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Animation 3.6 Enzyme Catalysis
If we were to extract the chemicals from a living cell and watch them react with one another, we'd probably have to wait a long time—perhaps longer than the normal life of the cell—to see many reactions take place. On their own, many of the chemicals react too slowly to support an organism's metabolism. Living cells circumvent this problem by producing biological catalysts, called enzymes. Enzymes lower the amount of energy required (activation energy) to trigger chemical reactions, making reactions more likely to occur and thereby increasing reaction rates. In the accompanying animation, we look at a reaction in which an enzyme holds a substrate molecule at the enzyme's active site and facilitates the molecule's conversion into a product. We will examine the relative rates of this reaction in the presence or absence of the enzyme, as well as in the presence of enzyme inhibitors.
Animation 3.7 Allosteric Regulation of Enzymes
Cells tightly regulate their enzymatic reactions, allowing necessary reactions to proceed while inhibiting unnecessary or damaging ones. One means of regulating enzyme action is allosteric regulation. In allosteric regulation, the covalent modification or noncovalent binding of a regulator to an enzyme can cause an enzyme to change shape and expose an active site. Negative regulation can work this way as well, with the active site becoming hidden.
Animation 1.1 Using Scientific Methodology
Regardless of the many different tools and methods used in research, all scientific investigations are based on observation and experimentation, key elements of the scientific method. The scientific method is one of the most powerful tools of modern science.
Often, science textbooks describe "the scientific method," as if there is a single, simple flow chart that all scientists follow. This is an oversimplification. Although such flow charts incorporate much of what scientists do, you should not conclude that scientists necessarily progress through the steps of the process in one prescribed, linear order. That said, we will introduce you to this traditional flow chart, which consists of five main steps: making observations; asking questions; forming hypotheses; making predictions based on the hypotheses; and testing the predictions by making additional observations or conducting experiments. We will highlight this version of the scientific method using an experiment on coral bleaching.
Animation 2.1 Chemical Bond Formation
If we take a purely mechanistic view of life, we can consider each living cell as an intricate web of chemical reactions. Atoms combine with other atoms to form molecules and then recombine again during other chemical reactions to form different molecules. These chemical reactions are the basis of a cell's structure and metabolism.
In the accompanying animation, we examine chemical bonds, which are the attractive forces between atoms. We focus, in particular, on the role of electrons in chemical bonds. The behavior of electrons explains most aspects of how atoms interact with each other in the living and nonliving world.
Animation 3.1 Macromolecules: Lipids
Although living cells are primarily made up of water, a number of other molecules are also abundant. Gigantic molecules, called macromolecules, populate a cell and provide it with important functions for life. For example, macromolecules provide structural support, a source of stored fuel, the ability to store and retrieve genetic information, and the ability to speed biochemical reactions. Four major types of macromolecules—proteins, carbohydrates, nucleic acids, and lipids—play these important roles in the life of a cell. In this tutorial, we examine the structures and functions of lipids.
Animation 4.1 Passive Transport
The cell membrane acts as a gatekeeper, allowing some substances to enter the cell, but excluding others. In other words, the membrane is selectively permeable. This selective permeability is an essential feature of the membranes of all living cells, because it provides them with the power to control their internal environments. The cell may use channels, carriers, or pumps to move substances from one side of a membrane to the other.
In this animation, we examine a type of transport across a membrane that requires no energy for a cell to perform. It is called passive transport. In passive transport, a substance moves across a membrane from a region of higher concentration to a region of lower concentration. Active transport (not shown here) is the opposite: it requires energy, moving a substance from a lower concentration to a higher concentration.
Animation 6.1 Signal Transduction and Cancer
A growth factor can trigger a cell to grow, differentiate, or divide. Many growth factors act by binding to a receptor on the cell's surface, causing the receptor to initiate a series of events inside the cell that lead to a cellular response, such as cell division. The sequence of molecular events and chemical reactions that lead to a cell's response is called a signal transduction pathway.
Signal transduction pathways are by necessity highly regulated. If a pathway triggered by a growth factor cannot turn off, for example, cells may continually divide without regulation—that is, become cancerous. In this animation we look at the events of one type of signal transduction pathway, as well as how a mutant protein (called RAS) in the cascade can result in cancer.
Animation 8.1 Independent Assortment of Alleles
As one of his many breeding experiments with pea plants, Gregor Mendel crossed plants that differed at two different gene loci. These experiments led him to the concept called Mendel's second law. According to this law, the alleles of two (or more) different gene pairs—for example, Rr and Yy—assort independently of each other during meiosis, such that a random combination of the genes from each pair winds up in the gametes.
Independent assortment occurs because chromosomes may be aligned in various ways in metaphase I of meiosis. However, keep in mind as you watch the animation that for two genes to assort independently they must reside on different chromosomes; or if they reside on the same chromosome, they must be located relatively far from each other along the chromosome's arms.
Animation 9.1 The Hershey–Chase Experiment
In 1952, Alfred Hershey and Martha Chase published a convincing demonstration that DNA (not protein) was the genetic material. The Hershey–Chase experiment was carried out with a virus, called bacteriophage T2, that infects bacteria. Bacteriophage T2 consists of little more than a DNA core packed inside a protein coat. Thus, the virus is made of the two materials that were, at the time, the leading candidates for the genetic material.
Animation 10.1 Transcription
For a protein-coding gene to be expressed, it must first be transcribed. In transcription, the code in the gene's DNA is converted into a complementary code in an RNA molecule. The RNA molecule then participates in the second phase of gene expression: translation. In translation, the code in the RNA is converted into an amino acid sequence in a protein. Transcription and translation are the main events of gene expression.
In the accompanying animation, we focus on transcription, which occurs in three phases: initiation, elongation, and termination.
Animation 11.1 The lac Operon
The bacterium E. coli has an efficient mechanism for metabolizing lactose. Three proteins that are important in lactose metabolism are all encoded in a single expressible unit of DNA, called the lac operon. The bacterium does not waste energy expressing these proteins if lactose is not present in the growth medium. It only makes these proteins when lactose is available to be metabolized.
In this tutorial, we examine how the presence of lactose turns on the expression of these lactose-metabolizing genes.
Animation 12.1 Sequencing the Genome
More than a thousand researchers throughout the world contributed to the first project to sequence the human genome. Their task, which they successfully completed in 2003, was to decode the DNA from each of 23 pairs of human chromosomes. Two groups undertook this sequencing task. One large, multinational, publicly funded group adopted an approach called hierarchical sequencing. This group's work is better known as the Human Genome Project. The other group, at a privately funded company, took an approach called shotgun sequencing.
This animated tutorial describes the methods used by the two groups, but keep in mind that technologies have changed a lot since then. The Human Genome Project was relatively slow, expensive, and labor intensive. It took 13 years and $2.7 billion to sequence one genome! In contrast, at the time of this writing, current methods allow researchers to sequence a human genome in just a few days for several thousand dollars.
Animation 13.1 Natural Selection
In 1858, two men, Charles Darwin and Alfred Russel Wallace, independently proposed a mechanism for evolution. Darwin named this mechanism natural selection. Natural selection requires variation among individuals in a population. In a particular environment, some traits of individuals are more advantageous than others. The individuals with the advantageous traits are able to survive better, and therefore they are also able to produce more offspring. In subsequent generations, there are relatively more individuals with the inherited advantageous traits. In this way, the population changes, or evolves, from one generation to the next.
In the accompanying animation, we examine natural selection in Texas Longhorn cattle.
Animation 14.1 Using Phylogenetic Analysis to Reconstruct Evolutionary History
In recent years, DNA sequences have become one of the most widely used sources for constructing phylogenetic trees. How can we test the accuracy of these construction efforts, considering that evolutionary events occurred in the past, mostly without human witnesses? Phylogenetic trees represent hypotheses of evolutionary relationships that can be explicitly tested using data. The example described in this animation does just that.
A group of investigators set up an experiment to track the evolution of a bacterial virus, called bacteriophage T7, in the laboratory. With the history of the T7 lineages known, the investigators could determine if a phylogenetic construction (based on the DNA sequences of the viruses at the endpoints of the lineages) matched the known history of the lineages.
