Preface

Abstract: Biology is designed for multi-semester biology courses for science majors. It is grounded on an evolutionary basis and includes exciting features that highlight careers in the biological sciences and everyday applications of the concepts at hand. To meet the needs of today’s instructors and students, some content has been strategically condensed while maintaining the overall scope and coverage of traditional texts for this course. Instructors can customize the book, adapting it to the approach that works best in their classroom. Biology also includes an innovative art program that incorporates critical thinking and clicker questions to help students understand—and apply—key concepts.

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About *Biology 2e*

*Biology 2e* (2nd edition) is designed to cover the scope and sequence requirements of a typical two-semester biology course for science majors. The text provides comprehensive coverage of foundational research and core biology concepts through an evolutionary lens. *Biology* includes rich features that engage students in scientific inquiry, highlight careers in the biological sciences, and offer everyday applications. The book also includes various types of practice and homework questions that help students understand — and apply — key concepts.

Additional resources

About the authors

**Contributing Authors and Reviewers**

Julie Adams, Aurora University

Summer Allen, Brown University

James Bader, Case Western Reserve University

David Bailey, St. Norbert College

Mark Belk, Brigham Young University

Nancy Boury, Iowa State University

Lisa Bonneau, Metropolitan Community College – Blue River

Graciela Brelles-Marino, California State University Pomona

Mark Browning, Purdue University

Sue Chaplin, University of St. Thomas

George Cline, Jacksonville State University

Deb Cook, Georgia Gwinnett College

Diane Day, Clayton State University

Frank Dirrigl, The University of Texas Pan American

Waneene Dorsey, Grambling State University

Nick Downey, University of Wisconsin La Crosse

Rick Duhrkopf, Baylor University

Kristy Duran, Adams State University

Stan Eisen, Christian Brothers University

Brent Ewers, University of Wyoming

Myriam Feldman, Lake Washington Institute of Technology

Michael Fine, Virginia Commonwealth University

Linda Flora, Delaware County Community College

Thomas Freeland, Walsh University

David Grisé, Texas A & M University – Corpus Christi

Andrea Hazard, SUNY Cortland

Michael Hedrick, University of North Texas

Linda Hensel, Mercer University

Mark Kopeny, University of Virginia

Norman Johnson, University of Massachusetts Amherst

Grace Lasker, Lake Washington Institute of Technology; Walden University

Sandy Latourelle, SUNY Plattsburgh

Theo Light, Shippensburg University

Clark Lindgren, Grinnell College

James Malcolm, University of Redlands

Mark Meade, Jacksonville State University

Richard Merritt, Houston Community College

James Mickle, North Carolina State University

Jasleen Mishra, Houston Community College

Dudley Moon, Albany College of Pharmacy and Health Sciences

Shobhana Natarajan, Brookhaven College

Jonas Okeagu, Fayetteville State University

Diana Oliveras, University of Colorado Boulder

John Peters, College of Charleston

Joel Piperberg, Millersville University

Johanna Porter-Kelley, Winston-Salem State University

Robyn Puffenbarger, Bridgewater College

Dennis Revie, California Lutheran University

Ann Rushing, Baylor University

Sangha Saha, City College of Chicago

Edward Saiff, Ramapo College of New Jersey

Brian Shmaefsky, Lone Star College System

Robert Sizemore, Alcorn State University

Marc Smith, Sinclair Community College

Frederick Spiegel, University of Arkansas

Frederick Sproull, La Roche College

Bob Sullivan, Marist College

Mark Sutherland, Hendrix College

Toure Thompson, Alabama A&M University

Scott Thomson, University of Wisconsin – Parkside

Allison van de Meene, University of Melbourne

Mary White, Southeastern Louisiana University

Steven Wilt, Bellarmine University

James Wise, Hampton University

Renna Wolfe

Virginia Young, Mercer University

Leslie Zeman, University of Washington

Daniel Zurek, Pittsburg State University

Shobhana Natarajan, Alcon Laboratories, Inc.

The Chemistry of Life

The Study of Life

Introduction

The Science of Biology

Abstract:
By the end of this section, you will be able to do the following:

* Identify the shared characteristics of the natural sciences
* Summarize the steps of the scientific method
* Compare inductive reasoning with deductive reasoning
* Describe the goals of basic science and applied science

The Process of Science

Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines? We can define science (from the Latin *scientia*, meaning “knowledge”) as knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method. It becomes clear from this definition that applying scientific method plays a major role in science. The scientific method is a method of research with defined steps that include experiments and careful observation.

The Scientific Method

Biologists study the living world by posing questions about it and seeking science-based responses. Known as scientific method, this approach is common to other sciences as well. The scientific method was used even in ancient times, but England’s Sir Francis Bacon (1561–1626) first documented it ([link]). He set up inductive methods for scientific inquiry. The scientific method is not used only by biologists; researchers from almost all fields of study can apply it as a logical, rational problem-solving method.

Two Types of Science: Basic Science and Applied Science

The scientific community has been debating for the last few decades about the value of different types of science. Is it valuable to pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth if we can apply it to solving a specific problem or to bettering our lives? This question focuses on the differences between two types of science: basic science and applied science.

Reporting Scientific Work

Whether scientific research is basic science or applied science, scientists must share their findings in order for other researchers to expand and build upon their discoveries. Collaboration with other scientists—when planning, conducting, and analyzing results—is important for scientific research. For this reason, important aspects of a scientist’s work are communicating with peers and disseminating results to peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the select few who are present. Instead, most scientists present their results in peer-reviewed manuscripts that are published in scientific journals. Peer-reviewed manuscripts are scientific papers that a scientist’s colleagues or peers review. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not the scientist’s work is suitable for publication. The process of peer review helps to ensure that the research in a scientific paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or different conditions to expand on the findings.

Themes and Concepts of Biology

Abstract:
By the end of this section, you will be able to do the following:

* Identify and describe the properties of life
* Describe the levels of organization among living things
* Recognize and interpret a phylogenetic tree
* List examples of different subdisciplines in biology

Properties of Life

All living organisms share several key characteristics or functions: order, sensitivity or response to the environment, reproduction, adaptation, growth and development, regulation/homeostasis, energy processing, and evolution. When viewed together, these eight characteristics serve to define life.

Levels of Organization of Living Things

Living things are highly organized and structured, following a hierarchy that we can examine on a scale from small to large. The atom is the smallest and most fundamental unit of matter that retains the properties of an element. It consists of a nucleus surrounded by electrons. Atoms form molecules. A molecule is a chemical structure consisting of at least two atoms held together by one or more chemical bonds. Many molecules that are biologically important are macromolecules, large molecules that are typically formed by polymerization (a polymer is a large molecule that is made by combining smaller units called monomers, which are simpler than macromolecules). An example of a macromolecule is deoxyribonucleic acid (DNA) ([link]), which contains the instructions for the structure and functioning of all living organisms.

The Diversity of Life

The fact that biology, as a science, has such a broad scope has to do with the tremendous diversity of life on earth. The source of this diversity is evolution, the process of gradual change in a population or species over time. Evolutionary biologists study the evolution of living things in everything from the microscopic world to ecosystems.

Branches of Biological Study

The scope of biology is broad and therefore contains many branches and subdisciplines. Biologists may pursue one of those subdisciplines and work in a more focused field. For instance, molecular biology and biochemistry study biological processes at the molecular and chemical level, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they are regulated. Microbiology, the study of microorganisms, is the study of the structure and function of single-celled organisms. It is quite a broad branch itself, and depending on the subject of study, there are also microbial physiologists, ecologists, and geneticists, among others.

The Chemical Foundation of Life

Introduction

Atoms, Isotopes, Ions, and Molecules: The Building Blocks

Abstract:
By the end of this section, you will be able to do the following:

* Define matter and elements
* Describe the interrelationship between protons, neutrons, and electrons
* Compare the ways in which electrons can be donated or shared between atoms
* Explain the ways in which naturally occurring elements combine to create molecules, cells, tissues, organ systems, and organisms

The Structure of the Atom

To understand how elements come together, we must first discuss the element's smallest component or building block, the atom. An atom is the smallest unit of matter that retains all of the element's chemical properties. For example, one gold atom has all of the properties of gold, like its chemical reactivity. A gold coin is simply a very large number of gold atoms molded into the shape of a coin and contains small amounts of other elements known as impurities. We cannot break down gold atoms into anything smaller while still retaining the properties of gold.

Atomic Number and Mass

Atoms of each element contain a characteristic number of protons and electrons. The number of protons determines an element’s atomic number, which scientists use to distinguish one element from another. The number of neutrons is variable, resulting in isotopes, which are different forms of the same atom that vary only in the number of neutrons they possess. Together, the number of protons and neutrons determine an element’s mass number, as [link] illustrates. Note that we disregard the small contribution of mass from electrons in calculating the mass number. We can use this approximation of mass to easily calculate how many neutrons an element has by simply subtracting the number of protons from the mass number. Since an element’s isotopes will have slightly different mass numbers, scientists also determine the atomic mass, which is the calculated mean of the mass number for its naturally occurring isotopes. Often, the resulting number contains a fraction. For example, the atomic mass of chlorine (Cl) is 35.45 because chlorine is composed of several isotopes, some (the majority) with atomic mass 35 (17 protons and 18 neutrons) and some with atomic mass 37 (17 protons and 20 neutrons).

Isotopes

Isotopes are different forms of an element that have the same number of protons but a different number of neutrons. Some elements—such as carbon, potassium, and uranium—have naturally occurring isotopes. Carbon-12 contains six protons, six neutrons, and six electrons; therefore, it has a mass number of 12 (six protons and six neutrons). Carbon-14 contains six protons, eight neutrons, and six electrons; its atomic mass is 14 (six protons and eight neutrons). These two alternate forms of carbon are isotopes. Some isotopes may emit neutrons, protons, and electrons, and attain a more stable atomic configuration (lower level of potential energy); these are radioactive isotopes, or radioisotopes. Radioactive decay (carbon-14 decaying to eventually become nitrogen-14) describes the energy loss that occurs when an unstable atom’s nucleus releases radiation.

The Periodic Table

The periodic table organizes and displays different elements. Devised by Russian chemist Dmitri Mendeleev (1834–1907) in 1869, the table groups elements that, although unique, share certain chemical properties with other elements. The properties of elements are responsible for their physical state at room temperature: they may be gases, solids, or liquids. Elements also have specific chemical reactivity, the ability to combine and to chemically bond with each other.

Electron Shells and the Bohr Model

Note that there is a connection between the number of protons in an element, the atomic number that distinguishes one element from another, and the number of electrons it has. In all electrically neutral atoms, the number of electrons is the same as the number of protons. Thus, each element, at least when electrically neutral, has a characteristic number of electrons equal to its atomic number.

Electron Orbitals

Although useful to explain the reactivity and chemical bonding of certain elements, the Bohr model does not accurately reflect how electrons spatially distribute themselves around the nucleus. They do not circle the nucleus like the earth orbits the sun, but we find them in electron orbitals. These relatively complex shapes result from the fact that electrons behave not just like particles, but also like waves. Mathematical equations from quantum mechanics, which scientists call wave functions, can predict within a certain level of probability where an electron might be at any given time. Scientists call the area where an electron is most likely to be found its orbital.

Chemical Reactions and Molecules

All elements are most stable when their outermost shell is filled with electrons according to the octet rule. This is because it is energetically favorable for atoms to be in that configuration and it makes them stable. However, since not all elements have enough electrons to fill their outermost shells, atoms form chemical bonds with other atoms thereby obtaining the electrons they need to attain a stable electron configuration. When two or more atoms chemically bond with each other, the resultant chemical structure is a molecule. The familiar water molecule, H2O, consists of two hydrogen atoms and one oxygen atom. These bond together to form water, as [link] illustrates. Atoms can form molecules by donating, accepting, or sharing electrons to fill their outer shells.

Ions and Ionic Bonds

Some atoms are more stable when they gain or lose an electron (or possibly two) and form ions. This fills their outermost electron shell and makes them energetically more stable. Because the number of electrons does not equal the number of protons, each ion has a net charge. Cations are positive ions that form by losing electrons. Negative ions form by gaining electrons, which we call anions. We designate anions by their elemental name and change the ending to “-ide”, thus the anion of chlorine is chloride, and the anion of sulfur is sulfide.

Covalent Bonds and Other Bonds and Interactions

Another way to satisfy the octet rule is by sharing electrons between atoms to form covalent bonds. These bonds are stronger and much more common than ionic bonds in the molecules of living organisms. We commonly find covalent bonds in carbon-based organic molecules, such as our DNA and proteins. We also find covalent bonds in inorganic molecules like H2O, CO2, and O2. The bonds may share one, two, or three pairs of electrons, making single, double, and triple bonds, respectively. The more covalent bonds between two atoms, the stronger their connection. Thus, triple bonds are the strongest.

Water

Abstract:
By the end of this section, you will be able to do the following:

* Describe the properties of water that are critical to maintaining life
* Explain why water is an excellent solvent
* Provide examples of water’s cohesive and adhesive properties
* Discuss the role of acids, bases, and buffers in homeostasis

Water’s Polarity

One of water’s important properties is that it is composed of polar molecules: the hydrogen and oxygen within water molecules (H2O) form polar covalent bonds. While there is no net charge to a water molecule, water's polarity creates a slightly positive charge on hydrogen and a slightly negative charge on oxygen, contributing to water’s properties of attraction. Water generates charges because oxygen is more electronegative than hydrogen, making it more likely that a shared electron would be near the oxygen nucleus than the hydrogen nucleus, thus generating the partial negative charge near the oxygen.

Water’s States: Gas, Liquid, and Solid

The formation of hydrogen bonds is an important quality of the liquid water that is crucial to life as we know it. As water molecules make hydrogen bonds with each other, water takes on some unique chemical characteristics compared to other liquids and, since living things have a high water content, understanding these chemical features is key to understanding life. In liquid water, hydrogen bonds constantly form and break as the water molecules slide past each other. The water molecules' motion (kinetic energy) causes the bonds to break due to the heat contained in the system. When the heat rises as water boils, the water molecules' higher kinetic energy causes the hydrogen bonds to break completely and allows water molecules to escape into the air as gas (steam or water vapor). Alternatively, when water temperature reduces and water freezes, the water molecules form a crystalline structure maintained by hydrogen bonding (there is not enough energy to break the hydrogen bonds) that makes ice less dense than liquid water, a phenomenon that we do not see when other liquids solidify.

Water’s High Heat Capacity

Water’s high heat capacity is a property that hydrogen bonding among water molecules causes. Water has the highest specific heat capacity of any liquid. We define specific heat as the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius. For water, this amount is one calorie. It therefore takes water a long time to heat and a long time to cool. In fact, water's specific heat capacity is about five times more than that of sand. This explains why the land cools faster than the sea. Due to its high heat capacity, warm blooded animals use water to more evenly disperse heat in their bodies: it acts in a similar manner to a car’s cooling system, transporting heat from warm places to cool places, causing the body to maintain a more even temperature.

Water’s Heat of Vaporization

Water also has a high heat of vaporization, the amount of energy required to change one gram of a liquid substance to a gas. A considerable amount of heat energy (586 cal) is required to accomplish this change in water. This process occurs on the water's surface. As liquid water heats up, hydrogen bonding makes it difficult to separate the liquid water molecules from each other, which is required for it to enter its gaseous phase (steam). As a result, water acts as a heat sink or heat reservoir and requires much more heat to boil than does a liquid such as ethanol (grain alcohol), whose hydrogen bonding with other ethanol molecules is weaker than water’s hydrogen bonding. Eventually, as water reaches its boiling point of 100° Celsius (212° Fahrenheit), the heat is able to break the hydrogen bonds between the water molecules, and the kinetic energy (motion) between the water molecules allows them to escape from the liquid as a gas. Even when below its boiling point, water’s individual molecules acquire enough energy from other water molecules such that some surface water molecules can escape and vaporize: we call this process evaporation.

Water’s Solvent Properties

Since water is a polar molecule with slightly positive and slightly negative charges, ions and polar molecules can readily dissolve in it. Therefore, we refer to water as a solvent, a substance capable of dissolving other polar molecules and ionic compounds. The charges associated with these molecules will form hydrogen bonds with water, surrounding the particle with water molecules. We refer to this as a sphere of hydration, or a hydration shell, as [link] illustrates and serves to keep the particles separated or dispersed in the water.

Water’s Cohesive and Adhesive Properties

Have you ever filled a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water forms a dome-like shape above the rim of the glass. This water can stay above the glass because of the property of cohesion. In cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together at the liquid-gas (water-air) interface, although there is no more room in the glass.

pH, Buffers, Acids, and Bases

The pH of a solution indicates its acidity or basicity.

${\text{H}}_{2}\text{O}\left(\text{I}\right)↔{\text{H}}^{+}\left(\text{aq}\right)+\text{O}{\text{H}}^{-}\left(\text{aq}\right)$You may have used litmus or pH paper, filter paper treated with a natural water-soluble dye for use as a pH indicator. It tests how much acid (acidity) or base (basicity) exists in a solution. You might have even used some to test whether the water in a swimming pool is properly treated. In both cases, the pH test measures hydrogen ions' concentration in a given solution.

Carbon

Abstract:
By the end of this section, you will be able to do the following:

* Explain why carbon is important for life
* Describe the role of functional groups in biological molecules

Hydrocarbons

Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane (CH4) described above. We often use hydrocarbons in our daily lives as fuels—like the propane in a gas grill or the butane in a lighter. The many covalent bonds between the atoms in hydrocarbons store a great amount of energy, which releases when these molecules burn (oxidize). Methane, an excellent fuel, is the simplest hydrocarbon molecule, with a central carbon atom bonded to four different hydrogen atoms, as [link] illustrates. The shape of its electron orbitals determines the shape of the methane molecule's geometry, where the atoms reside in three dimensions. The carbons and the four hydrogen atoms form a tetrahedron, with four triangular faces. For this reason, we describe methane as having tetrahedral geometry.

Isomers

The three-dimensional placement of atoms and chemical bonds within organic molecules is central to understanding their chemistry. We call molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds isomers. Structural isomers (like butane and isobutane in [link]a) differ in the placement of their covalent bonds: both molecules have four carbons and ten hydrogens (C4H10), but the different atom arrangement within the molecules leads to differences in their chemical properties. For example, butane is suited for use as a fuel for cigarette lighters and torches; whereas, isobutane is suited for use as a refrigerant and a propellant in spray cans.

Enantiomers

Enantiomers are molecules that share the same chemical structure and chemical bonds but differ in the three-dimensional placement of atoms so that they are non-superimposable mirror images. [link] shows an amino acid alanine example, where the two structures are nonsuperimposable. In nature, the L-forms of amino acids are predominant in proteins. Some D forms of amino acids are seen in the cell walls of bacteria and polypeptides in other organisms. Similarly, the D-form of glucose is the main product of photosynthesis and we rarely see the molecule's L-form in nature.

Functional Groups

Functional groups are groups of atoms that occur within molecules and confer specific chemical properties to those molecules. We find them along the “carbon backbone” of macromolecules. Chains and/or rings of carbon atoms with the occasional substitution of an element such as nitrogen or oxygen form this carbon backbone. Molecules with other elements in their carbon backbone are substituted hydrocarbons.

Biological Macromolecules

Introduction

Synthesis of Biological Macromolecules

Abstract:
By the end of this section, you will be able to do the following:

* Understand macromolecule synthesis
* Explain dehydration (or condensation) and hydrolysis reactions

Dehydration Synthesis

Most macromolecules are made from single subunits, or building blocks, called monomers. The monomers combine with each other using covalent bonds to form larger molecules known as polymers. In doing so, monomers release water molecules as byproducts. This type of reaction is dehydration synthesis, which means “to put together while losing water.”

Hydrolysis

Polymers break down into monomers during hydrolysis. A chemical reaction occurs when inserting a water molecule across the bond. Breaking a covalent bond with this water molecule in the compound achieves this ([link]). During these reactions, the polymer breaks into two components: one part gains a hydrogen atom (H+) and the other gains a hydroxyl molecule (OH–) from a split water molecule.

Carbohydrates

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the role of carbohydrates in cells and in the extracellular materials of animals and plants
* Explain carbohydrate classifications
* List common monosaccharides, disaccharides, and polysaccharides

Molecular Structures

The stoichiometric formula (CH2O)*n*, where *n* is the number of carbons in the molecule represents carbohydrates. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This formula also explains the origin of the term “carbohydrate”: the components are carbon (“carbo”) and the components of water (hence, “hydrate”). Scientists classify carbohydrates into three subtypes: monosaccharides, disaccharides, and polysaccharides.

Benefits of Carbohydrates

Are carbohydrates good for you? Some people believe that carbohydrates are bad and they should avoid them. Some diets completely forbid carbohydrate consumption, claiming that a low-carbohydrate diet helps people to lose weight faster. However, carbohydrates have been an important part of the human diet for thousands of years. Artifacts from ancient civilizations show the presence of wheat, rice, and corn in our ancestors’ storage areas.

Lipids

Abstract:
By the end of this section, you will be able to do the following:

* Describe the four major types of lipids
* Explain the role of fats in storing energy
* Differentiate between saturated and unsaturated fatty acids
* Describe phospholipids and their role in cells
* Define the basic structure of a steroid and some steroid functions
* Explain how cholesterol helps maintain the plasma membrane's fluid nature

Fats and Oils

A fat molecule consists of two main components—glycerol and fatty acids. Glycerol is an organic compound (alcohol) with three carbons, five hydrogens, and three hydroxyl (OH) groups. Fatty acids have a long chain of hydrocarbons to which a carboxyl group is attached, hence the name “fatty acid.” The number of carbons in the fatty acid may range from 4 to 36. The most common are those containing 12–18 carbons. In a fat molecule, the fatty acids attach to each of the glycerol molecule's three carbons with an ester bond through an oxygen atom ([link]).

Waxes

Wax covers some aquatic birds' feathers and some plants' leaf surfaces. Because of waxes' hydrophobic nature, they prevent water from sticking on the surface ([link]). Long fatty acid chains esterified to long-chain alcohols comprise waxes.

Phospholipids

Phospholipids are major plasma membrane constituents that comprise cells' outermost layer. Like fats, they are comprised of fatty acid chains attached to a glycerol or sphingosine backbone. However, instead of three fatty acids attached as in triglycerides, there are two fatty acids forming diacylglycerol, and a modified phosphate group occupies the glycerol backbone's third carbon ([link]). A phosphate group alone attached to a diacylglycerol does not qualify as a phospholipid. It is phosphatidate (diacylglycerol 3-phosphate), the precursor of phospholipids. An alcohol modifies the phosphate group. Phosphatidylcholine and phosphatidylserine are two important phospholipids that are in plasma membranes.

Steroids

Unlike the phospholipids and fats that we discussed earlier, steroids have a fused ring structure. Although they do not resemble the other lipids, scientists group them with them because they are also hydrophobic and insoluble in water. All steroids have four linked carbon rings and several of them, like cholesterol, have a short tail ([link]). Many steroids also have the –OH functional group, which puts them in the alcohol classification (sterols).

Proteins

Abstract:
By the end of this section, you will be able to do the following:

* Describe the functions proteins perform in the cell and in tissues
* Discuss the relationship between amino acids and proteins
* Explain the four levels of protein organization
* Describe the ways in which protein shape and function are linked

Types and Functions of Proteins

Enzymes, which living cells produce, are catalysts in biochemical reactions (like digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon which it acts. The enzyme may help in breakdown, rearrangement, or synthesis reactions. We call enzymes that break down their substrates catabolic enzymes. Those that build more complex molecules from their substrates are anabolic enzymes, and enzymes that affect the rate of reaction are catalytic enzymes. Note that all enzymes increase the reaction rate and, therefore, are organic catalysts. An example of an enzyme is salivary amylase, which hydrolyzes its substrate amylose, a component of starch.

Amino Acids

Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (*α*) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group ([link]).

Protein Structure

As we discussed earlier, a protein's shape is critical to its function. For example, an enzyme can bind to a specific substrate at an active site. If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind to the substrate. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.

Denaturation and Protein Folding

Each protein has its own unique sequence and shape that chemical interactions hold together. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape without losing its primary sequence in what scientists call denaturation. Denaturation is often reversible because the polypeptide's primary structure is conserved in the process if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to loss of function. One example of irreversible protein denaturation is frying an egg. The albumin protein in the liquid egg white denatures when placed in a hot pan. Not all proteins denature at high temperatures. For instance, bacteria that survive in hot springs have proteins that function at temperatures close to boiling. The stomach is also very acidic, has a low pH, and denatures proteins as part of the digestion process; however, the stomach's digestive enzymes retain their activity under these conditions.

Nucleic Acids

Abstract:
By the end of this section, you will be able to do the following:

* Describe nucleic acids' structure and define the two types of nucleic acids
* Explain DNA's structure and role
* Explain RNA's structure and roles

DNA and RNA

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope.

DNA Double-Helix Structure

DNA has a double-helix structure ([link]). The sugar and phosphate lie on the outside of the helix, forming the DNA's backbone. The nitrogenous bases are stacked in the interior, like a pair of staircase steps. Hydrogen bonds bind the pairs to each other. Every base pair in the double helix is separated from the next base pair by 0.34 nm. The helix's two strands run in opposite directions, meaning that the 5′ carbon end of one strand will face the 3′ carbon end of its matching strand. (Scientists call this an antiparallel orientation and is important to DNA replication and in many nucleic acid interactions.)

RNA

Ribonucleic acid, or RNA, is mainly involved in the process of protein synthesis under the direction of DNA. RNA is usually single-stranded and is comprised of ribonucleotides that are linked by phosphodiester bonds. A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and the phosphate group.

The Cell

Cell Structure

Introduction

Studying Cells

Abstract:
By the end of this section, you will be able to do the following:

* Describe the role of cells in organisms
* Compare and contrast light microscopy and electron microscopy
* Summarize cell theory

Microscopy

Cells vary in size. With few exceptions, we cannot see individual cells with the naked eye, so scientists use microscopes (micro- = “small”; -scope = “to look at”) to study them. A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs.

Cell Theory

The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s. Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed “animalcules.”

Prokaryotic Cells

Abstract:
By the end of this section, you will be able to do the following:

* Name examples of prokaryotic and eukaryotic organisms
* Compare and contrast prokaryotic and eukaryotic cells
* Describe the relative sizes of different cells
* Explain why cells must be small

Components of Prokaryotic Cells

All cells share four common components: 1) a plasma membrane, an outer covering that separates the cell’s interior from its surrounding environment; 2) cytoplasm, consisting of a jelly-like cytosol within the cell in which there are other cellular components; 3) DNA, the cell's genetic material; and 4) ribosomes, which synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways.

Eukaryotic Cells

Abstract:
By the end of this section, you will be able to do the following:

* Describe the structure of eukaryotic cells
* Compare animal cells with plant cells
* State the role of the plasma membrane
* Summarize the functions of the major cell organelles

The Plasma Membrane

Like prokaryotes, eukaryotic cells have a plasma membrane ([link]), a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule with two fatty acid chains and a phosphate-containing group. The plasma membrane controls the passage of organic molecules, ions, water, and oxygen into and out of the cell. Wastes (such as carbon dioxide and ammonia) also leave the cell by passing through the plasma membrane.

The Cytoplasm

The cytoplasm is the cell's entire region between the plasma membrane and the nuclear envelope (a structure we will discuss shortly). It is comprised of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals ([link]). Even though the cytoplasm consists of 70 to 80 percent water, it has a semi-solid consistency, which comes from the proteins within it. However, proteins are not the only organic molecules in the cytoplasm. Glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are also there. Ions of sodium, potassium, calcium, and many other elements also dissolve in the cytoplasm. Many metabolic reactions, including protein synthesis, take place in the cytoplasm.

The Nucleus

Typically, the nucleus is the most prominent organelle in a cell ([link]). The nucleus (plural = nuclei) houses the cell’s DNA and directs the synthesis of ribosomes and proteins. Let’s look at it in more detail ([link]).

Ribosomes

Ribosomes are the cellular structures responsible for protein synthesis. When we view them through an electron microscope, ribosomes appear either as clusters (polyribosomes) or single, tiny dots that float freely in the cytoplasm. They may be attached to the plasma membrane's cytoplasmic side or the endoplasmic reticulum's cytoplasmic side and the nuclear envelope's outer membrane ([link]). Electron microscopy shows us that ribosomes, which are large protein and RNA complexes, consist of two subunits, large and small ([link]). Ribosomes receive their “orders” for protein synthesis from the nucleus where the DNA transcribes into messenger RNA (mRNA). The mRNA travels to the ribosomes, which translate the code provided by the sequence of the nitrogenous bases in the mRNA into a specific order of amino acids in a protein. Amino acids are the building blocks of proteins.

Mitochondria

Scientists often call mitochondria (singular = mitochondrion) “powerhouses” or “energy factories” of both plant and animal cells because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. ATP represents the cell's short-term stored energy. Cellular respiration is the process of making ATP using the chemical energy in glucose and other nutrients. In mitochondria, this process uses oxygen and produces carbon dioxide as a waste product. In fact, the carbon dioxide that you exhale with every breath comes from the cellular reactions that produce carbon dioxide as a byproduct.

Peroxisomes

Peroxisomes are small, round organelles enclosed by single membranes. They carry out oxidation reactions that break down fatty acids and amino acids. They also detoxify many poisons that may enter the body. (Many of these oxidation reactions release hydrogen peroxide, H2O2, which would be damaging to cells; however, when these reactions are confined to peroxisomes, enzymes safely break down the H2O2 into oxygen and water.) For example, peroxisomes in liver cells detoxify alcohol. Glyoxysomes, which are specialized peroxisomes in plants, are responsible for converting stored fats into sugars. Plant cells contain many different types of peroxisomes that play a role in metabolism, pathogene defense, and stress response, to mention a few.

Vesicles and Vacuoles

Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Other than the fact that vacuoles are somewhat larger than vesicles, there is a very subtle distinction between them. Vesicle membranes can fuse with either the plasma membrane or other membrane systems within the cell. Additionally, some agents such as enzymes within plant vacuoles break down macromolecules. The vacuole's membrane does not fuse with the membranes of other cellular components.

Animal Cells versus Plant Cells

At this point, you know that each eukaryotic cell has a plasma membrane, cytoplasm, a nucleus, ribosomes, mitochondria, peroxisomes, and in some, vacuoles, but there are some striking differences between animal and plant cells. While both animal and plant cells have microtubule organizing centers (MTOCs), animal cells also have centrioles associated with the MTOC: a complex we call the centrosome. Animal cells each have a centrosome and lysosomes; whereas, most plant cells do not. Plant cells have a cell wall, chloroplasts and other specialized plastids, and a large central vacuole; whereas, animal cells do not.

The Endomembrane System and Proteins

Abstract:
By the end of this section, you will be able to do the following:

* List the components of the endomembrane system
* Recognize the relationship between the endomembrane system and its functions

The Endoplasmic Reticulum

The endoplasmic reticulum (ER) ([link]) is a series of interconnected membranous sacs and tubules that collectively modifies proteins and synthesizes lipids. However, these two functions take place in separate areas of the ER: the rough ER and the smooth ER, respectively.

The Golgi Apparatus

We have already mentioned that vesicles can bud from the ER and transport their contents elsewhere, but where do the vesicles go? Before reaching their final destination, the lipids or proteins within the transport vesicles still need sorting, packaging, and tagging so that they end up in the right place. Sorting, tagging, packaging, and distributing lipids and proteins takes place in the Golgi apparatus (also called the Golgi body), a series of flattened membranous sacs ([link]).

Lysosomes

In addition to their role as the digestive component and organelle-recycling facility of animal cells, lysosomes are part of the endomembrane system. Lysosomes also use their hydrolytic enzymes to destroy pathogens (disease-causing organisms) that might enter the cell. A good example of this occurs in macrophages, a group of white blood cells which are part of your body’s immune system. In a process that scientists call phagocytosis or endocytosis, a section of the macrophage's plasma membrane invaginates (folds in) and engulfs a pathogen. The invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle fuses with a lysosome. The lysosome’s hydrolytic enzymes then destroy the pathogen ([link]).

The Cytoskeleton

Abstract:
By the end of this section, you will be able to do the following:

* Describe the cytoskeleton
* Compare the roles of microfilaments, intermediate filaments, and microtubules
* Compare and contrast cilia and flagella
* Summarize the differences among the components of prokaryotic cells, animal cells, and plant cells

Microfilaments

Of the three types of protein fibers in the cytoskeleton, microfilaments are the narrowest. They function in cellular movement, have a diameter of about 7 nm, and are comprised of two globular protein intertwined strands, which we call actin ([link]). For this reason, we also call microfilaments actin filaments.

Intermediate Filaments

Several strands of fibrous proteins that are wound together comprise intermediate filaments ([link]). Cytoskeleton elements get their name from the fact that their diameter, 8 to 10 nm, is between those of microfilaments and microtubules.

Microtubules

As their name implies, microtubules are small hollow tubes. Polymerized dimers of α-tubulin and β-tubulin, two globular proteins, comprise the microtubule's walls ([link]). With a diameter of about 25 nm, microtubules are cytoskeletons' widest components. They help the cell resist compression, provide a track along which vesicles move through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. Like microfilaments, microtubules can disassemble and reform quickly.

Connections between Cells and Cellular Activities

Abstract:
By the end of this section, you will be able to do the following:

* Describe the extracellular matrix
* List examples of the ways that plant cells and animal cells communicate with adjacent cells
* Summarize the roles of tight junctions, desmosomes, gap junctions, and plasmodesmata

Extracellular Matrix of Animal Cells

While cells in most multicellular organisms release materials into the extracellular space, animal cells will be discussed as an example. The primary components of these materials are proteins, and the most abundant protein is collagen. Collagen fibers are interwoven with proteoglycans, which are carbohydrate-containing protein molecules. Collectively, we call these materials the extracellular matrix ([link]). Not only does the extracellular matrix hold the cells together to form a tissue, but it also allows the cells within the tissue to communicate with each other. How can this happen?

Intercellular Junctions

Cells can also communicate with each other via direct contact, or intercellular junctions. There are differences in the ways that plant and animal and fungal cells communicate. Plasmodesmata are junctions between plant cells; whereas, animal cell contacts include tight junctions, gap junctions, and desmosomes.

Structure and Function of Plasma Membranes

Introduction

Components and Structure

Abstract:
By the end of this section, you will be able to do the following:

* Understand the cell membrane fluid mosaic model
* Describe phospholipid, protein, and carbohydrate functions in membranes
* Discuss membrane fluidity

Fluid Mosaic Model

Scientists identified the plasma membrane in the 1890s, and its chemical components in 1915. The principal components they identified were lipids and proteins. In 1935, Hugh Davson and James Danielli proposed the plasma membrane's structure. This was the first model that others in the scientific community widely accepted. It was based on the plasma membrane's “railroad track” appearance in early electron micrographs. Davson and Danielli theorized that the plasma membrane's structure resembles a sandwich. They made the analogy of proteins to bread, and lipids to the filling. In the 1950s, advances in microscopy, notably transmission electron microscopy (TEM), allowed researchers to see that the plasma membrane's core consisted of a double, rather than a single, layer. In 1972, S.J. Singer and Garth L. Nicolson proposed a new model that provides microscopic observations and better explains plasma membrane function.

Membrane Fluidity

The membrane's mosaic characteristic helps to illustrate its nature. The integral proteins and lipids exist in the membrane as separate but loosely attached molecules. These resemble the separate, multicolored tiles of a mosaic picture, and they float, moving somewhat with respect to one another. The membrane is not like a balloon, however, that can expand and contract; rather, it is fairly rigid and can burst if penetrated or if a cell takes in too much water. However, because of its mosaic nature, a very fine needle can easily penetrate a plasma membrane without causing it to burst, and the membrane will flow and self-seal when one extracts the needle.

Passive Transport

Abstract:
By the end of this section, you will be able to do the following:

* Explain why and how passive transport occurs
* Understand the osmosis and diffusion processes
* Define tonicity and its relevance to passive transport

Selective Permeability

Plasma membranes are asymmetric: the membrane's interior is not identical to its exterior. There is a considerable difference between the array of phospholipids and proteins between the two leaflets that form a membrane. On the membrane's interior, some proteins serve to anchor the membrane to cytoskeleton's fibers. There are peripheral proteins on the membrane's exterior that bind extracellular matrix elements. Carbohydrates, attached to lipids or proteins, are also on the plasma membrane's exterior surface. These carbohydrate complexes help the cell bind required substances in the extracellular fluid. This adds considerably to plasma membrane's selective nature ([link]).

Diffusion

Diffusion is a passive process of transport. A single substance moves from a high concentration to a low concentration area until the concentration is equal across a space. You are familiar with diffusion of substances through the air. For example, think about someone opening a bottle of ammonia in a room filled with people. The ammonia gas is at its highest concentration in the bottle. Its lowest concentration is at the room's edges. The ammonia vapor will diffuse, or spread away, from the bottle, and gradually, increasingly more people will smell the ammonia as it spreads. Materials move within the cell’s cytosol by diffusion, and certain materials move through the plasma membrane by diffusion ([link]). Diffusion expends no energy. On the contrary, concentration gradients are a form of potential energy, which dissipates as the gradient is eliminated.

Facilitated transport

In facilitated transport, or facilitated diffusion, materials diffuse across the plasma membrane with the help of membrane proteins. A concentration gradient exists that would allow these materials to diffuse into the cell without expending cellular energy. However, these materials are polar molecule ions that the cell membrane's hydrophobic parts repel. Facilitated transport proteins shield these materials from the membrane's repulsive force, allowing them to diffuse into the cell.

Osmosis

Osmosis is the movement of free water molecules through a semipermeable membrane according to the water's concentration gradient across the membrane, which is inversely proportional to the solutes' concentration. While diffusion transports material across membranes and within cells, osmosis transports *only water* across a membrane and the membrane limits the solutes' diffusion in the water. Not surprisingly, the aquaporins that facilitate water movement play a large role in osmosis, most prominently in red blood cells and the membranes of kidney tubules.

Tonicity

Tonicity describes how an extracellular solution can change a cell's volume by affecting osmosis. A solution's tonicity often directly correlates with the solution's osmolarity. Osmolarity describes the solution's total solute concentration. A solution with low osmolarity has a greater number of water molecules relative to the number of solute particles. A solution with high osmolarity has fewer water molecules with respect to solute particles. In a situation in which a membrane permeable to water, though not to the solute separates two different osmolarities, water will move from the membrane's side with lower osmolarity (and more water) to the side with higher osmolarity (and less water). This effect makes sense if you remember that the solute cannot move across the membrane, and thus the only component in the system that can move—the water—moves along its own concentration gradient. An important distinction that concerns living systems is that osmolarity measures the number of particles (which may be molecules) in a solution. Therefore, a solution that is cloudy with cells may have a lower osmolarity than a solution that is clear, if the second solution contains more dissolved molecules than there are cells.

Tonicity in Living Systems

In a hypotonic environment, water enters a cell, and the cell swells. In an isotonic condition, the relative solute and solvent concentrations are equal on both membrane sides. There is no net water movement; therefore, there is no change in the cell's size. In a hypertonic solution, water leaves a cell and the cell shrinks. If either the hypo- or hyper- condition goes to excess, the cell’s functions become compromised, and the cell may be destroyed.

Active Transport

Abstract:
By the end of this section, you will be able to do the following:

* Understand how electrochemical gradients affect ions
* Distinguish between primary active transport and secondary active transport

Electrochemical Gradient

We have discussed simple concentration gradients—a substance's differential concentrations across a space or a membrane—but in living systems, gradients are more complex. Because ions move into and out of cells and because cells contain proteins that do not move across the membrane and are mostly negatively charged, there is also an electrical gradient, a difference of charge, across the plasma membrane. The interior of living cells is electrically negative with respect to the extracellular fluid in which they are bathed, and at the same time, cells have higher concentrations of potassium (K+) and lower concentrations of sodium (Na+) than the extracellular fluid. Thus in a living cell, the concentration gradient of Na+ tends to drive it into the cell, and its electrical gradient (a positive ion) also drives it inward to the negatively charged interior. However, the situation is more complex for other elements such as potassium. The electrical gradient of K+, a positive ion, also drives it into the cell, but the concentration gradient of K+ drives K+ *out* of the cell ([link]). We call the combined concentration gradient and electrical charge that affects an ion its electrochemical gradient.

Primary Active Transport

The primary active transport that functions with the active transport of sodium and potassium allows secondary active transport to occur. The second transport method is still active because it depends on using energy as does primary transport ([link]).

Secondary Active Transport (Co-transport)

Secondary active transport uses the kinetic energy of the sodium ions to bring other compounds, against their concentration gradient into the cell. As sodium ion concentrations build outside of the plasma membrane because of the primary active transport process, this creates an electrochemical gradient. If a channel protein exists and is open, the sodium ions will move down its concentration gradient across the membrane. This movement transports other substances that must be attached to the same transport protein in order for the sodium ions to move across the membrane ([link]). Many amino acids, as well as glucose, enter a cell this way. This secondary process also stores high-energy hydrogen ions in the mitochondria of plant and animal cells in order to produce ATP. The potential energy that accumulates in the stored hydrogen ions translates into kinetic energy as the ions surge through the channel protein ATP synthase, and that energy then converts ADP into ATP.

Bulk Transport

Abstract:
By the end of this section, you will be able to do the following:

* Describe endocytosis, including phagocytosis, pinocytosis, and receptor-mediated endocytosis
* Understand the process of exocytosis

Endocytosis

Endocytosis is a type of active transport that moves particles, such as large molecules, parts of cells, and even whole cells, into a cell. There are different endocytosis variations, but all share a common characteristic: the cell's plasma membrane invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle containing itself in a newly created intracellular vesicle formed from the plasma membrane.

Exocytosis

The reverse process of moving material into a cell is the process of exocytosis. Exocytosis is the opposite of the processes we discussed above in that its purpose is to expel material from the cell into the extracellular fluid. Waste material is enveloped in a membrane and fuses with the plasma membrane's interior. This fusion opens the membranous envelope on the cell's exterior, and the waste material expels into the extracellular space ([link]). Other examples of cells releasing molecules via exocytosis include extracellular matrix protein secretion and neurotransmitter secretion into the synaptic cleft by synaptic vesicles.

Metabolism

Introduction

Energy and Metabolism

Abstract:
By the end of this section, you will be able to do the following:

* Explain metabolic pathways and describe the two major types
* Discuss how chemical reactions play a role in energy transfer

Carbohydrate Metabolism

Sugar (a simple carbohydrate) metabolism (chemical reactions) is a classic example of the many cellular processes that use and produce energy. Living things consume sugar as a major energy source, because sugar molecules have considerable energy stored within their bonds. The following equation describes the breakdown of glucose, a simple sugar:

Metabolic Pathways

The processes of making and breaking down sugar molecules illustrate two types of metabolic pathways. A metabolic pathway is a series of interconnected biochemical reactions that convert a substrate molecule or molecules, step-by-step, through a series of metabolic intermediates, eventually yielding a final product or products. In the case of sugar metabolism, the first metabolic pathway synthesized sugar from smaller molecules, and the other pathway broke sugar down into smaller molecules. Scientists call these two opposite processes—the first requiring energy and the second producing energy—anabolic (building) and catabolic (breaking down) pathways, respectively. Consequently, building (anabolism) and degradation (catabolism) comprise metabolism.

Potential, Kinetic, Free, and Activation Energy

Abstract:
By the end of this section, you will be able to do the following:

* Define “energy”
* Explain the difference between kinetic and potential energy
* Discuss the concepts of free energy and activation energy
* Describe endergonic and exergonic reactions

Energy Types

When an object is in motion, there is energy. For example, an airplane in flight produces considerable energy. This is because moving objects are capable of enacting a change, or doing work. Think of a wrecking ball. Even a slow-moving wrecking ball can do considerable damage to other objects. However, a wrecking ball that is not in motion is incapable of performing work. Energy with objects in motion is kinetic energy. A speeding bullet, a walking person, rapid molecule movement in the air (which produces heat), and electromagnetic radiation like light all have kinetic energy.

Free Energy

After learning that chemical reactions release energy when energy-storing bonds break, an important next question is how do we quantify and express the chemical reactions with the associated energy? How can we compare the energy that releases from one reaction to that of another reaction? We use a measurement of free energy to quantitate these energy transfers. Scientists call this free energy Gibbs free energy (abbreviated with the letter G) after Josiah Willard Gibbs, the scientist who developed the measurement. According to the second law of thermodynamics, all energy transfers involve losing some energy in an unusable form such as heat, resulting in entropy. Gibbs free energy specifically refers to the energy that takes place with a chemical reaction that is available after we account for entropy. In other words, Gibbs free energy is usable energy, or energy that is available to do work.

Activation Energy

There is another important concept that we must consider regarding endergonic and exergonic reactions. Even exergonic reactions require a small amount of energy input before they can proceed with their energy-releasing steps. These reactions have a net release of energy, but still require some initial energy. Scientists call this small amount of energy input necessary for all chemical reactions to occur the activation energy (or free energy of activation) abbreviated as EA ([link]).

The Laws of Thermodynamics

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the concept of entropy
* Explain the first and second laws of thermodynamics

The First Law of Thermodynamics

The first law of thermodynamics deals with the total amount of energy in the universe. It states that this total amount of energy is constant. In other words, there has always been, and always will be, exactly the same amount of energy in the universe. Energy exists in many different forms. According to the first law of thermodynamics, energy may transfer from place to place or transform into different forms, but it cannot be created or destroyed. The transfers and transformations of energy take place around us all the time. Light bulbs transform electrical energy into light energy. Gas stoves transform chemical energy from natural gas into heat energy. Plants perform one of the most biologically useful energy transformations on earth: that of converting sunlight energy into the chemical energy stored within organic molecules ([link]). [link] examples of energy transformations.

The Second Law of Thermodynamics

A living cell’s primary tasks of obtaining, transforming, and using energy to do work may seem simple. However, the second law of thermodynamics explains why these tasks are harder than they appear. None of the energy transfers that we have discussed, along with all energy transfers and transformations in the universe, is completely efficient. In every energy transfer, some amount of energy is lost in a form that is unusable. In most cases, this form is heat energy. Thermodynamically, scientists define heat energy as energy that transfers from one system to another that is not doing work. For example, when an airplane flies through the air, it loses some of its energy as heat energy due to friction with the surrounding air. This friction actually heats the air by temporarily increasing air molecule speed. Likewise, some energy is lost as heat energy during cellular metabolic reactions. This is good for warm-blooded creatures like us, because heat energy helps to maintain our body temperature. Strictly speaking, no energy transfer is completely efficient, because some energy is lost in an unusable form.

ATP: Adenosine Triphosphate

Abstract:
By the end of this section, you will be able to do the following:

* Explain ATP's role as the cellular energy currency
* Describe how energy releases through ATP hydrolysis

Enzymes

Abstract:
By the end of this section, you will be able to do the following:

* Describe the role of enzymes in metabolic pathways
* Explain how enzymes function as molecular catalysts
* Discuss enzyme regulation by various factors

Enzyme Active Site and Substrate Specificity

The chemical reactants to which an enzyme binds are the enzyme’s substrates. There may be one or more substrates, depending on the particular chemical reaction. In some reactions, a single-reactant substrate breaks down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction, both become modified, and leave the reaction as two products. The location within the enzyme where the substrate binds is the enzyme’s active site. This is where the “action” happens. Since enzymes are proteins, there is a unique combination of amino acid residues (also side chains, or R groups) within the active site. Different properties characterize each residue. These can be large or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or negatively charged, or neutral. The unique combination of amino acid residues, their positions, sequences, structures, and properties, creates a very specific chemical environment within the active site. This specific environment is suited to bind, albeit briefly, to a specific chemical substrate (or substrates). Due to this jigsaw puzzle-like match between an enzyme and its substrates (which adapts to find the best fit between the transition state and the active site), enzymes are known for their specificity. The “best fit” results from the shape and the amino acid functional group’s attraction to the substrate. There is a specifically matched enzyme for each substrate and, thus, for each chemical reaction; however, there is flexibility as well.

Metabolism Control Through Enzyme Regulation

It would seem ideal to have a scenario in which all the encoded enzymes in an organism’s genome existed in abundant supply and functioned optimally under all cellular conditions, in all cells, at all times. In reality, this is far from the case. A variety of mechanisms ensure that this does not happen. Cellular needs and conditions vary from cell to cell, and change within individual cells over time. The required enzymes and energetic demands of stomach cells are different from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive cell works much harder to process and break down nutrients during the time that closely follows a meal compared with many hours after a meal. As these cellular demands and conditions vary, so do the amounts and functionality of different enzymes.

Cellular Respiration

Introduction

Energy in Living Systems

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the importance of electrons in the transfer of energy in living systems
* Explain how ATP is used by cells as an energy source

Electrons and Energy

The removal of an electron from a molecule (oxidizing it), results in a decrease in potential energy in the oxidized compound. However, the electron (sometimes as part of a hydrogen atom) does not remain unbonded in the cytoplasm of a cell. Rather, the electron is shifted to a second compound, reducing the second compound. *The shift of an electron from one compound to another removes some potential energy from the first compound (the oxidized compound) and increases the potential energy of the second compound (the reduced compound).* The transfer of electrons between molecules is important because most of the energy stored in atoms and used to fuel cell functions is in the form of high-energy electrons. The transfer of energy in the form of high-energy electrons allows the cell to transfer and use energy in an incremental fashion—in small packages rather than in a single, destructive burst. This chapter focuses on the extraction of energy from food; you will see that as you track the path of the transfers, you are tracking the path of electrons moving through metabolic pathways.

ATP in Living Systems

A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would result in excessive thermal motion that could damage and then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. How? It functions similarly to a rechargeable battery.

Glycolysis

Abstract:
By the end of this section, you will be able to do the following:

* Describe the overall result in terms of molecules produced during the chemical breakdown of glucose by glycolysis
* Compare the output of glycolysis in terms of ATP molecules and NADH molecules produced

First Half of Glycolysis (Energy-Requiring Steps)

**Step 1**. The first step in glycolysis ([link]) is catalyzed by hexokinase, an enzyme with broad specificity that catalyzes the phosphorylation of six-carbon sugars. Hexokinase phosphorylates glucose using ATP as the source of the phosphate, producing glucose-6-phosphate, a more reactive form of glucose. This reaction prevents the phosphorylated glucose molecule from continuing to interact with the GLUT proteins, and it can no longer leave the cell because the negatively charged phosphate will not allow it to cross the hydrophobic interior of the plasma membrane.

Second Half of Glycolysis (Energy-Releasing Steps)

So far, glycolysis has cost the cell two ATP molecules and produced two small, three-carbon sugar molecules. Both of these molecules will proceed through the second half of the pathway, and sufficient energy will be extracted to pay back the two ATP molecules used as an initial investment and produce a profit for the cell of two additional ATP molecules and two even higher-energy NADH molecules.

Outcomes of Glycolysis

Glycolysis begins with glucose and produces two pyruvate molecules, four new ATP molecules, and two molecules of NADH. (Note: two ATP molecules are used in the first half of the pathway to prepare the six-carbon ring for cleavage, so the cell has a *net gain of two ATP molecules* and two NADH molecules for its use). If the cell cannot catabolize the pyruvate molecules further, it will harvest only two ATP molecules from one molecule of glucose. Mature mammalian red blood cells do not have mitochondria and thus are not capable of aerobic respiration—the process in which organisms convert energy in the presence of oxygen—and glycolysis is their sole source of ATP. If glycolysis is interrupted, these cells lose their ability to maintain their sodium-potassium pumps, and eventually, they die.

Oxidation of Pyruvate and the Citric Acid Cycle

Abstract:
By the end of this section, you will be able to do the following:

* Explain how a circular pathway, such as the citric acid cycle, fundamentally differs from a linear biochemical pathway, such as glycolysis
* Describe how pyruvate, the product of glycolysis, is prepared for entry into the citric acid cycle

Breakdown of Pyruvate

In order for pyruvate, the product of glycolysis, to enter the next pathway, it must undergo several changes. The conversion is a three-step process ([link]).

Acetyl CoA to CO2

In the presence of oxygen, acetyl CoA delivers its acetyl (2C) group to a four-carbon molecule, oxaloacetate, to form citrate, a six-carbon molecule with three carboxyl groups; this pathway will harvest the remainder of the extractable energy from what began as a glucose molecule and release the remaining four CO2 molecules. This single pathway is called by different names: the citric acid cycle (for the first intermediate formed—citric acid, or citrate—when acetate joins to the oxaloacetate), the TCA cycle (because citric acid or citrate and isocitrate are tricarboxylic acids), and the Krebs cycle, after Hans Krebs, who first identified the steps in the pathway in the 1930s in pigeon flight muscles.

Citric Acid Cycle

Like the conversion of pyruvate to acetyl CoA, the citric acid cycle takes place in the matrix of mitochondria. Almost all of the enzymes of the citric acid cycle are soluble, with the single exception of the enzyme succinate dehydrogenase, which is embedded in the inner membrane of the mitochondrion. Unlike glycolysis, the citric acid cycle is a closed loop: the last part of the pathway regenerates the compound used in the first step. The eight steps of the cycle are a series of redox, dehydration, hydration, and decarboxylation reactions that produce two carbon dioxide molecules, one GTP/ATP, and the reduced carriers NADH and FADH2 ([link]). *This is considered an aerobic pathway because the NADH and FADH2 produced must transfer their electrons to the next pathway in the system, which will use oxygen.* If this transfer does not occur, the oxidation steps of the citric acid cycle also do not occur. Note that the citric acid cycle produces very little ATP directly and does not directly consume oxygen.

