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About *Concepts of Biology*

*Concepts of Biology* is designed for the single-semester introduction to biology course for non-science majors, which for many students is their only college-level science course. As such, this course represents an important opportunity for students to develop the necessary knowledge, tools, and skills to make informed decisions as they continue with their lives. Rather than being mired down with facts and vocabulary, the typical non-science major student needs information presented in a way that is easy to read and understand. Even more importantly, the content should be meaningful. Students do much better when they understand why biology is relevant to their everyday lives. For these reasons,
*Concepts of Biology* 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. We also strive to show the interconnectedness of topics within this extremely broad discipline. In order to meet the needs of today’s instructors and students, we maintain the overall organization and coverage found in most syllabi for this course. A strength of
*Concepts of Biology* is that instructors can customize the book, adapting it to the approach that works best in their classroom. Concepts of 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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Learning Resources

**Wiley Plus for Biology-Fall 2013 Pilot** WileyPLUS provides an engaging online environment for effective teaching and learning. WileyPLUS builds students’ confidence because it takes the guesswork out of studying by providing a clear roadmap; what to do, how to do it, and if they did it right. With WileyPLUS, students take more initiative. Therefore, the course has a greater impact on their learning experience. Adaptive tools provide students with a personal, adaptive learning experience so they can build their proficiency on topics and use their study time most effectively. Please let us know if you would like to participate in a Fall 2013 Pilot.

Additional Resources

The Cellular Foundation of Life

Introduction to Biology

Introduction

Themes and Concepts of Biology

Abstract:
By the end of this section, you will be able to:
* Identify and describe the properties of life
* Describe the levels of organization among living things
* List examples of different sub disciplines in biology

Properties of Life

All groups of living organisms share several key characteristics or functions: order, sensitivity or response to stimuli, 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 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 a chemical bond. Many molecules that are biologically important are macromolecules, large molecules that are typically formed by combining smaller units called monomers. An example of a macromolecule is deoxyribonucleic acid (DNA) ([link]), which contains the instructions for the functioning of the organism that contains it.

The Diversity of Life

The science of biology is very broad in scope because there is a tremendous diversity of life on Earth. The source of this diversity is evolution, the process of gradual change during which new species arise from older species. 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 sub disciplines. Biologists may pursue one of those sub disciplines and work in a more focused field. For instance, molecular biology studies biological processes at the molecular level, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they are regulated. Microbiology is the study of the structure and function of microorganisms. 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 Process of Science

Abstract:
By the end of this section, you will be able to:
* Identify the shared characteristics of the natural sciences
* Understand the process of scientific inquiry
* Compare inductive reasoning with deductive reasoning
* Describe the goals of basic science and applied science

The Nature of Science

Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines? Science (from the Latin *scientia,* meaning "knowledge") can be defined as knowledge about the natural world.

Hypothesis Testing

Biologists study the living world by posing questions about it and seeking science-based responses. This approach is common to other sciences as well and is often referred to as the scientific method. The scientific method was used even in ancient times, but it was first documented by England’s Sir Francis Bacon (1561–1626) ([link]), who set up inductive methods for scientific inquiry. The scientific method is not exclusively used by biologists but can be applied to almost anything as a logical problem-solving method.

Basic 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 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 for other researchers to expand and build upon their discoveries. Communication and collaboration within and between sub disciplines of science are key to the advancement of knowledge in science. For this reason, an important aspect of a scientist’s work is disseminating results and communicating with peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the limited few who are present. Instead, most scientists present their results in peer-reviewed articles that are published in scientific journals. Peer-reviewed articles are scientific papers that are reviewed, usually anonymously by a scientist’s colleagues, or peers. 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 described 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.

Chemistry of Life

Introduction

The Building Blocks of Molecules

Abstract:
By the end of this section, you will be able to:
* Describe matter and elements
* Describe the interrelationship between protons, neutrons, and electrons, and the ways in which electrons can be donated or shared between atoms

Atoms

An atom is the smallest component of an element that retains all of the chemical properties of that element. For example, one hydrogen atom has all of the properties of the element hydrogen, such as it exists as a gas at room temperature, and it bonds with oxygen to create a water molecule. Hydrogen atoms cannot be broken down into anything smaller while still retaining the properties of hydrogen. If a hydrogen atom were broken down into subatomic particles, it would no longer have the properties of hydrogen.

Chemical Bonds

How elements interact with one another depends on how their electrons are arranged and how many openings for electrons exist at the outermost region where electrons are present in an atom. Electrons exist at energy levels that form shells around the nucleus. The closest shell can hold up to two electrons. The closest shell to the nucleus is always filled first, before any other shell can be filled. Hydrogen has one electron; therefore, it has only one spot occupied within the lowest shell. Helium has two electrons; therefore, it can completely fill the lowest shell with its two electrons. If you look at the periodic table, you will see that hydrogen and helium are the only two elements in the first row. This is because they only have electrons in their first shell. Hydrogen and helium are the only two elements that have the lowest shell and no other shells.

Water

Abstract:
By the end of this section, you will be able to:
* Describe the properties of water that are critical to maintaining life

Water Is Polar

The hydrogen and oxygen atoms within water molecules form polar covalent bonds. The shared electrons spend more time associated with the oxygen atom than they do with hydrogen atoms. There is no overall charge to a water molecule, but there is a slight positive charge on each hydrogen atom and a slight negative charge on the oxygen atom. Because of these charges, the slightly positive hydrogen atoms repel each other and form the unique shape seen in [link]. Each water molecule attracts other water molecules because of the positive and negative charges in the different parts of the molecule. Water also attracts other polar molecules (such as sugars), forming hydrogen bonds. When a substance readily forms hydrogen bonds with water, it can dissolve in water and is referred to as hydrophilic (“water-loving”). Hydrogen bonds are not readily formed with nonpolar substances like oils and fats ([link]). These nonpolar compounds are hydrophobic (“water-fearing”) and will not dissolve in water.

Water Stabilizes Temperature

The hydrogen bonds in water allow it to absorb and release heat energy more slowly than many other substances. Temperature is a measure of the motion (kinetic energy) of molecules. As the motion increases, energy is higher and thus temperature is higher. Water absorbs a great deal of energy before its temperature rises. Increased energy disrupts the hydrogen bonds between water molecules. Because these bonds can be created and disrupted rapidly, water absorbs an increase in energy and temperature changes only minimally. This means that water moderates temperature changes within organisms and in their environments. As energy input continues, the balance between hydrogen-bond formation and destruction swings toward the destruction side. More bonds are broken than are formed. This process results in the release of individual water molecules at the surface of the liquid (such as a body of water, the leaves of a plant, or the skin of an organism) in a process called evaporation. Evaporation of sweat, which is 90 percent water, allows for cooling of an organism, because breaking hydrogen bonds requires an input of energy and takes heat away from the body.

Water Is an Excellent Solvent

Because water is polar, with slight positive and negative charges, ionic compounds and polar molecules can readily dissolve in it. Water is, therefore, what is referred to as a solvent—a substance capable of dissolving another substance. The charged particles will form hydrogen bonds with a surrounding layer of water molecules. This is referred to as a sphere of hydration and serves to keep the particles separated or dispersed in the water. In the case of table salt (NaCl) mixed in water ([link]), the sodium and chloride ions separate, or dissociate, in the water, and spheres of hydration are formed around the ions. A positively charged sodium ion is surrounded by the partially negative charges of oxygen atoms in water molecules. A negatively charged chloride ion is surrounded by the partially positive charges of hydrogen atoms in water molecules. These spheres of hydration are also referred to as hydration shells. The polarity of the water molecule makes it an effective solvent and is important in its many roles in living systems.

Water Is Cohesive

Have you ever filled up a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water actually 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-air (gas) interface, although there is no more room in the glass. Cohesion gives rise to surface tension, the capacity of a substance to withstand rupture when placed under tension or stress. When you drop a small scrap of paper onto a droplet of water, the paper floats on top of the water droplet, although the object is denser (heavier) than the water. This occurs because of the surface tension that is created by the water molecules. Cohesion and surface tension keep the water molecules intact and the item floating on the top. It is even possible to “float” a steel needle on top of a glass of water if you place it gently, without breaking the surface tension ([link]).

Buffers, pH, Acids, and Bases

The pH of a solution is a measure of its acidity or bascicity. You have probably used litmus paper, paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator, to test how much acid or base (basicity) exists in a solution. You might have even used some to make sure the water in an outdoor swimming pool is properly treated. In both cases, this pH test measures the amount of hydrogen ions that exists in a given solution. High concentrations of hydrogen ions yield a low pH, whereas low levels of hydrogen ions result in a high pH. The overall concentration of hydrogen ions is inversely related to its pH and can be measured on the pH scale ([link]). Therefore, the more hydrogen ions present, the lower the pH; conversely, the fewer hydrogen ions, the higher the pH.

Biological Molecules

Abstract:
By the end of this section, you will be able to:
* Describe the ways in which carbon is critical to life
* Explain the impact of slight changes in amino acids on organisms
* Describe the four major types of biological molecules
* Understand the functions of the four major types of molecules

Carbon

It is often said that life is “carbon-based.” This means that carbon atoms, bonded to other carbon atoms or other elements, form the fundamental components of many, if not most, of the molecules found uniquely in living things. Other elements play important roles in biological molecules, but carbon certainly qualifies as the “foundation” element for molecules in living things. It is the bonding properties of carbon atoms that are responsible for its important role.

Carbon Bonding

Carbon contains four electrons in its outer shell. Therefore, it can form four covalent bonds with other atoms or molecules. The simplest organic carbon molecule is methane (CH4), in which four hydrogen atoms bind to a carbon atom ([link]).

Carbohydrates

Carbohydrates are macromolecules with which most consumers are somewhat familiar. To lose weight, some individuals adhere to “low-carb” diets. Athletes, in contrast, often “carb-load” before important competitions to ensure that they have sufficient energy to compete at a high level. Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources of carbohydrates. Carbohydrates provide energy to the body, particularly through glucose, a simple sugar. Carbohydrates also have other important functions in humans, animals, and plants.

Lipids

Lipids include a diverse group of compounds that are united by a common feature. Lipids are hydrophobic (“water-fearing”), or insoluble in water, because they are nonpolar molecules. This is because they are hydrocarbons that include only nonpolar carbon-carbon or carbon-hydrogen bonds. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of lipids called fats. Lipids also provide insulation from the environment for plants and animals ([link]). For example, they help keep aquatic birds and mammals dry because of their water-repelling nature. Lipids are also the building blocks of many hormones and are an important constituent of the plasma membrane. Lipids include fats, oils, waxes, phospholipids, and steroids.

Proteins

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of different proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence.

Nucleic Acids

Nucleic acids are key macromolecules in the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell.

DNA Double-Helical Structure

DNA has a double-helical structure ([link]). It is composed of two strands, or polymers, of nucleotides. The strands are formed with bonds between phosphate and sugar groups of adjacent nucleotides. The strands are bonded to each other at their bases with hydrogen bonds, and the strands coil about each other along their length, hence the “double helix” description, which means a double spiral.

Cell Structure and Function

Introduction

How Cells Are Studied

Abstract:
By the end of this section, you will be able to:
* Describe the roles of cells in organisms
* Compare and contrast light microscopy and electron microscopy
* Summarize the cell theory

Microscopy

Cells vary in size. With few exceptions, individual cells are too small to be seen with the naked eye, so scientists use microscopes to study them. A microscope is an instrument that magnifies an object. Most images of cells are taken with a microscope and are called micrographs.

Cell Theory

The microscopes we use today are far more complex than those used in the 1600s by Antony van Leeuwenhoek, a Dutch shopkeeper who had great skill in crafting lenses. Despite the limitations of his now-ancient lenses, van Leeuwenhoek observed the movements of protists (a type of single-celled organism) and sperm, which he collectively termed “animalcules.”

Comparing Prokaryotic and Eukaryotic Cells

Abstract:
By the end of this section, you will be able to:
* Name examples of prokaryotic and eukaryotic organisms
* Compare and contrast prokaryotic cells and eukaryotic cells
* Describe the relative sizes of different kinds of cells

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 region within the cell in which other cellular components are found; 3) DNA, the genetic material of the cell; and 4) ribosomes, particles that synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways.

Eukaryotic Cells

In nature, the relationship between form and function is apparent at all levels, including the level of the cell, and this will become clear as we explore eukaryotic cells. The principle “form follows function” is found in many contexts. For example, birds and fish have streamlined bodies that allow them to move quickly through the medium in which they live, be it air or water. It means that, in general, one can deduce the function of a structure by looking at its form, because the two are matched.

Cell Size

At 0.1–5.0 µm in diameter, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10–100 µm ([link]). The small size of prokaryotes allows ions and organic molecules that enter them to quickly spread to other parts of the cell. Similarly, any wastes produced within a prokaryotic cell can quickly move out. However, larger eukaryotic cells have evolved different structural adaptations to enhance cellular transport. Indeed, the large size of these cells would not be possible without these adaptations. In general, cell size is limited because volume increases much more quickly than does cell surface area. As a cell becomes larger, it becomes more and more difficult for the cell to acquire sufficient materials to support the processes inside the cell, because the relative size of the surface area across which materials must be transported declines.

Eukaryotic Cells

Abstract:
By the end of this section, you will be able to:
* Describe the structure of eukaryotic plant and animal cells
* State the role of the plasma membrane
* Summarize the functions of the major cell organelles
* Describe the cytoskeleton and extracellular matrix

The Plasma Membrane

Like prokaryotes, eukaryotic cells have a plasma membrane ([link]) made up of a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule composed of two fatty acid chains, a glycerol backbone, and a phosphate group. The plasma membrane regulates the passage of some substances, such as organic molecules, ions, and water, preventing the passage of some to maintain internal conditions, while actively bringing in or removing others. Other compounds move passively across the membrane.

The Cytoplasm

The cytoplasm comprises the contents of a cell between the plasma membrane and the nuclear envelope (a structure to be discussed shortly). It is made up 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 found in the cytoplasm. Glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are found there too. Ions of sodium, potassium, calcium, and many other elements are also dissolved in the cytoplasm. Many metabolic reactions, including protein synthesis, take place in the cytoplasm.

The Cytoskeleton

If you were to remove all the organelles from a cell, would the plasma membrane and the cytoplasm be the only components left? No. Within the cytoplasm, there would still be ions and organic molecules, plus a network of protein fibers that helps to maintain the shape of the cell, secures certain organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independently. Collectively, this network of protein fibers is known as the cytoskeleton. There are three types of fibers within the cytoskeleton: microfilaments, also known as actin filaments, intermediate filaments, and microtubules ([link]).

The Endomembrane System

The endomembrane system (*endo* = within) is a group of membranes and organelles ([link]) in eukaryotic cells that work together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, and vesicles, the endoplasmic reticulum and Golgi apparatus, which we will cover shortly. Although not technically *within* the cell, the plasma membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous organelles.

Ribosomes

Ribosomes are the cellular structures responsible for protein synthesis. When viewed through an electron microscope, free ribosomes appear as either clusters or single tiny dots floating freely in the cytoplasm. Ribosomes may be attached to either the cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum ([link]). Electron microscopy has shown that ribosomes consist of large and small subunits. Ribosomes are enzyme complexes that are responsible for protein synthesis.

Mitochondria

Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. The formation of ATP from the breakdown of glucose is known as cellular respiration. Mitochondria are oval-shaped, double-membrane organelles ([link]) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae, which increase the surface area of the inner membrane. The area surrounded by the folds is called the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration.

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. Alcohol is detoxified by peroxisomes in liver cells. A byproduct of these oxidation reactions is hydrogen peroxide, H2O2, which is contained within the peroxisomes to prevent the chemical from causing damage to cellular components outside of the organelle. Hydrogen peroxide is safely broken down by peroxisomal enzymes into water and oxygen.

Animal Cells versus Plant Cells

Despite their fundamental similarities, there are some striking differences between animal and plant cells (see [link]). Animal cells have centrioles, centrosomes (discussed under the cytoskeleton), and lysosomes, whereas plant cells do not. Plant cells have a cell wall, chloroplasts, plasmodesmata, and plastids used for storage, and a large central vacuole, whereas animal cells do not.

Extracellular Matrix of Animal Cells

Most animal cells release materials into the extracellular space. The primary components of these materials are glycoproteins and the protein collagen. Collectively, these materials are called 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.

Intercellular Junctions

Cells can also communicate with each other by direct contact, referred to as intercellular junctions. There are some differences in the ways that plant and animal cells do this. Plasmodesmata (singular = plasmodesma) are junctions between plant cells, whereas animal cell contacts include tight and gap junctions, and desmosomes.

The Cell Membrane

Abstract:
By the end of this section, you will be able to:
* Understand the fluid mosaic model of membranes
* Describe the functions of phospholipids, proteins, and carbohydrates in membranes

Fluid Mosaic Model

In 1972, S. J. Singer and Garth L. Nicolson proposed a new model of the plasma membrane that, compared to earlier understanding, better explained both microscopic observations and the function of the plasma membrane. This was called the fluid mosaic model. The model has evolved somewhat over time, but still best accounts for the structure and functions of the plasma membrane as we now understand them. The fluid mosaic model describes the structure of the plasma membrane as a mosaic of components—including phospholipids, cholesterol, proteins, and carbohydrates—in which the components are able to flow and change position, while maintaining the basic integrity of the membrane. Both phospholipid molecules and embedded proteins are able to diffuse rapidly and laterally in the membrane. The fluidity of the plasma membrane is necessary for the activities of certain enzymes and transport molecules within the membrane. Plasma membranes range from 5–10 nm thick. As a comparison, human red blood cells, visible via light microscopy, are approximately 8 µm thick, or approximately 1,000 times thicker than a plasma membrane. ([link])

Passive Transport

Abstract:
By the end of this section, you will be able to:
* Explain why and how passive transport occurs
* Understand the processes of osmosis and diffusion
* Define tonicity and describe its relevance to passive transport

Selective Permeability

Plasma membranes are asymmetric, meaning that despite the mirror image formed by the phospholipids, the interior of the membrane is not identical to the exterior of the membrane. Integral proteins that act as channels or pumps work in one direction. Carbohydrates, attached to lipids or proteins, are also found on the exterior surface of the plasma membrane. These carbohydrate complexes help the cell bind substances that the cell needs in the extracellular fluid. This adds considerably to the selective nature of plasma membranes.

Diffusion

Diffusion is a passive process of transport. A single substance tends to move from an area of high concentration to an area of low concentration until the concentration is equal across the space. You are familiar with diffusion of substances through the air. For example, think about someone opening a bottle of perfume in a room filled with people. The perfume is at its highest concentration in the bottle and is at its lowest at the edges of the room. The perfume vapor will diffuse, or spread away, from the bottle, and gradually, more and more people will smell the perfume 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. Rather the different concentrations of materials in different areas are a form of potential energy, and diffusion is the dissipation of that potential energy as materials move down their concentration gradients, from high to low.

