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About *Biology for AP® Courses*

*Biology for AP® Courses* covers the scope and sequence requirements of a typical two-semester Advanced Placement® biology course. The text provides comprehensive coverage of core biology concepts and foundational research through an evolutionary lens. *Biology for AP® Courses* was designed to meet and exceed the requirements of the College Board’s AP® Biology framework while allowing significant flexibility for instructors. Each section of the book includes an introduction based on the AP® curriculum as well as rich features that engage students in scientific practice and AP® test preparation. It also highlights careers and research opportunities in the biological sciences.

Additional resources

About the authors

Curriculum Framework for AP® Biology

The Chemistry of Life

The Study of Life

Introduction

The Science of Biology

Themes and Concepts of Biology

The Chemical Foundation of Life

Introduction

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

Water

Carbon

Biological Macromolecules

Introduction

Synthesis of Biological Macromolecules

Carbohydrates

Lipids

Proteins

Nucleic Acids

The Cell

Cell Structure

Introduction

Studying Cells

Prokaryotic Cells

Eukaryotic Cells

The Endomembrane System and Proteins

Cytoskeleton

Connections between Cells and Cellular Activities

Structure and Function of Plasma Membranes

Introduction

Components and Structure

Passive Transport

Active Transport

Bulk Transport

Metabolism

Introduction

Energy and Metabolism

Potential, Kinetic, Free, and Activation Energy

The Laws of Thermodynamics

ATP: Adenosine Triphosphate

Enzymes

Cellular Respiration

Introduction

Energy in Living Systems

Glycolysis

Oxidation of Pyruvate and the Citric Acid Cycle

Oxidative Phosphorylation

Metabolism without Oxygen

Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways

Regulation of Cellular Respiration

Photosynthesis

Introduction

Overview of Photosynthesis

The Light-Dependent Reaction of Photosynthesis

Using Light to Make Organic Molecules

Cell Communication

Introduction

Signaling Molecules and Cellular Receptors

Propagation of the Signal

Response to the Signal

Signaling in Single-Celled Organisms

Cell Reproduction

Introduction

Cell Division

The Cell Cycle

Control of the Cell Cycle

Cancer and the Cell Cycle

Prokaryotic Cell Division

Genetics

Meiosis and Sexual Reproduction

Introduction

The Process of Meiosis

Sexual Reproduction

Mendel's Experiments and Heredity

Introduction

Mendel’s Experiments and the Laws of Probability

Characteristics and Traits

Laws of Inheritance

Modern Understandings of Inheritance

Introduction

Chromosomal Theory and Genetic Linkages

Chromosomal Basis of Inherited Disorders

DNA Structure and Function

Introduction

Historical Basis of Modern Understanding

DNA Structure and Sequencing

Basics of DNA Replication

DNA Replication in Prokaryotes

DNA Replication in Eukaryotes

DNA Repair

Genes and Proteins

Introduction

The Genetic Code

Prokaryotic Transcription

Eukaryotic Transcription

RNA Processing in Eukaryotes

Ribosomes and Protein Synthesis

Gene Regulation

Introduction

Regulation of Gene Expression

Prokaryotic Gene Regulation

Eukaryotic Epigenetic Gene Regulation

Eukaryotic Transcriptional Gene Regulation

Eukaryotic Post-transcriptional Gene Regulation

Eukaryotic Translational and Post-translational Gene Regulation

Cancer and Gene Regulation

Biotechnology and Genomics

Introduction

Biotechnology

Mapping Genomes

Whole-Genome Sequencing

Applying Genomics

Genomics and Proteomics

Evolutionary Processes

Evolution and Origin of Species

Introduction

Understanding Evolution

The Origin of Life

Humans have adopted many theories regarding the origin of life over the course of our time on Earth. Early civilizations believed that life was created by supernatural forces. Organisms were “hand-made” to be perfectly adapted to their environment and, therefore, did not change over time. Some early thinkers, such as the Greek philosopher Aristotle, believed that organisms belonged to a ladder of increasing complexity. Based on this understanding, scientists such as Carolus Linnaeus attempted to organize all living things into classification schemes that demonstrated an increasing complexity of life.

Formation of New Species

Speciation

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

Reconnection and Rates of Speciation

The Evolution of Populations

Introduction

Population Evolution

Population Genetics

Adaptive Evolution

No Perfect Organism

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

Phylogenies and the History of Life

Introduction

Organizing Life on Earth

Determining Evolutionary Relationships

Perspectives on the Phylogenetic Tree

Limitations to the Classic Model

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

Biological Diversity

Viruses

Introduction

Viral Evolution, Morphology, and Classification

Virus Infection and Hosts

Different Hosts and Their Viruses

As you’ve learned, viruses are often very specific as to which hosts and which cells within the host they will infect. This feature of a virus makes it specific to one or a few species of life on Earth. On the other hand, so many different types of viruses exist on Earth that nearly every living organism has its own set of viruses that tries to infect its cells. Even the smallest and simplest of cells, prokaryotic bacteria, may be attacked by specific types of viruses.