Animation 15.1 Pattern Formation in the Drosophila Embryo
The fruit fly Drosophila melanogaster, like other arthropods, is composed of numerous body segments. The fly has several fused head segments, three thoracic segments, eight abdominal segments, and a terminal segment at the end of the abdomen. In the adult fly, these segments are clearly unique, in that a head segment has antennae, but a thoracic segment has legs instead, and an abdominal segment has neither.
About 24 hours after fertilization, a larva appears with distinct segments. The segments all look similar, but their fates to become different adult segments is already determined. Several types of genes are expressed sequentially in the embryo to define these segments. The genes involved in each step code for transcription factors, which in turn control the synthesis of other transcription factors acting on the next set of genes. The genes expressed at the end of this cascade code for proteins that carry out the functions of the cell.
Animation 16.1 Speciation Mechanisms
How does a single species give rise to two or more different species? This concept, called speciation, requires that a single population of organisms divide into two or more populations that no longer interbreed. Without interbreeding, there is no gene flow between the populations, and these populations may then evolve separately into distinct species. There are many definitions for what a species is, but we will begin with biologist Ernst Mayr's 1940 definition, in which he states that species are groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups. We will extend this to say that if two individuals of different species do mate and produce offspring, that those offspring would not be fertile.
In the accompanying animation, we examine two mechanisms of establishing a barrier to gene flow, leading to speciation.
Animation 17.1 Movement of Continents
The continents on which we live are on the move, albeit at an average rate of only several centimeters each year. The continents move because they ride on top of gigantic plates that, in turn, float on a molten layer of Earth, called the mantle. Energy, released from radioactive decay in Earth's core, heats up the mantle and sets up convection currents that propel the plates around Earth's surface. The movement of the plates, and the continents that ride on them, is called continental drift.
At times in Earth's history, the continents have coalesced into giant landmasses, but at other times they have traveled away from each other. The positions of the continents affect Earth's climate, the sea levels, the distributions of organisms, as well as the birth and extinction of species. In addition to depicting continental drift, this animation also provides a summary of the state of life at each corresponding period in Earth's history.
Animation 18.1 The Primary Divisions of Life
Genetic studies indicate that modern life descended from a common ancestor. The last universal common ancestor likely existed more than three billion years ago. Over the course of evolution, it appears that two main lines of descent, drawn as branches on a tree of life, have sprung from the last universal common ancestor: Bacteria and Archaea. A third group—the Eukarya—evolved from within the Archaea.
Animation 19.1 Family Tree of Chloroplasts
A number of distantly related groups of protists, as well as all plants, contain chloroplasts. The chloroplasts come in a number of different types; they may be surrounded by two, three, or four membranes, and they may contain different types of photosynthetic pigments.
Despite these differences, all chloroplasts trace back to the engulfment of an ancestral cyanobacterium by a larger eukaryotic cell—an event called primary endosymbiosis. In endosymbiosis, one organism lives inside another organism.
In the accompanying animation, we focus on this event of primary endosymbiosis and the subsequent evolution of chloroplasts in plants and several types of protists.
Animation 20.1 Life Cycle of a Moss
A moss is a member of the plant phylum Bryophyta. These plants, along with the liverworts (Hepatophyta) and hornworts (Anthocerophyta), lack well-developed vascular systems. They lack a distinctive kind of fluid-conducting cell—the tracheid—and are referred to collectively as nonvascular land plants.
The life cycle of a moss, like all plants, is characterized by an alternation of generations. A diploid generation, called the sporophyte, follows a haploid generation, called the gametophyte, which is in turn followed by the next sporophyte generation.
Animation 21.1 Life Cycle of a Zygospore Fungus
Black bread mold is the common name for a species of fungus called Rhizopus stolonifer. Despite its name, this fungus also attacks substrates other than bread, including cheese and a variety of fruits and vegetables. Rhizopus grows by extending filaments, called hyphae, along the surface of a substrate and by penetrating the substrate with rootlike structures (also made up of hyphae) called rhizoids. Like all fungi, Rhizopus digests its food outside its body and then transports the digested nutrients inside.
Rhizopus is classified in the group Zygomycota, the zygospore fungi. The name for this group comes from the only diploid structure—called the zygosporangium—that exists in the entire life cycles of these organisms. In the accompanying animation we depict the life cycle of a zygospore fungus, which includes both sexual and asexual reproduction.
Animation 22.1 Life Cycle of a Cnidarian
The cnidarians include jellyfishes, sea anemones, corals, and hydrozoans. Of the roughly 11,000 living cnidarian species, all but a few live in the oceans. The smallest cnidarians can hardly be seen without a microscope. The largest known jellyfish is 2.5 meters in diameter, and some colonial species can reach lengths in excess of 30 meters.
The life cycle of many cnidarians has two distinct stages, one sessile and the other motile, although one or the other of these stages is absent in some groups. Obelia (a hydrozoan) is an example of a cnidarian with a life cycle alternating between polyp (sessile, with asexual reproduction through budding) and medusa (motile, with sexual reproduction) generations.
Animation 23.1 Secondary Growth: The Vascular Cambium
The trunk of a tree owes its woody girth to a phenomenon called secondary growth. In secondary growth, a plant grows wider. Contrast this to primary growth, in which a plant grows taller. Secondary growth occurs within a thin layer of actively dividing cells, called the vascular cambium, which lies between the plant's xylem and phloem.
Some stems and roots remain slender and show little or no growth in diameter, but in many eudicots, stems and roots thicken considerably. In the accompanying animation, we study the process of secondary growth in the stem of a woody eudicot.
Animation 24.1 Nitrogen and Iron Deficiencies
Plants require a variety of mineral elements from the soil or from another medium in which they grow. If a plant's growth medium lacks an essential mineral element, the plant will display a characteristic set of symptoms before it dies. Nitrogen and iron are essential mineral elements for plants. Plants deficient in these elements are stunted in growth and show yellowing symptoms in their leaves. In the accompanying animation, we describe the yellowing symptoms of nitrogen and iron deficiencies.
Animation 25.1 Tropisms
Plants require light for growth and survival, so it makes sense that plant shoots would have mechanisms to maximize their exposure to light. Two different kinds of phenomena help plants do this: phototropism, which is growth toward or away from light, and gravitropism, which is growth toward or away from the force of gravity. In shoots, phototropism and gravitropism are mediated in part by a hormone, called auxin, which travels asymmetrically in the shoot and stimulates cell elongation. In an accompanying animation, we examine the movements of auxin along the shoot and the subsequent growth of the seedling during phototropism and gravitropism.
In another animation, we study the kinds of experiments—similar to those first performed by Charles Darwin and his son Francis—that determined the location of the light sensor in shoots. These experiments were performed on canary grass seedlings, which have a sheath, called a coleoptile, that grows in the direction of a light source.
Animation 26.1 Double Fertilization
Flowering plants are capable of both asexual and sexual reproduction. In sexual reproduction, which is the subject of the accompanying animation, a haploid sperm cell fuses with a haploid egg cell to form a diploid zygote, which develops into an embryo. In addition to this fertilization event, there is a second event involving another sperm cell and a second cell within the female's reproductive tissue. The product of this second event is a triploid cell that develops into the developing embryo's food supply.
Animation 27.1 Signaling between Plants and Pathogens
Like animals, plants have a number of ways of protecting themselves against disease. Their first line of defense is their outer layer of tissue—the epidermis or cork—which is generally covered with a barrier of waxes, cutin, or suberin. However, if a pathogen, such as a virus, bacterium, or fungus, penetrates this barrier, the plant responds by producing other protective molecules. Plants and pathogens have evolved together such that pathogens have mechanisms to attack and penetrate plants, and plants have evolved mechanisms to kill the pathogens and limit the infection.
Animation 28.1 The Hypothalamus
Most organisms operate within a relatively narrow range of body temperatures. The body temperature of humans can vary only a few degrees from 37°C without serious consequences. The main problem is that at too high a temperature, proteins change conformation and begin to denature. At too low a temperature, chemical reactions slow down too much. At 0°C and below, ice crystals form within cells and destroy them. However, the diverse animals of the world have numerous adaptations for surviving changes in body temperatures and for living in a wide range of environmental temperatures.