Facilitated transport

In facilitated transport, also called facilitated diffusion, material moves across the plasma membrane with the assistance of transmembrane proteins down a concentration gradient (from high to low concentration) without the expenditure of cellular energy. However, the substances that undergo facilitated transport would otherwise not diffuse easily or quickly across the plasma membrane. The solution to moving polar substances and other substances across the plasma membrane rests in the proteins that span its surface. The material being transported is first attached to protein or glycoprotein receptors on the exterior surface of the plasma membrane. This allows the material that is needed by the cell to be removed from the extracellular fluid. The substances are then passed to specific integral proteins that facilitate their passage, because they form channels or pores that allow certain substances to pass through the membrane. The integral proteins involved in facilitated transport are collectively referred to as transport proteins, and they function as either channels for the material or carriers.

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. Whereas diffusion transports material across membranes and within cells, osmosis transports *only water* across a membrane and the membrane limits the diffusion of solutes in the water. Osmosis is a special case of diffusion. Water, like other substances, moves from an area of high concentration of free water molecules to one of low free water molecule concentration. Imagine a beaker with a semipermeable membrane, separating the two sides or halves ([link]). On both sides of the membrane, the water level is the same, but there are different concentrations on each side of a dissolved substance, or solute, that cannot cross the membrane. If the volume of the water is the same, but the concentrations of solute are different, then there are also different concentrations of water, the solvent, on either side of the membrane.

Tonicity

Tonicity describes the amount of solute in a solution. The measure of the tonicity of a solution, or the total amount of solutes dissolved in a specific amount of solution, is called its osmolarity. Three terms—hypotonic, isotonic, and hypertonic—are used to relate the osmolarity of a cell to the osmolarity of the extracellular fluid that contains the cells. In a hypotonic solution, such as tap water, the extracellular fluid has a lower concentration of solutes than the fluid inside the cell, and water enters the cell. (In living systems, the point of reference is always the cytoplasm, so the prefix *hypo*- means that the extracellular fluid has a lower concentration of solutes, or a lower osmolarity, than the cell cytoplasm.) It also means that the extracellular fluid has a higher concentration of water than does the cell. In this situation, water will follow its concentration gradient and enter the cell. This may cause an animal cell to burst, or lyse.

Active Transport

Abstract:
By the end of this section, you will be able to:
* Understand how electrochemical gradients affect ions
* Describe endocytosis, including phagocytosis, pinocytosis, and receptor-mediated endocytosis
* Understand the process of exocytosis

Electrochemical Gradient

We have discussed simple concentration gradients—differential concentrations of a substance across a space or a membrane—but in living systems, gradients are more complex. Because cells contain proteins, most of which are negatively charged, and because ions move into and out of cells, there is 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; at the same time, cells have higher concentrations of potassium (K+) and lower concentrations of sodium (Na+) than does the extracellular fluid. Thus, in a living cell, the concentration gradient and electrical gradient of Na+ promotes diffusion of the ion into the cell, and the electrical gradient of Na+ (a positive ion) tends to drive it inward to the negatively charged interior. The situation is more complex, however, for other elements such as potassium. The electrical gradient of K+ promotes diffusion of the ion *into* the cell, but the concentration gradient of K+ promotes diffusion *out* of the cell ([link]). The combined gradient that affects an ion is called its electrochemical gradient, and it is especially important to muscle and nerve cells.

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 variations of endocytosis, but all share a common characteristic: The plasma membrane of the cell invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle being contained in a newly created vacuole that is formed from the plasma membrane.

Exocytosis

In contrast to these methods of moving material into a cell is the process of exocytosis. Exocytosis is the opposite of the processes discussed above in that its purpose is to expel material from the cell into the extracellular fluid. A particle enveloped in membrane fuses with the interior of the plasma membrane. This fusion opens the membranous envelope to the exterior of the cell, and the particle is expelled into the extracellular space ([link]).

How Cells Obtain Energy

Introduction

Energy and Metabolism

Abstract:
By the end of this section, you will be able to:
* Explain what metabolic pathways are
* State the first and second laws of thermodynamics
* Explain the difference between kinetic and potential energy
* Describe endergonic and exergonic reactions
* Discuss how enzymes function as molecular catalysts

Metabolic Pathways

Consider the metabolism of sugar. This is a classic example of one of the many cellular processes that use and produce energy. Living things consume sugars as a major energy source, because sugar molecules have a great deal of energy stored within their bonds. For the most part, photosynthesizing organisms like plants produce these sugars. During photosynthesis, plants use energy (originally from sunlight) to convert carbon dioxide gas (CO2) into sugar molecules (like glucose: C6H12O6). They consume carbon dioxide and produce oxygen as a waste product. This reaction is summarized as:

Energy

Thermodynamics refers to the study of energy and energy transfer involving physical matter. The matter relevant to a particular case of energy transfer is called a system, and everything outside of that matter is called the surroundings. For instance, when heating a pot of water on the stove, the system includes the stove, the pot, and the water. Energy is transferred within the system (between the stove, pot, and water). There are two types of systems: open and closed. In an open system, energy can be exchanged with its surroundings. The stovetop system is open because heat can be lost to the air. A closed system cannot exchange energy with its surroundings.

Thermodynamics

The first law of thermodynamics states that the total amount of energy in the universe is constant and conserved. 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 be transferred from place to place or transformed 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 and heat 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 the energy of sunlight to chemical energy stored within organic molecules ([link]). Some examples of energy transformations are shown in [link].

Potential and Kinetic Energy

When an object is in motion, there is energy associated with that object. Think of a wrecking ball. Even a slow-moving wrecking ball can do a great deal of damage to other objects. Energy associated with objects in motion is called kinetic energy ([link]). A speeding bullet, a walking person, and the rapid movement of molecules in the air (which produces heat) all have kinetic energy.

Free and Activation Energy

After learning that chemical reactions release energy when energy-storing bonds are broken, an important next question is the following: How is the energy associated with these chemical reactions quantified and expressed? How can the energy released from one reaction be compared to that of another reaction? A measurement of free energy is used to quantify these energy transfers. Recall that according to the second law of thermodynamics, all energy transfers involve the loss of some amount of energy in an unusable form such as heat. Free energy specifically refers to the energy associated with a chemical reaction that is available after the losses are accounted for. In other words, free energy is usable energy, or energy that is available to do work.

Enzymes

A substance that helps a chemical reaction to occur is called a catalyst, and the molecules that catalyze biochemical reactions are called enzymes. Most enzymes are proteins and perform the critical task of lowering the activation energies of chemical reactions inside the cell. Most of the reactions critical to a living cell happen too slowly at normal temperatures to be of any use to the cell. Without enzymes to speed up these reactions, life could not persist. Enzymes do this by binding to the reactant molecules and holding them in such a way as to make the chemical bond-breaking and -forming processes take place more easily. It is important to remember that enzymes do not change whether a reaction is exergonic (spontaneous) or endergonic. This is because they do not change the free energy of the reactants or products. They only reduce the activation energy required for the reaction to go forward ([link]). In addition, an enzyme itself is unchanged by the reaction it catalyzes. Once one reaction has been catalyzed, the enzyme is able to participate in other reactions.

Glycolysis

Abstract:
By the end of this section, you will be able to:
* Explain how ATP is used by the cell as an energy source
* Describe the overall result in terms of molecules produced of the breakdown of glucose by glycolysis

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 denature enzymes and other proteins, and thus destroy the cell. Rather, a cell must be able to store energy safely and release it for use only as needed. Living cells accomplish this using ATP, which can be used to fill any energy need of the cell. How? It functions as a rechargeable battery.

Glycolysis

You have read that nearly all of the energy used by living things comes to them in the bonds of the sugar, glucose. Glycolysis is the first step in the breakdown of glucose to extract energy for cell metabolism. Many living organisms carry out glycolysis as part of their metabolism. Glycolysis takes place in the cytoplasm of most prokaryotic and all eukaryotic cells.

Citric Acid Cycle and Oxidative Phosphorylation

Abstract:
By the end of this section, you will be able to:
* Describe the location of the citric acid cycle and oxidative phosphorylation in the cell
* Describe the overall outcome of the citric acid cycle and oxidative phosphorylation in terms of the products of each
* Describe the relationships of glycolysis, the citric acid cycle, and oxidative phosphorylation in terms of their inputs and outputs.

The Citric Acid Cycle

In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into mitochondria, which are sites of cellular respiration. If oxygen is available, aerobic respiration will go forward. In mitochondria, pyruvate will be transformed into a two-carbon acetyl group (by removing a molecule of carbon dioxide) that will be picked up by a carrier compound called coenzyme A (CoA), which is made from vitamin B5. The resulting compound is called acetyl CoA. ([link]). Acetyl CoA can be used in a variety of ways by the cell, but its major function is to deliver the acetyl group derived from pyruvate to the next pathway in glucose catabolism.

Oxidative Phosphorylation

You have just read about two pathways in glucose catabolism—glycolysis and the citric acid cycle—that generate ATP. Most of the ATP generated during the aerobic catabolism of glucose, however, is not generated directly from these pathways. Rather, it derives from a process that begins with passing electrons through a series of chemical reactions to a final electron acceptor, oxygen. These reactions take place in specialized protein complexes located in the inner membrane of the mitochondria of eukaryotic organisms and on the inner part of the cell membrane of prokaryotic organisms. The energy of the electrons is harvested and used to generate an electrochemical gradient across the inner mitochondrial membrane. The potential energy of this gradient is used to generate ATP. The entirety of this process is called oxidative phosphorylation.

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 mitochondrial membrane. The NADH generated from glycolysis cannot easily enter mitochondria. Thus, electrons are picked up on the inside of the mitochondria by either NAD+ or FAD+. Fewer ATP molecules are generated when FAD+ acts as a carrier. NAD+ is used as the electron transporter in the liver and FAD+ in the brain, so ATP yield depends on the tissue being considered.

Fermentation

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

Lactic Acid Fermentation

The fermentation method used by animals and some bacteria like those in yogurt is lactic acid fermentation ([link]). This occurs routinely in mammalian red blood cells and in skeletal muscle that has insufficient oxygen supply to allow aerobic respiration to continue (that is, in muscles used to the point of fatigue). In muscles, lactic acid produced by fermentation must be removed by the blood circulation and brought to the liver for further metabolism. The chemical reaction of lactic acid fermentation is the following:

Alcohol Fermentation

Another familiar fermentation process is alcohol fermentation ([link]), which produces ethanol, an alcohol. The alcohol fermentation reaction is the following:

Anaerobic Cellular Respiration

Certain prokaryotes, including some species of bacteria and Archaea, use anaerobic respiration. For example, the group of Archaea 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 and Archaea, most of which are anaerobic ([link]), reduce sulfate to hydrogen sulfide to regenerate NAD+ from NADH.

Connections to Other Metabolic Pathways

Abstract:
By the end of this section, you will be able to:
* Discuss the way 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 a short-term energy storage molecule in animals. When there is adequate ATP present, excess glucose is converted into glycogen for storage. Glycogen is made and stored in the liver and muscle. Glycogen will be taken out of storage if blood sugar levels drop. The presence of glycogen in muscle cells as a source of glucose allows ATP to be produced for a longer time during exercise.

Connections of Proteins to Glucose Metabolism

Proteins are broken down by a variety of enzymes in cells. Most of the time, amino acids are recycled into new proteins. If there are excess amino acids, however, or if the body is in a state of famine, some amino acids will be shunted into pathways of glucose catabolism. 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 from the nitrogen originating in amino acids, and it leaves the body in urine.

Connections of Lipids to Glucose Metabolism

The lipids that are connected to the glucose pathways are 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 CoA and proceeds in only one direction. The process cannot be reversed, and ATP is not produced.

Photosynthesis

Introduction

Overview of Photosynthesis

Abstract:
By the end of this section, you will be able to:
* Summarize the process of photosynthesis
* Explain the relevance of photosynthesis to other living things
* Identify the reactants and products of photosynthesis
* Describe the main structures involved in photosynthesis

Solar Dependence and Food Production

Some organisms can carry out photosynthesis, whereas others cannot. An autotroph is an organism that can produce its own food. The Greek roots of the word *autotroph* mean “self” (*auto*) “feeder” (*troph*). Plants are the best-known autotrophs, but others exist, including certain types of bacteria and algae ([link]). Oceanic algae contribute enormous quantities of food and oxygen to global food chains. Plants are also photoautotrophs, a type of autotroph that uses sunlight and carbon from carbon dioxide to synthesize chemical energy in the form of carbohydrates. All organisms carrying out photosynthesis require sunlight.

Main Structures and Summary of Photosynthesis

Photosynthesis requires sunlight, carbon dioxide, and water as starting reactants ([link]). After the process is complete, photosynthesis releases oxygen and produces carbohydrate molecules, most commonly glucose. These sugar molecules contain the energy that living things need to survive.

The Two Parts of Photosynthesis

Photosynthesis takes place in two stages: the light-dependent reactions and the Calvin cycle. In the light-dependent reactions, which take place at the thylakoid membrane, chlorophyll absorbs energy from sunlight and then converts it into chemical energy with the use of water. The light-dependent reactions release oxygen from the hydrolysis of water as a byproduct. In the Calvin cycle, which takes place in the stroma, the chemical energy derived from the light-dependent reactions drives both the capture of carbon in carbon dioxide molecules and the subsequent assembly of sugar molecules. The two reactions use carrier molecules to transport the energy from one to the other. The carriers that move energy from the light-dependent reactions to the Calvin cycle reactions can be thought of as “full” because they bring energy. After the energy is released, the “empty” energy carriers return to the light-dependent reactions to obtain more energy. The two-stage, two-location photosynthesis process was discovered by Joan Mary Anderson, whose continuing work over the subsequent decades provided much of our understanding of the process, the membranes, and the chemicals involved.

The Light-Dependent Reactions of Photosynthesis

Abstract:
By the end of this section, you will be able to:
* Explain how plants absorb energy from sunlight
* Describe how the wavelength of light affects its energy and color
* 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). Humans can see only a fraction of this energy, which is referred to as “visible light.” The manner in which solar energy travels can be described and measured as waves. Scientists can determine the amount of energy of a wave by measuring its wavelength, the distance between two consecutive, similar points in a series of waves, such as from crest to crest or trough to trough ([link]).

Absorption of Light

Light energy enters the process of photosynthesis when pigments absorb the light. In plants, pigment molecules absorb only visible light for photosynthesis. The visible light seen by humans as white light actually exists in a rainbow of colors. Certain objects, such as a prism or a drop of water, disperse white light to reveal these colors to the human eye. The visible light portion of the electromagnetic spectrum is perceived by the human eye as a rainbow of colors, with violet and blue having shorter wavelengths and, therefore, higher energy. At the other end of the spectrum toward red, the wavelengths are longer and have lower energy.

Understanding Pigments

Different kinds of pigments exist, and each absorbs only certain wavelengths (colors) of visible light. Pigments reflect the color of the wavelengths that they cannot absorb.

How Light-Dependent Reactions Work

The overall purpose of the light-dependent reactions is to convert light energy into chemical energy. This chemical energy will be used by the Calvin cycle to fuel the assembly of sugar molecules.

Generating an Energy Carrier: ATP

In the light-dependent reactions, energy absorbed by sunlight is stored by two types of energy-carrier molecules: ATP and NADPH. The energy that these molecules carry is stored in a bond that holds a single atom or group of atoms to the molecule. For ATP, it is a phosphate group, and for NADPH, it is a hydrogen atom. Recall that NADH was a similar molecule that carried energy in the mitochondrion from the citric acid cycle to the electron transport chain. When these molecules release energy into the Calvin cycle, they each lose either atoms or groups of atoms to become the lower-energy molecules ADP and NADP+.

Generating Another Energy Carrier: NADPH

The remaining function of the light-dependent reaction is to generate the other energy-carrier molecule, NADPH. As the electron from the electron transport chain arrives at photosystem I, it is re-energized with another photon captured by chlorophyll. The energy from this electron drives the formation of NADPH from NADP+ and a hydrogen ion (H+). Now that the solar energy is stored in energy carriers, it can be used to make a sugar molecule.

The Calvin Cycle

Abstract:
By the end of this section, you will be able to:
* Describe the Calvin cycle
* Define carbon fixation
* Explain how photosynthesis works in the energy cycle of all living organisms

The Interworkings of the Calvin Cycle

In plants, carbon dioxide (CO2) enters the leaf through the stomata and diffuses into the mesophyll cells and into the stroma of the chloroplast—the site of the Calvin cycle reactions where sugar is synthesized. The reactions are named after Melvin Calvin, the scientist who discovered them, and reference the fact that the reactions function as a cycle. Others call it the Calvin-Benson cycle to include the name of another scientist involved in its discovery, Andrew Benson ([link]).

Photosynthesis in Prokaryotes

The two parts of photosynthesis—the light-dependent reactions and the Calvin cycle—have been described, as they take place in chloroplasts. However, prokaryotes, such as cyanobacteria, lack membrane-bound organelles. Prokaryotic photosynthetic autotrophic organisms have infoldings of the plasma membrane for chlorophyll attachment and photosynthesis ([link]). It is here that organisms like cyanobacteria can carry out photosynthesis.

The Energy Flow

Living things access energy by breaking down carbohydrate molecules. However, if plants make carbohydrate molecules, why would they need to break them down? Carbohydrates are storage molecules for energy in all living things. Although energy can be stored in molecules like ATP, carbohydrates are much more stable and efficient reservoirs for chemical energy. Photosynthetic organisms also carry out the reactions of respiration to harvest the energy that they have stored in carbohydrates, for example, plants have mitochondria in addition to chloroplasts.

Cell Division and Genetics

Reproduction at the Cellular Level

Introduction

The Genome

Abstract:
By the end of this section, you will be able to:
* Describe the prokaryotic and eukaryotic genome
* Distinguish between chromosomes, genes, and traits

Genomic DNA

Before discussing the steps a cell undertakes to replicate, a deeper understanding of the structure and function of a cell’s genetic information is necessary. A cell’s complete complement of DNA 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. 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.

The Cell Cycle

Abstract:
By the end of this section, you will be able to:
* Describe the three stages of interphase
* Discuss the behavior of chromosomes during mitosis and how the cytoplasmic content divides during cytokinesis
* Define the quiescent G0 phase
* Explain how the three internal control checkpoints occur at the end of G1, at the G2–M transition, and during metaphase

Interphase

During interphase, the cell undergoes normal processes while also preparing for cell division. For a cell to move from interphase to 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

To make two daughter cells, the contents of the nucleus and the cytoplasm must be divided. The mitotic phase is a multistep process during which the duplicated chromosomes are aligned, separated, and moved to opposite poles of the cell, and then the cell is divided into two new identical daughter cells. The first portion of the mitotic phase, mitosis, is composed of five stages, which accomplish nuclear division. The second portion of the mitotic phase, called cytokinesis, is the physical separation of the cytoplasmic components into two daughter cells.

G0 Phase

Not all cells adhere to the classic cell-cycle pattern in which a newly formed daughter cell immediately enters interphase, closely followed by the mitotic phase. Cells in the G0 phase are not actively preparing to divide. The cell is in a quiescent (inactive) stage, having exited the cell cycle. Some cells enter G0 temporarily 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 ([link]).

Regulation at Internal Checkpoints

It is essential that daughter cells 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 the abnormal cell. To prevent a compromised cell from continuing to divide, there are internal control mechanisms that operate at three main cell cycle checkpoints at which the cell cycle can be stopped until conditions are favorable. These checkpoints occur near the end of G1, at the G2–M transition, and during metaphase ([link]).

