This action might not be possible to undo. Are you sure you want to continue?
Life’s basic characteristic is a high degree of order. Each level of biological organization has emergent properties. Biological organization is based on a hierarchy of structural levels, each building on the levels below. At the lowest level are atoms that are ordered into complex biological molecules. Biological molecules are organized into structures called organelles, the components of cells. Cells are the fundamental unit of structure and function of living things. Some organisms consist of a single cell; others are multicellular aggregates of specialized cells. Whether multicellular or unicellular, all organisms must accomplish the same functions: uptake and processing of nutrients, excretion of wastes, response to environmental stimuli, and reproduction. Multicellular organisms exhibit three major structural levels above the cell: similar cells are grouped into tissues, several tissues coordinate to form organs, and several organs form an organ system. For example, to coordinate locomotory movements, sensory information travels from sense organs to the brain, where nervous tissues composed of billions of interconnected neurons—supported by connective tissue—coordinate signals that travel via other neurons to the individual muscle cells. Organisms belong to populations, localized groups of organisms belonging to the same species. Populations of several species in the same area comprise a biological community. Populations interact with their physical environment to form an ecosystem. The biosphere consists of all the environments on Earth that are inhabited by life. Order: atom, molecule, organelle, cell, tissue, organ, organism, population, community.
Concept 1.4 Evolution accounts for life’s unity and diversity
• • • • • • • • • • • • • • • • • • • • •
The history of life is a saga of a changing Earth billions of years old, inhabited by a changing cast of living forms. Charles Darwin brought evolution into focus in 1859 when he presented two main concepts in one of the most important and controversial books ever written, On the Origin of Species by Natural Selection. Darwin’s first point was that contemporary species arose from a succession of ancestors through “descent with modification.” This term captured the duality of life’s unity and diversity: unity in the kinship among species that descended from common ancestors and diversity in the modifications that evolved as species branched from their common ancestors. Darwin’s second point was his mechanism for descent with modification: natural selection. Darwininferred natural selection by connecting two observations: Observation 1: Individual variation. Individuals in a population of any species vary in many heritable traits. Observation 2: Overpopulation and competition. Any population can potentially produce far more offspring than the environment can support. This creates a struggle for existence among variant members of a population. Inference: Unequal reproductive success. Darwin inferred that those individuals with traits best suited to the local environment would leave more healthy, fertile offspring. Inference: Evolutionary adaptation. Unequal reproductive success can lead to adaptation of a population to its environment. Over generations, heritable traits that enhance survival and reproductive success will tend to increase in frequency among a population’s individuals. The population evolves. Natural selection, by its cumulative effects over vast spans of time, can produce new species from ancestral species. For example, a population fragmented into several isolated populations in different environments may gradually diversify into many species as each population adapts over many generations to different environmental problems. Fourteen species of finches found on the Galápagos Islands diversified after an ancestral finch species reached the archipelago from the South American mainland. Each species is adapted to exploit different food sources on different islands. Biologists’ diagrams of evolutionary relationships generally take a treelike form. Just as individuals have a family tree, each species is one twig of a branching tree of life. Similar species like the Galápagos finches share a recent common ancestor. Finches share a more distant ancestor with all other birds. The common ancestor of all vertebrates is even more ancient. Trace life back far enough, and there is a shared ancestor of all living things. All of life is connected through its long evolutionary history.