Humans and other mammals have a regulatory system for maintaining their body temperatures very close to their set points. Found in a region of the brain called the hypothalamus, this regulatory system acts as a kind of thermostat, receiving temperature information from sensory receptors and sending commands to controlled systems—the tissues and organs that respond by heating or cooling the body.
Animation 29.1 Circadian Rhythms
Biological rhythms are set by an internal clock, or pacemaker. These rhythms persist even in the absence of external cues. Many animals show rhythms in activity and physiological measures that repeat each day, month, or year. The internal clock that drives a circadian (daily) rhythm can be synchronized to time cues in the environment, such as the light/dark cycle. This process of synchronization to an external stimulus is called entrainment.
Although the existence of biological rhythms has been apparent for quite some time, a detailed analysis of this phenomenon required the development of appropriate methods for measuring ongoing behavior over an extended period of time. This animation shows examples of several experiments that demonstrate how biological rhythms can be measured and how the existence of internal clocks can be revealed.
Animation 30.1 Airflow in Birds
The respiratory system of birds is amazingly efficient. In addition to the lungs, where gas exchange occurs, the bird's respiratory system includes groups of air sacs. This arrangement of respiratory structures allows air to flow in one direction through the lungs. Therefore, all air that passes through the lungs of a bird is fresh, with a high percentage of oxygen.
In the accompanying animation, we examine the route that air takes as it passes through the respiratory system of a bird.
Animation 31.1 The Resting Membrane Potential
Neurons process information in the form of electrical signals (nerve impulses or action potentials) that travel along their axons (long extensions of cell membrane). Electrical charges move across the membrane as charged ions, but the cell membranes of most cells, including neurons, are relatively impermeable to charged ions. However, proteins that act as ion channels and ion pumps are embedded in the cell membrane and make it possible for ions to move, or to be moved, selectively across the membrane.
In this animation, we review how ion channels are responsible for a voltage difference (called the resting potential) across the cell membrane of a neuron.
Animation 32.1 The Hypothalamus and Negative Feedback
The hypothalamus is a small, yet vitally important, brain region that integrates the body's two communication systems: the endocrine and nervous systems. It links the two by sending and receiving signals from other regions of the nervous system while also controlling the body's "master gland"—the pituitary gland. The pituitary, in turn, controls most other endocrine organs of the body.
The interaction between the hypothalamus, pituitary, and other endocrine glands is known as the hypothalamic–pituitary–endocrine axis. In one animation, we examine the hypothalamic control of the pituitary gland, and we show the endocrine glands that the pituitary controls. In another, we examine a phenomenon called a negative feedback loop, in which hormones from endocrine glands influence the action of the hypothalamus.
Animation 33.1 Molecular Mechanisms of Muscle Contraction
An animal performs most of its behavior through the contraction and relaxation of muscles. Skeletal muscles have an organization in which bundles of protein filaments make up muscle cells, and bundles of muscle cells make up muscles. Muscle cells are the products of the fusion of many different cells, so each muscle cell contains many nuclei. The subcellular organization of a muscle cell also includes the previously mentioned bundles of protein filaments, called myofibrils. Lying end-to-end within these myofibrils are the actual contractile units, the sarcomeres. When the sarcomeres within a muscle cell contract, the muscle itself contracts and shortens. In the accompanying animation, we examine the mechanism by which a sarcomere shortens during contraction.
Animation 34.1 Fertilization in a Sea Urchin Egg
The union of the haploid sperm and the haploid egg in fertilization creates a single diploid cell, called a zygote, which will develop into an embryo. Fertilization does more, however, than just restore the full genetic complement of the animal. The processes associated with fertilization help the egg and sperm get together, prevent the union of the sperm and egg of different species, and guarantee that only one sperm will enter and activate the egg metabolically. In the accompanying animation, we examine fertilization using an invertebrate animal—a sea urchin—as an example.
Animation 35.1 Early Asymmetry in the Embryo
Cloning experiments have shown that cell nuclei do not undergo irreversible changes early in development. All cells retain the complete genetic code from which an entire organism can be produced. Still, not all cells behave the same way during development. Cells eventually differentiate to become the diverse tissues and structures of the body. Generalizing, we may say that differentiation results from differential gene expression—that is, from the differential regulation of transcription, posttranscriptional events such as mRNA splicing, and translation in different cell types.
Some differences in gene expression patterns are the result of cytoplasmic differences between cells. One such cytoplasmic difference is the emergence of distinct "top" and "bottom" ends of an organism or structure; such a difference is called polarity. Polarity is established early in development, and reflects differences between one end of an organism and the other—the head versus the tail, for example.
Animation 31.6 Information Processing in the Spinal Cord
In a spinal reflex, sensory (afferent) signals enter the spinal cord and are converted to motor (efferent) signals without any participation from the brain. The simplest type of spinal reflex involves two neurons communicating through one synapse, and is called a monosynaptic reflex. Most spinal circuits are more complex and involve multiple synapses. For example, the withdrawal of a limb in response to a painful stimulus is controlled by several sets of neurons that control antagonistic sets of muscles.
The accompanying animation depicts a spinal reflex that involves multiple sets of neurons and antagonistic sets of muscles.
Animation 36.1 Cells of the Immune System
White blood cells (also called leukocytes) are diverse cell types of the immune system that are specialized for specific functions. There are two major groups of white blood cells: phagocytes and lymphocytes. Phagocytes are large cells that engulf pathogens and other substances by phagocytosis. Some phagocytes are involved in both innate immunity (the first and nonspecific line of defense against pathogens) and adaptive immunity (a slower to develop, but longer-lasting defense against a specific pathogen). In particular, macrophages and dendritic cells play key roles in communicating between the innate and adaptive immune systems. Lymphocytes include B cells and T cells, which are involved in adaptive immunity; and natural killer cells, which are involved in both innate and adaptive immunity.
Animation 37.1 The Costs of Defending a Territory
In order to improve their survival and reproductive success, some animals will establish a territory and restrict access to its resources, whether those resources be food or access to receptive females. The animal will advertise that it owns the area and, if necessary, chase others away. But advertising and chasing takes time and energy that could have been used for other beneficial purposes, such as foraging for food and watching out for predators. Ecologists often use a cost-benefit approach to establish a framework for understanding the evolution of this type of behavior.
Experiments by Catherine Marler and Michael Moore on Yarrow's spiny lizards provide insight into the energetic costs of defending a territory.
Animation 38.1 Rain Shadow
Earth's spin and the latitudinal gradient in solar energy input both contribute to prevailing wind patterns at Earth's surface. These surface winds—the northeast trades, the southeast trades, the westerlies, and the easterlies—blow primarily in certain directions at certain latitudes around the globe. For example, the westerlies are prevailing winds that blow from west to east at latitudes between 30 and 60 degrees north or south of the equator. Most of North America receives weather from the westerlies.
Regional climates on Earth are influenced by prevailing surface winds, the spatial arrangement of water and land, and by land topography. In the accompanying animation, we examine the causes of a rain shadow, which is a region of low precipitation on the leeward (wind-protected) side of a mountain range.
Animation 39.1 Dispersal Corridors
Each organism in an ecosystem requires a habitat of sufficient size to find food, grow, and reproduce. Some species require large ranges and may become extinct if their habitats shrink.
Humans are continually encroaching on the world's natural habitats. We log forests for wood, replace forests and grasslands with agricultural plots, or eliminate these habitats to accommodate urban sprawl. As human activity destroys habitats, an important question to ask is how much of a natural ecosystem must be left intact for the resident species to continue to thrive? That is, do small patches of habitat adequately preserve the various species, or must these species have access to large, undisturbed regions? Do corridors between patches allow species in the patches to persist over time?
In the accompanying animation, we depict experiments in which researchers test the effects of habitat fragmentation and the presence of corridors on the extinction of species.
Animation 40.1 Mutualism
A mutualism is a type of interaction between species that benefits both. There are few, if any, taxonomic limits on the formation of mutualisms; animals, for example, can form mutualistic associations with other animals, with plants, and with a wide range of microorganisms. Mutualistic interactions often arise in environments where resources are in short supply. Consequently, many mutualisms involve an exchange of food for housing or defense. In another type of mutualism, many sessile organisms, particularly flowering plants, rely on more mobile species for mating or dispersal. In the animation, mutualistic partners exchange food and housing for defense.