Cancer and the Cell Cycle

Abstract:
By the end of this section, you will be able to:
* Explain how cancer is caused by uncontrolled cell division
* Understand how proto-oncogenes are normal cell genes that, when mutated, become oncogenes
* Describe how tumor suppressors function to stop the cell cycle until certain events are completed
* 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, 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, a protein involved in cell-cycle regulation, to be activated before it should be 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 undertake further cell divisions, the mutation would not be propagated and no harm comes to the organism. However, if the atypical daughter cells are able to divide further, the subsequent generation of cells will likely 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 genes that code for the negative regulator proteins, the type of regulator that—when activated—can prevent the cell from undergoing uncontrolled division. The collective function of the best-understood tumor suppressor gene proteins, retinoblastoma protein (RB1), p53, and p21, is to put up a roadblock to cell-cycle progress 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.

Prokaryotic Cell Division

Abstract:
By the end of this section, you will be able to:
* Describe the process of binary fission in prokaryotes
* Explain how FtsZ and tubulin proteins are examples of homology

Binary Fission

The cell division process of prokaryotes, called binary fission, is a less complicated and much quicker process than cell division in eukaryotes. Because of the speed of bacterial cell division, populations of bacteria can grow very rapidly. The single, circular DNA chromosome of bacteria is not enclosed in a nucleus, but instead occupies a specific location, the nucleoid, within the cell. As in eukaryotes, the DNA of the nucleoid is associated with proteins that aid in packaging the molecule into a compact size. The packing proteins of bacteria are, however, related to some of the proteins involved in the chromosome compaction of eukaryotes.

The Cellular Basis of Inheritance

Introduction

Sexual Reproduction

Abstract:
By the end of this section, you will be able to:
* Explain that variation among offspring is a potential evolutionary advantage resulting from sexual reproduction
* Describe the three different life-cycle strategies among sexual multicellular organisms and their commonalities

Life Cycles of Sexually Reproducing Organisms

Fertilization and meiosis alternate in sexual life cycles. What happens between these two events depends on the organism. The process of meiosis reduces the resulting gamete’s chromosome number by half. Fertilization, the joining of two haploid gametes, restores the diploid condition. There are three main categories of life cycles in multicellular organisms: diploid-dominant, in which the multicellular diploid stage is the most obvious life stage (and there is no multicellular haploid stage), as with most animals including humans; haploid-dominant, in which the multicellular haploid stage is the most obvious life stage (and there is no multicellular diploid stage), as with all fungi and some algae; and alternation of generations, in which the two stages, haploid and diploid, are apparent to one degree or another depending on the group, as with plants and some algae.

Meiosis

Abstract:
By the end of this section, you will be able to:
* Describe the behavior of chromosomes during meiosis
* Describe cellular events during meiosis
* Explain the differences between meiosis and mitosis
* Explain the mechanisms within meiosis that generate genetic variation among the products of meiosis

Interphase

Meiosis is preceded by an interphase consisting of the G1, S, and G2 phases, which are nearly identical to the phases preceding mitosis. The G1 phase is the first phase of interphase and is focused on cell growth. In the S phase, the DNA of the chromosomes is replicated. Finally, in the G2 phase, the cell undergoes the final preparations for meiosis.

Meiosis I

Early in prophase I, the chromosomes can be seen clearly microscopically. As the nuclear envelope begins to break down, the proteins associated with homologous chromosomes bring the pair close to each other. The tight pairing of the homologous chromosomes is called synapsis. In synapsis, the genes on the chromatids of the homologous chromosomes are precisely aligned with each other. An exchange of chromosome segments between non-sister homologous chromatids occurs and is called crossing over. This process is revealed visually after the exchange as chiasmata (singular = *chiasma*) ([link]).

Meiosis II

In meiosis II, the connected sister chromatids remaining in the haploid cells from meiosis I will be split to form four haploid cells. In some species, cells enter a brief interphase, or interkinesis, that lacks an S phase, before entering meiosis II. Chromosomes are not duplicated during interkinesis. The two cells produced in meiosis I go through the events of meiosis II in synchrony. Overall, meiosis II resembles the mitotic division of a haploid cell.

Comparing Meiosis and Mitosis

Mitosis and meiosis, which are both forms of division of the nucleus in eukaryotic cells, share some similarities, but also exhibit distinct differences that lead to their very different outcomes. Mitosis is a single nuclear division that results in two nuclei, usually partitioned into two new cells. The nuclei resulting from a mitotic division are genetically identical to the original. They have the same number of sets of chromosomes: one in the case of haploid cells, and two in the case of diploid cells. On the other hand, meiosis is two nuclear divisions that result in four nuclei, usually partitioned into four new cells. The nuclei resulting from meiosis are never genetically identical, and they contain one chromosome set only—this is half the number of the original cell, which was diploid ([link]).

Variations in Meiosis

Abstract:
By the end of this section, you will be able to:
* Explain how nondisjunction leads to differences in chromosome number
* Describe how errors in chromosome structure occur through inversions and translocations

Disorders in Chromosome Number

The isolation and microscopic observation of chromosomes 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, including 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 ([link]).

Chromosome Structural Rearrangements

Cytologists have characterized numerous structural rearrangements in chromosomes, including partial duplications, deletions, inversions, and translocations. Duplications and deletions often produce offspring that survive but exhibit physical and mental abnormalities. Cri-du-chat (from the French for “cry of the cat”) is a syndrome associated with nervous system abnormalities and identifiable physical features that results from a deletion of most of the small arm of chromosome 5 ([link]). Infants with this genotype emit a characteristic high-pitched cry upon which the disorder’s name is based.

Patterns of Inheritance

Introduction

Mendel’s Experiments

Abstract:
By the end of this section, you will be able to:
* Explain the scientific reasons for the success of Mendel’s experimental work
* Describe the expected outcomes of monohybrid crosses involving dominant and recessive alleles

Mendel’s Crosses

Mendel’s seminal work was accomplished using the garden pea, *Pisum sativum*, to study inheritance. This species naturally self-fertilizes, meaning that pollen encounters ova within the same flower. Because every pea plant has both male reproductive organs and female reproductive organs, each plant produces both types of gametes required for reproduction—both pollen and ova. In plants, just as in animals, reproductive organs are classified by the size of the gametes produced. The organs producing the smaller pollen are called male reproductive organs, while the organs producing the larger ova are called female reproductive organs.

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 and reported results from thousands of F2 plants.

Laws of Inheritance

Abstract:
By the end of this section, you will be able to:
* Explain the relationship between genotypes and phenotypes in dominant and recessive gene systems
* Use a Punnett square to calculate the expected proportions of genotypes and phenotypes in a monohybrid cross
* Explain Mendel’s law of segregation and independent assortment in terms of genetics and the events of meiosis
* Explain the purpose and methods of a test cross

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 the physically visible and the non-expressed alleles, is called its genotype. Mendel’s hybridization experiments demonstrate the difference between phenotype and genotype. For example, the phenotypes that Mendel observed in his crosses between pea plants with differing traits are connected to the diploid genotypes of the plants in the P, F1, and F2 generations. We will use a second trait that Mendel investigated, seed color, as an example. Seed color is governed by a single gene with two alleles. The yellow-seed allele is dominant and the green-seed allele is recessive. When true-breeding plants were cross-fertilized, in which one parent had yellow seeds and one had green seeds, all of the F1 hybrid offspring had yellow seeds. That is, the hybrid offspring were phenotypically identical to the true-breeding parent with yellow seeds. However, we know that the allele donated by the parent with green seeds was not simply lost because it reappeared in some of the F2 offspring ([link]). Therefore, the F1 plants must have been genotypically different from the parent with yellow seeds.

Monohybrid Cross and the Punnett Square

When fertilization occurs between two true-breeding parents that differ by only the characteristic being studied, the process is called a monohybrid cross, and the resulting offspring are called monohybrids. Mendel performed seven types of monohybrid crosses, each involving contrasting traits for different characteristics. Out of these crosses, all of the F1 offspring had the phenotype of one parent, and the F2 offspring had a 3:1 phenotypic ratio. On the basis of these results, 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.

Law of Segregation

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 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. This process was not understood by the scientific community during Mendel’s lifetime ([link]).

Law of 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. 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 wrinkled, green seeds (*rryy*) and another that has round, yellow seeds (*RRYY*). Because each parent is homozygous, the law of segregation indicates that the gametes for the wrinkled–green plant all are *ry*, and the gametes for the round–yellow plant are all *RY*. Therefore, the F1 generation of offspring all are *RrYy* ([link]).

Extensions of the Laws of Inheritance

Abstract:
By the end of this section, you will be able to:
* Identify non-Mendelian inheritance patterns such as incomplete dominance, codominance, multiple alleles, and sex linkage from the results of crosses
* Explain the effect of linkage and recombination on gamete genotypes
* Explain the phenotypic outcomes of epistatic effects among genes

Alternatives to Dominance and Recessiveness

Mendel’s experiments with pea plants suggested that: 1) two types of “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, with 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.” Since then, genetic studies in other organisms 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.

Linked Genes Violate the Law of Independent Assortment

Although all of Mendel’s pea plant 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 us 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.

Molecular Biology and Biotechnology

Molecular Biology

Introduction

The Structure of DNA

Abstract:
By the end of this section, you will be able to:
* Describe the structure of DNA
* Describe how eukaryotic and prokaryotic DNA is arranged in the cell

The Structure of RNA

There is a second nucleic acid in all cells called ribonucleic acid, or RNA. Like DNA, RNA is a polymer of nucleotides. Each of the nucleotides in RNA is made up of a nitrogenous base, a five-carbon sugar, and a phosphate group. In the case of RNA, the five-carbon sugar is ribose, not deoxyribose. Ribose has a hydroxyl group at the 2' carbon, unlike deoxyribose, which has only a hydrogen atom ([link]).

How DNA Is Arranged in the Cell

DNA is a working molecule; it must be replicated when a cell is ready to divide, and it must be “read” to produce the molecules, such as proteins, to carry out the functions of the cell. For this reason, the DNA is protected and packaged in very specific ways. In addition, DNA molecules can be very long. Stretched end-to-end, the DNA molecules in a single human cell would come to a length of about 2 meters. Thus, the DNA for a cell must be packaged in a very ordered way to fit and function within a structure (the cell) that is not visible to the naked eye. The chromosomes of prokaryotes are much simpler than those of eukaryotes in many of their features ([link]). Most prokaryotes contain a single, circular chromosome that is found in an area in the cytoplasm called the nucleoid.

DNA Replication

Abstract:
By the end of this section, you will be able to:
* Explain the process of DNA replication
* Explain the importance of telomerase to DNA replication
* Describe mechanisms of DNA repair

DNA Replication in Eukaryotes

Because eukaryotic genomes are very complex, DNA replication is a very complicated process that involves several enzymes and other proteins. It occurs in three main stages: initiation, elongation, and termination.

DNA Repair

DNA polymerase can make mistakes while adding nucleotides. It edits the DNA by proofreading every newly added base. Incorrect bases are removed and replaced by the correct base, and then polymerization continues ([link]**a**). Most mistakes are corrected during replication, although when this does not happen, the mismatch repair mechanism is employed. Mismatch repair enzymes recognize the wrongly incorporated base and excise it from the DNA, replacing it with the correct base ([link]**b**). In yet another type of repair, nucleotide excision repair, the DNA double strand is unwound and separated, the incorrect bases are removed along with a few bases on the 5' and 3' end, and these are replaced by copying the template with the help of DNA polymerase ([link]**c**). Nucleotide excision repair is particularly important in correcting thymine dimers, which are primarily caused by ultraviolet light. In a thymine dimer, two thymine nucleotides adjacent to each other on one strand are covalently bonded to each other rather than their complementary bases. If the dimer is not removed and repaired it will lead to a mutation. Individuals with flaws in their nucleotide excision repair genes show extreme sensitivity to sunlight and develop skin cancers early in life.

Transcription

Abstract:
By the end of this section, you will be able to:
* Explain the central dogma
* Explain the main steps of transcription
* Describe how eukaryotic mRNA is processed

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 sequences of mRNAs, which in turn specify the sequences of proteins.

Transcription: from DNA to mRNA

Both prokaryotes and eukaryotes perform fundamentally the same process of transcription, with the important difference of the membrane-bound nucleus in eukaryotes. With the genes bound in the nucleus, transcription occurs in the nucleus of the cell and the mRNA transcript must be transported to the cytoplasm. The prokaryotes, which include bacteria and archaea, lack membrane-bound nuclei and other organelles, and transcription occurs in the cytoplasm of the cell. In both prokaryotes and eukaryotes, transcription occurs in three main stages: initiation, elongation, and termination.

Eukaryotic RNA Processing

The newly transcribed eukaryotic mRNAs must undergo several processing steps before they can be transferred from the nucleus to the cytoplasm and translated into a protein. The additional steps involved in eukaryotic mRNA maturation create a molecule that is much more stable than a prokaryotic mRNA. For example, eukaryotic mRNAs last for several hours, whereas the typical prokaryotic mRNA lasts no more than five seconds.

Translation

Abstract:
By the end of this section, you will be able to:
* Describe the different steps in protein synthesis
* Discuss the role of ribosomes in protein synthesis
* Describe the genetic code and how the nucleotide sequence determines the amino acid and the protein sequence

The Protein Synthesis Machinery

In addition to the mRNA template, many other molecules contribute to the process of translation. The composition of each component may vary across species; for instance, ribosomes may consist of different numbers of ribosomal RNAs (rRNA) 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 ([link]).

The Genetic Code

To summarize what we know to this point, the cellular process of transcription generates messenger RNA (mRNA), a mobile molecular copy of one or more genes with an alphabet of A, C, G, and uracil (U). Translation of the mRNA template converts nucleotide-based genetic information into a protein product. Protein sequences consist of 20 commonly occurring amino acids; therefore, it can be said that the protein alphabet consists of 20 letters. Each amino acid is defined by a three-nucleotide sequence called the triplet codon. The relationship between a nucleotide codon and its corresponding amino acid is called the genetic code.

The Mechanism of Protein Synthesis

Just 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 will explore how translation occurs in *E. coli*, a representative prokaryote, and specify any differences between prokaryotic and eukaryotic translation.

How Genes Are Regulated

Abstract:
By the end of this section, you will be able to:
* Discuss why every cell does not express all of its genes
* Describe how prokaryotic gene expression occurs at the transcriptional level
* Understand that eukaryotic gene expression 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 becomes a functional protein in a cell. The process occurs in both prokaryotic and eukaryotic cells, just in slightly different fashions.

Biotechnology

Introduction

Cloning and Genetic Engineering

Abstract:
By the end of this section, you will be able to:
* Explain the basic techniques used to manipulate genetic material
* Explain molecular and reproductive cloning

Manipulating Genetic Material

To accomplish the applications described above, biotechnologists must be able to extract, manipulate, and analyze nucleic acids.

Cloning

In general, cloning means the creation of a perfect replica. Typically, the word is used to describe the creation of a genetically identical copy. 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 copy short stretches of DNA—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.

Genetic Engineering

Using recombinant DNA technology to modify an organism’s DNA to achieve desirable traits is called genetic engineering. Addition of foreign DNA in the form of recombinant DNA vectors that are generated by molecular cloning is the most common method of genetic engineering. An organism that receives the recombinant DNA is called a genetically modified organism (GMO). If the foreign DNA that is introduced comes from a different species, the host organism is called transgenic. Bacteria, plants, and animals have been genetically modified since the early 1970s for academic, medical, agricultural, and industrial purposes. These applications will be examined in more detail in the next module.

Biotechnology in Medicine and Agriculture

Abstract:
By the end of this section, you will be able to:
* Describe uses of biotechnology in medicine
* Describe uses of biotechnology in agriculture

Genetic Diagnosis and Gene Therapy

The process of testing for suspected genetic defects before administering treatment is called genetic diagnosis by genetic testing. In some cases in which a genetic disease is present in an individual’s family, family members may be advised to undergo genetic testing. For example, mutations in the *BRCA* genes may increase the likelihood of developing breast, ovarian, and some other cancers. A person with breast cancer can be screened for these mutations. If one of the high-risk mutations is found, relatives may also wish to be screened for that particular mutation, or simply be more vigilant for the occurrence of cancers. Genetic testing is also offered for fetuses (or embryos with in vitro fertilization) to determine the presence or absence of disease-causing genes in families with specific debilitating diseases.

Production of Vaccines, Antibiotics, and Hormones

Traditional vaccination strategies use weakened or inactive forms of microorganisms or viruses to stimulate the immune system. Modern techniques use specific genes of microorganisms cloned into vectors and mass-produced in bacteria to make large quantities of specific substances to stimulate the immune system. The substance is then used as a vaccine. In some cases, such as the H1N1 flu vaccine, genes cloned from the virus have been used to combat the constantly changing strains of this virus.

Transgenic Animals

Although several recombinant proteins used in medicine are successfully produced in bacteria, some proteins need a eukaryotic animal host for proper processing. For this reason, genes have been cloned and expressed in animals such as sheep, goats, chickens, and mice. Animals that have been modified to express recombinant DNA are called transgenic animals ([link]).

Transgenic Plants

Manipulating the DNA of plants (creating genetically modified organisms, or GMOs) has helped to create desirable traits such as disease resistance, herbicide, and pest 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.

Genomics and Proteomics

Abstract:
By the end of this section, you will be able to:
* Define genomics and proteomics
* Define whole genome sequencing
* Explain different applications of genomics and proteomics

Mapping Genomes

Genome mapping is the process of finding the location of genes on each chromosome. The maps that are created are comparable to the maps that we use to navigate streets. A genetic map is an illustration that lists genes and their location on a chromosome. Genetic maps provide the big picture (similar to a map of interstate highways) and use genetic markers (similar to landmarks). A genetic marker is a gene or sequence on a chromosome that shows genetic linkage with a trait of interest. The genetic marker tends to be inherited with the gene of interest, and one measure of distance between them is the recombination frequency during meiosis. Early geneticists called this linkage analysis.

Whole Genome Sequencing

Although there have been significant advances in the medical sciences in recent years, doctors are still confounded by many diseases and researchers are using whole genome sequencing to get to the bottom of the problem. Whole genome sequencing is a process that determines the DNA sequence of an entire genome. Whole genome sequencing is a brute-force approach to problem solving when there is a genetic basis at the core of a disease. Several laboratories now provide services to sequence, analyze, and interpret entire genomes.

Applying Genomics

The introduction of DNA sequencing and whole genome sequencing projects, particularly the Human Genome Project, has expanded the applicability of DNA sequence information. Genomics is now being used in a wide variety of fields, such as metagenomics, pharmacogenomics, and mitochondrial genomics. The most commonly known application of genomics is to understand and find cures for diseases.

Evolution and the Diversity of Life

Evolution and Its Processes

Introduction

Discovering How Populations Change

Abstract:
By the end of this section, you will be able to:
* Explain how Darwin’s theory of evolution differed from the current view at the time
* Describe how the present-day theory of evolution was developed
* Describe how population genetics is used to study the evolution of populations

Charles Darwin and Natural Selection

The actual mechanism for evolution was independently conceived of and described by two naturalists, Charles Darwin and Alfred Russell Wallace, in the mid-nineteenth century. Importantly, each 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*, visiting 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 in 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 that each had a unique beak shape ([link]). He observed both that these finches closely resembled another finch species on the mainland of South America and that the group of species in the Galápagos formed a graded series of beak sizes and shapes, with very small differences between the most similar. Darwin imagined that the island species might be all species modified from one original mainland species. In 1860, he wrote, “Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends.”[footnote]

Charles Darwin, *Journal of Researches into the Natural History and Geology of the Countries Visited during the Voyage of H.M.S. Beagle Round the World, under the Command of Capt. Fitz Roy, R.N*, 2nd. ed. (London: John Murray, 1860), http://www.archive.org/details/journalofresea00darw.