Concept 1.5 Biologists use various forms of inquiry to explore life
Page | 1
• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •
The word science is derived from a Latin verb meaning “to know.” At the heart of science is inquiry, people asking questions about nature and focusing on specific questions that can be answered. The process of science blends two types of exploration: discovery science and hypothesis-based science. Discovery science is mostly about discovering nature. Hypothesis-based science is mostly about explaining nature. Most scientific inquiry combines the two approaches. Discovery science describes natural structures and processes as accurately as possible through careful observation and analysis of data. Discovery science built our understanding of cell structure and is expanding our databases of genomes of diverse species. Observation is the use of the senses to gather information, which is recorded as data. Data can be qualitative or quantitative. Quantitative data are numerical measurements. Qualitative data may be in the form of recorded descriptions. Jane Goodall has spent decades recording her observations of chimpanzee behavior during field research in Gambia. She has also collected volumes of quantitative data over that time. Discovery science can lead to important conclusions based on inductive reasoning. Through induction, we derive generalizations based on a large number of specific observations. In science, inquiry frequently involves the proposing and testing of hypotheses. A hypothesis is a tentative answer to a well-framed question. It is usually an educated postulate, based on past experience and the available data of discovery science. A scientific hypothesis makes predictions that can be tested by recording additional observations or by designing experiments. A type of logic called deduction is built into hypothesis-based science. In deductive reasoning, reasoning flows from the general to the specific. From general premises, we extrapolate to a specific result that we should expect if the premises are true. In hypothesis-based science, deduction usually takes the form of predictions about what we should expect if a particular hypothesis is correct. We test the hypothesis by performing the experiment to see whether or not the results are as predicted. Deductive logic takes the form of “If . . . then” logic. Scientific hypotheses must be testable. There must be some way to check the validity of the idea. Scientific hypotheses must be falsifiable. There must be some observation or experiment that could reveal if a hypothesis is actually not true. The ideal in hypothesis-based science is to frame two or more alternative hypotheses and design experiments to falsify them. No amount of experimental testing can prove a hypothesis. A hypothesis gains support by surviving various tests that could falsify it, while testing falsifies alternative hypotheses. Facts, in the form of verifiable observations and repeatable experimental results, are the prerequisites of science.
We can explore the scientific method.
• • • • • • • • • • • • •
There is an idealized process of inquiry called the scientific method. Very few scientific inquiries adhere rigidly to the sequence of steps prescribed by the textbook scientific method. Discovery science has contributed a great deal to our understanding of nature without most of the steps of the so-called scientific method. We will consider a case study of scientific research. This case begins with a set of observations and generalizations from discovery science. Many poisonous animals have warning coloration that signals danger to potential predators. Imposter species mimic poisonous species, although they are harmless. An example is the bee fly, a nonstinging insect that mimics a honeybee. What is the function of such mimicry? What advantage does it give the mimic? In 1862, Henry Bates proposed that mimics benefit when predators mistake them for harmful species. This deception may lower the mimic’s risk of predation. In 2001, David and Karin Pfennig and William Harcombe of the University of North Carolina designed a set of field experiments to test Bates’s mimicry hypothesis. In North and South Carolina, a poisonous snake called the eastern coral snake has warning red, yellow, and black coloration.
Page | 2
• • • • • • • • • • • • • • • • • • • • • •
Predators avoid these snakes. It is unlikely that predators learn to avoid coral snakes, as a strike is usually lethal. Natural selection may have favored an instinctive recognition and avoidance of the warning coloration of the coral snake. The nonpoisonous scarlet king snake mimics the ringed coloration of the coral snake. Both king snakes and coral snake live in the Carolinas, but the king snake’s range also extends into areas without coral snakes. The distribution of these two species allowed the Pfennigs and Harcombe to test a key prediction of the mimicry hypothesis. Mimicry should protect the king snake from predators, but only in regions where coral snakes live. Predators in non–coral snake areas should attack king snakes more frequently than predators that live in areas where coral snakes are present. To test the mimicry hypothesis, Harcombe made hundreds of artificial snakes. The experimental group had the red, black, and yellow ring pattern of king snakes. The control group had plain, brown coloring. Equal numbers of both types were placed at field sites, including areas where coral snakes are absent. After four weeks, the scientists retrieved the fake snakes and counted bite or claw marks. Foxes, coyotes, raccoons, and black bears attacked snake models. The data fit the predictions of the mimicry hypothesis. The ringed snakes were attacked by predators less frequently than the brown snakes only within the geographic range of the coral snakes. The snake mimicry experiment provides an example of how scientists design experiments to test the effect of one variable by canceling out the effects of unwanted variables. The design is called a controlled experiment. An experimental group (artificial king snakes) is compared with a control group (artificial brown snakes). The experimental and control groups differ only in the one factor the experiment is designed to test—the effect of the snake’s coloration on the behavior of predators. The brown artificial snakes allowed the scientists to rule out such variables as predator density and temperature as possible determinants of number of predator attacks. Scientists do not control the experimental environment by keeping all variables constant. Researchers usually “control” unwanted variables, not by eliminating them but by canceling their effects using control groups.