Animation 41.1 Succession after Glacial Retreat
When ecological communities are disturbed, they sometimes recover their original characteristics, although not necessarily precisely their original species, through a process called succession. In other cases, termed ecological transitions, disturbance leads instead to the eventual development of a community that is distinctly different from the original community.
The patterns of ecological succession are varied, but the species that colonize a site soon after the disturbance often alter environmental conditions so that they become favorable or unfavorable for other species. A good example is the change in the plant community that followed the retreat of a glacier in Glacier Bay, Alaska, over the last 200 years. No human observer was present to record changes over the 200-year period, but ecologists have inferred the temporal pattern of succession by measuring plant communities on gravel deposits that were exposed by retreating glaciers at different times.
Animation 42.1 The Global Water Cycle
Water cycles from oceans, to land, and back to oceans in a flow known as the hydrologic cycle. The sun drives the hydrologic cycle by providing the energy to evaporate surface waters. Most of the evaporation occurs from the oceans, and a portion of the evaporated ocean water then falls on land. Gravity completes the hydrologic cycle by driving water from the land back to the oceans via rivers, coastal runoff, and subterranean flows.
Animation 3.2 Macromolecules: Carbohydrates
Although living cells are primarily made up of water, a number of other molecules are also abundant. Gigantic molecules, called macromolecules, populate a cell and provide it with important functions for life. For example, macromolecules provide structural support, a source of stored fuel, the ability to store and retrieve genetic information, and the ability to speed biochemical reactions. Four major types of macromolecules—proteins, carbohydrates, nucleic acids, and lipids—play these important roles in the life of a cell. In this tutorial, we examine the structures and functions of carbohydrates.
Animation 4.2 Active Transport
This animation illustrates the two types of active transport across cellular membranes: primary active transport and secondary active transport.
In order to control its internal environment, a cell must often expend energy to bring substances into or out of the cell. Energy is required in active transport, processes in which a cell moves a substance across a membrane from a region of lower concentration to a region of higher concentration. In other words, the cell moves the substance against its concentration gradient. In contrast, passive transport (not shown here) occurs when a substance moves from a region of higher concentration to a region of lower concentration; the substance rushes into or out of the cell by diffusion and requires no input of energy to do so.
When a cell expends ATP directly during active transport, the process is called primary active transport. Using another energy source, such as the potential energy stored in an ion gradient, is secondary active transport.
Animation 5.2 Two Experiments Demonstrate the Chemiosmotic Mechanism
Cells rely on energy carriers, most notably ATP, to perform cellular work. ATP fuels so many reactions that a person may use as many as 1025 of these molecules every day. The process for making ATP during cellular respiration (in mitochondria) and photosynthesis (in chloroplasts) is known as chemiosmosis.
In chemiosmosis, proton (H+) diffusion is coupled to ATP synthesis. When protons build up on one side of a membrane, they form an electrochemical gradient across the membrane. The proton concentration gradient and the electric charge difference constitute a source of potential energy called the proton-motive force. This force tends to drive the protons back across the membrane. Protons diffuse across the membrane through a specific proton channel, called ATP synthase, which couples proton flow with the formation of ATP.
The chemiosmotic mechanism was first proposed by Peter Mitchell in 1961 and has since been widely confirmed through experimentation, beginning with an experiment using chloroplasts.
Animation 6.2 Signal Transduction Pathway
When a person unexpectedly comes face to face with a grizzly bear, his or her body quickly shunts blood away from the skin and digestive system and toward the muscles. The heart also beats faster, and the liver releases glucose molecules that provide emergency fuel for what is called the "fight-or-flight" response.
In the fight-or-flight response, the adrenal glands release the hormone epinephrine, which serves as a signal within the body. Certain cells, including liver and muscle cells, can detect the signal, after which they process the signal and respond to it. The entire sequence—from signal reception to cellular response—is referred to as a signal transduction pathway.
Animation 7.2 Meiosis
Sexual reproduction requires meiosis, a process in which a parent cell divides to produce cells with half the genetic material of the parent. A diploid parent cell, for example, divides to make four haploid cells. In sexual reproduction, haploid gametes from two individuals then combine to produce a diploid zygote. An offspring resulting from sexual reproduction is genetically different from both parents.
In the accompanying animation, we examine the events of meiosis, using a model cell with two pairs of chromosomes. One chromosome of each pair is maternally derived, while the other is paternally derived; each is distinguished by different colors. The colors allow us to track two mechanisms of producing unique daughter cells: independent assortment of chromosomes and the phenomenon of crossing over.
Animation 8.2 Alleles That Do Not Assort Independently
In the 1850s, Austrian monk Gregor Mendel experimented with pea plants to unravel the basic principles of inheritance. His findings were ignored at the time, but later, when scientists learned about chromosomes and the process of meiosis, Mendel's theory gained prominence as the physical basis of inheritability became clearer. One of the principles Mendel described, now called Mendel's second law, was that alleles of different genes assort independently during gamete formation. Since Mendel's time, we have discovered that the law of independent assortment applies to many genes, but is not universal. When geneticist T. H. Morgan began studying the genetics of fruit flies, he discovered that some genes sort together when they are located on the same chromosome.
Animation 9.2 The Meselson–Stahl Experiment
In the 1950s, details of the genetic material, DNA, began to pour out of laboratories. First, James Watson and Francis Crick built a model for the double helical structure of DNA, showing that one strand consists of a sequence of bases that are complementary to the bases in the opposite strand. These scientists also suggested a model for the replication of DNA that would allow a cell to copy its genetic material and pass down exact replicas to daughter cells. Each old strand of the double helix would serve as a template to make a new strand. Although the simplicity of their replication model was compelling, no data yet existed to prove that it was correct.
A few years after Watson and Crick published their DNA structural model, the scientists Matthew Meselson and Franklin Stahl designed an elegant experiment to determine how DNA replicates.
Animation 10.2 RNA Splicing
The protein-coding genes of a eukaryote typically contain regions of DNA that serve no coding function. Noncoding regions, called introns, interrupt the coding regions, called exons.
When the gene is transcribed into RNA, both the coding and noncoding regions are copied. However, a eukaryotic cell has a mechanism for removing the introns from RNA. In a process called RNA splicing, a newly transcribed RNA molecule is cut at the intron-exon boundaries, its introns are discarded, and its exons are joined together. RNA splicing occurs within the nucleus before the RNA migrates to the cytoplasm. In the cytoplasm, ribosomes translate the RNA—now containing uninterrupted coding information—into protein.
Animation 11.2 The trp Operon
Tryptophan is one of the 20 amino acid building blocks that cells need for making proteins. The genes for the biosynthesis of tryptophan are clustered together under the control of a single promoter. This cluster of genes and their regulatory sequences is called the trp operon. When the availability of tryptophan is low, E. coli bacteria express the trp operon genes. When plenty of tryptophan is available, these genes are repressed. In this animation, we examine the expression and repression of the trp operon.
Animation 12.2 High-Throughput Sequencing
The first decade of the new millennium has seen rapid development of high-throughput sequencing methods—fast, cheap ways to sequence and analyze large genomes. The techniques are often referred to as massively parallel DNA sequencing, because thousands or millions of sequencing reactions are run at the same time to greatly speed up the process. The methods use miniaturization techniques first developed for the electronics industry, as well as the principles of DNA replication, often in combination with the polymerase chain reaction (PCR).
High-throughput sequencing methods are evolving rapidly. This animation describes two high-throughput methods. In one method, DNA is amplified on a solid surface and then sequenced using fluorescently labeled nucleotides. In the second method, the DNA is amplified by PCR on microbeads and analyzed by pyrosequencing using the enzyme luciferase to produce a light reaction.
Animation 15.2 Modularity
All insect species on Earth have exactly six legs—a pair on each of three thoracic (middle) body segments. Look at the larger group of arthropods, however, and you will see a striking variation in leg number, including finding legs on abdominal segments. These dramatic differences in morphology represent changes in self-contained body units (modules). The modular changes can arise through relatively small changes in key regulatory genes. In this tutorial we will examine an example of such modular changes in insects. We will also see how relatively small changes in the timing or place of expression of key regulatory genes can affect the morphology of different species—in this case comparing the hindlimbs of ducks (webbing) to those of chickens (no webbing).