The Modern Synthesis

The mechanisms of inheritance, genetics, were not understood at the time Darwin and Wallace were developing their idea of natural selection. This lack of understanding was a stumbling block to comprehending many aspects of evolution. In fact, blending inheritance was the predominant (and incorrect) genetic theory of the time, which made it difficult to understand how natural selection might operate. Darwin and Wallace were unaware of the genetics work by Austrian monk Gregor Mendel, which was published in 1866, not long after publication of *On the Origin of Species*. Mendel’s work was rediscovered in the early twentieth century at which time geneticists were rapidly coming to an understanding of the basics of inheritance. Initially, the newly discovered particulate nature of genes made it difficult for biologists to understand how gradual evolution could occur. But over the next few decades genetics and evolution were integrated in what became known as the modern synthesis—the coherent understanding of the relationship between natural selection and genetics that took shape by the 1940s and is generally accepted today. In sum, the modern synthesis describes how evolutionary pressures, such as natural selection, can affect a population’s genetic makeup, and, in turn, how this can result in the gradual evolution of populations and species. The theory also connects this gradual change of a population over time, called microevolution, with the processes that gave rise to new species and higher taxonomic groups with widely divergent characters, called macroevolution.

Population Genetics

Recall that a gene for a particular character may have several variants, or alleles, 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 make up the population. Mendel followed alleles as they were inherited from parent to offspring. In the early twentieth century, biologists began to study what happens to all the alleles in a population in a field of study known as population genetics.

Mechanisms of Evolution

Abstract:
By the end of this section, you will be able to:
* Describe the four basic causes of evolution: natural selection, mutation, genetic drift, and gene flow
* Explain how each evolutionary force can influence the allele frequencies of a population

Natural Selection

Natural selection has already been discussed. Alleles are expressed in a phenotype. Depending on the environmental conditions, the phenotype confers an advantage or disadvantage to the individual with the phenotype relative to the other phenotypes in the population. If it is an advantage, then that individual will likely have more offspring than individuals with the other phenotypes, and this will mean that the allele behind the phenotype will have greater representation in the next generation. If conditions remain the same, those offspring, which are carrying the same allele, will also benefit. Over time, the allele will increase in frequency in the population.

Mutation

Mutation is a source of new alleles in a population. Mutation is a change in the DNA sequence of the gene. A mutation can change one allele into another, but the net effect is a change in frequency. The change in frequency resulting from mutation is small, so its effect on evolution is small unless it interacts with one of the other factors, such as selection. A mutation may produce an allele that is selected against, selected for, or selectively neutral. Harmful mutations are removed from the population by selection and will generally only be found in very low frequencies equal to the mutation rate. Beneficial mutations will spread through the population through selection, although that initial spread is slow. Whether or not a mutation is beneficial or harmful is determined by whether it helps an organism survive to sexual maturity and reproduce. It should be noted that mutation is the ultimate source of genetic variation in all populations—new alleles, and, therefore, new genetic variations arise through mutation.

Genetic Drift

Another way a population’s allele frequencies can change is genetic drift ([link]), which is simply the effect of chance. Genetic drift is most important in small populations. Drift would be completely absent in a population with infinite individuals, but, of course, no population is this large. Genetic drift occurs because the alleles in an offspring generation are a random sample of the alleles in the parent generation. Alleles may or may not make it into the next generation due to chance events including mortality of an individual, events affecting finding a mate, and even the events affecting which gametes end up in fertilizations. If one individual in a population of ten individuals happens to die before it leaves any offspring to the next generation, all of its genes—a tenth of the population’s gene pool—will be suddenly lost. In a population of 100, that 1 individual represents only 1 percent of the overall gene pool; therefore, it has much less impact on the population’s genetic structure and is unlikely to remove all copies of even a relatively rare allele.

Gene Flow

Another important evolutionary force is gene flow, or the flow of alleles in and out of a population resulting from the migration of individuals or gametes ([link]). While some populations are fairly stable, others experience more flux. Many plants, for example, send their seeds far and wide, by wind or in the guts of animals; these seeds may introduce alleles common in the source population to a new population in which they are rare.

Evidence of Evolution

Abstract:
By the end of this section, you will be able to:
* Explain sources of evidence for evolution
* Define homologous and vestigial structures

Fossils

Fossils provide solid evidence that organisms from the past are not the same as those found today; fossils show the gradual evolutionary changes over time. Scientists determine the age of fossils and categorize them all over the world to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past, and shows the evolution of form over millions of years ([link]). For example, highly detailed fossil records have been recovered for sequences of species in the evolution of whales and modern horses. The fossil record of horses in North America is especially rich and many contain transition fossils: those showing intermediate anatomy between earlier and later forms. The fossil record extends back to a dog-like ancestor some 55 million years ago that gave rise to the first horse-like species 55 to 42 million years ago in the genus *Eohippus*. The series of fossils tracks the change in anatomy resulting from a gradual drying trend that changed the landscape from a forested one to a prairie. Successive fossils show the evolution of teeth shapes and foot and leg anatomy to a grazing habit, with adaptations for escaping predators, for example in species of *Mesohippus* found from 40 to 30 million years ago. Later species showed gains in size, such as those of *Hipparion*, which existed from about 23 to 2 million years ago. The fossil record shows several adaptive radiations in the horse lineage, which is now much reduced to only one genus, *Equus*, with several species.

Anatomy and Embryology

Another type of evidence for evolution is the presence of structures in organisms that share the same basic form. For example, the bones in the appendages of a human, dog, bird, and whale all share the same overall construction ([link]). That similarity results from their origin in the appendages of a common ancestor. Over time, evolution led to changes in the shapes and sizes of these bones in different species, but they have maintained the same overall layout, evidence of descent from a common ancestor. Scientists call these synonymous parts homologous structures. Some structures exist in organisms that have no apparent function at all, and appear to be residual parts from a past ancestor. For example, some snakes have pelvic bones despite having no legs because they descended from reptiles that did have legs. These unused structures without function are called vestigial structures. Other examples of vestigial structures are wings on flightless birds (which may have other functions), leaves on some cacti, traces of pelvic bones in whales, and the sightless eyes of cave animals.

Biogeography

The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, for example the unique flora and fauna of northern continents that formed from the supercontinent Laurasia and of the southern continents that formed from the supercontinent Gondwana. The presence of Proteaceae in Australia, southern Africa, and South America is best explained by the plant family’s presence there prior to the southern supercontinent Gondwana breaking up ([link]).

Molecular Biology

Like anatomical structures, the structures of the molecules of life reflect descent with modification. Evidence of a common ancestor for all of life is reflected in the universality of DNA as the genetic material and of the near universality of the genetic code and the machinery of DNA replication and expression. Fundamental divisions in life between the three domains are reflected in major structural differences in otherwise conservative structures such as the components of ribosomes and the structures of membranes. In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences—exactly the pattern that would be expected from descent and diversification from a common ancestor.

Speciation

Abstract:
By the end of this section, you will be able to:
* Describe the definition of species and how species are identified as different
* Explain allopatric and sympatric speciation
* Describe adaptive radiation

Speciation through Geographic Separation

A geographically continuous population has a gene pool that is relatively homogeneous. Gene flow, the movement of alleles across the range of the species, is relatively free because individuals can move and then mate with individuals in their new location. Thus, the frequency of an allele at one end of a distribution will be similar to the frequency of the allele at the other end. When populations become geographically discontinuous that free-flow of alleles is prevented. 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 more and more 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. Different histories of genetic drift, enhanced because the populations are smaller than the parent population, will also lead to divergence.

Speciation without Geographic Separation

Can divergence occur if no physical barriers are in place to separate individuals who continue to live and reproduce in the same habitat? A number of mechanisms for sympatric speciation have been proposed and studied.

Common Misconceptions about Evolution

Abstract:
By the end of this section, you will be able to:
* Identify common misconceptions about evolution
* Identify common criticisms of evolution

Evolution Is Just a Theory

Critics of the theory of evolution dismiss its importance by purposefully confounding the everyday usage of the word “theory” with the way scientists use the word. In science, a “theory” is understood to be a concept that has been extensively tested and supported over time. We have a theory of the atom, a theory of gravity, and the theory of relativity, each of which describes what scientists understand to be facts about the world. In the same way, the theory of evolution describes facts about the living world. As such, a theory in science has survived significant efforts to discredit it by scientists, who are naturally skeptical. While theories can sometimes be overturned or revised, this does not lessen their weight but simply reflects the constantly evolving state of scientific knowledge. In contrast, a “theory” in common vernacular means a guess or suggested explanation for something. This meaning is more akin to the concept of a “hypothesis” used by scientists, which is a tentative explanation for something that is proposed to either be supported or disproved. When critics of evolution say evolution is “just a theory,” they are implying that there is little evidence supporting it and that it is still in the process of being rigorously tested. This is a mischaracterization. If this were the case, geneticist Theodosius Dobzhansky would not have said that “nothing in biology makes sense, except in the light of evolution.”[footnote]

Theodosius Dobzhansky. “Biology, Molecular and Organismic.” *American Zoologist* 4, no. 4 (1964): 449.

Individuals Evolve

An individual is born with the genes it has—these do not change as the individual ages. Therefore, an individual cannot evolve or adapt through natural selection. Evolution is the change in genetic composition of a population over time, specifically over generations, resulting from differential reproduction of individuals with certain alleles. Individuals do change over their lifetime, but this is called development; it involves changes programmed by the set of genes the individual acquired at birth in coordination with the individual’s environment. When thinking about the evolution of a characteristic, it is probably best to think about the change of the average value of the characteristic in the population over time. For example, when natural selection leads to bill-size change in medium ground finches in the Galápagos, this does not mean that individual bills on the finches are changing. If one measures the average bill size among all individuals in the population at one time, and then measures the average bill size in the population several years later after there has been a strong selective pressure, this average value may be different as a result of evolution. Although some individuals may survive from the first time to the second, those individuals will still have the same bill size. However, there may be enough new individuals with different bill sizes to change the average bill size.

Evolution Explains the Origin of Life

It is a common misunderstanding that evolution includes an explanation of life’s origins. Some of the theory’s critics complain that it cannot explain the origin of life. The theory does not try to explain the origin of life. The theory of evolution explains how populations change over time and how life diversifies—the origin of species. It does not shed light on the beginnings of life including the origins of the first cells, which is how life is defined. The mechanisms of the origin of life on Earth are a particularly difficult problem because it occurred a very long time ago, over a very long time, and presumably just occurred once. Importantly, biologists believe that the presence of life on Earth precludes the possibility that the events that led to life on Earth can be repeated because the intermediate stages would immediately become food for existing living things. The early stages of life included the formation of organic molecules such as carbohydrates, amino acids, or nucleotides. If these were formed from inorganic precursors today, they would simply be broken down by living things. The early stages of life also probably included more complex aggregations of molecules into enclosed structures with an internal environment, a boundary layer of some form, and the external environment. Such structures, if they were formed now, would be quickly consumed or broken down by living organisms.

Organisms Evolve on Purpose

Statements such as “organisms evolve in response to a change in an environment,” are quite common. There are two easy misunderstandings possible with such a statement. First of all, the statement must not be understood to mean that individual organisms evolve, as was discussed above. The statement is shorthand for “a population evolves in response to a changing environment.” However, a second misunderstanding may arise by interpreting the statement to mean that the evolution is somehow intentional. A changed environment results in some individuals in the population, those with particular phenotypes, benefiting and, therefore, producing proportionately more offspring than other phenotypes. This results in change in the population if the characters are genetically determined.

Evolution Is Controversial among Scientists

The theory of evolution was controversial when it was first proposed in 1859, yet within 20 years virtually every working biologist had accepted evolution as the explanation for the diversity of life. The rate of acceptance was extraordinarily rapid, partly because Darwin had amassed an impressive body of evidence. The early controversies involved both scientific arguments against the theory and the arguments of religious leaders. It was the arguments of the biologists that were resolved after a short time, while the arguments of religious leaders have persisted to this day.

Other Theories Should Be Taught

A common argument from some people is that alternative theories to evolution should be taught in public schools. Critics of evolution use this strategy to create uncertainty about the validity of the theory without offering actual evidence. In fact, there are no viable alternative scientific theories to evolution. The last such theory, proposed by Lamarck in the nineteenth century, was replaced by the theory of natural selection. A single exception was a research program in the Soviet Union based on Lamarck’s theory during the early twentieth century that set that country’s agricultural research back decades. Special creation is not a viable alternative scientific theory because it is not a scientific theory, since it relies on an untestable explanation. Intelligent design, despite the claims of its proponents, is also not a scientific explanation. This is because intelligent design posits the existence of an unknown designer of living organisms and their systems. Whether the designer is unknown or supernatural, it is a cause that cannot be measured; therefore, it is not a scientific explanation. There are two reasons not to teach nonscientific theories. First, these explanations for the diversity of life lack scientific usefulness because they do not, and cannot, give rise to research programs that promote our understanding of the natural world. Experiments cannot test non-material explanations for natural phenomena. For this reason, teaching these explanations as science in public schools is not in the public interest. Second, in the United States, it is illegal to teach them as science because the U.S. Supreme Court and lower courts have ruled that the teaching of religious belief, such as special creation or intelligent design, violates the establishment clause of the First Amendment of the U.S. Constitution, which prohibits government sponsorship of a particular religion.

Diversity of Life

Introduction

Organizing Life on Earth

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

The Levels of Classification

Taxonomy (which literally means “arrangement law”) is the science of naming and grouping species to construct an internationally shared classification system. The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish naturalist) uses a hierarchical model. A hierarchical system has levels and each group at one of the levels includes groups at the next lowest level, so that at the lowest level each member belongs to a series of nested groups. An analogy is the nested series of directories on the main disk drive of a computer. For example, in the most inclusive grouping, scientists divide organisms into three domains: Bacteria, Archaea, and Eukarya. Within each domain is a second level called a kingdom. Each domain contains several kingdoms. Within kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species.

Classification and Phylogeny

Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and relationships between organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. The hierarchical classification of groups nested within more inclusive groups is reflected in diagrams. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past because one cannot go back through time to confirm the proposed relationships.

Limitations of Phylogenetic Trees

It is 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 different surroundings or after the evolution of a major new adaptation, they may look quite different from each other, even more so 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 salamanders (within the frog lineage) do not; yet on the surface, lizards and salamanders appear more similar than the lizards and rabbits.

Determining Evolutionary Relationships

Abstract:
By the end of this section, you will be able to:
* Compare homologous and analogous traits
* Discuss the purpose of cladistics

Two Measures of Similarity

Organisms that share similar physical features *and* genetic sequences tend to be more closely related than those that do not. Features that overlap both morphologically and genetically are referred to as homologous structures; the similarities stem from common evolutionary paths. For example, as shown in [link], the bones in the wings of bats and birds, the arms of humans, and the foreleg of a horse are homologous structures. Notice the structure is not simply a single bone, but rather a grouping of several bones arranged in a similar way in each organism even though the elements of the structure may have changed shape and size.

Building Phylogenetic Trees

How do scientists construct phylogenetic trees? Presently, the most accepted method for constructing phylogenetic trees is a method called cladistics. This method sorts organisms into clades, groups of organisms that are most closely related to each other and the ancestor from which they descended. For example, in [link], all of the organisms in the shaded region evolved from a single ancestor that had amniotic eggs. Consequently, all of these organisms also have amniotic eggs and make a single clade, also called a monophyletic group. Clades must include the ancestral species and all of the descendants from a branch point.

Diversity of Microbes, Fungi, and Protists

Introduction

Prokaryotic Diversity

Abstract:
By the end of this section, you will be able to:
* Describe the evolutionary history of prokaryotes
* Describe the basic structure of a typical prokaryote
* Identify bacterial diseases that caused historically important plagues and epidemics
* Describe the uses of prokaryotes in food processing and bioremediation

Prokaryotic Diversity

The advent of DNA sequencing provided immense insight into the relationships and origins of prokaryotes that were not possible using traditional methods of classification. A major insight identified two groups of prokaryotes that were found to be as different from each other as they were from eukaryotes. This recognition of prokaryotic diversity forced a new understanding of the classification of all life and brought us closer to understanding the fundamental relationships of all living things, including ourselves.

Biofilms

Until a couple of decades ago, microbiologists thought 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. A biofilm is a microbial community held together in a gummy-textured matrix, consisting primarily of polysaccharides secreted by the organisms, together with some proteins and nucleic acids. Biofilms grow attached to surfaces. Some of the best-studied biofilms are composed of prokaryotes, although fungal biofilms have also been described.

Characteristics of Prokaryotes

There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common structures: a plasma membrane that functions as a barrier for the cell and separates the cell from its environment; cytoplasm, a jelly-like substance inside the cell; genetic material (DNA and RNA); and ribosomes, where protein synthesis takes place. Prokaryotes come in various shapes, but many fall into three categories: cocci (spherical), bacilli (rod-shaped), and spirilla (spiral-shaped) ([link]).

The Prokaryotic Cell

Recall that prokaryotes ([link]) are unicellular organisms that lack organelles surrounded by membranes. Therefore, they do not have a nucleus but instead have a single chromosome—a piece of circular DNA located in an area of the cell called the nucleoid. Most prokaryotes have a cell wall lying outside the plasma membrane. The composition of the cell wall differs significantly between the domains Bacteria and Archaea (and their cell walls also differ from the eukaryotic cell walls found in plants and fungi.) The cell wall functions as a protective layer and is responsible for the organism’s shape. Some other structures are present in some prokaryotic species, but not in others. For example, the capsule found in some species enables the organism to attach to surfaces and protects it from dehydration. Some species may also have flagella (singular, flagellum) used for locomotion, and pili (singular, pilus) used for attachment to surfaces and to other bacteria for conjugation. Plasmids, which consist of small, circular pieces of DNA outside of the main chromosome, are also present in many species of bacteria.

Reproduction

Reproduction in prokaryotes is primarily asexual and takes place by binary fission. Recall that the DNA of a prokaryote exists usually as a single, circular chromosome. Prokaryotes do not undergo mitosis. Rather, the chromosome loop is replicated, and the two resulting copies attached to the plasma membrane move apart as the cell grows in a process called binary fission. 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, but prokaryotes can alter their genetic makeup in three ways.

How Prokaryotes Obtain Energy and Carbon

Prokaryotes are metabolically diverse organisms. Prokaryotes fill many niches on Earth, including being involved in nutrient cycles such as the nitrogen and carbon cycles, decomposing dead organisms, and growing and multiplying inside living organisms, including humans. Different prokaryotes can use different sources of energy to assemble macromolecules from smaller molecules. Phototrophs obtain their energy from sunlight. Chemotrophs obtain their energy from chemical compounds.

Bacterial Diseases in Humans

Devastating pathogen-borne diseases and plagues, both viral and bacterial in nature, have affected and continue to affect humans. It is worth noting that all pathogenic prokaryotes are Bacteria; there are no known pathogenic Archaea in humans or any other organism. Pathogenic organisms evolved alongside humans. In the past, the true cause of these diseases was not understood, and some cultures thought that diseases were a spiritual punishment or were mistaken about material causes. Over time, people came to realize that staying apart from afflicted persons, improving sanitation, and properly disposing of the corpses and personal belongings of victims of illness reduced their own chances of getting sick.