Let’s look at the nature of science.
• • • • • • • • • • • • • • • • • • • •
There are limitations to the kinds of questions that science can address. These limits are set by science’s requirements that hypotheses are testable and falsifiable and that observations and experimental results be repeatable. The limitations of science are set by its naturalism. Science seeks natural causes for natural phenomena. Science cannot support or falsify supernatural explanations, which are outside the bounds of science. Everyday use of the term theory implies an untested speculation. The term theory has a very different meaning in science. A scientific theory is much broader in scope than a hypothesis. This is a hypothesis: “Mimicking poisonous snakes is an adaptation that protects nonpoisonous snakes from predators.” This is a theory: “Evolutionary adaptations evolve by natural selection.” A theory is general enough to generate many new, specific hypotheses that can be tested. Compared to any one hypothesis, a theory is generally supported by a much more massive body of evidence. The theories that become widely adopted in science (such as the theory of adaptation by natural selection) explain many observations and are supported by a great deal of evidence. In spite of the body of evidence supporting a widely accepted theory, scientists may have to modify or reject theories when new evidence is found. As an example, the five-kingdom theory of biological diversity eroded as new molecular methods made it possible to test some of the hypotheses about the relationships between living organisms. Scientists may construct models in the form of diagrams, graphs, computer programs, or mathematical equations. Models may range from lifelike representations to symbolic schematics. Science is an intensely social activity. Most scientists work in teams, which often include graduate and undergraduate students. Both cooperation and competition characterize scientific culture.
Page | 3
• • • • • • • • • • • •
Scientists attempt to confirm each other’s observations and may repeat experiments. They share information through publications, seminars, meetings, and personal communication. Scientists may be very competitive when converging on the same research question. Science as a whole is embedded in the culture of its times. For example, recent increases in the proportion of women in biology have had an impact on the research being performed. For instance, there has been a switch in focus in studies of the mating behavior of animals from competition among males for access to females to the role that females play in choosing mates. Recent research has revealed that females prefer bright coloration that “advertises” a male’s vigorous health, a behavior that enhances a female’s probability of having healthy offspring. Some philosophers of science argue that scientists are so influenced by cultural and political values that science is no more objective than other ways of “knowing nature.” At the other extreme are those who view scientific theories as though they were natural laws. The reality of science is somewhere in between. The cultural milieu affects scientific fashion, but need for repeatability in observation and hypothesis testing distinguishes science from other fields. If there is “truth” in science, it is based on a preponderance of the available evidence.