Oxidative Phosphorylation

Abstract:
By the end of this section, you will be able to do the following:

* Describe how electrons move through the electron transport chain and explain what happens to their energy levels during this process
* Explain how a proton (H+) gradient is established and maintained by the electron transport chain

Electron Transport Chain

The electron transport chain ([link]) is the last component of aerobic respiration and is the only part of glucose metabolism that uses atmospheric oxygen. Oxygen continuously diffuses into plant tissues (typically through stomata), as well as into fungi and bacteria; however, in animals, oxygen enters the body through a variety of respiratory systems. Electron transport is a series of redox reactions that resembles a relay race or bucket brigade in that electrons are passed rapidly from one component to the next, to the endpoint of the chain where the electrons reduce molecular oxygen and, along with associated protons, produces water. There are four complexes composed of proteins, labeled I through IV in [link], and the aggregation of these four complexes, together with associated mobile, accessory electron carriers, is called the electron transport chain. The electron transport chain is present with multiple copies in the inner mitochondrial membrane of eukaryotes and within the plasma membrane of prokaryotes.

Chemiosmosis

In chemiosmosis, the free energy from the series of redox reactions just described is used to pump hydrogen ions (protons) across the mitochondrial membrane. The uneven distribution of H+ ions across the membrane establishes both concentration and electrical gradients (thus, an electrochemical gradient), owing to the hydrogen ions’ positive charge and their aggregation on one side of the membrane.

ATP Yield

The number of ATP molecules generated from the catabolism of glucose varies. For example, the number of hydrogen ions that the electron transport chain complexes can pump through the membrane varies between species. Another source of variance stems from the shuttle of electrons across the membranes of the mitochondria. (The NADH generated from glycolysis cannot easily enter mitochondria.) Thus, electrons are picked up on the inside of mitochondria by either NAD+ or FAD+. As you have learned earlier, these FAD+ molecules can transport fewer ions; consequently, fewer ATP molecules are generated when FAD+ acts as a carrier. NAD+ is used as the electron transporter in the liver and FAD+ acts in the brain.

Metabolism without Oxygen

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the fundamental difference between anaerobic cellular respiration and fermentation
* Describe the type of fermentation that readily occurs in animal cells and the conditions that initiate that fermentation

Anaerobic Cellular Respiration

Certain prokaryotes, including some species in the domains Bacteria and Archaea, use anaerobic respiration. For example, a group of archaeans called methanogens reduces carbon dioxide to methane to oxidize NADH. These microorganisms are found in soil and in the digestive tracts of ruminants, such as cows and sheep. Similarly, sulfate-reducing bacteria, most of which are anaerobic ([link]), reduce sulfate to hydrogen sulfide to regenerate NAD+ from NADH.

Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the ways in which carbohydrate metabolic pathways, glycolysis, and the citric acid cycle interrelate with protein and lipid metabolic pathways
* Explain why metabolic pathways are not considered closed systems

Connections of Other Sugars to Glucose Metabolism

Glycogen, a polymer of glucose, is an energy storage molecule in animals. When there is adequate ATP present, excess glucose is stored as glycogen in both liver and muscle cells. The glycogen will be hydrolyzed into glucose 1-phosphate monomers (G-1-P) if blood sugar levels drop. The presence of glycogen as a source of glucose allows ATP to be produced for a longer period of time during exercise. Glycogen is broken down into glucose-1-phosphate (G-1-P) and converted into glucose-6-phosphate (G-6-P) in both muscle and liver cells, and this product enters the glycolytic pathway.

Connections of Proteins to Glucose Metabolism

Proteins are hydrolyzed by a variety of enzymes in cells. Most of the time, the amino acids are recycled into the synthesis of new proteins. If there are excess amino acids, however, or if the body is in a state of starvation, some amino acids will be shunted into the pathways of glucose catabolism ([link]). It is very important to note that each amino acid must have its amino group removed prior to entry into these pathways. The amino group is converted into ammonia. In mammals, the liver synthesizes urea from two ammonia molecules and a carbon dioxide molecule. Thus, urea is the principal waste product in mammals, produced from the nitrogen originating in amino acids, and it leaves the body in urine. It should be noted that amino acids can be synthesized from the intermediates and reactants in the cellular respiration cycle.

Connections of Lipid and Glucose Metabolisms

The lipids connected to the glucose pathway include cholesterol and triglycerides. Cholesterol is a lipid that contributes to cell membrane flexibility and is a precursor of steroid hormones. The synthesis of cholesterol starts with acetyl groups and proceeds in only one direction. The process cannot be reversed.

Regulation of Cellular Respiration

Abstract:
By the end of this section, you will be able to do the following:

* Describe how feedback inhibition would affect the production of an intermediate or product in a pathway
* Identify the mechanism that controls the rate of the transport of electrons through the electron transport chain

Regulatory Mechanisms

A variety of mechanisms is used to control cellular respiration. Some type of control exists at each stage of glucose metabolism. Access of glucose to the cell can be regulated using the GLUT (glucose transporter) proteins that transport glucose ([link]). Different forms of the GLUT protein control passage of glucose into the cells of specific tissues.

Control of Catabolic Pathways

Enzymes, proteins, electron carriers, and pumps that play roles in glycolysis, the citric acid cycle, and the electron transport chain tend to catalyze nonreversible reactions. In other words, if the initial reaction takes place, the pathway is committed to proceeding with the remaining reactions. Whether a particular enzyme activity is released depends upon the energy needs of the cell (as reflected by the levels of ATP, ADP, and AMP).

Photosynthesis

Introduction

Overview of Photosynthesis

Abstract:
By the end of this section, you will be able to do the following:

* Explain the significance of photosynthesis to other living organisms
* Describe the main structures involved in photosynthesis
* Identify the substrates and products of photosynthesis

Main Structures and Summary of Photosynthesis

Photosynthesis is a multi-step process that requires specific wavelengths of visible sunlight, carbon dioxide (which is low in energy), and water as substrates ([link]). After the process is complete, it releases oxygen and produces glyceraldehyde-3-phosphate (G3P), as well as simple carbohydrate molecules (high in energy) that can then be converted into glucose, sucrose, or any of dozens of other sugar molecules. These sugar molecules contain energy and the energized carbon that all living things need to survive.

Basic Photosynthetic Structures

In plants, photosynthesis generally takes place in leaves, which consist of several layers of cells. The process of photosynthesis occurs in a middle layer called the mesophyll. The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called stomata (singular: stoma), which also play roles in the regulation of gas exchange and water balance. The stomata are typically located on the underside of the leaf, which helps to minimize water loss due to high temperatures on the upper surface of the leaf. Each stoma is flanked by guard cells that regulate the opening and closing of the stomata by swelling or shrinking in response to osmotic changes.

The Two Parts of Photosynthesis

Photosynthesis takes place in two sequential stages: the light-dependent reactions and the light-independent reactions. In the light-dependent reactions, energy from sunlight is absorbed by chlorophyll and that energy is converted into stored chemical energy. In the light-independent reactions, the chemical energy harvested during the light-dependent reactions drives the assembly of sugar molecules from carbon dioxide. Therefore, although the light-independent reactions do not use light as a reactant, they require the products of the light-dependent reactions to function. In addition, however, several enzymes of the light-independent reactions are activated by light. The light-dependent reactions utilize certain molecules to temporarily store the energy: These are referred to as *energy carriers*. The energy carriers that move energy from light-dependent reactions to light-independent reactions can be thought of as “full” because they are rich in energy. After the energy is released, the “empty” energy carriers return to the light-dependent reaction to obtain more energy. [link] illustrates the components inside the chloroplast where the light-dependent and light-independent reactions take place.

The Light-Dependent Reactions of Photosynthesis

Abstract:
By the end of this section, you will be able to do the following:

* Explain how plants absorb energy from sunlight
* Describe short and long wavelengths of light
* Describe how and where photosynthesis takes place within a plant

What Is Light Energy?

The sun emits an enormous amount of electromagnetic radiation (solar energy in a spectrum from very short gamma rays to very long radio waves). Humans can see only a tiny fraction of this energy, which we refer to as “visible light.” The manner in which solar energy travels is described as waves. Scientists can determine the amount of energy of a wave by measuring its wavelength (shorter wavelengths are more powerful than longer wavelengths)—the distance between consecutive crest points of a wave. Therefore, a single wave is measured from two consecutive points, such as from crest to crest or from trough to trough ([link]).

Absorption of Light

Light energy initiates the process of photosynthesis when pigments absorb specific wavelengths of visible light. Organic pigments, whether in the human retina or the chloroplast thylakoid, have a narrow range of energy levels that they can absorb. Energy levels lower than those represented by red light are insufficient to raise an orbital electron to an excited (quantum) state. Energy levels higher than those in blue light will physically tear the molecules apart, in a process called bleaching. Our retinal pigments can only “see” (absorb) wavelengths between 700 nm and 400 nm of light, a spectrum that is therefore called visible light. For the same reasons, plants, pigment molecules absorb only light in the wavelength range of 700 nm to 400 nm; plant physiologists refer to this range for plants as photosynthetically active radiation.

How Light-Dependent Reactions Work

The overall function of light-dependent reactions is to convert solar energy into chemical energy in the form of NADPH and ATP. This chemical energy supports the light-independent reactions and fuels the assembly of sugar molecules. The light-dependent reactions are depicted in [link]. Protein complexes and pigment molecules work together to produce NADPH and ATP. The numbering of the photosystems is derived from the order in which they were discovered, not in the order of the transfer of electrons.

Using Light Energy to Make Organic Molecules

Abstract:
By the end of this section, you will be able to do the following:

* Describe the Calvin cycle
* Define carbon fixation
* Explain how photosynthesis works in the energy cycle of all living organisms

The Calvin Cycle

In plants, carbon dioxide (CO2) enters the leaves through stomata, where it diffuses over short distances through intercellular spaces until it reaches the mesophyll cells. Once in the mesophyll cells, CO2 diffuses into the stroma of the chloroplast—the site of light-independent reactions of photosynthesis. These reactions actually have several names associated with them. Another term, the Calvin cycle, is named for the man who discovered it, and because these reactions function as a cycle. Others call it the Calvin-Benson cycle to include the name of another scientist involved in its discovery. The most outdated name is “dark reaction,” because light is not directly required ([link]). However, the term dark reaction can be misleading because it implies incorrectly that the reaction only occurs at night or is independent of light, which is why most scientists and instructors no longer use it.

The Energy Flow

Whether the organism is a bacterium, plant, or animal, all living things access energy by breaking down carbohydrate and other carbon-rich organic molecules. But if plants make carbohydrate molecules, why would they need to break them down, especially when it has been shown that the gas organisms release as a “waste product” (CO2) acts as a substrate for the formation of more food in photosynthesis? Remember, living things need energy to perform life functions. In addition, an organism can either make its own food or eat another organism—either way, the food still needs to be broken down. Finally, in the process of breaking down food, called cellular respiration, heterotrophs release needed energy and produce “waste” in the form of CO2 gas.

Cell Communication

Introduction

Signaling Molecules and Cellular Receptors

Abstract:
By the end of this section, you will be able to do the following:

* Describe four types of signaling mechanisms found in multicellular organisms
* Compare internal receptors with cell-surface receptors
* Recognize the relationship between a ligand’s structure and its mechanism of action

Forms of Signaling

There are four categories of chemical signaling found in multicellular organisms: paracrine signaling, endocrine signaling, autocrine signaling, and direct signaling across gap junctions ([link]). The main difference between the different categories of signaling is the distance that the signal travels through the organism to reach the target cell. We should note here that not all cells are affected by the same signals.

Types of Receptors

Receptors are protein molecules in the target cell or on its surface that bind ligand. There are two types of receptors, internal receptors and cell-surface receptors.

Signaling Molecules

Produced by signaling cells and the subsequent binding to receptors in target cells, ligands act as chemical signals that travel to the target cells to coordinate responses. The types of molecules that serve as ligands are incredibly varied and range from small proteins to small ions like calcium (Ca2+).

Propagation of the Signal

Abstract:
By the end of this section, you will be able to do the following:

* Explain how the binding of a ligand initiates signal transduction throughout a cell
* Recognize the role of phosphorylation in the transmission of intracellular signals
* Evaluate the role of second messengers in signal transmission

Binding Initiates a Signaling Pathway

After the ligand binds to the cell-surface receptor, the activation of the receptor’s intracellular components sets off a chain of events that is called a signaling pathway, sometimes called a signaling cascade. In a signaling pathway, second messengers–enzymes–and activated proteins interact with specific proteins, which are in turn activated in a chain reaction that eventually leads to a change in the cell’s environment ([link]), such as an increase in metabolism or specific gene expression. The events in the cascade occur in a series, much like a current flows in a river. Interactions that occur before a certain point are defined as upstream events, and events after that point are called downstream events.

Methods of Intracellular Signaling

The induction of a signaling pathway depends on the modification of a cellular component by an enzyme. There are numerous enzymatic modifications that can occur, and they are recognized in turn by the next component downstream. The following are some of the more common events in intracellular signaling.

Response to the Signal

Abstract:
By the end of this section, you will be able to do the following:

* Describe how signaling pathways direct protein expression, cellular metabolism, and cell growth
* Identify the function of PKC in signal transduction pathways
* Recognize the role of apoptosis in the development and maintenance of a healthy organism

Gene Expression

Some signal transduction pathways regulate the transcription of RNA. Others regulate the translation of proteins from mRNA. An example of a protein that regulates translation in the nucleus is the MAP kinase ERK. The MAPK/ERK pathway (also known as the Ras-Raf-MEK-ERK pathway) is a chain of proteins in the cell that communicates a signal from a receptor on the surface of the cell to the nuclear DNA. ERK is activated in a phosphorylation cascade when epidermal growth factor (EGF) binds the EGF receptor (see [link]). Upon phosphorylation, ERK enters the nucleus and activates a protein kinase that, in turn, regulates protein translation ([link]).

Increase in Cellular Metabolism

The result of another signaling pathway affects muscle cells. The activation of β-adrenergic receptors in muscle cells by adrenaline leads to an increase in cyclic AMP (cAMP) inside the cell. Also known as epinephrine, adrenaline is a hormone (produced by the adrenal gland located on top of the kidney) that readies the body for short-term emergencies. Cyclic AMP activates PKA (protein kinase A), which in turn phosphorylates two enzymes. The first enzyme promotes the degradation of glycogen by activating intermediate glycogen phosphorylase kinase (GPK) that in turn activates glycogen phosphorylase (GP) that catabolizes glycogen into its constituent glucose monomers. (Recall that your body converts excess glucose to glycogen for short-term storage. When energy is needed, glycogen is quickly reconverted to glucose.) Phosphorylation of the second enzyme, glycogen synthase (GS), inhibits its ability to form glycogen from glucose. In this manner, a muscle cell obtains a ready pool of glucose by activating its formation via glycogen degradation and by inhibiting the use of glucose to form glycogen, thus preventing a futile cycle of glycogen degradation and synthesis. The glucose is then available for use by the muscle cell in response to a sudden surge of adrenaline—the “fight or flight” reflex.

Cell Growth

Cell signaling pathways also play a major role in cell division. Cells do not normally divide unless they are stimulated by signals from other cells. The ligands that promote cell growth are called growth factors. Most growth factors bind to cell-surface receptors that are linked to tyrosine kinases. These cell-surface receptors are called receptor tyrosine kinases (RTKs). Activation of RTKs initiates a signaling pathway that includes a G-protein called RAS, which activates the MAP kinase pathway described earlier. The enzyme MAP kinase then stimulates the expression of proteins that interact with other cellular components to initiate cell division.

Cell Death

When a cell is damaged, superfluous, or potentially dangerous to an organism, a cell can initiate a mechanism to trigger programmed cell death, or apoptosis. Apoptosis allows a cell to die in a controlled manner that prevents the release of potentially damaging molecules from inside the cell. There are many internal checkpoints that monitor a cell’s health; if abnormalities are observed, a cell can spontaneously initiate the process of apoptosis. However, in some cases, such as a viral infection or uncontrolled cell division due to cancer, the cell’s normal checks and balances fail. External signaling can also initiate apoptosis. For example, most normal animal cells have receptors that interact with the extracellular matrix, a network of glycoproteins that provides structural support for cells in an organism. The binding of cellular receptors to the extracellular matrix initiates a signaling cascade within the cell. However, if the cell moves away from the extracellular matrix, the signaling ceases, and the cell undergoes apoptosis. This system keeps cells from traveling through the body and proliferating out of control, as happens with tumor cells that metastasize.

Termination of the Signal Cascade

The aberrant signaling often seen in tumor cells is proof that the termination of a signal at the appropriate time can be just as important as the initiation of a signal. One method of stopping a specific signal is to degrade the ligand or remove it so that it can no longer access its receptor. One reason that hydrophobic hormones like estrogen and testosterone trigger long-lasting events is because they bind carrier proteins. These proteins allow the insoluble molecules to be soluble in blood, but they also protect the hormones from degradation by circulating enzymes.

Signaling in Single-Celled Organisms

Abstract:
By the end of this section, you will be able to do the following:

* Describe how single-celled yeasts use cell signaling to communicate with one another
* Relate the role of quorum sensing to the ability of some bacteria to form biofilms

Signaling in Yeast

Yeasts are eukaryotes (fungi), and the components and processes found in yeast signals are similar to those of cell-surface receptor signals in multicellular organisms. Budding yeasts ([link]) are able to participate in a process that is similar to sexual reproduction that entails two haploid cells (cells with one-half the normal number of chromosomes) combining to form a diploid cell (a cell with two sets of each chromosome, which is what normal body cells contain). In order to find another haploid yeast cell that is prepared to mate, budding yeasts secrete a signaling molecule called mating factor. When mating factor binds to cell-surface receptors in other yeast cells that are nearby, they stop their normal growth cycles and initiate a cell signaling cascade that includes protein kinases and GTP-binding proteins that are similar to G-proteins.

Signaling in Bacteria

Signaling in bacteria enables bacteria to monitor extracellular conditions, ensure that there are sufficient amounts of nutrients, and ensure that hazardous situations are avoided. There are circumstances, however, when bacteria communicate with each other.

Cell Reproduction

Introduction

Cell Division

Abstract:
By the end of this section, you will be able to do the following:

* Describe the structure of prokaryotic and eukaryotic genomes
* Distinguish between chromosomes, genes, and traits
* Describe the mechanisms of chromosome compaction

Genomic DNA

Before discussing the steps a cell must undertake to replicate and divide its DNA, a deeper understanding of the structure and function of a cell’s genetic information is necessary. A cell’s DNA, packaged as a double-stranded DNA molecule, is called its genome. In prokaryotes, the genome is composed of a single, double-stranded DNA molecule in the form of a loop or circle ([link]). The region in the cell containing this genetic material is called a nucleoid. Some prokaryotes also have smaller loops of DNA called plasmids that are not essential for normal growth. Bacteria can exchange these plasmids with other bacteria, sometimes receiving beneficial new genes that the recipient can add to their chromosomal DNA. *Antibiotic resistance* is one trait that often spreads through a bacterial colony through plasmid exchange from resistant donors to recipient cells.

Eukaryotic Chromosomal Structure and Compaction

If the DNA from all 46 chromosomes in a human cell nucleus were laid out end-to-end, it would measure approximately two meters; however, its diameter would be only 2 nm! Considering that the size of a typical human cell is about 10 µm (100,000 cells lined up to equal one meter), DNA must be *tightly packaged* to fit in the cell’s nucleus. At the same time, it must also be readily accessible for the genes to be expressed. For this reason, the long strands of DNA are condensed into compact chromosomes during certain stages of the cell cycle. There are a number of ways that chromosomes are compacted.

The Cell Cycle

Abstract:
By the end of this section, you will be able to do the following:

* Describe the three stages of interphase
* Discuss the behavior of chromosomes during karyokinesis/mitosis
* Explain how the cytoplasmic content is divided during cytokinesis
* Define the quiescent G0 phase

Interphase

During interphase, the cell undergoes normal growth processes while also preparing for cell division. In order for a cell to move from interphase into the mitotic phase, many internal and external conditions must be met. The three stages of interphase are called *G1, S, and G2.*

The Mitotic Phase

The mitotic phase is a multistep process during which the duplicated chromosomes are aligned, separated, and move into two new, identical daughter cells. The first portion of the mitotic phase is called karyokinesis, or nuclear division. As we have just seen, the second portion of the mitotic phase (and often viewed as a process separate from and following mitosis) is called cytokinesis—the physical separation of the cytoplasmic components into the two daughter cells.

G0 Phase

Not all cells adhere to the classic cell-cycle pattern in which a newly formed daughter cell immediately enters the preparatory phases of interphase, closely followed by the mitotic phase, and cytokinesis. Cells in G0 phase are not actively preparing to divide. The cell is in a quiescent (inactive) stage that occurs when cells exit the cell cycle. Some cells enter G0 temporarily due to environmental conditions such as availability of nutrients, or stimulation by growth factors. The cell will remain in this phase until conditions improve or until an external signal triggers the onset of G1. Other cells that never or rarely divide, such as mature cardiac muscle and nerve cells, remain in G0 permanently.

Control of the Cell Cycle

Abstract:
By the end of this section, you will be able to do the following:

* Understand how the cell cycle is controlled by mechanisms that are both internal and external to the cell
* Explain how the three internal “control checkpoints” occur at the end of G1, at the G2/M transition, and during metaphase
* Describe the molecules that control the cell cycle through positive and negative regulation

Regulation of the Cell Cycle by External Events

Both the initiation and inhibition of cell division are triggered by events external to the cell when it is about to begin the replication process. An event may be as simple as the death of nearby cells or as sweeping as the release of growth-promoting hormones, such as human growth hormone (HGH or hGH). A lack of HGH can *inhibit* cell division, resulting in dwarfism, whereas too much HGH can result in gigantism. Crowding of cells can also inhibit cell division. In contrast, a factor that can initiate cell division is the size of the cell: As a cell grows, it becomes physiologically inefficient due to its decreasing surface-to-volume ratio. The solution to this problem is to divide.

Regulation at Internal Checkpoints

It is essential that the daughter cells produced be exact duplicates of the parent cell. Mistakes in the duplication or distribution of the chromosomes lead to mutations that may be passed forward to every new cell produced from an abnormal cell. To prevent a compromised cell from continuing to divide, there are internal control mechanisms that operate at three main cell-cycle checkpoints: A checkpoint is one of several points in the eukaryotic cell cycle at which the progression of a cell to the next stage in the cycle can be halted until conditions are favorable. These checkpoints occur near the end of G1, at the G2/M transition, and during metaphase ([link]).

Regulator Molecules of the Cell Cycle

In addition to the internally controlled checkpoints, there are two groups of intracellular molecules that regulate the cell cycle. These regulatory molecules either promote progress of the cell to the next phase (positive regulation) or halt the cycle (negative regulation). Regulator molecules may act individually, or they can influence the activity or production of other regulatory proteins. Therefore, the failure of a single regulator may have almost no effect on the cell cycle, especially if more than one mechanism controls the same event. However, the effect of a deficient or non-functioning regulator can be wide-ranging and possibly fatal to the cell if multiple processes are affected.

Cancer and the Cell Cycle

Abstract:
By the end of this section, you will be able to do the following:

* Describe how cancer is caused by uncontrolled cell growth
* Understand how proto-oncogenes are normal cell genes that, when mutated, become oncogenes
* Describe how tumor suppressors function
* Explain how mutant tumor suppressors cause cancer

Proto-oncogenes

The genes that code for the positive cell-cycle regulators are called proto-oncogenes. Proto-oncogenes are normal genes that, when mutated in certain ways, become oncogenes—genes that cause a cell to become cancerous. Consider what might happen to the cell cycle in a cell with a recently acquired oncogene. In most instances, the alteration of the DNA sequence will result in a less functional (or non-functional) protein. The result is detrimental to the cell and will likely prevent the cell from completing the cell cycle; however, the organism is not harmed because the mutation will not be carried forward. If a cell cannot reproduce, the mutation is not propagated and the damage is minimal. Occasionally, however, a gene mutation causes a change that increases the activity of a positive regulator. For example, a mutation that allows Cdk to be activated without being partnered with cyclin could push the cell cycle past a checkpoint before all of the required conditions are met. If the resulting daughter cells are too damaged to undergo further cell divisions, the mutation would not be propagated and no harm would come to the organism. However, if the atypical daughter cells are able to undergo further cell divisions, subsequent generations of cells may accumulate even more mutations, some possibly in additional genes that regulate the cell cycle.

Tumor Suppressor Genes

Like proto-oncogenes, many of the negative cell-cycle regulatory proteins were discovered in cells that had become cancerous. Tumor suppressor genes are segments of DNA that code for negative regulator proteins, the type of regulators that, when activated, can prevent the cell from undergoing uncontrolled division. The collective function of the best-understood tumor suppressor gene proteins, Rb, p53, and p21, is to put up a roadblock to cell-cycle progression until certain events are completed. A cell that carries a mutated form of a negative regulator might not be able to halt the cell cycle if there is a problem. Tumor suppressors are similar to brakes in a vehicle: Malfunctioning brakes can contribute to a car crash!

Prokaryotic Cell Division

Abstract:
By the end of this section, you will be able to do the following:

* Describe the process of binary fission in prokaryotes
* Explain how FtsZ and tubulin proteins are examples of homology

Binary Fission

Due to the relative simplicity of the prokaryotes, the cell division process is a less complicated and much more rapid process than cell division in eukaryotes. As a review of the general information on cell division we discussed at the beginning of this chapter, recall that the single, circular DNA chromosome of bacteria occupies a specific location, the nucleoid region, within the cell ([link]). Although the DNA of the nucleoid is associated with proteins that aid in packaging the molecule into a compact size, there are no histone proteins and thus no nucleosomes in prokaryotes. The packing proteins of bacteria are, however, related to the cohesin and condensin proteins involved in the chromosome compaction of eukaryotes.

Genetics

Meiosis and Sexual Reproduction

Introduction

The Process of Meiosis

Abstract:
By the end of this section, you will be able to do the following:

* Describe the behavior of chromosomes during meiosis, and the differences between the first and second meiotic divisions
* Describe the cellular events that take place during meiosis
* Explain the differences between meiosis and mitosis
* Explain the mechanisms within the meiotic process that produce genetic variation among the haploid gametes

Meiosis I

Meiosis is preceded by an interphase consisting of G1, S, and G2 phases, which are nearly identical to the phases preceding mitosis. The G1 phase (the “first gap phase”) is focused on cell growth. During the S phase—the second phase of interphase—the cell copies or *replicates* the DNA of the chromosomes. Finally, in the G2 phase (the “second gap phase”) the cell undergoes the final preparations for meiosis.

Meiosis II

In some species, cells enter a brief interphase, or interkinesis, before entering meiosis II. Interkinesis lacks an S phase, so chromosomes are not duplicated. The two cells produced in meiosis I go through the events of meiosis II in synchrony. During meiosis II, the sister chromatids within the two daughter cells separate, forming four new haploid gametes. The mechanics of meiosis II are similar to mitosis, except that each dividing cell has only one set of homologous chromosomes, each with two chromatids. Therefore, each cell has half the number of sister chromatids to separate out as a diploid cell undergoing mitosis. In terms of chromosomal content, cells at the start of meiosis II are similar to haploid cells in G2, preparing to undergo mitosis.

Comparing Meiosis and Mitosis

Mitosis and meiosis are both forms of division of the nucleus in eukaryotic cells. They share some similarities, but also exhibit a number of distinct processes that lead to very different outcomes ([link]). Mitosis is a single nuclear division that results in two nuclei that are usually partitioned into two new cells. The nuclei resulting from a mitotic division are genetically identical to the original nucleus. They have the same number of sets of chromosomes: one set in the case of haploid cells and two sets in the case of diploid cells. In contrast, meiosis consists of two nuclear divisions resulting in four nuclei that are usually partitioned into four new, genetically distinct cells. The four nuclei produced during meiosis are not genetically identical, and they contain one chromosome set only. This is half the number of chromosome sets of the original cell, which is diploid.

Sexual Reproduction

Abstract:
By the end of this section, you will be able to do the following:

* Explain that meiosis and sexual reproduction are highly evolved traits
* Identify variation among offspring as a potential evolutionary advantage of sexual reproduction
* Describe the three different life-cycle types among sexually reproducing multicellular organisms.

Life Cycles of Sexually Reproducing Organisms

Fertilization and meiosis alternate in sexual life cycles. What happens between these two events depends on the organism’s “reproductive strategy.” The process of meiosis reduces the chromosome number by half. Fertilization, the joining of two haploid gametes, restores the diploid condition. Some organisms have a multicellular diploid stage that is most obvious and only produce haploid reproductive cells. Animals, including humans, have this type of life cycle. Other organisms, such as fungi, have a multicellular haploid stage that is most obvious. Plants and some algae have alternation of generations, in which they have multicellular diploid and haploid life stages that are apparent to different degrees depending on the group.

Mendel's Experiments and Heredity

Introduction

Mendel’s Experiments and the Laws of Probability

Abstract:
By the end of this section, you will be able to do the following:

* Describe the scientific reasons for the success of Mendel’s experimental work
* Describe the expected outcomes of monohybrid crosses involving dominant and recessive alleles
* Apply the sum and product rules to calculate probabilities

Mendel’s Model System

Mendel’s seminal work was accomplished using the garden pea, *Pisum sativum*, to study inheritance. This species naturally self-fertilizes, such that pollen encounters ova within individual flowers. The flower petals remain sealed tightly until after pollination, preventing pollination from other plants. The result is highly inbred, or “true-breeding,” pea plants. These are plants that always produce offspring that look like the parent. By experimenting with true-breeding pea plants, Mendel avoided the appearance of unexpected traits in offspring that might occur if the plants were not true breeding. The garden pea also grows to maturity within one season, meaning that several generations could be evaluated over a relatively short time. Finally, large quantities of garden peas could be cultivated simultaneously, allowing Mendel to conclude that his results did not come about simply by chance.

Mendelian Crosses

Mendel performed hybridizations, which involve mating two true-breeding individuals that have different traits. In the pea, which is naturally self-pollinating, this is done by manually transferring pollen from the anther of a mature pea plant of one variety to the stigma of a separate mature pea plant of the second variety. In plants, pollen carries the male gametes (sperm) to the stigma, a sticky organ that traps pollen and allows the sperm to move down the pistil to the female gametes (ova) below. To prevent the pea plant that was receiving pollen from self-fertilizing and confounding his results, Mendel painstakingly removed all of the anthers from the plant’s flowers before they had a chance to mature.

Garden Pea Characteristics Revealed the Basics of Heredity

In his 1865 publication, Mendel reported the results of his crosses involving seven different characteristics, each with two contrasting traits. A trait is defined as a variation in the physical appearance of a heritable characteristic. The characteristics included plant height, seed texture, seed color, flower color, pea pod size, pea pod color, and flower position. For the characteristic of flower color, for example, the two contrasting traits were white versus violet. To fully examine each characteristic, Mendel generated large numbers of F1 and F2 plants, reporting results from 19,959 F2 plants alone. His findings were consistent.

Probability Basics

Probabilities are mathematical measures of likelihood. The empirical probability of an event is calculated by dividing the number of times the event occurs by the total number of opportunities for the event to occur. It is also possible to calculate theoretical probabilities by dividing the number of times that an event is *expected* to occur by the number of times that it could occur. Empirical probabilities come from observations, like those of Mendel. Theoretical probabilities, on the other hand, come from knowing how the events are produced and assuming that the probabilities of individual outcomes are equal. A probability of one for some event indicates that it is guaranteed to occur, whereas a probability of zero indicates that it is guaranteed not to occur. An example of a genetic event is a round seed produced by a pea plant.

Characteristics and Traits

Abstract:
By the end of this section, you will be able to do the following:

* Explain the relationship between genotypes and phenotypes in dominant and recessive gene systems
* Develop a Punnett square to calculate the expected proportions of genotypes and phenotypes in a monohybrid cross
* Explain the purpose and methods of a test cross
* Identify non-Mendelian inheritance patterns such as incomplete dominance, codominance, recessive lethals, multiple alleles, and sex linkage

Phenotypes and Genotypes

Two alleles for a given gene in a diploid organism are expressed and interact to produce physical characteristics. The observable traits expressed by an organism are referred to as its phenotype. An organism’s underlying genetic makeup, consisting of both physically visible and non-expressed alleles, is called its genotype. Mendel’s hybridization experiments demonstrate the difference between phenotype and genotype. When true-breeding plants in which one parent had yellow pods and one had green pods were cross-fertilized, all of the F1 hybrid offspring had yellow pods. That is, the hybrid offspring were phenotypically identical to the true-breeding parent with yellow pods. However, we know that the allele donated by the parent with green pods was not simply lost because it reappeared in some of the F2 offspring. Therefore, the F1 plants must have been genotypically different from the parent with yellow pods.

The Punnett Square Approach for a Monohybrid Cross

When fertilization occurs between two true-breeding parents that differ in only one characteristic, the process is called a monohybrid cross, and the resulting offspring are monohybrids. Mendel performed seven monohybrid crosses involving contrasting traits for each characteristic. On the basis of his results in F1 and F2 generations, Mendel postulated that each parent in the monohybrid cross contributed one of two paired unit factors to each offspring, and every possible combination of unit factors was equally likely.

Alternatives to Dominance and Recessiveness

Mendel’s experiments with pea plants suggested that: (1) two “units” or alleles exist for every gene; (2) alleles maintain their integrity in each generation (no blending); and (3) in the presence of the dominant allele, the recessive allele is hidden and makes no contribution to the phenotype. Therefore, recessive alleles can be “carried” and not expressed by individuals. Such heterozygous individuals are sometimes referred to as “carriers.” Further genetic studies in other plants and animals have shown that much more complexity exists, but that the fundamental principles of Mendelian genetics still hold true. In the sections to follow, we consider some of the extensions of Mendelism. If Mendel had chosen an experimental system that exhibited these genetic complexities, it’s possible that he would not have understood what his results meant.

Laws of Inheritance

Abstract:
By the end of this section, you will be able to do the following:

* Explain Mendel’s law of segregation and independent assortment in terms of genetics and the events of meiosis
* Use the forked-line method and the probability rules to calculate the probability of genotypes and phenotypes from multiple gene crosses
* Explain the effect of linkage and recombination on gamete genotypes
* Explain the phenotypic outcomes of epistatic effects between genes

Pairs of Unit Factors, or Genes

Mendel proposed first that paired unit factors of heredity were transmitted faithfully from generation to generation by the dissociation and reassociation of paired factors during gametogenesis and fertilization, respectively. After he crossed peas with contrasting traits and found that the recessive trait resurfaced in the F2 generation, Mendel deduced that hereditary factors must be inherited as discrete units. This finding contradicted the belief at that time that parental traits were blended in the offspring.

Alleles Can Be Dominant or Recessive

Mendel’s law of dominance states that in a heterozygote, one trait will conceal the presence of another trait for the same characteristic. Rather than both alleles contributing to a phenotype, the dominant allele will be expressed exclusively. The recessive allele will remain “latent” but will be transmitted to offspring by the same manner in which the dominant allele is transmitted. The recessive trait will only be expressed by offspring that have two copies of this allele ([link]), and these offspring will breed true when self-crossed.

Equal Segregation of Alleles

Observing that true-breeding pea plants with contrasting traits gave rise to F1 generations that all expressed the dominant trait and F2 generations that expressed the dominant and recessive traits in a 3:1 ratio, Mendel proposed the law of segregation. This law states that paired unit factors (genes) must segregate equally into gametes such that offspring have an equal likelihood of inheriting either factor. For the F2 generation of a monohybrid cross, the following three possible combinations of genotypes could result: homozygous dominant, heterozygous, or homozygous recessive. Because heterozygotes could arise from two different pathways (receiving one dominant and one recessive allele from either parent), and because heterozygotes and homozygous dominant individuals are phenotypically identical, the law supports Mendel’s observed 3:1 phenotypic ratio. The equal segregation of alleles is the reason we can apply the Punnett square to accurately predict the offspring of parents with known genotypes. The physical basis of Mendel’s law of segregation is the first division of meiosis, in which the homologous chromosomes with their different versions of each gene are segregated into daughter nuclei. The role of the meiotic segregation of chromosomes in sexual reproduction was not understood by the scientific community during Mendel’s lifetime.

Independent Assortment

Mendel’s law of independent assortment states that genes do not influence each other with regard to the sorting of alleles into gametes, and every possible combination of alleles for every gene is equally likely to occur. The independent assortment of genes can be illustrated by the dihybrid cross, a cross between two true-breeding parents that express different traits for two characteristics. Consider the characteristics of seed color and seed texture for two pea plants, one that has green, wrinkled seeds (*yyrr*) and another that has yellow, round seeds (*YYRR*). Because each parent is homozygous, the law of segregation indicates that the gametes for the green/wrinkled plant all are *yr*, and the gametes for the yellow/round plant are all *YR*. Therefore, the F1 generation of offspring all are *YyRr* ([link]).

Linked Genes Violate the Law of Independent Assortment

Although all of Mendel’s pea characteristics behaved according to the law of independent assortment, we now know that some allele combinations are not inherited independently of each other. Genes that are located on separate non-homologous chromosomes will always sort independently. However, each chromosome contains hundreds or thousands of genes, organized linearly on chromosomes like beads on a string. The segregation of alleles into gametes can be influenced by linkage, in which genes that are located physically close to each other on the same chromosome are more likely to be inherited as a pair. However, because of the process of recombination, or “crossover,” it is possible for two genes on the same chromosome to behave independently, or as if they are not linked. To understand this, let’s consider the biological basis of gene linkage and recombination.

Epistasis

Mendel’s studies in pea plants implied that the sum of an individual’s phenotype was controlled by genes (or as he called them, unit factors), such that every characteristic was distinctly and completely controlled by a single gene. In fact, single observable characteristics are almost always under the influence of multiple genes (each with two or more alleles) acting in unison. For example, at least eight genes contribute to eye color in humans.

Modern Understandings of Inheritance

Introduction

Chromosomal Theory and Genetic Linkage

Abstract:
By the end of this section, you will be able to do the following:

* Discuss Sutton’s Chromosomal Theory of Inheritance
* Describe genetic linkage
* Explain the process of homologous recombination, or crossing over
* Describe chromosome creation
* Calculate the distances between three genes on a chromosome using a three-point test cross

Chromosomal Theory of Inheritance

The speculation that chromosomes might be the key to understanding heredity led several scientists to examine Mendel’s publications and reevaluate his model in terms of chromosome behavior during mitosis and meiosis. In 1902, Theodor Boveri observed that proper sea urchin embryonic development does not occur unless chromosomes are present. That same year, Walter Sutton observed chromosome separation into daughter cells during meiosis ([link]). Together, these observations led to the Chromosomal Theory of Inheritance, which identified chromosomes as the genetic material responsible for Mendelian inheritance.

Genetic Linkage and Distances

Mendel’s work suggested that traits are inherited independently of each other. Morgan identified a 1:1 correspondence between a segregating trait and the X chromosome, suggesting that random chromosome segregation was the physical basis of Mendel’s model. This also demonstrated that linked genes disrupt Mendel’s predicted outcomes. That each chromosome can carry many linked genes explains how individuals can have many more traits than they have chromosomes. However, researchers in Morgan’s laboratory suggested that alleles positioned on the same chromosome were not always inherited together. During meiosis, linked genes somehow became unlinked.

Chromosomal Basis of Inherited Disorders

Abstract:
By the end of this section, you will be able to do the following:

* Describe how a karyogram is created
* Explain how nondisjunction leads to disorders in chromosome number
* Compare disorders that aneuploidy causes
* Describe how errors in chromosome structure occur through inversions and translocations

Chromosome Identification

Chromosome isolation and microscopic observation forms the basis of cytogenetics and is the primary method by which clinicians detect chromosomal abnormalities in humans. A karyotype is the number and appearance of chromosomes, and includes their length, banding pattern, and centromere position. To obtain a view of an individual’s karyotype, cytologists photograph the chromosomes and then cut and paste each chromosome into a chart, or karyogram. Another name is an ideogram ([link]).

Chromosome Number Disorders

Of all of the chromosomal disorders, chromosome number abnormalities are the most obviously identifiable from a karyogram. Chromosome number disorders include duplicating or losing entire chromosomes, as well as changes in the number of complete sets of chromosomes. They are caused by nondisjunction, which occurs when homologous chromosome pairs or sister chromatids fail to separate during meiosis. Misaligned or incomplete synapsis, or a spindle apparatus dysfunction that facilitates chromosome migration, can cause nondisjunction. The risk of nondisjunction occurring increases with the parents' age.

Aneuploidy

Scientists call an individual with the appropriate number of chromosomes for their species euploid. In humans, euploidy corresponds to 22 pairs of autosomes and one pair of sex chromosomes. An individual with an error in chromosome number is described as aneuploid, a term that includes monosomy (losing one chromosome) or trisomy (gaining an extraneous chromosome). Monosomic human zygotes missing any one copy of an autosome invariably fail to develop to birth because they lack essential genes. This underscores the importance of “gene dosage” in humans. Most autosomal trisomies also fail to develop to birth; however, duplications of some smaller chromosomes (13, 15, 18, 21, or 22) can result in offspring that survive for several weeks to many years. Trisomic individuals suffer from a different type of genetic imbalance: an excess in gene dose. Individuals with an extra chromosome may synthesize an abundance of the gene products, which that chromosome encodes. This extra dose (150 percent) of specific genes can lead to a number of functional challenges and often precludes development. The most common trisomy among viable births is that of chromosome 21, which corresponds to Down Syndrome. Short stature and stunted digits, facial distinctions that include a broad skull and large tongue, and significant developmental delays characterize individuals with this inherited disorder. We can correlate the incidence of Down syndrome with maternal age. Older people are more likely to become pregnant with fetuses carrying the trisomy 21 genotype ([link]).

Polyploidy

We call an individual with more than the correct number of chromosome sets (two for diploid species) polyploid. For instance, fertilizing an abnormal diploid egg with a normal haploid sperm would yield a triploid zygote. Polyploid animals are extremely rare, with only a few examples among the flatworms, crustaceans, amphibians, fish, and lizards. Polyploid animals are sterile because meiosis cannot proceed normally and instead produces mostly aneuploid daughter cells that cannot yield viable zygotes. Rarely, polyploid animals can reproduce asexually by haplodiploidy, in which an unfertilized egg divides mitotically to produce offspring. In contrast, polyploidy is very common in the plant kingdom, and polyploid plants tend to be larger and more robust than euploids of their species ([link]).

Sex Chromosome Nondisjunction in Humans

Humans display dramatic deleterious effects with autosomal trisomies and monosomies. Therefore, it may seem counterintuitive that human females and males can function normally, despite carrying different numbers of the X chromosome. Rather than a gain or loss of autosomes, variations in the number of sex chromosomes occur with relatively mild effects. In part, this happens because of the molecular process X inactivation. Early in development, when female mammalian embryos consist of just a few thousand cells (relative to trillions in the newborn), one X chromosome in each cell inactivates by tightly condensing into a quiescent (dormant) structure, or a Barr body. The chance that an X chromosome (maternally or paternally derived) inactivates in each cell is random, but once this occurs, all cells derived from that one will have the same inactive X chromosome or Barr body. By this process, females compensate for their double genetic dose of X chromosome. In so-called “tortoiseshell” cats, we observe embryonic X inactivation as color variegation ([link]). Females that are heterozygous for an X-linked coat color gene will express one of two different coat colors over different regions of their body, corresponding to whichever X chromosome inactivates in that region's embryonic cell progenitor.

Duplications and Deletions

In addition to losing or gaining an entire chromosome, a chromosomal segment may duplicate or lose itself. Duplications and deletions often produce offspring that survive but exhibit abnormalities. Duplicated chromosomal segments may fuse to existing chromosomes or may be free in the nucleus. Cri-du-chat (from the French for “cry of the cat”) is a syndrome that occurs with nervous system abnormalities and identifiable physical features that result from a deletion of most 5p (the small arm of chromosome 5) ([link]). Infants with this genotype emit a characteristic high-pitched cry on which the disorder’s name is based.

Chromosomal Structural Rearrangements

Cytologists have characterized numerous structural rearrangements in chromosomes, but chromosome inversions and translocations are the most common. We can identify both during meiosis by the adaptive pairing of rearranged chromosomes with their former homologs to maintain appropriate gene alignment. If the genes on two homologs are not oriented correctly, a recombination event could result in losing genes from one chromosome and gaining genes on the other. This would produce aneuploid gametes.

DNA Structure and Function

Introduction

Historical Basis of Modern Understanding

Abstract:
By the end of this section, you will be able to do the following:

* Explain transformation of DNA
* Describe the key experiments that helped identify that DNA is the genetic material
* State and explain Chargaff’s rules

DNA Structure and Sequencing

Abstract:
By the end of this section, you will be able to do the following:

* Describe the structure of DNA
* Explain the Sanger method of DNA sequencing
* Discuss the similarities and differences between eukaryotic and prokaryotic DNA

DNA Sequencing Techniques

Until the 1990s, the sequencing of DNA (reading the sequence of DNA) was a relatively expensive and long process. Using radiolabeled nucleotides also compounded the problem through safety concerns. With currently available technology and automated machines, the process is cheaper, safer, and can be completed in a matter of hours. Fred Sanger developed the sequencing method used for the human genome sequencing project, which is widely used today ([link]).

Basics of DNA Replication

Abstract:
By the end of this section, you will be able to do the following:

* Explain how the structure of DNA reveals the replication process
* Describe the Meselson and Stahl experiments

DNA Replication in Prokaryotes

Abstract:
By the end of this section, you will be able to do the following:

* Explain the process of DNA replication in prokaryotes
* Discuss the role of different enzymes and proteins in supporting this process

DNA Replication in Eukaryotes

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the similarities and differences between DNA replication in eukaryotes and prokaryotes
* State the role of telomerase in DNA replication

Telomere replication

Unlike prokaryotic chromosomes, eukaryotic chromosomes are linear. As you’ve learned, the enzyme DNA pol can add nucleotides only in the 5' to 3' direction. In the leading strand, synthesis continues until the end of the chromosome is reached. On the lagging strand, DNA is synthesized in short stretches, each of which is initiated by a separate primer. When the replication fork reaches the end of the linear chromosome, there is no way to replace the primer on the 5’ end of the lagging strand. The DNA at the ends of the chromosome thus remains unpaired, and over time these ends, called **telomeres,** may get progressively shorter as cells continue to divide.

DNA Repair

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the different types of mutations in DNA
* Explain DNA repair mechanisms

Genes and Proteins

Introduction

The Genetic Code

Abstract:
By the end of this section, you will be able to do the following:

* Explain the “central dogma” of DNA-protein synthesis
* Describe the genetic code and how the nucleotide sequence prescribes the amino acid and the protein sequence

The Central Dogma: DNA Encodes RNA; RNA Encodes Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma ([link]), which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis, while keeping the DNA itself intact and protected. The copying of DNA to RNA is relatively straightforward, with one nucleotide being added to the mRNA strand for every nucleotide read in the DNA strand. The translation to protein is a bit more complex because three mRNA nucleotides correspond to one amino acid in the polypeptide sequence. However, the translation to protein is still systematic and colinear, such that nucleotides 1 to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino acid 2, and so on.

Prokaryotic Transcription

Abstract:
By the end of this section, you will be able to do the following:

* List the different steps in prokaryotic transcription
* Discuss the role of promoters in prokaryotic transcription
* Describe how and when transcription is terminated

Initiation of Transcription in Prokaryotes

Prokaryotes do not have membrane-enclosed nuclei. Therefore, the processes of transcription, translation, and mRNA degradation can all occur simultaneously. The intracellular level of a bacterial protein can quickly be amplified by multiple transcription and translation events that occur concurrently on the same DNA template. Prokaryotic genomes are very compact, and prokaryotic transcripts often cover more than one gene or cistron (a coding sequence for a single protein). Polycistronic mRNAs are then translated to produce more than one kind of protein.

Elongation and Termination in Prokaryotes

The transcription elongation phase begins with the release of the *σ* subunit from the polymerase. The dissociation of *σ* allows the core enzyme to proceed along the DNA template, synthesizing mRNA in the 5' to 3' direction at a rate of approximately 40 nucleotides per second. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it. The base pairing between DNA and RNA is not stable enough to maintain the stability of the mRNA synthesis components. Instead, the RNA polymerase acts as a stable linker between the DNA template and the nascent RNA strands to ensure that elongation is not interrupted prematurely.

Prokaryotic Termination Signals

Once a gene is transcribed, the prokaryotic polymerase needs to be instructed to dissociate from the DNA template and liberate the newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals. One is protein-based and the other is RNA-based. Rho-dependent termination is controlled by the rho (ρ) protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase encounters a run of G nucleotides on the DNA template and it stalls. As a result, the rho protein collides with the polymerase. The interaction with rho releases the mRNA from the transcription bubble.

Eukaryotic Transcription

Abstract:
By the end of this section, you will be able to do the following:

* List the steps in eukaryotic transcription
* Discuss the role of RNA polymerases in transcription
* Compare and contrast the three RNA polymerases
* Explain the significance of transcription factors

Initiation of Transcription in Eukaryotes

Unlike the prokaryotic polymerase that can bind to a DNA template on its own, eukaryotes require several other proteins, called transcription factors, to first bind to the promoter region and then to help recruit the appropriate polymerase.

Eukaryotic Elongation and Termination

Following the formation of the preinitiation complex, the polymerase is released from the other transcription factors, and elongation is allowed to proceed as it does in prokaryotes with the polymerase synthesizing pre-mRNA in the 5' to 3' direction. As discussed previously, RNA polymerase II transcribes the major share of eukaryotic genes, so in this section we will focus on how this polymerase accomplishes elongation and termination.

RNA Processing in Eukaryotes

Abstract:
By the end of this section, you will be able to do the following:

* Describe the different steps in RNA processing
* Understand the significance of exons, introns, and splicing for mRNAs
* Explain how tRNAs and rRNAs are processed

mRNA Processing

The eukaryotic pre-mRNA undergoes extensive processing before it is ready to be translated. Eukaryotic protein-coding sequences are not continuous, as they are in prokaryotes. The coding sequences (exons) are interrupted by noncoding introns, which must be removed to make a translatable mRNA. The additional steps involved in eukaryotic mRNA maturation also create a molecule with a much longer half-life than a prokaryotic mRNA. Eukaryotic mRNAs last for several hours, whereas the typical *E. coli* mRNA lasts no more than five seconds.

Processing of tRNAs and rRNAs

The tRNAs and rRNAs are structural molecules that have roles in protein synthesis; however, these RNAs are not themselves translated. Pre-rRNAs are transcribed, processed, and assembled into ribosomes in the nucleolus. Pre-tRNAs are transcribed and processed in the nucleus and then released into the cytoplasm where they are linked to free amino acids for protein synthesis.

Ribosomes and Protein Synthesis

Abstract:
By the end of this section, you will be able to do the following:

* Describe the different steps in protein synthesis
* Discuss the role of ribosomes in protein synthesis

The Protein Synthesis Machinery

In addition to the mRNA template, many molecules and macromolecules contribute to the process of translation. The composition of each component may vary across species; for example, ribosomes may consist of different numbers of rRNAs and polypeptides depending on the organism. However, the general structures and functions of the protein synthesis machinery are comparable from bacteria to human cells. Translation requires the input of an mRNA template, ribosomes, tRNAs, and various enzymatic factors. (Note: A ribosome can be thought of as an enzyme whose amino acid binding sites are specified by mRNA.)

The Mechanism of Protein Synthesis

As with mRNA synthesis, protein synthesis can be divided into three phases: *initiation, elongation, and termination*. The process of translation is similar in prokaryotes and eukaryotes. Here we’ll explore how translation occurs in *E. coli*, a representative prokaryote, and specify any differences between prokaryotic and eukaryotic translation.

Protein Folding, Modification, and Targeting

During and after translation, individual amino acids may be chemically modified, signal sequences appended, and the new protein “folded” into a distinct three-dimensional structure as a result of intramolecular interactions. A signal sequence is a short sequence at the amino end of a protein that directs it to a specific cellular compartment. These sequences can be thought of as the protein’s “train ticket” to its ultimate destination, and are recognized by signal-recognition proteins that act as conductors. For instance, a specific signal sequence terminus will direct a protein to the mitochondria or chloroplasts (in plants). Once the protein reaches its cellular destination, the signal sequence is usually clipped off.

Gene Expression

Introduction

Regulation of Gene Expression

Abstract:
By the end of this section, you will be able to do the following:

* Discuss why every cell does not express all of its genes all of the time
* Describe how prokaryotic gene regulation occurs at the transcriptional level
* Discuss how eukaryotic gene regulation occurs at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels

Prokaryotic versus Eukaryotic Gene Expression

To understand how gene expression is regulated, we must first understand how a gene codes for a functional protein in a cell. The process occurs in both prokaryotic and eukaryotic cells, just in slightly different manners.

Prokaryotic Gene Regulation

Abstract:
By the end of this section, you will be able to do the following:

* Describe the steps involved in prokaryotic gene regulation
* Explain the roles of activators, inducers, and repressors in gene regulation

The *trp* Operon: A Repressible Operon

Bacteria such as *Escherichia coli* need amino acids to survive, and are able to synthesize many of them. Tryptophan is one such amino acid that *E. coli* can either ingest from the environment or synthesize using enzymes that are encoded by five genes. These five genes are next to each other in what is called the tryptophan (*trp*) operon ([link]). The genes are transcribed into a single mRNA, which is then translated to produce all five enzymes. If tryptophan is present in the environment, then *E. coli* does not need to synthesize it and the *trp* operon is switched off. However, when tryptophan availability is low, the switch controlling the operon is turned on, the mRNA is transcribed, the enzyme proteins are translated, and tryptophan is synthesized.