Historical Perspective

There are records of infectious diseases as far back as 3,000 B.C. A number of significant pandemics caused by Bacteria have been documented over several hundred years. Some of the largest pandemics led to the decline of cities and cultures. Many were zoonoses that appeared with the domestication of animals, as in the case of tuberculosis. A zoonosis is a disease that infects animals but can be transmitted from animals to humans.

The Antibiotic Crisis

The word antibiotic comes from the Greek *anti*, meaning “against,” and *bios*, meaning “life.” An antibiotic is an organism-produced chemical that is hostile to the growth of other organisms. Today’s news and media often address concerns about an antibiotic crisis. Are antibiotics that were used to treat bacterial infections easily treatable 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 of these questions challenge the healthcare community.

Foodborne Diseases

Prokaryotes are everywhere: They readily colonize the surface of any type of material, and food is not an exception. Outbreaks of bacterial infection related to food consumption are common. A foodborne disease (colloquially called “food poisoning”) is an illness resulting from the consumption of food contaminated with pathogenic bacteria, viruses, or other parasites. Although the United States has one of the safest food supplies in the world, the Center 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.”[footnote]

http://www.cdc.gov/ecoli/2006/september, Centers for Disease Control and Prevention, “Multi-state outbreak of *E. coli* O157:H7 infections from spinach,” September-October (2006).

Beneficial Prokaryotes

Not all prokaryotes are pathogenic. On the contrary, pathogens represent only a very small percentage of the diversity of the microbial world. In fact, our life and all life on this planet would not be possible without prokaryotes.

Prokaryotes, and Food and Beverages

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. However, humans have used prokaryotes to create products before the term biotechnology was even coined. And some of the goods and services are as simple as cheese, yogurt, sour cream, vinegar, cured sausage, sauerkraut, and fermented seafood that contains both bacteria and archaea ([link]).

http://www.cbd.int/convention/articles/?a=cbd-02http://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 (pesticides and fertilizers) that leach from soil into groundwater. Certain toxic metals, such as selenium and arsenic compounds, can also be removed from water by bioremediation. The reduction of ${\text{SeO}}_{4}^{{2}^{-}}$

 to ${\text{SeO}}_{3}^{{2}^{-}}$
 and to Se0 (metallic selenium) is a method used to remove selenium ions from water. Mercury is an example of a toxic metal that can be removed from an environment by bioremediation. Mercury is an active ingredient of some pesticides; it is used in industry and is also a byproduct of certain industries, such as battery production. 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 Hg2+ to Hg0, which is nontoxic to humans.

Eukaryotic Origins

Abstract:
By the end of this section, you will be able to:
* Describe the endosymbiotic theory
* Explain the origin of mitochondria and chloroplasts

Endosymbiosis

The origin of eukaryotic cells was largely a mystery until a revolutionary hypothesis was comprehensively examined in the 1960s by Lynn Margulis. The endosymbiotic theory states that eukaryotes are a product of one prokaryotic cell engulfing another, one living within another, and evolving together over time until the separate cells were no longer recognizable as such. This once-revolutionary hypothesis had immediate persuasiveness and is now widely accepted, with work progressing on uncovering the steps involved in this evolutionary process as well as the key players. It has become clear that many nuclear eukaryotic genes and the molecular machinery responsible for replicating and expressing those genes appear closely related to the Archaea. On the other hand, the metabolic organelles and the genes responsible for many energy-harvesting processes had their origins in bacteria. Much remains to be clarified about how this relationship occurred; this continues to be an exciting field of discovery in biology. Several endosymbiotic events likely contributed to the origin of the eukaryotic cell.

Protists

Abstract:
By the end of this section, you will be able to:
* Describe the main characteristics of protists
* Describe important pathogenic species of protists
* Describe the roles of protists as food sources and as decomposers

Characteristics of Protists

There are over 100,000 described living species of protists, and it is unclear how many undescribed species may exist. Since many protists live in symbiotic relationships with other organisms and these relationships are often species specific, there is a huge potential for undescribed protist diversity that matches the diversity of the hosts. As the catchall term for eukaryotic organisms that are not animals, plants, fungi, or any single phylogenetically related group, it is not surprising that few characteristics are common to all protists.

How Protists Obtain Energy

Protists exhibit many forms of nutrition and may be aerobic or anaerobic. Photosynthetic protists (photoautotrophs) are characterized by the presence of chloroplasts. Other protists are heterotrophs 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]). This vesicle then fuses with a lysosome, 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 through exocytosis.

Reproduction

Protists reproduce by a variety of mechanisms. Most are capable some form of asexual reproduction, such as binary fission to produce two daughter cells, or multiple fission to divide simultaneously into many daughter cells. Others produce tiny buds that go on to divide and grow to the size of the parental protist. Sexual reproduction, involving meiosis and fertilization, is common among protists, and many protist species can switch from asexual to sexual reproduction when necessary. Sexual reproduction is often associated with periods when nutrients are depleted or environmental changes occur. Sexual reproduction may allow the protist to recombine genes and produce new variations of progeny that may be better suited to surviving in the new environment. However, sexual reproduction is also often associated with cysts that are a protective, resting stage. Depending on their habitat, the cysts may be particularly resistant to temperature extremes, desiccation, or low pH. This strategy also allows certain protists to “wait out” stressors until their environment becomes more favorable for survival or until they are carried (such as by wind, water, or transport on a larger organism) to a different environment because cysts exhibit virtually no cellular metabolism.

Protist Diversity

With the advent of DNA sequencing, the relationships among protist groups and between protist groups and other eukaryotes are beginning to become clearer. Many relationships that were based on morphological similarities are being replaced by new relationships based on genetic similarities. Protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon is called convergent evolution. It is one reason why protist classification is so challenging. The emerging classification scheme groups the entire domain Eukaryota into six “supergroups” that contain all of the protists as well as animals, plants, and fungi ([link]); these include the Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, and Opisthokonta. The supergroups are believed to be monophyletic; all organisms within each supergroup are believed to have evolved from a single common ancestor, and thus all members are most closely related to each other than to organisms outside that group. There is still evidence lacking for the monophyly of some groups.

Human Pathogens

Many protists are pathogenic parasites that must infect other organisms to survive and propagate. Protist parasites include the causative agents of malaria, African sleeping sickness, 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]**a**). Grape plants infected with *P*. *viticola* appear stunted and have discolored withered leaves. The spread of downy mildew caused the near collapse of the French wine industry in the nineteenth century.

Beneficial Protists

Protists play critically important ecological roles as producers particularly in the world’s oceans. They are equally important on the other end of food webs as decomposers.

Fungi

Abstract:
By the end of this section, you will be able to:
* List the characteristics of fungi
* Describe fungal parasites and pathogens of plants and infections in humans
* Describe the importance of fungi to the environment
* Summarize the beneficial role of fungi in food and beverage preparation and in the chemical and pharmaceutical industry

Cell Structure and Function

Fungi are eukaryotes and as such have a complex cellular organization. As eukaryotes, fungal cells contain a membrane-bound nucleus. A few types of fungi have structures comparable to the plasmids (loops of DNA) seen in bacteria. Fungal cells also contain mitochondria and a complex system of internal membranes, including the endoplasmic reticulum and Golgi apparatus.

Fungal Diversity

The kingdom Fungi contains four major divisions that were established according to their mode of sexual reproduction. Unrelated fungi that reproduce without a sexual cycle, are placed for convenience in a fifth division, and a sixth major fungal group that does not fit well with any of the previous five has recently been described. Not all mycologists agree with this scheme. Rapid advances in molecular biology and the sequencing of 18S rRNA (a component of ribosomes) continue to reveal new and different relationships between the various categories of fungi.

Pathogenic Fungi

Many fungi have negative impacts on other species, including humans and the organisms they depend on for food. Fungi may be parasites, pathogens, and, in a very few cases, predators.

Plant Parasites and Pathogens

The production of enough good-quality crops is essential to our existence. Plant diseases have ruined crops, bringing widespread famine. Most plant pathogens are fungi that cause tissue decay and eventual death of the host ([link]). In addition to destroying plant tissue directly, some plant pathogens spoil crops by producing potent toxins. 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. Fungi attack animals directly by colonizing and destroying tissues. Humans and other animals can be poisoned by eating toxic mushrooms or foods contaminated by fungi. In addition, individuals who display hypersensitivity to molds and spores 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 adversely affect the eukaryotic animal host.

Beneficial Fungi

Fungi play a crucial role in the balance of ecosystems. They colonize most habitats on Earth, preferring dark, moist conditions. They can thrive in seemingly hostile environments, such as the tundra, thanks to a most successful symbiosis with photosynthetic organisms, like lichens. Fungi are not obvious in the way that large animals or tall trees are. Yet, like bacteria, they are major decomposers of nature. With their versatile metabolism, fungi break down organic matter that is insoluble and would not be recycled otherwise.

Diversity of Plants

Introduction

The Plant Kingdom

Abstract:
By the end of this section, you will be able to:
* Describe the major characteristics of the plant kingdom
* Discuss the challenges to plant life on land
* Describe the adaptations that allowed plants to colonize land

Plant Adaptations to Life on Land

As organisms adapt to life on land, they have to contend with several challenges in the terrestrial environment. Water has been described as “the stuff of life.” The cell’s interior—the medium in which most small molecules dissolve and diffuse, and in which the majority of the chemical reactions of metabolism take place—is a watery soup. 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, their aerial structures are likely to dry out. Water provides buoyancy to organisms that live in aquatic habitats. On land, plants need to develop structural support in air—a medium that does not give the same lift. Additionally, the male and female gametes must reach one another using new strategies because swimming is no longer possible. Finally, both gametes and zygotes must be protected from drying out. The successful land plants evolved strategies to deal with all of these challenges, although not all adaptations appeared at once. Some species did not move far from an aquatic environment, whereas others left the water and went on to conquer the driest environments on Earth.

Additional Land Plant Adaptations

As plants adapted to dry land and became independent of the constant presence of water in damp habitats, new organs and structures made their appearance. Early land plants did not grow above a few inches off the ground, and on these low mats, they competed for light. By evolving 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). The evolution of vascular tissue for the distribution of water and solutes was a necessary prerequisite for plants to evolve larger bodies. The vascular system contains xylem and phloem tissues. Xylem conducts water and minerals taken from the soil up to the shoot; phloem transports food derived from photosynthesis throughout the entire plant. The root system that evolved to take up water and minerals also anchored the increasingly taller shoot in the soil.

The Major Divisions of Land Plants

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 formed of specialized cells for the transport of water and nutrients are referred to as nonvascular plants. The bryophytes, liverworts, mosses, and hornworts are seedless and nonvascular, and likely appeared early in land plant evolution. Vascular plants developed a network of cells that conduct water and solutes through the plant body. The first vascular plants appeared in the late Ordovician (461–444 million years ago) 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. They do not produce seeds, which are embryos with their stored food reserves protected by a hard casing. The seed plants 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 plants, the flowering plants, or angiosperms, which protect their seeds inside chambers at the center of a flower. The walls of these chambers later develop into fruits.

Seedless Plants

Abstract:
By the end of this section, you will be able to:
* Describe the distinguishing traits of the three types of bryophytes
* Identify the new traits that first appear in seedless vascular plants
* Describe the major classes of seedless vascular plants

Bryophytes

Bryophytes, an informal grouping of the nonvascular plants, are the closest extant relative of early terrestrial plants. The first bryophytes most probably appeared in the Ordovician period, about 490 million years ago. Because of the lack of lignin—the tough polymer in cell walls in the stems of vascular plants—and other resistant structures, the likelihood of bryophytes forming fossils is rather small, though some spores made up of sporopollenin have been discovered that have been attributed to early bryophytes. By the Silurian period (440 million years ago), however, vascular plants had spread throughout the continents. This fact is used as evidence that nonvascular plants must have preceded the Silurian period.

Liverworts

Liverworts (Marchantiophyta) may be viewed as the plants most closely related to the ancestor that moved to land. Liverworts have colonized many habitats on Earth and diversified to more than 6,000 existing species ([link]**a**). Some gametophytes form lobate green structures, as seen in [link]**b**. The shape is similar to the lobes of the liver and, hence, provides the origin of the common name given to the division.

Hornworts

The hornworts (Anthocerotophyta) have colonized a variety of habitats on land, although they are never far from a source of moisture. There are about 100 described species of hornworts. The dominant phase of the life cycle of hornworts is the short, blue-green gametophyte. The sporophyte is the defining characteristic of the group. It is a long and narrow pipe-like structure that emerges from the parent gametophyte and maintains growth throughout the life of the plant ([link]).

Mosses

More than 12,000 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, their shallow rhizoids allow them to fasten to a substrate without digging into the frozen soil. They slow down erosion, store moisture and soil nutrients, and provide shelter for small animals and food for larger herbivores, such as the musk ox. Mosses are very sensitive to air pollution and are used to monitor the quality of air. The sensitivity of mosses to copper salts makes these salts a common ingredient of compounds marketed to eliminate mosses in lawns ([link]).

Vascular Plants

The vascular plants are the dominant and most conspicuous group of land plants. There are about 275,000 species of vascular plants, which represent more than 90 percent of Earth’s vegetation. Several evolutionary innovations explain their success and their spread to so many habitats.

Seedless Vascular Plants

By the Late Devonian period (385 million years ago), plants had evolved vascular tissue, well-defined leaves, and root systems. With these advantages, plants increased in height and size. During the Carboniferous period (359–299 million years ago), swamp forests of club mosses and horsetails, with some specimens reaching more than 30 meters tall, 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 lifecycle.

Seed Plants: Gymnosperms

Abstract:
By the end of this section, you will be able to:
* Discuss the type of seeds produced by gymnosperms, as well as other characteristics of gymnosperms
* List the four groups of modern-day gymnosperms and provide examples of each

The Evolution of Seed Plants

In seed plants, the evolutionary trend led to a dominant sporophyte generation, in which the larger and more ecologically significant generation for a species is the diploid plant. At the same time, the trend led to a reduction in the size of the gametophyte, from a conspicuous structure to a microscopic cluster of cells enclosed in the tissues of the sporophyte. Lower vascular plants, such as club mosses and ferns, are mostly homosporous (produce only one type of spore). In contrast, all seed plants, or spermatophytes, are heterosporous, forming two types of spores: megaspores (female) and microspores (male). Megaspores develop into female gametophytes that produce eggs, and microspores mature into male gametophytes that generate sperm. Because gametophyte maturation depends on water and nutrient supply from the dominant sporophyte tissue, they are not free-living, as are the gametophytes of seedless vascular plants. Heterosporous seedless plants are seen as the evolutionary forerunners of seed plants.

Gymnosperms

Gymnosperms (“naked seed”) are a diverse group of seed plants and are paraphyletic. Paraphyletic groups do not include descendants of a single common ancestor. Gymnosperm characteristics include naked seeds, separate female and male gametes, pollination by wind, and tracheids, which transport water and solutes in the vascular system.

Diversity of Gymnosperms

Modern gymnosperms are classified into four major divisions and comprise about 1,000 described species. Coniferophyta, Cycadophyta, and Ginkgophyta are similar in their production of secondary cambium (cells that generate the vascular system of the trunk or stem) and their pattern of seed development, but are not closely related phylogenetically to each other. Gnetophyta are considered the closest group to angiosperms because they produce true xylem tissue that contains both tracheids and vessel elements.

Seed Plants: Angiosperms

Abstract:
By the end of this section, you will be able to:
* Describe the main parts of a flower and their purpose
* Detail the life cycle of an angiosperm
* Discuss the two main groups into which flower plants are divided, as well as explain how basal angiosperms differ from others

Flowers

Flowers are modified leaves or sporophylls organized around a central stalk. Although they vary greatly in appearance, all flowers contain the same structures: sepals, petals, pistils, and stamens. A whorl of sepals (the calyx) is located at the base of the peduncle, or stem, and encloses the floral bud before it opens. 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—this led botanists to coin the word tepal. Petals (collectively the corolla) are located inside the whorl of sepals and usually display vivid colors to attract pollinators. Flowers pollinated by wind are usually small and dull. The sexual organs are located at the center of the flower.

Fruit

The seed forms in an ovary, which enlarges as the seeds grow. As the seed develops, the walls of the ovary also thicken and form the fruit. In botany, a fruit is a fertilized and fully grown, ripened ovary. Many foods commonly called vegetables are actually fruit. Eggplants, zucchini, string beans, and bell peppers are all technically fruit because they contain seeds and are derived from the thick ovary tissue. Acorns and winged maple keys, whose scientific name is a samara, are also fruit.

The Life Cycle of an Angiosperm

The adult, or sporophyte, phase is the main phase in an angiosperm’s life cycle. Like gymnosperms, angiosperms are heterosporous. They produce microspores, which develop into pollen grains (the male gametophytes), and megaspores, which form an ovule containing the female gametophytes. Inside the anthers’ microsporangia ([link]), male microsporocytes divide by meiosis, generating haploid microspores that 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.

Diversity of Angiosperms

Angiosperms are classified in a single division, the Anthophyta. Modern angiosperms appear to be a monophyletic group, which means that they originate from a single ancestor. Flowering plants are divided into two major groups, according to the structure of the cotyledons, the pollen grains, and other features: monocots, which include grasses and lilies, and eudicots or dicots, a polyphyletic group. Basal angiosperms are a group of plants that are believed to have branched off before the separation into monocots and eudicots because they exhibit traits from both groups. They are categorized separately in many classification schemes, and correspond to a grouping known as the Magnoliidae. The Magnoliidae group is comprised of magnolia trees, laurels, water lilies, and the pepper family.

The Role of Seed Plants

Without seed plants, life as we know it would not be possible. Plants play a key role in the maintenance of terrestrial ecosystems through the stabilization of soils, cycling of carbon, and climate moderation. Large tropical forests release oxygen and act as carbon dioxide “sinks.” Seed plants provide shelter to many life forms, as well as food for herbivores, thereby indirectly feeding carnivores. Plant secondary metabolites are used for medicinal purposes and industrial production. Virtually all animal life is dependent on plants for survival.

Diversity of Animals

Introduction

Features of the Animal Kingdom

Abstract:
By the end of this section, you will be able to:
* List the features that distinguish the animal kingdom from other kingdoms
* Explain the processes of animal reproduction and embryonic development
* Describe the hierarchy of basic animal classification
* Compare and contrast the embryonic development of protostomes and deuterostomes

Complex Tissue Structure

A hallmark trait of animals is specialized structures that are differentiated to perform unique functions. As multicellular organisms, most animals develop specialized cells that group together into tissues with specialized functions. A tissue is a collection of similar cells that had a common embryonic origin. There are four main types of animal tissues: nervous, muscle, connective, and epithelial. Nervous tissue contains neurons, or nerve cells, which transmit nerve impulses. Muscle tissue contracts to cause all types of body movement from locomotion of the organism to movements within the body itself. Animals also have specialized connective tissues that provide many functions, including transport and structural support. Examples of connective tissues include blood and bone. Connective tissue is comprised of cells separated by extracellular material made of organic and inorganic materials, such as the protein and mineral deposits of bone. Epithelial tissue covers the internal and external surfaces of organs inside the animal body and the external surface of the body of the organism.