Prevention and Treatment of Viral Infections

Other Acellular Entities: Prions and Viroids

Prokaryotes: Bacteria and Archaea

Introduction

Prokaryotic Diversity

The Ecology of Biofilms

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

Structure of Prokaryotes

Prokaryotic Metabolism

Bacterial Diseases in Humans

Beneficial Prokaryotes

Plant Structure and Function

Plant Form and Physiology

Introduction

The Plant Body

Stems

Roots

Leaves

Leaf Arrangement

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

Transport of Water and Solutes in Plants

Plant Sensory Systems and Responses

Animal Structure and Function

The Animal Body: Basic Form and Function

Introduction

Animal Form and Function

Animal Primary Tissues

Homeostasis

Animal Nutrition and the Digestive System

Introduction

Digestive Systems

Nutrition and Energy Production

Digestive System Processes

Digestive System Regulation

The Nervous System

Introduction

Neurons and Glial Cells

How Neurons Communicate

The Central Nervous System

The Peripheral Nervous System

Nervous System Disorders

Sensory Systems

Introduction

Sensory Processes

Somatosensation

Taste and Smell

Hearing and Vestibular Sensation

Vision

Higher Processing

The myelinated axons of ganglion cells make up the optic nerves. Within the nerves, different axons carry different qualities of the visual signal. Some axons constitute the magnocellular (big cell) pathway, which carries information about form, movement, depth, and differences in brightness. Other axons constitute the parvocellular (small cell) pathway, which carries information on color and fine detail. Some visual information projects directly back into the brain, while other information crosses to the opposite side of the brain. This crossing of optical pathways produces the distinctive optic chiasma (Greek, for “crossing”) found at the base of the brain and allows us to coordinate information from both eyes.

The Endocrine System

Introduction

Types of Hormones

How Hormones Work

Regulation of Body Processes

Regulation of Hormone Production

Endocrine Glands

The Musculoskeletal System

Introduction

Types of Skeletal Systems

Bone

Bone Tissue

Bones are considered organs because they contain various types of tissue, such as blood, connective tissue, nerves, and bone tissue. Osteocytes, the living cells of bone tissue, form the mineral matrix of bones. There are two types of bone tissue: compact and spongy.

Joints and Skeletal Movement

Muscle Contraction and Locomotion

The Respiratory System

Introduction

Systems of Gas Exchange

Direct Diffusion

For small multicellular organisms, diffusion across the outer membrane is sufficient to meet their oxygen needs. Gas exchange by direct diffusion across surface membranes is efficient for organisms less than 1 mm in diameter. In simple organisms, such as cnidarians and flatworms, every cell in the body is close to the external environment. Their cells are kept moist and gases diffuse quickly via direct diffusion. Flatworms are small, literally flat worms, which ‘breathe’ through diffusion across the outer membrane ([link]). The flat shape of these organisms increases the surface area for diffusion, ensuring that each cell within the body is close to the outer membrane surface and has access to oxygen. If the flatworm had a cylindrical body, then the cells in the center would not be able to get oxygen.

Skin and Gills

Earthworms and amphibians use their skin (integument) as a respiratory organ. A dense network of capillaries lies just below the skin and facilitates gas exchange between the external environment and the circulatory system. The respiratory surface must be kept moist in order for the gases to dissolve and diffuse across cell membranes.

Tracheal Systems

Insect respiration is independent of its circulatory system; therefore, the blood does not play a direct role in oxygen transport. Insects have a highly specialized type of respiratory system called the tracheal system, which consists of a network of small tubes that carries oxygen to the entire body. The tracheal system is the most direct and efficient respiratory system in active animals. The tubes in the tracheal system are made of a polymeric material called chitin.

Mammalian Systems

In mammals, pulmonary ventilation occurs via inhalation (breathing). During inhalation, air enters the body through the **nasal cavity** located just inside the nose ([link]). As air passes through the nasal cavity, the air is warmed to body temperature and humidified. The respiratory tract is coated with mucus to seal the tissues from direct contact with air. Mucus is high in water. As air crosses these surfaces of the mucous membranes, it picks up water. These processes help equilibrate the air to the body conditions, reducing any damage that cold, dry air can cause. Particulate matter that is floating in the air is removed in the nasal passages via mucus and cilia. The processes of warming, humidifying, and removing particles are important protective mechanisms that prevent damage to the trachea and lungs. Thus, inhalation serves several purposes in addition to bringing oxygen into the respiratory system.

Protective Mechanisms

The air that organisms breathe contains **particulate matter** such as dust, dirt, viral particles, and bacteria that can damage the lungs or trigger allergic immune responses. The respiratory system contains several protective mechanisms to avoid problems or tissue damage. In the nasal cavity, hairs and mucus trap small particles, viruses, bacteria, dust, and dirt to prevent their entry.

Gas Exchange across Respiratory Surfaces

Basic Principles of Gas Exchange

Gas exchange during respiration occurs primarily through diffusion. Diffusion is a process in which transport is driven by a concentration gradient. Gas molecules move from a region of high concentration to a region of low concentration. Blood that is low in oxygen concentration and high in carbon dioxide concentration undergoes gas exchange with air in the lungs. The air in the lungs has a higher concentration of oxygen than that of oxygen-depleted blood and a lower concentration of carbon dioxide. This concentration gradient allows for gas exchange during respiration.

Lung Volumes and Capacities

Different animals have different lung capacities based on their activities. Cheetahs have evolved a much higher lung capacity than humans; it helps provide oxygen to all the muscles in the body and allows them to run very fast. Elephants also have a high lung capacity. In this case, it is not because they run fast but because they have a large body and must be able to take up oxygen in accordance with their body size.

Gas Pressure and Respiration

The respiratory process can be better understood by examining the properties of gases. Gases move freely, but gas particles are constantly hitting the walls of their vessel, thereby producing gas pressure.

Gas Exchange across the Alveoli

In the body, oxygen is used by cells of the body’s tissues and carbon dioxide is produced as a waste product. The ratio of carbon dioxide production to oxygen consumption is the **respiratory quotient (RQ)**. RQ varies between 0.7 and 1.0. If just glucose were used to fuel the body, the RQ would equal one. One mole of carbon dioxide would be produced for every mole of oxygen consumed. Glucose, however, is not the only fuel for the body. Protein and fat are also used as fuels for the body. Because of this, less carbon dioxide is produced than oxygen is consumed and the RQ is, on average, about 0.7 for fat and about 0.8 for protein.