Each element consists of unique atoms. An atom is the smallest unit of matter that still retains the properties of an element. Atoms are composed of even smaller parts, called subatomic particles. Two of these, neutrons and protons, are packed together to form a dense core, the atomic nucleus, at the center of an atom. Electrons can be visualized as forming a cloud of negative charge around the nucleus. Each electron has one unit of negative charge. Each proton has one unit of positive charge. Neutrons are electrically neutral. The attractions between the positive charges in the nucleus and the negative charges of the electrons keep the electrons in the vicinity of the nucleus. A neutron and a proton are almost identical in mass, about 1.7 × 10−24 gram per particle. For convenience, a smaller unit of measure, the dalton, is used to measure the mass of subatomic particles, atoms, or molecules. The mass of a neutron or a proton is close to 1 dalton. The mass of an electron is about 1/2000 that of a neutron or proton. Therefore, we typically ignore the contribution of electrons when determining the total mass of an atom. All atoms of a particular element have the same number of protons in their nuclei. This number of protons is the element’s unique atomic number. The atomic number is written as a subscript before the symbol for the element. For example, 2He means that an atom of helium has 2 protons in its nucleus. Unless otherwise indicated, atoms have equal numbers of protons and electrons and, therefore, no net charge. Therefore, the atomic number tells us the number of protons and the number of electrons that are found in a neutral atom of a specific element. The mass number is the sum of the number of protons and neutrons in the nucleus of an atom. Therefore, we can determine the number of neutrons in an atom by subtracting the number of protons (the atomic number) from the mass number. The mass number is written as a superscript before an element’s symbol (for example, 4He). The atomic weight of an atom, a measure of its mass, can be approximated by the mass number. While all atoms of a given element have the same number of protons, they may differ in the number of neutrons. Two atoms of the same element that differ in the number of neutrons are called isotopes. In nature, an element occurs as a mixture of isotopes. For example, 99% of carbon atoms have 6 neutrons (12C). Most of the remaining 1% of carbon atoms have 7 neutrons (13C) while the rarest carbon isotope, with 8 neutrons, is 14C. Most isotopes are stable; they do not tend to lose particles. Both 12C and 13C are stable isotopes. The nuclei of some isotopes are unstable and decay spontaneously, emitting particles and energy. 14C is one of these unstable isotopes, or radioactive isotopes. When 14C decays, one of its neutrons is converted to a proton and an electron. This converts 14C to 14N, transforming the atom to a different element. Radioactive isotopes have many applications in biological research. Radioactive decay rates can be used to date fossils. Radioactive isotopes can be used to trace atoms through metabolic processes. Radioactive isotopes are also used to diagnose medical disorders. The molecular formula indicates the number and types of atoms present in a single molecule. H2 is the molecular formula for hydrogen gas. Oxygen needs to add 2 electrons to the 6 already present to complete its valence shell.
Page | 4
sodium has a full valence shell (the second) and chlorine has a full valence shell (the third). radioactive tracers can be used with imaging instruments to monitor chemical processes in the body. Each pH unit represents a tenfold difference in H+ and OH− concentrations. The chemical equilibrium between carbonic acid and bicarbonate acts as a pH regulator. These interactions typically result in the atoms remaining close together. calcium (Ca). The attraction of an atom for the shared electrons of a covalent bond is called its electronegativity. Two oxygen atoms can form a molecule by sharing two pairs of valence electrons. usually near pH 7. When two atoms that differ in electronegativity bond. Compounds with a polar covalent bond have regions of partial negative charge near the strongly electronegative atom and regions of partial positive charge near the weakly electronegative atom. The chemical processes in the cell can be disrupted by changes to the H+ and OH− concentrations away from their normal values. The strongest chemical bonds are covalent bonds and ionic bonds. Most biological fluids have pH values in the range of 6 to 8. the