Animation 16.2 Founder Events and Allopatric Specialization
Sometimes, one species diverges into two by a process called speciation. Speciation can occur when a population becomes divided by an insurmountable physical barrier, such as a mountain range or a body of water. This process is called allopatric speciation, and it is thought to be the way that most new species form. Genetic divergence between the two geographically divided populations can arise for a variety of reasons, often because their environments become different from each other.
Allopatric speciation can also result when a small number of individuals from a population cross an existing barrier and create a new, isolated population. Such a population differs from its parent population because of a phenomenon called the founder effect—the small group of founding individuals has only an incomplete representation of the gene pool of its parent population.
Animation 19.2 Digestive Vacuoles
The modern eukaryotic cell differs from its prokaryotic precursors in several key characteristics. Eukaryotic cells have a nucleus, organelles, and a cytoskeleton, as well as specialized vesicular structures called vacuoles.
One type of vacuole, the digestive vacuole, is found in many protists. Digestive vacuoles handle the processes of digestion and excretion for the cell.
Animation 20.2 Life Cycle of a Conifer
Firs, cedars, spruce, and pines rank among the great vegetation formations of the world. All of these trees belong to one group of gymnosperms—the conifers, or cone-bearers. Gymnosperms derive their name (which means "naked-seeded") from the fact that their ovules and seeds are not protected by ovary or fruit tissue.
In conifers, the same diploid sporophyte plant has both pollen-producing strobili and egg-producing cones. Most conifer ovules—which, upon fertilization, develop into seeds—are borne exposed on the upper surfaces of the modified branches that form the scales of the cone. At maturity, the scales of the cones separate, and the seeds are released into the air to be carried sometimes considerable distances by the wind.
Animation 22.2 An Overview of the Protostomes
The protostomes are arguably the most successful group of animals on Earth. They are the most diverse group, with more than one million species described for arthropods alone. Also, the protostomes contain the nematodes, which probably make up the most abundant and universally distributed of all animal groups.
The protostomes can be divided into two major clades—the lophotrochozoans (including bryozoans, annelids, and mollusks) and the ecdysozoans (including nematodes and arthropods)—largely on the basis of DNA sequence analysis.
Animation 24.2 Xylem Transport
Scientists have proposed various models to explain the ascent of xylem sap from roots to leaves. One model was based on the idea that root pressure pushed the liquid up the stem. Although root pressure does exist, it cannot account for the ascent of sap in trees. The current model of xylem transport relies on an alternative to pushing: pulling. The evaporative loss of water from the leaves indirectly generates a pulling force—tension—on the water in the apoplast of the leaves, which pulls the xylem sap upward.
Animation 25.2 Went's Experiment
Experiments by Charles and Francis Darwin demonstrated that the tip of a plant's shoot senses light, and that some kind of chemical signal travels from the tip to the growing region. The shoot responds to this signal by bending the toward the light.
In the 1920s, Dutch botanist Frits Went attempted to isolate the chemical signal from the tips of oat coleoptiles. This animation follows a recreation of his experiment and provides an opportunity for you to predict some of his experimental results.
Animation 26.2 The Effect of Interrupted Days and Nights
For flowering plants to cross pollinate, they must produce flowers at the same time of year. How do plants that may be different in size or age synchronize their flowering? In the 1930s, James Bonner and Karl Hamner discovered that the key flowering trigger in some plants is the length of night, which explains why a species will flower during a particular season year after year.
For historical reasons, plants are described as short-day or long-day plants, rather than the more appropriate long-night and short-night plants. Day-neutral plants, in which the flowering trigger does not depend on a specific length of darkness, are perhaps more common than short- or long-day plants. In this animation, we will examine flowering experiments performed on cocklebur, a short-day plant.
Animation 28.2 Insulin and Glucose Regulation
Glucose in the blood provides a source of fuel for all tissues of the body. Blood glucose levels are highest during the absorptive period after a meal, during which the stomach and small intestine are breaking down food and circulating glucose to the bloodstream. Blood glucose levels are the lowest during the postabsorptive period, when the stomach and small intestines are empty. Despite having food only periodically in the digestive tract, the body works to maintain relatively stable levels of circulatory glucose throughout the day.
The body maintains blood glucose homeostasis mainly through the action of two hormones secreted by the pancreas. These hormones are insulin, which is released when glucose levels are high, and glucagon, which is released when glucose levels are low. The accompanying animation depicts the functions of these hormones in blood glucose regulation.
Animation 29.2 Time-Compensated Solar Compass
A bird uses a variety of cues to navigate accurately. One cue is the direction of the sun. However, because the sun is continually changing its position in the sky, a bird also needs other information—such as the time of day—to determine what the sun's position means.
In the accompanying animation, we describe an experiment that tests whether pigeons use what is called a time-compensated solar compass to determine compass directions. That is, does a pigeon use an internal clock, called a circadian rhythm, to assess the time of day and thereby interpret the sun's position in the sky?
Animation 30.2 Airflow in Mammals
Airflow through the respiratory system of mammals is tidal, meaning that air flows in by the same route that it leaves. When at rest, the average adult human breathes in and out about half a liter of air with each breath. This is called our tidal volume. When this fresh air enters the lungs, it mixes with stale air—typically 2 liters worth—before it hits the respiratory surfaces in the alveoli (air sacs) of the lungs. Because the stale air has a low partial pressure of oxygen, tidal breathing is not an optimally efficient means of gas exchange.
Breathing in mammals is driven by pressure changes in the thoracic cavity. In the accompanying animation, we focus on the mechanics of tidal breathing in humans, and, in particular, we examine the muscles and membranes that are important in this ventilation of the lungs.
Animation 31.2 The Action Potential
The creation and conduction of action potentials represents a fundamental means of communication in the nervous system. Action potentials represent rapid reversals in voltage across the cell membrane of axons. These rapid reversals are mediated by voltage-gated ion channels found in the cell membrane. The distribution of voltage-gated channels along the axon enables the conduction of the action potential from the nerve cell body to the axon terminal. At the synapse, the electrical signal is converted to a chemical signal that is then propagated to the postsynaptic neuron.
Animation 32.2 Complete Metamorphosis
When an insect grows and develops, it must periodically shed its rigid exoskeleton in a process called molting. In place of the old tight exoskeleton, the insect grows a new loose one that provides the insect with room to grow larger. Many insect species also transform in body structure as they molt from a juvenile to an adult form—a process called metamorphosis.
Several hormones control insect molting and development. In the accompanying animation, we look at these hormones and the events in the life of the silkworm moth, Hyalophora cecropia. This insect undergoes complete metamorphosis—the radical transformation that occurs when the caterpillar develops into the adult moth.
Animation 33.2 Smooth Muscle Action
Smooth muscle provides the contractile force for most of our internal organs, including the digestive tract, urinary bladder, uterus, and blood vessels. Structurally, smooth muscle cells are usually long and spindle-shaped and, unlike skeletal muscle, each cell has only a single nucleus. The actin and myosin filaments in smooth muscle are not arranged in a regular pattern like that in skeletal muscle, and the cells therefore have a "smooth" appearance, rather than the striated appearance of skeletal muscle, when viewed under a microscope.
In many organs, smooth muscle cells are arranged in sheets, with individual cells in electrical contact with one another through gap junctions. As a result, an action potential generated in one smooth muscle cell can quickly spread to all the cells in the sheet. Thus, the cells in the sheet can contract in a coordinated fashion. In the digestive tract, a coordinated, spreading wave of smooth muscle contraction will push the contents through its central lumen. This process is called peristalsis.
Animation 34.2 The Menstrual Cycle
A human female is born with a million or so immature eggs, or oocytes, within each of her ovaries. These oocytes are arrested at an early stage of meiosis. Most of these oocytes will die before they ever have a chance to mature, and by the time a woman reaches sexual maturity, each ovary contains about 200,000 oocytes. Every month, a dozen of these oocytes re-initiate their development, but usually only one of them makes it to full maturity.