Breathing

Types of Breathing

Amphibians have evolved multiple ways of breathing. Young amphibians, like tadpoles, use gills to breathe, and they don’t leave the water. Some amphibians retain gills for life. As the tadpole grows, the gills disappear and lungs grow. These lungs are primitive and not as evolved as mammalian lungs. Adult amphibians are lacking or have a reduced diaphragm, so breathing via lungs is forced. The other means of breathing for amphibians is diffusion across the skin. To aid this diffusion, amphibian skin must remain moist.

The Mechanics of Human Breathing

Boyle’s Law is the gas law that states that in a closed space, pressure and volume are inversely related. As volume decreases, pressure increases and vice versa ([link]). The relationship between gas pressure and volume helps to explain the mechanics of breathing.

The Work of Breathing

The number of breaths per minute is the **respiratory rate**. On average, under non-exertion conditions, the human respiratory rate is 12–15 breaths/minute. The respiratory rate contributes to the **alveolar ventilation**, or how much air moves into and out of the alveoli. Alveolar ventilation prevents carbon dioxide buildup in the alveoli. There are two ways to keep the alveolar ventilation constant: increase the respiratory rate while decreasing the tidal volume of air per breath (shallow breathing), or decrease the respiratory rate while increasing the tidal volume per breath. In either case, the ventilation remains the same, but the work done and type of work needed are quite different. Both tidal volume and respiratory rate are closely regulated when oxygen demand increases.

Dead Space: V/Q Mismatch

Pulmonary circulation pressure is very low compared to that of the systemic circulation. It is also independent of cardiac output. This is because of a phenomenon called **recruitment**, which is the process of opening airways that normally remain closed when cardiac output increases. As cardiac output increases, the number of capillaries and arteries that are perfused (filled with blood) increases. These capillaries and arteries are not always in use but are ready if needed. At times, however, there is a mismatch between the amount of air (ventilation, V) and the amount of blood (perfusion, Q) in the lungs. This is referred to as **ventilation/perfusion (V/Q) mismatch**.

Transport of Gases in Human Bodily Fluids

Transport of Oxygen in the Blood

Although oxygen dissolves in blood, only a small amount of oxygen is transported this way. Only 1.5 percent of oxygen in the blood is dissolved directly into the blood itself. Most oxygen—98.5 percent—is bound to a protein called hemoglobin and carried to the tissues.

Transport of Carbon Dioxide in the Blood

Carbon dioxide molecules are transported in the blood from body tissues to the lungs by one of three methods: dissolution directly into the blood, binding to hemoglobin, or carried as a bicarbonate ion. Several properties of carbon dioxide in the blood affect its transport. First, carbon dioxide is more soluble in blood than oxygen. About 5 to 7 percent of all carbon dioxide is dissolved in the plasma. Second, carbon dioxide can bind to plasma proteins or can enter red blood cells and bind to hemoglobin. This form transports about 10 percent of the carbon dioxide. When carbon dioxide binds to hemoglobin, a molecule called **carbaminohemoglobin** is formed. Binding of carbon dioxide to hemoglobin is reversible. Therefore, when it reaches the lungs, the carbon dioxide can freely dissociate from the hemoglobin and be expelled from the body.

The Circulatory System

Introduction

Overview of the Circulatory System

Circulatory System Architecture

The circulatory system is effectively a network of cylindrical vessels: the arteries, veins, and capillaries that emanate from a pump, the heart. In all vertebrate organisms, as well as some invertebrates, this is a closed-loop system, in which the blood is not free in a cavity. In a **closed circulatory system**, blood is contained inside blood vessels and circulates **unidirectionally** from the heart around the systemic circulatory route, then returns to the heart again, as illustrated in [link]**a**. As opposed to a closed system, arthropods—including insects, crustaceans, and most mollusks—have an open circulatory system, as illustrated in [link]**b**. In an **open circulatory system**, the blood is not enclosed in the blood vessels but is pumped into a cavity called a **hemocoel** and is called **hemolymph** because the blood mixes with the **interstitial fluid**. As the heart beats and the animal moves, the hemolymph circulates around the organs within the body cavity and then reenters the hearts through openings called **ostia**. This movement allows for gas and nutrient exchange. An open circulatory system does not use as much energy as a closed system to operate or to maintain; however, there is a trade-off with the amount of blood that can be moved to metabolically active organs and tissues that require high levels of oxygen. In fact, one reason that insects with wing spans of up to two feet wide (70 cm) are not around today is probably because they were outcompeted by the arrival of birds 150 million years ago. Birds, having a closed circulatory system, are thought to have moved more agilely, allowing them to get food faster and possibly to prey on the insects.

Circulatory System Variation in Animals

The circulatory system varies from simple systems in invertebrates to more complex systems in vertebrates. The simplest animals, such as the sponges (Porifera) and rotifers (Rotifera), do not need a circulatory system because diffusion allows adequate exchange of water, nutrients, and waste, as well as dissolved gases, as shown in [link]**a**. Organisms that are more complex but still only have two layers of cells in their body plan, such as jellies (Cnidaria) and comb jellies (Ctenophora) also use diffusion through their epidermis and internally through the gastrovascular compartment. Both their internal and external tissues are bathed in an aqueous environment and exchange fluids by diffusion on both sides, as illustrated in [link]**b**. Exchange of fluids is assisted by the pulsing of the jellyfish body.

Components of the Blood

The Role of Blood in the Body

Blood, like the human blood illustrated in [link] is important for regulation of the body’s systems and homeostasis. Blood helps maintain homeostasis by stabilizing pH, temperature, osmotic pressure, and by eliminating excess heat. Blood supports growth by distributing nutrients and hormones, and by removing waste. Blood plays a protective role by transporting clotting factors and platelets to prevent blood loss and transporting the disease-fighting agents or **white blood cells** to sites of infection.