Catabolite Activator Protein (CAP): A Transcriptional Activator

Just as the *trp* operon is negatively regulated by tryptophan molecules, there are proteins that bind to the promoter sequences that act as positive regulators to turn genes on and activate them. For example, when glucose is scarce, *E. coli* bacteria can turn to other sugar sources for fuel. To do this, new genes to process these alternate sugars must be transcribed. When glucose levels drop, cyclic AMP (cAMP) begins to accumulate in the cell. The cAMP molecule is a signaling molecule that is involved in glucose and energy metabolism in *E. coli*. Accumulating cAMP binds to the positive regulator catabolite activator protein (CAP), a protein that binds to the promoters of operons which control the processing of alternative sugars. When cAMP binds to CAP, the complex then binds to the promoter region of the genes that are needed to use the alternate sugar sources ([link]). In these operons, a CAP-binding site is located upstream of the RNA-polymerase-binding site in the promoter. CAP binding stabilizes the binding of RNA polymerase to the promoter region and increases transcription of the associated protein-coding genes.

The *lac* Operon: An Inducible Operon

The third type of gene regulation in prokaryotic cells occurs through *inducible operons*, which have proteins that bind to activate or repress transcription depending on the local environment and the needs of the cell. The *lac* operon is a typical inducible operon. As mentioned previously, *E. coli* is able to use other sugars as energy sources when glucose concentrations are low. One such sugar source is lactose. The *lac* operon encodes the genes necessary to acquire and process the lactose from the local environment. The Z gene of the *lac* operon encodes beta-galactosidase, which breaks lactose down to glucose and galactose.

Eukaryotic Epigenetic Gene Regulation

Abstract:
By the end of this section, you will be able to do the following:

* Explain how chromatin remodeling controls transcriptional access
* Describe how access to DNA is controlled by histone modification
* Describe how DNA methylation is related to epigenetic gene changes

Epigenetic Control: Regulating Access to Genes within the Chromosome

The human genome encodes over 20,000 genes, with hundreds to thousands of genes on each of the 23 human chromosomes. The DNA in the nucleus is precisely wound, folded, and compacted into chromosomes so that it will fit into the nucleus. It is also organized so that specific segments can be accessed as needed by a specific cell type.

Eukaryotic Transcription Gene Regulation

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the role of transcription factors in gene regulation
* Explain how enhancers and repressors regulate gene expression

The Promoter and the Transcription Machinery

Genes are organized to make the control of gene expression easier. The promoter region is immediately upstream of the coding sequence. This region can be short (only a few nucleotides in length) or quite long (hundreds of nucleotides long). The longer the promoter, the more available space for proteins to bind. This also adds more control to the transcription process. The length of the promoter is gene-specific and can differ dramatically between genes. Consequently, the level of control of gene expression can also differ quite dramatically between genes. The purpose of the promoter is to bind transcription factors that control the initiation of transcription.

Enhancers and Transcription

In some eukaryotic genes, there are additional regions that help increase or enhance transcription. These regions, called enhancers, are not necessarily close to the genes they enhance. They can be located upstream of a gene, within the coding region of the gene, downstream of a gene, or may be thousands of nucleotides away.

Turning Genes Off: Transcriptional Repressors

Like prokaryotic cells, eukaryotic cells also have mechanisms to prevent transcription. Transcriptional repressors can bind to promoter or enhancer regions and block transcription. Like the transcriptional activators, repressors respond to external stimuli to prevent the binding of activating transcription factors.

Eukaryotic Post-transcriptional Gene Regulation

Abstract:
By the end of this section, you will be able to do the following:

* Understand RNA splicing and explain its role in regulating gene expression
* Describe the importance of RNA stability in gene regulation

RNA Splicing, the First Stage of Post-transcriptional Control

In eukaryotic cells, the RNA transcript often contains regions, called introns, that are removed prior to translation. The regions of RNA that code for protein are called exons. ([link]). After an RNA molecule has been transcribed, but prior to its departure from the nucleus to be translated, the RNA is processed and the introns are removed by splicing. Splicing is done by spliceosomes, ribonucleoprotein complexes that can recognize the two ends of the intron, cut the transcript at those two points, and bring the exons together for ligation.

Control of RNA Stability

Before the mRNA leaves the nucleus, it is given two protective "caps" that prevent the ends of the strand from degrading during its journey. 5' and 3' exonucleases can degrade unprotected RNAs. The 5' cap, which is placed on the 5' end of the mRNA, is usually composed of a methylated guanosine triphosphate molecule (GTP). The GTP is placed "backward" on the 5' end of the mRNA, so that the 5' carbons of the GTP and the terminal nucleotide are linked through three phosphates. The poly-A tail, which is attached to the 3' end, is usually composed of a long chain of adenine nucleotides. These changes protect the two ends of the RNA from exonuclease attack.

Eukaryotic Translational and Post-translational Gene Regulation

Abstract:
By the end of this section, you will be able to do the following:

* Understand the process of translation and discuss its key factors
* Describe how the initiation complex controls translation
* Explain the different ways in which the post-translational control of gene expression takes place

The Initiation Complex and Translation Rate

Like transcription, translation is controlled by proteins that bind and initiate the process. In translation, the complex that assembles to start the process is referred to as the translation initiation complex. In eukaryotes, translation is initiated by binding the initiating met-tRNAi to the 40S ribosome. This tRNA is brought to the 40S ribosome by a protein initiation factor, eukaryotic initiation factor-2 (eIF-2). The eIF-2 protein binds to the high-energy molecule guanosine triphosphate (GTP). The tRNA-eIF2-GTP complex then binds to the 40S ribosome. A second complex forms on the mRNA. Several different initiation factors recognize the 5' cap of the mRNA and proteins bound to the poly-A tail of the same mRNA, forming the mRNA into a loop. The cap-binding protein eIF4F brings the mRNA complex together with the 40S ribosome complex. The ribosome then scans along the mRNA until it finds a start codon AUG. When the anticodon of the initiator tRNA and the start codon are aligned, the GTP is hydrolyzed, the initiation factors are released, and the large 60S ribosomal subunit binds to form the translation complex. The binding of eIF-2 to the RNA is controlled by phosphorylation. If eIF-2 is phosphorylated, it undergoes a conformational change and cannot bind to GTP. Therefore, the initiation complex cannot form properly and translation is impeded ([link]). When eIF-2 remains unphosphorylated, the initiation complex can form normally and translation can proceed.

Chemical Modifications, Protein Activity, and Longevity

Proteins can be chemically modified with the addition of groups including methyl, phosphate, acetyl, and ubiquitin groups. The addition or removal of these groups from proteins regulates their activity or the length of time they exist in the cell. Sometimes these modifications can regulate where a protein is found in the cell—for example, in the nucleus, in the cytoplasm, or attached to the plasma membrane.

Cancer and Gene Regulation

Abstract:
By the end of this section, you will be able to do the following:

* Describe how changes to gene expression can cause cancer
* Explain how changes to gene expression at different levels can disrupt the cell cycle
* Discuss how understanding regulation of gene expression can lead to better drug design

Cancer: Disease of Altered Gene Expression

Cancer can be described as a disease of altered gene expression. There are many proteins that are turned on or off (gene activation or gene silencing) that dramatically alter the overall activity of the cell. A gene that is not normally expressed in that cell can be switched on and expressed at high levels. This can be the result of gene mutation or changes in gene regulation (epigenetic, transcription, post-transcription, translation, or post-translation).

Cancer and Epigenetic Alterations

Silencing genes through epigenetic mechanisms is also very common in cancer cells. There are characteristic modifications to histone proteins and DNA that are associated with silenced genes. In cancer cells, the DNA in the promoter region of silenced genes is methylated on cytosine DNA residues in CpG islands. Histone proteins that surround that region lack the acetylation modification that is present when the genes are expressed in normal cells. This combination of DNA methylation and histone deacetylation (epigenetic modifications that lead to gene silencing) is commonly found in cancer. When these modifications occur, the gene present in that chromosomal region is silenced. Increasingly, scientists understand how epigenetic changes are altered in cancer. Because these changes are temporary and can be reversed—for example, by preventing the action of the histone deacetylase protein that removes acetyl groups, or by DNA methyl transferase enzymes that add methyl groups to cytosines in DNA—it is possible to design new drugs and new therapies to take advantage of the reversible nature of these processes. Indeed, many researchers are testing how a silenced gene can be switched back on in a cancer cell to help re-establish normal growth patterns.

Cancer and Transcriptional Control

Alterations in cells that give rise to cancer can affect the transcriptional control of gene expression. Mutations that activate transcription factors, such as increased phosphorylation, can increase the binding of a transcription factor to its binding site in a promoter. This could lead to increased transcriptional activation of that gene that results in modified cell growth. Alternatively, a mutation in the DNA of a promoter or enhancer region can increase the binding ability of a transcription factor. This could also lead to the increased transcription and aberrant gene expression that is seen in cancer cells.

Cancer and Post-transcriptional Control

Changes in the post-transcriptional control of a gene can also result in cancer. Recently, several groups of researchers have shown that specific cancers have altered expression of miRNAs. Because miRNAs bind to the 3' UTR of RNA molecules to degrade them, overexpression of these miRNAs could be detrimental to normal cellular activity. Too many miRNAs could dramatically decrease the RNA population, leading to a decrease in protein expression. Several studies have demonstrated a change in the miRNA population in specific cancer types. It appears that the subset of miRNAs expressed in breast cancer cells is quite different from the subset expressed in lung cancer cells or even from normal breast cells. This suggests that alterations in miRNA activity can contribute to the growth of breast cancer cells. These types of studies also suggest that if some miRNAs are specifically expressed only in cancer cells, they could be potential drug targets. It would, therefore, be conceivable that new drugs that turn off miRNA expression in cancer could be an effective method to treat cancer.

Cancer and Translational/Post-translational Control

There are many examples of how translational or post-translational modifications of proteins arise in cancer. Modifications are found in cancer cells from the increased translation of a protein to changes in protein phosphorylation to alternative splice variants of a protein. An example of how the expression of an alternative form of a protein can have dramatically different outcomes is seen in colon cancer cells. The c-Flip protein, a protein involved in mediating the cell-death pathway, comes in two forms: long (c-FLIPL) and short (c-FLIPS). Both forms appear to be involved in initiating controlled cell-death mechanisms in normal cells. However, in colon cancer cells, expression of the long form results in increased cell growth instead of cell death. Clearly, the expression of the wrong protein dramatically alters cell function and contributes to the development of cancer.

New Drugs to Combat Cancer: Targeted Therapies

Scientists are using what is known about the regulation of gene expression in disease states, including cancer, to develop new ways to treat and prevent disease development. Many scientists are designing drugs on the basis of the gene expression patterns within individual tumors. This idea, that therapy and medicines can be tailored to an individual, has given rise to the field of personalized medicine. With an increased understanding of gene regulation and gene function, medicines can be designed to specifically target diseased cells without harming healthy cells. Some new medicines, called targeted therapies, have exploited the overexpression of a specific protein or the mutation of a gene to develop a new medication to treat disease. One such example is the use of anti-EGF receptor medications to treat the subset of breast cancer tumors that have very high levels of the EGF protein. Undoubtedly, more targeted therapies will be developed as scientists learn more about how gene expression changes can cause cancer.

Biotechnology and Genomics

Introduction

Biotechnology

Abstract:
By the end of this section, you will be able to do the following:

* Describe gel electrophoresis
* Explain molecular and reproductive cloning
* Describe biotechnology uses in medicine and agriculture

Basic Techniques to Manipulate Genetic Material (DNA and RNA)

To understand the basic techniques used to work with nucleic acids, remember that nucleic acids are macromolecules made of nucleotides (a sugar, a phosphate, and a nitrogenous base) linked by phosphodiester bonds. The phosphate groups on these molecules each have a net negative charge. An entire set of DNA molecules in the nucleus is called the genome. DNA has two complementary strands linked by hydrogen bonds between the paired bases. Exposure to high temperatures (DNA denaturation) can separate the two strands and cooling can reanneal them. The DNA polymerase enzyme can replicate the DNA. Unlike DNA, which is located in the eukaryotic cells' nucleus, RNA molecules leave the nucleus. The most common type of RNA that researchers analyze is the messenger RNA (mRNA) because it represents the protein-coding genes that are actively expressed. However, RNA molecules present some other challenges to analysis, as they are often less stable than DNA.

Molecular Cloning

In general, the word “cloning” means the creation of a perfect replica; however, in biology, the re-creation of a whole organism is referred to as “reproductive cloning.” Long before attempts were made to clone an entire organism, researchers learned how to reproduce desired regions or fragments of the genome, a process that is referred to as molecular cloning. The technique offered methods to create new medicines and to overcome difficulties with existing ones. When Lydia Villa-Komaroff, working in the Gilbert Lab at Harvard, published the first paper outlining the technique for producing synthetic insulin, diabetes researchers and patients received new hope in fighting the disease. Insulin at that time was only produced using pig and cow pancreases, and the life-saving substance was often in short supply. Synthetic insulin, once mass produced, would solve that problem for many patients. These early discoveries led to the "BioTech Boom," and spurred continued research and funding for newer and better ways to improve health.

Cellular Cloning

Unicellular organisms, such as bacteria and yeast, naturally produce clones of themselves when they replicate asexually by binary fission; this is known as cellular cloning. The nuclear DNA duplicates by the process of mitosis, which creates an exact replica of the genetic material.

Reproductive Cloning

Reproductive cloning is a method scientists use to clone or identically copy an entire multicellular organism. Most multicellular organisms undergo reproduction by sexual means, which involves genetic hybridization of two individuals (parents), making it impossible to generate an identical copy or a clone of either parent. Recent advances in biotechnology have made it possible to artificially induce mammal asexual reproduction in the laboratory.

Genetic Engineering

Genetic engineering is the alteration of an organism’s genotype using recombinant DNA technology to modify an organism’s DNA to achieve desirable traits. The addition of foreign DNA in the form of recombinant DNA vectors generated by molecular cloning is the most common method of genetic engineering. The organism that receives the recombinant DNA is a genetically modified organism (GMO). If the foreign DNA comes from a different species, the host organism is transgenic. Scientists have genetically modified bacteria, plants, and animals since the early 1970s for academic, medical, agricultural, and industrial purposes. In the US, GMOs such as Roundup-ready soybeans and borer-resistant corn are part of many common processed foods.

Biotechnology in Medicine and Agriculture

It is easy to see how biotechnology can be used for medicinal purposes. Knowledge of the genetic makeup of our species, the genetic basis of heritable diseases, and the invention of technology to manipulate and fix mutant genes provides methods to treat the disease. Biotechnology in agriculture can enhance resistance to disease, pest, and environmental stress, and improve both crop yield and quality.

Production of Vaccines, Antibiotics, and Hormones

Traditional vaccination strategies use weakened or inactive forms of microorganisms to mount the initial immune response. Modern techniques use the genes of microorganisms cloned into vectors to mass produce the desired antigen. Doctors then introduce the antigen into the body to stimulate the primary immune response and trigger immune memory. The medical field has used genes cloned from the influenza virus to combat the constantly changing strains of this virus.

Transgenic Animals

Although several recombinant proteins in medicine are successfully produced in bacteria, some proteins require a eukaryotic animal host for proper processing. For this reason, the desired genes are cloned and expressed in animals, such as sheep, goats, chickens, and mice. We call animals that have been modified to express recombinant DNA transgenic animals. Several human proteins are expressed in transgenic sheep and goat milk, and some are expressed in chicken eggs. Scientists have used mice extensively for expressing and studying recombinant gene and mutation effects.

Transgenic Plants

Manipulating the DNA of plants (i.e., creating GMOs) has helped to create desirable traits, such as disease resistance, herbicide and pesticide resistance, better nutritional value, and better shelf-life ([link]). Plants are the most important source of food for the human population. Farmers developed ways to select for plant varieties with desirable traits long before modern-day biotechnology practices were established.

Mapping Genomes

Abstract:
By the end of this section, you will be able to do the following:

* Define genomics
* Describe genetic and physical maps
* Describe genomic mapping methods

Genetic Maps

The study of genetic maps begins with linkage analysis, a procedure that analyzes the recombination frequency between genes to determine if they are linked or show independent assortment. Scientists used the term *linkage* before the discovery of DNA. Early geneticists relied on observing phenotypic changes to understand an organism’s genotype. Shortly after Gregor Mendel (the father of modern genetics) proposed that traits were determined by what we now call genes, other researchers observed that different traits were often inherited together, and thereby deduced that the genes were physically linked by their location on the same chromosome. Gene mapping relative to each other based on linkage analysis led to developing the first genetic maps.

Physical Maps

A physical map provides detail of the actual physical distance between genetic markers, as well as the number of nucleotides. There are three methods scientists use to create a physical map: cytogenetic mapping, radiation hybrid mapping, and sequence mapping. Cytogenetic mapping uses information from microscopic analysis of stained chromosome sections ([link]). It is possible to determine the approximate distance between genetic markers using cytogenetic mapping, but not the exact distance (number of base pairs). Radiation hybrid mapping uses radiation, such as x-rays, to break the DNA into fragments. We can adjust the radiation amount to create smaller or larger fragments. This technique overcomes the limitation of genetic mapping, and we can adjust the radiation so that increased or decreased recombination frequency does not affect it. Sequence mapping resulted from DNA sequencing technology that allowed for creating detailed physical maps with distances measured in terms of the number of base pairs. Creating genomic libraries and complementary DNA (cDNA) libraries (collections of cloned sequences or all DNA from a genome) has sped the physical mapping process. A genetic site that scientists use to generate a physical map with sequencing technology (a sequence-tagged site, or STS) is a unique sequence in the genome with a known exact chromosomal location. An expressed sequence tag (EST) and a single sequence length polymorphism (SSLP) are common STSs. An EST is a short STS that we can identify with cDNA libraries, while we obtain SSLPs from known genetic markers, which provide a link between genetic and physical maps.

Genetic and Physical Maps Integration

Genetic maps provide the outline and physical maps provide the details. It is easy to understand why both genome mapping technique types are important to show the big picture. Scientists use information from each technique in combination to study the genome. Scientists are using genomic mapping with different model organisms for research. Genome mapping is still an ongoing process, and as researchers develop more advanced techniques, they expect more breakthroughs. Genome mapping is similar to completing a complicated puzzle using every piece of available data. Mapping information generated in laboratories all over the world goes into central databases, such as GenBank at the National Center for Biotechnology Information (NCBI). Researchers are making efforts for the information to be more easily accessible to other researchers and the general public. Just as we use global positioning systems instead of paper maps to navigate through roadways, NCBI has created a genome viewer tool to simplify the data-mining process.

Whole-Genome Sequencing

Abstract:
By the end of this section, you will be able to do the following:

* Describe three types of sequencing
* Define whole-genome sequencing

Strategies Used in Sequencing Projects

The basic sequencing technique used in all modern day sequencing projects is the chain termination method (also known as the dideoxy method), which Fred Sanger developed in the 1970s. The chain termination method involves DNA replication of a single-stranded template by using a primer and a regular deoxynucleotide (dNTP), which is a monomer, or a single DNA unit. The primer and dNTP mix with a small proportion of fluorescently labeled dideoxynucleotides (ddNTPs). The ddNTPs are monomers that are missing a hydroxyl group (–OH) at the site at which another nucleotide usually attaches to form a chain ([link]). Scientists label each ddNTP with a different color of fluorophore. Every time a ddNTP incorporates in the growing complementary strand, it terminates the DNA replication process, which results in multiple short strands of replicated DNA that each terminate at a different point during replication. When gel electrophoresis processes the reaction mixture after separating into single strands, the multiple newly replicated DNA strands form a ladder because of the differing sizes. Because the ddNTPs are fluorescently labeled, each band on the gel reflects the DNA strand’s size and the ddNTP that terminated the reaction. The different colors of the fluorophore-labeled ddNTPs help identify the ddNTP incorporated at that position. Reading the gel on the basis of each band’s color on the ladder produces the template strand’s sequence ([link]).

Use of Whole-Genome Sequences of Model Organisms

British biochemist and Nobel Prize winner Fred Sanger used a bacterial virus, the bacteriophage fx174 (5368 base pairs), to completely sequence the first genome. Other scientists later sequenced several other organelle and viral genomes. American biotechnologist, biochemist, geneticist, and businessman Craig Venter sequenced the bacterium *Haemophilus influenzae* in the 1980s. Approximately 74 different laboratories collaborated on sequencing the genome of the yeast *Saccharomyces cerevisiae*, which began in 1989 and was completed in 1996, because it was 60 times bigger than any other genome sequencing. By 1997, the genome sequences of two important model organisms were available: the bacterium *Escherichia coli* K12 and the yeast *Saccharomyces cerevisiae*. We now know the genomes of other model organisms, such as the mouse *Mus musculus*, the fruit fly *Drosophila melanogaster*, the nematode *Caenorhabditis. elegans*, and humans *Homo sapiens*. Researchers perform extensive basic research in model organisms because they can apply the information to genetically similar organisms. A model organism is a species that researchers use as a model to understand the biological processes in other species that the model organism represents. Having entire genomes sequenced helps with the research efforts in these model organisms. The process of attaching biological information to gene sequences is genome annotation. Annotating gene sequences helps with basic experiments in molecular biology, such as designing PCR primers and RNA targets.

Genome Sequence Uses

DNA microarrays are methods that scientists use to detect gene expression by analyzing different DNA fragments that are fixed to a glass slide or a silicon chip to identify active genes and sequences. We can discover almost one million genotypic abnormalities using microarrays; whereas, whole-genome sequencing can provide information about all six billion base pairs in the human genome. Although studying genome sequencing medical applications is interesting, this discipline dwells on abnormal gene function. Knowing about the entire genome will allow researchers to discover future onset diseases and other genetic disorders early. This will allow for more informed decisions about lifestyle, medication, and having children. Genomics is still in its infancy, although someday it may become routine to use whole-genome sequencing to screen every newborn to detect genetic abnormalities.

Applying Genomics

Abstract:
By the end of this section, you will be able to do the following:

* Explain pharmacogenomics
* Define polygenic

Predicting Disease Risk at the Individual Level

Predicting disease risk involves screening currently healthy individuals by genome analysis at the individual level. Health care professionals can recommend intervention with lifestyle changes and drugs before disease onset. However, this approach is most applicable when the problem resides within a single gene defect. Such defects only account for approximately 5 percent of diseases in developed countries. Most of the common diseases, such as heart disease, are multi-factored or polygenic, which is a phenotypic characteristic that involves two or more genes, and also involve environmental factors such as diet. In April 2010, scientists at Stanford University published the genome analysis of a healthy individual (Stephen Quake, a scientist at Stanford University, who had his genome sequenced. The analysis predicted his propensity to acquire various diseases. The medical team performed a risk assessment to analyze Quake’s percentage of risk for 55 different medical conditions. The team found a rare genetic mutation, which showed him to be at risk for sudden heart attack. The results also predicted that Quake had a 23 percent risk of developing prostate cancer and a 1.4 percent risk of developing Alzheimer’s. The scientists used databases and several publications to analyze the genomic data. Even though genomic sequencing is becoming more affordable and analytical tools are becoming more reliable, researchers still must address ethical issues surrounding genomic analysis at a population level.

Pharmacogenomics and Toxicogenomics

Pharmacogenomics, or toxicogenomics, involves evaluating drug effectiveness and safety on the basis of information from an individual's genomic sequence. We can study genomic responses to drugs using experimental animals (such as laboratory rats or mice) or live cells in the laboratory before embarking on studies with humans. Studying changes in gene expression could provide information about the transcription profile in the drug's presence, which we can use as an early indicator of the potential for toxic effects. For example, genes involved in cellular growth and controlled cell death, when disturbed, could lead to cancerous cell growth. Genome-wide studies can also help to find new genes involved in drug toxicity. Medical professionals can use personal genome sequence information to prescribe medications that will be most effective and least toxic on the basis of the individual patient’s genotype. The gene signatures may not be completely accurate, but medical professionals can test them further before pathologic symptoms arise.

Microbial Genomics: Metagenomics

Traditionally, scholars have taught microbiology with the view that it is best to study microorganisms under pure culture conditions. This involves isolating a single cell type and culturing it in the laboratory. Because microorganisms can go through several generations in a matter of hours, their gene expression profiles adapt to the new laboratory environment very quickly. In addition, the vast majority of bacterial species resist culturing in isolation. Most microorganisms do not live as isolated entities, but in microbial communities or biofilms. For all of these reasons, pure culture is not always the best way to study microorganisms. Metagenomics is the study of the collective genomes of multiple species that grow and interact in an environmental niche. Metagenomics can be used to identify new species more rapidly and to analyze the effect of pollutants on the environment ([link]).

Microbial Genomics: Creation of New Biofuels

Knowledge of the genomics of microorganisms is being used to find better ways to harness biofuels from algae and cyanobacteria. The primary sources of fuel today are coal, oil, wood, and other plant products, such as ethanol. Although plants are renewable resources, there is still a need to find more alternative renewable sources of energy to meet our population’s energy demands. The microbial world is one of the largest resources for genes that encode new enzymes and produce new organic compounds, and it remains largely untapped. Microorganisms are used to create products, such as enzymes that are used in research, antibiotics, and other antimicrobial mechanisms. Microbial genomics is helping to develop diagnostic tools, improved vaccines, new disease treatments, and advanced environmental cleanup techniques.

Mitochondrial Genomics

Mitochondria are intracellular organelles that contain their own DNA. Mitochondrial DNA mutates at a rapid rate and scientists often use it to study evolutionary relationships. Another feature that makes studying the mitochondrial genome interesting is that the mitochondrial DNA in most multicellular organisms passes from the mother during the fertilization process. For this reason, scientists often use mitochondrial genomics to trace genealogy.

Genomics in Agriculture

Genomics can reduce the trials and failures involved in scientific research to a certain extent, which could improve agricultural crop yield quality and quantity. Linking traits to genes or gene signatures helps improve crop breeding to generate hybrids with the most desirable qualities. Scientists use genomic data to identify desirable traits, and then transfer those traits to a different organism. Researchers are discovering how genomics can improve agricultural production's quality and quantity. For example, scientists could use desirable traits to create a useful product or enhance an existing product, such as making a drought-sensitive crop more tolerant of the dry season.

Genomics and Proteomics

Abstract:
By the end of this section, you will be able to do the following:

* Explain systems biology
* Describe a proteome
* Define protein signature

Basic Techniques in Protein Analysis

The ultimate goal of proteomics is to identify or compare the proteins expressed from a given genome under specific conditions, study the interactions between the proteins, and use the information to predict cell behavior or develop drug targets. Just as scientists analyze the genome using the basic DNA sequencing technique, proteomics requires techniques for protein analysis. The basic technique for protein analysis, analogous to DNA sequencing, is mass spectrometry. Mass spectrometry identifies and determines a molecule's characteristics. Advances in spectrometry have allowed researchers to analyze very small protein samples. X-ray crystallography, for example, enables scientists to determine a protein crystal's three-dimensional structure at atomic resolution. Another protein imaging technique, nuclear magnetic resonance (NMR), uses atoms' magnetic properties to determine the protein's three-dimensional structure in aqueous solution. Scientists have also used protein microarrays to study protein interactions. Large-scale adaptations of the basic two-hybrid screen ([link]) have provided the basis for protein microarrays. Scientists use computer software to analyze the vast amount of data for proteomic analysis.

Cancer Proteomics

Researchers are studying patients' genomes and proteomes to understand the genetic basis of diseases. The most prominent disease researchers are studying with proteomic approaches is cancer. These approaches improve screening and early cancer detection. Researchers are able to identify proteins whose expression indicates the disease process. An individual protein is a biomarker; whereas, a set of proteins with altered expression levels is a protein signature. For a biomarker or protein signature to be useful as a candidate for early cancer screening and detection, they must secrete in body fluids, such as sweat, blood, or urine, such that health professionals can perform large-scale screenings in a noninvasive fashion. The current problem with using biomarkers for early cancer detection is the high rate of false-negative results. A false negative is an incorrect test result that should have been positive. In other words, many cancer cases go undetected, which makes biomarkers unreliable. Some examples of protein biomarkers in cancer detection are CA-125 for ovarian cancer and PSA for prostate cancer. Protein signatures may be more reliable than biomarkers to detect cancer cells. Researchers are also using proteomics to develop individualized treatment plans, which involves predicting whether or not an individual will respond to specific drugs and the side effects that the individual may experience. Researchers also use proteomics to predict the possibility of disease recurrence.

Evolutionary Processes

Evolution and the Origin of Species

Introduction

Understanding Evolution

Abstract:
By the end of this section, you will be able to do the following:

* Describe how scientists developed the present-day theory of evolution
* Define adaptation
* Explain convergent and divergent evolution
* Describe homologous and vestigial structures
* Discuss misconceptions about the theory of evolution

Charles Darwin and Natural Selection

In the mid-nineteenth century, two naturalists, Charles Darwin and Alfred Russel Wallace, independently conceived and described the actual mechanism for evolution. Importantly, each naturalist spent time exploring the natural world on expeditions to the tropics. From 1831 to 1836, Darwin traveled around the world on *H.M.S. Beagle*, including stops in South America, Australia, and the southern tip of Africa. Wallace traveled to Brazil to collect insects in the Amazon rainforest from 1848 to 1852 and to the Malay Archipelago from 1854 to 1862. Darwin’s journey, like Wallace’s later journeys to the Malay Archipelago, included stops at several island chains, the last being the Galápagos Islands west of Ecuador. On these islands, Darwin observed species of organisms on different islands that were clearly similar, yet had distinct differences. For example, the ground finches inhabiting the Galápagos Islands comprised several species with a unique beak shape ([link]). The species on the islands had a graded series of beak sizes and shapes with very small differences between the most similar. He observed that these finches closely resembled another finch species on the South American mainland. Darwin imagined that the island species might be species modified from one of the original mainland species. Upon further study, he realized that each finch's varied beaks helped the birds acquire a specific type of food. For example, seed-eating finches had stronger, thicker beaks for breaking seeds, and insect-eating finches had spear-like beaks for stabbing their prey.

Processes and Patterns of Evolution

Natural selection can only take place if there is variation, or differences, among individuals in a population. Importantly, these differences must have some genetic basis; otherwise, the selection will not lead to change in the next generation. This is critical because nongenetic reasons can cause variation among individuals such as an individual's height because of better nutrition rather than different genes.

Evidence of Evolution

The evidence for evolution is compelling and extensive. Looking at every level of organization in living systems, biologists see the signature of past and present evolution. Darwin dedicated a large portion of his book, *On the* *Origin of Species*, to identifying patterns in nature that were consistent with evolution, and since Darwin, our understanding has become clearer and broader.

Misconceptions of Evolution

Although the theory of evolution generated some controversy when Darwin first proposed it, biologists almost universally accepted it, particularly younger biologists, within 20 years after publication of *On the* *Origin of Species*. Nevertheless, the theory of evolution is a difficult concept and misconceptions about how it works abound.

Formation of New Species

Abstract:
By the end of this section, you will be able to do the following:

* Define species and describe how scientists identify species as different
* Describe genetic variables that lead to speciation
* Identify prezygotic and postzygotic reproductive barriers
* Explain allopatric and sympatric speciation
* Describe adaptive radiation

Species and the Ability to Reproduce

A species is a group of individual organisms that interbreed and produce fertile, viable offspring. According to this definition, one species is distinguished from another when, in nature, it is not possible for matings between individuals from each species to produce fertile offspring.

Speciation

The biological definition of species, which works for sexually reproducing organisms, is a group of actual or potential interbreeding individuals. There are exceptions to this rule. Many species are similar enough that hybrid offspring are possible and may often occur in nature, but for the majority of species this rule generally holds. The presence in nature of hybrids between similar species suggests that they may have descended from a single interbreeding species, and the speciation process may not yet be completed.

Allopatric Speciation

A geographically continuous population has a gene pool that is relatively homogeneous. Gene flow, the movement of alleles across a species' range, is relatively free because individuals can move and then mate with individuals in their new location. Thus, an allele's frequency at one end of a distribution will be similar to the allele's frequency at the other end. When populations become geographically discontinuous, it prevents alleles' free-flow. When that separation lasts for a period of time, the two populations are able to evolve along different trajectories. Thus, their allele frequencies at numerous genetic loci gradually become increasingly different as new alleles independently arise by mutation in each population. Typically, environmental conditions, such as climate, resources, predators, and competitors for the two populations will differ causing natural selection to favor divergent adaptations in each group.

Sympatric Speciation

Can divergence occur if no physical barriers are in place to separate individuals who continue to live and reproduce in the same habitat? The answer is yes. We call the process of speciation within the same space sympatric. The prefix “sym” means same, so “sympatric” means “same homeland” in contrast to “allopatric” meaning “other homeland.” Scientists have proposed and studied many mechanisms.

Reproductive Isolation

Given enough time, the genetic and phenotypic divergence between populations will affect characters that influence reproduction: if individuals of the two populations were brought together, mating would be less likely, but if mating occurred, offspring would be nonviable or infertile. Many types of diverging characters may affect the reproductive isolation, the ability to interbreed, of the two populations.

Reconnection and Speciation Rates

Abstract:
By the end of this section, you will be able to do the following:

* Describe pathways of species evolution in hybrid zones
* Explain the two major theories on rates of speciation

Reconnection

After speciation, two species may recombine or even continue interacting indefinitely. Individual organisms will mate with any nearby individual with whom they are capable of breeding. We call an area where two closely related species continue to interact and reproduce, forming hybrids a hybrid zone. Over time, the hybrid zone may change depending on the fitness of the hybrids and the reproductive barriers ([link]). If the hybrids are less fit than the parents, speciation reinforcement occurs, and the species continue to diverge until they can no longer mate and produce viable offspring. If reproductive barriers weaken, fusion occurs and the two species become one. Barriers remain the same if hybrids are fit and reproductive: stability may occur and hybridization continues.

Varying Rates of Speciation

Scientists around the world study speciation, documenting observations both of living organisms and those found in the fossil record. As their ideas take shape and as research reveals new details about how life evolves, they develop models to help explain speciation rates. In terms of how quickly speciation occurs, we can observe two current patterns: gradual speciation model and punctuated equilibrium model.

The Evolution of Populations

Introduction

Population Evolution

Abstract:
By the end of this section, you will be able to do the following:

* Define population genetics and describe how scientists use population genetics in studying population evolution
* Define the Hardy-Weinberg principle and discuss its importance

Population Genetics

Recall that a gene for a particular character may have several alleles, or variants, that code for different traits associated with that character. For example, in the ABO blood type system in humans, three alleles determine the particular blood-type carbohydrate on the surface of red blood cells. Each individual in a population of diploid organisms can only carry two alleles for a particular gene, but more than two may be present in the individuals that comprise the population. Mendel followed alleles as they were inherited from parent to offspring. In the early twentieth century, biologists in the area of population genetics began to study how selective forces change a population through changes in allele and genotypic frequencies.

Hardy-Weinberg Principle of Equilibrium

In the early twentieth century, English mathematician Godfrey Hardy and German physician Wilhelm Weinberg stated the principle of equilibrium to describe the population's genetic makeup. The theory, which later became known as the Hardy-Weinberg principle of equilibrium, states that a population’s allele and genotype frequencies are inherently stable— unless some kind of evolutionary force is acting upon the population, neither the allele nor the genotypic frequencies would change. The Hardy-Weinberg principle assumes an infinitely large population and conditions with no mutations, migration, emigration, or selective pressure for or against genotype. While no population can satisfy those conditions, the principle offers a useful model against which to compare real population changes.

Population Genetics

Abstract:
By the end of this section, you will be able to do the following:

* Describe the different types of variation in a population
* Explain why only natural selection can act upon heritable variation
* Describe genetic drift and the bottleneck effect
* Explain how each evolutionary force can influence a population's allele frequencies

Genetic variability

Natural selection and some of the other evolutionary forces can only act on heritable traits, namely an organism’s genetic code. Because alleles are passed from parent to offspring, those that confer beneficial traits or behaviors may be selected, while deleterious alleles may not. Acquired traits, for the most part, are not heritable. For example, if an athlete works out in the gym every day, building up muscle strength, the athlete’s offspring will not necessarily grow up to be a body builder. If there is a genetic basis for the ability to run fast, on the other hand, a parent may pass this to a child.

Genetic Drift

The theory of natural selection stems from the observation that some individuals in a population are more likely to survive longer and have more offspring than others; thus, they will pass on more of their genes to the next generation. A big, powerful male gorilla, for example, is much more likely than a smaller, weaker one to become the population’s silverback, the pack’s leader who mates far more than the other males of the group. The pack leader will father more offspring, who share half of his genes, and are likely to also grow bigger and stronger like their father. Over time, the genes for bigger size will increase in frequency in the population, and the population will, as a result, grow larger on average. That is, this would occur if this particular selection pressure, or driving selective force, were the only one acting on the population. In other examples, better camouflage or a stronger resistance to drought might pose a selection pressure.

Gene Flow

Another important evolutionary force is gene flow: the flow of alleles in and out of a population due to the migration of individuals or gametes ([link]). While some populations are fairly stable, others experience more flux. Many plants, for example, send their pollen far and wide, by wind or by bird, to pollinate other populations of the same species some distance away. Even a population that may initially appear to be stable, such as a pride of lions, can experience its fair share of immigration and emigration as developing males leave their mothers to seek out a new pride with genetically unrelated females. This variable flow of individuals in and out of the group not only changes the population's gene structure, but it can also introduce new genetic variation to populations in different geological locations and habitats.

Mutation

Mutations are changes to an organism’s DNA and are an important driver of diversity in populations. Species evolve because of mutations accumulating over time. The appearance of new mutations is the most common way to introduce novel genotypic and phenotypic variability. Some mutations are unfavorable or harmful and are quickly eliminated from the population by natural selection. Others are beneficial and will spread through the population. Whether or not a mutation is beneficial or harmful is determined by whether it helps an organism survive to sexual maturity and reproduce. Some mutations do not do anything and can linger, unaffected by natural selection, in the genome. Some can have a dramatic effect on a gene and the resulting phenotype.

Nonrandom Mating

If individuals nonrandomly mate with their peers, the result can be a changing population. There are many reasons nonrandom mating occurs. One reason is simple mate choice. For example, female peahens may prefer peacocks with bigger, brighter tails. Natural selection picks traits that lead to more mating selections for an individual. One common form of mate choice, called assortative mating, is an individual’s preference to mate with partners who are phenotypically similar to themselves.

Environmental Variation

Genes are not the only players involved in determining population variation. Other factors, such as the environment ([link]) also influence phenotypes. A beachgoer is likely to have darker skin than a city dweller, for example, due to regular exposure to the sun, an environmental factor. For some species, the environment determines some major characteristics, such as sex. For example, some turtles and other reptiles have temperature-dependent sex determination (TSD). TSD means that individuals develop into males if their eggs are incubated within a certain temperature range, or females at a different temperature range.

Adaptive Evolution

Abstract:
By the end of this section, you will be able to do the following:

* Explain the different ways natural selection can shape populations
* Describe how these different forces can lead to different outcomes in terms of the population variation

Stabilizing Selection

If natural selection favors an average phenotype, selecting against extreme variation, the population will undergo stabilizing selection ([link]). In a mouse population that live in the woods, for example, natural selection is likely to favor mice that best blend in with the forest floor and are less likely for predators to spot. Assuming the ground is a fairly consistent shade of brown, those mice whose fur is most closely matched to that color will be most likely to survive and reproduce, passing on their genes for their brown coat. Mice that carry alleles that make them a bit lighter or a bit darker will stand out against the ground and be more likely to fall victim to predation. As a result of this selection, the population’s genetic variability will decrease.

Directional Selection

When the environment changes, populations will often undergo directional selection ([link]), which selects for phenotypes at one end of the spectrum of existing variation. A classic example of this type of selection is the evolution of the peppered moth in eighteenth- and nineteenth-century England. Prior to the Industrial Revolution, the moths were predominately light in color, which allowed them to blend in with the light-colored trees and lichens in their environment. However, as soot began spewing from factories, the trees darkened, and the light-colored moths became easier for predatory birds to spot. Over time, the frequency of the moth's melanic form increased because they had a higher survival rate in habitats affected by air pollution because their darker coloration blended with the sooty trees. Similarly, the hypothetical mouse population may evolve to take on a different coloration if something were to cause the forest floor where they live to change color. The result of this type of selection is a shift in the population’s genetic variability toward the new, fit phenotype.

Diversifying Selection

Sometimes two or more distinct phenotypes can each have their advantages for natural selection, while the intermediate phenotypes are, on average, less fit. Scientists call this diversifying selection ([link]) We see this in many animal populations that have multiple male forms. Large, dominant alpha males use brute force to obtain mates, while small males can sneak in for furtive copulations with the females in an alpha male’s territory. In this case, both the alpha males and the “sneaking” males will be selected for, but medium-sized males, who can’t overtake the alpha males and are too big to sneak copulations, are selected against. Diversifying selection can also occur when environmental changes favor individuals on either end of the phenotypic spectrum. Imagine a mouse population living at the beach where there is light-colored sand interspersed with patches of tall grass. In this scenario, light-colored mice that blend in with the sand would be favored, as well as dark-colored mice that can hide in the grass. Medium-colored mice, alternatively would not blend in with either the grass or the sand, and thus predators would most likely eat them. The result of this type of selection is increased genetic variability as the population becomes more diverse.

Frequency-Dependent Selection

Another type of selection, frequency-dependent selection, favors phenotypes that are either common (positive frequency-dependent selection) or rare (negative frequency-dependent selection). We can observe an interesting example of this type of selection in a unique group of Pacific Northwest lizards. Male common side-blotched lizards come in three throat-color patterns: orange, blue, and yellow. Each of these forms has a different reproductive strategy: orange males are the strongest and can fight other males for access to their females. Blue males are medium-sized and form strong pair bonds with their mates. Yellow males ([link]) are the smallest, and look a bit like females, which allows them to sneak copulations. Like a game of rock-paper-scissors, orange beats blue, blue beats yellow, and yellow beats orange in the competition for females. That is, the big, strong orange males can fight off the blue males to mate with the blue’s pair-bonded females, the blue males are successful at guarding their mates against yellow sneaker males, and the yellow males can sneak copulations from the potential mates of the large, polygynous orange males.

Sexual Selection

Males and females of certain species are often quite different from one another in ways beyond the reproductive organs. Males are often larger, for example, and display many elaborate colors and adornments, like the peacock’s tail, while females tend to be smaller and duller in decoration. We call such differences sexual dimorphisms ([link]), which arise in many populations, particularly animal populations, where there is more variability in the male's reproductive success than that of the females. That is, some males—often the bigger, stronger, or more decorated males—obtain the vast majority of the total matings, while others receive none. This can occur because the males are better at fighting off other males, or because females will choose to mate with the bigger or more decorated males. In either case, this variation in reproductive success generates a strong selection pressure among males to obtain those matings, resulting in the evolution of bigger body size and elaborate ornaments to attract the females’ attention. Females, however, tend to achieve a handful of selected matings; therefore, they are more likely to select more desirable males.

No Perfect Organism

Natural selection is a driving force in evolution and can generate populations that are better adapted to survive and successfully reproduce in their environments. However, natural selection cannot produce the perfect organism. Natural selection can only select on existing variation in the population. It does not create anything from scratch. Thus, it is limited by a population’s existing genetic variability and whatever new alleles arise through mutation and gene flow.

Phylogenies and the History of Life

Introduction

Organizing Life on Earth

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the need for a comprehensive classification system
* List the different levels of the taxonomic classification system
* Describe how systematics and taxonomy relate to phylogeny
* Discuss a phylogenetic tree's components and purpose

Phylogenetic Trees

Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships. In other words, we can construct a “tree of life” to illustrate when different organisms evolved and to show the relationships among different organisms ([link]).

Limitations of Phylogenetic Trees

It may be easy to assume that more closely related organisms look more alike, and while this is often the case, it is not always true. If two closely related lineages evolved under significantly varied surroundings, it is possible for the two groups to appear more different than other groups that are not as closely related. For example, the phylogenetic tree in [link] shows that lizards and rabbits both have amniotic eggs; whereas, frogs do not. Yet lizards and frogs appear more similar than lizards and rabbits.

Classification Levels

Taxonomy (which literally means “arrangement law”) is the science of classifying organisms to construct internationally shared classification systems with each organism placed into increasingly more inclusive groupings. Think about a grocery store's organization. One large space is divided into departments, such as produce, dairy, and meats. Then each department further divides into aisles, then each aisle into categories and brands, and then finally a single product. We call this organization from larger to smaller, more specific categories a hierarchical system.

Determining Evolutionary Relationships

Abstract:
By the end of this section, you will be able to do the following:

* Compare homologous and analogous traits
* Discuss the purpose of cladistics
* Describe maximum parsimony

Two Options for Similarities

In general, organisms that share similar physical features and genomes are more closely related than those that do not. We refer to such features that overlap both morphologically (in form) and genetically as homologous structures. They stem from developmental similarities that are based on evolution. For example, the bones in bat and bird wings have homologous structures. This is an example of morphological homology ([link]).

Building Phylogenetic Trees

How do scientists construct phylogenetic trees? After they sort the homologous and analogous traits, scientists often organize the homologous traits using cladistics. This system sorts organisms into clades: groups of organisms that descended from a single ancestor. For example, in [link], all the organisms in the orange region evolved from a single ancestor that had amniotic eggs. Consequently, these organisms also have amniotic eggs and make a single clade, or a monophyletic group. Clades must include all descendants from a branch point.

Perspectives on the Phylogenetic Tree

Abstract:
By the end of this section, you will be able to do the following:

* Describe horizontal gene transfer
* Illustrate how prokaryotes and eukaryotes transfer genes horizontally
* Identify the web and ring models of phylogenetic relationships and describe how they differ from the original phylogenetic tree concept

Limitations to the Classic Model

Classical thinking about prokaryotic evolution, included in the classic tree model, is that species evolve clonally. That is, they produce offspring themselves with only random mutations causing the descent into the variety of modern-day and extinct species known to science. This view is somewhat complicated in eukaryotes that reproduce sexually, but the laws of Mendelian genetics explain the variation in offspring, again, to be a result of a mutation within the species. Scientists did not consider the concept of genes transferring between unrelated species as a possibility until relatively recently. Horizontal gene transfer (HGT), or lateral gene transfer, is the transfer of genes between unrelated species. HGT is an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model. Genes pass between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to understanding phylogenetic relationships.

Horizontal Gene Transfer

Horizontal gene transfer (HGT) is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission from parent(s) to offspring. These transfers allow even distantly related species to share genes, influencing their phenotypes. Scientists believe that HGT is more prevalent in prokaryotes, but that this process transfers only about 2% of the prokaryotic genome. Some researchers believe such estimates are premature: we must view the actual importance of HGT to evolutionary processes as a work in progress. As scientists investigate this phenomenon more thoroughly, they may reveal more HGT. Many scientists believe that HGT and mutation are (especially in prokaryotes) a significant source of genetic variation, which is the raw material in the natural selection process. These transfers may occur between any two species that share an intimate relationship ([link]).

Genome Fusion and Eukaryote Evolution

Scientists believe the ultimate in HGT occurs through genome fusion between different prokaryote species when two symbiotic organisms become endosymbiotic. This occurs when one species is taken inside another species' cytoplasm, which ultimately results in a genome consisting of genes from both the endosymbiont and the host. This mechanism is an aspect of the Endosymbiont Theory, which most biologists accept as the mechanism whereby eukaryotic cells obtained their mitochondria and chloroplasts. However, the role of endosymbiosis in developing the nucleus is more controversial. Scientists believe that nuclear and mitochondrial DNA have different (separate) evolutionary origins, with the mitochondrial DNA being derived from the
bacteria's circular genomes engulfed by ancient prokaryotic cells. We can regard mitochondrial DNA as the smallest chromosome. Interestingly enough, mitochondrial DNA is inherited only from females. The mitochondrial DNA degrades in sperm when the sperm degrades in the fertilized egg or in other instances when the mitochondria located in the sperm's flagellum fails to enter the egg.

Web and Network Models

Recognizing the importance of HGT, especially in prokaryote evolution, has caused some to propose abandoning the classic “tree of life” model. In 1999, W. Ford Doolittle proposed a phylogenetic model that resembles a web or a network more than a tree. The hypothesis is that eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms. As [link]a shows, some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development to the new eukaryotes; whereas, other species transferred the bacteria that gave rise to chloroplasts. Scientists often call this model the “web of life.” In an effort to save the tree analogy, some have proposed using the *Ficus* tree ([link]b) with its multiple trunks as a phylogenetic way to represent a diminished evolutionary role for HGT.

Ring of Life Models

Others have proposed abandoning any tree-like model of phylogeny in favor of a ring structure, the so-called “ring of life” ([link]). This is a phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes. Lake, again using the conditioned reconstruction algorithm, proposes a ring-like model in which species of all three domains—Archaea, Bacteria, and Eukarya—evolved from a single pool of gene-swapping prokaryotes. His laboratory proposes that this structure is the best fit for data from extensive DNA analyses performed in his laboratory, and that the ring model is the only one that adequately takes HGT and genomic fusion into account. However, other phylogeneticists remain highly skeptical of this model.

Biological Diversity

Viruses

Introduction

Viral Evolution, Morphology, and Classification

Abstract:
By the end of this section, you will be able to do the following:

* Describe how viruses were first discovered and how they are detected
* Discuss three hypotheses about how viruses evolved
* Describe the general structure of a virus
* Recognize the basic shapes of viruses
* Understand past and emerging classification systems for viruses
* Describe the basis for the Baltimore classification system

Discovery and Detection

Viruses were first discovered after the development of a porcelain filter—the Chamberland-Pasteur filter—that could remove all bacteria visible in the microscope from any liquid sample. In 1886, Adolph Meyer demonstrated that a disease of tobacco plants—tobacco mosaic disease—could be transferred from a diseased plant to a healthy one via liquid plant extracts. In 1892, Dmitri Ivanowski showed that this disease could be transmitted in this way even after the Chamberland-Pasteur filter had removed all viable bacteria from the extract. Still, it was many years before it was proved that these “filterable” infectious agents were not simply very small bacteria but were a new type of very small, disease-causing particle.

Evolution of Viruses

Although biologists have a significant amount of knowledge about how present-day viruses mutate and adapt, much less is known about how viruses originated in the first place. When exploring the evolutionary history of most organisms, scientists can look at fossil records and similar historic evidence. However, viruses do not fossilize, as far as we know, so researchers must extrapolate from investigations of how today’s viruses evolve and by using biochemical and genetic information to create speculative virus histories.

Viral Morphology

Viruses are noncellular, meaning they are biological entities that do not have a cellular structure. They therefore lack most of the components of cells, such as organelles, ribosomes, and the plasma membrane. A virion consists of a nucleic acid core, an outer protein coating or capsid, and sometimes an outer envelope made of protein and phospholipid membranes derived from the host cell. Viruses may also contain additional proteins, such as enzymes, within the capsid or attached to the viral genome. The most obvious difference between members of different viral families is the variation in their morphology, which is quite diverse. An interesting feature of viral complexity is that the complexity of the host does not necessarily correlate with the complexity of the virion. In fact, some of the most complex virion structures are found in the bacteriophages—viruses that infect the simplest living organisms, bacteria.

The Challenge of Virus Classification

Because most viruses probably evolved from different ancestors, the systematic methods that scientists have used to classify prokaryotic and eukaryotic cells are not very useful. If viruses represent “remnants” of different organisms, then even genomic or protein analysis is not useful. Why?, *Because viruses have no common genomic sequence that they all share*. For example, the 16S rRNA sequence so useful for constructing prokaryote phylogenies is of no use for a creature with no ribosomes! Biologists have used several classification systems in the past. Viruses were initially grouped by shared morphology. Later, groups of viruses were classified by the type of nucleic acid they contained, DNA or RNA, and whether their nucleic acid was single- or double-stranded. However, these earlier classification methods grouped viruses differently, because they were based on different sets of characters of the virus. The most commonly used classification method today is called the Baltimore classification scheme, and is based on how messenger RNA (mRNA) is generated in each particular type of virus.

Virus Infections and Hosts

Abstract:
By the end of this section, you will be able to do the following:

* List the steps of replication and explain what occurs at each step
* Describe the lytic and lysogenic cycles of virus replication
* Explain the transmission of plant and animal viruses
* Discuss some of the diseases caused by plant and animal viruses
* Discuss the economic impact of plant and animal viruses

Steps of Virus Infections

A virus must use its host-cell processes to replicate. The viral replication cycle can produce dramatic biochemical and structural changes in the host cell, which may cause cell damage. These changes, called cytopathic effects, can change cell functions or even destroy the cell. Some infected cells, such as those infected by the common cold virus known as rhinovirus, die through lysis (bursting) or apoptosis (programmed cell death or “cell suicide”), releasing all progeny virions at once. The symptoms of viral diseases result both from such cell damage caused by the virus and from the immune response to the virus, which attempts to control and eliminate the virus from the body.

Different Hosts and Their Viruses

As you’ve learned, viruses often infect very specific hosts, as well as specific cells within the host. This feature of a virus makes it specific to one or a few species of life on Earth. On the other hand, so many different types of viruses exist on Earth that nearly every living organism has its own set of *viruses* trying to infect its cells. Even prokaryotes, the smallest and simplest of cells, may be attacked by specific types of viruses. In the following section, we will look at some of the features of viral infection of prokaryotic cells. As we have learned, viruses that infect bacteria are called *bacteriophages* ([link]). Archaea have their own similar viruses.

Bacteriophages

Most bacteriophages are dsDNA viruses, which use host enzymes for DNA replication and RNA transcription. Phage particles must bind to specific surface receptors and actively insert the genome into the host cell. (The complex tail structures seen in many bacteriophages are actively involved in getting the viral genome across the prokaryotic cell wall.) When infection of a cell by a bacteriophage results in the production of new virions, the infection is said to be *productive*. If the virions are released by bursting the cell, the virus replicates by means of a *lytic cycle* ([link]). An example of a lytic bacteriophage is T4, which infects *Escherichia coli* found in the human intestinal tract. Sometimes, however, a virus can remain within the cell without being released. For example, when a temperate bacteriophage infects a bacterial cell, it replicates by means of a *lysogenic cycle* ([link]), and the viral genome is incorporated into the genome of the host cell. When the phage DNA is incorporated into the host-cell genome, it is called a prophage. An example of a lysogenic bacteriophage is the λ (lambda) virus, which also infects the *E*. *coli* bacterium. Viruses that infect plant or animal cells may sometimes undergo infections where they are not producing virions for long periods. An example is the animal *herpesviruses*, including herpes simplex viruses, the cause of oral and genital herpes in humans. In a process called latency, these viruses can exist in nervous tissue for long periods of time without producing new virions, only to leave latency periodically and cause lesions in the skin where the virus replicates. Even though there are similarities between lysogeny and latency, the term lysogenic cycle is usually reserved to describe bacteriophages. Latency will be described in more detail in the next section.