valence shell. collectively they are strong and play important biological roles. To maintain cellular pH values at a constant level. Most of the remaining 4% of an organism’s weight consists of phosphorus (P). and the pH = 7. ranging from 1 to 14. both atoms are no longer neutral. oxygen (O). The equilibrium shifts left or right as other metabolic processes add or remove H+ from the solution. Each atom can count both electrons toward its goal of filling the valence shell. with one valence electron in its third shell. Chapter 3: The pH scale. and potassium (K). Buffers typically consist of a weak acid and its corresponding base. they do not share the electron pair equally and form a polar covalent bond. A small change in pH actually indicates a substantial change in H+ and OH− concentrations. Four elements—carbon (C). with each atom contributing one. A covalent bond between atoms that have similar electronegativities is also nonpolar. The chemical behavior of an atom depends mostly on the number of electrons in its outermost shell. Hydrogen bondsform when a hydrogen atom already covalently bonded to a strongly electronegative atom is attracted to another strongly electronegative atom. About 25 of the 92 natural elements are known to be essential for life. but have charges and are called ions. which dissociates to yield a bicarbonate ion and a hydrogen ion. This energy can destroy molecules within living cells. If electrons in a covalent bond are shared equally. drawing the structural formula. Molecules or atoms in close proximity can be attracted by these fleeting charge differences. hydrogen. Lithium has one valence electron. Atoms with the same number of valence electrons have similar chemical behaviors. Buffers resist changes to the pH of a solution when H+ or OH− is added to the solution. and nitrogen (N)—make up 96% of living matter. the human stomach has strongly acidic digestive juice with a pH of about 2. After the transfer. For example. The pH of a neutral solution is 7. While individual bonds (ionic. neon has eight. We can abbreviate the structure of the molecule by substituting a line for each pair of shared electrons. These atoms have formed a double covalent bond. Trace elementsare required by an organism but only in minute quantities. For example. transfers this electron to chlorine. values for [OH−] can be easily calculated from the product relationship. Two or more atoms held together by covalent bonds constitute a molecule. and basic solutions have pH values greater than 7. Also. Atoms with incomplete valence shells can interact with each other by sharing or transferring valence electrons. Buffers accept hydrogen ions from the solution when they are in excess and donate hydrogen ions when they have been depleted. then they can share a pair of electrons. van der Waals) are weak and temporary. hydrogen (H). pH = − log [H+] or [H+] = 10−pH In a neutral solution. Values for pH decline as [H+] increase. Electrons in the valence shell are known as valence electrons. the bonds of CH4 are nonpolar. A covalent bond between two atoms of the same element is always nonpolar. the energy emitted in radioactive decay is hazardous to life. Page | 5 . Now. An atom with a completed valence shell. The severity of damage depends on the type and amount of radiation that the organism absorbs. Acidic solutions have pH values less than 7. sodium. sulfur (S). with 7 valence electrons in its third shell. However. compresses the range of concentrations by employing logarithms. like neon. Because carbon and hydrogen do not differ greatly in electronegativities. held by attractions called chemical bonds. then this is a nonpolar covalent bond. [H+] = 10−7 M. Strongly electronegative atoms attempt to pull the shared electrons toward themselves. is nonreactive. A covalent bond is formed by the sharing of a pair of valence electrons by two atoms. if two hydrogen atoms come close enough that their 1s orbitals overlap. While useful in research and medicine. biological fluids have buffers. One important buffer in human blood and other biological solutions is carbonic acid. The bonds between oxygen and hydrogen in water are polar covalent because oxygen has a much higher electronegativity than does hydrogen. creating van der Waals interactions. If two atoms come close enough that their unshared orbitals overlap. While the pH scale is based on [H+]. they will share their newly paired electrons. An ionic bond can form if two atoms are so unequal in their attraction for valence electrons that one atom strips an electron completely from the other.