White Blood Cells

White blood cells, also called leukocytes (leuko = white), make up approximately one percent by volume of the cells in blood. The role of white blood cells is very different than that of red blood cells: they are primarily involved in the immune response to identify and target pathogens, such as invading bacteria, viruses, and other foreign organisms. White blood cells are formed continually; some only live for hours or days, but some live for years.

Platelets and Coagulation Factors

Blood must clot to heal wounds and prevent excess blood loss. Small cell fragments called platelets (thrombocytes) are attracted to the wound site where they adhere by extending many projections and releasing their contents. These contents activate other platelets and also interact with other coagulation factors, which convert fibrinogen, a water-soluble protein present in blood serum into fibrin (a non-water soluble protein), causing the blood to clot. Many of the clotting factors require vitamin K to work, and vitamin K deficiency can lead to problems with blood clotting. Many platelets converge and stick together at the wound site forming a platelet plug (also called a fibrin clot), as illustrated in [link]**b**. The plug or clot lasts for a number of days and stops the loss of blood. Platelets are formed from the disintegration of larger cells called megakaryocytes, like that shown in [link]**a**. For each megakaryocyte, 2000–3000 platelets are formed with 150,000 to 400,000 platelets present in each cubic millimeter of blood. Each platelet is disc shaped and 2–4 μm in diameter. They contain many small vesicles but do not contain a nucleus.

Plasma and Serum

The liquid component of blood is called plasma, and it is separated by spinning or centrifuging the blood at high rotations (3000 rpm or higher). The blood cells and platelets are separated by centrifugal forces to the bottom of a specimen tube. The upper liquid layer, the plasma, consists of 90 percent water along with various substances required for maintaining the body’s pH, osmotic load, and for protecting the body. The plasma also contains the coagulation factors and antibodies.

Mammalian Heart and Blood Vessels

Structure of the Heart

The heart muscle is asymmetrical as a result of the distance blood must travel in the pulmonary and systemic circuits. Since the right side of the heart sends blood to the pulmonary circuit it is smaller than the left side which must send blood out to the whole body in the systemic circuit, as shown in [link]. In humans, the heart is about the size of a clenched fist; it is divided into four chambers: two atria and two ventricles. There is one atrium and one ventricle on the right side and one atrium and one ventricle on the left side. The atria are the chambers that receive blood, and the ventricles are the chambers that pump blood. The right atrium receives deoxygenated blood from the **superior vena cava**, which drains blood from the jugular vein that comes from the brain and from the veins that come from the arms, as well as from the **inferior vena cava** which drains blood from the veins that come from the lower organs and the legs. In addition, the right atrium receives blood from the coronary sinus which drains deoxygenated blood from the heart itself. This deoxygenated blood then passes to the right ventricle through the **atrioventricular valve** or the **tricuspid valve**, a flap of connective tissue that opens in only one direction to prevent the backflow of blood. The valve separating the chambers on the left side of the heart valve is called the biscuspid or mitral valve. After it is filled, the right ventricle pumps the blood through the pulmonary arteries, by-passing the **semilunar valve** (or pulmonic valve) to the lungs for re-oxygenation. After blood passes through the pulmonary arteries, the right semilunar valves close preventing the blood from flowing backwards into the right ventricle. The left atrium then receives the oxygen-rich blood from the lungs via the pulmonary veins. This blood passes through the **bicuspid valve** or mitral valve (the atrioventricular valve on the left side of the heart) to the left ventricle where the blood is pumped out through **aorta**, the major artery of the body, taking oxygenated blood to the organs and muscles of the body. Once blood is pumped out of the left ventricle and into the aorta, the aortic semilunar valve (or aortic valve) closes preventing blood from flowing backward into the left ventricle. This pattern of pumping is referred to as double circulation and is found in all mammals.

The Cardiac Cycle

The main purpose of the heart is to pump blood through the body; it does so in a repeating sequence called the cardiac cycle. The **cardiac cycle** is the coordination of the filling and emptying of the heart of blood by electrical signals that cause the heart muscles to contract and relax. The human heart beats over 100,000 times per day. In each cardiac cycle, the heart contracts (**systole**), pushing out the blood and pumping it through the body; this is followed by a relaxation phase (**diastole**), where the heart fills with blood, as illustrated in [link]. The atria contract at the same time, forcing blood through the atrioventricular valves into the ventricles. Closing of the atrioventricular valves produces a monosyllabic “lup” sound. Following a brief delay, the ventricles contract at the same time forcing blood through the semilunar valves into the aorta and the artery transporting blood to the lungs (via the pulmonary artery). Closing of the semilunar valves produces a monosyllabic “dup” sound.

Arteries, Veins, and Capillaries

The blood from the heart is carried through the body by a complex network of blood vessels ([link]). **Arteries** take blood away from the heart. The main artery is the aorta that branches into major arteries that take blood to different limbs and organs. These major arteries include the carotid artery that takes blood to the brain, the brachial arteries that take blood to the arms, and the thoracic artery that takes blood to the thorax and then into the hepatic, renal, and gastric arteries for the liver, kidney, and stomach, respectively. The iliac artery takes blood to the lower limbs. The major arteries diverge into minor arteries, and then smaller vessels called **arterioles**, to reach more deeply into the muscles and organs of the body.

Blood Flow and Blood Pressure Regulation

How Blood Flows Through the Body

Blood is pushed through the body by the action of the pumping heart. With each rhythmic pump, blood is pushed under high pressure and velocity away from the heart, initially along the main artery, the aorta. In the aorta, the blood travels at 30 cm/sec. As blood moves into the arteries, arterioles, and ultimately to the capillary beds, the rate of movement slows dramatically to about 0.026 cm/sec, one-thousand times slower than the rate of movement in the aorta. While the diameter of each individual arteriole and capillary is far narrower than the diameter of the aorta, and according to the law of continuity, fluid should travel faster through a narrower diameter tube, the rate is actually slower due to the overall diameter of all the combined capillaries being far greater than the diameter of the individual aorta.