The cycle in which an oocyte matures, erupts from the ovary, and then travels down the oviduct to the uterus is called the ovarian cycle. The cycle varies in length, lasting on average 28 days. The ovarian cycle is tightly coordinated with the uterine cycle, in which the lining of the uterus grows and prepares for an embryo to implant. If, by the end of the cycle, the oocyte has not been fertilized and an embryo has not implanted, then the lining of the uterus sloughs off in a process called menses, or menstruation.
Animation 35.2 Gastrulation in a Frog Embryo
In frog development, a zygote undergoes a series of cell divisions that result in the formation of a blastula, a fluid-filled ball of cells. Based on the pattern of cleavage, the cells of the blastula, called blastomeres, contain cytoplasm with slightly different contents. Some of these blastomeres are essential in triggering the next phase of development, called gastrulation.
In gastrulation, the blastula rearranges, with sheets of blastomeres from the outside of the embryo entering the embryo's interior. Cells move into contact with new cells, allowing unique intercellular communications that lead to cell determination and differentiation. By the end of gastrulation, three embryonic germ layers—endoderm, mesoderm, and ectoderm—take their positions in the embryo. These layers ultimately give rise to specific tissues and organs that make up the adult body plan.
Animation 36.2 Humoral Immune Response
The humoral immune response is one of two main arms of the immune system. In this response, the immune system triggers specific B cells to proliferate and secrete large amounts of their specific antibodies. These antibodies can then combat a particular microorganism or virus and thereby stop an infection.
The humoral immune response has an activation phase and effector phase. During the activation phase, helper T (TH) cells become activated against a particular antigen. In the effector phase, activated TH cells trigger specific B cells to proliferate and release antibodies. These antibodies then bind to the invader and fight the infection.
Animation 37.2 Foraging Behavior
How does an animal choose what food to eat? One might assume that natural selection has influenced the foraging behaviors of animals, and that most animals forage efficiently, spending the least energy to gain the most nutrients.
The accompanying animation is based on the results of an experiment on the feeding behavior of bluegill sunfish. Ecologists performed laboratory experiments with these fish to determine their foraging strategies when presented with different sizes of the water flea Daphnia. Before performing the experiment, the investigators predicted that in an environment stocked with low densities of all three sizes of prey, the bluegills would take every water flea that they encountered, but that in an environment with abundant large water fleas, the fish would ignore the smaller ones.
Animation 41.2 Island Biogeography in the Florida Keys
On a global scale, the distribution and diversity of organisms—the patterns of biogeography—vary among the different biomes, from continent to continent, and with latitude. On a smaller scale, other factors influence species diversity. Small islands tend to have fewer species than large islands, and islands close to a mainland (a species pool) tend to have more species than islands far away. The theory of island biogeography relates the size of an island and its distance from a mainland with the number of species an island maintains. The accompanying animation describes this theory as well as an experiment that tests it using mangrove islands in the Florida Keys.
Animation 42.2 The Global Nitrogen Cycle
Nitrogen passes between living organisms and the nonliving world in a biogeochemical cycle known as the global nitrogen cycle. In organisms, this element is one of the most abundant and is required in DNA, RNA, and proteins. In our largest nitrogen reservoir—the atmosphere—nitrogen gas (N2) is the most abundant gas, making up 78% of the air we breath. Although it is ubiquitous in the environment, nitrogen gas is not accessible to most living organisms. Only certain types of bacteria—the nitrogen fixers—can break the N2 triple bond and thereby tap this atmospheric reservoir. In addition to nitrogen-fixing bacteria, humans have also been converting nitrogen gas into other chemical forms to make fertilizers. Both natural and industrial nitrogen fixation convert nitrogen into usable forms that the rest of life on Earth can use.
Animation 3.3 Macromolecules: Nucleic Acids
Although living cells are primarily made up of water, a number of other molecules are also abundant. Gigantic molecules, called macromolecules, populate a cell and provide it with important functions for life. For example, macromolecules provide structural support, a source of stored fuel, the ability to store and retrieve genetic information, and the ability to speed biochemical reactions. Four major types of macromolecules—proteins, carbohydrates, nucleic acids, and lipids—play these important roles in the life of a cell. In this tutorial, we examine the structures and functions of nucleic acids.
Animation 4.3 Endocytosis and Exocytosis
This animation illustrates how a cell takes up an LDL particle by means of endocytosis and then uses a lysosome to destroy the particle. The animation begins with an overview of the cell membrane and an LDL particle, then moves to close-ups showing the molecular interactions of the structures.
The cell membrane acts as a barrier that allows certain substances to pass freely, but blocks the passage of others. Large molecules, such as proteins, polysaccharides, and nucleic acids are too large and too charged or polar to slip easily through the plasma membrane. If a cell takes them in, or releases them, it does so by the processes of endocytosis or exocytosis. In endocytosis, the cell's membrane surrounds a part of the exterior environment and buds off as an internal vesicle. In exocytosis, an internal vesicle fuses with the plasma membrane and thereby releases its contents to the outside of the cell.
Animation 5.3 The Source of the Oxygen Produced by Photosynthesis
All photosynthetic eukaryotic cells contain chloroplasts that use the radiant energy of sunlight to convert carbon dioxide and water into carbohydrates. As a byproduct of photosynthesis, oxygen gas is also released into the atmosphere through tiny openings in the leaves called stomata. The carbohydrates produced by photosynthesis provide us with an important energy source, while the oxygen is a critical component of the air we breathe.
The reactants and products of photosynthesis have been known since the early 1800s. At first, it was generally assumed that the oxygen released as a byproduct of photosynthesis came from the carbon dioxide. However, the question was not definitely answered until the early 1940s, and the result was surprising to many.
Animation 9.3 DNA Replication and Polymerization
Before dividing into daughter cells, a cell first replicates its DNA. During this process, the parental DNA unwinds, and each strand of a double helix acts as a template for new DNA synthesis. Because the resulting DNA molecules consist of one parental, or conserved, strand and one new strand, DNA replication is referred to as semiconservative. The accompanying animations show DNA replication at two different levels: molecular and chromosomal.
Animation 10.3 Deciphering the Genetic Code
DNA consists of a code language with just four letters, known as bases, making up a variety of words, known as codons, that are three letters in length. The four bases are strung together linearly along chromosomes, and in humans make up the 3-billion base pairs worth of sequences in the human genome. How did scientists first learn to interpret the genetic code? Some of the first clues appeared serendipitously as researchers studied aspects of gene expression. Later, researchers probed in earnest, setting up specific experiments to decipher the code used in RNA molecules. Marshall Nirenberg and his colleagues gathered the bulk of the data.
Animation 11.3 Initiation of Transcription
Of the approximately 21,000 protein-coding genes in human cells, only a fraction of these are expressed in any one cell type, or at any particular time in development, or at any one stage in the cell cycle. The ability for a gene to be transcribed depends on the presence of numerous proteins.
Animation 12.3 DNA Microarray Technology
The science of genomics faces two major quantitative challenges. First, there are very large numbers of genes in eukaryotic genomes. Second, there are myriad distinct patterns of gene expression in different tissues at different times. For example, the cells of a skin cancer at its early stage may have a unique mRNA "fingerprint" that differs from those of normal skin cells and cells from a more advanced skin cancer. In such a case, the pattern of gene expression could provide invaluable information to a clinician trying to characterize a patient's tumor.
Patterns of gene expression can be analyzed with a thumbnail-sized invention called a DNA microarray ("gene chip"), one of the most powerful new tools to emerge from genome studies. A DNA microarray is made with thousands of DNA sequences attached to the microarray in a grid pattern. The attached sequences act as probes and tell a researcher whether a test sample contains a particular DNA or RNA sequence.
Animation 19.3 Life Cycle of the Malarial Parasite
Some microbial eukaryotes are pathogens that cause serious diseases in humans and other vertebrates. The best-known pathogenic protists are members of the genus Plasmodium, a highly specialized group of apicomplexans that spend part of their life cycle in mosquitoes of the genus Anopheles and part as parasites in human red blood cells, where they are the cause of malaria. In terms of the number of people affected, malaria is one of the world's three most serious infectious diseases: it infects over 350 million people, and kills over 1 million people, each year. On average, about two people die from malaria every minute of every day—most of them in sub-Saharan Africa, although malaria occurs in more than 100 countries. This tutorial describes the life cycle of the malarial parasite.