Plant Viruses

Most plant viruses, like the tobacco mosaic virus, have single-stranded (+) RNA genomes. However, there are also plant viruses in most other virus categories. Unlike bacteriophages, plant viruses do not have active mechanisms for delivering the viral genome across the protective cell wall. For a plant virus to enter a new host plant, some type of mechanical damage must occur. This damage is often caused by weather, insects, animals, fire, or human activities like farming or landscaping. Movement from cell to cell within a plant can be facilitated by viral modification of plasmodesmata (cytoplasmic threads that pass from one plant cell to the next). Additionally, plant offspring may inherit viral diseases from parent plants. Plant viruses can be transmitted by a variety of vectors, through contact with an infected plant’s sap, by living organisms such as insects and nematodes, and through pollen. The transfer of a virus from one plant to another is known as horizontal transmission, whereas the inheritance of a virus from a parent is called vertical transmission.

Animal Viruses

Animal viruses, unlike the viruses of plants and bacteria, do not have to penetrate a cell wall to gain access to the host cell. The virus may even induce the host cell to cooperate in the infection process. Non-enveloped or “naked” animal viruses may enter cells in two different ways. As a protein in the viral capsid binds to its receptor on the host cell, the virus may be taken inside the cell via a vesicle during the normal cell process of *receptor-mediated endocytosis*. An alternative method of cell penetration used by non-enveloped viruses is for capsid proteins to undergo shape changes after binding to the receptor, creating channels in the host cell membrane. The viral genome is then “injected” into the host cell through these channels in a manner analogous to that used by many bacteriophages.

Prevention and Treatment of Viral Infections

Abstract:
By the end of this section, you will be able to do the following:

* Identify major viral illnesses that affect humans
* Compare vaccinations and anti-viral drugs as medical approaches to viruses

Vaccines for Prevention

The primary method of controlling viral disease is by vaccination, which is intended to prevent outbreaks by building immunity to a virus or virus family ([link]). Vaccines may be prepared using live viruses, killed viruses, or molecular subunits of the virus. Note that the killed viral vaccines and subunit viruses are both incapable of causing disease, nor is there any valid evidence that vaccinations contribute to autism.

Vaccines and Antiviral Drugs for Treatment

In some cases, vaccines can be used to treat an active viral infection. The concept behind this is that by giving the vaccine, immunity is boosted without adding more disease-causing virus. In the case of *rabies*, a fatal neurological disease transmitted via the saliva of rabies virus-infected animals, the progression of the disease from the time of the animal bite to the time it enters the central nervous system may be two weeks or longer. This is enough time to vaccinate individuals who suspect that they have been bitten by a rabid animal, and their boosted immune response is sufficient to prevent the virus from entering nervous tissue. Thus, the potentially fatal neurological consequences of the disease are averted, and the individual only has to recover from the infected bite. This approach is also being used for the treatment of Ebola, one of the fastest and most deadly viruses on Earth. Transmitted by bats and great apes, this disease can cause death in 70 to 90 percent of infected humans within two weeks. Using newly developed vaccines that *boost the immune response* in this way, there is hope that affected individuals will be better able to control the virus, potentially saving a greater percentage of infected persons from a rapid and very painful death.

Other Acellular Entities: Prions and Viroids

Abstract:
By the end of this section, you will be able to do the following:

* Describe prions and their basic properties
* Define viroids and their targets of infection

Prions

Prions, so-called because they are proteinaceous, are infectious particles—smaller than viruses—that contain no nucleic acids (neither DNA nor RNA). Historically, the idea of an infectious agent that did not use nucleic acids was considered impossible, but pioneering work by Nobel Prize-winning biologist Stanley Prusiner has convinced the majority of biologists that such agents do indeed exist.

Viroids

Viroids are plant pathogens: small, single-stranded, circular RNA particles that are much simpler than a virus. They do not have a capsid or outer envelope, but like viruses can reproduce only within a host cell. Viroids do not, however, manufacture any proteins, and they only produce a single, specific RNA molecule. Human diseases caused by viroids have yet to be identified.

Prokaryotes: Bacteria and Archaea

Introduction

Prokaryotic Diversity

Abstract:
By the end of this section, you will be able to do the following:

* Describe the evolutionary history of prokaryotes
* Discuss the distinguishing features of extremophiles
* Explain why it is difficult to culture prokaryotes

Prokaryotes, the First Inhabitants of Earth

When and where did cellular life begin? What were the conditions on Earth when life began? We now know that prokaryotes were likely the first forms of cellular life on Earth, and they existed for billions of years before plants and animals appeared. The Earth and its moon are dated at about 4.54 billion years in age. This estimate is based on evidence from radiometric dating of meteorite material together with other substrate material from Earth and the moon. Early Earth had a very different atmosphere (contained less molecular oxygen) than it does today and was subjected to strong solar radiation; thus, the first organisms probably would have flourished where they were more protected, such as in the deep ocean or far beneath the surface of the Earth. Strong volcanic activity was common on Earth at this time, so it is likely that these first organisms—the first prokaryotes—were adapted to very high temperatures. Because early Earth was prone to geological upheaval and volcanic eruption, and was subject to bombardment by mutagenic radiation from the sun, the first organisms were prokaryotes that must have withstood these harsh conditions.

Microbes Are Adaptable: Life in Moderate and Extreme Environments

Some organisms have developed strategies that allow them to survive harsh conditions. Almost all prokaryotes have a cell wall, a protective structure that allows them to survive in both hypertonic and hypotonic aqueous conditions. Some soil bacteria are able to form *endospores* that resist heat and drought, thereby allowing the organism to survive until favorable conditions recur. These adaptations, along with others, allow bacteria to remain the most abundant life form in all terrestrial and aquatic ecosystems.

The Ecology of Biofilms

Some prokaryotes may be unculturable because they require the presence of other prokaryotic species. Until a couple of decades ago, microbiologists used to think of prokaryotes as isolated entities living apart. This model, however, does not reflect the true ecology of prokaryotes, most of which prefer to live in communities where they can interact. As we have seen, a biofilm is a microbial community ([link]) held together in a gummy-textured matrix that consists primarily of polysaccharides secreted by the organisms, together with some proteins and nucleic acids. Biofilms typically grow attached to surfaces. Some of the best-studied biofilms are composed of prokaryotes, although fungal biofilms have also been described, as well as some composed of a mixture of fungi and bacteria.

Structure of Prokaryotes: Bacteria and Archaea

Abstract:
By the end of this section, you will be able to do the following:

* Describe the basic structure of a typical prokaryote
* Describe important differences in structure between Archaea and Bacteria

The Prokaryotic Cell

Recall that prokaryotes are unicellular organisms that lack membrane-bound organelles or other internal membrane-bound structures ([link]). Their chromosome—usually single—consists of a piece of circular, double-stranded DNA located in an area of the cell called the nucleoid. Most prokaryotes have a cell wall outside the plasma membrane. The cell wall functions as a protective layer, and it is responsible for the organism’s shape. Some bacterial species have a capsule outside the cell wall. The capsule enables the organism to attach to surfaces, protects it from dehydration and attack by phagocytic cells, and makes pathogens more resistant to our immune responses. Some species also have flagella (singular, flagellum) used for locomotion, and pili (singular, pilus) used for attachment to surfaces including the surfaces of other cells. Plasmids, which consist of extra-chromosomal DNA, are also present in many species of bacteria and archaea.

Reproduction

Reproduction in prokaryotes is *asexual* and usually takes place by binary fission. (Recall that the DNA of a prokaryote is a single, circular chromosome.) Prokaryotes do not undergo mitosis; instead, the chromosome is replicated and the two resulting copies separate from one another, due to the growth of the cell. The prokaryote, now enlarged, is pinched inward at its equator and the two resulting cells, which are *clones*, separate. Binary fission does not provide an opportunity for genetic recombination or genetic diversity, but prokaryotes can share genes by three other mechanisms.

Prokaryotic Metabolism

Abstract:
By the end of this section, you will be able to do the following:

* Identify the macronutrients needed by prokaryotes, and explain their importance
* Describe the ways in which prokaryotes get energy and carbon for life processes
* Describe the roles of prokaryotes in the carbon and nitrogen cycles

Needs of Prokaryotes

The diverse environments and ecosystems on Earth have a wide range of conditions in terms of temperature, available nutrients, acidity, salinity, oxygen availability, and energy sources. Prokaryotes are very well equipped to make their living out of a vast array of nutrients and environmental conditions. To live, prokaryotes need a source of energy, a source of carbon, and some additional nutrients.

Role of Prokaryotes in Ecosystems

Prokaryotes are ubiquitous: There is no niche or ecosystem in which they are not present. Prokaryotes play many roles in the environments they occupy. The roles they play in the carbon and nitrogen cycles are vital to life on Earth. In addition, the current scientific consensus suggests that metabolically interactive prokaryotic communities may have been the basis for the emergence of eukaryotic cells.

Bacterial Diseases in Humans

Abstract:
By the end of this section, you will be able to do the following:

* Identify bacterial diseases that caused historically important plagues and epidemics
* Describe the link between biofilms and foodborne diseases
* Explain how overuse of antibiotics may be creating “super bugs”
* Explain the importance of MRSA with respect to the problems of antibiotic resistance

Long History of Bacterial Disease

There are records about infectious diseases as far back as 3000 B.C. A number of significant pandemics caused by bacteria have been documented over several hundred years. Some of the most memorable pandemics led to the decline of cities and entire nations.

Emerging and Re-emerging Diseases

The distribution of a particular disease is *dynamic*. Changes in the environment, the pathogen, or the host population can dramatically impact the spread of a disease. According to the World Health Organization (WHO), an emerging disease ([link]) is one that has appeared in a population for the first time, or that may have existed previously but is rapidly increasing in incidence or geographic range. This definition also includes *re-emerging diseases* that were previously under control. Approximately 75 percent of recently emerging infectious diseases affecting humans are zoonotic diseases. Zoonoses are diseases that primarily infect animals but can be transmitted to humans; some are of viral origin and some are of bacterial origin. Brucellosis is an example of a prokaryotic zoonosis that is re-emerging in some regions, and *necrotizing fasciitis* (commonly known as flesh-eating bacteria) has been increasing in virulence for the last 80 years for unknown reasons.

Foodborne Diseases

Prokaryotes are everywhere: They readily colonize the surface of any type of material, and food is not an exception. Most of the time, prokaryotes colonize food and food-processing equipment in the form of a *biofilm*, as we have discussed earlier. Outbreaks of bacterial infection related to food consumption are common. A foodborne disease (commonly called “food poisoning”) is an illness resulting from the consumption the pathogenic bacteria, viruses, or other parasites that contaminate food. Although the United States has one of the safest food supplies in the world, the U.S. Centers for Disease Control and Prevention (CDC) has reported that “76 million people get sick, more than 300,000 are hospitalized, and 5,000 Americans die each year from foodborne illness.”

Biofilms and Disease

Recall that biofilms are microbial communities that are very difficult to destroy. They are responsible for diseases such as Legionnaires’ disease, otitis media (ear infections), and various infections in patients with cystic fibrosis. They produce dental plaque and colonize catheters, prostheses, transcutaneous and orthopedic devices, contact lenses, and internal devices such as pacemakers. They also form in open wounds and burned tissue. In healthcare environments, biofilms grow on hemodialysis machines, mechanical ventilators, shunts, and other medical equipment. In fact, 65 percent of all infections acquired in the hospital (nosocomial infections) are attributed to biofilms. Biofilms are also related to diseases contracted from food because they colonize the surfaces of vegetable leaves and meat, as well as food-processing equipment that isn’t adequately cleaned.

Antibiotics: Are We Facing a Crisis?

The word *antibiotic* comes from the Greek *anti* meaning “against” and *bios* meaning “life.” An antibiotic is a chemical, produced either by microbes or synthetically, that is hostile to or prevents the growth of other organisms. Today’s media often address concerns about an antibiotic crisis. Are the antibiotics that easily treated bacterial infections in the past becoming obsolete? Are there new “superbugs”—bacteria that have evolved to become more resistant to our arsenal of antibiotics? Is this the beginning of the end of antibiotics? All these questions challenge the healthcare community.

Beneficial Prokaryotes

Abstract:
By the end of this section, you will be able to do the following:

* Explain the need for nitrogen fixation and how it is accomplished
* Describe the beneficial effects of bacteria that colonize our skin and digestive tracts
* Identify prokaryotes used during the processing of food
* Describe the use of prokaryotes in bioremediation

Cooperation between Bacteria and Eukaryotes: Nitrogen Fixation

Nitrogen is a very important element to living things, because it is part of nucleotides and amino acids that are the building blocks of nucleic acids and proteins, respectively. Nitrogen is usually the most limiting element in terrestrial ecosystems, with atmospheric nitrogen, N2, providing the largest pool of available nitrogen. However, eukaryotes cannot use atmospheric, gaseous nitrogen to synthesize macromolecules. Fortunately, nitrogen can be “fixed,” meaning it is converted into a more accessible form—ammonia (NH3)—either biologically or abiotically.

Early Biotechnology: Cheese, Bread, Wine, Beer, and Yogurt

According to the United Nations Convention on Biological Diversity, biotechnology is “any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use."[footnote] The concept of “specific use” involves some sort of commercial application. Genetic engineering, artificial selection, antibiotic production, and cell culture are current topics of study in biotechnology and will be described in later chapters. However, humans were using prokaryotes before the term biotechnology was even coined. Some of the products of this early biotechnology are as familiar as cheese, bread, wine, beer, and yogurt, which employ both bacteria and other microbes, such as yeast, a fungus ([link]).

http://www.cbd.int/convention/articles/?a=cbd-02, United Nations Convention on Biological Diversity: Article 2: Use of Terms.

Using Prokaryotes to Clean up Our Planet: Bioremediation

Microbial bioremediation is the use of prokaryotes (or microbial metabolism) to remove pollutants. Bioremediation has been used to remove agricultural chemicals (e.g., pesticides, fertilizers) that leach from soil into groundwater and the subsurface. Certain toxic metals and oxides, such as selenium and arsenic compounds, can also be removed from water by bioremediation. The reduction of SeO4-2 to SeO3-2 and to Se0 (metallic selenium) is a method used to remove selenium ions from water. Mercury (Hg) is an example of a toxic metal that can be removed from an environment by bioremediation. As an active ingredient of some pesticides, mercury is used in industry and is also a by-product of certain processes, such as battery production. Methyl mercury is usually present in very low concentrations in natural environments, but it is highly toxic because it accumulates in living tissues. Several species of bacteria can carry out the biotransformation of toxic mercury into nontoxic forms. These bacteria, such as *Pseudomonas aeruginosa*, can convert Hg+2 into Hg0, which is nontoxic to humans.

Protists

Introduction

Eukaryotic Origins

Abstract:
By the end of this section, you will be able to do the following:

* List the unifying characteristics of eukaryotes
* Describe what scientists know about the origins of eukaryotes based on the last common ancestor
* Explain the endosymbiotic theory

Characteristics of Eukaryotes

Data from these fossils, as well as from the study of living genomes, have led comparative biologists to conclude that living eukaryotes are all descendants of a single common ancestor. Mapping the characteristics found in all major groups of eukaryotes reveals that the following characteristics are present in at least some of the members of each major lineage, or during some part of their life cycle, and therefore must have been present in the *last common ancestor*.

Endosymbiosis and the Evolution of Eukaryotes

Before we discuss the origins of eukaryotes, it is first important to understand that all extant eukaryotes are likely the descendants of a chimera-like organism that was a composite of a host cell and the cell(s) of an alpha-proteobacterium that “took up residence” inside it. This major theme in the origin of eukaryotes is known as endosymbiosis, one cell engulfing another such that the engulfed cell survives and both cells benefit. Over many generations, a symbiotic relationship can result in two organisms that depend on each other so completely that neither could survive on its own. Endosymbiotic events likely contributed to the origin of the last common ancestor of today’s eukaryotes and to later diversification in certain lineages of eukaryotes ([link]). Similar endosymbiotic associations are not uncommon in living eukaryotes. Before explaining this further, it is necessary to consider metabolism in prokaryotes.

Characteristics of Protists

Abstract:
By the end of this section, you will be able to do the following:

* Describe the cell structure characteristics of protists
* Describe the metabolic diversity of protists
* Describe the life cycle diversity of protists

Cell Structure

The cells of protists are among the most elaborate of all cells. Multicellular plants, animals, and fungi are embedded among the protists in eukaryotic phylogeny. In most plants and animals and some fungi, complexity arises out of *multicellularity*, *tissue specialization,* and subsequent interaction because of these features. Although a rudimentary form of multicellularity exists among some of the organisms labelled as “protists,” those that have remained unicellular show how complexity can evolve in the absence of true multicellularity, with the differentiation of cellular morphology and function. A few protists live as colonies that behave in some ways as a group of free-living cells and in other ways as a multicellular organism. Some protists are composed of enormous, multinucleate, single cells that look like amorphous blobs of slime, or in other cases, like ferns. In some species of protists, the nuclei are different sizes and have distinct roles in protist cell function.

Metabolism

Protists exhibit many forms of nutrition and may be aerobic or anaerobic. Those that store energy by photosynthesis belong to a group of *photoautotrophs* and are characterized by the presence of chloroplasts. Other protists are *heterotrophic* and consume organic materials (such as other organisms) to obtain nutrition. Amoebas and some other heterotrophic protist species ingest particles by a process called *phagocytosis*, in which the cell membrane engulfs a food particle and brings it inward, pinching off an intracellular membranous sac, or vesicle, called a food vacuole ([link]). In some protists, food vacuoles can be formed anywhere on the body surface, whereas in others, they may be restricted to the base of a specialized feeding structure. The vesicle containing the ingested particle, the phagosome, then fuses with a lysosome containing hydrolytic enzymes to produce a phagolysosome, and the food particle is broken down into small molecules that can diffuse into the cytoplasm and be used in cellular metabolism. Undigested remains ultimately are expelled from the cell via *exocytosis*.

Motility

The majority of protists are motile, but different types of protists have evolved varied modes of movement ([link]). Some protists have one or more flagella, which they rotate or whip. Others are covered in rows or tufts of tiny cilia that they beat in a coordinated manner to swim. Still others form cytoplasmic extensions called *pseudopodia* anywhere on the cell, anchor the pseudopodia to a substrate, and pull themselves forward. Some protists can move toward or away from a stimulus, a movement referred to as taxis. For example, movement toward light, termed phototaxis, is accomplished by coupling their locomotion strategy with a light-sensing organ.

Life Cycles

Protists reproduce by a variety of mechanisms. Most undergo some form of *asexual reproduction*, such as binary fission, to produce two daughter cells. In protists, binary fission can be divided into transverse or longitudinal, depending on the axis of orientation; sometimes *Paramecium* exhibits this method. Some protists such as the true slime molds exhibit multiple fission and simultaneously divide into many daughter cells. Others produce tiny buds that go on to divide and grow to the size of the parental protist.

Habitats

Nearly all protists exist in some type of aquatic environment, including freshwater and marine environments, damp soil, and even snow. Several protist species are parasites that infect animals or plants. A few protist species live on dead organisms or their wastes, and contribute to their decay.

Groups of Protists

Abstract:
By the end of this section, you will be able to do the following:

* Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes
* Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes
* Identify defining features of protists in each of the six supergroups of eukaryotes.

Archaeplastida

Molecular evidence supports the hypothesis that all Archaeplastida are descendents of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium. The protist members of the group include the red algae and green algae. It was from a common ancestor of these protists that the land plants evolved, since their closest relatives are found in this group. The red and green algae include unicellular, multicellular, and colonial forms. A variety of algal life cycles exists, but the most complex is alternation of generations, in which both haploid and diploid stages are multicellular. A diploid sporophyte contains cells that undergo meiosis to produce haploid spores. The spores germinate and grow into a haploid gametophyte, which then makes gametes by mitosis. The gametes fuse to form a zygote that grows into a diploid sporophyte. Alternation of generations is seen in some species of Archaeplastid algae, as well as some species of Stramenopiles ([link]). In some species, the gametophyte and sporophyte look quite different, while in others they are nearly indistinguishable.

Amoebozoa

Like the Archaeplastida, the Amoebozoa include species with single cells, species with large multinucleated cells, and species that have multicellular phases. Amoebozoan cells characteristically exhibit pseudopodia that extend like tubes or flat lobes. These pseudopods project outward from anywhere on the cell surface and can anchor to a substrate. The protist then transports its cytoplasm into the pseudopod, thereby moving the entire cell. This type of motion is similar to the cytoplasmic streaming used to move organelles in the Archaeplastida, and is also used by other protists as a means of locomotion or as a method to distribute nutrients and oxygen. The Amoebozoa include both free-living and parasitic species.

Opisthokonta

The Opisthokonts are named for the single posterior flagellum seen in flagellated cells of the group. The flagella of other protists are anterior and their movement pulls the cells along, while the opisthokonts are pushed. Protist members of the opisthokonts include the animal-like choanoflagellates, which are believed to resemble the common ancestor of sponges and perhaps, all animals. Choanoflagellates include unicellular and colonial forms ([link]), and number about 244 described species. In these organisms, the single, apical flagellum is surrounded by a contractile collar composed of microvilli. The collar is used to filter and collect bacteria for ingestion by the protist. A similar feeding mechanism is seen in the collar cells of sponges, which suggests a possible connection between choanoflagellates and animals.

Rhizaria

The Rhizaria supergroup includes many of the amoebas with thin threadlike, needle-like or root-like pseudopodia ([link]), rather than the broader lobed pseudopodia of the Amoebozoa. Many rhizarians make elaborate and beautiful tests—armor-like coverings for the body of the cell—composed of calcium carbonate, silicon, or strontium salts. Rhizarians have important roles in both carbon and nitrogen cycles. When rhizarians die, and their tests sink into deep water, the carbonates are out of reach of most decomposers, locking carbon dioxide away from the atmosphere. In general, this process by which carbon is transported deep into the ocean is described as the biological carbon pump, because carbon is “pumped” to the ocean depths where it is inaccessible to the atmosphere as carbon dioxide. The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels. Foraminiferans are unusual in that they are the only eukaryotes known to participate in the nitrogen cycle by denitrification, an activity usually served only by prokaryotes.

Chromalveolata

Current evidence suggests that species classified as chromalveolates are derived from a common ancestor that engulfed a photosynthetic red algal cell, which itself had already evolved chloroplasts from an endosymbiotic relationship with a photosynthetic prokaryote. Therefore, the ancestor of chromalveolates is believed to have resulted from a secondary endosymbiotic event. However, some chromalveolates appear to have lost red alga-derived plastid organelles or lack plastid genes altogether. Therefore, this supergroup should be considered a hypothesis-based working group that is subject to change. Chromalveolates include very important photosynthetic organisms, such as diatoms, brown algae, and significant disease agents in animals and plants. The chromalveolates can be subdivided into alveolates and stramenopiles.

Excavata

Many of the protist species classified into the supergroup Excavata are asymmetrical, single-celled organisms with a feeding groove “excavated” from one side. This supergroup includes heterotrophic predators, photosynthetic species, and parasites. Its subgroups are the diplomonads, parabasalids, and euglenozoans. The group includes a variety of modified mitochondria, as well as chloroplasts derived from green algae by secondary endosymbiosis. Many of the euglenozoans are free-living, but most diplomonads and parabasalids are symbionts or parasites.

Ecology of Protists

Abstract:
By the end of this section, you will be able to do the following:

* Describe the role that protists play in the ecosystem
* Describe important pathogenic species of protists

Primary Producers/Food Sources

Protists are essential sources of food and provide nutrition for many other organisms. In some cases, as with zooplankton, protists are consumed directly. Alternatively, photosynthetic protists serve as producers of nutrition for other organisms. *Paramecium bursaria* and several other species of ciliates are *mixotrophic* due to a symbiotic relationship with green algae. This is a temporary version of the secondarily endosymbiotic chloroplast found in *Euglena*. But these symbiotic associations are not restricted to protists. For instance, photosynthetic dinoflagellates called *zooxanthellae* provide nutrients for the coral polyps ([link]) that house them, giving corals a boost of energy to secrete their calcium carbonate skeleton. In turn, the corals provide the protist with a protected environment and the compounds needed for photosynthesis. This type of symbiotic relationship is important in nutrient-poor environments. Without dinoflagellate symbionts, corals lose algal pigments in a process called *coral bleaching*, and they eventually die. This explains why reef-building corals typically do not reside in waters deeper than 20 meters: insufficient light reaches those depths for dinoflagellates to photosynthesize.

Human Pathogens

As we have seen, a pathogen is anything that causes disease. Parasitic organisms live in or on a host organism and harm the organism. A small number of protists are serious pathogenic parasites that must infect other organisms to survive and propagate. For example, protist parasites include the causative agents of malaria, African sleeping sickness, amoebic encephalitis, and waterborne gastroenteritis in humans. Other protist pathogens prey on plants, effecting massive destruction of food crops.

Plant Parasites

Protist parasites of terrestrial plants include agents that destroy food crops. The oomycete *Plasmopara viticola* parasitizes grape plants, causing a disease called *downy mildew* ([link]). Grape plants infected with *P*. *viticola* appear stunted and have discolored, withered leaves. The spread of downy mildew nearly collapsed the French wine industry in the nineteenth century.

Protist Decomposers

The fungus-like protist *saprobes* are specialized to absorb nutrients from nonliving organic matter, such as dead organisms or their wastes. For instance, many types of oomycetes grow on dead animals or algae. Saprobic protists have the essential function of returning inorganic nutrients to the soil and water. This process allows for new plant growth, which in turn generates sustenance for other organisms along the food chain. Indeed, without saprobe species, such as protists, fungi, and bacteria, life would cease to exist as all organic carbon became “tied up” in dead organisms.

Fungi

Introduction

Characteristics of Fungi

Abstract:
By the end of this section, you will be able to do the following:

* List the characteristics of fungi
* Describe the composition of the mycelium
* Describe the mode of nutrition of fungi
* Explain sexual and asexual reproduction in fungi

Cell Structure and Function

Fungi are eukaryotes, and as such, have a complex cellular organization. As eukaryotes, fungal cells contain a membrane-bound nucleus. The DNA in the nucleus is represented by multiple linear molecules wrapped around histone proteins, as is observed in other eukaryotic cells. A few types of fungi have accessory genomic structures comparable to bacterial plasmids (loops of DNA); however, the horizontal transfer of genetic information that occurs between one bacterium and another rarely occurs in fungi. Fungal cells also contain mitochondria and a complex system of internal membranes, including the endoplasmic reticulum and Golgi apparatus.

Reproduction

Fungi reproduce sexually and/or asexually. Some fungi reproduce both sexually and asexually, while other fungi reproduce only asexually (by mitosis).

Classifications of Fungi

Abstract:
By the end of this section, you will be able to do the following:

* Identify fungi and place them into the five major phyla according to current classification
* Describe each phylum in terms of major representative species and patterns of reproduction

Chytridiomycota: The Chytrids

The only class in the Phylum Chytridiomycota is the Chytridiomycetes. The chytrids are the simplest and most primitive Eumycota, or true fungi. The evolutionary record shows that the first recognizable chytrids appeared during the late pre-Cambrian period, more than 500 million years ago. Like all fungi, chytrids have chitin in their cell walls, but one group of chytrids has both cellulose and chitin in the cell wall. Most chytrids are unicellular; however, a few form multicellular organisms and hyphae, which have no septa between cells (coenocytic). The Chytrids are the only fungi that have retained flagella. They produce both gametes and diploid zoospores that swim with the help of a single flagellum. An unusual feature of the chytrids is that both male and female gametes are flagellated.

Zygomycota: The Conjugated Fungi

The zygomycetes are a relatively small group of fungi belonging to the Phylum Zygomycota. They include the familiar bread mold, *Rhizopus stolonifer*, which rapidly propagates on the surfaces of breads, fruits, and vegetables. Most species are saprobes, living off decaying organic material; a few are parasites, particularly of insects. Zygomycetes play a considerable commercial role. For example, the metabolic products of some species of *Rhizopus* are intermediates in the synthesis of semi-synthetic steroid hormones.

Ascomycota: The Sac Fungi

The majority of known fungi belong to the Phylum Ascomycota, which is characterized by the formation of an ascus (plural, asci), a sac-like structure that contains haploid *ascospores*. Filamentous ascomycetes produce hyphae divided by perforated septa, allowing streaming of cytoplasm from one cell to another. Conidia and asci, which are used respectively for asexual and sexual reproduction, are usually separated from the vegetative hyphae by blocked (non-perforated) septa. Many ascomycetes are of commercial importance. Some play a beneficial role for humanity, such as the yeasts used in baking, brewing, and wine fermentation, and directly as food delicacies such as truffles and morels. *Aspergillus oryzae* is used in the fermentation of rice to produce sake. Other ascomycetes parasitize plants and animals, including humans. For example, fungal pneumonia poses a significant threat to AIDS patients who have a compromised immune system. Ascomycetes not only infest and destroy crops directly; they also produce poisonous secondary metabolites that make crops unfit for consumption.

Basidiomycota: The Club Fungi

The fungi in the Phylum Basidiomycota are easily recognizable under a light microscope by their club-shaped fruiting bodies called basidia (singular, basidium), which are the swollen terminal cells of hyphae. The basidia, which are the reproductive organs of these fungi, are often contained within the familiar mushroom, commonly seen in fields after rain, on the supermarket shelves, and growing on your lawn ([link]). These mushroom-producing basidiomycetes are sometimes referred to as *“gill fungi”* because of the presence of gill-like structures on the underside of the cap. The gills are actually *compacted hyphae* on which the basidia are borne. This group also includes shelf fungi, which cling to the bark of trees like small shelves. In addition, the basidiomycota include smuts and rusts, which are important plant pathogens. Most edible fungi belong to the Phylum Basidiomycota; however, some basidiomycota are inedible and produce deadly toxins. For example, *Cryptococcus neoformans* causes severe respiratory illness. The infamous death cap mushroom (*Amanita phalloides*) is related to the fly agaric seen at the beginning of the previous section.

Asexual Ascomycota and Basidiomycota

Imperfect fungi—those that do not display a sexual phase—were formerly classified in the form phylum Deuteromycota, an invalid taxon no longer used in the present, ever-developing classification of organisms. While Deuteromycota was once a classification taxon, recent molecular analysis has shown that some of the members classified in this group belong to the Ascomycota ([link]) or the Basidiomycota. Because some members of this group have not yet been appropriately classified, they are less well described in comparison to members of other fungal taxa. Most imperfect fungi live on land, with a few aquatic exceptions. They form visible mycelia with a fuzzy appearance and are commonly known as mold.

Glomeromycota

The Glomeromycota is a newly established phylum that comprises about 230 species, all of which are involved in close associations with the roots of trees. Fossil records indicate that trees and their root symbionts share a long evolutionary history. It appears that nearly all members of this family form arbuscular mycorrhizae: the hyphae interact with the root cells forming a mutually beneficial association in which the plants supply the carbon source and energy in the form of carbohydrates to the fungus, and the fungus supplies essential minerals from the soil to the plant. The exception is *Geosiphon pyriformis*, which hosts the cyanobacterium *Nostoc* as an endosymbiont.

Ecology of Fungi

Abstract:
By the end of this section, you will be able to do the following:

* Describe the role of fungi in various ecosystems
* Describe mutualistic relationships of fungi with plant roots and photosynthetic organisms
* Describe the beneficial relationship between some fungi and insects

Habitats

Although fungi are primarily associated with humid and cool environments that provide a supply of organic matter, they colonize a surprising diversity of habitats, from seawater to human skin and mucous membranes. Chytrids are found primarily in aquatic environments. Other fungi, such as *Coccidioides immitis*, which causes pneumonia when its spores are inhaled, thrive in the dry and sandy soil of the southwestern United States. Fungi that parasitize coral reefs live in the ocean. However, most members of the Kingdom Fungi grow on the forest floor, where the dark and damp environment is rich in decaying debris from plants and animals. In these environments, fungi play a major role as decomposers and recyclers, making it possible for members of the other kingdoms to be supplied with nutrients and live.

Decomposers and Recyclers

The food web would be incomplete without organisms that decompose organic matter ([link]). Some elements—such as nitrogen and phosphorus—are required in large quantities by biological systems, and yet are not abundant in the environment. The action of fungi releases these elements from decaying matter, making them available to other living organisms. Trace elements present in low amounts in many habitats are essential for growth, and would remain tied up in rotting organic matter if fungi and bacteria did not return them to the environment via their metabolic activity.

Mutualistic Relationships

Symbiosis is the ecological interaction between two organisms that live together. This definition does not describe the type or quality of the interaction. When both members of the association benefit, the symbiotic relationship is called mutualistic. Fungi form mutualistic associations with many types of organisms, including cyanobacteria, algae, plants, and animals.

Fungivores

Animal dispersal is important for some fungi because an animal may carry fungal spores considerable distances from the source. Fungal spores are rarely completely degraded in the gastrointestinal tract of an animal, and many are able to germinate when they are passed in the feces. Some “dung fungi” actually require passage through the digestive system of herbivores to complete their lifecycle. The black truffle—a prized gourmet delicacy—is the fruiting body of an underground ascomycete. Almost all truffles are ectomycorrhizal, and are usually found in close association with trees. Animals eat truffles and disperse the spores. In Italy and France, truffle hunters use female pigs to sniff out truffles (female pigs are attracted to truffles because the fungus releases a volatile compound closely related to a pheromone produced by male pigs.)

Fungal Parasites and Pathogens

Abstract:
By the end of this section, you will be able to do the following:

* Describe some fungal parasites and pathogens of plants
* Describe the different types of fungal infections in humans
* Explain why antifungal therapy is hampered by the similarity between fungal and animal cells

Plant Parasites and Pathogens

The production of sufficient high-quality crops is essential to human existence. Unfortunately, plant diseases have ruined many crops throughout human agricultural history, sometimes creating widespread famine. Many plant pathogens are fungi that cause tissue decay and the eventual death of the host ([link]). In addition to destroying plant tissue directly, some plant pathogens spoil crops by producing potent toxins that can further damage and kill the host plant. Fungi are also responsible for food spoilage and the rotting of stored crops. For example, the fungus *Claviceps purpurea* causes ergot, a disease of cereal crops (especially of rye). Although the fungus reduces the yield of cereals, the effects of the ergot's alkaloid toxins on humans and animals are of much greater significance. In animals, the disease is referred to as *ergotism*. The most common signs and symptoms are convulsions, hallucination, gangrene, and loss of milk in cattle. The active ingredient of ergot is *lysergic acid*, which is a precursor of the drug LSD. Smuts, rusts, and powdery or downy mildew are other examples of common fungal pathogens that affect crops.

Animal and Human Parasites and Pathogens

Fungi can affect animals, including humans, in several ways. A mycosis is a fungal disease that results from infection and direct damage due to the growth and infiltration of the fungus. Fungi attack animals directly by colonizing and destroying tissues. Mycotoxicosis is the poisoning of humans (and other animals) by foods contaminated by fungal toxins (mycotoxins). Mycetismus specifically describes the ingestion of preformed toxins in poisonous mushrooms. In addition, individuals who display hypersensitivity to molds and spores may develop strong and dangerous allergic reactions. Fungal infections are generally very difficult to treat because, unlike bacteria, fungi are eukaryotes. Antibiotics only target prokaryotic cells, whereas compounds that kill fungi also harm the eukaryotic animal host.

Importance of Fungi in Human Life

Abstract:
By the end of this section, you will be able to do the following:

* Describe the importance of fungi to the balance of the environment
* Summarize the role of fungi in agriculture and food and beverage preparation
* Describe the importance of fungi in the chemical and pharmaceutical industries
* Discuss the role of fungi as model organisms

Seedless Plants

Introduction

Early Plant Life

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the challenges to plant life on land
* Describe the adaptations that allowed plants to colonize the land
* Describe the timeline of plant evolution and the impact of land plants on other living things

Plant Adaptations to Life on Land

As organisms adapted to life on land, they had to contend with several challenges in the terrestrial environment. Water has been described as “the stuff of life.” The cell’s interior is a thick soup: in this medium, most small molecules dissolve and diffuse, and the majority of the chemical reactions of metabolism take place. Desiccation, or drying out, is a constant danger for an organism exposed to air. Even when parts of a plant are close to a source of water, the aerial structures are likely to dry out. Water also provides buoyancy to organisms. On land, plants need to develop structural support in a medium that does not give the same lift as water. The organism is also subject to bombardment by mutagenic radiation, because air does not filter out ultraviolet rays of sunlight. Additionally, the male gametes must reach the female gametes using new strategies, because swimming is no longer possible. Therefore, both gametes and zygotes must be protected from desiccation. The successful land plants developed strategies to deal with all of these challenges. Not all adaptations appeared at once. Some species never moved very far from the aquatic environment, whereas others went on to conquer the driest environments on Earth.

Additional Land Plant Adaptations

As plants adapted to dry land and became independent from the constant presence of water in damp habitats, new organs and structures made their appearance. Early land plants did not grow more than a few inches off the ground, competing for light on these low mats. By developing a shoot and growing taller, individual plants captured more light. Because air offers substantially less support than water, land plants incorporated more rigid molecules in their stems (and later, tree trunks). In small plants such as single-celled algae, simple diffusion suffices to distribute water and nutrients throughout the organism. However, for plants to evolve larger forms, the evolution of a conductive tissue for the distribution of water and solutes was a prerequisite. The evolution of vascular tissue in plants met both of these needs. The vascular system contains two types of conductive tissue: xylem and phloem. Xylem conducts water and minerals absorbed from the soil up to the shoot, while phloem transports food derived from photosynthesis throughout the entire plant. In xylem, the cells walls are reinforced with lignin, whose tough hydrophobic polymers help prevent the seepage of water across the xylem cell walls. Lignin also adds to the strength of these tissues in supporting the plant. The vascular tissues extend into the root of land plants. The root system evolved to take up water and minerals from the soil, and to anchor the increasingly taller shoot in the soil.

Evolution of Land Plants

No discussion of the evolution of plants on land can be undertaken without a brief review of the timeline of the geological eras. The early era, known as the Paleozoic, is divided into six periods. It starts with the Cambrian period, followed by the Ordovician, Silurian, Devonian, Carboniferous, and Permian. The major event to mark the Ordovician, more than 500 million years ago, was the colonization of land by the ancestors of modern land plants. Fossilized cells, cuticles, and spores of early land plants have been dated as far back as the Ordovician period in the early Paleozoic era. The oldest-known vascular plants have been identified in deposits from the Devonian. One of the richest sources of information is the Rhynie chert, a sedimentary rock deposit found in Rhynie, Scotland ([link]), where embedded fossils of some of the earliest vascular plants have been identified.

The Major Divisions of Land Plants

The green algae and land plants are grouped together into a subphylum called the Streptophyta, and thus are called Streptophytes. In a further division, land plants are classified into two major groups according to the absence or presence of vascular tissue, as detailed in [link]. Plants that lack vascular tissue, which is formed of specialized cells for the transport of water and nutrients, are referred to as non-vascular plants. Liverworts, mosses, and hornworts are seedless, non-vascular plants that likely appeared early in land plant evolution. Vascular plants developed a network of cells that conduct water and solutes. The first vascular plants appeared in the late Ordovician (500 to 435 MYA) and were probably similar to lycophytes, which include club mosses (not to be confused with the mosses) and the pterophytes (ferns, horsetails, and whisk ferns). Lycophytes and pterophytes are referred to as seedless vascular plants, because they do not produce seeds. The seed plants, or spermatophytes, form the largest group of all existing plants, and hence dominate the landscape. Seed plants include gymnosperms, most notably conifers, which produce “naked seeds,” and the most successful of all plants, the flowering plants (angiosperms). Angiosperms protect their seeds inside chambers at the center of a flower; the walls of the chamber later develop into a fruit.

Green Algae: Precursors of Land Plants

Abstract:
By the end of this section, you will be able to do the following:

* Describe the traits shared by green algae and land plants
* Explain why charophytes are considered the closest algal relative to land plants
* Explain how current phylogenetic relationships are reshaped by comparative analysis of DNA sequences

Streptophytes

Until recently, all photosynthetic eukaryotes were classified as members of the kingdom Plantae. The brown and golden algae, however, are now reassigned to the protist supergroup Chromalveolata. This is because apart from their ability to capture light energy and fix CO2, they lack many structural and biochemical traits that are characteristic of plants. The plants are now classified, along with the red and green algae, in the protist supergroup Archaeplastida. Green algae contain the same carotenoids and chlorophyll a and b as land plants, whereas other algae have different accessory pigments and types of chlorophyll molecules in addition to chlorophyll a. Both green algae and land plants also store carbohydrates as starch. Their cells contain chloroplasts that display a dizzying variety of shapes, and their cell walls contain cellulose, as do land plants. Which of the green algae to include among the plants has not been phylogenetically resolved.

Reproduction of Green Algae

Green algae reproduce both asexually, by fragmentation or dispersal of spores, or sexually, by producing gametes that fuse during fertilization. In a single-celled organism such as *Chlamydomonas*, there is no mitosis after fertilization. In the multicellular *Ulva*, a sporophyte grows by mitosis after fertilization (and thus exhibits alternation of generations). Both *Chlamydomonas* and *Ulva* produce flagellated gametes.

Charophytes

The charophytes include several different algal orders that have each been suggested to be the closest relatives of the land plants: the Charales, the Zygnematales, and the Coleochaetales. The Charales can be traced back 420 million years. They live in a range of freshwater habitats and vary in size from a few millimeters to a meter in length. The representative genus is *Chara* ([link]), often called muskgrass or skunkweed because of its unpleasant smell. Large cells form the *thallus*: the main stem of the alga. Branches arising from the nodes are made of smaller cells. Male and female reproductive structures are found on the nodes, and the sperm have flagella. Although *Chara* looks superficially like some land plants, a major difference is that the stem has no supportive tissue. However, the Charales exhibit a number of traits that are significant for adaptation to land life. They produce the compounds *lignin* and *sporopollenin*, and form plasmodesmata that connect the cytoplasm of adjacent cells. Although the life cycle of the Charales is haplontic (the main form is haploid, and diploid zygotes are formed but have a brief existence), the egg, and later, the zygote, form in a protected chamber on the haploid parent plant.

Bryophytes

Abstract:
By the end of this section, you will be able to do the following:

* Identify the main characteristics of bryophytes
* Describe the distinguishing traits of liverworts, hornworts, and mosses
* Chart the development of land adaptations in the bryophytes
* Describe the events in the bryophyte lifecycle

Liverworts

Liverworts (Marchantiophyta) are currently classified as the plants most closely related to the ancestor of vascular plants that adapted to terrestrial environments. In fact, liverworts have colonized every terrestrial habitat on Earth and diversified to more than 7000 existing species ([link]). Lobate liverworts form a flat thallus, with lobes that have a vague resemblance to the lobes of the liver ([link]), which accounts for the name given to the phylum. Leafy liverworts have tiny leaflike structures attached to a stalk. Several leafy liverworts are shown in [link].

Hornworts

The defining characteristic of the hornworts (*Anthocerotophyta*) is the narrow, pipe-like sporophyte. Hornworts have colonized a variety of habitats on land, although they are never far from a source of moisture. The short, blue-green gametophyte is the dominant phase of the life cycle of a hornwort. The sporophytes emerge from the parent gametophyte and continue to grow throughout the life of the plant ([link]).

Mosses

The mosses are the most numerous of the non-vascular plants. More than 10,000 species of mosses have been catalogued. Their habitats vary from the tundra, where they are the main vegetation, to the understory of tropical forests. In the tundra, the mosses’ shallow rhizoids allow them to fasten to a substrate without penetrating the frozen soil. Mosses slow down erosion, store moisture and soil nutrients, and provide shelter for small animals as well as food for larger herbivores, such as the musk ox. Mosses are very sensitive to air pollution and are used to monitor air quality. They are also sensitive to copper salts, so these salts are a common ingredient of compounds marketed to eliminate mosses from lawns.

Seedless Vascular Plants

Abstract:
By the end of this section, you will be able to do the following:

* Identify the new traits that first appear in seedless tracheophytes
* Discuss how each trait is important for adaptation to life on land
* Identify the classes of seedless tracheophytes
* Describe the life cycle of a fern
* Explain the role of seedless plants in the ecosystem

Vascular Tissue: Xylem and Phloem

The first plant fossils that show the presence of vascular tissue date to the Silurian period, about 430 million years ago. The simplest arrangement of conductive cells shows a pattern of xylem at the center surrounded by phloem. Xylem is the tissue responsible for the storage and long-distance transport of water and nutrients, as well as the transfer of water-soluble growth factors from the organs of synthesis to the target organs. The tissue consists of conducting cells, known as tracheids, and supportive filler tissue, called parenchyma. Xylem conductive cells incorporate the compound lignin into their walls, and are thus described as lignified. Lignin itself is a complex polymer: It is impermeable to water and confers mechanical strength on vascular tissue. With their rigid cell walls, the xylem cells provide support to the plant and allow it to achieve impressive heights. Tall plants have a selective advantage by being able to reach unfiltered sunlight and disperse their spores or seeds away from the parent plant, thus expanding the species’ range. By growing higher than other plants, tall trees cast their shadows on shorter plants and thereby outcompete them for water and precious nutrients in the soil.

Roots: Support for the Plant

Roots are not well-preserved in the fossil record. Nevertheless, it seems that roots appeared later in evolution than vascular tissue. The development of an extensive network of roots represented a significant new feature of vascular plants. Thin rhizoids attached bryophytes to the substrate, but these rather flimsy filaments did not provide a strong anchor for the plant; nor did they absorb substantial amounts of water and nutrients. In contrast, roots, with their prominent vascular tissue system, transfer water and minerals from the soil to the rest of the plant. The extensive network of roots that penetrates deep into the soil to reach sources of water also stabilizes plants by acting as a ballast or anchor. The majority of roots establish a symbiotic relationship with fungi, forming mutualistic mycorrhizae, which benefit the plant by greatly increasing the surface area for absorption of water, soil minerals, and nutrients.

Leaves, Sporophylls, and Strobili

A third innovation marks the seedless vascular plants. Accompanying the prominence of the sporophyte and the development of vascular tissue, the appearance of true leaves improved their photosynthetic efficiency. Leaves capture more sunlight with their increased surface area by employing more chloroplasts to trap light energy and convert it to chemical energy, which is then used to fix atmospheric carbon dioxide into carbohydrates. The carbohydrates are exported to the rest of the plant by the conductive cells of phloem tissue.

Ferns and Other Seedless Vascular Plants

By the late Devonian period, plants had evolved vascular tissue, well-defined leaves, and root systems. With these advantages, plants increased in height and size. During the Carboniferous period (360 to 300 MYA), swamp forests of club mosses and horsetails—some specimens reaching heights of more than 30 m (100 ft)—covered most of the land. These forests gave rise to the extensive coal deposits that gave the Carboniferous its name. In seedless vascular plants, the sporophyte became the dominant phase of the life cycle.

The Importance of Seedless Plants

Mosses and liverworts are often the first macroscopic organisms to colonize an area, both in a primary succession—where bare land is settled for the first time by living organisms, or in a secondary succession—where soil remains intact after a catastrophic event wipes out many existing species. Their spores are carried by the wind, birds, or insects. Once mosses and liverworts are established, they provide food and shelter for other plant species. In a hostile environment, like the tundra where the soil is frozen, bryophytes grow well because they do not have roots and can dry and rehydrate quickly once water is again available. Mosses are at the base of the food chain in the tundra biome. Many species—from small herbivorous insects to musk oxen and reindeer—depend on mosses for food. In turn, predators feed on the herbivores, which are the primary consumers. Some reports indicate that bryophytes make the soil more amenable to colonization by other plants. Because they establish symbiotic relationships with nitrogen-fixing cyanobacteria, mosses replenish the soil with nitrogen.

Seed Plants

Introduction

Evolution of Seed Plants

Abstract:
By the end of this section, you will be able to do the following:

* Describe the two major innovations that allowed seed plants to reproduce in the absence of water
* Explain when seed plants first appeared and when gymnosperms became the dominant plant group
* Discuss the purpose of pollen grains and seeds
* Describe the significance of angiosperms bearing both flowers and fruit

Evolution of Gymnosperms

The fossil plant *Elkinsia polymorpha*, a "seed fern" from the Devonian period—about 400 million years ago—is considered the earliest seed plant known to date. Seed ferns ([link]) produced their seeds along their branches, in structures called cupules that enclosed and protected the ovule—the female gametophyte and associated tissues—which develops into a seed upon fertilization. Seed plants resembling modern tree ferns became more numerous and diverse in the coal swamps of the Carboniferous period.

Evolution of Angiosperms

The roughly 200 million years between the appearance of the gymnosperms and the flowering plants gives us some appreciation for the evolutionary experimentation that ultimately produced flowers and fruit. Angiosperms (“seed in a vessel”) produce a flower containing male and/or female reproductive structures. Fossil evidence ([link]) indicates that flowering plants first appeared about 125 million years ago in the Lower Cretaceous (late in the Mesozoic era), and were rapidly diversifying by about 100 million years ago in the Middle Cretaceous. Earlier traces of angiosperms are scarce. Fossilized pollen recovered from Jurassic geological material has been attributed to angiosperms. A few early Cretaceous rocks show clear imprints of leaves resembling angiosperm leaves. By the mid-Cretaceous, a staggering number of diverse flowering plants crowd the fossil record. The same geological period is also marked by the appearance of many modern groups of insects, suggesting that pollinating insects played a key role in the evolution of flowering plants.

Gymnosperms

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the type of seeds produced by gymnosperms, as well as other characteristics of gymnosperms
* Identify the geological era dominated by the gymnosperms and describe the conditions to which they were adapted
* List the four groups of modern-day gymnosperms and provide examples of each
* Describe the life cycle of a typical gymnosperm

Life Cycle of a Conifer

Pine trees are conifers (coniferous = cone bearing) and carry both male and female sporophylls on the same mature sporophyte. Therefore, they are monoecious plants. Like all gymnosperms, pines are heterosporous and generate two different types of spores (male microspores and female megaspores). Male and female spores develop in different strobili, with small male cones and larger female cones. In the male cones, or staminate cones, the microsporocytes undergo meiosis and the resultant haploid microspores give rise to male gametophytes or “pollen grains” by mitosis. Each pollen grain consists of just a few haploid cells enclosed in a tough wall reinforced with sporopollenin. In the spring, large amounts of yellow pollen are released and carried by the wind. Some gametophytes will land on a female cone. Pollination is defined as the initiation of pollen tube growth. The pollen tube develops slowly, and the generative cell in the pollen grain produces two haploid sperm or generative nuclei by mitosis. At fertilization, one of the haploid sperm nuclei will unite with the haploid nucleus of an egg cell.

Diversity of Gymnosperms

Modern gymnosperms are classified into four phyla. Coniferophyta, Cycadophyta, and Ginkgophyta are similar in their pattern of seed development and also in their production of *secondary cambium* (cells that generate the vascular system of the trunk or stem and are partially specialized for water transportation). However, the three phyla are not closely related phylogenetically to each other. Gnetophyta are considered the closest group to angiosperms because they produce true xylem tissue, with vessels as well as the tracheids found in the rest of the gymnosperms. It is possible that vessel elements arose independently in the two groups

Angiosperms

Abstract:
By the end of this section, you will be able to do the following:

* Explain why angiosperms are the dominant form of plant life in most terrestrial ecosystems
* Describe the main parts of a flower and their functions
* Detail the life cycle of a typical gymnosperm and angiosperm
* Discuss the similarities and differences between the two main groups of flowering plants

Flowers

Flowers are modified leaves, or sporophylls, organized around a central receptacle. Although they vary greatly in appearance, virtually all flowers contain the same structures: sepals, petals, carpels, and stamens. The peduncle typically attaches the flower to the plant proper. A whorl of sepals (collectively called the calyx) is located at the base of the peduncle and encloses the unopened floral bud. Sepals are usually photosynthetic organs, although there are some exceptions. For example, the corolla in lilies and tulips consists of three sepals and three petals that look virtually identical. Petals, collectively the corolla, are located inside the whorl of sepals and may display vivid colors to attract pollinators. Sepals and petals together form the perianth. The sexual organs, the *female gynoecium* and *male androecium* are located at the center of the flower. Typically, the sepals, petals, and stamens are attached to the receptacle at the base of the gynoecium, but the gynoecium may also be located deeper in the receptacle, with the other floral structures attached above it.

The Life Cycle of an Angiosperm

The adult or sporophyte phase is the main phase of an angiosperm’s life cycle ([link]). Like gymnosperms, angiosperms are heterosporous. Therefore, they produce microspores, which will generate pollen grains as the male gametophytes, and *megaspores*, which will form an ovule that contains female gametophytes. Inside the anther’s microsporangia, male sporocytes divide by meiosis to generate haploid microspores, which, in turn, undergo mitosis and give rise to pollen grains. Each pollen grain contains two cells: one generative cell that will divide into two sperm and a second cell that will become the pollen tube cell.

Fruit

As the seed develops, the walls of the ovary thicken and form the fruit. The seed forms in an ovary, which also enlarges as the seeds grow. Many foods commonly called vegetables are actually fruits. Eggplants, zucchini, string beans, tomatoes, and bell peppers are all technically fruits because they contain seeds and are derived from the thick ovary tissue. Acorns are true nuts, and winged maple “helicopter seeds” or whirligigs (whose botanical name is *samara*) are also fruits. Botanists classify fruit into more than two dozen different categories, only a few of which are actually fleshy and sweet.