Blood Pressure

The pressure of the blood flow in the body is produced by the hydrostatic pressure of the fluid (blood) against the walls of the blood vessels. Fluid will move from areas of high to low hydrostatic pressures. In the arteries, the hydrostatic pressure near the heart is very high and blood flows to the arterioles where the rate of flow is slowed by the narrow openings of the arterioles. During systole, when new blood is entering the arteries, the artery walls stretch to accommodate the increase of pressure of the extra blood; during diastole, the walls return to normal because of their elastic properties. The blood pressure of the systole phase and the diastole phase, graphed in [link], gives the two pressure readings for blood pressure. For example, 120/80 indicates a reading of 120 mm Hg during the systole and 80 mm Hg during diastole. Throughout the cardiac cycle, the blood continues to empty into the arterioles at a relatively even rate. This resistance to blood flow is called **peripheral resistance**.

Blood Pressure Regulation

Cardiac output is the volume of blood pumped by the heart in one minute. It is calculated by multiplying the number of heart contractions that occur per minute (heart rate) times the **stroke volume** (the volume of blood pumped into the aorta per contraction of the left ventricle). Therefore, cardiac output can be increased by increasing heart rate, as when exercising. However, cardiac output can also be increased by increasing stroke volume, such as if the heart contracts with greater strength. Stroke volume can also be increased by speeding blood circulation through the body so that more blood enters the heart between contractions. During heavy exertion, the blood vessels relax and increase in diameter, offsetting the increased heart rate and ensuring adequate oxygenated blood gets to the muscles. Stress triggers a decrease in the diameter of the blood vessels, consequently increasing blood pressure. These changes can also be caused by nerve signals or hormones, and even standing up or lying down can have a great effect on blood pressure.

Osmotic Regulation and Excretion

Introduction

Osmoregulation and Osmotic Balance

Need for Osmoregulation

Biological systems constantly interact and exchange water and nutrients with the environment by way of consumption of food and water and through excretion in the form of sweat, urine, and feces. Without a mechanism to regulate osmotic pressure, or when a disease damages this mechanism, there is a tendency to accumulate toxic waste and water, which can have dire consequences.

Transport of Electrolytes across Cell Membranes

Electrolytes, such as sodium chloride, ionize in water, meaning that they dissociate into their component ions. In water, sodium chloride (NaCl), dissociates into the sodium ion (Na+) and the chloride ion (Cl–). The most important ions, whose concentrations are
very closely regulated in body fluids, are the cations sodium (Na+), potassium (K+), calcium (Ca+2),
magnesium (Mg+2), and the anions chloride (Cl–), carbonate (CO3–2), bicarbonate (HCO3–), and phosphate(PO3–). Electrolytes are lost from the body during urination and perspiration. For this
reason, athletes are encouraged to replace electrolytes and fluids during periods of increased activity and perspiration.

Concept of Osmolality and Milliequivalent

In order to calculate osmotic pressure, it is necessary to understand how solute concentrations are measured. The unit for measuring solutes is the **mole**. One mole is defined as the gram molecular weight of the solute. For example, the molecular weight of sodium chloride is 58.44. Thus, one mole of sodium chloride weighs 58.44 grams. The **molarity** of a solution is the number of moles of solute per liter of solution. The **molality** of a solution is the number of moles of solute per kilogram of solvent. If the solvent is water, one kilogram of water is equal to one liter of water. While molarity and molality are used to express the concentration of solutions, electrolyte concentrations are usually expressed in terms of milliequivalents per liter (mEq/L): the mEq/L is equal to the ion concentration (in millimoles) multiplied by the number of electrical charges on the ion. The unit of milliequivalent takes into consideration the ions present in the solution (since electrolytes form ions in aqueous solutions) and the charge on the ions.

Osmoregulators and Osmoconformers

Persons lost at sea without any fresh water to drink are at risk of severe dehydration because the human body cannot adapt to drinking seawater, which is hypertonic in comparison to body fluids. Organisms such as goldfish that can tolerate only a relatively narrow range of salinity are referred to as stenohaline. About 90 percent of all bony fish are restricted to either freshwater or seawater. They are incapable of osmotic regulation in the opposite environment. It is possible, however, for a few fishes like salmon to spend part of their life in fresh water and part in sea water. Organisms like the salmon and molly that can tolerate a relatively wide range of salinity are referred to as euryhaline organisms. This is possible because some fish have evolved **osmoregulatory** mechanisms to survive in all kinds of aquatic environments. When they live in fresh water, their bodies tend to take up water because the environment is relatively hypotonic, as illustrated in [link]**a**. In such hypotonic environments, these fish do not drink much water. Instead, they pass a lot of very dilute urine, and they achieve electrolyte balance by active transport of salts through the gills. When they move to a hypertonic marine environment, these fish start drinking sea water; they excrete the excess salts through their gills and their urine, as illustrated in [link]**b**. Most marine invertebrates, on the other hand, may be isotonic with sea water (**osmoconformers**). Their body fluid concentrations conform to changes in seawater concentration. Cartilaginous fishes’ salt composition of the blood is similar to bony fishes; however, the blood of sharks contains the organic compounds urea and trimethylamine oxide (TMAO). This does not mean that their electrolyte composition is similar to that of sea water. They achieve isotonicity with the sea by storing large concentrations of urea. These animals that secrete urea are called ureotelic animals. TMAO stabilizes proteins in the presence of high urea levels, preventing the disruption of peptide bonds that would occur in other animals exposed to similar levels of urea. Sharks are cartilaginous fish with a rectal gland to secrete salt and assist in osmoregulation.