Animal Reproduction and Development

Most animals have diploid body (somatic) cells and a small number of haploid reproductive (gamete) cells produced through meiosis. Some exceptions exist: For example, in bees, wasps, and ants, the male is haploid because it develops from an unfertilized egg. Most animals undergo sexual reproduction, while many also have mechanisms of asexual reproduction.

Classification Features of Animals

Animals are classified according to morphological and developmental characteristics, such as a body plan. With the exception of sponges, the animal body plan is symmetrical. This means that their distribution of body parts is balanced along an axis. Additional characteristics that contribute to animal classification include the number of tissue layers formed during development, the presence or absence of an internal body cavity, and other features of embryological development.

Sponges and Cnidarians

Abstract:
By the end of this section, you will be able to:
* Describe the organizational features of the simplest animals
* Describe the organizational features of cnidarians

Sponges

Animals in subkingdom Parazoa represent the simplest animals and include the sponges, or phylum Porifera ([link]). All sponges are aquatic and the majority of species are marine. Sponges live in intimate contact with water, which plays a role in their feeding, gas exchange, and excretion. Much of the body structure of the sponge is dedicated to moving water through the body so it can filter out food, absorb dissolved oxygen, and eliminate wastes.

Cnidarians

The phylum Cnidaria includes animals that show radial or biradial symmetry and are diploblastic. Nearly all (about 99 percent) cnidarians are marine species. Cnidarians have specialized cells known as cnidocytes (“stinging cells”) containing organelles called nematocysts. These cells are concentrated around the mouth and tentacles of the animal and can immobilize prey with toxins. Nematocysts contain coiled threads that may bear barbs. The outer wall of the cell has a hairlike projection that is sensitive to touch. When touched, the cells fire the toxin-containing coiled threads that can penetrate and stun the predator or prey (see [link]).

Flatworms, Nematodes, and Arthropods

Abstract:
By the end of this section, you will be able to:
* Describe the structure and systems of flatworms
* Describe the structural organization of nematodes
* Compare the internal systems and the appendage specialization of arthropods

Flatworms

The relationships among flatworms, or phylum Platyhelminthes, is being revised and the description here will follow the traditional groupings. Most flatworms are parasitic, including important parasites of humans. Flatworms have three embryonic germ layers that give rise to surfaces covering tissues, internal tissues, and the lining of the digestive system. The epidermal tissue is a single layer of cells or a layer of fused cells covering a layer of circular muscle above a layer of longitudinal muscle. The mesodermal tissues include support cells and secretory cells that secrete mucus and other materials to the surface. The flatworms are acoelomate, so their bodies contain no cavities or spaces between the outer surface and the inner digestive tract.

Nematodes

The phylum Nematoda, or roundworms, includes more than 28,000 species with an estimated 16,000 parasitic species. The name Nematoda is derived from the Greek word “nemos,” which means “thread.” Nematodes are present in all habitats and are extremely common, although they are usually not visible ([link]).

Arthropoda

The name “arthropoda” means “jointed legs,” which aptly describes each of the enormous number of species belonging to this phylum. Arthropoda dominate the animal kingdom with an estimated 85 percent of known species, with many still undiscovered or undescribed. The principal characteristics of all the animals in this phylum are functional segmentation of the body and the presence of jointed appendages ([link]). As members of Ecdysozoa, arthropods also have an exoskeleton made principally of chitin. Arthropoda is the largest phylum in the animal world in terms of numbers of species, and insects form the single largest group within this phylum. Arthropods are true coelomate animals and exhibit prostostomic development.

Mollusks and Annelids

Abstract:
By the end of this section, you will be able to:
* Describe the unique anatomical features of mollusks
* Describe the features of an animal classified in phylum Annelida

Phylum Mollusca

Mollusca is the predominant phylum in marine environments, where it is estimated that 23 percent of all known marine species belong to this phylum. It is the second most diverse phylum of animals with over 75,000 described species. The name “mollusca” signifies a soft body, as the earliest descriptions of mollusks came from observations of unshelled, soft-bodied cuttlefish (squid relatives). Although mollusk body forms vary, they share key characteristics, such as a ventral, muscular foot that is typically used for locomotion; the visceral mass, which contains most of the internal organs of the animal; and a dorsal mantle, which is a flap of tissue over the visceral mass that creates a space called the mantle cavity. The mantle may or may not secrete a shell of calcium carbonate. In addition, many mollusks have a scraping structure at the mouth, called a radula ([link]).

Annelida

Phylum Annelida are segmented worms 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 name of the phylum is derived from the Latin word *annellus*, which means a small ring. Approximately 16,500 species have been described. The phylum includes earthworms, polychaete worms, and leeches. Like mollusks, annelids exhibit protostomic development.

Physiological Processes of Annelida

The skin of annelids is protected by a cuticle that is thinner than the cuticle of the ecdysozoans and does not need to be molted for growth. Chitinous hairlike extensions, anchored in the skin and projecting from the cuticle, called chaetae, are present in every segment in most groups. The chaetae are a defining character of annelids. Polychaete worms have paired, unjointed limbs called parapodia on each segment used for locomotion and breathing. Beneath the cuticle there are two layers of muscle, one running around its circumference (circular) and one running the length of the worm (longitudinal). Annelids have a true coelom in which organs are distributed and bathed in coelomic fluid. Annelids possess a well-developed complete digestive system with specialized organs: mouth, muscular pharynx, esophagus, and crop. A cross-sectional view of a body segment of an earthworm is shown in [link]; each segment is limited by a membrane that divides the body cavity into compartments.

Annelid Diversity

Phylum Annelida includes the classes Polychaeta and Clitellata ([link]); the latter contains subclasses Oligochaeta, Hirudinoidea, and Branchiobdellida.

Echinoderms and Chordates

Abstract:
By the end of this section, you will be able to:
* Describe the distinguishing characteristics of echinoderms
* Describe the distinguishing characteristics of chordates

Echinoderms

Echinodermata are named for their spiny skin (from the Greek “echinos” meaning “spiny” and “dermos” meaning “skin”). The phylum includes about 7,000[footnote] described living species, such as sea stars, sea cucumbers, sea urchins, sand dollars, and brittle stars. Echinodermata are exclusively marine.

“Number of Living Species in Australia and the World,” A.D. Chapman, Australia Biodiversity Information Services, last modified August 26, 2010, http://www.environment.gov.au/biodiversity/abrs/publications/other/species-numbers/2009/03-exec-summary.html.

Physiological Processes of Echinoderms

Echinoderms have a unique system for gas exchange, nutrient circulation, and locomotion called the water vascular system. The system consists of a central ring canal and radial canals extending along each arm. Water circulates through these structures allowing for gas, nutrient, and waste exchange. A structure on top of the body, called the madreporite, regulates the amount of water in the water vascular system. “Tube feet,” which protrude through openings in the endoskeleton, may be expanded or contracted using the hydrostatic pressure in the system. The system allows for slow movement, but a great deal of power, as witnessed when the tube feet latch on to opposite halves of a bivalve mollusk, like a clam, and slowly, but surely pull the shells apart, exposing the flesh within.

Echinoderm Diversity

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

Chordates

The majority of species in the phylum Chordata are found in the subphylum Vertebrata, which include many species with which we are familiar. The vertebrates contain more than 60,000 described species, divided into major groupings of the lampreys, fishes, amphibians, reptiles, birds, and mammals.

Invertebrate Chordates

In addition to the vertebrates, the phylum Chordata contains two clades of invertebrates: Urochordata (tunicates) and Cephalochordata (lancelets). Members of these groups possess the four distinctive features of chordates at some point during their development.

Vertebrates

Abstract:
By the end of this section, you will be able to:
* Describe the difference between jawless and jawed fishes
* Explain the main characteristics of amphibians, reptiles, and birds
* Describe the derived characteristics in birds that facilitate flight
* Name and describe the distinguishing features of the three main groups of mammals
* Describe the derived features that distinguish primates from other animals

Fishes

Modern fishes include an estimated 31,000 species. Fishes were the earliest vertebrates, and jawless fishes were the earliest of these. Jawless fishes—the present day hagfishes and lampreys—have a distinct cranium and complex sense organs including eyes, distinguishing them from the invertebrate chordates. The jawed fishes evolved later and are extraordinarily diverse today. Fishes are active feeders, rather than sessile, suspension feeders.

Amphibians

Amphibians are vertebrate tetrapods. Amphibia includes frogs, salamanders, and caecilians. The term amphibian means “dual life,” which is a reference to the metamorphosis that many frogs undergo from a tadpole to an adult and the mixture of aquatic and terrestrial environments in their life cycle. Amphibians evolved in the Devonian period and were the earliest terrestrial tetrapods.

Reptiles and Birds

The amniotes—reptiles, birds, and mammals—are distinguished from amphibians by their terrestrially adapted (shelled) egg and an embryo protected by amniotic membranes. The evolution of amniotic membranes meant that the embryos of amniotes could develop within an aquatic environment inside the egg. This led to less dependence on a water environment for development and allowed the amniotes to invade drier areas. This was a significant evolutionary change that distinguished them from amphibians, which were restricted to moist environments due to their shell-less eggs. Although the shells of various amniotic species vary significantly, they all allow retention of water. The membranes of the amniotic egg also allowed gas exchange and sequestering of wastes within the enclosure of an eggshell. The shells of bird eggs are composed of calcium carbonate and are hard and brittle, but possess pores for gas and water exchange. The shells of reptile eggs are more leathery and pliable. Most mammals do not lay eggs; however, even with internal gestation, amniotic membranes are still present.

Mammals

Mammals are vertebrates that have hair and mammary glands used to provide nutrition for their young. Certain features of the jaw, skeleton, skin, and internal anatomy are also unique to mammals. The presence of hair is one of the key characteristics of a mammal. Although it is not very extensive in some groups, such as whales, hair has many important functions for mammals. Mammals are endothermic, and hair provides insulation by trapping a layer of air close to the body to retain metabolic heat. Hair also serves as a sensory mechanism through specialized hairs called vibrissae, better known as whiskers. These attach to nerves that transmit touch information, which is particularly useful to nocturnal or burrowing mammals. Hair can also provide protective coloration.

Animal Structure and Function

The Body’s Systems

Introduction

Homeostasis and Osmoregulation

Abstract:
By the end of this section, you will be able to:
* Explain the concept of homeostasis
* Describe thermoregulation of endothermic and ectothermic animals
* Explain how the kidneys serve as the main osmoregulatory organs in the human body

Homeostasis

The goal of homeostasis is the maintenance of equilibrium around a specific value of some aspect of the body or its cells 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 activities of the system so the value moves back toward the set point. For instance, if the body becomes too warm, adjustments are made to cool the animal. If glucose levels in the blood rise after a meal, adjustments are made to lower them and to get the nutrient into tissues that need it or to store it for later use.

Thermoregulation

Animals can be divided into two groups: those that maintain a constant body temperature in the face of differing environmental temperatures, and those that have a body temperature that is the same as their environment and thus varies with the environmental temperature. Animals that do not have internal control of their body temperature are called ectotherms. The body temperature of these organisms is generally similar to the temperature of the environment, although the individual organisms may do things that keep their bodies slightly below or above the environmental temperature. This can include burrowing underground on a hot day or resting in the sunlight on a cold day. The ectotherms have been called cold-blooded, a term that may not apply to an animal in the desert with a very warm body temperature.

Osmoregulation

Osmoregulation is the process of maintaining salt and water balance (osmotic balance) across membranes within the body. The fluids inside and surrounding cells are composed of water, electrolytes, and nonelectrolytes. An electrolyte is a compound that dissociates into ions when dissolved in water. A nonelectrolyte, in contrast, does not dissociate into ions in water. The body’s fluids include blood plasma, fluid that exists within cells, and the interstitial fluid that exists in the spaces between cells and tissues of the body. The membranes of the body (both the membranes around cells and the “membranes” made of cells lining body cavities) are semipermeable membranes. Semipermeable membranes are permeable to certain types of solutes and to water, but typically cell membranes are impermeable to solutes.

Digestive System

Abstract:
By the end of this section, you will be able to:
* Explain the processes of digestion and absorption
* 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
* Describe the essential nutrients required for cellular function that cannot be synthesized by the animal body
* Describe how excess carbohydrates and energy are stored in the body

The Human Digestive System

The process of digestion begins in the mouth with the intake of food ([link]). The teeth play an important role in masticating (chewing) or physically breaking food into smaller particles. The enzymes present in saliva also begin to chemically break down food. The food is then swallowed and enters the esophagus—a long tube that connects the mouth to the stomach. Using peristalsis, or wave-like smooth-muscle contractions, the muscles of the esophagus push the food toward the stomach. The stomach contents are extremely acidic, with a pH between 1.5 and 2.5. This acidity kills microorganisms, breaks down food tissues, and activates digestive enzymes. Further breakdown of food takes place in the small intestine where bile produced by the liver, and enzymes produced by the small intestine and the pancreas, continue the process of digestion. The smaller molecules are absorbed into the blood stream through the epithelial cells lining the walls of the small intestine. The waste material travels on to the large intestine where water is absorbed and the drier waste material is compacted into feces; it is stored until it is excreted through the anus.

Nutrition

The human diet should be well balanced to provide nutrients required for bodily function and the minerals and vitamins required for maintaining structure and regulation necessary for good health and reproductive capability ([link]).

Circulatory and Respiratory Systems

Abstract:
By the end of this section, you will be able to:
* Describe the passage of air from the outside environment to the lungs
* Describe the function of the circulatory system
* Describe the cardiac cycle
* Explain how blood flows through the body

The Respiratory System

Take a breath in and hold it. Wait several seconds and then let it out. Humans, when they are not exerting themselves, breathe approximately 15 times per minute on average. This equates to about 900 breaths an hour or 21,600 breaths per day. With every inhalation, air fills the lungs, and with every exhalation, it rushes back out. That air is doing more than just inflating and deflating the lungs in the chest cavity. The air contains oxygen that crosses the lung tissue, enters the bloodstream, and travels to organs and tissues. There, oxygen is exchanged for carbon dioxide, which is a cellular waste material. Carbon dioxide exits the cells, enters the bloodstream, travels back to the lungs, and is expired out of the body during exhalation.

The Circulatory System

The circulatory system is a network of vessels—the arteries, veins, and capillaries—and a pump, the heart. In all vertebrate organisms this is a closed-loop system, in which the blood is largely separated from the body’s other extracellular fluid compartment, the interstitial fluid, which is the fluid bathing the cells. Blood circulates inside blood vessels and circulates unidirectionally from the heart around one of two circulatory routes, then returns to the heart again; this is a closed circulatory system. Open circulatory systems are found in invertebrate animals in which the circulatory fluid bathes the internal organs directly even though it may be moved about with a pumping heart.

The Heart

The heart is a complex muscle that consists of two pumps: one that pumps blood through pulmonary circulation to the lungs, and the other that pumps blood through systemic circulation to the rest of the body’s tissues (and the heart itself).

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 flow of blood through the heart coordinated by electrochemical signals that cause the heart muscle to contract and relax. In each cardiac cycle, a sequence of contractions pushes out the blood, pumping it through the body; this is followed by a relaxation phase, where the heart fills with blood. These two phases are called the systole (contraction) and diastole (relaxation), respectively ([link]). The signal for contraction begins at a location on the outside of the right atrium. The electrochemical signal moves from there across the atria causing them to contract. The contraction of the atria forces blood through the valves into the ventricles. Closing of these valves caused by the contraction of the ventricles produces a “lub” sound. The signal has, by this time, passed down the walls of the heart, through a point between the right atrium and right ventricle. The signal then causes the ventricles to contract. The ventricles contract together forcing blood into the aorta and the pulmonary arteries. Closing of the valves to these arteries caused by blood being drawn back toward the heart during ventricular relaxation produces a monosyllabic “dub” sound.

Blood Vessels

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 of the systemic circulation is the aorta; it branches into major arteries that take blood to different limbs and organs. The aorta and arteries near the heart have heavy but elastic walls that respond to and smooth out the pressure differences caused by the beating heart. Arteries farther away from the heart have more muscle tissue in their walls that can constrict to affect flow rates of blood. 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.

Endocrine System

Abstract:
By the end of this section, you will be able to:
* List the different types of hormones and explain their roles in maintaining homeostasis
* Explain how hormones work
* Explain how hormone production is regulated
* Describe the role of different glands in the endocrine system
* Explain how the different glands work together to maintain homeostasis

Hormones

Maintaining homeostasis within the body requires the coordination of many different systems and organs. One mechanism of communication between neighboring cells, and between cells and tissues in distant parts of the body, occurs through the release of chemicals called hormones. Hormones are released into body fluids, usually blood, which carries them to their target cells where they elicit a response. The cells that secrete hormones are often located in specific organs, called endocrine glands, and the cells, tissues, and organs that secrete hormones make up the endocrine system. Examples of endocrine organs include the pancreas, which produces the hormones insulin and glucagon to regulate blood-glucose levels, the adrenal glands, which produce hormones such as epinephrine and norepinephrine that regulate responses to stress, and the thyroid gland, which produces thyroid hormones that regulate metabolic rates.

How Hormones Work

Hormones cause changes in target cells by binding to specific cell-surface or intracellular hormone receptors, molecules embedded in the cell membrane or floating in the cytoplasm with a binding site that matches a binding site on the hormone molecule. In this way, even though hormones circulate throughout the body and come into contact with many different cell types, they only affect cells that possess the necessary receptors. Receptors for a specific hormone may be found on or in many different cells or may be limited to a small number of specialized cells. For example, thyroid hormones act on many different tissue types, stimulating metabolic activity throughout the body. Cells can have many receptors for the same hormone but often also possess receptors for different types of hormones. The number of receptors that respond to a hormone determines the cell’s sensitivity to that hormone, and the resulting cellular response. Additionally, the number of receptors available to respond to a hormone can change over time, resulting in increased or decreased cell sensitivity. In up-regulation, the number of receptors increases in response to rising hormone levels, making the cell more sensitive to the hormone and allowing for more cellular activity. When the number of receptors decreases in response to rising hormone levels, called down-regulation, cellular activity is reduced.

Endocrine Glands

The endocrine glands secrete hormones into the surrounding interstitial fluid; those hormones then diffuse into blood and are carried to various organs and tissues within the body. The endocrine glands include the pituitary, thyroid, parathyroid, adrenal glands, gonads, pineal, and pancreas.

Regulation of Hormone Production

Hormone production and release are primarily controlled by negative feedback, as described in the discussion on homeostasis. In this way, the concentration of hormones in blood is maintained within a narrow range. For example, the anterior pituitary signals the thyroid to release thyroid hormones. Increasing levels of these hormones in the blood then give feedback to the hypothalamus and anterior pituitary to inhibit further signaling to the thyroid gland ([link]).

Musculoskeletal System

Abstract:
By the end of this section, you will be able to:
* Discuss the axial and appendicular parts of the skeletal system
* Explain the role of joints in skeletal movement
* Explain the role of muscles in locomotion

Skeletal System

The human skeleton is an endoskeleton that consists of 206 bones in the adult. An endoskeleton develops within the body rather than outside like the exoskeleton of insects. The skeleton has five main functions: providing support to the body, storing minerals and lipids, producing blood cells, protecting internal organs, and allowing for movement. The skeletal system in vertebrates is divided into the axial skeleton (which consists of the skull, vertebral column, and rib cage), and the appendicular skeleton (which consists of limb bones, the pectoral or shoulder girdle, and the pelvic girdle).