Diversity of Angiosperms

Angiosperms are classified in a single phylum: the Anthophyta. Modern angiosperms appear to be a monophyletic group, which as you may recall means that they originated from a single ancestor. Within the angiosperms are three major groups: basal angiosperms, monocots, and dicots. Basal angiosperms are a group of plants that are believed to have branched off before the separation of the monocots and eudicots, because they exhibit traits from both groups. They are categorized separately in most classification schemes. The basal angiosperms include *Amborella*, water lilies, the Magnoliids (magnolia trees, laurels, and spice peppers), and a group called the Austrobaileyales, which includes the star anise. The monocots and dicots are differentiated on the basis of the structure of the cotyledons, pollen grains, and other structures. Monocots include grasses and lilies, and the dicots form a multi-branched group that includes (among many others) roses, cabbages, sunflowers, and mints.

The Role of Seed Plants

Abstract:
By the end of this section, you will be able to do the following:

* Explain how angiosperm diversity is due, in part, to multiple complex interactions with animals
* Describe ways in which pollination occurs
* Discuss the roles that plants play in ecosystems and how deforestation threatens plant biodiversity

Animals and Plants: Herbivory

Coevolution of flowering plants and insects is a hypothesis that has received much attention and support, especially because both angiosperms and insects diversified at about the same time in the middle Mesozoic. Many authors have attributed the diversity of plants and insects to both pollination and herbivory, or the consumption of plants by insects and other animals. Herbivory is believed to have been as much a driving force as pollination. Coevolution of herbivores and plant defenses is easily and commonly observed in nature. Unlike animals, most plants cannot outrun predators or use mimicry to hide from hungry animals (although mimicry has been used to entice pollinators). A sort of arms race exists between plants and herbivores. To “combat” herbivores, some plant seeds—such as acorn and unripened persimmon—are high in alkaloids and therefore unsavory to some animals. Other plants are protected by bark, although some animals developed specialized mouth pieces to tear and chew vegetal material. Spines and thorns ([link]) deter most animals, except for mammals with thick fur, and some birds have specialized beaks to get past such defenses.

Animals and Plants: Pollination

Flowers pollinated by wind are usually small, feathery, and visually inconspicuous. *Grasses* are a successful group of flowering plants that are wind pollinated. They produce large amounts of powdery pollen carried over large distances by the wind. Some large trees such as oaks, maples, and birches are also wind pollinated.

The Importance of Seed Plants in Human Life

Seed plants are the foundation of human diets across the world ([link]). Many societies eat almost exclusively vegetarian fare and depend solely on seed plants for their nutritional needs. A few crops (rice, wheat, and potatoes) dominate the agricultural landscape. Many crops were developed during the agricultural revolution, when human societies made the transition from nomadic hunter–gatherers to horticulture and agriculture. Cereals, rich in carbohydrates, provide the staple of many human diets. Beans and nuts supply proteins. Fats are derived from crushed seeds, as is the case for peanut and rapeseed (canola) oils, or fruits such as olives. Animal husbandry also consumes large quantities of crop plants.

Biodiversity of Plants

Biodiversity ensures a resource for new food crops and medicines. Plant life balances ecosystems, protects watersheds, mitigates erosion, moderates our climate, and provides shelter for many animal species. Threats to plant diversity, however, come from many sources. The explosion of the human population, especially in tropical countries where birth rates are highest and economic development is in full swing, is leading to devastating human encroachment into forested areas. To feed the growing population, humans need to obtain arable land, so there has been and continues to be massive clearing of trees. The need for more energy to power larger cities and economic growth therein leads to the construction of dams, the consequent flooding of ecosystems, and increased emissions of pollutants. Other threats to tropical forests come from poachers, who log trees for their precious wood. Ebony and Brazilian rosewood, both on the endangered list, are examples of tree species driven almost to extinction by indiscriminate logging. This unfortunate practice continues unabated today largely due to lack of population control and political willpower.

Introduction to Animal Diversity

Introduction

Features of the Animal Kingdom

Abstract:
By the end of this section, you will be able to do the following:

* List the features that distinguish the kingdom Animalia from other kingdoms
* Explain the processes of animal reproduction and embryonic development
* Describe the roles that Hox genes play in development

Complex Tissue Structure

Many of the specialized tissues of animals are associated with the requirements and hazards of seeking and processing food. This explains why animals typically have evolved special structures associated with specific methods of food capture and complex digestive systems supported by accessory organs. Sensory structures help animals navigate their environment, detect food sources (and avoid becoming a food source for other animals!). Movement is driven by muscle tissue attached to supportive structures like bone or chitin, and is coordinated by neural communication. Animal cells may also have unique structures for intercellular communication (such as gap junctions). The evolution of nerve tissues and muscle tissues has resulted in animals’ unique ability to rapidly sense and respond to changes in their environment. This allows animals to survive in environments where they must compete with other species to meet their nutritional demands.

Animal Reproduction and Development

Most animals are diploid organisms, meaning that their body (somatic) cells are diploid and haploid reproductive (gamete) cells are produced through meiosis. Some exceptions exist: for example, in bees, wasps, and ants, the male is haploid because it develops from unfertilized eggs. Most animals undergo sexual reproduction. However, a few groups, such as cnidarians, flatworms, and roundworms, may also undergo asexual reproduction, in which offspring originate from part of the parental body.

Features Used to Classify Animals

Abstract:
By the end of this section, you will be able to do the following:

* Explain the differences in animal body plans that support basic animal classification
* Compare and contrast the embryonic development of protostomes and deuterostomes

Animal Characterization Based on Body Symmetry

At a very basic level of classification, true animals can be largely divided into three groups based on the type of symmetry of their body plan: radially symmetrical, bilaterally symmetrical, and asymmetrical. Asymmetry is seen in two modern clades, the Parazoa ([link]a) and Placozoa. (Although we should note that the ancestral fossils of the Parazoa apparently exhibited bilateral symmetry.) One clade, the Cnidaria ([link]b,c), exhibits radial or biradial symmetry: Ctenophores have rotational symmetry ([link]e). Bilateral symmetry is seen in the largest of the clades, the Bilateria ([link]d); however the Echinodermata are bilateral as larvae and metamorphose secondarily into radial adults. All types of symmetry are well suited to meet the unique demands of a particular animal’s lifestyle.

Animal Characterization Based on Features of Embryological Development

Most animal species undergo a separation of tissues into germ layers during embryonic development. Recall that these germ layers are formed during *gastrulation*, and that each germ layer typically gives rise to specific types of embryonic tissues and organs. Animals develop either two or three embryonic germ layers ([link]). The animals that display radial, biradial, or rotational symmetry develop two germ layers, an inner layer (*endoderm* or *mesendoderm*) and an outer layer (*ectoderm*). These animals are called diploblasts, and have a nonliving middle layer between the endoderm and ectoderm (although individual cells may be distributed through this middle layer, there is no *coherent* third layer of tissue). The four clades considered to be diploblastic have different levels of complexity and different developmental pathways, although there is little information about development in Placozoa. More complex animals (usually those with bilateral symmetry) develop three tissue layers: an inner layer (endoderm), an outer layer (ectoderm), and a middle layer (mesoderm). Animals with three tissue layers are called triploblasts.

Animal Phylogeny

Abstract:
By the end of this section, you will be able to do the following:

* Interpret the metazoan phylogenetic tree
* Describe the types of data that scientists use to construct and revise animal phylogeny
* List some of the relationships within the modern phylogenetic tree that have been discovered as a result of modern molecular data

Constructing an Animal Phylogenetic Tree

The current understanding of evolutionary relationships among animal, or Metazoa, phyla begins with the distinction between animals with *true differentiated tissues*, called Eumetazoa, and animal phyla that do not have true differentiated tissues, such as the sponges (Porifera) and the Placozoa. Similarities between the feeding cells of sponges (choanocytes) and choanoflagellate protists ([link]) have been used to suggest that Metazoa evolved from a common ancestral organism that resembled the modern colonial choanoflagellates.

Modern Advances in Phylogenetic Understanding Come from Molecular Analyses

The phylogenetic groupings are continually being debated and refined by evolutionary biologists. Each year, new evidence emerges that further alters the relationships described by a phylogenetic tree diagram.

The Evolutionary History of the Animal Kingdom

Abstract:
By the end of this section, you will be able to do the following:

* Describe the features that characterized the earliest animals and approximately when they appeared on earth
* Explain the significance of the Cambrian period for animal evolution and the changes in animal diversity that took place during that time
* Describe some of the unresolved questions surrounding the Cambrian explosion
* Discuss the implications of mass animal extinctions that have occurred in evolutionary history

Pre-Cambrian Animal Life

The time before the Cambrian period is known as the Ediacaran Period (from about 635 million years ago to 543 million years ago), the final period of the late Proterozoic Neoproterozoic Era ([link]). Ediacaran fossils were first found in the Ediacaran hills of Southern Australia. There are no living representatives of these species, which have left impressions that look like those of feathers or coins ([link]). It is believed that early animal life, termed *Ediacaran biota*, evolved from protists at this time.

The Cambrian Explosion of Animal Life

If the fossils of the Ediacaran and Cryogenian periods are enigmatic, those of the following Cambrian period are far less so, and include body forms similar to those living today. The Cambrian period, occurring between approximately 542–488 million years ago, marks the most rapid evolution of new animal phyla and animal diversity in Earth’s history. The rapid diversification of animals that appeared during this period, including most of the animal phyla in existence today, is often referred to as the Cambrian explosion ([link]). Animals resembling echinoderms, mollusks, worms, arthropods, and chordates arose during this period. What may have been a top predator of this period was an arthropod-like creature named *Anomalocaris*, over a meter long, with compound eyes and spiky tentacles. Obviously, all these Cambrian animals already exhibited complex structures, so their ancestors must have existed much earlier.

Post-Cambrian Evolution and Mass Extinctions

The periods that followed the Cambrian during the Paleozoic Era are marked by further animal evolution and the emergence of many new orders, families, and species. As animal phyla continued to diversify, new species adapted to new ecological niches. During the Ordovician period, which followed the Cambrian period, plant life first appeared on land. This change allowed formerly aquatic animal species to invade land, feeding directly on plants or decaying vegetation. Continual changes in temperature and moisture throughout the remainder of the Paleozoic Era due to continental plate movements encouraged the development of new adaptations to terrestrial existence in animals, such as limbed appendages in amphibians and epidermal scales in reptiles.

Invertebrates

Introduction

Phylum Porifera

Abstract:
By the end of this section, you will be able to do the following:

* Describe the organizational features of the simplest multicellular organisms
* Explain the various body forms and bodily functions of sponges

Morphology of Sponges

There are at least 5,000 named species of sponges, likely with thousands more yet to be classified. The morphology of the simplest sponges takes the shape of an irregular cylinder with a large central cavity, the spongocoel, occupying the inside of the cylinder ([link]). Water enters into the spongocoel through numerous pores, or *ostia*, that create openings in the body wall. Water entering the spongocoel is expelled via a large common opening called the osculum. However, we should note that sponges exhibit a range of diversity in body forms, including variations in the size and shape of the spongocoel, as well as the number and arrangement of feeding chambers within the body wall. In some sponges, multiple feeding chambers open off of a central spongocoel and in others, several feeding chambers connecting to one another may lie between the entry pores and the spongocoel.

Physiological Processes in Sponges

Sponges, despite being simple organisms, regulate their different physiological processes through a variety of mechanisms. These processes regulate their metabolism, reproduction, and locomotion.

Phylum Cnidaria

Abstract:
By the end of this section, you will be able to do the following:

* Compare structural and organization characteristics of Porifera and Cnidaria
* Describe the progressive development of tissues and their relevance to animal complexity
* Identify the two general body forms found in the Cnidaria
* Describe the identifying features of the major cnidarian classes

Class Anthozoa

The class Anthozoa ("flower animals") includes sea anemones ([link]), sea pens, and corals, with an estimated number of 6,100 described species. Sea anemones are usually brightly colored and can attain a size of 1.8 to 10 cm in diameter. Individual animals are cylindrical in shape and are attached directly to a substrate.

Class Scyphozoa

Class Scyphozoa ("cup animals") includes all (and only) the marine jellies, with about 200 known species. The medusa is the prominent stage in the life cycle, although there is a polyp stage in the life cycle of most species. Most jellies range from 2 to 40 cm in length but the largest scyphozoan species, *Cyanea capillata*, can reach a size of two meters in diameter. Scyphozoans display a characteristic bell-like morphology ([link]).

Class Cubozoa

This class includes jellies that have a box-shaped medusa, or a bell that is square in cross-section, and are colloquially known as “box jellyfish.” These species may achieve sizes of 15 to 25 cm, but typically members of the Cubozoa are not as large as those of the Scyphozoa. However, cubozoans display overall morphological and anatomical characteristics that are similar to those of the scyphozoans. A prominent difference between the two classes is the arrangement of tentacles. The cubozoans contain muscular pads called pedalia at the corners of the square bell canopy, with one or more tentacles attached to each pedalium. In some cases, the digestive system may extend into the pedalia. Nematocysts may be arranged in a spiral configuration along the tentacles; this arrangement helps to effectively subdue and capture prey. Cubozoans include the most venomous of all the cnidarians ([link]).

Class Hydrozoa

Hydrozoa is a diverse group that includes nearly 3,200 species; most are marine, although some freshwater species are known ([link]). Most species exhibit both polypoid and medusoid forms in their lifecycles, although the familiar *Hydra* has only the polyp form. The medusoid form has a muscular veil or velum below the margin of the bell and for this reason is called a *hydromedusa*. In contrast, the medusoid form of Scyphozoa lacks a velum and is termed a *scyphomedusa*.

Superphylum Lophotrochozoa: Flatworms, Rotifers, and Nemerteans

Abstract:
By the end of this section, you will be able to do the following:

* Describe the unique anatomical and morphological features of flatworms, rotifers, and Nemertea
* Identify an important extracoelomic cavity found in Nemertea
* Explain the key features of Platyhelminthes and their importance as parasites

Phylum Platyhelminthes

The flatworms are acoelomate organisms that include many free-living and parasitic forms. The flatworms possess neither a lophophore nor trochophore larvae, although the larvae of one group of flatworms, the Polycladida (named after its many-branched digestive tract), are considered to be homologous to trochophore larvae. Spiral cleavage is also seen in the polycladids and other basal flatworm groups. The developmental pattern of some of the free-living forms is obscured by a phenomenon called "*blastomere anarchy*," in which a sort of temporary feeding larva forms, followed by a regrouping of cells within the embryo that gives rise to a second-stage embryo. However, both the monophyly of the flatworms and their placement in the Lophotrochozoa has been supported by molecular analyses.

Phylum Rotifera

The rotifers ("wheel-bearer") belong to a group of microscopic (about 100 µm to 2 mm) mostly aquatic animals that get their name from the corona—a pair of ciliated feeding structures that appear to rotate when viewed under the light microscope ([link]). Although their taxonomic status is currently in flux, one treatment places the rotifers in three classes: Bdelloidea, Monogononta, and Seisonidea. In addition, the parasitic “spiny headed worms” currently in phylum Acanthocephala, appear to be modified rotifers and will probably be placed into the group in the near future. Undoubtedly the rotifers will continue to be revised as more phylogenetic evidence becomes available.

Phylum Nemertea

The Nemertea are colloquially known as *ribbon worms* or proboscis worms. Most species of phylum Nemertea are marine and predominantly benthic (bottom dwellers), with an estimated 900 known species. However, nemerteans have been recorded in freshwater and very damp terrestrial habitats as well. Most nemerteans are carnivores, feeding on worms, clams, and crustaceans. Some species are scavengers, and some, like *Malacobdella grossa*, have also evolved commensal relationships with mollusks. Economically important species have at times devastated commercial fishing of clams and crabs. Nemerteans have almost no predators and two species are sold as fish bait.

Superphylum Lophotrochozoa: Molluscs and Annelids

Abstract:
By the end of this section, you will be able to do the following:

* Describe the unique anatomical and morphological features of molluscs and annelids
* Describe the formation of the coelom
* Identify an important extracoelomic cavity in molluscs
* Describe the major body regions of Mollusca and how they vary in different molluscan classes
* Discuss the advantages of true body segmentation
* Describe the features of animals classified in phylum Annelida

Phylum Mollusca

The name “Mollusca” means “soft” body, since the earliest descriptions of molluscs came from observations of “squishy,” unshelled cuttlefish. Molluscs are predominantly a marine group of animals; however, they are also known to inhabit freshwater as well as terrestrial habitats. This enormous phylum includes chitons, tusk shells, snails, slugs, nudibranchs, sea butterflies, clams, mussels, oysters, squids, octopuses, and nautiluses. Molluscs display a wide range of morphologies in each class and subclass, but share a few key characteristics ([link]). The chief locomotor structure is usually a muscular foot. Most internal organs are contained in a region called the visceral mass. Overlying the visceral mass is a fold of tissue called the mantle; within the cavity formed by the mantle are respiratory structures called gills, that typically fold over the visceral mass. The mouths of most mollusks, except bivalves (e.g., clams) contain a specialized feeding organ called a radula, an abrasive tonguelike structure. Finally, the mantle secretes a calcium-carbonate-hardened shell in most molluscs, although this is greatly reduced in the class Cephalopoda, which contains the octopuses and squids.

Phylum Annelida

Phylum Annelida comprises the true, segmented worms. These animals are found in marine, terrestrial, and freshwater habitats, but the presence of water or humidity is a critical factor for their survival in terrestrial habitats. The annelids are often called “segmented worms” due to their key characteristic of metamerism, or true segmentation. Approximately 22,000 species have been described in phylum Annelida, which includes polychaete worms (marine annelids with multiple appendages), and oligochaetes (earthworms and leeches). Some animals in this phylum show parasitic and commensal symbioses with other species in their habitat.

Superphylum Ecdysozoa: Nematodes and Tardigrades

Abstract:
By the end of this section, you will be able to do the following:

* Describe the structural organization of nematodes
* Describe the importance of Caenorhabditis elegans in research
* Describe the features of Tardigrades

Superphylum Ecdysozoa

The superphylum Ecdysozoa contains an incredibly large number of species. This is because it contains two of the most diverse animal groups: phylum Nematoda (the roundworms) and phylum Arthropoda (the arthropods). The most prominent distinguishing feature of ecdysozoans is the cuticle—a tough, but flexible exoskeleton that protects these animals from water loss, predators, and other dangers of the external environment. One small phylum within the Ecdysozoa, with exceptional resistance to desiccation and other environmental hazards, is the Tardigrada. The nematodes, tardigrades, and arthropods all belong to the superphylum Ecdysozoa, which is believed to be monophyletic—a clade consisting of all evolutionary descendants from one common ancestor. All members of this superphylum periodically go through a molting process that culminates in ecdysis—the actual shedding of the old exoskeleton. (The term “ecdysis” translates roughly as “take off” or “strip.”) During the molting process, old cuticle is replaced by a new cuticle, which is secreted beneath it, and which will last until the next growth period.

Phylum Nematoda

The Nematoda, like other members of the superphylum Ecdysozoa, are triploblastic and possess an embryonic mesoderm that is sandwiched between the ectoderm and endoderm. They are also bilaterally symmetrical, meaning that a longitudinal section will divide them into right and left sides that are superficially symmetrical. In contrast with flatworms, nematodes are pseudocoelomates and show a tubular morphology and circular cross-section. Nematodes include both free-living and parasitic forms.

Phylum Tardigrada

The tardigrades ("slow-steppers") comprise a phylum of inconspicuous little animals living in marine, freshwater, or damp terrestrial environments throughout the world. They are commonly called "water bears" because of their plump bodies and the large claws on their stubby legs. There are over 1,000 species, most of which are less than 1 mm in length. A chitinous cuticle covers the body surface and may be divided into plates ([link]). Tardigrades are known for their ability to enter a state called cryptobiosis, which provides them with resistance to multiple environmental challenges, including desiccation, very low temperatures, vacuum, high pressure, and radiation. They can suspend their metabolic activity for years, and survive the loss of up to 99% of their water content. Their remarkable resistance has recently been attributed to unique proteins that replace water in their cells and protect their internal cell structure and their DNA from damage.

Superphylum Ecdysozoa: Arthropods

Abstract:
By the end of this section, you will be able to do the following:

* Compare the internal systems and appendage specializations of phylum Arthropoda
* Discuss the environmental importance of arthropods
* Discuss the reasons for arthropod success and abundance

Phylum Arthropoda

The name “arthropoda” means “jointed feet.” The name aptly describes the invertebrates included in this phylum. Arthropods have probably always dominated the animal kingdom in terms of number of species and likely will continue to do so: An estimated 85 percent of all known species are included in this phylum! In effect, life on Earth could conceivably be called the Age of Arthropods beginning nearly 500 million years ago.

Superphylum Deuterostomia

Abstract:
By the end of this section, you will be able to do the following:

* Describe the distinguishing characteristics of echinoderms
* Describe the distinguishing characteristics of chordates

Phylum Echinodermata

Echinodermata are named after their “prickly skin” (from the Greek “echinos” meaning “prickly” and “dermos” meaning “skin”). This phylum is a collection of about 7,000 described living species of exclusively marine, bottom-dwelling organisms. Sea stars ([link]), sea cucumbers, sea urchins, sand dollars, and brittle stars are all examples of echinoderms.

Classes of Echinoderms

This phylum is divided into five extant classes: Asteroidea (sea stars), Ophiuroidea (brittle stars), Echinoidea (sea urchins and sand dollars), Crinoidea (sea lilies or feather stars), and Holothuroidea (sea cucumbers) ([link]).

Phylum Chordata

Animals in the phylum Chordata share five key features that appear at some stage of their development: a notochord, a dorsal hollow nerve cord, pharyngeal slits, a post-anal tail, and an endostyle/thyroid gland that secretes iodinated hormones. In some groups, some of these traits are present only during embryonic development. In addition to containing vertebrate classes, the phylum Chordata contains two clades of “invertebrates”: Urochordata (tunicates, salps, and larvaceans) and Cephalochordata (lancelets). Most tunicates live on the ocean floor and are suspension feeders. Lancelets are suspension feeders that feed on phytoplankton and other microorganisms. The invertebrate chordates will be discussed more extensively in the following chapter.

Vertebrates

Introduction

Chordates

Abstract:
By the end of this section, you will be able to do the following:

* Describe the distinguishing characteristics of chordates
* Identify the derived characters of craniates that sets them apart from other chordates
* Describe the developmental fate of the notochord in vertebrates

Characteristics of Chordata

Animals in the phylum Chordata share five key characteristics that appear at some stage during their development: a notochord, a dorsal hollow (tubular) nerve cord, pharyngeal gill arches or slits, a post-anal tail, and an endostyle/thyroid gland ([link]). In some groups, some of these key characteristics are present only during embryonic development.

Chordates and the Evolution of Vertebrates

Two clades of chordates are invertebrates: Cephalochordata and Urochordata. Members of these groups also possess the five distinctive features of chordates at some point during their development.

Subphylum Vertebrata (Craniata)

A cranium is a bony, cartilaginous, or fibrous structure surrounding the brain, jaw, and facial bones ([link]). Most bilaterally symmetrical animals have a head; of these, those that have a cranium comprise the clade Craniata/Vertebrata, which includes the primitively jawless Myxini (hagfishes), Petromyzontida (lampreys), and all of the organisms called “vertebrates.” (We should note that the Myxini have a cranium but lack a backbone.)

Fishes

Abstract:
By the end of this section, you will be able to do the following:

* Describe the difference between jawless and jawed fishes
* Discuss the distinguishing features of sharks and rays compared to other modern fishes

Jawless Fishes: Superclass Agnatha

Jawless fishes (Agnatha) are craniates representing an ancient vertebrate lineage that arose over 550 million years ago. In the past, hagfishes and lampreys were sometimes recognized as separate clades within the Agnatha, primarily because lampreys were regarded as true vertebrates, whereas hagfishes were not. However, recent molecular data, both from rRNA and mtDNA, as well as embryological data, provide strong support for the hypothesis that living agnathans—previously called *cyclostomes*—are monophyletic, and thus share recent common ancestry. The discussion below, for convenience, separates the modern “cyclostomes” into the class Myxini and class Petromyzontida. The defining features of the living jawless fishes are the lack of jaws and lack of paired lateral appendages (fins). They also lack internal ossification and scales, although these are not defining features of the clade.

Gnathostomes: Jawed Fishes

Gnathostomes, or “jaw-mouths,” are vertebrates that possess true jaws—a milestone in the evolution of the vertebrates. In fact, one of the most significant developments in early vertebrate evolution was the development of the jaw: a hinged structure attached to the cranium that allows an animal to grasp and tear its food. Jaws were probably derived from the first pair of gill arches supporting the gills of jawless fishes.

Amphibians

Abstract:
By the end of this section, you will be able to do the following:

* Describe the important difference between the life cycle of amphibians and the life cycles of other vertebrates
* Distinguish between the characteristics of Urodela, Anura, and Apoda
* Describe the evolutionary history of amphibians

Characteristics of Amphibians

As tetrapods, most amphibians are characterized by four well-developed limbs. In some species of salamanders, hindlimbs are reduced or absent, but all caecilians are (secondarily) limbless. An important characteristic of extant amphibians is a moist, permeable skin that is achieved via mucus glands. Most water is taken in across the skin rather than by drinking. The skin is also one of three respiratory surfaces used by amphibians. The other two are the lungs and the buccal (mouth) cavity. Air is taken first into the mouth through the nostrils, and then pushed by positive pressure into the lungs by elevating the throat and closing the nostrils.

Evolution of Amphibians

The fossil record provides evidence of the first tetrapods: now-extinct amphibian species dating to nearly 400 million years ago. Evolution of tetrapods from lobe-finned freshwater fishes (similar to coelacanths and lungfish) represented a significant change in body plan from one suited to organisms that respired and swam in water, to organisms that breathed air and moved onto land; these changes occurred over a span of 50 million years during the Devonian period.

Modern Amphibians

Amphibia comprises an estimated 6,770 extant species that inhabit tropical and temperate regions around the world. All living species are classified in the subclass Lissamphibia ("smooth-amphibian"), which is divided into three clades: Urodela (“tailed”), the salamanders; Anura (“tail-less”), the frogs; and Apoda (“legless ones”), the caecilians.

Reptiles

Abstract:
By the end of this section, you will be able to do the following:

* Describe the main characteristics of amniotes
* Explain the difference between anapsids, synapsids, and diapsids, and give an example of each
* Identify the characteristics of reptiles
* Discuss the evolution of reptiles

Characteristics of Amniotes

The amniotic egg is the key characteristic of amniotes. In amniotes that lay eggs, the shell of the egg provides protection for the developing embryo while being permeable enough to allow for the exchange of carbon dioxide and oxygen. The *albumin*, or egg white, outside of the chorion provides the embryo with water and protein, whereas the fattier egg yolk contained in the yolk sac provides nutrients for the embryo, as is the case with the eggs of many other animals, such as amphibians. Here are the functions of the extraembryonic membranes:

Evolution of Amniotes

The first amniotes evolved from tetrapod ancestors approximately 340 million years ago during the Carboniferous period. The early amniotes quickly diverged into two main lines: *synapsids* and *sauropsids*. Synapsids included the *therapsids*, a clade from which mammals evolved. Sauropsids were further divided into *anapsids* and *diapsids*. Diapsids gave rise to the reptiles, including the dinosaurs and birds. The key differences between the synapsids, anapsids, and diapsids are the structures of the skull and the number of *temporal fenestrae* (“windows”) behind each eye ([link]). Temporal fenestrae are post-orbital openings in the skull that allow muscles to expand and lengthen. Anapsids have no temporal fenestrae, synapsids have one (fused ancestrally from two fenestrae), and diapsids have two (although many diapsids such as birds have highly modified diapsid skulls). Anapsids include extinct organisms and traditionally included turtles. However, more recent molecular and fossil evidence clearly shows that turtles arose within the diapsid line and secondarily lost the temporal fenestrae; thus they appear to be anapsids because modern turtles do not have fenestrae in the temporal bones of the skull. The canonical diapsids include dinosaurs, birds, and all other extinct and living reptiles.

Characteristics of Reptiles

Reptiles are tetrapods. Limbless reptiles—snakes and legless lizards—are classified as tetrapods because they are descended from four-limbed ancestors. Reptiles lay calcareous or leathery eggs enclosed in shells on land. Even aquatic reptiles return to the land to lay eggs. They usually reproduce sexually with internal fertilization. Some species display ovoviviparity, with the eggs remaining in the mother’s body until they are ready to hatch. In ovoviviparous reptiles, most nutrients are supplied by the egg yolk, while the chorioallantois assists with respiration. Other species are viviparous, with the offspring born alive, with their development supported by a yolk sac-placenta, a chorioallantoic-placenta, or both.

Evolution of Reptiles

Reptiles originated approximately 300 million years ago during the Carboniferous period. One of the oldest known amniotes is *Casineria*, which had both amphibian and reptilian characteristics. One of the earliest undisputed reptile fossils was *Hylonomus*, a lizardlike animal about 20 cm long. Soon after the first amniotes appeared, they diverged into three groups—synapsids, anapsids, and diapsids—during the Permian period. The Permian period also saw a second major divergence of diapsid reptiles into stem archosaurs (predecessors of thecodonts, crocodilians, dinosaurs, and birds) and lepidosaurs (predecessors of snakes and lizards). These groups remained inconspicuous until the Triassic period, when the archosaurs became the dominant terrestrial group possibly due to the extinction of large-bodied anapsids and synapsids during the Permian-Triassic extinction. About 250 million years ago, archosaurs radiated into the pterosaurs and both saurischian “lizard hip” and ornithischian “bird-hip” dinosaurs (see below).

Archosaurs: Dinosaurs

Dinosaurs (“fearfully-great lizard”) include the Saurischia (“lizard-hipped”) with a simple, three-pronged pelvis, and Ornithischia (“bird-hipped”) dinosaurs with a more complex pelvis, superficially similar to that of birds. However, it is a fact that birds evolved from the saurischian “lizard hipped” lineage, *not* the ornithischian “bird hip” lineage. Dinosaurs and their theropod descendants, the birds, are remnants of what was formerly a hugely diverse group of reptiles, some of which like *Argentinosaurus* were nearly 40 meters (130 feet) in length and weighed at least 80,000 kg (88 tons). They were the largest land animals to have lived, challenging and perhaps exceeding the great blue whale in size, but probably not weight—which could be greater than 200 tons.

Archosaurs: Pterosaurs

More than 200 species of pterosaurs have been described, and in their day, beginning about 230 million years ago, they were the undisputed rulers of the Mesozoic skies for over 170 million years. Recent fossils suggest that hundreds of pterosaur species may have lived during any given period, dividing up the environment much like birds do today. Pterosaurs came in amazing sizes and shapes, ranging in size from that of a small song bird to that of the enormous *Quetzalcoatlus northropi*, which stood nearly 6 meters (19 feet) high and had a wingspan of nearly 14 meters (40 feet). This monstrous pterosaur, named after the Aztec god Quetzalcoatl, the feathered flying serpent that contributed largely to the creation of humankind, may have been the largest flying animal that ever evolved!

Modern Reptiles

Class Reptilia includes many diverse species that are classified into four living clades. There are the 25 species of Crocodilia, two species of Sphenodontia, approximately 9,200 Squamata species, and about 325 species of Testudines.

Birds

Abstract:
By the end of this section, you will be able to do the following:

* Describe the evolutionary history of birds
* Describe the derived characteristics in birds that facilitate flight

Characteristics of Birds

Birds are endothermic, and more specifically, **homeothermic**—meaning that they usually maintain an elevated and constant body temperature, which is significantly above the average body temperature of most mammals. This is, in part, due to the fact that active flight—especially the hovering skills of birds such as hummingbirds—requires enormous amounts of energy, which in turn necessitates a high metabolic rate. Like mammals (which are also endothermic and homeothermic and covered with an insulating pelage), birds have several different types of feathers that together keep “heat” (infrared energy) within the core of the body, away from the surface where it can be lost by radiation and convection to the environment.

Evolution of Birds

Thanks to amazing new fossil discoveries in China, the evolutionary history of birds has become clearer, even though bird bones do not fossilize as well as those of other vertebrates. As we’ve seen earlier, birds are highly modified diapsids, but rather than having two fenestrations or openings in their skulls behind the eye, the skulls of modern birds are so specialized that it is difficult to see any trace of the original diapsid condition.

The Evolution of Flight in Birds

There are two basic hypotheses that explain how flight may have evolved in birds: the *arboreal (“tree”) hypothesis* and the *terrestrial (“land”) hypothesis*. The arboreal hypothesis posits that tree-dwelling precursors to modern birds jumped from branch to branch using their feathers for gliding before becoming fully capable of flapping flight. In contrast to this, the terrestrial hypothesis holds that running (perhaps pursuing active prey such as small cursorial animals) was the stimulus for flight. In this scenario, wings could be used to capture prey and were preadapted for balance and flapping flight. Ostriches, which are large flightless birds, hold their wings out when they run, possibly for balance. However, this condition may represent a behavioral relict of the clade of flying birds that were their ancestors. It seems more likely that small feathered arboreal dinosaurs, were capable of gliding (and flapping) from tree to tree and branch to branch, improving the chances of escaping enemies, finding mates, and obtaining prey such as flying insects. This early flight behavior would have also greatly increased the opportunity for species dispersal.

Mammals

Abstract:
By the end of this section, you will be able to do the following:

* Name and describe the distinguishing features of the three main groups of mammals
* Describe the likely line of evolutionary descent that produced mammals
* List some derived features that may have arisen in response to mammals’ need for constant, high-level metabolism
* Identify the major clades of eutherian mammals

Characteristics of Mammals

The presence of hair, composed of the protein keratin, is one of the most obvious characteristics of mammals. Although it is not very extensive or obvious on some species (such as whales), hair has many important functions for most mammals. Mammals are endothermic, and hair traps a boundary layer of air close to the body, retaining heat generated by metabolic activity. Along with insulation, hair can serve as a sensory mechanism via specialized hairs called *vibrissae*, better known as whiskers. Vibrissae attach to nerves that transmit information about tactile vibration produced by sound sensation, which is particularly useful to nocturnal or burrowing mammals. Hair can also provide protective coloration or be part of social signaling, such as when an animal’s hair stands “on end” to warn enemies, or possibly to make the mammal “look bigger” to predators.

Evolution of Mammals

Mammals are synapsids, meaning they have a single, ancestrally fused, postorbital opening in the skull. They are the only living synapsids, as earlier forms became extinct by the Jurassic period. The early non-mammalian synapsids can be divided into two groups, the pelycosaurs and the therapsids. Within the therapsids, a group called the cynodonts are thought to have been the ancestors of mammals ([link]).

Living Mammals

There are three major groups of living mammals: *monotremes* (*prototheria*), *marsupials* (*metatheria*), and *placental* (*eutheria*) mammals. The eutherians and the marsupials together comprise a clade of therian mammals, with the monotremes forming a sister clade to both metatherians and eutherians.

The Evolution of Primates

Abstract:
By the end of this section, you will be able to do the following:

* Describe the derived features that distinguish primates from other animals
* Describe the defining features of the major groups of primates
* Identify the major hominin precursors to modern humans
* Explain why scientists are having difficulty determining the true lines of descent in hominids

Characteristics of Primates

All primate species possess adaptations for climbing trees, as they all descended from tree-dwellers. This arboreal heritage of primates has resulted in hands and feet that are adapted for climbing, or brachiation (swinging through trees using the arms). These adaptations include, but are not limited to: 1) a rotating shoulder joint, 2) a big toe that is widely separated from the other toes (except humans) and thumbs sufficiently separated from fingers to allow for gripping branches, and 3) stereoscopic vision, two overlapping fields of vision from the eyes, which allows for the perception of depth and gauging distance. Other characteristics of primates are brains that are larger than those of most other mammals, claws that have been modified into flattened nails, typically only one offspring per pregnancy, and a trend toward holding the body upright.

Evolution of Primates

The first primate-like mammals are referred to as proto-primates. They were roughly similar to squirrels and tree shrews in size and appearance. The existing fossil evidence (mostly from North Africa) is very fragmented. These proto-primates remain largely mysterious creatures until more fossil evidence becomes available. Although genetic evidence suggests that primates diverged from other mammals about 85 MYA, the oldest known primate-like mammals with a relatively robust fossil record date to about 65 MYA. Fossils like the proto-primate *Plesiadapis* (although some researchers do not agree that *Plesiadapis* was a proto-primate) had some features of the teeth and skeleton in common with true primates. They were found in North America and Europe in the Cenozoic and went extinct by the end of the Eocene.

Human Evolution

The family Hominidae of order Primates includes the hominoids: the great apes and humans ([link]). Evidence from the fossil record and from a comparison of human and chimpanzee DNA suggests that humans and chimpanzees diverged from a common hominoid ancestor approximately six million years ago. Several species evolved from the evolutionary branch that includes humans, although our species is the only surviving member. The term hominin is used to refer to those species that evolved after this split of the primate line, thereby designating species that are more closely related to humans than to chimpanzees. A number of marker features differentiate humans from the other hominoids, including bipedalism or upright posture, increase in the size of the brain, and a fully opposable thumb that can touch the little finger. Bipedal hominins include several groups that were probably part of the modern human lineage—*Australopithecus*, *Homo habilis*, and *Homo erectus*—and several non-ancestral groups that can be considered “cousins” of modern humans, such as Neanderthals and Denisovans.

Plant Structure and Function

Plant Form and Physiology

Introduction

The Plant Body

Abstract:
By the end of this section, you will be able to do the following:

* Describe the shoot organ system and the root organ system
* Distinguish between meristematic tissue and permanent tissue
* Identify and describe the three regions where plant growth occurs
* Summarize the roles of dermal tissue, vascular tissue, and ground tissue
* Compare simple plant tissue with complex plant tissue

Plant Organ Systems

In plants, just as in animals, similar cells working together form a tissue. When different types of tissues work together to perform a unique function, they form an organ; organs working together form organ systems. Vascular plants have two distinct organ systems: a shoot system, and a root system. The shoot system consists of two portions: the vegetative (non-reproductive) parts of the plant, such as the leaves and the stems, and the reproductive parts of the plant, which include flowers and fruits. The shoot system generally grows above ground, where it absorbs the light needed for photosynthesis. The root system, which supports the plants and absorbs water and minerals, is usually underground. [link] shows the organ systems of a typical plant.

Plant Tissues

Plants are multicellular eukaryotes with tissue systems made of various cell types that carry out specific functions. Plant tissue systems fall into one of two general types: meristematic tissue, and permanent (or non-meristematic) tissue. Cells of the meristematic tissue are found in meristems, which are plant regions of continuous cell division and growth. Meristematic tissue cells are either undifferentiated or incompletely differentiated, and they continue to divide and contribute to the growth of the plant. In contrast, permanent tissue consists of plant cells that are no longer actively dividing.

Stems

Abstract:
By the end of this section, you will be able to do the following:

* Describe the main function and basic structure of stems
* Compare and contrast the roles of dermal tissue, vascular tissue, and ground tissue
* Distinguish between primary growth and secondary growth in stems
* Summarize the origin of annual rings
* List and describe examples of modified stems

Stem Anatomy

The stem and other plant organs arise from the ground tissue, and are primarily made up of simple tissues formed from three types of cells: parenchyma, collenchyma, and sclerenchyma cells.

Growth in Stems

Growth in plants occurs as the stems and roots lengthen. Some plants, especially those that are woody, also increase in thickness during their life span. The increase in length of the shoot and the root is referred to as primary growth, and is the result of cell division in the shoot apical meristem. Secondary growth is characterized by an increase in thickness or girth of the plant, and is caused by cell division in the lateral meristem. [link] shows the areas of primary and secondary growth in a plant. Herbaceous plants mostly undergo primary growth, with hardly any secondary growth or increase in thickness. Secondary growth or “wood” is noticeable in woody plants; it occurs in some dicots, but occurs very rarely in monocots.

Stem Modifications

Some plant species have modified stems that are especially suited to a particular habitat and environment ([link]). A rhizome is a modified stem that grows horizontally underground and has nodes and internodes. Vertical shoots may arise from the buds on the rhizome of some plants, such as ginger and ferns. Corms are similar to rhizomes, except they are more rounded and fleshy (such as in gladiolus). Corms contain stored food that enables some plants to survive the winter. Stolons are stems that run almost parallel to the ground, or just below the surface, and can give rise to new plants at the nodes. Runners are a type of stolon that runs above the ground and produces new clone plants at nodes at varying intervals: strawberries are an example. Tubers are modified stems that may store starch, as seen in the potato (*Solanum* sp.). Tubers arise as swollen ends of stolons, and contain many adventitious or unusual buds (familiar to us as the “eyes” on potatoes). A bulb, which functions as an underground storage unit, is a modification of a stem that has the appearance of enlarged fleshy leaves emerging from the stem or surrounding the base of the stem, as seen in the iris.

Roots

Abstract:
By the end of this section, you will be able to do the following:

* Identify the two types of root systems
* Describe the three zones of the root tip and summarize the role of each zone in root growth
* Describe the structure of the root
* List and describe examples of modified roots

Types of Root Systems

Root systems are mainly of two types ([link]). Dicots have a tap root system, while monocots have a fibrous root system. A tap root system has a main root that grows down vertically, and from which many smaller lateral roots arise. Dandelions are a good example; their tap roots usually break off when trying to pull these weeds, and they can regrow another shoot from the remaining root. A tap root system penetrates deep into the soil. In contrast, a fibrous root system is located closer to the soil surface, and forms a dense network of roots that also helps prevent soil erosion (lawn grasses are a good example, as are wheat, rice, and corn). Some plants have a combination of tap roots and fibrous roots. Plants that grow in dry areas often have deep root systems, whereas plants growing in areas with abundant water are likely to have shallower root systems.

Root Growth and Anatomy

Root growth begins with seed germination. When the plant embryo emerges from the seed, the radicle of the embryo forms the root system. The tip of the root is protected by the root cap, a structure exclusive to roots and unlike any other plant structure. The root cap is continuously replaced because it gets damaged easily as the root pushes through soil. The root tip can be divided into three zones: a zone of cell division, a zone of elongation, and a zone of maturation and differentiation ([link]). The zone of cell division is closest to the root tip; it is made up of the actively dividing cells of the root meristem. The zone of elongation is where the newly formed cells increase in length, thereby lengthening the root. Beginning at the first root hair is the zone of cell maturation where the root cells begin to differentiate into special cell types. All three zones are in the first centimeter or so of the root tip.

Root Modifications

Root structures may be modified for specific purposes. For example, some roots are bulbous and store starch. Aerial roots and prop roots are two forms of aboveground roots that provide additional support to anchor the plant. Tap roots, such as carrots, turnips, and beets, are examples of roots that are modified for food storage ([link]).

Leaves

Abstract:
By the end of this section, you will be able to do the following:

* Identify the parts of a typical leaf
* Describe the internal structure and function of a leaf
* Compare and contrast simple leaves and compound leaves
* List and describe examples of modified leaves

Structure of a Typical Leaf

Each leaf typically has a leaf blade called the lamina, which is also the widest part of the leaf. Some leaves are attached to the plant stem by a petiole. Leaves that do not have a petiole and are directly attached to the plant stem are called sessile leaves. Small green appendages usually found at the base of the petiole are known as stipules. Most leaves have a midrib, which travels the length of the leaf and branches to each side to produce veins of vascular tissue. The edge of the leaf is called the margin. [link] shows the structure of a typical eudicot leaf.

Leaf Arrangement

The arrangement of leaves on a stem is known as phyllotaxy. The number and placement of a plant’s leaves will vary depending on the species, with each species exhibiting a characteristic leaf arrangement. Leaves are classified as either alternate, spiral, or opposite. Plants that have only one leaf per node have leaves that are said to be either alternate—meaning the leaves alternate on each side of the stem in a flat plane—or spiral, meaning the leaves are arrayed in a spiral along the stem. In an opposite leaf arrangement, two leaves arise at the same point, with the leaves connecting opposite each other along the branch. If there are three or more leaves connected at a node, the leaf arrangement is classified as whorled.

Leaf Form

Leaves may be simple or compound ([link]). In a simple leaf, the blade is either completely undivided—as in the banana leaf—or it has lobes, but the separation does not reach the midrib, as in the maple leaf. In a compound leaf, the leaf blade is completely divided, forming leaflets, as in the locust tree. Each leaflet may have its own stalk, but is attached to the rachis. A palmately compound leaf resembles the palm of a hand, with leaflets radiating outwards from one point. Examples include the leaves of poison ivy, the buckeye tree, or the familiar houseplant *Schefflera* sp. (common name “umbrella plant”). Pinnately compound leaves take their name from their feather-like appearance; the leaflets are arranged along the midrib, as in rose leaves (*Rosa* sp.), or the leaves of hickory, pecan, ash, or walnut trees.

Leaf Structure and Function

The outermost layer of the leaf is the epidermis; it is present on both sides of the leaf and is called the upper and lower epidermis, respectively. Botanists call the upper side the adaxial surface (or adaxis) and the lower side the abaxial surface (or abaxis). The epidermis helps in the regulation of gas exchange. It contains stomata ([link]): openings through which the exchange of gases takes place. Two guard cells surround each stoma, regulating its opening and closing.

Leaf Adaptations

Coniferous plant species that thrive in cold environments, like spruce, fir, and pine, have leaves that are reduced in size and needle-like in appearance. These needle-like leaves have sunken stomata and a smaller surface area: two attributes that aid in reducing water loss. In hot climates, plants such as cacti have leaves that are reduced to spines, which in combination with their succulent stems, help to conserve water. Many aquatic plants have leaves with wide lamina that can float on the surface of the water, and a thick waxy cuticle on the leaf surface that repels water.

Transport of Water and Solutes in Plants

Abstract:
By the end of this section, you will be able to do the following:

* Define water potential and explain how it is influenced by solutes, pressure, gravity, and the matric potential
* Describe how water potential, evapotranspiration, and stomatal regulation influence how water is transported in plants
* Explain how photosynthates are transported in plants

Water Potential

Plants are phenomenal hydraulic engineers. Using only the basic laws of physics and the simple manipulation of potential energy, plants can move water to the top of a 116-meter-tall tree ([link]a). Plants can also use hydraulics to generate enough force to split rocks and buckle sidewalks ([link]b). Plants achieve this because of water potential.

Movement of Water and Minerals in the Xylem

Solutes, pressure, gravity, and matric potential are all important for the transport of water in plants. Water moves from an area of higher total water potential (higher Gibbs free energy) to an area of lower total water potential. Gibbs free energy is the energy associated with a chemical reaction that can be used to do work. This is expressed as ΔΨ.

Transportation of Photosynthates in the Phloem

Plants need an energy source to grow. In seeds and bulbs, food is stored in polymers (such as starch) that are converted by metabolic processes into sucrose for newly developing plants. Once green shoots and leaves are growing, plants are able to produce their own food by photosynthesizing. The products of photosynthesis are called photosynthates, which are usually in the form of simple sugars such as sucrose.

Plant Sensory Systems and Responses

Abstract:
By the end of this section, you will be able to do the following:

* Describe how red and blue light affect plant growth and metabolic activities
* Discuss gravitropism
* Understand how hormones affect plant growth and development
* Describe thigmotropism, thigmonastism, and thigmogenesis
* Explain how plants defend themselves from predators and respond to wounds

Plant Responses to Light

Plants have a number of sophisticated uses for light that go far beyond their ability to photosynthesize low-molecular-weight sugars using only carbon dioxide, light, and water. Photomorphogenesis is the growth and development of plants in response to light. It allows plants to optimize their use of light and space. Photoperiodism is the ability to use light to track time. Plants can tell the time of day and time of year by sensing and using various wavelengths of sunlight. Phototropism is a directional response that allows plants to grow towards, or even away from, light.

Plant Responses to Gravity

Whether or not they germinate in the light or in total darkness, shoots usually sprout up from the ground, and roots grow downward into the ground. A plant laid on its side in the dark will send shoots upward when given enough time. Gravitropism ensures that roots grow into the soil and that shoots grow toward sunlight. Growth of the shoot apical tip upward is called negative gravitropism, whereas growth of the roots downward is called positive gravitropism.

Growth Responses

A plant’s sensory response to external stimuli relies on chemical messengers (hormones). Plant hormones affect all aspects of plant life, from flowering to fruit setting and maturation, and from phototropism to leaf fall. Potentially every cell in a plant can produce plant hormones. They can act in their cell of origin or be transported to other portions of the plant body, with many plant responses involving the synergistic or antagonistic interaction of two or more hormones. In contrast, animal hormones are produced in specific glands and transported to a distant site for action, and they act alone.

Plant Responses to Wind and Touch

The shoot of a pea plant winds around a trellis, while a tree grows on an angle in response to strong prevailing winds. These are examples of how plants respond to touch or wind.

Defense Responses against Herbivores and Pathogens

Plants face two types of enemies: herbivores and pathogens. Herbivores both large and small use plants as food, and actively chew them. Pathogens are agents of disease. These infectious microorganisms, such as fungi, bacteria, and nematodes, live off of the plant and damage its tissues. Plants have developed a variety of strategies to discourage or kill attackers.

Soil and Plant Nutrition

Introduction

Nutritional Requirements of Plants

Abstract:
By the end of this section, you will be able to do the following:

* Describe how plants obtain nutrients
* List the elements and compounds required for proper plant nutrition
* Describe an essential nutrient

The Chemical Composition of Plants

Since plants require nutrients in the form of elements such as carbon and potassium, it is important to understand the chemical composition of plants. The majority of volume in a plant cell is water; it typically comprises 80 to 90 percent of the plant’s total weight. Soil is the water source for land plants, and can be an abundant source of water, even if it appears dry. Plant roots absorb water from the soil through root hairs and transport it up to the leaves through the xylem. As water vapor is lost from the leaves, the process of transpiration and the polarity of water molecules (which enables them to form hydrogen bonds) draws more water from the roots up through the plant to the leaves ([link]). Plants need water to support cell structure, for metabolic functions, to carry nutrients, and for photosynthesis.

Essential Nutrients

Plants require only light, water, and about 20 elements to support all their biochemical needs: these 20 elements are called essential nutrients ([link]). For an element to be regarded as essential, three criteria are required: 1) a plant cannot complete its life cycle without the element; 2) no other element can perform the function of the element; and 3) the element is directly involved in plant nutrition.

The Soil

Abstract:
By the end of this section, you will be able to do the following:

* Describe how soils are formed
* Explain soil composition
* Describe a soil profile

Soil Composition

Soil consists of these major components ([link]):

Soil Formation

Soil formation is the consequence of a combination of biological, physical, and chemical processes. Soil should ideally contain 50 percent solid material and 50 percent pore space. About one-half of the pore space should contain water, and the other half should contain air. The organic component of soil serves as a cementing agent, returns nutrients to the plant, allows soil to store moisture, makes soil tillable for farming, and provides energy for soil microorganisms. Most soil microorganisms—bacteria, algae, or fungi—are dormant in dry soil, but become active once moisture is available.

Physical Properties of the Soil

Soils are named and classified based on their horizons. The soil profile has four distinct layers: 1) O horizon; 2) A horizon; 3) B horizon, or subsoil; and 4) C horizon, or soil base ([link]). The O horizon has freshly decomposing organic matter—humus—at its surface, with decomposed vegetation at its base. Humus enriches the soil with nutrients and enhances soil moisture retention. Topsoil—the top layer of soil—is usually two to three inches deep, but this depth can vary considerably. For instance, river deltas like the Mississippi River delta have deep layers of topsoil. Topsoil is rich in organic material; microbial processes occur there, and it is the “workhorse” of plant production. The A horizon consists of a mixture of organic material with inorganic products of weathering, and it is therefore the beginning of true mineral soil. This horizon is typically darkly colored because of the presence of organic matter. In this area, rainwater percolates through the soil and carries materials from the surface. The B horizon is an accumulation of mostly fine material that has moved downward, resulting in a dense layer in the soil. In some soils, the B horizon contains nodules or a layer of calcium carbonate. The C horizon, or soil base, includes the parent material, plus the organic and inorganic material that is broken down to form soil. The parent material may be either created in its natural place, or transported from elsewhere to its present location. Beneath the C horizon lies bedrock.

Nutritional Adaptations of Plants

Abstract:
By the end of this section, you will be able to do the following:

* Understand the nutritional adaptations of plants
* Describe mycorrhizae
* Explain nitrogen fixation

Nitrogen Fixation: Root and Bacteria Interactions

Nitrogen is an important macronutrient because it is part of nucleic acids and proteins. Atmospheric nitrogen, which is the diatomic molecule N2, or dinitrogen, is the largest pool of nitrogen in terrestrial ecosystems. However, plants cannot take advantage of this nitrogen because they do not have the necessary enzymes to convert it into biologically useful forms. However, nitrogen can be “fixed,” which means that it can be converted to ammonia (NH3) through biological, physical, or chemical processes. As you have learned, biological nitrogen fixation (BNF) is the conversion of atmospheric nitrogen (N2) into ammonia (NH3), exclusively carried out by prokaryotes such as soil bacteria or cyanobacteria. Biological processes contribute 65 percent of the nitrogen used in agriculture. The following equation represents the process:

Mycorrhizae: The Symbiotic Relationship between Fungi and Roots

A nutrient depletion zone can develop when there is rapid soil solution uptake, low nutrient concentration, low diffusion rate, or low soil moisture. These conditions are very common; therefore, most plants rely on fungi to facilitate the uptake of minerals from the soil. Fungi form symbiotic associations called mycorrhizae with plant roots, in which the fungi actually are integrated into the physical structure of the root. The fungi colonize the living root tissue during active plant growth.

Nutrients from Other Sources

Some plants cannot produce their own food and must obtain their nutrition from outside sources. This may occur with plants that are parasitic or saprophytic. Some plants are mutualistic symbionts, epiphytes, or insectivorous.