The Kidneys and Osmoregulatory Organs

Kidneys: The Main Osmoregulatory Organ

The **kidneys**, illustrated in [link], are a pair of bean-shaped structures that are located just below and posterior to the liver in the peritoneal cavity. The adrenal glands sit on top of each kidney and are also called the suprarenal glands. Kidneys filter blood and purify it. All the blood in the human body is filtered many times a day by the kidneys; these organs use up almost 25 percent of the oxygen absorbed through the lungs to perform this function. Oxygen allows the kidney cells to efficiently manufacture chemical energy in the form of ATP through aerobic respiration. The filtrate coming out of the kidneys is called **urine**.

Kidney Structure

Externally, the kidneys are surrounded by three layers, illustrated in [link]. The outermost layer is a tough connective tissue layer called the **renal fascia**. The second layer is called the **perirenal fat capsule**, which helps anchor the kidneys in place. The third and innermost layer is the **renal capsule**. Internally, the kidney has three regions—an outer **cortex**, a **medulla** in the middle, and the **renal pelvis** in the region called the **hilum** of the kidney. The hilum is the concave part of the bean-shape where blood vessels and nerves enter and exit the kidney; it is also the point of exit for the ureters. The renal cortex is granular due to the presence of **nephrons**—the functional unit of the kidney. The medulla consists of multiple pyramidal tissue masses, called the **renal pyramids**. In between the pyramids are spaces called **renal columns** through which the blood vessels pass. The tips of the pyramids, called renal papillae, point toward the renal pelvis. There are, on average, eight renal pyramids in each kidney. The renal pyramids along with the adjoining cortical region are called the **lobes of the kidney**. The renal pelvis leads to the **ureter** on the outside of the kidney. On the inside of the kidney, the renal pelvis branches out into two or three extensions called the major **calyces**, which further branch into the minor calyces. The ureters are urine-bearing tubes that exit the kidney and empty into the **urinary bladder**.

Kidney Function and Physiology

Kidneys filter blood in a three-step process. First, the nephrons filter blood that runs through the capillary network in the glomerulus. Almost all solutes, except for proteins, are filtered out into the glomerulus by a process called **glomerular filtration**. Second, the filtrate is collected in the renal tubules. Most of the solutes get reabsorbed in the PCT by a process called **tubular reabsorption**. In the loop of Henle, the filtrate continues to exchange solutes and water with the renal medulla and the peritubular capillary network. Water is also reabsorbed during this step. Then, additional solutes and wastes are secreted into the kidney tubules during **tubular secretion**, which is, in essence, the opposite process to tubular reabsorption. The collecting ducts collect filtrate coming from the nephrons and fuse in the medullary papillae. From here, the papillae deliver the filtrate, now called urine, into the minor calyces that eventually connect to the ureters through the renal pelvis. This entire process is illustrated in [link].

Excretion Systems

Contractile Vacuoles in Microorganisms

The most fundamental feature of life is the presence of a cell. In other words, a cell is the simplest functional unit of a life. Bacteria are unicellular, prokaryotic organisms that have some of the least complex life processes in place; however, prokaryotes such as bacteria do not contain membrane-bound vacuoles. The cells of microorganisms like bacteria, protozoa, and fungi are bound by cell membranes and use them to interact with the environment. Some cells, including some leucocytes in humans, are able to engulf food by endocytosis—the formation of vesicles by involution of the cell membrane within the cells. The same vesicles are able to interact and exchange metabolites with the intracellular environment. In some unicellular eukaryotic organisms such as the amoeba, shown in [link], cellular wastes and excess water are excreted by exocytosis, when the contractile vacuoles merge with the cell membrane and expel wastes into the environment. Contractile vacuoles (CV) should not be confused with vacuoles, which store food or water.

Flame Cells of Planaria and Nephridia of Worms

As multi-cellular systems evolved to have organ systems that divided the metabolic needs of the body, individual organs evolved to perform the excretory function. Planaria are flatworms that live in fresh water. Their excretory system consists of two tubules connected to a highly branched duct system. The cells in the tubules are called **flame cells** (or **protonephridia**) because they have a cluster of cilia that looks like a flickering flame when viewed under the microscope, as illustrated in [link]**a**. The cilia propel waste matter down the tubules and out of the body through excretory pores that open on the body surface; cilia also draw water from the interstitial fluid, allowing for filtration. Any valuable metabolites are recovered by reabsorption. Flame cells are found in flatworms, including parasitic tapeworms and free-living planaria. They also maintain the organism’s osmotic balance.

Malpighian Tubules of Insects

**Malpighian tubules** are found lining the gut of some species of arthropods, such as the bee illustrated in [link]. They are usually found in pairs and the number of tubules varies with the species of insect. Malpighian tubules are convoluted, which increases their surface area, and they are lined with **microvilli** for reabsorption and maintenance of osmotic balance. Malpighian tubules work cooperatively with specialized glands in the wall of the rectum. Body fluids are not filtered as in the case of nephridia; urine is produced by tubular secretion mechanisms by the cells lining the Malpighian tubules that are bathed in hemolymph (a mixture of blood and interstitial fluid that is found in insects and other arthropods as well as most mollusks). Metabolic wastes like uric acid freely diffuse into the tubules. There are exchange pumps lining the tubules, which actively transport H+ ions into the cell and K+ or Na+ ions out; water passively follows to form urine. The secretion of ions alters the osmotic pressure which draws water, electrolytes, and nitrogenous waste (uric acid) into the tubules. Water and electrolytes are reabsorbed when these organisms are faced with low-water environments, and uric acid is excreted as a thick paste or powder. Not dissolving wastes in water helps these organisms to conserve water; this is especially important for life in dry environments.