Joints and Skeletal Movement

The point at which two or more bones meet is called a joint, or articulation. Joints are responsible for movement, such as the movement of limbs, and stability, such as the stability found in the bones of the skull.

Muscles

Muscles allow for movement such as walking, and they also facilitate bodily processes such as respiration and digestion. The body contains three types of muscle tissue: skeletal muscle, cardiac muscle, and smooth muscle ([link]).

Skeletal Muscle Fiber Structure and Function

Each skeletal muscle fiber is a skeletal muscle cell. 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. They attach to the plasma membrane, called the sarcolemma, at their ends, so that as myofibrils shorten, the entire muscle cell contracts ([link]).

Nervous System

Abstract:
By the end of this section, you will be able to:
* Describe the form and function of a neuron
* Describe the basic parts and functions of the central nervous system
* Describe the basic parts and functions of the peripheral nervous system

Neurons and Glial Cells

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.

How Neurons Communicate

All functions performed by the nervous system—from a simple motor reflex to more advanced functions like making a memory or a decision—require neurons to communicate with one another. Neurons communicate between the axon of one neuron and the dendrites, and sometimes the cell body, of another neuron across the gap between them, known as the synaptic cleft. When an action potential reaches the end of an axon it stimulates the release of neurotransmitter molecules into the synaptic cleft between the synaptic knob of the axon and the post-synaptic membrane of the dendrite or soma of the next cell. The neurotransmitter is released through exocytosis of vesicles containing the neurotransmitter molecules. The neurotransmitter diffuses across the synaptic cleft and binds to receptors in the post-synaptic membrane. These receptor molecules are chemically regulated ion channels and will open, allowing sodium to enter the cell. If sufficient neurotransmitter has been released an action potential may be initiated in the next cell, but this is not guaranteed. If insufficient neurotransmitter is released the nerve signal will die at this point. There are a number of different neurotransmitters that are specific to neuron types that have specific functions.

The Central Nervous System

The central nervous system (CNS) is made up of the brain and spinal cord and is covered with three layers of protective coverings called meninges (“meninges” is derived from the Greek and means “membranes”) ([link]). The outermost layer is the dura mater, the middle layer is the web-like arachnoid mater, and the inner layer is the pia mater, which directly contacts and covers the brain and spinal cord. The space between the arachnoid and pia maters is filled with cerebrospinal fluid (CSF). The brain floats in CSF, which acts as a cushion and shock absorber.

The 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, cerebellum, brainstem, and retinas. The outermost part of the brain is a thick piece of nervous system tissue called the cerebral cortex. The cerebral cortex, limbic system, and basal ganglia make up the two cerebral hemispheres. A thick fiber bundle called the corpus callosum (corpus = “body”; callosum = “tough”) connects the two hemispheres. Although there are some brain functions that are localized more to one hemisphere than the other, the functions of the two hemispheres are largely redundant. In fact, sometimes (very rarely) an entire hemisphere is removed to treat severe epilepsy. While patients do suffer some deficits following the surgery, they can have surprisingly few problems, especially when the surgery is performed on children who have very immature nervous systems.

Spinal cord

Connecting to the brainstem and extending down the body through the spinal column is the spinal cord. 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 meninges and the bones of the vertebral 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 ([link]). Axons make up the “white matter” and neuron and glia cell bodies (and interneurons) make up the “gray matter.” Axons and cell bodies in the dorsa spinal cord convey mostly sensory information from the body to the brain. Axons and cell bodies in the spinal cord primarily transmit signals controlling movement from the brain to the body.

The Peripheral Nervous System

The peripheral nervous system (PNS) is the connection between the central nervous system and the rest of the body. The PNS can be broken down into the autonomic nervous system, which controls bodily functions without conscious control, and the sensory-somatic nervous system, which transmits sensory information from the skin, muscles, and sensory organs to the CNS and sends motor commands from the CNS to the muscles.

The Immune System and Disease

Introduction

Viruses

Abstract:
By the end of this section, you will be able to:
* Describe how viruses were first discovered and how they are detected
* Explain the detailed steps of viral replication
* Describe how vaccines are used in prevention and treatment of viral diseases

How Viruses Replicate

Viruses were first discovered after the development of a porcelain filter, called the Chamberland-Pasteur filter, which could remove all bacteria visible under 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 through 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 proven that these “filterable” infectious agents were not simply very small bacteria but were a new type of tiny, disease-causing particle.

Viruses and Disease

Viruses cause a variety of diseases in animals, including humans, ranging from the common cold to potentially fatal illnesses like meningitis ([link]). These diseases can be treated by antiviral drugs or by vaccines, but some viruses, such as HIV, are capable of avoiding the immune response and mutating so as to become resistant to antiviral drugs.

Innate Immunity

Abstract:
By the end of this section, you will be able to:
* Describe the body’s innate physical and chemical defenses
* Explain the inflammatory response
* Describe the complement system

External and Chemical Barriers

The body has significant physical barriers to potential pathogens. The skin contains the protein keratin, which resists physical entry into cells. Other body surfaces, particularly those associated with body openings, are protected by the mucous membranes. The sticky mucus provides a physical trap for pathogens, preventing their movement deeper into the body. The openings of the body, such as the nose and ears, are protected by hairs that catch pathogens, and the mucous membranes of the upper respiratory tract have cilia that constantly move pathogens trapped in the mucus coat up to the mouth.

Internal Defenses

When pathogens enter the body, the innate immune system responds with a variety of internal defenses. These include the inflammatory response, phagocytosis, natural killer cells, and the complement system. White blood cells in the blood and lymph recognize pathogens as foreign to the body. A white blood cell is larger than a red blood cell, is nucleated, and is typically able to move using amoeboid locomotion. Because they can move on their own, white blood cells can leave the blood to go to infected tissues. For example, a monocyte is a type of white blood cell that circulates in the blood and lymph and develops into a macrophage after it moves into infected tissue. A macrophage is a large cell that engulfs foreign particles and pathogens. Mast cells are produced in the same way as white blood cells, but unlike circulating white blood cells, mast cells take up residence in connective tissues and especially mucosal tissues. They are responsible for releasing chemicals in response to physical injury. They also play a role in the allergic response, which will be discussed later in the chapter.

Adaptive Immunity

Abstract:
By the end of this section, you will be able to:
* Explain adaptive immunity
* Describe cell-mediated immune response and humoral immune response
* Describe immune tolerance

B and T Cells

Lymphocytes, which are white blood cells, are formed with other blood cells in the red bone marrow found in many flat bones, such as the shoulder or pelvic bones. The two types of lymphocytes of the adaptive immune response are B and T cells ([link]). Whether an immature lymphocyte becomes a B cell or T cell depends on where in the body it matures. The B cells remain in the bone marrow to mature (hence the name “B” for “bone marrow”), while T cells migrate to the thymus, where they mature (hence the name “T” for “thymus”).

Humoral Immune Response

As mentioned, an antigen is a molecule that stimulates a response in the immune system. Not every molecule is antigenic. B cells participate in a chemical response to antigens present in the body by producing specific antibodies that circulate throughout the body and bind with the antigen whenever it is encountered. This is known as the humoral immune response. As discussed, during maturation of B cells, a set of highly specific B cells are produced that have many antigen receptor molecules in their membrane ([link]).

Cell-Mediated Immunity

Unlike B cells, T lymphocytes are unable to recognize pathogens without assistance. Instead, dendritic cells and macrophages first engulf and digest pathogens into hundreds or thousands of antigens. Then, an antigen-presenting cell (APC) detects, engulfs, and informs the adaptive immune response about an infection. When a pathogen is detected, these APCs will engulf and break it down through phagocytosis. Antigen fragments will then be transported to the surface of the APC, where they will serve as an indicator to other immune cells. A dendritic cell is an immune cell that mops up antigenic materials in its surroundings and presents them on its surface. Dendritic cells are located in the skin, the linings of the nose, lungs, stomach, and intestines. These positions are ideal locations to encounter invading pathogens. Once they are activated by pathogens and mature to become APCs they migrate to the spleen or a lymph node. Macrophages also function as APCs. After phagocytosis by a macrophage, the phagocytic vesicle fuses with an intracellular lysosome. Within the resulting phagolysosome, the components are broken down into fragments; the fragments are then loaded onto MHC class II molecules and are transported to the cell surface for antigen presentation ([link]). Helper T cells cannot properly respond to an antigen unless it is processed and embedded in an MHC class II molecule. The APCs express MHC class II on their surfaces, and when combined with a foreign antigen, these complexes signal an invader.

Immunological Memory

The adaptive immune system has a memory component that allows for a rapid and large response upon reinvasion of the same pathogen. During the adaptive immune response to a pathogen that has not been encountered before, known as the primary immune 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 ([link]). A memory cell is an antigen-specific B or T lymphocyte that does not differentiate into an effector cell during the primary immune response, but that can immediately become an effector cell on reexposure to the same pathogen. As the infection is cleared and pathogenic stimuli subside, the effectors are no longer needed and they undergo apoptosis. In contrast, the memory cells persist in the circulation.

The Lymphatic System

Lymph is the watery fluid that bathes tissues and organs and contains protective white blood cells but does not contain erythrocytes. Lymph moves about the body through the lymphatic system, which is made up of vessels, lymph ducts, lymph glands, and organs, such as tonsils, adenoids, thymus, and spleen.

Mucosal Immune System

The innate and adaptive immune responses compose the systemic immune system (affecting the whole body), which is distinct from the mucosal immune system. Mucosa associated lymphoid tissue (MALT) is a crucial component of a functional immune system because mucosal surfaces, such as the nasal passages, are the first tissues onto which inhaled or ingested pathogens are deposited. The mucosal tissue includes the mouth, pharynx, and esophagus, and the gastrointestinal, respiratory, and urogenital tracts.

Immune Tolerance

The immune system has to be regulated to prevent wasteful, unnecessary responses to harmless substances, and more importantly, so that it does not attack “self.” The acquired ability to prevent an unnecessary or harmful immune response to a detected foreign substance known not to cause disease, or self-antigens, is described as immune tolerance. The primary mechanism for developing immune tolerance to self-antigens occurs during the selection for weakly self-binding cells during T and B lymphocyte maturation. There are populations of T cells that suppress the immune response to self-antigens and that suppress the immune response after the infection has cleared to minimize host cell damage induced by inflammation and cell lysis. Immune tolerance is especially well developed in the mucosa of the upper digestive system because of the tremendous number of foreign substances (such as food proteins) that APCs of the oral cavity, pharynx, and gastrointestinal mucosa encounter. Immune tolerance is brought about by specialized APCs in the liver, lymph nodes, small intestine, and lung that present harmless antigens to a diverse population of regulatory T (Treg) cells, specialized lymphocytes that suppress local inflammation and inhibit the secretion of stimulatory immune factors. The combined result of Treg cells is to prevent immunologic activation and inflammation in undesired tissue compartments and to allow the immune system to focus on pathogens instead.

Disruptions in the Immune System

Abstract:
By the end of this section, you will be able to:
* Describe hypersensitivity
* Define autoimmunity

Immunodeficiency

Immunodeficiency is a failure, insufficiency, or delay in the response of the immune system, which may be acquired or inherited. Immunodeficiency can allow pathogens or tumor cells to gain a foothold and replicate or proliferate to high enough levels so that the immune system becomes overwhelmed. Immunodeficiency can be acquired as a result of infection with certain pathogens that attack the cells of the immune system itself (such as HIV), chemical exposure (including certain medical treatments such as chemotherapy), malnutrition, or extreme stress. For instance, radiation exposure can destroy populations of lymphocytes and elevate an individual’s susceptibility to infections and cancer. Rarely, primary immunodeficiencies that are present from birth may also occur. For example, severe combined immunodeficiency disease (SCID) is a condition in which children are born without functioning B or T cells.

Hypersensitivities

A maladaptive immune response toward harmless foreign substances or self-antigens that occur after tissue sensitization is termed a hypersensitivity. Types of hypersensitivities include immediate, delayed, and autoimmune. A large proportion of the human population is affected by one or more types of hypersensitivity.

Animal Reproduction and Development

Introduction

How Animals Reproduce

Abstract:
By the end of this section, you will be able to:
* Describe advantages and disadvantages of asexual and sexual reproduction
* Discuss asexual reproduction methods
* Discuss sexual reproduction methods
* Discuss internal and external methods of fertilization

Asexual Reproduction

Asexual reproduction occurs in prokaryotic microorganisms (bacteria and archaea) and in many eukaryotic, single-celled and multi-celled organisms. There are several ways that animals reproduce asexually, the details of which vary among individual species.

Sexual Reproduction

Sexual reproduction is the combination of reproductive cells from two individuals to form genetically unique offspring. The nature of the individuals that produce the two kinds of gametes can vary, having for example separate sexes or multiple sexes in each individual. Sex determination, the mechanism that determines which sex an individual develops into, also can vary.

Sex Determination

Pioneering scientist Nettie Stevens was the first to observe chromosomal differences between the different sexes of organisms. Using a microscope to observe mealworm cells, she noted that one chromosome was notably different between females and males, and she concluded that those chromosomes were the most likely determinants of the worms' sex. She later studied other insects, and her discoveries were confirmed by other scientists. (Stevens was initially denied credit due to her gender, but later publications acknowledged her critical role.) Mammalian sex is determined genetically by the combination of X and Y chromosomes. Individuals homozygous for X (XX) are female and heterozygous individuals (XY) are male. In mammals, 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

The fusion of a sperm and an egg is a process called fertilization. This can occur either inside (internal fertilization) or outside (external fertilization) the body of the female. Humans provide an example of the former, whereas frog reproduction is an example of the latter.

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 spawning may be triggered by environmental signals, such as 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). Frogs, corals, squid, and octopuses also spawn ([link]).

Development and Organogenesis

Abstract:
By the end of this section, you will be able to:
* Explain how the embryo forms from the zygote
* Discuss the role of cleavage and gastrulation in animal development
* Describe organogenesis

Early Embryonic Development

Fertilization is the process in which gametes (an egg and sperm) fuse to form a zygote ([link]). To ensure that the offspring has only one complete diploid set of chromosomes, only one sperm must fuse with one egg. In mammals, a layer called the zona pellucida protects the egg. At the tip of the head of a sperm cell is a structure like a lysosome called the acrosome, which contains enzymes. When a sperm binds to the zona pellucida, a series of events, called the acrosomal reactions, take place. These reactions, involving enzymes from the acrosome, allow the sperm plasma membrane to fuse with the egg plasma membrane and permit the sperm nucleus to transfer into the ovum. The nuclear membranes of the egg and sperm break down and the two haploid nuclei fuse to form a diploid nucleus or genome.

Human Reproduction

Abstract:
By the end of this section, you will be able to:
* Describe human testicular and ovarian reproductive anatomies
* Describe spermatogenesis and oogenesis and discuss their differences and similarities
* Describe the role of hormones in human reproduction
* Describe the roles of reproductive hormones

Human Reproductive Anatomy

The reproductive tissues of male and female humans develop similarly *in utero* until about the seventh week of gestation when, in some cases, a low level of the hormone testosterone is released from the gonads. Testosterone causes the primitive gonads to differentiate into sexual organs, such as the scrotum and penis. When testosterone is absent, the primitive gonads develop into 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. Thus the male and female anatomies arise from a divergence in the development of what were once common embryonic structures.

Gametogenesis (Spermatogenesis and Oogenesis)

Gametogenesis, the production of sperm and eggs, involves the process of meiosis. During meiosis, two nuclear 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 and its associated cell divisions 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 Reproduction

The human reproductive cycles are controlled by the interaction of hormones from the hypothalamus and anterior pituitary with hormones from reproductive tissues and organs. The hypothalamus monitors and causes the release of hormones from the anterior pituitary gland. When the reproductive hormone is required, the hypothalamus sends a gonadotropin-releasing hormone (GnRH) to the anterior pituitary. This causes the release of follicle stimulating hormone (FSH) and luteinizing hormone (LH) from the anterior pituitary into the blood. Although these hormones are named after their functions in female reproduction, they are produced in both sexes and play important roles in controlling reproduction. Other hormones have specific functions in the male and female reproductive systems.

Female Hormones

The control of reproduction in females is more complex. The female reproductive cycle is divided into the ovarian cycle and the menstrual cycle. The ovarian cycle governs the preparation of endocrine tissues and release of eggs, while the menstrual cycle governs the preparation and maintenance of the uterine lining ([link]). These cycles are coordinated over a 22–32 day cycle, with an average length of 28 days.

Gestation

Pregnancy begins with the fertilization of an egg and continues through to the birth of the individual. The length of time of gestation, or the gestation period, in humans is 266 days and is similar in other great apes.

Ecology

Population and Community Ecology

Introduction

Population Demographics and Dynamics

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

Populations are characterized by their population size (total number of individuals) and their population density (number of individuals per unit area). A population may have a large number of individuals that are distributed densely, or sparsely. There are also populations with small numbers of individuals that may be dense or very sparsely distributed in a local area. Population size can affect potential for adaptation because it affects the amount of genetic variation present in the population. Density can have effects on interactions within a population such as competition for food and the ability of individuals to find a mate. Smaller organisms tend to be more densely distributed than larger organisms ([link]).

Species Distribution

In addition to measuring density, further information about a population can be obtained by looking at the distribution of the individuals throughout their range. A species distribution pattern is the distribution of individuals within a habitat at a particular point in time—broad categories of patterns are used to describe them.

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. These population characteristics are often displayed in a life table.

Population Growth and Regulation

Abstract:
By the end of this section, you will be able to:
* Explain the characteristics of and differences between exponential and logistic growth patterns
* Give examples of exponential and logistic growth in natural populations
* 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

Population Growth

The two simplest models of population growth use deterministic equations (equations that do not account for random events) to describe the rate of change in the size of a population over time. The first of these models, exponential growth, describes theoretical populations that increase in numbers without any limits to their growth. The second model, logistic growth, introduces limits to reproductive growth that become more intense as the population size increases. Neither model adequately describes natural populations, but they provide points of comparison.

Logistic Growth

Extended 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 are more likely to survive and pass on the traits that made them successful 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

The logistic model of population growth, while valid in many natural populations and a useful model, is a simplification of real-world population dynamics. Implicit in the model is that the carrying capacity of the environment does not change, which is not the case. The carrying capacity varies annually. For example, some summers are hot and dry whereas others are cold and wet; in many areas, the carrying capacity during the winter is much lower than it is during the summer. Also, natural events such as earthquakes, volcanoes, and fires can alter an environment and hence its carrying capacity. Additionally, populations do not usually exist in isolation. They share the environment with other species, competing with them for the same resources (interspecific competition). These factors are also important to understanding how a specific population will grow.

Density-dependent Regulation

Most density-dependent factors are biological in nature and include predation, inter- and intraspecific competition, and parasites. Usually, the denser a population is, the greater its mortality rate. For example, during intra- and interspecific competition, the reproductive rates of the species will usually be lower, reducing their populations’ rate of growth. In addition, low prey density increases the mortality of its predator because it has more difficulty locating its food source. Also, when the population is denser, diseases spread more rapidly among the members of the population, which affect the mortality rate.