Symbionts

A symbiont is a plant in a symbiotic relationship, with special adaptations such as mycorrhizae or nodule formation ([link] and [link]).

Insectivorous Plants

An insectivorous plant has specialized leaves to attract and digest insects. The Venus flytrap is popularly known for its insectivorous mode of nutrition, and has leaves that work as traps ([link]). The minerals it obtains from prey compensate for those lacking in the boggy (low pH) soil of its native North Carolina coastal plains. There are three sensitive hairs in the center of each half of each leaf. The edges of each leaf are covered with long spines. Nectar secreted by the plant attracts flies to the leaf. When a fly touches the sensory hairs, the leaf immediately closes. Next, fluids and enzymes break down the prey and minerals are absorbed by the leaf. Since this plant is popular in the horticultural trade, it is threatened in its original habitat.

Plant Reproduction

Introduction

Reproductive Development and Structure

Abstract:
By the end of this section, you will be able to do the following:

* Describe the two stages of a plant’s lifecycle
* Compare and contrast male and female gametophytes and explain how they form in angiosperms
* Describe the reproductive structures of a plant
* Describe the components of a complete flower
* Describe the development of microsporangium and megasporangium in gymnosperms

Sexual Reproduction in Angiosperms

The lifecycle of angiosperms follows the alternation of generations explained previously. The haploid gametophyte alternates with the diploid sporophyte during the sexual reproduction process of angiosperms. Flowers contain the plant’s reproductive structures.

Sexual Reproduction in Gymnosperms

As with angiosperms, the lifecycle of a gymnosperm is also characterized by alternation of generations. In conifers such as pines, the green leafy part of the plant is the sporophyte, and the cones contain the male and female gametophytes ([link]). The female cones are larger than the male cones and are positioned towards the top of the tree; the small, male cones are located in the lower region of the tree. Because the pollen is shed and blown by the wind, this arrangement makes it difficult for a gymnosperm to self-pollinate.

Angiosperms versus Gymnosperms

Gymnosperm reproduction differs from that of angiosperms in several ways ([link]). In angiosperms, the female gametophyte exists in an enclosed structure—the ovule—which is within the ovary; in gymnosperms, the female gametophyte is present on exposed bracts of the female cone. Double fertilization is a key event in the lifecycle of angiosperms, but is completely absent in gymnosperms. The male and female gametophyte structures are present on separate male and female cones in gymnosperms, whereas in angiosperms, they are a part of the flower. Lastly, wind plays an important role in pollination in gymnosperms because pollen is blown by the wind to land on the female cones. Although many angiosperms are also wind-pollinated, animal pollination is more common.

Pollination and Fertilization

Abstract:
By the end of this section, you will be able to do the following:

* Describe what must occur for plant fertilization
* Explain cross-pollination and the ways in which it takes place
* Describe the process that leads to the development of a seed
* Define double fertilization

Pollination by Insects

Bees are perhaps the most important pollinator of many garden plants and most commercial fruit trees ([link]). The most common species of bees are bumblebees and honeybees. Since bees cannot see the color red, bee-pollinated flowers usually have shades of blue, yellow, or other colors. Bees collect energy-rich pollen or nectar for their survival and energy needs. They visit flowers that are open during the day, are brightly colored, have a strong aroma or scent, and have a tubular shape, typically with the presence of a nectar guide. A nectar guide includes regions on the flower petals that are visible only to bees, and not to humans; it helps to guide bees to the center of the flower, thus making the pollination process more efficient. The pollen sticks to the bees’ fuzzy hair, and when the bee visits another flower, some of the pollen is transferred to the second flower. Recently, there have been many reports about the declining population of honeybees. Many flowers will remain unpollinated and not bear seed if honeybees disappear. The impact on commercial fruit growers could be devastating.

Pollination by Bats

In the tropics and deserts, bats are often the pollinators of nocturnal flowers such as agave, guava, and morning glory. The flowers are usually large and white or pale-colored; thus, they can be distinguished from the dark surroundings at night. The flowers have a strong, fruity, or musky fragrance and produce large amounts of nectar. They are naturally large and wide-mouthed to accommodate the head of the bat. As the bats seek the nectar, their faces and heads become covered with pollen, which is then transferred to the next flower.

Pollination by Birds

Many species of small birds, such as the hummingbird ([link]) and sun birds, are pollinators for plants such as orchids and other wildflowers. Flowers visited by birds are usually sturdy and are oriented in such a way as to allow the birds to stay near the flower without getting their wings entangled in the nearby flowers. The flower typically has a curved, tubular shape, which allows access for the bird’s beak. Brightly colored, odorless flowers that are open during the day are pollinated by birds. As a bird seeks energy-rich nectar, pollen is deposited on the bird’s head and neck and is then transferred to the next flower it visits. Botanists have been known to determine the range of extinct plants by collecting and identifying pollen from 200-year-old bird specimens from the same site.

Pollination by Wind

Most species of conifers, and many angiosperms, such as grasses, maples and oaks, are pollinated by wind. Pine cones are brown and unscented, while the flowers of wind-pollinated angiosperm species are usually green, small, may have small or no petals, and produce large amounts of pollen. Unlike the typical insect-pollinated flowers, flowers adapted to pollination by wind do not produce nectar or scent. In wind-pollinated species, the microsporangia hang out of the flower, and, as the wind blows, the lightweight pollen is carried with it ([link]). The flowers usually emerge early in the spring, before the leaves, so that the leaves do not block the movement of the wind. The pollen is deposited on the exposed feathery stigma of the flower ([link]).

Pollination by Water

Some weeds, such as Australian sea grass and pond weeds, are pollinated by water. The pollen floats on water, and when it comes into contact with the flower, it is deposited inside the flower.

Double Fertilization

After pollen is deposited on the stigma, it must germinate and grow through the style to reach the ovule. The microspores, or the pollen, contain two cells: the pollen tube cell and the generative cell. The pollen tube cell grows into a pollen tube through which the generative cell travels. The germination of the pollen tube requires water, oxygen, and certain chemical signals. As it travels through the style to reach the embryo sac, the pollen tube’s growth is supported by the tissues of the style. In the meantime, if the generative cell has not already split into two cells, it now divides to form two sperm cells. The pollen tube is guided by the chemicals secreted by the synergids present in the embryo sac, and it enters the ovule sac through the micropyle. Of the two sperm cells, one sperm fertilizes the egg cell, forming a diploid zygote; the other sperm fuses with the two polar nuclei, forming a triploid cell that develops into the endosperm. Together, these two fertilization events in angiosperms are known as double fertilization ([link]). After fertilization is complete, no other sperm can enter. The fertilized ovule forms the seed, whereas the tissues of the ovary become the fruit, usually enveloping the seed.

Development of Fruit and Fruit Types

After fertilization, the ovary of the flower usually develops into the fruit. Fruits are usually associated with having a sweet taste; however, not all fruits are sweet. Botanically, the term “fruit” is used for a ripened ovary. In most cases, flowers in which fertilization has taken place will develop into fruits, and flowers in which fertilization has not taken place will not. Some fruits develop from the ovary and are known as true fruits, whereas others develop from other parts of the female gametophyte and are known as accessory fruits. The fruit encloses the seeds and the developing embryo, thereby providing it with protection. Fruits are of many types, depending on their origin and texture. The sweet tissue of the blackberry, the red flesh of the tomato, the shell of the peanut, and the hull of corn (the tough, thin part that gets stuck in your teeth when you eat popcorn) are all fruits. As the fruit matures, the seeds also mature.

Fruit and Seed Dispersal

The fruit has a single purpose: seed dispersal. Seeds contained within fruits need to be dispersed far from the mother plant, so they may find favorable and less competitive conditions in which to germinate and grow.

Asexual Reproduction

Abstract:
By the end of this section, you will be able to do the following:

* Compare the mechanisms and methods of natural and artificial asexual reproduction
* Describe the advantages and disadvantages of natural and artificial asexual reproduction
* Discuss plant life spans

Natural Methods of Asexual Reproduction

Natural methods of asexual reproduction include strategies that plants have developed to self-propagate. Many plants—like ginger, onion, gladioli, and dahlia—continue to grow from buds that are present on the surface of the stem. In some plants, such as the sweet potato, adventitious roots or runners can give rise to new plants ([link]). In *Bryophyllum* and kalanchoe, the leaves have small buds on their margins. When these are detached from the plant, they grow into independent plants; or, they may start growing into independent plants if the leaf touches the soil. Some plants can be propagated through cuttings alone.

Artificial Methods of Asexual Reproduction

These methods are frequently employed to give rise to new, and sometimes novel, plants. They include grafting, cutting, layering, and micropropagation.

Plant Life Spans

The length of time from the beginning of development to the death of a plant is called its life span. The life cycle, on the other hand, is the sequence of stages a plant goes through from seed germination to seed production of the mature plant. Some plants, such as annuals, only need a few weeks to grow, produce seeds and die. Other plants, such as the bristlecone pine, live for thousands of years. Some bristlecone pines have a documented age of 4,500 years ([link]). Even as some parts of a plant, such as regions containing meristematic tissue—the area of active plant growth consisting of undifferentiated cells capable of cell division—continue to grow, some parts undergo programmed cell death (apoptosis). The cork found on stems, and the water-conducting tissue of the xylem, for example, are composed of dead cells.

Animal Structure and Function

The Animal Body: Basic Form and Function

Introduction

Animal Form and Function

Abstract:
By the end of this section, you will be able to do the following:

* Describe the various types of body plans that occur in animals
* Describe limits on animal size and shape
* Relate bioenergetics to body size, levels of activity, and the environment

Body Plans

Animal body plans follow set patterns related to symmetry. They are asymmetrical, radial, or bilateral in form as illustrated in [link]. Asymmetrical animals are animals with no pattern or symmetry; an example of an asymmetrical animal is a sponge. Radial symmetry, as illustrated in [link], describes when an animal has an up-and-down orientation: any plane cut along its longitudinal axis through the organism produces equal halves, but not a definite right or left side. This plan is found mostly in aquatic animals, especially organisms that attach themselves to a base, like a rock or a boat, and extract their food from the surrounding water as it flows around the organism. Bilateral symmetry is illustrated in the same figure by a goat. The goat also has an upper and lower component to it, but a plane cut from front to back separates the animal into definite right and left sides. Additional terms used when describing positions in the body are anterior (front), posterior (rear), dorsal (toward the back), and ventral (toward the stomach). Bilateral symmetry is found in both land-based and aquatic animals; it enables a high level of mobility.

Limits on Animal Size and Shape

Animals with bilateral symmetry that live in water tend to have a fusiform shape: this is a tubular shaped body that is tapered at both ends. This shape decreases the drag on the body as it moves through water and allows the animal to swim at high speeds. [link] lists the maximum speed of various animals. Certain types of sharks can swim at fifty kilometers per hour and some dolphins at 32 to 40 kilometers per hour. Land animals frequently travel faster, although the tortoise and snail are significantly slower than cheetahs. Another difference in the adaptations of aquatic and land-dwelling organisms is that aquatic organisms are constrained in shape by the forces of drag in the water since water has higher viscosity than air. On the other hand, land-dwelling organisms are constrained mainly by gravity, and drag is relatively unimportant. For example, most adaptations in birds are for gravity not for drag.

Limiting Effects of Diffusion on Size and Development

The exchange of nutrients and wastes between a cell and its watery environment occurs through the process of diffusion. All living cells are bathed in liquid, whether they are in a single-celled organism or a multicellular one. Diffusion is effective over a specific distance and limits the size that an individual cell can attain. If a cell is a single-celled microorganism, such as an amoeba, it can satisfy all of its nutrient and waste needs through diffusion. If the cell is too large, then diffusion is ineffective and the center of the cell does not receive adequate nutrients nor is it able to effectively dispel its waste.

Animal Bioenergetics

All animals must obtain their energy from food they ingest or absorb. These nutrients are converted to adenosine triphosphate (ATP) for short-term storage and use by all cells. Some animals store energy for slightly longer times as glycogen, and others store energy for much longer times in the form of triglycerides housed in specialized adipose tissues. No energy system is one hundred percent efficient, and an animal’s metabolism produces waste energy in the form of heat. If an animal can conserve that heat and maintain a relatively constant body temperature, it is classified as a warm-blooded animal and called an endotherm. The insulation used to conserve the body heat comes in the forms of fur, fat, or feathers. The absence of insulation in ectothermic animals increases their dependence on the environment for body heat.

Animal Body Planes and Cavities

A standing vertebrate animal can be divided by several planes. A sagittal plane divides the body into right and left portions. A midsagittal plane divides the body exactly in the middle, making two equal right and left halves. A frontal plane (also called a coronal plane) separates the front from the back. A transverse plane (or, horizontal plane) divides the animal into upper and lower portions. This is sometimes called a cross section, and, if the transverse cut is at an angle, it is called an oblique plane. [link] illustrates these planes on a goat (a four-legged animal) and a human being.

Animal Primary Tissues

Abstract:
By the end of this section, you will be able to do the following:

* Describe epithelial tissues
* Discuss the different types of connective tissues in animals
* Describe three types of muscle tissues
* Describe nervous tissue

Epithelial Tissues

Epithelial tissues cover the outside of organs and structures in the body and line the lumens of organs in a single layer or multiple layers of cells. The types of epithelia are classified by the shapes of cells present and the number of layers of cells. Epithelia composed of a single layer of cells is called simple epithelia; epithelial tissue composed of multiple layers is called stratified epithelia. [link] summarizes the different types of epithelial tissues.

Connective Tissues

Connective tissues are made up of a matrix consisting of living cells and a nonliving substance, called the ground substance. The ground substance is made of an organic substance (usually a protein) and an inorganic substance (usually a mineral or water). The principal cell of connective tissues is the fibroblast. This cell makes the fibers found in nearly all of the connective tissues. Fibroblasts are motile, able to carry out mitosis, and can synthesize whichever connective tissue is needed. Macrophages, lymphocytes, and, occasionally, leukocytes can be found in some of the tissues. Some tissues have specialized cells that are not found in the others. The matrix in connective tissues gives the tissue its density. When a connective tissue has a high concentration of cells or fibers, it has proportionally a less dense matrix.

Muscle Tissues

There are three types of muscle in animal bodies: smooth, skeletal, and cardiac. They differ by the presence or absence of striations or bands, the number and location of nuclei, whether they are voluntarily or involuntarily controlled, and their location within the body. [link] summarizes these differences.

Nervous Tissues

Nervous tissues are made of cells specialized to receive and transmit electrical impulses from specific areas of the body and to send them to specific locations in the body. The main cell of the nervous system is the neuron, illustrated in [link]. The large structure with a central nucleus is the cell body of the neuron. Projections from the cell body are either dendrites specialized in receiving input or a single axon specialized in transmitting impulses. Some glial cells are also shown. Astrocytes regulate the chemical environment of the nerve cell, and oligodendrocytes insulate the axon so the electrical nerve impulse is transferred more efficiently. Other glial cells that are not shown support the nutritional and waste requirements of the neuron. Some of the glial cells are phagocytic and remove debris or damaged cells from the tissue. A nerve consists of neurons and glial cells.

Homeostasis

Abstract:
By the end of this section, you will be able to do the following:

* Define homeostasis
* Describe the factors affecting homeostasis
* Discuss positive and negative feedback mechanisms used in homeostasis
* Describe thermoregulation of endothermic and ectothermic animals

Homeostatic Process

The goal of homeostasis is the maintenance of equilibrium around a point or value called a set point. While there are normal fluctuations from the set point, the body’s systems will usually attempt to go back to this point. A change in the internal or external environment is called a stimulus and is detected by a receptor; the response of the system is to adjust the deviation parameter toward the set point. For instance, if the body becomes too warm, adjustments are made to cool the animal. If the blood’s glucose rises after a meal, adjustments are made to lower the blood glucose level by getting the nutrient into tissues that need it or to store it for later use.

Control of Homeostasis

When a change occurs in an animal’s environment, an adjustment must be made. The receptor senses the change in the environment, then sends a signal to the control center (in most cases, the brain) which in turn generates a response that is signaled to an effector. The effector is a muscle (that contracts or relaxes) or a gland that secretes. Homeostatsis is maintained by negative feedback loops. Positive feedback loops actually push the organism further out of homeostasis, but may be necessary for life to occur. Homeostasis is controlled by the nervous and endocrine system of mammals.

Homeostasis: Thermoregulation

Body temperature affects body activities. Generally, as body temperature rises, enzyme activity rises as well. For every ten degree centigrade rise in temperature, enzyme activity doubles, up to a point. Body proteins, including enzymes, begin to denature and lose their function with high heat (around 50oC for mammals). Enzyme activity will decrease by half for every ten degree centigrade drop in temperature, to the point of freezing, with a few exceptions. Some fish can withstand freezing solid and return to normal with thawing.

Endotherms and Ectotherms

Animals can be divided into two groups: some maintain a constant body temperature in the face of differing environmental temperatures, while others have a body temperature that is the same as their environment and thus varies with the environment. Animals that rely on external temperatures to set their body temperature are ectotherms. This group has been called cold-blooded, but the term may not apply to an animal in the desert with a very warm body temperature. In contrast to ectotherms, poikilotherms are animals with constantly varying internal temperatures. An animal that maintains a constant body temperature in the face of environmental changes is called a homeotherm. Endotherms are animals that rely on internal sources for maintenance of relatively constant body temperature in varying environmental temperatures. These animals are able to maintain a level of metabolic activity at cooler temperature, which an ectotherm cannot due to differing enzyme levels of activity. It is worth mentioning that some ectotherms and poikilotherms have relatively constant body temperatures due to the constant environmental temperatures in their habitats. These animals are so-called ectothermic homeotherms, like some deep sea fish species.

Heat Conservation and Dissipation

Animals conserve or dissipate heat in a variety of ways. In certain climates, endothermic animals have some form of insulation, such as fur, fat, feathers, or some combination thereof. Animals with thick fur or feathers create an insulating layer of air between their skin and internal organs. Polar bears and seals live and swim in a subfreezing environment and yet maintain a constant, warm, body temperature. The arctic fox, for example, uses its fluffy tail as extra insulation when it curls up to sleep in cold weather. Mammals have a residual effect from shivering and increased muscle activity: arrector pili muscles cause “goose bumps,” causing small hairs to stand up when the individual is cold; this has the intended effect of increasing body temperature. Mammals use layers of fat to achieve the same end. Loss of significant amounts of body fat will compromise an individual’s ability to conserve heat.

Neural Control of Thermoregulation

The nervous system is important to thermoregulation, as illustrated in [link]. The processes of homeostasis and temperature control are centered in the hypothalamus of the advanced animal brain.

Animal Nutrition and the Digestive System

Introduction

Digestive Systems

Abstract:
By the end of this section, you will be able to do the following:

* Explain the processes of digestion and absorption
* Compare and contrast different types of digestive systems
* Explain the specialized functions of the organs involved in processing food in the body
* Describe the ways in which organs work together to digest food and absorb nutrients

Herbivores, Omnivores, and Carnivores

Herbivores are animals whose primary food source is plant-based. Examples of herbivores, as shown in [link] include vertebrates like deer, koalas, and some bird species, as well as invertebrates such as crickets and caterpillars. These animals have evolved digestive systems capable of handling large amounts of plant material. Herbivores can be further classified into frugivores (fruit-eaters), granivores (seed eaters), nectivores (nectar feeders), and folivores (leaf eaters).

Invertebrate Digestive Systems

Animals have evolved different types of digestive systems to aid in the digestion of the different foods they consume. The simplest example is that of a gastrovascular cavity and is found in organisms with only one opening for digestion. Platyhelminthes (flatworms), Ctenophora (comb jellies), and Cnidaria (coral, jelly fish, and sea anemones) use this type of digestion. Gastrovascular cavities, as shown in [link]a, are typically a blind tube or cavity with only one opening, the “mouth”, which also serves as an “anus”. Ingested material enters the mouth and passes through a hollow, tubular cavity. Cells within the cavity secrete digestive enzymes that breakdown the food. The food particles are engulfed by the cells lining the gastrovascular cavity.

Vertebrate Digestive Systems

Vertebrates have evolved more complex digestive systems to adapt to their dietary needs. Some animals have a single stomach, while others have multi-chambered stomachs. Birds have developed a digestive system adapted to eating unmasticated food.

Parts of the Digestive System

The vertebrate digestive system is designed to facilitate the transformation of food matter into the nutrient components that sustain organisms.

Nutrition and Energy Production

Abstract:
By the end of this section, you will be able to do the following:

* Explain why an animal’s diet should be balanced and meet the needs of the body
* Define the primary components of food
* Describe the essential nutrients required for cellular function that cannot be synthesized by the animal body
* Explain how energy is produced through diet and digestion
* Describe how excess carbohydrates and energy are stored in the body

Food Requirements

What are the fundamental requirements of the animal diet? The animal diet should be well balanced and provide nutrients required for bodily function and the minerals and vitamins required for maintaining structure and regulation necessary for good health and reproductive capability. These requirements for a human are illustrated graphically in [link]

Food Energy and ATP

Animals need food to obtain energy and maintain homeostasis. Homeostasis is the ability of a system to maintain a stable internal environment even in the face of external changes to the environment. For example, the normal body temperature of humans is 37°C (98.6°F). Humans maintain this temperature even when the external temperature is hot or cold. It takes energy to maintain this body temperature, and animals obtain this energy from food.

Digestive System Processes

Abstract:
By the end of this section, you will be able to do the following:

* Describe the process of digestion
* Detail the steps involved in digestion and absorption
* Define elimination
* Explain the role of both the small and large intestines in absorption

Ingestion

The large molecules found in intact food cannot pass through the cell membranes. Food needs to be broken into smaller particles so that animals can harness the nutrients and organic molecules. The first step in this process is ingestion. Ingestion is the process of taking in food through the mouth. In vertebrates, the teeth, saliva, and tongue play important roles in mastication (preparing the food into bolus). While the food is being mechanically broken down, the enzymes in saliva begin to chemically process the food as well. The combined action of these processes modifies the food from large particles to a soft mass that can be swallowed and can travel the length of the esophagus.

Digestion and Absorption

Digestion is the mechanical and chemical breakdown of food into small organic fragments. It is important to breakdown macromolecules into smaller fragments that are of suitable size for absorption across the digestive epithelium. Large, complex molecules of proteins, polysaccharides, and lipids must be reduced to simpler particles such as simple sugar before they can be absorbed by the digestive epithelial cells. Different organs play specific roles in the digestive process. The animal diet needs carbohydrates, protein, and fat, as well as vitamins and inorganic components for nutritional balance. How each of these components is digested is discussed in the following sections.

Elimination

The final step in digestion is the elimination of undigested food content and waste products. The undigested food material enters the colon, where most of the water is reabsorbed. Recall that the colon is also home to the microflora called “intestinal flora” that aid in the digestion process. The semi-solid waste is moved through the colon by peristaltic movements of the muscle and is stored in the rectum. As the rectum expands in response to storage of fecal matter, it triggers the neural signals required to set up the urge to eliminate. The solid waste is eliminated through the anus using peristaltic movements of the rectum.

Digestive System Regulation

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the role of neural regulation in digestive processes
* Explain how hormones regulate digestion

Neural Responses to Food

In reaction to the smell, sight, or thought of food, like that shown in [link], the first response is that of salivation. The salivary glands secrete more saliva in response to stimulation by the autonomic nervous system triggered by food in preparation for digestion. Simultaneously, the stomach begins to produce hydrochloric acid to digest the food. Recall that the peristaltic movements of the esophagus and other organs of the digestive tract are under the control of the brain. The brain prepares these muscles for movement as well. When the stomach is full, the part of the brain that detects satiety signals fullness. There are three overlapping phases of gastric control—the cephalic phase, the gastric phase, and the intestinal phase—each requires many enzymes and is under neural control as well.

Hormonal Responses to Food

The endocrine system controls the response of the various glands in the body and the release of hormones at the appropriate times.

The Nervous System

Introduction

Neurons and Glial Cells

Abstract:
By the end of this section, you will be able to do the following:

* List and describe the functions of the structural components of a neuron
* List and describe the four main types of neurons
* Compare the functions of different types of glial cells

Neurons

The nervous system of the common laboratory fly, *Drosophila melanogaster*, contains around 100,000 neurons, the same number as a lobster. This number compares to 75 million in the mouse and 300 million in the octopus. A human brain contains around 86 billion neurons. Despite these very different numbers, the nervous systems of these animals control many of the same behaviors—from basic reflexes to more complicated behaviors like finding food and courting mates. The ability of neurons to communicate with each other as well as with other types of cells underlies all of these behaviors.

Glia

While glia are often thought of as the supporting cast of the nervous system, the number of glial cells in the brain actually outnumbers the number of neurons by a factor of ten. Neurons would be unable to function without the vital roles that are fulfilled by these glial cells. Glia guide developing neurons to their destinations, buffer ions and chemicals that would otherwise harm neurons, and provide myelin sheaths around axons. Scientists have recently discovered that they also play a role in responding to nerve activity and modulating communication between nerve cells. When glia do not function properly, the result can be disastrous—most brain tumors are caused by mutations in glia.

How Neurons Communicate

Abstract:
By the end of this section, you will be able to do the following:

* Describe the basis of the resting membrane potential
* Explain the stages of an action potential and how action potentials are propagated
* Explain the similarities and differences between chemical and electrical synapses
* Describe long-term potentiation and long-term depression

Nerve Impulse Transmission within a Neuron

For the nervous system to function, neurons must be able to send and receive signals. These signals are possible because each neuron has a charged cellular membrane (a voltage difference between the inside and the outside), and the charge of this membrane can change in response to neurotransmitter molecules released from other neurons and environmental stimuli. To understand how neurons communicate, one must first understand the basis of the baseline or ‘resting’ membrane charge.

Synaptic Transmission

The synapse or “gap” is the place where information is transmitted from one neuron to another. Synapses usually form between axon terminals and dendritic spines, but this is not universally true. There are also axon-to-axon, dendrite-to-dendrite, and axon-to-cell body synapses. The neuron transmitting the signal is called the presynaptic neuron, and the neuron receiving the signal is called the postsynaptic neuron. Note that these designations are relative to a particular synapse—most neurons are both presynaptic and postsynaptic. There are two types of synapses: chemical and electrical.

Signal Summation

Sometimes a single EPSP is strong enough to induce an action potential in the postsynaptic neuron, but often multiple presynaptic inputs must create EPSPs around the same time for the postsynaptic neuron to be sufficiently depolarized to fire an action potential. This process is called summation and occurs at the axon hillock, as illustrated in [link]. Additionally, one neuron often has inputs from many presynaptic neurons—some excitatory and some inhibitory—so IPSPs can cancel out EPSPs and vice versa. It is the net change in postsynaptic membrane voltage that determines whether the postsynaptic cell has reached its threshold of excitation needed to fire an action potential. Together, synaptic summation and the threshold for excitation act as a filter so that random “noise” in the system is not transmitted as important information.

Synaptic Plasticity

Synapses are not static structures. They can be weakened or strengthened. They can be broken, and new synapses can be made. Synaptic plasticity allows for these changes, which are all needed for a functioning nervous system. In fact, synaptic plasticity is the basis of learning and memory. Two processes in particular, long-term potentiation (LTP) and long-term depression (LTD) are important forms of synaptic plasticity that occur in synapses in the hippocampus, a brain region that is involved in storing memories.

The Central Nervous System

Abstract:
By the end of this section, you will be able to do the following:

* Identify the spinal cord, cerebral lobes, and other brain areas on a diagram of the brain
* Describe the basic functions of the spinal cord, cerebral lobes, and other brain areas

Brain

The brain is the part of the central nervous system that is contained in the cranial cavity of the skull. It includes the cerebral cortex, limbic system, basal ganglia, thalamus, hypothalamus, and cerebellum. There are three different ways that a brain can be sectioned in order to view internal structures: a sagittal section cuts the brain left to right, as shown in [link]b, a coronal section cuts the brain front to back, as shown in [link]a, and a horizontal section cuts the brain top to bottom.

Spinal Cord

Connecting to the brainstem and extending down the body through the spinal column is the spinal cord, shown in [link]. The spinal cord is a thick bundle of nerve tissue that carries information about the body to the brain and from the brain to the body. The spinal cord is contained within the bones of the vertebrate column but is able to communicate signals to and from the body through its connections with spinal nerves (part of the peripheral nervous system). A cross-section of the spinal cord looks like a white oval containing a gray butterfly-shape, as illustrated in [link]. Myelinated axons make up the “white matter” and neuron and glial cell bodies make up the “gray matter.” Gray matter is also composed of interneurons, which connect two neurons each located in different parts of the body. Axons and cell bodies in the dorsal (facing the back of the animal) spinal cord convey mostly sensory information from the body to the brain. Axons and cell bodies in the ventral (facing the front of the animal) spinal cord primarily transmit signals controlling movement from the brain to the body.

The Peripheral Nervous System

Abstract:
By the end of this section, you will be able to do the following:

* Describe the organization and functions of the sympathetic and parasympathetic nervous systems
* Describe the organization and function of the sensory-somatic nervous system

Autonomic Nervous System

The autonomic nervous system serves as the relay between the CNS and the internal organs. It controls the lungs, the heart, smooth muscle, and exocrine and endocrine glands. The autonomic nervous system controls these organs largely without conscious control; it can continuously monitor the conditions of these different systems and implement changes as needed. Signaling to the target tissue usually involves two synapses: a preganglionic neuron (originating in the CNS) synapses to a neuron in a ganglion that, in turn, synapses on the target organ, as illustrated in [link]. There are two divisions of the autonomic nervous system that often have opposing effects: the sympathetic nervous system and the parasympathetic nervous system.

Sensory-Somatic Nervous System

The sensory-somatic nervous system is made up of cranial and spinal nerves and contains both sensory and motor neurons. Sensory neurons transmit sensory information from the skin, skeletal muscle, and sensory organs to the CNS. Motor neurons transmit messages about desired movement from the CNS to the muscles to make them contract. Without its sensory-somatic nervous system, an animal would be unable to process any information about its environment (what it sees, feels, hears, and so on) and could not control motor movements. Unlike the autonomic nervous system, which has two synapses between the CNS and the target organ, sensory and motor neurons have only one synapse—one ending of the neuron is at the organ and the other directly contacts a CNS neuron. Acetylcholine is the main neurotransmitter released at these synapses.

Nervous System Disorders

Abstract:
By the end of this section, you will be able to do the following:

* Describe the symptoms, potential causes, and treatment of several examples of nervous system disorders

Neurodegenerative Disorders

Neurodegenerative disorders are illnesses characterized by a loss of nervous system functioning that are usually caused by neuronal death. These diseases generally worsen over time as more and more neurons die. The symptoms of a particular neurodegenerative disease are related to where in the nervous system the death of neurons occurs. Spinocerebellar ataxia, for example, leads to neuronal death in the cerebellum. The death of these neurons causes problems in balance and walking. Neurodegenerative disorders include Huntington’s disease, amyotrophic lateral sclerosis, Alzheimer’s disease and other types of dementia disorders, and Parkinson’s disease. Here, Alzheimer’s and Parkinson’s disease will be discussed in more depth.

Neurodevelopmental Disorders

Neurodevelopmental disorders occur when the development of the nervous system is disturbed. There are several different classes of neurodevelopmental disorders. Some, like Down Syndrome, cause intellectual deficits. Others specifically affect communication, learning, or the motor system. Some disorders like autism spectrum disorder and attention deficit/hyperactivity disorder have complex symptoms.

Other Neurological Disorders

There are several other neurological disorders that cannot be easily placed in the above categories. These include chronic pain conditions, cancers of the nervous system, epilepsy disorders, and stroke. Epilepsy and stroke are discussed below.

Sensory Systems

Introduction

Sensory Processes

Abstract:
By the end of this section, you will be able to do the following:

* Identify the general and special senses in humans
* Describe three important steps in sensory perception
* Explain the concept of just-noticeable difference in sensory perception

Reception

The first step in sensation is reception, which is the activation of sensory receptors by stimuli such as mechanical stimuli (being bent or squished, for example), chemicals, or temperature. The receptor can then respond to the stimuli. The region in space in which a given sensory receptor can respond to a stimulus, be it far away or in contact with the body, is that receptor’s receptive field. Think for a moment about the differences in receptive fields for the different senses. For the sense of touch, a stimulus must come into contact with the body. For the sense of hearing, a stimulus can be a moderate distance away (some baleen whale sounds can propagate for many kilometers). For vision, a stimulus can be very far away; for example, the visual system perceives light from stars at enormous distances.

Transduction

The most fundamental function of a sensory system is the translation of a sensory signal to an electrical signal in the nervous system. This takes place at the sensory receptor, and the change in electrical potential that is produced is called the receptor potential. How is sensory input, such as pressure on the skin, changed to a receptor potential? In this example, a type of receptor called a mechanoreceptor (as shown in [link]) possesses specialized membranes that respond to pressure. Disturbance of these dendrites by compressing them or bending them opens gated ion channels in the plasma membrane of the sensory neuron, changing its electrical potential. Recall that in the nervous system, a positive change of a neuron’s electrical potential (also called the membrane potential), depolarizes the neuron. Receptor potentials are graded potentials: the magnitude of these graded (receptor) potentials varies with the strength of the stimulus. If the magnitude of depolarization is sufficient (that is, if membrane potential reaches a threshold), the neuron will fire an action potential. In most cases, the correct stimulus impinging on a sensory receptor will drive membrane potential in a positive direction, although for some receptors, such as those in the visual system, this is not always the case.

Perception

Perception is an individual’s interpretation of a sensation. Although perception relies on the activation of sensory receptors, perception happens not at the level of the sensory receptor, but at higher levels in the nervous system, in the brain. The brain distinguishes sensory stimuli through a sensory pathway: action potentials from sensory receptors travel along neurons that are dedicated to a particular stimulus. These neurons are dedicated to that particular stimulus and synapse with particular neurons in the brain or spinal cord.

Somatosensation

Abstract:
By the end of this section, you will be able to do the following:

* Describe four important mechanoreceptors in human skin
* Describe the topographical distribution of somatosensory receptors between glabrous and hairy skin
* Explain why the perception of pain is subjective

Somatosensory Receptors

Sensory receptors are classified into five categories: mechanoreceptors, thermoreceptors, proprioceptors, pain receptors (nociceptors), and chemoreceptors. These categories are based on the nature of stimuli each receptor class transduces. What is commonly referred to as “touch” involves more than one kind of stimulus and more than one kind of receptor. Mechanoreceptors in the skin are described as encapsulated (that is, surrounded by a capsule) or unencapsulated (a group that includes free nerve endings). A free nerve ending, as its name implies, is an unencapsulated dendrite of a sensory neuron. Free nerve endings are the most common nerve endings in skin, and they extend into the middle of the epidermis. Free nerve endings are sensitive to painful stimuli, to hot and cold, and to light touch. They are slow to adjust to a stimulus and so are less sensitive to abrupt changes in stimulation.

Thermoreception

In addition to Krause end bulbs that detect cold and Ruffini endings that detect warmth, there are different types of cold receptors on some free nerve endings: thermoreceptors, located in the dermis, skeletal muscles, liver, and hypothalamus, that are activated by different temperatures. Their pathways into the brain run from the spinal cord through the thalamus to the primary somatosensory cortex. Warmth and cold information from the face travels through one of the cranial nerves to the brain. You know from experience that a tolerably cold or hot stimulus can quickly progress to a much more intense stimulus that is no longer tolerable. Any stimulus that is too intense can be perceived as pain because temperature sensations are conducted along the same pathways that carry pain sensations.

Pain

Pain is the name given to nociception, which is the neural processing of injurious stimuli in response to tissue damage. Pain is caused by true sources of injury, such as contact with a heat source that causes a thermal burn or contact with a corrosive chemical. But pain also can be caused by harmless stimuli that mimic the action of damaging stimuli, such as contact with capsaicins, the compounds that cause peppers to taste hot and which are used in self-defense pepper sprays and certain topical medications. Peppers taste “hot” because the protein receptors that bind capsaicin open the same calcium channels that are activated by warm receptors.

Taste and Smell

Abstract:
By the end of this section, you will be able to do the following:

* Explain in what way smell and taste stimuli differ from other sensory stimuli
* Identify the five primary tastes that can be distinguished by humans
* Explain in anatomical terms why a dog’s sense of smell is more acute than a human’s

Tastes and Odors

Both taste and odor stimuli are molecules taken in from the environment. The primary tastes detected by humans are sweet, sour, bitter, salty, and umami. The first four tastes need little explanation. The identification of umami as a fundamental taste occurred fairly recently—it was identified in 1908 by Japanese scientist Kikunae Ikeda while he worked with seaweed broth, but it was not widely accepted as a taste that could be physiologically distinguished until many years later. The taste of umami, also known as savoriness, is attributable to the taste of the amino acid L-glutamate. In fact, monosodium glutamate, or MSG, is often used in cooking to enhance the savory taste of certain foods. What is the adaptive value of being able to distinguish umami? Savory substances tend to be high in protein.

Reception and Transduction

Odorants (odor molecules) enter the nose and dissolve in the olfactory epithelium, the mucosa at the back of the nasal cavity (as illustrated in [link]). The olfactory epithelium is a collection of specialized olfactory receptors in the back of the nasal cavity that spans an area about 5 cm2 in humans. Recall that sensory cells are neurons. An olfactory receptor, which is a dendrite of a specialized neuron, responds when it binds certain molecules inhaled from the environment by sending impulses directly to the olfactory bulb of the brain. Humans have about 12 million olfactory receptors, distributed among hundreds of different receptor types that respond to different odors. Twelve million seems like a large number of receptors, but compare that to other animals: rabbits have about 100 million, most dogs have about 1 billion, and bloodhounds—dogs selectively bred for their sense of smell—have about 4 billion. The overall size of the olfactory epithelium also differs between species, with that of bloodhounds, for example, being many times larger than that of humans.

Smell and Taste in the Brain

Olfactory neurons project from the olfactory epithelium to the olfactory bulb as thin, unmyelinated axons. The olfactory bulb is composed of neural clusters called glomeruli, and each glomerulus receives signals from one type of olfactory receptor, so each glomerulus is specific to one odorant. From glomeruli, olfactory signals travel directly to the olfactory cortex and then to the frontal cortex and the thalamus. Recall that this is a different path from most other sensory information, which is sent directly to the thalamus before ending up in the cortex. Olfactory signals also travel directly to the amygdala, thereafter reaching the hypothalamus, thalamus, and frontal cortex. The last structure that olfactory signals directly travel to is a cortical center in the temporal lobe structure important in spatial, autobiographical, declarative, and episodic memories. Olfaction is finally processed by areas of the brain that deal with memory, emotions, reproduction, and thought.

Hearing and Vestibular Sensation

Abstract:
By the end of this section, you will be able to do the following:

* Describe the relationship of amplitude and frequency of a sound wave to attributes of sound
* Trace the path of sound through the auditory system to the site of transduction of sound
* Identify the structures of the vestibular system that respond to gravity

Sound

Auditory stimuli are sound waves, which are mechanical, pressure waves that move through a medium, such as air or water. There are no sound waves in a vacuum since there are no air molecules to move in waves. The speed of sound waves differs, based on altitude, temperature, and medium, but at sea level and a temperature of 20º C (68º F), sound waves travel in the air at about 343 meters per second.

Reception of Sound

In mammals, sound waves are collected by the external, cartilaginous part of the ear called the auricle, then travel through the auditory canal and cause vibration of the thin diaphragm called the tympanum or ear drum, the innermost part of the outer ear (illustrated in [link]). Interior to the tympanum is the middle ear. The middle ear holds three small bones called the ossicles, which transfer energy from the moving tympanum to the inner ear. The three ossicles are the malleus (also known as the hammer), the incus (the anvil), and stapes (the stirrup). The aptly named stapes looks very much like a stirrup. The three ossicles are unique to mammals, and each plays a role in hearing. The malleus attaches at three points to the interior surface of the tympanic membrane. The incus attaches the malleus to the stapes. In humans, the stapes is not long enough to reach the tympanum. If we did not have the malleus and the incus, then the vibrations of the tympanum would never reach the inner ear. These bones also function to collect force and amplify sounds. The ear ossicles are homologous to bones in a fish mouth: the bones that support gills in fish are thought to be adapted for use in the vertebrate ear over evolutionary time. Many animals (frogs, reptiles, and birds, for example) use the stapes of the middle ear to transmit vibrations to the inner ear.

Transduction of Sound

Vibrating objects, such as vocal cords, create sound waves or pressure waves in the air. When these pressure waves reach the ear, the ear transduces this mechanical stimulus (pressure wave) into a nerve impulse (electrical signal) that the brain perceives as sound. The pressure waves strike the tympanum, causing it to vibrate. The mechanical energy from the moving tympanum transmits the vibrations to the three bones of the middle ear. The stapes transmits the vibrations to a thin diaphragm called the oval window, which is the outermost structure of the inner ear. The structures of the inner ear are found in the labyrinth, a bony, hollow structure that is the most interior portion of the ear. Here, the energy from the sound wave is transferred from the stapes through the flexible oval window and to the fluid of the cochlea. The vibrations of the oval window create pressure waves in the fluid (perilymph) inside the cochlea. The cochlea is a whorled structure, like the shell of a snail, and it contains receptors for transduction of the mechanical wave into an electrical signal (as illustrated in [link]). Inside the cochlea, the basilar membrane is a mechanical analyzer that runs the length of the cochlea, curling toward the cochlea’s center.

Vestibular Information

The stimuli associated with the vestibular system are linear acceleration (gravity) and angular acceleration and deceleration. Gravity, acceleration, and deceleration are detected by evaluating the inertia on receptive cells in the vestibular system. Gravity is detected through head position. Angular acceleration and deceleration are expressed through turning or tilting of the head.

Vision

Abstract:
By the end of this section, you will be able to do the following:

* Explain how electromagnetic waves differ from sound waves
* Trace the path of light through the eye to the point of the optic nerve
* Explain tonic activity as it is manifested in photoreceptors in the retina

Light

As with auditory stimuli, light travels in waves. The compression waves that compose sound must travel in a medium—a gas, a liquid, or a solid. In contrast, light is composed of electromagnetic waves and needs no medium; light can travel in a vacuum ([link]). The behavior of light can be discussed in terms of the behavior of waves and also in terms of the behavior of the fundamental unit of light—a packet of electromagnetic radiation called a photon. A glance at the electromagnetic spectrum shows that visible light for humans is just a small slice of the entire spectrum, which includes radiation that we cannot see as light because it is below the frequency of visible red light and above the frequency of visible violet light.

Anatomy of the Eye

The photoreceptive cells of the eye, where transduction of light to nervous impulses occurs, are located in the retina (shown in [link]) on the inner surface of the back of the eye. But light does not impinge on the retina unaltered. It passes through other layers that process it so that it can be interpreted by the retina ([link]b). The cornea, the front transparent layer of the eye, and the crystalline lens, a transparent convex structure behind the cornea, both refract (bend) light to focus the image on the retina. The iris, which is conspicuous as the colored part of the eye, is a circular muscular ring lying between the lens and cornea that regulates the amount of light entering the eye. In conditions of high ambient light, the iris contracts, reducing the size of the pupil at its center. In conditions of low light, the iris relaxes and the pupil enlarges.

Transduction of Light

The rods and cones are the site of transduction of light to a neural signal. Both rods and cones contain photopigments. In vertebrates, the main photopigment, rhodopsin, has two main parts ([link]): an opsin, which is a membrane protein (in the form of a cluster of α-helices that span the membrane), and retinal—a molecule that absorbs light. When light hits a photoreceptor, it causes a shape change in the retinal, altering its structure from a bent (*cis*) form of the molecule to its linear (*trans*) isomer. This isomerization of retinal activates the rhodopsin, starting a cascade of events that ends with the closing of Na+ channels in the membrane of the photoreceptor. Thus, unlike most other sensory neurons (which become depolarized by exposure to a stimulus) visual receptors become hyperpolarized and thus driven away from threshold ([link]).

Higher Processing

The myelinated axons of ganglion cells make up the optic nerves. Within the nerves, different axons carry different qualities of the visual signal. Some axons constitute the magnocellular (big cell) pathway, which carries information about form, movement, depth, and differences in brightness. Other axons constitute the parvocellular (small cell) pathway, which carries information on color and fine detail. Some visual information projects directly back into the brain, while other information crosses to the opposite side of the brain. This crossing of optical pathways produces the distinctive optic chiasma (Greek, for “crossing”) found at the base of the brain and allows us to coordinate information from both eyes.

The Endocrine System

Introduction

Types of Hormones

Abstract:
By the end of this section, you will be able to do the following:

* List the different types of hormones
* Explain their role in maintaining homeostasis

Lipid-Derived Hormones (or Lipid-soluble Hormones)

Most lipid hormones are derived from cholesterol and thus are structurally similar to it, as illustrated in [link]. The primary class of lipid hormones in humans is the steroid hormones. Chemically, these hormones are usually ketones or alcohols; their chemical names will end in “-ol” for alcohols or “-one” for ketones. Examples of steroid hormones include estrogens (such as estradiol) and androgens (such as testosterone), both of which regulate bone and tissue development in all humans.

Amino Acid-Derived Hormones

The amino acid-derived hormones are relatively small molecules that are derived from the amino acids tyrosine and tryptophan, shown in [link]. If a hormone is amino acid-derived, its chemical name will end in “-ine”. Examples of amino acid-derived hormones include epinephrine and norepinephrine, which are synthesized in the medulla of the adrenal glands, and thyroxine, which is produced by the thyroid gland. The pineal gland in the brain makes and secretes melatonin which regulates sleep cycles.

Peptide Hormones

The structure of peptide hormones is that of a polypeptide chain (chain of amino acids). The peptide hormones include molecules that are short polypeptide chains, such as antidiuretic hormone and oxytocin produced in the brain and released into the blood in the posterior pituitary gland. This class also includes small proteins, like growth hormones produced by the pituitary, and large glycoproteins such as follicle-stimulating hormone produced by the pituitary. [link] illustrates these peptide hormones.

How Hormones Work

Abstract:
By the end of this section, you will be able to do the following:

* Explain how hormones work
* Discuss the role of different types of hormone receptors

Intracellular Hormone Receptors

Lipid-derived (soluble) hormones such as steroid hormones diffuse across the membranes of the endocrine cell. Once outside the cell, they bind to transport proteins that keep them soluble in the bloodstream. At the target cell, the hormones are released from the carrier protein and diffuse across the lipid bilayer of the plasma membrane of cells. The steroid hormones pass through the plasma membrane of a target cell and adhere to intracellular receptors residing in the cytoplasm or in the nucleus. The cell signaling pathways induced by the steroid hormones regulate specific genes on the cell's DNA. The hormones and receptor complex act as transcription regulators by increasing or decreasing the synthesis of mRNA molecules of specific genes. This, in turn, determines the amount of corresponding protein that is synthesized by altering gene expression. This protein can be used either to change the structure of the cell or to produce enzymes that catalyze chemical reactions. In this way, the steroid hormone regulates specific cell processes as illustrated in [link].

Plasma Membrane Hormone Receptors

Amino acid-derived hormones (with the exception of thyroxine) and polypeptide hormones are not lipid-derived (lipid-soluble) and therefore cannot diffuse through the plasma membrane of cells. Lipid insoluble hormones bind to receptors on the outer surface of the plasma membrane, via plasma membrane hormone receptors. Unlike steroid hormones, lipid insoluble hormones do not directly affect the target cell because they cannot enter the cell and act directly on DNA. Binding of these hormones to a cell surface receptor results in activation of a signaling pathway; this triggers intracellular activity and carries out the specific effects associated with the hormone. In this way, nothing passes through the cell membrane; the hormone that binds at the surface remains at the surface of the cell while the intracellular product remains inside the cell. The hormone that initiates the signaling pathway is called a first messenger, which activates a second messenger in the cytoplasm, as illustrated in [link].

Regulation of Body Processes

Abstract:
By the end of this section, you will be able to do the following:

* Explain how hormones regulate the excretory system
* Discuss the role of hormones in the reproductive system
* Describe how hormones regulate metabolism
* Explain the role of hormones in different diseases

Hormonal Regulation of the Excretory System

Maintaining a proper water balance in the body is important to avoid dehydration or over-hydration (hyponatremia). The water concentration of the body is monitored by osmoreceptors in the hypothalamus, which detect the concentration of electrolytes in the extracellular fluid. The concentration of electrolytes in the blood rises when there is water loss caused by excessive perspiration, inadequate water intake, or low blood volume due to blood loss. An increase in blood electrolyte levels results in a neuronal signal being sent from the osmoreceptors in hypothalamic nuclei. The pituitary gland has two components: anterior and posterior. The anterior pituitary is composed of glandular cells that secrete protein hormones. The posterior pituitary is an extension of the hypothalamus. It is composed largely of neurons that are continuous with the hypothalamus.

Hormonal Regulation of the Reproductive System

Regulation of the reproductive system is a process that requires the action of hormones from the pituitary gland, the adrenal cortex, and the gonads. During puberty in both males and females, the hypothalamus produces gonadotropin-releasing hormone (GnRH), which stimulates the production and release of follicle-stimulating hormone (FSH) and luteinizing hormone (LH) from the anterior pituitary gland. These hormones regulate the gonads (testes in males and ovaries in females) and therefore are called gonadotropins. In both males and females, FSH stimulates gamete production and LH stimulates production of hormones by the gonads. An increase in gonad hormone levels inhibits GnRH production through a negative feedback loop.

Hormonal Regulation of Metabolism

Blood glucose levels vary widely over the course of a day as periods of food consumption alternate with periods of fasting. Insulin and glucagon are the two hormones primarily responsible for maintaining homeostasis of blood glucose levels. Additional regulation is mediated by the thyroid hormones.

Hormonal Control of Blood Calcium Levels

Regulation of blood calcium concentrations is important for generation of muscle contractions and nerve impulses, which are electrically stimulated. If calcium levels get too high, membrane permeability to sodium decreases and membranes become less responsive. If calcium levels get too low, membrane permeability to sodium increases and convulsions or muscle spasms can result.

Hormonal Regulation of Growth

Hormonal regulation is required for the growth and replication of most cells in the body. Growth hormone (GH), produced by the anterior portion of the pituitary gland, accelerates the rate of protein synthesis, particularly in skeletal muscle and bones. Growth hormone has direct and indirect mechanisms of action. The first direct action of GH is stimulation of triglyceride breakdown (lipolysis) and release into the blood by adipocytes. This results in a switch by most tissues from utilizing glucose as an energy source to utilizing fatty acids. This process is called a glucose-sparing effect. In another direct mechanism, GH stimulates glycogen breakdown in the liver; the glycogen is then released into the blood as glucose. Blood glucose levels increase as most tissues are utilizing fatty acids instead of glucose for their energy needs. The GH mediated increase in blood glucose levels is called a diabetogenic effect because it is similar to the high blood glucose levels seen in diabetes mellitus.

Hormonal Regulation of Stress

When a threat or danger is perceived, the body responds by releasing hormones that will ready it for the “fight-or-flight” response. The effects of this response are familiar to anyone who has been in a stressful situation: increased heart rate, dry mouth, and hair standing up.

Regulation of Hormone Production

Abstract:
By the end of this section, you will be able to do the following:

* Explain how hormone production is regulated
* Discuss the different stimuli that control hormone levels in the body

Humoral Stimuli

The term “humoral” is derived from the term “humor,” which refers to bodily fluids such as blood. A humoral stimulus refers to the control of hormone release in response to changes in extracellular fluids such as blood or the ion concentration in the blood. For example, a rise in blood glucose levels triggers the pancreatic release of insulin. Insulin causes blood glucose levels to drop, which signals the pancreas to stop producing insulin in a negative feedback loop.

Hormonal Stimuli

Hormonal stimuli refers to the release of a hormone in response to another hormone. A number of endocrine glands release hormones when stimulated by hormones released by other endocrine glands. For example, the hypothalamus produces hormones that stimulate the anterior portion of the pituitary gland. The anterior pituitary in turn releases hormones that regulate hormone production by other endocrine glands. The anterior pituitary releases the thyroid-stimulating hormone, which then stimulates the thyroid gland to produce the hormones T3 and T4. As blood concentrations of T3 and T4 rise, they inhibit both the pituitary and the hypothalamus in a negative feedback loop.

Neural Stimuli

In some cases, the nervous system directly stimulates endocrine glands to release hormones, which is referred to as neural stimuli. Recall that in a short-term stress response, the hormones epinephrine and norepinephrine are important for providing the bursts of energy required for the body to respond. Here, neuronal signaling from the sympathetic nervous system directly stimulates the adrenal medulla to release the hormones epinephrine and norepinephrine in response to stress.

Endocrine Glands

Abstract:
By the end of this section, you will be able to do the following:

* Describe the role of different glands in the endocrine system
* Explain how the different glands work together to maintain homeostasis

Hypothalamic-Pituitary Axis

The hypothalamus in vertebrates integrates the endocrine and nervous systems. The hypothalamus is an endocrine organ located in the diencephalon of the brain. It receives input from the body and other brain areas and initiates endocrine responses to environmental changes. The hypothalamus acts as an endocrine organ, synthesizing hormones and transporting them along axons to the posterior pituitary gland. It synthesizes and secretes regulatory hormones that control the endocrine cells in the anterior pituitary gland. The hypothalamus contains autonomic centers that control endocrine cells in the adrenal medulla via neuronal control.

Thyroid Gland

The thyroid gland is located in the neck, just below the larynx and in front of the trachea, as shown in [link]. It is a butterfly-shaped gland with two lobes that are connected by the isthmus. It has a dark red color due to its extensive vascular system. When the thyroid swells due to dysfunction, it can be felt under the skin of the neck.

Parathyroid Glands

Most people have four parathyroid glands; however, the number can vary from two to six. These glands are located on the posterior surface of the thyroid gland, as shown in [link]. Normally, there is a superior gland and an inferior gland associated with each of the thyroid’s two lobes. Each parathyroid gland is covered by connective tissue and contains many secretory cells that are associated with a capillary network.