Nitrogenous Wastes

Nitrogenous Waste in Terrestrial Animals: The Urea Cycle

The **urea cycle** is the primary mechanism by which mammals convert ammonia to urea. Urea is made in the liver and excreted in urine. The overall chemical reaction by which ammonia is converted to urea is 2 NH3 (ammonia) + CO2 + 3 ATP + H2O → H2N-CO-NH2 (urea) + 2 ADP + 4 Pi + AMP.

Nitrogenous Waste in Birds and Reptiles: Uric Acid

Birds, reptiles, and most terrestrial arthropods convert toxic ammonia to **uric acid** or the closely related compound guanine (guano) instead of urea. Mammals also form some uric acid during breakdown of nucleic acids. Uric acid is a compound similar to purines found in nucleic acids. It is water insoluble and tends to form a white paste or powder; it is excreted by birds, insects, and reptiles. Conversion of ammonia to uric acid requires more energy and is much more complex than conversion of ammonia to urea [link].

Hormonal Control of Osmoregulatory Functions

Epinephrine and Norepinephrine

Epinephrine and norepinephrine are released by the adrenal medulla and nervous system respectively. They are the flight/fight hormones that are released when the body is under extreme stress. During stress, much of the body’s energy is used to combat imminent danger. Kidney function is halted temporarily by epinephrine and norepinephrine. These hormones function by acting directly on the smooth muscles of blood vessels to constrict them. Once the afferent arterioles are constricted, blood flow into the nephrons stops. These hormones go one step further and trigger the **renin-angiotensin-aldosterone** system.

Mineralocorticoids

Mineralocorticoids are hormones synthesized by the adrenal cortex that affect osmotic balance. Aldosterone is a mineralocorticoid that regulates sodium levels in the blood. Almost all of the sodium in the blood is reclaimed by the renal tubules under the influence of aldosterone. Because sodium is always reabsorbed by active transport and water follows sodium to maintain osmotic balance, aldosterone manages not only sodium levels but also the water levels in body fluids. In contrast, the aldosterone also stimulates potassium secretion concurrently with sodium reabsorption. In contrast, absence of aldosterone means that no sodium gets reabsorbed in the renal tubules and all of it gets excreted in the urine. In addition, the daily dietary potassium load is not secreted and the retention of K+ can cause a dangerous increase in plasma K+ concentration. Patients who have Addison's disease have a failing adrenal cortex and cannot produce aldosterone. They lose sodium in their urine constantly, and if the supply is not replenished, the consequences can be fatal.

Antidiurectic Hormone

As previously discussed, antidiuretic hormone or ADH (also called **vasopressin**), as the name suggests, helps the body conserve water when body fluid volume, especially that of blood, is low. It is formed by the hypothalamus and is stored and released from the posterior pituitary. It acts by inserting aquaporins in the collecting ducts and promotes reabsorption of water. ADH also acts as a vasoconstrictor and increases blood pressure during hemorrhaging.

Atrial Natriuretic Peptide Hormone

The atrial natriuretic peptide (ANP) lowers blood pressure by acting as a **vasodilator**. It is released by cells in the atrium of the heart in response to high blood pressure and in patients with sleep apnea. ANP affects salt release, and because water passively follows salt to maintain osmotic balance, it also has a diuretic effect. ANP also prevents sodium reabsorption by the renal tubules, decreasing water reabsorption (thus acting as a diuretic) and lowering blood pressure. Its actions suppress the actions of aldosterone, ADH, and renin.

The Immune System

Introduction

Innate Immune Response

Adaptive Immune Response

Immunological Memory

The adaptive immune system possesses a memory component that allows for an efficient and dramatic response upon reinvasion of the same pathogen. Memory is handled by the adaptive immune system with little reliance on cues from the innate response. During the adaptive immune response to a pathogen that has not been encountered before, called a primary response, plasma cells secreting antibodies and differentiated T cells increase, then plateau over time. As B and T cells mature into effector cells, a subset of the naïve populations differentiates into B and T memory cells with the same antigen specificities, as illustrated in [link].

Antibodies

Antibodies of the Mucosal Immune System

Antibodies synthesized by the mucosal immune system include IgA and IgM. Activated B cells differentiate into mucosal plasma cells that synthesize and secrete dimeric IgA, and to a lesser extent, pentameric IgM. Secreted IgA is abundant in tears, saliva, breast milk, and in secretions of the gastrointestinal and respiratory tracts. Antibody secretion results in a local humoral response at epithelial surfaces and prevents infection of the mucosa by binding and neutralizing pathogens.

Disruptions in the Immune System

Immunodeficiency

Failures, insufficiencies, or delays at any level of the immune response can allow pathogens or tumor cells to gain a foothold and replicate or proliferate to high enough levels that the immune system becomes overwhelmed. **Immunodeficiency** is the failure, insufficiency, or delay in the response of the immune system, which may be acquired or inherited. Immunodeficiency can be acquired as a result of infection with certain pathogens (such as HIV), chemical exposure (including certain medical treatments), malnutrition, or possibly by extreme stress. For instance, radiation exposure can destroy populations of lymphocytes and elevate an individual’s susceptibility to infections and cancer. Dozens of genetic disorders result in immunodeficiencies, including Severe Combined Immunodeficiency (SCID), Bare lymphocyte syndrome, and MHC II deficiencies. Rarely, primary immunodeficiencies that are present from birth may occur. Neutropenia is one form in which the immune system produces a below-average number of neutrophils, the body’s most abundant phagocytes. As a result, bacterial infections may go unrestricted in the blood, causing serious complications.