Animation 20.3 Life Cycle of an Angiosperm
The oldest fossil evidence of angiosperms dates back to about 150 million years ago. The angiosperms radiated explosively beginning 65 million years ago and became the dominant plant life on Earth. The name angiosperm ("enclosed seed") is drawn from a distinctive character of these plants: the ovules and seeds are enclosed in a modified leaf called a carpel. The carpel protects the ovules and seeds and often interacts with incoming pollen to prevent self-pollination, thus favoring cross-pollination and increasing genetic diversity.
The life cycle of angiosperms, like all land plants, alternates between a diploid sporophyte generation and a haploid gametophyte generation. Angiosperms represent the extreme end of a trend in the evolution of vascular plants: the sporophyte generation becomes larger and more independent of the gametophyte, while the gametophyte becomes smaller and more dependent on the sporophyte.
Animation 22.3 An Overview of the Deuterostomes
It may surprise you to learn that both you and a sea urchin are deuterostomes. Adult sea stars, sea urchins, and sea cucumbers—the most familiar echinoderms—look so different from adult vertebrates (fishes, frogs, lizards, birds, and mammals) that it may be difficult to believe all these animals are closely related. The evidence that all deuterostomes share a common ancestor that is not shared with the protostomes includes early developmental patterns and phylogenetic analysis of gene sequences, factors that are not apparent in the forms of the adult animals.
Animation 24.3 The Pressure Flow Model
A plant transports dissolved sugars and amino acids in solution through a component of its vascular tissue called the phloem. The movement of fluid in the phloem, a process called translocation, can occur in any direction, up or down the plant. However, the fluid typically flows from source cells to sink cells. Source cells are cells that produce sugars and pump them into the phloem, whereas sink cells are cells that do not make enough sugars for their own growth and metabolism and must import them from the phloem.
The mechanism of phloem translocation is described in a model of phloem function called the pressure flow model. The accompanying animations describe this model, both in the plant and in a laboratory simulation.
Animation 25.3 Auxin Affects Cell Walls
Auxin is a plant hormone involved in many aspects of plant growth and development. One function of auxin is to trigger cell elongation in shoots. Auxin's action in shoots can be deduced from Arabidopsis thaliana plants that do not make auxin, because these plants are short, and supplying them with the hormone reverses this phenotype. Auxin also mediates phototropism, in which cells elongate more on one side of a shoot, causing the plant to bend toward light.
Plant cell elongation requires two elements: high turgor pressure inside the plant cell and a loosening of the cell wall so that the turgor pressure and additional incoming water can force the cell to expand. In this tutorial, we focus on how auxin loosens the cell wall—a process described as the acid growth hypothesis.
Animation 30.3 The Cardiac Cycle
The human heart is the circulatory system's pump, which forces blood through the blood vessels of the body. To pump blood, the muscle tissue of the heart contracts. The contraction begins in the upper two chambers of the heart, called the atria, and then proceeds to the lower two chambers, the ventricles. A complete contraction and relaxation of the heart is a single heartbeat, also called a cardiac cycle.
In the accompanying animation, we examine the events of the cardiac cycle, which can be divided into a phase in which the ventricles are contracted (systole) and a phase in which the ventricles are relaxed (diastole). We also correlate these phases of the cycle with the changing pressures in the ventricles and aorta and the changing blood volume in the ventricles.
Animation 31.3 Synaptic Transmission
The ability of our nervous system to orchestrate complex behaviors, deal with complex concepts, and learn and remember depends upon communication between vast numbers of neurons. Communication between neurons occurs at specialized junctions called synapses. The most common type of synapse in the brain is the chemical synapse—one in which chemical messages released by a presynaptic cell induce changes in a postsynaptic cell. Neurons also communicate with muscle cells through chemical synapses. The classic synapse that has been extensively studied is the neuromuscular junction—the synapse through which a motor neuron causes a muscle cell to contract.
This animation depicts the events that are involved in transmitting the signal from the nerve ending of a motor neuron to a muscle cell at a chemical synapse using the neurotransmitter acetylcholine (ACh).
Animation 35.3 Tissue Transplants Reveal the Process of Determination
One of the most exciting stories in animal development is the discovery of how cells in the embryo become committed to their specific fate. After a sperm joins with an egg, the zygote goes through an initial series of rapid cell divisions that subdivides the cytoplasm into a mass of smaller undifferentiated cells. Cell fate-regulating molecules in the form of mRNAs or proteins become asymmetrically distributed starting at the one-cell stage. This uneven distribution of molecules is maintained through successive divisions and provides positional information that results in the determination of cells—their commitment to a particular role in the body plan. An orderly series of cell movements, called gastrulation, then creates multiple cell layers and sets up new cell-to-cell contacts that trigger further steps of development.
In the accompanying animation, we examine the experiments conducted by German biologist Hans Spemann and his student Hilde Mangold, in which they determined how the embryo becomes organized.
Animation 36.3 A B Cell Builds an Antibody
One of the key features of the immune system is that it can defend the body against a great diversity of invaders. It is capable of recognizing millions of molecular features, called antigenic determinants, which any invading organisms or molecules might display.
Some of the immune system's power to respond to this diversity comes from the action of certain protein molecules, called antibodies or immunoglobulins. Each of the millions of B cells in the immune system produces a unique type of antibody. Each unique antibody, in turn, can bind to a particular antigenic determinant. When a B cell develops from a precursor cell into a mature cell, it undergoes an unusual genetic process in which it rearranges its immunoglobulin genes. DNA segments are randomly rearranged and joined, and some DNA is permanently deleted. The resulting immunoglobulin genes are unique and code for the unique antibodies that each mature B cell produces.
Animation 41.3 Fragmentation Effects
When habitats are destroyed or made uninhabitable, the organisms living there are lost. But habitat loss affects even those remaining habitats that are not destroyed. As habitat fragments become smaller and more isolated, the fragments become more disturbed by "edge effects," in which an ecological community is changed by physical and biological factors coming from an adjacent community.
In 1979, researchers initiated a study on habitat patches in the rainforest north of the city of Manaus, Brazil, which highlighted the importance of edge effects. The rainforest in the study area was continuous at the time, but was scheduled to be logged. One of the key findings of the research was that the smaller fragments were disturbed to a greater extent by surrounding influences than were the larger fragments.
Animation 42.3 The Global Carbon Cycle
The elements that make up the living and nonliving components of ecosystems are recycled. Organisms capture material, perform chemical transformations, and release materials back into circulation. In the accompanying animation, we focus on the carbon cycle, describing the flow of this element in its various chemical forms as it moves through organisms and the physical environment—the atmosphere, oceans, fresh waters, and land.
In the illustrations in this animation, arrows of differing widths are used to represent the magnitudes of the fluxes (flow rates) as the element moves from a source, which gives up a substance, to a sink, which takes in the substance.
Animation 3.4 Macromolecules: Proteins
Although living cells are primarily made up of water, a number of other molecules are also abundant. Gigantic molecules, called macromolecules, populate a cell and provide it with important functions for life. For example, macromolecules provide structural support, a source of stored fuel, the ability to store and retrieve genetic information, and the ability to speed biochemical reactions. Four major types of macromolecules—proteins, carbohydrates, nucleic acids, and lipids—play these important roles in the life of a cell. In this tutorial, we examine the structures and functions of proteins.
Animation 4.4 The Golgi Apparatus
This animation explains the role the Golgi apparatus plays in the production and distribution of some of the proteins produced in the cell. The path of these proteins is followed, starting with their production in the ER, through their transport via vesicles through the cisternae of the Golgi, to their release outside the cell.
In eukaryotic cells, the endoplasmic reticulum (ER) and the Golgi apparatus are part of an elaborate network of membrane compartments called the endomembrane system. These organelles work together to make and process many of the proteins, lipids, and carbohydrates that the cell uses or exports. The subset of cellular proteins that begin their journeys in the ER are those that will be exported from the cell, incorporated into membranes, or moved into organelles of the endomembrane system, such as lysosomes. In this animation, we examine the path of some of these proteins, from their production in the ER, to their transport through the Golgi, to their release from the cell.