Adrenal Glands

The adrenal glands are associated with the kidneys; one gland is located on top of each kidney as illustrated in [link]. The adrenal glands consist of an outer adrenal cortex and an inner adrenal medulla. These regions secrete different hormones.

Pancreas

The pancreas, illustrated in [link], is an elongated organ that is located between the stomach and the proximal portion of the small intestine. It contains both exocrine cells that excrete digestive enzymes and endocrine cells that release hormones. It is sometimes referred to as a heterocrine gland because it has both endocrine and exocrine functions.

Pineal Gland

The pineal gland produces melatonin. The rate of melatonin production is affected by the photoperiod. Collaterals from the visual pathways innervate the pineal gland. During the day photoperiod, little melatonin is produced; however, melatonin production increases during the dark photoperiod (night). In some mammals, melatonin has an inhibitory affect on reproductive functions by decreasing production and maturation of sperm, oocytes, and reproductive organs. Melatonin is an effective antioxidant, protecting the CNS from free radicals such as nitric oxide and hydrogen peroxide. Lastly, melatonin is involved in biological rhythms, particularly circadian rhythms such as the sleep-wake cycle and eating habits.

Gonads

The gonads—the testes and ovaries—produce steroid hormones. The testes produce androgens, testosterone being the most prominent, which allow for the growth and development of the testes and penis, increased skeletal and muscular growth, enlargement of the larynx, increased growth and redistribution of body hair, and the production of sperm cells. The ovaries produce estradiol and progesterone, which cause secondary sex characteristics and prepare the body for childbirth.

Organs with Secondary Endocrine Functions

There are several organs whose primary functions are non-endocrine but that also possess endocrine functions. These include the heart, kidneys, intestines, thymus, gonads, and adipose tissue.

The Musculoskeletal System

Introduction

Types of Skeletal Systems

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the different types of skeletal systems
* Explain the role of the human skeletal system
* Compare and contrast different skeletal systems

Hydrostatic Skeleton

A hydrostatic skeleton is a skeleton formed by a fluid-filled compartment within the body, called the coelom. The organs of the coelom are supported by the aqueous fluid, which also resists external compression. This compartment is under hydrostatic pressure because of the fluid and supports the other organs of the organism. This type of skeletal system is found in soft-bodied animals such as sea anemones, earthworms, Cnidaria, and other invertebrates ([link]).

Exoskeleton

An exoskeleton is an external skeleton that consists of a hard encasement on the surface of an organism. For example, the shells of crabs and insects are exoskeletons ([link]). This skeleton type provides defence against predators, supports the body, and allows for movement through the contraction of attached muscles. As with vertebrates, muscles must cross a joint inside the exoskeleton. Shortening of the muscle changes the relationship of the two segments of the exoskeleton. Arthropods such as crabs and lobsters have exoskeletons that consist of 30–50 percent chitin, a polysaccharide derivative of glucose that is a strong but flexible material. Chitin is secreted by the epidermal cells. The exoskeleton is further strengthened by the addition of calcium carbonate in organisms such as the lobster. Because the exoskeleton is acellular, arthropods must periodically shed their exoskeletons because the exoskeleton does not grow as the organism grows.

Endoskeleton

An endoskeleton is a skeleton that consists of hard, mineralized structures located within the soft tissue of organisms. An example of a primitive endoskeletal structure is the spicules of sponges. The bones of vertebrates are composed of tissues, whereas sponges have no true tissues ([link]). Endoskeletons provide support for the body, protect internal organs, and allow for movement through contraction of muscles attached to the skeleton.

Human Axial Skeleton

The axial skeleton forms the central axis of the body and includes the bones of the skull, ossicles of the middle ear, hyoid bone of the throat, vertebral column, and the thoracic cage (ribcage) ([link]). The function of the axial skeleton is to provide support and protection for the brain, the spinal cord, and the organs in the ventral body cavity. It provides a surface for the attachment of muscles that move the head, neck, and trunk, performs respiratory movements, and stabilizes parts of the appendicular skeleton.

Human Appendicular Skeleton

The appendicular skeleton is composed of the bones of the upper limbs (which function to grasp and manipulate objects) and the lower limbs (which permit locomotion). It also includes the pectoral girdle, or shoulder girdle, that attaches the upper limbs to the body, and the pelvic girdle that attaches the lower limbs to the body ([link]).

Bone

Abstract:
By the end of this section, you will be able to do the following:

* Classify the different types of bones in the skeleton
* Explain the role of the different cell types in bone
* Explain how bone forms during development

Bone Tissue

Bones are considered organs because they contain various types of tissue, such as blood, connective tissue, nerves, and bone tissue. Osteocytes, the living cells of bone tissue, form the mineral matrix of bones. There are two types of bone tissue: compact and spongy.

Cell Types in Bones

Bone consists of four types of cells: osteoblasts, osteoclasts, osteocytes, and osteoprogenitor cells. Osteoblasts are bone cells that are responsible for bone formation. Osteoblasts synthesize and secrete the organic part and inorganic part of the extracellular matrix of bone tissue, and collagen fibers. Osteoblasts become trapped in these secretions and differentiate into less active osteocytes. Osteoclasts are large bone cells with up to 50 nuclei. They remove bone structure by releasing lysosomal enzymes and acids that dissolve the bony matrix. These minerals, released from bones into the blood, help regulate calcium concentrations in body fluids. Bone may also be resorbed for remodeling, if the applied stresses have changed. Osteocytes are mature bone cells and are the main cells in bony connective tissue; these cells cannot divide. Osteocytes maintain normal bone structure by recycling the mineral salts in the bony matrix. Osteoprogenitor cells are squamous stem cells that divide to produce daughter cells that differentiate into osteoblasts. Osteoprogenitor cells are important in the repair of fractures.

Development of Bone

Ossification, or osteogenesis, is the process of bone formation by osteoblasts. Ossification is distinct from the process of calcification; whereas calcification takes place during the ossification of bones, it can also occur in other tissues. Ossification begins approximately six weeks after fertilization in an embryo. Before this time, the embryonic skeleton consists entirely of fibrous membranes and hyaline cartilage. The development of bone from fibrous membranes is called intramembranous ossification; development from hyaline cartilage is called endochondral ossification. Bone growth continues until approximately age 25. Bones can grow in thickness throughout life, but after age 25, ossification functions primarily in bone remodeling and repair.

Intramembranous Ossification

Intramembranous ossification is the process of bone development from fibrous membranes. It is involved in the formation of the flat bones of the skull, the mandible, and the clavicles. Ossification begins as mesenchymal cells form a template of the future bone. They then differentiate into osteoblasts at the ossification center. Osteoblasts secrete the extracellular matrix and deposit calcium, which hardens the matrix. The non-mineralized portion of the bone or osteoid continues to form around blood vessels, forming spongy bone. Connective tissue in the matrix differentiates into red bone marrow in the fetus. The spongy bone is remodeled into a thin layer of compact bone on the surface of the spongy bone.

Growth of Bone

Long bones continue to lengthen, potentially until adolescence, through the addition of bone tissue at the epiphyseal plate. They also increase in width through appositional growth.

Bone Remodeling and Repair

Bone renewal continues after birth into adulthood. Bone remodeling is the replacement of old bone tissue by new bone tissue. It involves the processes of bone deposition by osteoblasts and bone resorption by osteoclasts. Normal bone growth requires vitamins D, C, and A, plus minerals such as calcium, phosphorous, and magnesium. Hormones such as parathyroid hormone, growth hormone, and calcitonin are also required for proper bone growth and maintenance.

Joints and Skeletal Movement

Abstract:
By the end of this section, you will be able to do the following:

* Classify the different types of joints on the basis of structure
* Explain the role of joints in skeletal movement

Classification of Joints on the Basis of Structure

There are two ways to classify joints: on the basis of their structure or on the basis of their function. The structural classification divides joints into bony, fibrous, cartilaginous, and synovial joints depending on the material composing the joint and the presence or absence of a cavity in the joint.

Classification of Joints on the Basis of Function

The functional classification divides joints into three categories: synarthroses, amphiarthroses, and diarthroses. A synarthrosis is a joint that is immovable. This includes sutures, gomphoses, and synchondroses. Amphiarthroses are joints that allow slight movement, including syndesmoses and symphyses. Diarthroses are joints that allow for free movement of the joint, as in synovial joints.

Movement at Synovial Joints

The wide range of movement allowed by synovial joints produces different types of movements. The movement of synovial joints can be classified as one of four different types: gliding, angular, rotational, or special movement.

Types of Synovial Joints

Synovial joints are further classified into six different categories on the basis of the shape and structure of the joint. The shape of the joint affects the type of movement permitted by the joint ([link]). These joints can be described as planar, hinge, pivot, condyloid, saddle, or ball-and-socket joints.

Muscle Contraction and Locomotion

Abstract:
By the end of this section, you will be able to do the following:

* Classify the different types of muscle tissue
* Explain the role of muscles in locomotion

Skeletal Muscle Fiber Structure

Each skeletal muscle fiber is a skeletal muscle cell. These cells are incredibly large, with diameters of up to 100 µm and lengths of up to 30 cm. The plasma membrane of a skeletal muscle fiber is called the sarcolemma. The sarcolemma is the site of action potential conduction, which triggers muscle contraction. Within each muscle fiber are myofibrils—long cylindrical structures that lie parallel to the muscle fiber. Myofibrils run the entire length of the muscle fiber, and because they are only approximately 1.2 µm in diameter, hundreds to thousands can be found inside one muscle fiber. They attach to the sarcolemma at their ends, so that as myofibrils shorten, the entire muscle cell contracts ([link]).

Sliding Filament Model of Contraction

For a muscle cell to contract, the sarcomere must shorten. However, thick and thin filaments—the components of sarcomeres—do not shorten. Instead, they slide by one another, causing the sarcomere to shorten while the filaments remain the same length. The sliding filament theory of muscle contraction was developed to fit the differences observed in the named bands on the sarcomere at different degrees of muscle contraction and relaxation. The mechanism of contraction is the binding of myosin to actin, forming cross-bridges that generate filament movement ([link]).

ATP and Muscle Contraction

The motion of muscle shortening occurs as myosin heads bind to actin and pull the actin inwards. This action requires energy, which is provided by ATP. Myosin binds to actin at a binding site on the globular actin protein. Myosin has another binding site for ATP at which enzymatic activity hydrolyzes ATP to ADP, releasing an inorganic phosphate molecule and energy.

Regulatory Proteins

When a muscle is in a resting state, actin and myosin are separated. To keep actin from binding to the active site on myosin, regulatory proteins block the molecular binding sites. Tropomyosin blocks myosin binding sites on actin molecules, preventing cross-bridge formation and preventing contraction in a muscle without nervous input. Troponin binds to tropomyosin and helps to position it on the actin molecule; it also binds calcium ions.

Excitation–Contraction Coupling

Excitation–contraction coupling is the link (transduction) between the action potential generated in the sarcolemma and the start of a muscle contraction. The trigger for calcium release from the sarcoplasmic reticulum into the sarcoplasm is a neural signal. Each skeletal muscle fiber is controlled by a motor neuron, which conducts signals from the brain or spinal cord to the muscle. The area of the sarcolemma on the muscle fiber that interacts with the neuron is called the motor end plate. The end of the neuron’s axon is called the synaptic terminal, and it does not actually contact the motor end plate. A small space called the synaptic cleft separates the synaptic terminal from the motor end plate. Electrical signals travel along the neuron’s axon, which branches through the muscle and connects to individual muscle fibers at a neuromuscular junction.

Control of Muscle Tension

Neural control initiates the formation of actin–myosin cross-bridges, leading to the sarcomere shortening involved in muscle contraction. These contractions extend from the muscle fiber through connective tissue to pull on bones, causing skeletal movement. The pull exerted by a muscle is called tension, and the amount of force created by this tension can vary. This enables the same muscles to move very light objects and very heavy objects. In individual muscle fibers, the amount of tension produced depends on the cross-sectional area of the muscle fiber and the frequency of neural stimulation.

The Respiratory System

Introduction

Systems of Gas Exchange

Abstract:
By the end of this section, you will be able to do the following:

* Describe the passage of air from the outside environment to the lungs
* Explain how the lungs are protected from particulate matter

Direct Diffusion

For small multicellular organisms, diffusion across the outer membrane is sufficient to meet their oxygen needs. Gas exchange by direct diffusion across surface membranes is efficient for organisms less than 1 mm in diameter. In simple organisms, such as cnidarians and flatworms, every cell in the body is close to the external environment. Their cells are kept moist and gases diffuse quickly via direct diffusion. Flatworms are small, literally flat worms, which ‘breathe’ through diffusion across the outer membrane ([link]). The flat shape of these organisms increases the surface area for diffusion, ensuring that each cell within the body is close to the outer membrane surface and has access to oxygen. If the flatworm had a cylindrical body, then the cells in the center would not be able to get oxygen.

Skin and Gills

Earthworms and amphibians use their skin (integument) as a respiratory organ. A dense network of capillaries lies just below the skin and facilitates gas exchange between the external environment and the circulatory system. The respiratory surface must be kept moist in order for the gases to dissolve and diffuse across cell membranes.

Tracheal Systems

Insect respiration is independent of its circulatory system; therefore, the blood does not play a direct role in oxygen transport. Insects have a highly specialized type of respiratory system called the tracheal system, which consists of a network of small tubes that carries oxygen to the entire body. The tracheal system is the most direct and efficient respiratory system in active animals. The tubes in the tracheal system are made of a polymeric material called chitin.

Mammalian Systems

In mammals, pulmonary ventilation occurs via inhalation (breathing). During inhalation, air enters the body through the nasal cavity located just inside the nose ([link]). As air passes through the nasal cavity, the air is warmed to body temperature and humidified. The respiratory tract is coated with mucus to seal the tissues from direct contact with air. Mucus is high in water. As air crosses these surfaces of the mucous membranes, it picks up water. These processes help equilibrate the air to the body conditions, reducing any damage that cold, dry air can cause. Particulate matter that is floating in the air is removed in the nasal passages via mucus and cilia. The processes of warming, humidifying, and removing particles are important protective mechanisms that prevent damage to the trachea and lungs. Thus, inhalation serves several purposes in addition to bringing oxygen into the respiratory system.

Protective Mechanisms

The air that organisms breathe contains particulate matter such as dust, dirt, viral particles, and bacteria that can damage the lungs or trigger allergic immune responses. The respiratory system contains several protective mechanisms to avoid problems or tissue damage. In the nasal cavity, hairs and mucus trap small particles, viruses, bacteria, dust, and dirt to prevent their entry.

Gas Exchange across Respiratory Surfaces

Abstract:
By the end of this section, you will be able to do the following:

* Name and describe lung volumes and capacities
* Understand how gas pressure influences how gases move into and out of the body

Basic Principles of Gas Exchange

Gas exchange during respiration occurs primarily through diffusion. Diffusion is a process in which transport is driven by a concentration gradient. Gas molecules move from a region of high concentration to a region of low concentration. Blood that is low in oxygen concentration and high in carbon dioxide concentration undergoes gas exchange with air in the lungs. The air in the lungs has a higher concentration of oxygen than that of oxygen-depleted blood and a lower concentration of carbon dioxide. This concentration gradient allows for gas exchange during respiration.

Lung Volumes and Capacities

Different animals have different lung capacities based on their activities. Cheetahs have evolved a much higher lung capacity than humans; it helps provide oxygen to all the muscles in the body and allows them to run very fast. Elephants also have a high lung capacity. In this case, it is not because they run fast but because they have a large body and must be able to take up oxygen in accordance with their body size.

Gas Pressure and Respiration

The respiratory process can be better understood by examining the properties of gases. Gases move freely, but gas particles are constantly hitting the walls of their vessel, thereby producing gas pressure.

Gas Exchange across the Alveoli

In the body, oxygen is used by cells of the body’s tissues and carbon dioxide is produced as a waste product. The ratio of carbon dioxide production to oxygen consumption is the respiratory quotient (RQ). RQ varies between 0.7 and 1.0. If just glucose were used to fuel the body, the RQ would equal one. One mole of carbon dioxide would be produced for every mole of oxygen consumed. Glucose, however, is not the only fuel for the body. Protein and fat are also used as fuels for the body. Because of this, less carbon dioxide is produced than oxygen is consumed and the RQ is, on average, about 0.7 for fat and about 0.8 for protein.

Breathing

Abstract:
By the end of this section, you will be able to do the following:

* Describe how the structures of the lungs and thoracic cavity control the mechanics of breathing
* Explain the importance of compliance and resistance in the lungs
* Discuss problems that may arise due to a V/Q mismatch

Types of Breathing

Amphibians have evolved multiple ways of breathing. Young amphibians, like tadpoles, use gills to breathe, and they don’t leave the water. Some amphibians retain gills for life. As the tadpole grows, the gills disappear and lungs grow. These lungs are primitive and not as evolved as mammalian lungs. Adult amphibians are lacking or have a reduced diaphragm, so breathing via lungs is forced. The other means of breathing for amphibians is diffusion across the skin. To aid this diffusion, amphibian skin must remain moist.

The Mechanics of Human Breathing

Boyle’s Law is the gas law that states that in a closed space, pressure and volume are inversely related. As volume decreases, pressure increases and vice versa ([link]). The relationship between gas pressure and volume helps to explain the mechanics of breathing.

The Work of Breathing

The number of breaths per minute is the respiratory rate. On average, under non-exertion conditions, the human respiratory rate is 12–15 breaths/minute. The respiratory rate contributes to the alveolar ventilation, or how much air moves into and out of the alveoli. Alveolar ventilation prevents carbon dioxide buildup in the alveoli. There are two ways to keep the alveolar ventilation constant: increase the respiratory rate while decreasing the tidal volume of air per breath (shallow breathing), or decrease the respiratory rate while increasing the tidal volume per breath. In either case, the ventilation remains the same, but the work done and type of work needed are quite different. Both tidal volume and respiratory rate are closely regulated when oxygen demand increases.

Dead Space: V/Q Mismatch

Pulmonary circulation pressure is very low compared to that of the systemic circulation. It is also independent of cardiac output. This is because of a phenomenon called recruitment, which is the process of opening airways that normally remain closed when cardiac output increases. As cardiac output increases, the number of capillaries and arteries that are perfused (filled with blood) increases. These capillaries and arteries are not always in use but are ready if needed. At times, however, there is a mismatch between the amount of air (ventilation, V) and the amount of blood (perfusion, Q) in the lungs. This is referred to as ventilation/perfusion (V/Q) mismatch.

Transport of Gases in Human Bodily Fluids

Abstract:
By the end of this section, you will be able to do the following:

* Describe how oxygen is bound to hemoglobin and transported to body tissues
* Explain how carbon dioxide is transported from body tissues to the lungs

Transport of Oxygen in the Blood

Although oxygen dissolves in blood, only a small amount of oxygen is transported this way. Only 1.5 percent of oxygen in the blood is dissolved directly into the blood itself. Most oxygen—98.5 percent—is bound to a protein called hemoglobin and carried to the tissues.

Transport of Carbon Dioxide in the Blood

Carbon dioxide molecules are transported in the blood from body tissues to the lungs by one of three methods: dissolution directly into the blood, binding to hemoglobin, or carried as a bicarbonate ion. Several properties of carbon dioxide in the blood affect its transport. First, carbon dioxide is more soluble in blood than oxygen. About 5 to 7 percent of all carbon dioxide is dissolved in the plasma. Second, carbon dioxide can bind to plasma proteins or can enter red blood cells and bind to hemoglobin. This form transports about 10 percent of the carbon dioxide. When carbon dioxide binds to hemoglobin, a molecule called carbaminohemoglobin is formed. Binding of carbon dioxide to hemoglobin is reversible. Therefore, when it reaches the lungs, the carbon dioxide can freely dissociate from the hemoglobin and be expelled from the body.

The Circulatory System

Introduction

Overview of the Circulatory System

Abstract:
By the end of this section, you will be able to do the following:

* Describe an open and closed circulatory system
* Describe interstitial fluid and hemolymph
* Compare and contrast the organization and evolution of the vertebrate circulatory system

Circulatory System Architecture

The circulatory system is effectively a network of cylindrical vessels: the arteries, veins, and capillaries that emanate from a pump, the heart. In all vertebrate organisms, as well as some invertebrates, this is a closed-loop system, in which the blood is not free in a cavity. In a closed circulatory system, blood is contained inside blood vessels and circulates unidirectionally from the heart around the systemic circulatory route, then returns to the heart again, as illustrated in [link]a. As opposed to a closed system, arthropods—including insects, crustaceans, and most mollusks—have an open circulatory system, as illustrated in [link]b. In an open circulatory system, the blood is not enclosed in the blood vessels but is pumped into a cavity called a hemocoel and is called hemolymph because the blood mixes with the interstitial fluid. As the heart beats and the animal moves, the hemolymph circulates around the organs within the body cavity and then reenters the hearts through openings called ostia. This movement allows for gas and nutrient exchange. An open circulatory system does not use as much energy as a closed system to operate or to maintain; however, there is a trade-off with the amount of blood that can be moved to metabolically active organs and tissues that require high levels of oxygen. In fact, one reason that insects with wing spans of up to two feet wide (70 cm) are not around today is probably because they were outcompeted by the arrival of birds 150 million years ago. Birds, having a closed circulatory system, are thought to have moved more agilely, allowing them to get food faster and possibly to prey on the insects.

Circulatory System Variation in Animals

The circulatory system varies from simple systems in invertebrates to more complex systems in vertebrates. The simplest animals, such as the sponges (Porifera) and rotifers (Rotifera), do not need a circulatory system because diffusion allows adequate exchange of water, nutrients, and waste, as well as dissolved gases, as shown in [link]a. Organisms that are more complex but still only have two layers of cells in their body plan, such as jellies (Cnidaria) and comb jellies (Ctenophora) also use diffusion through their epidermis and internally through the gastrovascular compartment. Both their internal and external tissues are bathed in an aqueous environment and exchange fluids by diffusion on both sides, as illustrated in [link]b. Exchange of fluids is assisted by the pulsing of the jellyfish body.

Components of the Blood

Abstract:
By the end of this section, you will be able to do the following:

* List the basic components of the blood
* Compare red and white blood cells
* Describe blood plasma and serum

The Role of Blood in the Body

Blood, like the human blood illustrated in [link] is important for regulation of the body’s systems and homeostasis. Blood helps maintain homeostasis by stabilizing pH, temperature, osmotic pressure, and by eliminating excess heat. Blood supports growth by distributing nutrients and hormones, and by removing waste. Blood plays a protective role by transporting clotting factors and platelets to prevent blood loss and transporting the disease-fighting agents or white blood cells to sites of infection.

Red Blood Cells

Red blood cells, or erythrocytes (erythro- = “red”; -cyte = “cell”), are specialized cells that circulate through the body delivering oxygen to cells; they are formed from stem cells in the bone marrow. In mammals, red blood cells are small biconcave cells that at maturity do not contain a nucleus or mitochondria and are only 7–8 µm in size. In birds and non-avian reptiles, a nucleus is still maintained in red blood cells.

White Blood Cells

White blood cells, also called leukocytes (leuko = white), make up approximately one percent by volume of the cells in blood. The role of white blood cells is very different than that of red blood cells: they are primarily involved in the immune response to identify and target pathogens, such as invading bacteria, viruses, and other foreign organisms. White blood cells are formed continually; some only live for hours or days, but some live for years.

Platelets and Coagulation Factors

Blood must clot to heal wounds and prevent excess blood loss. Small cell fragments called platelets (thrombocytes) are attracted to the wound site where they adhere by extending many projections and releasing their contents. These contents activate other platelets and also interact with other coagulation factors, which convert fibrinogen, a water-soluble protein present in blood serum into fibrin (a non-water soluble protein), causing the blood to clot. Many of the clotting factors require vitamin K to work, and vitamin K deficiency can lead to problems with blood clotting. Many platelets converge and stick together at the wound site forming a platelet plug (also called a fibrin clot), as illustrated in [link]b. The plug or clot lasts for a number of days and stops the loss of blood. Platelets are formed from the disintegration of larger cells called megakaryocytes, like that shown in [link]a. For each megakaryocyte, 2000–3000 platelets are formed with 150,000 to 400,000 platelets present in each cubic millimeter of blood. Each platelet is disc shaped and 2–4 μm in diameter. They contain many small vesicles but do not contain a nucleus.

Plasma and Serum

The liquid component of blood is called plasma, and it is separated by spinning or centrifuging the blood at high rotations (3000 rpm or higher). The blood cells and platelets are separated by centrifugal forces to the bottom of a specimen tube. The upper liquid layer, the plasma, consists of 90 percent water along with various substances required for maintaining the body’s pH, osmotic load, and for protecting the body. The plasma also contains the coagulation factors and antibodies.

Mammalian Heart and Blood Vessels

Abstract:
By the end of this section, you will be able to do the following:

* Describe the structure of the heart and explain how cardiac muscle is different from other muscles
* Describe the cardiac cycle
* Explain the structure of arteries, veins, and capillaries, and how blood flows through the body

Structure of the Heart

The heart muscle is asymmetrical as a result of the distance blood must travel in the pulmonary and systemic circuits. Since the right side of the heart sends blood to the pulmonary circuit it is smaller than the left side which must send blood out to the whole body in the systemic circuit, as shown in [link]. In humans, the heart is about the size of a clenched fist; it is divided into four chambers: two atria and two ventricles. There is one atrium and one ventricle on the right side and one atrium and one ventricle on the left side. The atria are the chambers that receive blood, and the ventricles are the chambers that pump blood. The right atrium receives deoxygenated blood from the superior vena cava, which drains blood from the jugular vein that comes from the brain and from the veins that come from the arms, as well as from the inferior vena cava which drains blood from the veins that come from the lower organs and the legs. In addition, the right atrium receives blood from the coronary sinus which drains deoxygenated blood from the heart itself. This deoxygenated blood then passes to the right ventricle through the atrioventricular valve or the tricuspid valve, a flap of connective tissue that opens in only one direction to prevent the backflow of blood. The valve separating the chambers on the left side of the heart valve is called the bicuspid or mitral valve. After it is filled, the right ventricle pumps the blood through the pulmonary arteries, bypassing the semilunar valve (or pulmonic valve) to the lungs for re-oxygenation. After blood passes through the pulmonary arteries, the right semilunar valves close preventing the blood from flowing backwards into the right ventricle. The left atrium then receives the oxygen-rich blood from the lungs via the pulmonary veins. This blood passes through the bicuspid valve or mitral valve (the atrioventricular valve on the left side of the heart) to the left ventricle where the blood is pumped out through the aorta, the major artery of the body, taking oxygenated blood to the organs and muscles of the body. Once blood is pumped out of the left ventricle and into the aorta, the aortic semilunar valve (or aortic valve) closes preventing blood from flowing backward into the left ventricle. This pattern of pumping is referred to as double circulation and is found in all mammals.

The Cardiac Cycle

The main purpose of the heart is to pump blood through the body; it does so in a repeating sequence called the cardiac cycle. The cardiac cycle is the coordination of the filling and emptying of the heart of blood by electrical signals that cause the heart muscles to contract and relax. The human heart beats over 100,000 times per day. In each cardiac cycle, the heart contracts (systole), pushing out the blood and pumping it through the body; this is followed by a relaxation phase (diastole), where the heart fills with blood, as illustrated in [link]. The atria contract at the same time, forcing blood through the atrioventricular valves into the ventricles. Closing of the atrioventricular valves produces a monosyllabic “lup” sound. Following a brief delay, the ventricles contract at the same time forcing blood through the semilunar valves into the aorta and the artery transporting blood to the lungs (via the pulmonary artery). Closing of the semilunar valves produces a monosyllabic “dup” sound.

Arteries, Veins, and Capillaries

The blood from the heart is carried through the body by a complex network of blood vessels ([link]). Arteries take blood away from the heart. The main artery is the aorta that branches into major arteries that take blood to different limbs and organs. These major arteries include the carotid artery that takes blood to the brain, the brachial arteries that take blood to the arms, and the thoracic artery that takes blood to the thorax and then into the hepatic, renal, and gastric arteries for the liver, kidney, and stomach, respectively. The iliac artery takes blood to the lower limbs. The major arteries diverge into minor arteries, and then smaller vessels called arterioles, to reach more deeply into the muscles and organs of the body.

Blood Flow and Blood Pressure Regulation

Abstract:
By the end of this section, you will be able to do the following:

* Describe the system of blood flow through the body
* Describe how blood pressure is regulated

How Blood Flows Through the Body

Blood is pushed through the body by the action of the pumping heart. With each rhythmic pump, blood is pushed under high pressure and velocity away from the heart, initially along the main artery, the aorta. In the aorta, the blood travels at 30 cm/sec. As blood moves into the arteries, arterioles, and ultimately to the capillary beds, the rate of movement slows dramatically to about 0.026 cm/sec, one-thousand times slower than the rate of movement in the aorta. While the diameter of each individual arteriole and capillary is far narrower than the diameter of the aorta, and according to the law of continuity, fluid should travel faster through a narrower diameter tube, the rate is actually slower due to the overall diameter of all the combined capillaries being far greater than the diameter of the individual aorta.

Blood Pressure

The pressure of the blood flow in the body is produced by the hydrostatic pressure of the fluid (blood) against the walls of the blood vessels. Fluid will move from areas of high to low hydrostatic pressures. In the arteries, the hydrostatic pressure near the heart is very high and blood flows to the arterioles where the rate of flow is slowed by the narrow openings of the arterioles. During systole, when new blood is entering the arteries, the artery walls stretch to accommodate the increase of pressure of the extra blood; during diastole, the walls return to normal because of their elastic properties. The blood pressure of the systole phase and the diastole phase, graphed in [link], gives the two pressure readings for blood pressure. For example, 120/80 indicates a reading of 120 mm Hg during the systole and 80 mm Hg during diastole. Throughout the cardiac cycle, the blood continues to empty into the arterioles at a relatively even rate. This resistance to blood flow is called peripheral resistance.

Blood Pressure Regulation

Cardiac output is the volume of blood pumped by the heart in one minute. It is calculated by multiplying the number of heart contractions that occur per minute (heart rate) times the stroke volume (the volume of blood pumped into the aorta per contraction of the left ventricle). Therefore, cardiac output can be increased by increasing heart rate, as when exercising. However, cardiac output can also be increased by increasing stroke volume, such as if the heart contracts with greater strength. Stroke volume can also be increased by speeding blood circulation through the body so that more blood enters the heart between contractions. During heavy exertion, the blood vessels relax and increase in diameter, offsetting the increased heart rate and ensuring adequate oxygenated blood gets to the muscles. Stress triggers a decrease in the diameter of the blood vessels, consequently increasing blood pressure. These changes can also be caused by nerve signals or hormones, and even standing up or lying down can have a great effect on blood pressure.

Osmotic Regulation and Excretion

Introduction

Osmoregulation and Osmotic Balance

Abstract:
By the end of this section, you will be able to do the following:

* Define osmosis and explain its role within molecules
* Explain why osmoregulation and osmotic balance are important body functions
* Describe active transport mechanisms
* Explain osmolarity and the way in which it is measured
* Describe osmoregulators or osmoconformers and how these tools allow animals to adapt to different environments

Need for Osmoregulation

Biological systems constantly interact and exchange water and nutrients with the environment by way of consumption of food and water and through excretion in the form of sweat, urine, and feces. Without a mechanism to regulate osmotic pressure, or when a disease damages this mechanism, there is a tendency to accumulate toxic waste and water, which can have dire consequences.

Transport of Electrolytes across Cell Membranes

Electrolytes, such as sodium chloride, ionize in water, meaning that they dissociate into their component ions. In water, sodium chloride (NaCl), dissociates into the sodium ion (Na+) and the chloride ion (Cl–). The most important ions, whose concentrations are
very closely regulated in body fluids, are the cations sodium (Na+), potassium (K+), calcium (Ca+2),
magnesium (Mg+2), and the anions chloride (Cl-), carbonate (CO3-2), bicarbonate (HCO3-), and phosphate(PO3-). Electrolytes are lost from the body during urination and perspiration. For this
reason, athletes are encouraged to replace electrolytes and fluids during periods of increased activity and perspiration.

Concept of Osmolality and Milliequivalent

In order to calculate osmotic pressure, it is necessary to understand how solute concentrations are measured. The unit for measuring solutes is the mole. One mole is defined as the gram molecular weight of the solute. For example, the molecular weight of sodium chloride is 58.44. Thus, one mole of sodium chloride weighs 58.44 grams. The molarity of a solution is the number of moles of solute per liter of solution. The molality of a solution is the number of moles of solute per kilogram of solvent. If the solvent is water, one kilogram of water is equal to one liter of water. While molarity and molality are used to express the concentration of solutions, electrolyte concentrations are usually expressed in terms of milliequivalents per liter (mEq/L): the mEq/L is equal to the ion concentration (in millimoles) multiplied by the number of electrical charges on the ion. The unit of milliequivalent takes into consideration the ions present in the solution (since electrolytes form ions in aqueous solutions) and the charge on the ions.

Osmoregulators and Osmoconformers

Persons lost at sea without any freshwater to drink are at risk of severe dehydration because the human body cannot adapt to drinking seawater, which is hypertonic in comparison to body fluids. Organisms such as goldfish that can tolerate only a relatively narrow range of salinity are referred to as stenohaline. About 90 percent of all bony fish are restricted to either freshwater or seawater. They are incapable of osmotic regulation in the opposite environment. It is possible, however, for a few fishes like salmon to spend part of their life in freshwater and part in seawater. Organisms like the salmon and molly that can tolerate a relatively wide range of salinity are referred to as euryhaline organisms. This is possible because some fish have evolved osmoregulatory mechanisms to survive in all kinds of aquatic environments. When they live in freshwater, their bodies tend to take up water because the environment is relatively hypotonic, as illustrated in [link]a. In such hypotonic environments, these fish do not drink much water. Instead, they pass a lot of very dilute urine, and they achieve electrolyte balance by active transport of salts through the gills. When they move to a hypertonic marine environment, these fish start drinking seawater; they excrete the excess salts through their gills and their urine, as illustrated in [link]b. Most marine invertebrates, on the other hand, may be isotonic with seawater (osmoconformers). Their body fluid concentrations conform to changes in seawater concentration. Cartilaginous fishes’ salt composition of the blood is similar to bony fishes; however, the blood of sharks contains the organic compounds urea and trimethylamine oxide (TMAO). This does not mean that their electrolyte composition is similar to that of seawater. They achieve isotonicity with the sea by storing large concentrations of urea. These animals that secrete urea are called ureotelic animals. TMAO stabilizes proteins in the presence of high urea levels, preventing the disruption of peptide bonds that would occur in other animals exposed to similar levels of urea. Sharks are cartilaginous fish with a rectal gland to secrete salt and assist in osmoregulation.

The Kidneys and Osmoregulatory Organs

Abstract:
By the end of this section, you will be able to do the following:

* Explain how the kidneys serve as the main osmoregulatory organs in mammalian systems
* Describe the structure of the kidneys and the functions of the parts of the kidney
* Describe how the nephron is the functional unit of the kidney and explain how it actively filters blood and generates urine
* Detail the three steps in the formation of urine: glomerular filtration, tubular reabsorption, and tubular secretion

Kidneys: The Main Osmoregulatory Organ

The kidneys, illustrated in [link], are a pair of bean-shaped structures that are located just below and posterior to the liver in the peritoneal cavity. The adrenal glands sit on top of each kidney and are also called the suprarenal glands. Kidneys filter blood and purify it. All the blood in the human body is filtered many times a day by the kidneys; these organs use up almost 25 percent of the oxygen absorbed through the lungs to perform this function. Oxygen allows the kidney cells to efficiently manufacture chemical energy in the form of ATP through aerobic respiration. The filtrate coming out of the kidneys is called urine.

Kidney Structure

Externally, the kidneys are surrounded by three layers, illustrated in [link]. The outermost layer is a tough connective tissue layer called the renal fascia. The second layer is called the perirenal fat capsule, which helps anchor the kidneys in place. The third and innermost layer is the renal capsule. Internally, the kidney has three regions—an outer cortex, a medulla in the middle, and the renal pelvis in the region called the hilum of the kidney. The hilum is the concave part of the bean-shape where blood vessels and nerves enter and exit the kidney; it is also the point of exit for the ureters. The renal cortex is granular due to the presence of nephrons—the functional unit of the kidney. The medulla consists of multiple pyramidal tissue masses, called the renal pyramids. In between the pyramids are spaces called renal columns through which the blood vessels pass. The tips of the pyramids, called renal papillae, point toward the renal pelvis. There are, on average, eight renal pyramids in each kidney. The renal pyramids along with the adjoining cortical region are called the lobes of the kidney. The renal pelvis leads to the ureter on the outside of the kidney. On the inside of the kidney, the renal pelvis branches out into two or three extensions called the major calyces, which further branch into the minor calyces. The ureters are urine-bearing tubes that exit the kidney and empty into the urinary bladder.

Kidney Function and Physiology

Kidneys filter blood in a three-step process. First, the nephrons filter blood that runs through the capillary network in the glomerulus. Almost all solutes, except for proteins, are filtered out into the glomerulus by a process called glomerular filtration. Second, the filtrate is collected in the renal tubules. Most of the solutes get reabsorbed in the PCT by a process called tubular reabsorption. In the loop of Henle, the filtrate continues to exchange solutes and water with the renal medulla and the peritubular capillary network. Water is also reabsorbed during this step. Then, additional solutes and wastes are secreted into the kidney tubules during tubular secretion, which is, in essence, the opposite process to tubular reabsorption. The collecting ducts collect filtrate coming from the nephrons and fuse in the medullary papillae. From here, the papillae deliver the filtrate, now called urine, into the minor calyces that eventually connect to the ureters through the renal pelvis. This entire process is illustrated in [link].

Excretion Systems

Abstract:
By the end of this section, you will be able to do the following:

* Explain how vacuoles, present in microorganisms, work to excrete waste
* Describe the way in which flame cells and nephridia in worms perform excretory functions and maintain osmotic balance
* Explain how insects use Malpighian tubules to excrete wastes and maintain osmotic balance

Contractile Vacuoles in Microorganisms

The most fundamental feature of life is the presence of a cell. In other words, a cell is the simplest functional unit of a life. Bacteria are unicellular, prokaryotic organisms that have some of the least complex life processes in place; however, prokaryotes such as bacteria do not contain membrane-bound vacuoles. The cells of microorganisms like bacteria, protozoa, and fungi are bound by cell membranes and use them to interact with the environment. Some cells, including some leucocytes in humans, are able to engulf food by endocytosis—the formation of vesicles by involution of the cell membrane within the cells. The same vesicles are able to interact and exchange metabolites with the intracellular environment. In some unicellular eukaryotic organisms such as the amoeba, shown in [link], cellular wastes and excess water are excreted by exocytosis, when the contractile vacuoles merge with the cell membrane and expel wastes into the environment. Contractile vacuoles (CV) should not be confused with vacuoles, which store food or water.

Flame Cells of Planaria and Nephridia of Worms

As multicellular systems evolved to have organ systems that divided the metabolic needs of the body, individual organs evolved to perform the excretory function. Planaria are flatworms that live in freshwater. Their excretory system consists of two tubules connected to a highly branched duct system. The cells in the tubules are called flame cells (or protonephridia) because they have a cluster of cilia that looks like a flickering flame when viewed under the microscope, as illustrated in [link]a. The cilia propel waste matter down the tubules and out of the body through excretory pores that open on the body surface; cilia also draw water from the interstitial fluid, allowing for filtration. Any valuable metabolites are recovered by reabsorption. Flame cells are found in flatworms, including parasitic tapeworms and free-living planaria. They also maintain the organism’s osmotic balance.

Malpighian Tubules of Insects

Malpighian tubules are found lining the gut of some species of arthropods, such as the bee illustrated in [link]. They are usually found in pairs and the number of tubules varies with the species of insect. Malpighian tubules are convoluted, which increases their surface area, and they are lined with microvilli for reabsorption and maintenance of osmotic balance. Malpighian tubules work cooperatively with specialized glands in the wall of the rectum. Body fluids are not filtered as in the case of nephridia; urine is produced by tubular secretion mechanisms by the cells lining the Malpighian tubules that are bathed in hemolymph (a mixture of blood and interstitial fluid that is found in insects and other arthropods as well as most mollusks). Metabolic wastes like uric acid freely diffuse into the tubules. There are exchange pumps lining the tubules, which actively transport H+ ions into the cell and K+ or Na+ ions out; water passively follows to form urine. The secretion of ions alters the osmotic pressure which draws water, electrolytes, and nitrogenous waste (uric acid) into the tubules. Water and electrolytes are reabsorbed when these organisms are faced with low-water environments, and uric acid is excreted as a thick paste or powder. Not dissolving wastes in water helps these organisms to conserve water; this is especially important for life in dry environments.

Nitrogenous Wastes

Abstract:
By the end of this section, you will be able to do the following:

* Compare and contrast the way in which aquatic animals and terrestrial animals can eliminate toxic ammonia from their systems
* Compare the major byproduct of ammonia metabolism in vertebrate animals to that of birds, insects, and reptiles

Nitrogenous Waste in Terrestrial Animals: The Urea Cycle

The urea cycle is the primary mechanism by which mammals convert ammonia to urea. Urea is made in the liver and excreted in urine. The overall chemical reaction by which ammonia is converted to urea is 2 NH3 (ammonia) + CO2 + 3 ATP + H2O → H2N-CO-NH2 (urea) + 2 ADP + 4 Pi + AMP.

Nitrogenous Waste in Birds and Reptiles: Uric Acid

Birds, reptiles, and most terrestrial arthropods convert toxic ammonia to uric acid or the closely related compound guanine (guano) instead of urea. Mammals also form some uric acid during breakdown of nucleic acids. Uric acid is a compound similar to purines found in nucleic acids. It is water insoluble and tends to form a white paste or powder; it is excreted by birds, insects, and reptiles. Conversion of ammonia to uric acid requires more energy and is much more complex than conversion of ammonia to urea [link].

Hormonal Control of Osmoregulatory Functions

Abstract:
By the end of this section, you will be able to do the following:

* Explain how hormonal cues help the kidneys synchronize the osmotic needs of the body
* Describe how hormones like epinephrine, norepinephrine, renin-angiotensin, aldosterone, anti-diuretic hormone, and atrial natriuretic peptide help regulate waste elimination, maintain correct osmolarity, and perform other osmoregulatory functions

Epinephrine and Norepinephrine

Epinephrine and norepinephrine are released by the adrenal medulla and nervous system respectively. They are the flight/fight hormones that are released when the body is under extreme stress. During stress, much of the body’s energy is used to combat imminent danger. Kidney function is halted temporarily by epinephrine and norepinephrine. These hormones function by acting directly on the smooth muscles of blood vessels to constrict them. Once the afferent arterioles are constricted, blood flow into the nephrons stops. These hormones go one step further and trigger the renin-angiotensin-aldosterone system.

Renin-Angiotensin-Aldosterone

The renin-angiotensin-aldosterone system, illustrated in [link] proceeds through several steps to produce angiotensin II, which acts to stabilize blood pressure and volume. Renin (secreted by a part of the juxtaglomerular complex) is produced by the granular cells of the afferent and efferent arterioles. Thus, the kidneys control blood pressure and volume directly. Renin acts on angiotensinogen, which is made in the liver and converts it to angiotensin I. Angiotensin converting enzyme (ACE) converts angiotensin I to angiotensin II. Angiotensin II raises blood pressure by constricting blood vessels. It also triggers the release of the mineralocorticoid aldosterone from the adrenal cortex, which in turn stimulates the renal tubules to reabsorb more sodium. Angiotensin II also triggers the release of anti-diuretic hormone (ADH) from the hypothalamus, leading to water retention in the kidneys. It acts directly on the nephrons and decreases glomerular filtration rate. Medically, blood pressure can be controlled by drugs that inhibit ACE (called ACE inhibitors).

Mineralocorticoids

Mineralocorticoids are hormones synthesized by the adrenal cortex that affect osmotic balance. Aldosterone is a mineralocorticoid that regulates sodium levels in the blood. Almost all of the sodium in the blood is reclaimed by the renal tubules under the influence of aldosterone. Because sodium is always reabsorbed by active transport and water follows sodium to maintain osmotic balance, aldosterone manages not only sodium levels but also the water levels in body fluids. In contrast, the aldosterone also stimulates potassium secretion concurrently with sodium reabsorption. In contrast, absence of aldosterone means that no sodium gets reabsorbed in the renal tubules and all of it gets excreted in the urine. In addition, the daily dietary potassium load is not secreted and the retention of K+ can cause a dangerous increase in plasma K+ concentration. Patients who have Addison's disease have a failing adrenal cortex and cannot produce aldosterone. They lose sodium in their urine constantly, and if the supply is not replenished, the consequences can be fatal.

Antidiuretic Hormone

As previously discussed, antidiuretic hormone or ADH (also called vasopressin), as the name suggests, helps the body conserve water when body fluid volume, especially that of blood, is low. It is formed by the hypothalamus and is stored and released from the posterior pituitary. It acts by inserting aquaporins in the collecting ducts and promotes reabsorption of water. ADH also acts as a vasoconstrictor and increases blood pressure during hemorrhaging.

Atrial Natriuretic Peptide Hormone

The atrial natriuretic peptide (ANP) lowers blood pressure by acting as a vasodilator. It is released by cells in the atrium of the heart in response to high blood pressure and in patients with sleep apnea. ANP affects salt release, and because water passively follows salt to maintain osmotic balance, it also has a diuretic effect. ANP also prevents sodium reabsorption by the renal tubules, decreasing water reabsorption (thus acting as a diuretic) and lowering blood pressure. Its actions suppress the actions of aldosterone, ADH, and renin.

The Immune System

Introduction

Innate Immune Response

Abstract:
By the end of this section, you will be able to do the following:

* Describe physical and chemical immune barriers
* Explain immediate and induced innate immune responses
* Discuss natural killer cells
* Describe major histocompatibility complex I molecules
* Summarize how the proteins in a complement system function to destroy extracellular pathogens

Physical and Chemical Barriers

Before any immune factors are triggered, the skin functions as a continuous, impassable barrier to potentially infectious pathogens. Pathogens are killed or inactivated on the skin by desiccation (drying out) and by the skin’s acidity. In addition, beneficial microorganisms that coexist on the skin compete with invading pathogens, preventing infection. Regions of the body that are not protected by skin (such as the eyes and mucus membranes) have alternative methods of defense, such as tears and mucus secretions that trap and rinse away pathogens, and cilia in the nasal passages and respiratory tract that push the mucus with the pathogens out of the body. Throughout the body are other defenses, such as the low pH of the stomach (which inhibits the growth of pathogens), blood proteins that bind and disrupt bacterial cell membranes, and the process of urination (which flushes pathogens from the urinary tract).

Pathogen Recognition

An infection may be intracellular or extracellular, depending on the pathogen. All viruses infect cells and replicate within those cells (intracellularly), whereas bacteria and other parasites may replicate intracellularly or extracellularly, depending on the species. The innate immune system must respond accordingly: by identifying the extracellular pathogen and/or by identifying host cells that have already been infected. When a pathogen enters the body, cells in the blood and lymph detect the specific pathogen-associated molecular patterns (PAMPs) on the pathogen’s surface. PAMPs are carbohydrate, polypeptide, and nucleic acid “signatures” that are expressed by viruses, bacteria, and parasites but which differ from molecules on host cells. The immune system has specific cells, described in [link] and shown in [link], with receptors that recognize these PAMPs. A macrophage is a large phagocytic cell that engulfs foreign particles and pathogens. Macrophages recognize PAMPs via complementary pattern recognition receptors (PRRs). PRRs are molecules on macrophages and dendritic cells which are in contact with the external environment. A monocyte is a type of white blood cell that circulates in the blood and lymph and differentiates into macrophages after it moves into infected tissue. Dendritic cells bind molecular signatures of pathogens and promote pathogen engulfment and destruction. Toll-like receptors (TLRs) are a type of PRR that recognizes molecules that are shared by pathogens but distinguishable from host molecules. TLRs are present in invertebrates as well as vertebrates, and appear to be one of the most ancient components of the immune system. TLRs have also been identified in the mammalian nervous system.

Natural Killer Cells

Lymphocytes are leukocytes that are histologically identifiable by their large, darkly staining nuclei; they are small cells with very little cytoplasm, as shown in [link]. Infected cells are identified and destroyed by natural killer (NK) cells, lymphocytes that can kill cells infected with viruses or tumor cells (abnormal cells that uncontrollably divide and invade other tissue). T cells and B cells of the adaptive immune system also are classified as lymphocytes. T cells are lymphocytes that mature in the thymus gland, and B cells are lymphocytes that mature in the bone marrow. NK cells identify intracellular infections, especially from viruses, by the altered expression of major histocompatibility complex (MHC) I molecules on the surface of infected cells. MHC I molecules are proteins on the surfaces of all nucleated cells, thus they are scarce on red blood cells and platelets which are non-nucleated. The function of MHC I molecules is to display fragments of proteins from the infectious agents within the cell to T cells; healthy cells will be ignored, while “non-self” or foreign proteins will be attacked by the immune system. MHC II molecules are found mainly on cells containing antigens (“non-self proteins”) and on lymphocytes. MHC II molecules interact with helper T cells to trigger the appropriate immune response, which may include the inflammatory response.

Complement

An array of approximately 20 types of soluble proteins, called a complement system, functions to destroy extracellular pathogens. Cells of the liver and macrophages synthesize complement proteins continuously; these proteins are abundant in the blood serum and are capable of responding immediately to infecting microorganisms. The complement system is so named because it is complementary to the antibody response of the adaptive immune system. Complement proteins bind to the surfaces of microorganisms and are particularly attracted to pathogens that are already bound by antibodies. Binding of complement proteins occurs in a specific and highly regulated sequence, with each successive protein being activated by cleavage and/or structural changes induced upon binding of the preceding protein(s). After the first few complement proteins bind, a cascade of sequential binding events follows in which the pathogen rapidly becomes coated in complement proteins.

Adaptive Immune Response

Abstract:
By the end of this section, you will be able to do the following:

* Explain adaptive immunity
* Compare and contrast adaptive and innate immunity
* Describe cell-mediated immune response and humoral immune response
* Describe immune tolerance

Antigen-presenting Cells

Unlike NK cells of the innate immune system, B cells (B lymphocytes) are a type of white blood cell that gives rise to antibodies, whereas T cells (T lymphocytes) are a type of white blood cell that plays an important role in the immune response. T cells are a key component in the cell-mediated response—the specific immune response that utilizes T cells to neutralize cells that have been infected with viruses and certain bacteria. There are three types of T cells: cytotoxic, helper, and suppressor T cells. Cytotoxic T cells destroy virus-infected cells in the cell-mediated immune response, and helper T cells play a part in activating both the antibody and the cell-mediated immune responses. Suppressor T cells deactivate T cells and B cells when needed, and thus prevent the immune response from becoming too intense.

T and B Lymphocytes

Lymphocytes in human circulating blood are approximately 80 to 90 percent T cells, shown in [link], and 10 to 20 percent B cells. Recall that the T cells are involved in the cell-mediated immune response, whereas B cells are part of the humoral immune response.

Immunological Memory

The adaptive immune system possesses a memory component that allows for an efficient and dramatic response upon reinvasion of the same pathogen. Memory is handled by the adaptive immune system with little reliance on cues from the innate response. During the adaptive immune response to a pathogen that has not been encountered before, called a primary response, plasma cells secreting antibodies and differentiated T cells increase, then plateau over time. As B and T cells mature into effector cells, a subset of the naïve populations differentiates into B and T memory cells with the same antigen specificities, as illustrated in [link].

Primary Centers of the Immune System

Although the immune system is characterized by circulating cells throughout the body, the regulation, maturation, and intercommunication of immune factors occur at specific sites. The blood circulates immune cells, proteins, and other factors through the body. Approximately 0.1 percent of all cells in the blood are leukocytes, which encompass monocytes (the precursor of macrophages) and lymphocytes. The majority of cells in the blood are erythrocytes (red blood cells). Lymph is a watery fluid that bathes tissues and organs with protective white blood cells and does not contain erythrocytes. Cells of the immune system can travel between the distinct lymphatic and blood circulatory systems, which are separated by interstitial space, by a process called extravasation (passing through to surrounding tissue).

Antibodies

Abstract:
By the end of this section, you will be able to do the following:

* Explain cross-reactivity
* Describe the structure and function of antibodies
* Discuss antibody production

Antibody Structure

An antibody molecule is comprised of four polypeptides: two identical heavy chains (large peptide units) that are partially bound to each other in a “Y” formation, which are flanked by two identical light chains (small peptide units), as illustrated in [link]. Bonds between the cysteine amino acids in the antibody molecule attach the polypeptides to each other. The areas where the antigen is recognized on the antibody are variable domains and the antibody base is composed of constant domains.

Antibody Functions

Differentiated plasma cells are crucial players in the humoral response, and the antibodies they secrete are particularly significant against extracellular pathogens and toxins. Antibodies circulate freely and act independently of plasma cells. Antibodies can be transferred from one individual to another to temporarily protect against infectious disease. For instance, a person who has recently produced a successful immune response against a particular disease agent can donate blood to a nonimmune recipient and confer temporary immunity through antibodies in the donor’s blood serum. This phenomenon is called passive immunity; it also occurs naturally during breastfeeding, which makes breastfed infants highly resistant to infections during the first few months of life.

Antibodies of the Mucosal Immune System

Antibodies synthesized by the mucosal immune system include IgA and IgM. Activated B cells differentiate into mucosal plasma cells that synthesize and secrete dimeric IgA, and to a lesser extent, pentameric IgM. Secreted IgA is abundant in tears, saliva, breast milk, and in secretions of the gastrointestinal and respiratory tracts. Antibody secretion results in a local humoral response at epithelial surfaces and prevents infection of the mucosa by binding and neutralizing pathogens.