Animal Reproduction and Development

Introduction

Reproduction Methods

Fertilization

Internal Fertilization

Internal fertilization occurs most often in land-based animals, although some aquatic animals also use this method. There are three ways that offspring are produced following internal fertilization. In **oviparity**, fertilized eggs are laid outside the female’s body and develop there, receiving nourishment from the yolk that is a part of the egg. This occurs in most bony fish, many reptiles, some cartilaginous fish, most amphibians, two mammals, and all birds. Reptiles and insects produce leathery eggs, while birds and turtles produce eggs with high concentrations of calcium carbonate in the shell, making them hard. Chicken eggs are an example of this second type.

Human Reproductive Anatomy and Gametogenesis

Hormonal Control of Human Reproduction

Fertilization and Early Embryonic Development

Organogenesis and Vertebrate Formation

Human Pregnancy and Birth

Ecology

Ecology and the Biosphere

Introduction

The Scope of Ecology

Biogeography

Terrestrial Biomes

Arctic Tundra

The Arctic tundra lies north of the subarctic boreal forest and is located throughout the Arctic regions of the northern hemisphere ([link]). The average winter temperature is -34 °C (-29.2 °F) and the average summer temperature is from 3 °C to 12 °C (37 °F–52 °F). Plants in the arctic tundra have a very short growing season of approximately 10–12 weeks. However, during this time, there are almost 24 hours of daylight and plant growth is rapid. The annual precipitation of the Arctic tundra is very low with little annual variation in precipitation. And, as in the boreal forests, there is little evaporation due to the cold temperatures.

Aquatic Biomes

Climate and the Effects of Global Climate Change

Climate and Weather

A common misconception about global climate change is that a specific weather event occurring in a particular region (for example, a very cool week in June in central Indiana) is evidence of global climate change. However, a cold week in June is a weather-related event and not a climate-related one. These misconceptions often arise because of confusion over the terms climate and weather.

Documented Results of Climate Change: Past and Present

Scientists have geological evidence of the consequences of long-ago climate change. Modern-day phenomena such as retreating glaciers and melting polar ice cause a continual rise in sea level. Meanwhile, changes in climate can negatively affect organisms.

Population and Community Ecology

Introduction

Population Demography

Demography

While population size and density describe a population at one particular point in time, scientists must use demography to study the dynamics of a population. Demography is the statistical study of population changes over time: birth rates, death rates, and life expectancies. Each of these measures, especially birth rates, may be affected by the population characteristics described above. For example, a large population size results in a higher birth rate because more potentially reproductive individuals are present. In contrast, a large population size can also result in a higher death rate because of competition, disease, and the accumulation of waste. Similarly, a higher population density or a clumped dispersion pattern results in more potential reproductive encounters between individuals, which can increase birth rate. Lastly, a female-biased sex ratio (the ratio of males to females) or age structure (the proportion of population members at specific age ranges) composed of many individuals of reproductive age can increase birth rates.

Life Histories and Natural Selection

Life History Patterns and Energy Budgets

Energy is required by all living organisms for their growth, maintenance, and reproduction; at the same time, energy is often a major limiting factor in determining an organism’s survival. Plants, for example, acquire energy from the sun via photosynthesis, but must expend this energy to grow, maintain health, and produce energy-rich seeds to produce the next generation. Animals have the additional burden of using some of their energy reserves to acquire food. Furthermore, some animals must expend energy caring for their offspring. Thus, all species have an energy budget: they must balance energy intake with their use of energy for metabolism, reproduction, parental care, and energy storage (such as bears building up body fat for winter hibernation).

Environmental Limits to Population Growth

Population Dynamics and Regulation

Modern Theories of Life History

The *r*- and *K*-selection theory, although accepted for decades and used for much groundbreaking research, has now been reconsidered, and many population biologists have abandoned or modified it. Over the years, several studies attempted to confirm the theory, but these attempts have largely failed. Many species were identified that did not follow the theory’s predictions. Furthermore, the theory ignored the age-specific mortality of the populations which scientists now know is very important. New **demographic-based models** of life history evolution have been developed which incorporate many ecological concepts included in *r*- and *K*-selection theory as well as population age structure and mortality factors.

Human Population Growth

Community Ecology

Behavioral Biology: Proximate and Ultimate Causes of Behavior

Sociobiology

Sociobiology is an interdisciplinary science originally popularized by social insect researcher E.O. Wilson in the 1970s. Wilson defined the science as “the extension of population biology and evolutionary theory to social organization.”[footnote]The main thrust of sociobiology is that animal and human behavior, including aggressiveness and other social interactions, can be explained almost solely in terms of genetics and natural selection. This science is controversial; noted scientists such as the late Stephen Jay Gould criticized the approach for ignoring the environmental effects on behavior. This is another example of the “nature versus nurture” debate of the role of genetics versus the role of environment in determining an organism’s characteristics.

Edward O. Wilson. *On Human Nature* (1978; repr., Cambridge: Harvard University Press, 2004), xx.

Ecosystems

Introduction

Ecology for Ecosystems

Energy Flow through Ecosystems

Biogeochemical Cycles

Conservation Biology and Biodiversity

Introduction

The Biodiversity Crisis

The Importance of Biodiversity to Human Life

Psychological and Moral Value

Finally, it has been argued that humans benefit psychologically from living in a biodiverse world. A chief proponent of this idea is entomologist E. O. Wilson. He argues that human evolutionary history has adapted us to live in a natural environment and that built environments generate stressors that affect human health and well-being. There is considerable research into the psychological regenerative benefits of natural landscapes that suggests the hypothesis may hold some truth. In addition, there is a moral argument that humans have a responsibility to inflict as little harm as possible on other species.

Threats to Biodiversity

Preserving Biodiversity

The Periodic Table of Elements

Geological Time

Measurements and the Metric System