Density-independent Regulation and Interaction with Density-dependent Factors

Many factors that are typically physical in nature cause mortality of a population regardless of its density. These factors include weather, natural disasters, and pollution. An individual deer will 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.

Demographic-Based Population Models

Population ecologists have hypothesized that suites of characteristics may evolve in species that lead to particular adaptations to their environments. These adaptations impact the kind of population growth their species experience. Life history characteristics such as birth rates, age at first reproduction, the numbers of offspring, and even death rates evolve just like anatomy or behavior, leading to adaptations that affect population growth. Population ecologists have described a continuum of life-history “strategies” with *K*-selected species on one end and *r*-selected species on the other. *K*-selected species are adapted to stable, predictable environments. Populations of *K*-selected species tend to exist close to their carrying capacity. These species tend to have larger, but fewer, offspring and contribute large amounts of resources to each offspring. Elephants would be an example of a *K*-selected species. *r*-selected species are adapted to unstable and unpredictable environments. They have large numbers of small offspring. Animals that are *r*-selected do not provide a lot of resources or parental care to offspring, and the offspring are relatively self-sufficient at birth. Examples of *r*-selected species are marine invertebrates such as jellyfish and plants such as the dandelion. The two extreme strategies are at two ends of a continuum on which real species life histories will exist. In addition, life history strategies do not need to evolve as suites, but can evolve independently of each other, so each species may have some characteristics that trend toward one extreme or the other.

The Human Population

Abstract:
By the end of this section, you will be able to:
* Discuss how human population growth can be exponential
* 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 in myriad ways. This ability is responsible for human population growth because it resets the carrying capacity and overcomes density-dependent growth regulation. Much of this ability is related to human intelligence, society, and communication. Humans construct shelters to protect themselves 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 in different age classes. Models that incorporate age structure allow better prediction of population growth, plus the ability to associate this growth with the level of economic development in a 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 ([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, and there is a high birth rate. 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 critics view this statement as an exaggeration, 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:
* 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 the predator-prey relationship. The narrowest definition of the predator-prey interaction describes individuals of one population that kill and then consume the individuals of another population. Population sizes of predators and prey in a community are not constant over time, and they may vary in cycles that appear to be related. The most often cited example of predator-prey population dynamics is seen in the cycling of the lynx (predator) and the snowshoe hare (prey), using 100 years of trapping data from North America ([link]). This cycling of predator and prey population sizes has a period of approximately ten years, with the predator population lagging one to two years behind the prey population. An apparent explanation for this pattern is that 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 numbers begin 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, 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. Ecologists have come to understand that all species have an ecological niche. A niche is the unique set of resources used by a species, which includes its interactions with other species. 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. This principle works because if there is an overlap in resource use and therefore competition between two species, then traits that lessen reliance on the shared resource will be selected for leading to evolution that reduces the overlap. If either species is unable to evolve to reduce competition, then the species that most efficiently exploits the resource will drive the other species to extinction. An experimental 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 are close, long-term interactions between individuals of different species. Symbioses may be commensal, in which one species benefits while the other is neither harmed nor benefited; mutualistic, in which both species benefit; or parasitic, in which the interaction harms one species and benefits the other.

Characteristics of Communities

Communities are complex systems that can be characterized by their structure (the number and size of populations and their interactions) and dynamics (how the members and their interactions change over time). Understanding community structure and dynamics allows us to minimize impacts on ecosystems and manage ecological communities we benefit from.

Community Dynamics

Community dynamics are the changes in community structure and composition over time, often following environmental disturbances such as volcanoes, earthquakes, storms, fires, and climate change. Communities with a relatively constant number of species are said to be at equilibrium. The equilibrium is dynamic with species identities and relationships changing over time, but maintaining relatively constant numbers. Following a disturbance, the community may or may not return to the equilibrium state.

Ecosystems and the Biosphere

Introduction

Energy Flow through Ecosystems

Abstract:
By the end of this section, you will be able to:
* Describe the basic types of ecosystems on Earth
* Differentiate between food chains and food webs and recognize the importance of each
* 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 ecosystems

Ecology of Ecosystems

Life in an ecosystem often involves competition for limited resources, which occurs both within a single species and between different species. Organisms compete for food, water, sunlight, space, and mineral nutrients. These resources provide the energy for metabolic processes and the matter to make up organisms’ physical structures. Other critical factors influencing community dynamics are the components of its physical environment: a habitat’s climate (seasons, sunlight, and rainfall), elevation, and geology. These can all be important environmental variables that determine which organisms can exist within a particular area.

Food Chains and Food Webs

A food chain is a linear sequence of organisms through which nutrients and energy pass as one organism eats another; the levels in the food chain are producers, primary consumers, higher-level consumers, and finally decomposers. These levels are used to describe ecosystem structure and dynamics. There is a single path through a food chain. Each organism in a food chain occupies a specific trophic level (energy level), its position in the food chain or food web.

How Organisms Acquire Energy in a Food Web

All living things require energy in one form or another. Energy is used by most complex metabolic pathways (usually in the form of ATP), especially those responsible for building large molecules from smaller compounds. Living organisms would not be able to assemble macromolecules (proteins, lipids, nucleic acids, and complex carbohydrates) from their monomers without a constant energy input.

Consequences of Food Webs: Biological Magnification

One of the most important consequences of ecosystem dynamics in terms of human impact is biomagnification. Biomagnification is the increasing concentration of persistent, toxic substances in organisms at each successive trophic level. These are substances that are fat soluble, not water soluble, and are stored in the fat reserves of each organism. Many substances have been shown to biomagnify, including classical studies with the pesticide dichlorodiphenyltrichloroethane (DDT), which were described in the 1960s bestseller, *Silent Spring* by Rachel Carson. DDT was a commonly used pesticide before its dangers to apex consumers, such as the bald eagle, became known. In aquatic ecosystems, organisms from each trophic level consumed many organisms in 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 devastating effects on these bird populations. 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:
* Discuss the biogeochemical cycles of water, carbon, nitrogen, phosphorus, and sulfur
* Explain how human activities have impacted these cycles and the resulting potential consequences for Earth

The Water Cycle

Water is essential for all living processes. The human body is more than one-half water and human cells are more than 70 percent water. Thus, most land animals need a supply of fresh water to survive. Of the stores of water on Earth, 97.5 percent is salt water ([link]). Of the remaining water, 99 percent is locked as underground water or ice. Thus, less than one percent of fresh water is present in lakes and rivers. Many living things are dependent on this small amount of surface fresh water supply, a lack of which can have important effects on ecosystem dynamics. 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. Although this pursuit of drinkable water has been ongoing throughout human history, the supply of fresh water continues to be a major issue in modern times.

The Carbon Cycle

Carbon is the fourth 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. Carbon compounds contain energy, and many of these compounds from plants and algae have remained stored as fossilized carbon, which humans use as fuel. Since the 1800s, the use of fossil fuels has accelerated. As global demand for Earth’s limited fossil fuel supplies has risen since the beginning of the Industrial Revolution, the amount of carbon dioxide in our atmosphere has increased as the fuels are burned. This increase in carbon dioxide has been associated with climate change and is a major environmental concern worldwide.

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. 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 acids 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, particularly freshwater, ecosystems.

The Sulfur Cycle

Sulfur is an essential element for the macromolecules of living things. As part of the amino acid cysteine, it is involved in the formation of proteins. As shown in [link], sulfur cycles between the oceans, land, and atmosphere. Atmospheric sulfur is found in the form of sulfur dioxide (SO2), which enters the atmosphere in three ways: first, from the decomposition of organic molecules; second, from volcanic activity and geothermal vents; and, third, from the burning of fossil fuels by humans.

Terrestrial Biomes

Abstract:
By the end of this section, you will be able to:
* Identify the two major abiotic factors that determine the type of terrestrial biome in an area
* Recognize distinguishing characteristics of each of the eight major terrestrial biomes

Tropical Forest

Tropical rainforests are also referred to as tropical wet forests. This biome is found in equatorial regions ([link]). Tropical rainforests are the most diverse terrestrial biome. This biodiversity is still largely unknown to science and is under extraordinary threat primarily through logging and deforestation for agriculture. Tropical rainforests have also been described as nature’s pharmacy because of the potential for new drugs that is largely hidden in the chemicals produced by the huge diversity of plants, animals, and other organisms. The vegetation is characterized by plants with spreading roots and broad leaves that fall off throughout the year, unlike the trees of deciduous forests that lose their leaves in one season. These forests are “evergreen,” year-round.

Savannas

Savannas are grasslands with scattered trees, and they are found in Africa, South America, and northern Australia ([link]). Savannas are hot, tropical areas with temperatures averaging from 24oC–29oC (75oF–84oF) and an annual rainfall of 51–127 cm (20–50 in). Savannas have an extensive dry season and consequent fires. As a result, scattered in 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 re-sprout after a fire.

Deserts

Subtropical deserts exist between 15o and 30o north and south latitude and are centered on the Tropic of Cancer and the Tropic of Capricorn ([link]). Deserts are frequently located on the downwind or lee side of mountain ranges, which create a rain shadow after prevailing winds drop their water content on the mountains. This is typical of the North American deserts, such as the Mohave and Sonoran deserts. Deserts in other regions, such as the Sahara Desert in northern Africa or the Namib Desert in southwestern Africa are dry because of the high-pressure, dry air descending at those latitudes. Subtropical deserts are very dry; evaporation typically exceeds precipitation. Subtropical hot deserts can have daytime soil surface temperatures above 60oC (140oF) and nighttime temperatures approaching 0oC (32oF). The temperature drops so far because there is little water vapor in the air to prevent radiative cooling of the land surface. 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. Some years may receive tiny amounts of rainfall, while others receive more. 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 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 is dominated by shrubs and is adapted to periodic fires, with some plants producing seeds that germinate only 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. Fire is a natural part of the maintenance of this biome and frequently threatens human habitation in this biome in the U.S. ([link]).

Temperate Grasslands

Temperate grasslands are found throughout central North America, where they are also known as prairies, and 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, which occurs in the spring, summer, and fall.

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 –30oC and 30oC (–22oF to 86oF) and drop to below freezing on an annual basis. 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 roughly between 50o and 60o north latitude across most of Canada, Alaska, Russia, and northern Europe ([link]). Boreal forests are also found above a certain elevation (and below high elevations where trees cannot grow) in mountain ranges throughout the Northern Hemisphere. 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 forests and is located throughout the Arctic regions of the Northern Hemisphere ([link]). Tundra also exists at elevations above the tree line on mountains. The average winter temperature is –34°C (–29.2°F) and the average summer temperature is 3°C–12°C (37°F –52°F). Plants in the Arctic tundra have a short growing season of approximately 50–60 days. However, during this time, there are almost 24 hours of daylight and plant growth is rapid. The annual precipitation of the Arctic tundra is low (15–25 cm or 6–10 in) with little annual variation in precipitation. And, as in the boreal forests, there is little evaporation because of the cold temperatures.

Aquatic and Marine Biomes

Abstract:
By the end of this section, you will be able to:
* Describe the effects of abiotic factors on the composition of plant and animal communities in aquatic biomes
* Compare the characteristics of the ocean zones
* Summarize the characteristics of standing water and flowing water in freshwater biomes

Marine Biomes

The ocean is a continuous body of salt water that is relatively uniform in chemical composition. It is a weak solution of mineral salts and decayed biological matter. Within the ocean, coral reefs are a second type 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 river, a source of fresh water, meets the ocean. Therefore, both fresh water and salt water are found in the same vicinity; mixing results in a diluted (brackish) salt water. Estuaries form protected areas where many of the offspring of crustaceans, mollusks, and fish begin their lives. Salinity is an important factor that influences the organisms and the adaptations of the organisms found in estuaries. The salinity of estuaries varies and is based on the rate of flow of its freshwater sources. 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 ([link]).

Freshwater Biomes

Freshwater biomes include lakes, ponds, and wetlands (standing water) as well as rivers and streams (flowing water). Humans rely on freshwater biomes to provide aquatic resources for drinking water, crop irrigation, sanitation, recreation, and industry. These various roles and human benefits are referred to as ecosystem services. Lakes and ponds are found in terrestrial landscapes and are therefore connected with abiotic and biotic factors influencing these terrestrial biomes.

Wetlands

Wetlands are environments in which the soil is either permanently or periodically saturated with water. Wetlands are different from lakes and ponds because wetlands exhibit a near continuous cover of emergent vegetation. Emergent vegetation consists of wetland plants that are rooted in the soil but have portions of leaves, stems, and flowers extending above the water’s surface. There are several types of wetlands including marshes, swamps, bogs, mudflats, and salt marshes ([link]).

Conservation and Biodiversity

Introduction

Importance of Biodiversity

Abstract:
By the end of this section, you will be able to:
* Describe biodiversity as the equilibrium of naturally fluctuating rates of extinction and speciation
* Identify benefits of biodiversity to humans

Types of Biodiversity

A common meaning of biodiversity is simply the number of species in a location or on Earth; for example, the American Ornithologists’ Union lists 2078 species of birds in North and Central America. This is one measure of the bird biodiversity on the continent. More sophisticated measures of diversity take into account the relative abundances of species. For example, a forest with 10 equally common species of trees is more diverse than a forest that has 10 species of trees wherein just one of those species makes up 95 percent of the trees rather than them being equally distributed. Biologists have also identified alternate measures of biodiversity, some of which are important in planning how to preserve biodiversity.

Patterns of Biodiversity

Biodiversity is not evenly distributed on the planet. Lake Victoria contained almost 500 species of cichlids (only one family of fishes present in the lake) before the introduction of an exotic species in the 1980s and 1990s caused a mass extinction. All of these species were found only in Lake Victoria, which is to say they were endemic. Endemic species are found in only one location. For example, the blue jay is endemic to North America, while the Barton Springs salamander is endemic to the mouth of one spring in Austin, Texas. Endemics with highly restricted distributions, like the Barton Springs salamander, are particularly vulnerable to extinction. Higher taxonomic levels, such as genera and families, can also be endemic.

Importance of Biodiversity

Loss of biodiversity eventually threatens other species we do not impact directly because of their interconnectedness; as species disappear from an ecosystem other species are threatened by the changes in available resources. Biodiversity is important to the survival and welfare of human populations because it has impacts on our health and our ability to feed ourselves through agriculture and harvesting populations of wild animals.

Threats to Biodiversity

Abstract:
By the end of this section, you will be able to:
* Identify significant threats to biodiversity
* Explain the effects of habitat loss, 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 habitat—whether it is a forest, coral reef, grassland, or flowing river—will kill the individuals in the species. Remove the entire habitat within the range of a species and, unless they are one of the few species that do well in human-built environments, the species will become extinct. Human destruction of habitats (habitats generally refer to the part of the ecosystem required by a particular species) 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. The orangutan in Borneo is listed as endangered by the International Union for Conservation of Nature (IUCN), but it is simply the most visible of thousands of species that will not survive the disappearance of the forests of 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 5-year estimate of global forest cover loss for the years from 2000 to 2005 was 3.1 percent. Much loss (2.4 percent) occurred in the humid tropics where forest loss is primarily from timber extraction. These losses certainly also represent the extinction of species unique to those areas.

Overharvesting

Overharvesting is a serious threat to many species, but particularly to aquatic species. There are many examples of regulated fisheries (including hunting of marine mammals and harvesting of crustaceans and other species) monitored by fisheries scientists that have nevertheless collapsed. The western Atlantic cod fishery is the most spectacular recent collapse. While it was a hugely productive fishery for 400 years, the introduction of modern factory trawlers in the 1980s and the pressure on the fishery led to it becoming unsustainable. The causes of fishery collapse are both economic and political in nature. Most fisheries are managed as a common resource, available to anyone willing to fish, even when the fishing territory lies within a country’s territorial waters. Common resources are subject to an economic pressure known as the tragedy of the commons, in which fishers have little motivation to exercise restraint in harvesting a fishery when they do not own the fishery. The general outcome of harvests of resources held in common is their overexploitation. While large fisheries are regulated to attempt to avoid this pressure, it still exists in the background. 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 drive toward fishing the population to extinction.

Exotic Species

Exotic species are species that have been intentionally or unintentionally introduced by humans into an ecosystem in which they did not evolve. Human transportation of people and goods, including the intentional transport of organisms for trade, has dramatically increased the introduction of species into new ecosystems. These new introductions are 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 warming trend presently underway, is recognized as a major extinction threat, particularly when combined with other threats such as habitat loss. Anthropogenic warming of the planet has been observed and is hypothesized to continue due to past and continuing emission of greenhouse gases, primarily carbon dioxide and methane, into the atmosphere caused by the burning of fossil fuels and deforestation. These gases decrease the degree to which Earth is able to radiate heat energy created by the sunlight that enters the atmosphere. The changes in climate and energy balance caused by increasing greenhouse gases are complex and our understanding of them depends on predictions generated from detailed computer models. Scientists generally agree the present warming trend is caused by humans and some of the likely effects include dramatic and dangerous climate changes in the coming decades. However, there is still debate and a lack of understanding about specific outcomes. Scientists disagree about the likely magnitude of the effects on extinction rates, with estimates ranging from 15 to 40 percent of species committed to extinction by 2050. Scientists do agree that climate change will alter regional climates, including rainfall and snowfall patterns, making habitats less hospitable to the species living in them. The warming trend will shift colder climates toward the north and south poles, forcing species to move with their adapted climate norms, but also to face 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 species had separate ranges. Now, their ranges are overlapping and there are documented cases of these two species mating and producing viable offspring. Changing climates also throw off the delicate timing adaptations that species have to seasonal food resources and breeding times. Scientists have already documented many contemporary mismatches to shifts in resource availability and timing.

Preserving Biodiversity

Abstract:
By the end of this section, you will be able to:
* Describe biodiversity as the equilibrium of naturally fluctuating rates of extinction and speciation
* Explain the legislative framework for conservation
* Identify the factors important in conservation preserve design
* Identify examples of the effects of habitat restoration
* Identify the role of zoos in biodiversity conservation

Change in Biodiversity through 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 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 reverse is true when extinction rates begin to overtake speciation rates. Throughout the history of life on Earth, as reflected in the fossil record, these two processes have fluctuated to a greater or lesser extent, sometimes leading to dramatic changes in the number of species on the planet as reflected in the fossil record ([link]).

Recent and Current Extinction Rates

A sixth, or Holocene, mass extinction has mostly to do with the activities of *Homo sapiens*. There are numerous recent extinctions of individual species that are recorded in human writings. Most of these are coincident with the expansion of the European colonies since the 1500s.

Estimates of Present-day Extinction Rates

Estimates of extinction rates are hampered by the fact that most extinctions are probably happening without being observed. The extinction of a bird or mammal is often noticed by humans, especially if it has been hunted or used in some other way. But there are many organisms that are less noticeable to humans (not necessarily of less value) and many that are undescribed.

Conservation of Biodiversity

The threats to biodiversity at the genetic, species, and ecosystem levels have been recognized for some time. In the United States, the first national park with land set aside to remain in a wilderness state was Yellowstone Park in 1872. However, attempts to preserve nature for various reasons have occurred for centuries. Today, the main efforts to preserve biodiversity involve legislative approaches to regulate human and corporate behavior, setting aside protected areas, and habitat restoration.

The Periodic Table of Elements

Geological Time

Measurements and the Metric System

Measurements and the Metric System