Animation 5.4 Photophosphorylation
Energy from the sun fuels most of life on Earth. In a process called photosynthesis, a variety of organisms—plants, algae, and cyanobacteria—capture solar energy and use it to fuel the creation of carbohydrates.
In plants, photosynthesis occurs in organelles, called chloroplasts, by two main metabolic pathways: the light reactions and the Calvin cycle (also called the light-independent reactions). In the light reactions, chloroplasts convert light energy into the chemical energy contained in the small molecules ATP and NADPH. The light-driven production of ATP from ADP and inorganic phosphate is called photophosphorylation.
Animation 9.4 Leading and Lagging Strand Synthesis
During DNA replication, the replication of one of the two strands of DNA proceeds in a relatively straightforward manner. DNA polymerase adds nucleotides continuously, following directly behind the unzipping replication fork. However, the replication of the second strand is far more complex. Because the two strands of DNA are antiparallel, DNA polymerase must replicate them in opposite directions. Therefore, the replication of the second strand follows in a direction opposite the replication fork, and it does so discontinuously, replicating a segment of DNA at a time. The two strands of DNA are referred to as leading- and lagging-strands, respectively.
Animation 10.4 Translation
A cell's DNA contains all of the information necessary to produce the hundreds or thousands of different proteins necessary for the cell's survival and function. In order to produce a protein, the cell must first transcribe the code contained in the DNA into a complementary mRNA code. The mRNA is then translated into a series of amino acids. The series of amino acids makes up all or part of the final protein.
This tutorial focuses on the second half of this process, called translation, or protein synthesis. Protein synthesis occurs on ribosomes, which serve as staging areas where mRNA and a series of amino acids—each carried on an adapter molecule called tRNA—come together. In addition to bringing these molecules together, ribosomes have catalytic activity—they facilitate the formation of peptide bonds between the amino acids in a growing polypeptide (protein) chain.
Animation 12.4 DNA Testing
Many techniques exist for testing whether a sample of DNA carries a mutation. In this animation, we explore the use of two different techniques for identifying whether an individual carries the sickle-cell allele of the β-globin gene.
One procedure is called allele-specific oligonucleotide hybridization. In allele-specific oligonucleotide hybridization, the binding of a probe to sample DNA indicates that a particular allele is present in the DNA.
The other procedure, DNA testing by allele-specific cleavage, uses restriction enzymes as diagnostic tools. Restriction enzymes are proteins that recognize and cut DNA at specific sequences. Allele-specific cleavage relies on the mutation in the disease allele either adding or eliminating a recognition site for a restriction enzyme.
Animation 22.4 Life Cycle of a Frog
The amphibians include three modern-day groups of animals: the legless, wormlike caecilians found in the tropics, the tail-less frogs and toads (collectively called anurans), and the tailed salamanders. Many of these animals live on dry land as adults, but the typical amphibian life cycle occurs at least partly in the water or in a moist environment. The dual life of these animals, on land and in the water, gives this group its name—Amphibia, meaning "double life."
Animation 31.4 Sound Transduction in the Human Ear
For humans, speech, music, and other environmental sounds form the basic elements of language, social relations, and adaptive response to environmental stimuli. Our auditory system can detect rapid changes of sound intensity (measured in decibels, dB) and frequency (measured in hertz, Hz). In humans, sound intensity and frequency roughly correspond to loudness and pitch.
The task of the auditory system is to convert changes in air pressure in the environment into the neural activity that permits our brain to perceive and attach meaning to the sounds that we hear.
Each part of the ear performs a specific function in hearing. The external ear captures, focuses, and filters sound. The middle ear concentrates sound energies. Finally, the inner ear transduces mechanical energy into neural activity.
Animation 35.4 Embryonic Stem Cells
One of the most exciting frontiers in medicine is the potential use of embryonic stem cells (ES cells) for treating a host of congenital, developmental, or degenerative diseases. Cell replacement strategies are particularly relevant for tissues and organs that have little capacity for self-repair.
ES cells possess two properties that make them especially well suited for cell therapy. First, they retain the flexibility to become any one of the more than 200 cell types that make up the human body. Given the right combination of signals, ES cells develop into mature cells that can function as neurons, muscle, bone, blood or other cell types. Stem cells with such flexibility are described as "pluripotent," to indicate their high potential to differentiate into a wide variety of cell types.
A second feature of embryonic stem cells is their ability to remain in an undifferentiated state and to divide indefinitely. This property of "self-renewal" means that virtually unlimited numbers of well-defined, genetically characterized cells can be produced in culture.
Animation 36.4 Cellular Immune Response
In the cellular immune response, cells of the immune system kill cells of the body that have been infected with a virus or that are cancerous. This response relies on the lethal talents of cytotoxic T (TC) cells. TC cells contain molecules, called perforin, that they release onto target cells. The perforin pokes holes in the target cells and thereby kills them.
The cellular immune response occurs in two phases. In the first, called the activation phase, TC cells that have the appropriate T-cell receptors are activated and triggered to divide repeatedly. In the second, called the effector phase, these activated TC cells encounter target cells and kill them.
Animation 42.4 Earth's Radiation Budget
To maintain a steady global temperature, Earth must emit the same amount of energy back into space as it receives from solar radiation. Earth's radiant energy balance is the accounting of the average annual energy gain from solar radiation versus the average annual loss from infrared radiation that leaves the Earth system. When the energy gain and energy loss are in balance, Earth neither heats up nor cools down.
Many physical factors of the Earth and its atmosphere play roles in Earth's radiant energy balance. Without the atmosphere, for instance, the average surface temperature on Earth would be about 35°C colder than it is at present. The warming of Earth that results from retention of heat in its atmosphere is called the greenhouse effect. Changes to the atmosphere, therefore, can change the temperature of Earth.
Animation D1 Gel Electrophoresis
Many of the procedures used in recombinant DNA technology rely on a researcher's ability to purify a DNA fragment of interest. In an important procedure called agarose gel electrophoresis, DNA fragments are separated by size as they move through a gel matrix. In this animation, we will examine how gel electrophoresis is performed and then describe a method called blotting, which allows researchers to identify the DNA fragments of interest along the length of a gel.
Animation 3.5 Synthesis of Prebiotic Molecules
It is impossible to know for certain how life on Earth began. Possibly, living organisms arrived from an extraterrestrial source, such as Mars, traveling on a meteor. Alternatively, the conditions on the early Earth might have allowed the formation of the large molecules unique to living things. There is some evidence for both the extraterrestrial-origin hypothesis, collected from meteorites that have landed on Earth, as well as the chemical evolution hypothesis.
In the 1950s, Stanley Miller and Harold Urey performed an experiment that was profoundly important in giving weight to speculations about the chemical origin of life on Earth and elsewhere in the universe. They set up an apparatus to create conditions that mimicked those thought to exist on the primitive Earth. They filled a chamber with gases such as methane, ammonia, hydrogen, and water vapor. Then they generated electrical sparks to simulate lightning.
Animation 5.5 Tracing the Pathway of CO2
Perhaps no chemical process has a greater impact on life than the conversion of atmospheric carbon dioxide and water into carbohydrates by photosynthetic plants. Photosynthesis can be divided into two major reaction pathways. The first pathway, driven by light energy from the sun, uses electron transport and photophosphorylation to produce ATP and NADPH. These energy-rich compounds are then utilized in the second pathway to convert carbon dioxide into carbohydrate molecules—a process called carbon fixation. This latter pathway, called the Calvin cycle, was first elucidated by Melvin Calvin and colleagues at UC Berkeley.
Animation 31.5 Photosensitivity
Sensitivity to light—photosensitivity—confers on the simplest animals the ability to orient to the sun and sky and gives more complex animals rapid and extremely detailed information about objects in their environment. It is not surprising that both simple and complex animals can sense and respond to light. What is remarkable is that across the entire range of animal species, evolution has conserved the same basis for photosensitivity: a family of pigments called rhodopsins. In this animation we will describe how rhodopsin molecules respond when stimulated by light energy and how that response is transduced into neural signals.