Disruptions in the Immune System

Abstract:
By the end of this section, you will be able to do the following:

* Describe hypersensitivity
* Define autoimmunity

Immunodeficiency

Failures, insufficiencies, or delays at any level of the immune response can allow pathogens or tumor cells to gain a foothold and replicate or proliferate to high enough levels that the immune system becomes overwhelmed. Immunodeficiency is the failure, insufficiency, or delay in the response of the immune system, which may be acquired or inherited. Immunodeficiency can be acquired as a result of infection with certain pathogens (such as HIV), chemical exposure (including certain medical treatments), malnutrition, or possibly by extreme stress. For instance, radiation exposure can destroy populations of lymphocytes and elevate an individual’s susceptibility to infections and cancer. Dozens of genetic disorders result in immunodeficiencies, including Severe Combined Immunodeficiency (SCID), Bare lymphocyte syndrome, and MHC II deficiencies. Rarely, primary immunodeficiencies that are present from birth may occur. Neutropenia is one form in which the immune system produces a below-average number of neutrophils, the body’s most abundant phagocytes. As a result, bacterial infections may go unrestricted in the blood, causing serious complications.

Hypersensitivities

Maladaptive immune responses toward harmless foreign substances or self antigens that occur after tissue sensitization are termed hypersensitivities. The types of hypersensitivities include immediate, delayed, and autoimmunity. A large proportion of the population is affected by one or more types of hypersensitivity.

Animal Reproduction and Development

Introduction

Reproduction Methods

Abstract:
By the end of this section, you will be able to do the following:

* Describe advantages and disadvantages of asexual and sexual reproduction
* Discuss asexual reproduction methods
* Discuss sexual reproduction methods

Asexual Reproduction

Asexual reproduction occurs in prokaryotic microorganisms (bacteria) and in some eukaryotic single-celled and multi-celled organisms. There are a number of ways that animals reproduce asexually.

Sexual Reproduction

Sexual reproduction is the combination of (usually haploid) reproductive cells from two individuals to form a third (usually diploid) unique offspring. Sexual reproduction produces offspring with novel combinations of genes. This can be an adaptive advantage in unstable or unpredictable environments. As humans, we are used to thinking of animals as having two separate sexes—male and female—determined at conception. However, in the animal kingdom, there are many variations on this theme.

Sex Determination

Mammalian sex determination is determined genetically by the presence of X and Y chromosomes. Individuals homozygous for X (XX) are female and heterozygous individuals (XY) are male. The presence of a Y chromosome causes the development of male characteristics and its absence results in female characteristics. The XY system is also found in some insects and plants.

Fertilization

Abstract:
By the end of this section, you will be able to do the following:

* Discuss internal and external methods of fertilization
* Describe the methods used by animals for development of offspring during gestation
* Describe the anatomical adaptations that occurred in animals to facilitate reproduction

External Fertilization

External fertilization usually occurs in aquatic environments where both eggs and sperm are released into the water. After the sperm reaches the egg, fertilization takes place. Most external fertilization happens during the process of spawning where one or several females release their eggs and the male(s) release sperm in the same area, at the same time. The release of the reproductive material may be triggered by water temperature or the length of daylight. Nearly all fish spawn, as do crustaceans (such as crabs and shrimp), mollusks (such as oysters), squid, and echinoderms (such as sea urchins and sea cucumbers). [link] shows salmon spawning in a shallow stream. Frogs, like those shown in [link], corals, molluscs, and sea cucumbers also spawn.

The Evolution of Reproduction

Once multicellular organisms evolved and developed specialized cells, some also developed tissues and organs with specialized functions. An early development in reproduction occurred in the Annelids. These organisms produce sperm and eggs from undifferentiated cells in their coelom and store them in that cavity. When the coelom becomes filled, the cells are released through an excretory opening or by the body splitting open. Reproductive organs evolved with the development of gonads that produce sperm and eggs. These cells went through meiosis, an adaptation of mitosis, which reduced the number of chromosomes in each reproductive cell by half, while increasing the number of cells through cell division.

Human Reproductive Anatomy and Gametogenesis

Abstract:
By the end of this section, you will be able to do the following:

* Describe human male and female reproductive anatomies
* Discuss the human sexual response
* Describe spermatogenesis and oogenesis and discuss their differences and similarities

Human Reproductive Anatomy

The reproductive tissues of male and female humans develop similarly *in utero* until, in some cases, a low level of the hormone testosterone is released from gonads. Testosterone causes the undeveloped tissues to differentiate into organs, such as the scrotum and penis. When testosterone is absent, the tissues continue to develop into structures such as the ovaries and labia. These cells are considered bipotential: one group of cells has the potential to develop into either type of reproductive structure. Primitive gonads become testes or ovaries. Tissues that produce a penis in males produce a clitoris in females. The tissue that will become the scrotum in a male becomes the labia in a female; that is, they are homologous structures.

Gametogenesis (Spermatogenesis and Oogenesis)

Gametogenesis, the production of sperm and eggs, takes place through the process of meiosis. During meiosis, two cell divisions separate the paired chromosomes in the nucleus and then separate the chromatids that were made during an earlier stage of the cell’s life cycle. Meiosis produces haploid cells with half of each pair of chromosomes normally found in diploid cells. The production of sperm is called spermatogenesis and the production of eggs is called oogenesis.

Hormonal Control of Human Reproduction

Abstract:
By the end of this chapter, you will be able to do the following:
* Describe the roles of male and female reproductive hormones
* Discuss the interplay of the ovarian and menstrual cycles
* Describe the process of menopause

Male Hormones

At the onset of puberty, the hypothalamus causes the release of FSH and LH into the male system for the first time. FSH enters the testes and stimulates the Sertoli cells to begin facilitating spermatogenesis using negative feedback, as illustrated in [link]. LH also enters the testes and stimulates the interstitial cells of Leydig to make and release testosterone into the testes and the blood.

Female Hormones

The control of reproduction in females is more complex. As with the male, the anterior pituitary hormones cause the release of the hormones FSH and LH. In addition, estrogens and progesterone are released from the developing follicles. Estrogen is the reproductive hormone in females that assists in endometrial regrowth, ovulation, and calcium absorption; it is also responsible for the secondary sexual characteristics of females. These include breast development, flaring of the hips, and a shorter period necessary for bone maturation. Progesterone assists in endometrial regrowth and inhibition of FSH and LH release.

Human Pregnancy and Birth

Abstract:
By the end of this section, you will be able to do the following:

* Explain fetal development during the three trimesters of gestation
* Describe labor and delivery
* Compare the efficacy and duration of various types of contraception
* Discuss causes of infertility and the therapeutic options available

Human Gestation

Twenty-four hours before fertilization, the egg has finished meiosis and becomes a mature oocyte. When fertilized (at conception) the egg becomes known as a zygote. The zygote travels through the oviduct to the uterus ([link]). The developing embryo must implant into the wall of the uterus within seven days, or it will deteriorate and die. The outer layers of the zygote (blastocyst) grow into the endometrium by digesting the endometrial cells, and wound healing of the endometrium closes up the blastocyst into the tissue. Another layer of the blastocyst, the chorion, begins releasing a hormone called human beta chorionic gonadotropin (*β*-HCG) which makes its way to the corpus luteum and keeps that structure active. This ensures adequate levels of progesterone that will maintain the endometrium of the uterus for the support of the developing embryo. Pregnancy tests determine the level of *β*-HCG in urine or serum. If the hormone is present, the test is positive.

Labor and Birth

Labor is the physical efforts of expulsion of the fetus and the placenta from the uterus during birth (parturition). Toward the end of the third trimester, estrogen causes receptors on the uterine wall to develop and bind the hormone oxytocin. At this time, the baby reorients, facing forward and down with the back or crown of the head engaging the cervix (uterine opening). This causes the cervix to stretch and nerve impulses are sent to the hypothalamus, which signals for the release of oxytocin from the posterior pituitary. The oxytocin causes the smooth muscle in the uterine wall to contract. At the same time, the placenta releases prostaglandins into the uterus, increasing the contractions. A positive feedback relay occurs between the uterus, hypothalamus, and the posterior pituitary to assure an adequate supply of oxytocin. As more smooth muscle cells are recruited, the contractions increase in intensity and force.

Contraception and Birth Control

The prevention of a pregnancy comes under the terms contraception or birth control. Strictly speaking, contraception refers to preventing the sperm and egg from joining. Both terms are, however, frequently used interchangeably.

Infertility

Infertility is the inability to conceive a child or carry a child to birth. About 75 percent of causes of infertility can be identified; these include diseases, such as sexually transmitted diseases that can cause scarring of the reproductive tubes in males or females, or developmental problems frequently related to abnormal hormone levels in one of the individuals. Inadequate nutrition, especially starvation, can delay menstruation. Stress can also lead to infertility. Short-term stress can affect hormone levels, while long-term stress can delay puberty and cause less frequent menstrual cycles. Other factors that affect fertility include toxins (such as cadmium), tobacco smoking, marijuana use, gonadal injuries, and aging.

Fertilization and Early Embryonic Development

Abstract:
By the end of this section, you will be able to do the following:

* Discuss how fertilization occurs
* Explain how the embryo forms from the zygote
* Discuss the role of cleavage and gastrulation in animal development

Fertilization

Fertilization, pictured in [link]a is the process in which gametes (an egg and sperm) fuse to form a zygote. The egg and sperm each contain one set of chromosomes. To ensure that the offspring has only one complete diploid set of chromosomes, only one sperm must fuse with one egg. In mammals, the egg is protected by a layer of extracellular matrix consisting mainly of glycoproteins called the zona pellucida. When a sperm binds to the zona pellucida, a series of biochemical events, called the acrosomal reactions, take place. In placental mammals, the acrosome contains digestive enzymes that initiate the degradation of the glycoprotein matrix protecting the egg and allowing the sperm plasma membrane to fuse with the egg plasma membrane, as illustrated in [link]b. The fusion of these two membranes creates an opening through which the sperm nucleus is transferred into the ovum. The nuclear membranes of the egg and sperm break down and the two haploid genomes condense to form a diploid genome.

Cleavage and Blastula Stage

The development of multi-cellular organisms begins from a single-celled zygote, which undergoes rapid cell division to form the blastula. The rapid, multiple rounds of cell division are termed cleavage. Cleavage is illustrated in ([link]a). After the cleavage has produced over 100 cells, the embryo is called a blastula. The blastula is usually a spherical layer of cells (the blastoderm) surrounding a fluid-filled or yolk-filled cavity (the blastocoel). Mammals at this stage form a structure called the blastocyst, characterized by an inner cell mass that is distinct from the surrounding blastula, shown in [link]b. During cleavage, the cells divide without an increase in mass; that is, one large single-celled zygote divides into multiple smaller cells. Each cell within the blastula is called a blastomere.

Gastrulation

The typical blastula is a ball of cells. The next stage in embryonic development is the formation of the body plan. The cells in the blastula rearrange themselves spatially to form three layers of cells. This process is called gastrulation. During gastrulation, the blastula folds upon itself to form the three layers of cells. Each of these layers is called a germ layer and each germ layer differentiates into different organ systems.

Organogenesis and Vertebrate Formation

Abstract:
By the end of this section, you will be able to do the following:

* Describe the process of organogenesis
* Identify the anatomical axes formed in vertebrates

Organogenesis

Organs form from the germ layers through the process of differentiation. During differentiation, the embryonic stem cells express specific sets of genes which will determine their ultimate cell type. For example, some cells in the ectoderm will express the genes specific to skin cells. As a result, these cells will differentiate into epidermal cells. The process of differentiation is regulated by cellular signaling cascades.

Vertebrate Axis Formation

Even as the germ layers form, the ball of cells still retains its spherical shape. However, animal bodies have lateral-medial (left-right), dorsal-ventral (back-belly), and anterior-posterior (head-feet) axes, illustrated in [link].

Ecology

Ecology and the Biosphere

Introduction

The Scope of Ecology

Abstract:
By the end of this section, you will be able to do the following:

* Define ecology and the four basic levels of ecological research
* Describe examples of the ways in which ecology requires the integration of different scientific disciplines
* Distinguish between abiotic and biotic components of the environment
* Recognize the relationship between abiotic and biotic components of the environment

Levels of Ecological Study

When a discipline such as biology is studied, it is often helpful to subdivide it into smaller, related areas. For instance, cell biologists interested in cell signaling need to understand the chemistry of the signal molecules (which are usually proteins) as well as the result of cell signaling. Ecologists interested in the factors that influence the survival of an endangered species might use mathematical models to predict how current conservation efforts affect endangered organisms.

Organismal Ecology

Researchers studying ecology at the organismal level are interested in the adaptations that enable individuals to live in specific habitats. These adaptations can be morphological, physiological, and behavioral. For instance, the Karner blue butterfly (*Lycaeides melissa samuelis*) ([link]) is considered a specialist because the females only *oviposit* (that is, lay eggs) on wild lupine (*Lupinus perennis*). This specific requirement and adaptation means that the Karner blue butterfly is completely dependent on the presence of wild lupine plants for its survival.

Population Ecology

A population is a group of *interbreeding organisms* that are members of the same species living in the same area at the same time. (Organisms that are all members of the same species are called conspecifics.) A population is identified, in part, by where it lives, and its area of population may have natural or artificial boundaries. Natural boundaries might be rivers, mountains, or deserts, while artificial boundaries may be mowed grass, manmade structures, or roads. The study of *population ecology* focuses on the number of individuals in an area and how and why population size changes over time.

Community Ecology

A biological community consists of the different species within an area, typically a three-dimensional space, and the interactions within and among these species. Community ecologists are interested in the processes driving these interactions and their consequences. Questions about *conspecific* interactions often focus on competition among members of the same species for a limited resource. Ecologists also study interactions between various species; members of different species are called heterospecifics. Examples of heterospecific interactions include predation, parasitism, herbivory, competition, and pollination. These interactions can have regulating effects on population sizes and can impact ecological and evolutionary processes affecting diversity.

Ecosystem Ecology

Ecosystem ecology is an extension of organismal, population, and community ecology. The ecosystem is composed of all the biotic components (living things) in an area along with the abiotic components (nonliving things) of that area. Some of the abiotic components include air, water, and soil. Ecosystem biologists ask questions about how nutrients and energy are stored and how they move among organisms and through the surrounding atmosphere, soil, and water.

Biogeography

Abstract:
By the end of this section, you will be able to do the following:

* Define biogeography
* List and describe abiotic factors that affect the global distribution of plant and animal species
* Compare the impact of abiotic forces on aquatic and terrestrial environments
* Summarize the effects of abiotic factors on net primary productivity

Biogeography

Biogeography is the study of the geographic distribution of living things and the *abiotic factors* that affect their distribution. Abiotic factors such as temperature and rainfall vary based mainly on latitude and elevation. As these abiotic factors change, the composition of plant and animal communities also changes. For example, if you were to begin a journey at the equator and walk north, you would notice gradual changes in plant communities. At the beginning of your journey, you would see tropical wet forests with broad-leaved evergreen trees, which are characteristic of plant communities found near the equator. As you continued to travel north, you would see these broad-leaved evergreen plants eventually give rise to seasonally dry forests with scattered trees. You would also begin to notice changes in temperature and moisture. At about 30 degrees north, these forests would give way to deserts, which are characterized by low precipitation and high insolation (sunlight).

Abiotic Factors Influencing Plant Growth

Temperature and moisture are important influences on plant production (primary productivity) and the amount of organic matter available as food (net primary productivity). Net primary productivity is an estimation of all of the organic matter available as food; it is calculated as the total amount of carbon fixed per year minus the amount that is oxidized during cellular respiration. In terrestrial environments, net primary productivity is estimated by measuring the above-ground biomass per unit area, which is the total mass of living plants, excluding roots (whose mass is very difficult to measure). This means that a large percentage of plant biomass which exists underground is not included in this measurement. Net primary productivity is an important variable when considering differences in biomes. Very productive biomes have a high level of aboveground biomass.

Terrestrial Biomes

Abstract:
By the end of this section, you will be able to do the following:

* Identify the two major abiotic factors that determine terrestrial biomes
* Recognize distinguishing characteristics of each of the eight major terrestrial biomes

Tropical Wet Forest

Tropical wet forests are also referred to as tropical rainforests. This biome is found in equatorial regions ([link]). The vegetation is characterized by plants with broad leaves that fall and are replaced throughout the year. Unlike the trees of deciduous forests, the trees in this biome do not have a seasonal loss of leaves associated with variations in temperature and sunlight; these forests are “evergreen” year-round.

Savannas

Savannas are grasslands with scattered trees, and they are located in Africa, South America, and northern Australia ([link]). Savannas are usually hot, tropical areas with temperatures averaging from 24 °C to 29 °C (75 °F to 84 °F) and an annual rainfall of 10–40 cm (3.9–15.7 in). Savannas have an extensive dry season; for this reason, forest trees do not grow as well as they do in the tropical wet forest (or other forest biomes). As a result, within the grasses and *forbs* (herbaceous flowering plants) that dominate the savanna, there are relatively few trees ([link]). Since fire is an important source of disturbance in this biome, plants have evolved well-developed root systems that allow them to quickly resprout after a fire.

Subtropical Deserts

Subtropical deserts exist between 15° and 30° north and south latitude and are centered on the Tropics of Cancer and Capricorn ([link]). This biome is very dry; in some years, evaporation exceeds precipitation. Subtropical hot deserts can have daytime soil surface temperatures above 60 °C (140 °F) and nighttime temperatures approaching 0 °C (32 °F). This is largely due to the lack of atmospheric water. In cold deserts, temperatures can be as high as 25 °C and can drop below -30 °C (-22 °F). Subtropical deserts are characterized by low annual precipitation of fewer than 30 cm (12 in) with little monthly variation and lack of predictability in rainfall. In some cases, the annual rainfall can be as low as 2 cm (0.8 in) in subtropical deserts located in central Australia (“the Outback”) and northern Africa.

Chaparral

The chaparral is also called the scrub forest and is found in California, along the Mediterranean Sea, and along the southern coast of Australia ([link]). The annual rainfall in this biome ranges from 65 cm to 75 cm (25.6–29.5 in), and the majority of the rain falls in the winter. Summers are very dry and many chaparral plants are dormant during the summertime. The chaparral vegetation, shown in [link], is dominated by shrubs adapted to periodic fires, with some plants producing seeds that only germinate after a hot fire. The ashes left behind after a fire are rich in nutrients like nitrogen that fertilize the soil and promote plant regrowth.

Temperate Grasslands

Temperate grasslands are found throughout central North America, where they are also known as *prairies*; they are also in Eurasia, where they are known as *steppes* ([link]). Temperate grasslands have pronounced annual fluctuations in temperature with hot summers and cold winters. The annual temperature variation produces specific growing seasons for plants. Plant growth is possible when temperatures are warm enough to sustain plant growth and when ample water is available, which occurs in the spring, summer, and fall. During much of the winter, temperatures are low, and water, which is stored in the form of ice, is not available for plant growth.

Temperate Forests

Temperate forests are the most common biome in eastern North America, Western Europe, Eastern Asia, Chile, and New Zealand ([link]). This biome is found throughout mid-latitude regions. Temperatures range between -30 °C and 30 °C (-22 °F to 86 °F) and drop to below freezing periodically during cold winters. These temperatures mean that temperate forests have defined growing seasons during the spring, summer, and early fall. Precipitation is relatively constant throughout the year and ranges between 75 cm and 150 cm (29.5–59 in).

Boreal Forests

The boreal forest, also known as taiga or coniferous forest, is found south of the Arctic Circle and across most of Canada, Alaska, Russia, and northern Europe ([link]). This biome has cold, dry winters and short, cool, wet summers. The annual precipitation is from 40 cm to 100 cm (15.7–39 in) and usually takes the form of snow. Little evaporation occurs because of the cold temperatures.

Arctic Tundra

The Arctic tundra lies north of the subarctic boreal forest and is located throughout the Arctic regions of the northern hemisphere ([link]). The average winter temperature is –34 °C (–29.2 °F) and the average summer temperature is from 3 °C to 12 °C (37 °F–52 °F). Plants in the arctic tundra have a very short growing season of approximately 10–12 weeks.

Aquatic Biomes

Abstract:
By the end of this section, you will be able to do the following:

* Describe the effects of abiotic factors on the composition of plant and animal communities in aquatic biomes
* Compare and contrast the characteristics of the ocean zones
* Summarize the characteristics of standing water and flowing water freshwater biomes

Abiotic Factors Influencing Aquatic Biomes

Like terrestrial biomes, aquatic biomes are influenced by a series of abiotic factors. The aquatic medium—water— has different physical and chemical properties than air, however. Even if the water in a pond or other body of water is perfectly clear (there are no suspended particles), water, on its own, absorbs light. As one descends into a deep body of water, there will eventually be a depth which the sunlight cannot reach. While there are some abiotic and biotic factors in a terrestrial ecosystem that might obscure light (like fog, dust, or insect swarms), usually these are not permanent features of the environment. The importance of light in aquatic biomes is central to the communities of organisms found in both freshwater and marine ecosystems. In freshwater systems, stratification due to differences in density is perhaps the most critical abiotic factor and is related to the energy aspects of light. The thermal properties of water (rates of heating and cooling and the ability to store much larger amounts of energy than the air) are significant to the function of marine systems and have major impacts on global climate and weather patterns. Marine systems are also influenced by large-scale physical water movements, such as currents; these are less important in most freshwater lakes.

Marine Biomes

The ocean is the largest marine biome. It is a continuous body of salt water that is relatively uniform in chemical composition; in fact, it is a weak solution of mineral salts and decayed biological matter. Within the ocean, coral reefs are a second kind of marine biome. Estuaries, coastal areas where salt water and fresh water mix, form a third unique marine biome.

Estuaries: Where the Ocean Meets Fresh Water

Estuaries are biomes that occur where a source of fresh water, such as a river, meets the ocean. Therefore, both fresh water and salt water are found in the same vicinity; mixing results in a diluted (*brackish*) saltwater. Estuaries form protected areas where many of the young offspring of crustaceans, molluscs, and fish begin their lives, which also creates important breeding grounds for other animals. Salinity is a very important factor that influences the organisms and the adaptations of the organisms found in estuaries. The salinity of estuaries varies considerably and is based on the rate of flow of its freshwater sources, which may depend on the seasonal rainfall. Once or twice a day, high tides bring salt water into the estuary. Low tides occurring at the same frequency reverse the current of salt water.

Freshwater Biomes

Freshwater biomes include lakes and ponds (standing water) as well as rivers and streams (flowing water). They also include wetlands, which will be discussed later. Humans rely on freshwater biomes to provide ecosystem benefits, which are aquatic resources for drinking water, crop irrigation, sanitation, and industry. Lakes and ponds are connected with abiotic and biotic factors influencing their terrestrial biomes.

Climate and the Effects of Global Climate Change

Abstract:
By the end of this section, you will be able to do the following:

* Define global climate change
* Summarize the effects of the Industrial Revolution on global atmospheric carbon dioxide concentration
* Describe three natural factors affecting long-term global climate
* List two or more greenhouse gases and describe their role in the greenhouse effect

Climate and Weather

A common misconception about global climate change is that a specific weather event occurring in a particular region (for example, a very cool week in June in central Indiana) provides evidence of global climate change. However, a cold week in June is a weather-related event and not a climate-related one. These misconceptions often arise because of confusion over the terms *climate* and *weather*.

Global Climate Change

Climate change can be understood by approaching three areas of study:

Documented Results of Climate Change: Past and Present

Scientists have geological evidence of the consequences of long-ago climate change. Modern-day phenomena such as retreating glaciers and melting polar ice cause a continual rise in sea level. Meanwhile, changes in climate can negatively affect organisms.

Population and Community Ecology

Introduction

Population Demography

Abstract:
By the end of this section, you will be able to do the following:

* Describe how ecologists measure population size and density
* Describe three different patterns of population distribution
* Use life tables to calculate mortality rates
* Describe the three types of survivorship curves and relate them to specific populations

Population Size and Density

The study of any population usually begins by determining how many individuals of a particular species exist, and how closely associated they are with each other. Within a particular habitat, a population can be characterized by its population size (*N*), the total number of individuals, and its population density, the number of individuals within a specific area or volume. Population size and density are the two main characteristics used to describe and understand populations. For example, populations with more individuals may be more stable than smaller populations based on their genetic variability, and thus their potential to adapt to the environment. Alternatively, a member of a population with low population density (more spread out in the habitat), might have more difficulty finding a mate to reproduce compared to a population of higher density. As is shown in [link], smaller organisms tend to be more densely distributed than larger organisms.

Species Distribution

In addition to measuring simple density, further information about a population can be obtained by looking at the distribution of the individuals. Species dispersion patterns (or distribution patterns) show the spatial relationship between members of a population within a habitat at a particular point in time. In other words, they show whether members of the species live close together or far apart, and what patterns are evident when they are spaced apart.

Demography

While population size and density describe a population at one particular point in time, scientists must use demography to study the dynamics of a population. Demography is the statistical study of population changes over time: birth rates, death rates, and life expectancies. Each of these measures, especially birth rates, may be affected by the population characteristics described above. For example, a large population size results in a higher birth rate because more potentially reproductive individuals are present. In contrast, a large population size can also result in a higher death rate because of competition, disease, and the accumulation of waste. Similarly, a higher population density or a clumped dispersion pattern results in more potential reproductive encounters between individuals, which can increase birth rate. Lastly, a female-biased sex ratio (the ratio of males to females) or age structure (the proportion of population members at specific age ranges) composed of many individuals of reproductive age can increase birth rates.

Life Histories and Natural Selection

Abstract:
By the end of this section, you will be able to do the following:

* Describe how life history patterns are influenced by natural selection
* Explain different life history patterns and how different reproductive strategies affect species’ survival

Life History Patterns and Energy Budgets

Energy is required by all living organisms for their growth, maintenance, and reproduction; at the same time, energy is often a major limiting factor in determining an organism’s survival. Plants, for example, acquire energy from the sun via photosynthesis, but must expend this energy to grow, maintain health, and produce energy-rich seeds to produce the next generation. Animals have the additional burden of using some of their energy reserves to acquire food. Furthermore, some animals must expend energy caring for their offspring. Thus, all species have an energy budget: they must balance energy intake with their use of energy for metabolism, reproduction, parental care, and energy storage (such as bears building up body fat for winter hibernation).

Environmental Limits to Population Growth

Abstract:
By the end of this section, you will be able to do the following:

* Explain the characteristics of and differences between exponential and logistic growth patterns
* Give examples of exponential and logistic growth in natural populations
* Describe how natural selection and environmental adaptation led to the evolution of particular life history patterns

Exponential Growth

Charles Darwin, in his theory of natural selection, was greatly influenced by the English clergyman Thomas Malthus. Malthus published a book in 1798 stating that populations with unlimited natural resources grow very rapidly, which represents an exponential growth, and then population growth decreases as resources become depleted, indicating a logistic growth.

Logistic Growth

Exponential growth is possible only when infinite natural resources are available; this is not the case in the real world. Charles Darwin recognized this fact in his description of the “struggle for existence,” which states that individuals will compete (with members of their own or other species) for limited resources. The successful ones will survive to pass on their own characteristics and traits (which we know now are transferred by genes) to the next generation at a greater rate (natural selection). To model the reality of limited resources, population ecologists developed the logistic growth model.

Population Dynamics and Regulation

Abstract:
By the end of this section, you will be able to do the following:

* Give examples of how the carrying capacity of a habitat may change
* Compare and contrast density-dependent growth regulation and density-independent growth regulation, giving examples
* Give examples of exponential and logistic growth in wild animal populations
* Describe how natural selection and environmental adaptation leads to the evolution of particular life-history patterns

Density-Dependent Regulation

Most density-dependent factors are biological in nature (biotic), and include predation, inter- and intraspecific competition, accumulation of waste, and diseases such as those caused by parasites. Usually, the denser a population is, the greater its mortality rate. For example, during intra- and interspecific competition, the reproductive rates of the individuals will usually be lower, reducing their population’s rate of growth. In addition, low prey density increases the mortality of its predator because it has more difficulty locating its food source.

Density-Independent Regulation and Interaction with Density-Dependent Factors

Many factors, typically physical or chemical in nature (abiotic), influence the mortality of a population regardless of its density, including weather, natural disasters, and pollution. An individual deer may be killed in a forest fire regardless of how many deer happen to be in that area. Its chances of survival are the same whether the population density is high or low. The same holds true for cold winter weather.

Life Histories of *K*-selected and *r*-selected Species

While reproductive strategies play a key role in life histories, they do not account for important factors like limited resources and competition. The regulation of population growth by these factors can be used to introduce a classical concept in population biology, that of *K*-selected versus *r*-selected species.

Modern Theories of Life History

By the second half of the twentieth century, the concept of K- and r-selected species was used extensively and successfully to study populations. The *r*- and *K*-selection theory, although accepted for decades and used for much groundbreaking research, has now been reconsidered, and many population biologists have abandoned or modified it. Over the years, several studies attempted to confirm the theory, but these attempts have largely failed. Many species were identified that did not follow the theory’s predictions. Furthermore, the theory ignored the age-specific mortality of the populations which scientists now know is very important. New demographic-based models of life history evolution have been developed which incorporate many ecological concepts included in *r*- and *K*-selection theory as well as population age structure and mortality factors.

Human Population Growth

Abstract:
By the end of this section, you will be able to do the following:

* Discuss exponential human population growth
* Explain how humans have expanded the carrying capacity of their habitat
* Relate population growth and age structure to the level of economic development in different countries
* Discuss the long-term implications of unchecked human population growth

Overcoming Density-Dependent Regulation

Humans are unique in their ability to alter their environment with the conscious purpose of increasing carrying capacity. This ability is a major factor responsible for human population growth and a way of overcoming density-dependent growth regulation. Much of this ability is related to human intelligence, society, and communication. Humans can construct shelter to protect them from the elements and have developed agriculture and domesticated animals to increase their food supplies. In addition, humans use language to communicate this technology to new generations, allowing them to improve upon previous accomplishments.

Age Structure, Population Growth, and Economic Development

The age structure of a population is an important factor in population dynamics. Age structure is the proportion of a population at different age ranges. Age structure allows better prediction of population growth, plus the ability to associate this growth with the level of economic development in the region. Countries with rapid growth have a pyramidal shape in their age structure diagrams, showing a preponderance of younger individuals, many of whom are of reproductive age or will be soon ([link]). This pattern is most often observed in underdeveloped countries where individuals do not live to old age because of less-than-optimal living conditions. Age structures of areas with slow growth, including developed countries such as the United States, still have a pyramidal structure, but with many fewer young and reproductive-aged individuals and a greater proportion of older individuals. Other developed countries, such as Italy, have zero population growth. The age structure of these populations is more conical, with an even greater percentage of middle-aged and older individuals. The actual growth rates in different countries are shown in [link], with the highest rates tending to be in the less economically developed countries of Africa and Asia.

Long-Term Consequences of Exponential Human Population Growth

Many dire predictions have been made about the world’s population leading to a major crisis called the “population explosion.” In the 1968 book *The Population Bomb*, biologist Dr. Paul R. Ehrlich wrote, “The battle to feed all of humanity is over. In the 1970s hundreds of millions of people will starve to death in spite of any crash programs embarked upon now. At this late date nothing can prevent a substantial increase in the world death rate.”[footnote] While many experts view this statement as incorrect based on evidence, the laws of exponential population growth are still in effect, and unchecked human population growth cannot continue indefinitely.

Paul R. Erlich, prologue to *The Population Bomb*, (1968; repr., New York: Ballantine, 1970).

Community Ecology

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the predator-prey cycle
* Give examples of defenses against predation and herbivory
* Describe the competitive exclusion principle
* Give examples of symbiotic relationships between species
* Describe community structure and succession

Predation and Herbivory

Perhaps the classical example of species interaction is predation: the consumption of prey by its predator. Nature shows on television highlight the drama of one living organism killing another. Populations of predators and prey in a community are not constant over time: in most cases, they vary in cycles that appear to be related. The most often cited example of predator-prey dynamics is seen in the cycling of the lynx (predator) and the snowshoe hare (prey), using nearly 200 year-old trapping data from North American forests ([link]). This cycle of predator and prey lasts approximately 10 years, with the predator population lagging 1–2 years behind that of the prey population. As the hare numbers increase, there is more food available for the lynx, allowing the lynx population to increase as well. When the lynx population grows to a threshold level, however, they kill so many hares that hare population begins to decline, followed by a decline in the lynx population because of scarcity of food. When the lynx population is low, the hare population size begins to increase due, at least in part, to low predation pressure, starting the cycle anew.

Competitive Exclusion Principle

Resources are often limited within a habitat and multiple species may compete to obtain them. All species have an ecological niche in the ecosystem, which describes how they acquire the resources they need and how they interact with other species in the community. The competitive exclusion principle states that two species cannot occupy the same niche in a habitat. In other words, different species cannot coexist in a community if they are competing for all the same resources. An example of this principle is shown in [link], with two protozoan species, *Paramecium aurelia* and *Paramecium caudatum*. When grown individually in the laboratory, they both thrive. But when they are placed together in the same test tube (habitat), *P. aurelia* outcompetes *P. caudatum* for food, leading to the latter’s eventual extinction.

Symbiosis

Symbiotic relationships, or symbioses (plural), are close interactions between individuals of different species over an extended period of time which impact the abundance and distribution of the associating populations. Most scientists accept this definition, but some restrict the term to only those species that are mutualistic, where both individuals benefit from the interaction. In this discussion, the broader definition will be used.

Characteristics of Communities

Communities are complex entities that can be characterized by their structure (the types and numbers of species present) and dynamics (how communities change over time). Understanding community structure and dynamics enables community ecologists to manage ecosystems more effectively.

Community Dynamics

Community dynamics are the changes in community structure and composition over time. Sometimes these changes are induced by environmental disturbances such as volcanoes, earthquakes, storms, fires, and climate change. Communities with a stable structure are said to be at equilibrium. Following a disturbance, the community may or may not return to the equilibrium state.

Behavioral Biology: Proximate and Ultimate Causes of Behavior

Abstract:
By the end of this section, you will be able to do the following:

* Compare innate and learned behavior
* Discuss how movement and migration behaviors are a result of natural selection
* Discuss the different ways members of a population communicate with each other
* Give examples of how species use energy for mating displays and other courtship behaviors
* Differentiate between various mating systems
* Describe different ways that species learn

Innate Behaviors: Movement and Migration

Innate or instinctual behaviors rely on response to stimuli. The simplest example of this is a reflex action, an involuntary and rapid response to stimulus. To test the “knee-jerk” reflex, a doctor taps the patellar tendon below the kneecap with a rubber hammer. The stimulation of the nerves leads to the reflex of extending the leg at the knee. This is similar to the reaction of someone who touches a hot stove and instinctually pulls their hand away. Even humans, with our great capacity to learn, still exhibit a variety of innate behaviors.

Innate Behaviors: Living in Groups

Not all animals live in groups, but even those that live relatively solitary lives, with the exception of those that can reproduce asexually, must mate. Mating usually involves one animal signaling another so as to communicate the desire to mate. There are several types of energy-intensive behaviors or displays associated with mating, called mating rituals. Other behaviors found in populations that live in groups are described in terms of which animal benefits from the behavior. In selfish behavior, only the animal in question benefits; in altruistic behavior, one animal’s actions benefit another animal; cooperative behavior describes when both animals benefit. All of these behaviors involve some sort of communication between population members.

Simple Learned Behaviors

The majority of the behaviors previously discussed were innate or at least have an innate component (variations on the innate behaviors may be learned). They are inherited and the behaviors do not change in response to signals from the environment. Conversely, learned behaviors, even though they may have instinctive components, allow an organism to adapt to changes in the environment and are modified by previous experiences. Simple learned behaviors include habituation and imprinting—both are important to the maturation process of young animals.

Conditioned Behavior

Conditioned behaviors are types of associative learning, where a stimulus becomes associated with a consequence. During operant conditioning, the behavioral response is modified by its consequences, with regards to its form, strength, or frequency.

Cognitive Learning

Classical and operant conditioning are inefficient ways for humans and other intelligent animals to learn. Some primates, including humans, are able to learn by imitating the behavior of others and by taking instructions. The development of complex language by humans has made cognitive learning, the manipulation of information using the mind, the most prominent method of human learning. In fact, that is how students are learning right now by reading this book. As students read, they can make mental images of objects or organisms and imagine changes to them, or behaviors by them, and anticipate the consequences. In addition to visual processing, cognitive learning is also enhanced by remembering past experiences, touching physical objects, hearing sounds, tasting food, and a variety of other sensory-based inputs. Cognitive learning is so powerful that it can be used to understand conditioning in detail. In the reverse scenario, conditioning cannot help someone learn about cognition.

Sociobiology

Sociobiology is an interdisciplinary science originally popularized by social insect researcher E.O. Wilson in the 1970s. Wilson defined the science as “the extension of population biology and evolutionary theory to social organization.”[footnote]The main thrust of sociobiology is that animal and human behavior, including aggressiveness and other social interactions, can be explained almost solely in terms of genetics and natural selection. This science is controversial; noted scientists such as the late Stephen Jay Gould criticized the approach for ignoring the environmental effects on behavior. This is another example of the “nature versus nurture” debate of the role of genetics versus the role of environment in determining an organism’s characteristics.

Edward O. Wilson. *On Human Nature* (1978; repr., Cambridge: Harvard University Press, 2004), xx.

Ecosystems

Introduction

Ecology of Ecosystems

Abstract:
By the end of this section, you will be able to do the following:

* Describe the basic ecosystem types
* Explain the methods that ecologists use to study ecosystem structure and dynamics
* Identify the different methods of ecosystem modeling
* Differentiate between food chains and food webs and recognize the importance of each

Food Chains and Food Webs

The term “food chain” is sometimes used metaphorically to describe human social situations. Individuals who are considered successful are seen as being at the top of the food chain, consuming all others for their benefit, whereas the less successful are seen as being at the bottom.

Research into Ecosystem Dynamics: Ecosystem Experimentation and Modeling

The study of the changes in ecosystem structure caused by changes in the environment (disturbances) or by internal forces is called ecosystem dynamics. Ecosystems are characterized using a variety of research methodologies. Some ecologists study ecosystems using controlled experimental systems, while some study entire ecosystems in their natural state, and others use both approaches.

Energy Flow through Ecosystems

Abstract:
By the end of this section, you will be able to do the following:

* Describe how organisms acquire energy in a food web and in associated food chains
* Explain how the efficiency of energy transfers between trophic levels affects ecosystem structure and dynamics
* Discuss trophic levels and how ecological pyramids are used to model them

How Organisms Acquire Energy in a Food Web

Energy is acquired by living things in three ways: photosynthesis, chemosynthesis, and the consumption and digestion of other living or previously living organisms by heterotrophs.

Productivity within Trophic Levels

Productivity within an ecosystem can be defined as the percentage of energy entering the ecosystem incorporated into biomass in a particular trophic level. Biomass is the total mass, in a unit area at the time of measurement, of living or previously living organisms within a trophic level. Ecosystems have characteristic amounts of biomass at each trophic level. For example, in the English Channel ecosystem the primary producers account for a biomass of 4 g/m2 (grams per square meter), while the primary consumers exhibit a biomass of 21 g/m2.

Ecological Efficiency: The Transfer of Energy between Trophic Levels

As illustrated in ([link]), as energy flows from primary producers through the various trophic levels, the ecosystem loses large amounts of energy. The main reason for this loss is the second law of thermodynamics, which states that whenever energy is converted from one form to another, there is a tendency toward disorder (entropy) in the system. In biologic systems, this energy takes the form of metabolic heat, which is lost when the organisms consume other organisms. In the Silver Springs ecosystem example ([link]), we see that the primary consumers produced 1103 kcal/m2/yr from the 7618 kcal/m2/yr of energy available to them from the primary producers. The measurement of energy transfer efficiency between two successive trophic levels is termed the trophic level transfer efficiency (TLTE) and is defined by the formula:

Modeling Ecosystems Energy Flow: Ecological Pyramids

The structure of ecosystems can be visualized with ecological pyramids, which were first described by the pioneering studies of Charles Elton in the 1920s. Ecological pyramids show the relative amounts of various parameters (such as number of organisms, energy, and biomass) across trophic levels.

Consequences of Food Webs: Biological Magnification

One of the most important environmental consequences of ecosystem dynamics is biomagnification. Biomagnification is the increasing concentration of persistent, toxic substances in organisms at each trophic level, from the primary producers to the apex consumers. Many substances have been shown to bioaccumulate, including the pesticide **d**ichloro**d**iphenyl**t**richloroethane (DDT), which was described in the 1960s bestseller, *Silent Spring*, by marine biologist Rachel Carson. DDT was a commonly used pesticide before its dangers became known. In some aquatic ecosystems, organisms from each trophic level consumed many organisms of the lower level, which caused DDT to increase in birds (apex consumers) that ate fish. Thus, the birds accumulated sufficient amounts of DDT to cause fragility in their eggshells. This effect increased egg breakage during nesting and was shown to have adverse effects on these bird populations. Carson's combination of scientific knowledge and illuminating writing helped raise awareness about overall environmental issues as well as the specifics of the pesticide. The use of DDT was banned in the United States in the 1970s.

Biogeochemical Cycles

Abstract:
By the end of this section, you will be able to do the following:

* Discuss the biogeochemical cycles of water, carbon, nitrogen, phosphorus, and sulfur
* Explain how human activities have impacted these cycles and the potential consequences for Earth

The Water (Hydrologic) Cycle

Water is the basis of all living processes on Earth. When examining the stores of water on Earth, 97.5 percent of it is non-potable salt water ([link]). Of the remaining water, 99 percent is locked underground as water or as ice. Thus, less than 1 percent of fresh water is easily accessible from lakes and rivers. Many living things, such as plants, animals, and fungi, are dependent on that small amount of fresh surface water, a lack of which can have massive effects on ecosystem dynamics. To be successful, organisms must adapt to fluctuating water supplies. Humans, of course, have developed technologies to increase water availability, such as digging wells to harvest groundwater, storing rainwater, and using desalination to obtain drinkable water from the ocean.

The Carbon Cycle

Carbon is the second most abundant element in living organisms. Carbon is present in all organic molecules, and its role in the structure of macromolecules is of primary importance to living organisms.

The Nitrogen Cycle

Getting nitrogen into the living world is difficult. Plants and phytoplankton are not equipped to incorporate nitrogen from the atmosphere (which exists as tightly bonded, triple covalent N2) even though this molecule comprises approximately 78 percent of the atmosphere. Nitrogen enters the living world via free-living and symbiotic bacteria, which incorporate nitrogen into their macromolecules through nitrogen fixation (conversion of N2). Cyanobacteria live in most aquatic ecosystems where sunlight is present; they play a key role in nitrogen fixation. Cyanobacteria are able to use inorganic sources of nitrogen to “fix” nitrogen. *Rhizobium* bacteria live symbiotically in the root nodules of legumes (such as peas, beans, and peanuts) and provide them with the organic nitrogen they need. (For example, gardeners often grow peas both for their produce and to naturally add nitrogen to the soil. This practice goes back to ancient times, even if the science has only been recently understood.) Free-living bacteria, such as *Azotobacter*, are also important nitrogen fixers.

The Phosphorus Cycle

Phosphorus is an essential nutrient for living processes; it is a major component of nucleic acid and phospholipids, and, as calcium phosphate, makes up the supportive components of our bones. Phosphorus is often the limiting nutrient (necessary for growth) in aquatic ecosystems ([link]).

The Sulfur Cycle

Sulfur is an essential element for the macromolecules of living things. As a part of the amino acid cysteine, it is involved in the formation of disulfide bonds within proteins, which help to determine their 3-D folding patterns, and hence their functions. As shown in [link], sulfur cycles between the oceans, land, and atmosphere. Atmospheric sulfur is found in the form of sulfur dioxide (SO2) and enters the atmosphere in three ways: from the decomposition of organic molecules, from volcanic activity and geothermal vents, and from the burning of fossil fuels by humans.

Conservation Biology and Biodiversity

Introduction

The Biodiversity Crisis

Abstract:
By the end of this section, you will be able to do the following:

* Define biodiversity in terms of species diversity and abundance
* Describe biodiversity as the equilibrium of naturally fluctuating rates of extinction and speciation
* Identify historical causes of high extinction rates in Earth’s history

Types of Biodiversity

Scientists generally accept that the term biodiversity describes the number and kinds of species and their abundance in a given location or on the planet. Species can be difficult to define, but most biologists still feel comfortable with the concept and are able to identify and count eukaryotic species in most contexts. Biologists have also identified alternate measures of biodiversity, some of which are important for planning how to preserve biodiversity.

Biodiversity Change through Geological Time

The number of species on the planet, or in any geographical area, is the result of an equilibrium of two evolutionary processes that are continuously ongoing: *speciation* and *extinction*. Both are natural “birth” and “death” processes of macroevolution. When speciation rates begin to outstrip extinction rates, the number of species will increase; likewise, the number of species will decrease when extinction rates begin to overtake speciation rates. Throughout Earth’s history, these two processes have fluctuated—sometimes leading to dramatic changes in the number of species on Earth as reflected in the fossil record ([link]).

The Importance of Biodiversity to Human Life

Abstract:
By the end of this section, you will be able to do the following:

* Identify chemical diversity benefits to humans
* Identify biodiversity components that support human agriculture
* Describe ecosystem services

Human Health

Archeological evidence indicates that humans have been using plants for medicinal uses for thousands of years. A Chinese document from approximately 2800 BC is believed to be the first written account of herbal remedies, and such references occur throughout the global historical record. Contemporary indigenous societies that live close to the land often retain broad knowledge of the medicinal uses of plants growing in their area. Most plants produce secondary plant compounds, which are toxins used to protect the plant from insects and other animals that eat them, but some of which also work as medication.

Agricultural Diversity

Since the beginning of human agriculture more than 10,000 years ago, human groups have been breeding and selecting crop varieties. This crop diversity matched the cultural diversity of highly subdivided populations of humans. For example, potatoes were domesticated beginning around 7,000 years ago in the central Andes of Peru and Bolivia. The potatoes grown in that region belong to seven species and the number of varieties likely is in the thousands. Even the Inca capital of Machu Picchu had numerous gardens growing varieties of potatoes. Each variety has been bred to thrive at particular elevations and soil and climate conditions. The diversity is driven by the diverse demands of the topography, the limited movement of people, and the demands created by crop rotation for different varieties that will do well in different fields.

Wild Food Sources

In addition to growing crops and raising animals for food, humans obtain food resources from wild populations, primarily fish populations. In fact, for approximately 1 billion people worldwide, aquatic resources provide the main source of animal protein. But since 1990, global fish production has declined, sometimes dramatically. Unfortunately, and despite considerable effort, few fisheries on the planet are managed for sustainability.

Psychological and Moral Value

Finally, it has been clearly shown that humans benefit psychologically from living in a biodiverse world. A chief proponent of this idea is Harvard entomologist E. O. Wilson. He argues that human evolutionary history has adapted us to live in a natural environment and that city environments generate psychological stressors that affect human health and well-being. There is considerable research into the psychological regenerative benefits of natural landscapes that suggests the hypothesis may hold some truth. In addition, there is a moral argument that humans have a responsibility to inflict as little harm as possible on other species.

Threats to Biodiversity

Abstract:
By the end of this section, you will be able to do the following:

* Identify significant threats to biodiversity
* Explain the effects of habitat loss, the introduction of exotic species, and hunting on biodiversity
* Identify the early and predicted effects of climate change on biodiversity

Habitat Loss

Humans rely on technology to modify their environment and replace certain functions that were once performed by the natural ecosystem. Other species cannot do this. Elimination of their ecosystem—whether it is a forest, a desert, a grassland, a freshwater estuarine, or a marine environment—will kill the individuals belonging to the species. The species will become extinct if we remove the entire habitat within the range of a species. Human destruction of habitats accelerated in the latter half of the twentieth century. Consider the exceptional biodiversity of Sumatra: it is home to one species of orangutan, a species of critically endangered elephant, and the Sumatran tiger, but half of Sumatra’s forest is now gone. The neighboring island of Borneo, home to the other species of orangutan, has lost a similar area of forest. Forest loss continues in protected areas of Borneo. All three species of orangutan are now listed as endangered by the International Union for Conservation of Nature (IUCN), but they are simply the most visible of thousands of species that will not survive the disappearance of the forests in Sumatra and Borneo. The forests are removed for timber and to plant palm oil plantations ([link]). Palm oil is used in many products including food products, cosmetics, and biodiesel in Europe. A five-year estimate of global forest cover loss for the years 2000–2005 was 3.1 percent. In the humid tropics where forest loss is primarily from timber extraction, 272,000 km2 was lost out of a global total of 11,564,000 km2 (or 2.4 percent). In the tropics, these losses certainly also represent the extinction of species because of high levels of endemism—species unique to a defined geographic location, and found nowhere else.

Overharvesting

Overharvesting is a serious threat to many species, but particularly to aquatic (both marine and freshwater) species. Despite regulation and monitoring, there are recent examples of fishery collapse. The western Atlantic cod fishery is the among the most significant. While it was a hugely productive fishery for 400 years, the introduction of modern factory trawlers in the 1980s caused it to become unsustainable. Fisheries collapse as a result of both economic and political factors. Fisheries are managed as a shared international resource even when the fishing territory lies within an individual country’s territorial waters. Common resources are subject to an economic pressure known as the tragedy of the commons, in which essentially no fisher has a motivation to exercise restraint in harvesting a fishery when it is not owned by that fisher. Overexploitation is a common outcome. This overexploitation is exacerbated when access to the fishery is open and unregulated and when technology gives fishers the ability to overfish. In a few fisheries, the biological growth of the resource is less than the potential growth of the profits made from fishing if that time and money were invested elsewhere. In these cases—whales are an example—economic forces will always drive toward fishing the population to extinction.

Exotic Species

Exotic species are species that have been intentionally or unintentionally introduced into an ecosystem in which they did not evolve. For example, Kudzu (*Pueraria lobata*), which is native to Japan, was introduced in the United States in 1876. It was later planted for soil conservation. Problematically, it grows too well in the southeastern United States—up to a foot a day. It is now an invasive pest species and covers over 7 million acres in the southeastern United States. If an introduced species is able to survive in its new habitat, that introduction is now reflected in the observed range of the species. Human transportation of people and goods, including the intentional transport of organisms for trade, has dramatically increased the introduction of species into new ecosystems, sometimes at distances that are well beyond the capacity of the species to ever travel itself and outside the range of the species’ natural predators.

Climate Change

Climate change, and specifically the *anthropogenic* (meaning, caused by humans) warming trend presently escalating, is recognized as a major extinction threat, particularly when combined with other threats such as habitat loss and the expansion of disease organisms. Scientists disagree about the likely magnitude of the effects, with extinction rate estimates ranging from 15 percent to 40 percent of species destined for extinction by 2050. Scientists do agree, however, that climate change will alter regional climates, including rainfall and snowfall patterns, making habitats less hospitable to the species living in them, in particular, the endemic species. The warming trend will shift colder climates toward the north and south poles, forcing species to move with their adapted climate norms while facing habitat gaps along the way. The shifting ranges will impose new competitive regimes on species as they find themselves in contact with other species not present in their historic range. One such unexpected species contact is between polar bears and grizzly bears. Previously, these two distinct species had separate ranges. Now, their ranges are overlapping and there are documented cases of these two species mating and producing viable offspring, which may or may not be viable crossing back to either parental species. Changing climates also throw off species’ delicate timed adaptations to seasonal food resources and breeding times. Many contemporary mismatches to shifts in resource availability and timing have already been documented.

Preserving Biodiversity

Abstract:
By the end of this section, you will be able to do the following:

* Identify new technologies and methods for describing biodiversity
* Explain the legislative framework for conservation
* Describe principles and challenges of conservation preserve design
* Identify examples of the effects of habitat restoration
* Discuss the role of zoos in biodiversity conservation

Measuring Biodiversity

The technology of molecular genetics and data processing and storage are maturing to the point where cataloguing the planet’s species in an accessible way is now feasible. DNA barcoding is one molecular genetic method, which takes advantage of rapid evolution in a mitochondrial gene (cytochrome c oxidase 1) present in eukaryotes, except for plants, to identify species using the sequence of portions of the gene. However, plants may be barcoded using a combination of chloroplast genes. Rapid mass sequencing machines make the molecular genetics portion of the work relatively inexpensive and quick. Computer resources store and make available the large volumes of data. Projects are currently underway to use DNA barcoding to catalog museum specimens, which have already been named and studied, as well as testing the method on less-studied groups. As of mid 2017, close to 200,000 named species had been barcoded. Early studies suggest there are significant numbers of undescribed species that looked too much like sibling species to previously be recognized as different. These now can be identified with DNA barcoding.

Changing Human Behavior

Legislation throughout the world has been enacted to protect species. The legislation includes international treaties as well as national and state laws. The Convention on International Trade in Endangered Species of Wild Fauna and Flora **(CITES)** treaty came into force in 1975. The treaty, and the national legislation that supports it, provides a legal framework for preventing approximately 33,000 listed species from being transported across nations’ borders, thus protecting them from being caught or killed when international trade is involved. The treaty is limited in its reach because it only deals with international movement of organisms or their parts. It is also limited by various countries’ ability or willingness to *enforce* the treaty and supporting legislation. The illegal trade in organisms and their parts is probably a market in the hundreds of millions of dollars. Illegal wildlife trade is monitored by another non-profit: Trade Records Analysis of Flora and Fauna in Commerce **(TRAFFIC)**.

Conservation in Preserves

Establishment of wildlife and ecosystem preserves is one of the key tools in conservation efforts. A preserve is an area of land set aside with varying degrees of protection for the organisms that exist within the boundaries of the preserve. Preserves can be effective in the short term for protecting both species and ecosystems, but they face challenges that scientists are still exploring to strengthen their viability as long-term solutions to the preservation of biodiversity *and* the prevention of extinction.

The Periodic Table of Elements

Geological Time

Measurements and the Metric System