creating an ammonium ion (NH4+). A calorie is released when 1 g of water cools by 1°C. To maintain cellular pH values at a constant level. When hydrochloric acid is added to water. Carbonic acid (H2CO3) is a weak acid: H2CO3 <=> HCO3− + H+ At equilibrium. a phenomenon called cohesion. Cohesion among water molecules plays a key role in the transport of water and dissolved nutrients against gravity in plants. Page | 6 . contributes too. is related to cohesion. The chemical equilibrium between carbonic acid and bicarbonate acts as a pH regulator. 1% of the H2CO3 molecules will be dissociated. or run on water without breaking the surface. The equilibrium shifts left or right as other metabolic processes add or remove H+ from the solution In a water molecule. as water adheres to the wall of the vessels. NaOH -> Na+ + OH− OH− + H+ -> H2O Solutions with more OH− than H+ are basic solutions. there will be a fixed ratio of products to reactants. two hydrogen atoms form single polar covalent bonds with an oxygen atom. An acid is a substance that increases the hydrogen ion concentration in a solution. Water stabilizes temperature because it has a high specific heat. Some animals can stand. Buffers resist changes to the pH of a solution when H+ or OH− is added to the solution. Each hydrogen bond lasts only a few trillionths of a second. hydrogen bonds hold water together. This upward pull is transmitted down to the roots.239 cal. Buffers accept hydrogen ions from the solution when they are in excess and donate hydrogen ions when they have been depleted. hydrogen ions dissociate from chloride ions: HCl -> H+ + Cl− Addition of an acid makes a solution more acidic. the binding and release of hydrogen ions are reversible. one convenient unit is the calorie (cal). For these molecules. They form. the kilocalorie (kcal) is more convenient. biological fluids have buffers. break. While there are several ways to measure heat energy. Water behaves as if covered by an invisible film. Collectively. Solutions in which concentrations of OH− and H+ are equal are neutral solutions. A kilocalorie is the amount of heat energy necessary to raise the temperature of 1000 g of water by 1°C. Adhesion. Buffers typically consist of a weak acid and its corresponding base. Some bases reduce the H+ concentration directly by accepting hydrogen ions. is equivalent to 0. One important buffer in human blood and other biological solutions is carbonic acid. about 1/20 as strong as covalent bonds. In any solution. These molecules dissociate completely in water.a measure of the force necessary to stretch or break the surface of a liquid.clinging of one substance to another. which then combines with H+ to form water. and reform with great frequency. Ammonia (NH3) acts as a base when the nitrogen’s unshared electron pair attracts a hydrogen ion from the solution. • • • • • • • • • • • • • • • • • • • • Because oxygen is more electronegative than hydrogen. One calorie is the amount of heat energy necessary to raise the temperature of one g of water by 1°C. Any substance that reduces the hydrogen ion concentration in a solution is a base. NH3 + H+ <=> NH4+ Other bases reduce H+ indirectly by dissociating to OH−. The regions near the two hydrogen atoms have a partial positive charge. walk. Solutions with more H+ than OH− are acidic solutions. which dissociates to yield a bicarbonate ion and a hydrogen ion. Water has a greater surface tension than most other liquids because hydrogen bonds among surface water molecules resist stretching or breaking the surface. The slightly negative regions of one water molecule are attracted to the slightly positive regions of nearby water molecules. a substantial percentage of all water molecules are bonded to their neighbors. Water molecules move from the roots to the leaves of a plant through water-conducting vessels. Other acids and bases (NH3) are weak acids or bases. Another common energy unit. Surface tension. the region around the oxygen atom has a partial negative charge. the product of the H+ and OH− concentrations is constant at 10−14. At any instant. A water molecule is a polar molecule in which opposite ends of the molecule have opposite charges. Some acids and bases (HCl and NaOH) are strong acids or bases. forming hydrogen bonds. Each water molecule can form hydrogen bonds with up to four neighbors. At equilibrium. creating a high level of structure. The hydrogen bonds joining water molecules are weak. Hydrogen bonds cause water molecules leaving the vessels to tug on molecules farther down. In many biological processes. other water molecules from vessels in the leaf replace them. Water has a variety of unusual properties because of the attraction between polar water molecules. the joule (J). As water molecules evaporate from a leaf.
water molecules cannot form hydrogen bonds with hydrophobic molecules. · All are hydrophilic and increase the solubility of organic compounds in water. In other words. · · Both are steroids with four fused carbon rings. Chapter 4: · The components of organic molecules that are most commonly involved in chemical reactions are known as functional groups. Water molecules form hydrogen bonds with the cellulose fibers of cotton. Water’s high specific heat is due to hydrogen bonding. Organic compounds with hydroxyl groups are alcohols. The specific heat of iron is 1/10 that of water. and their names typically end in -ol. which forms a polar covalent bond to the carbon skeleton. its giant cellulose molecules are too large to dissolve in water. can dissolve in water if they have ionic and polar regions. carboxyl. its major constituent. the basic structure of testosterone (a male sex hormone) and estradiol (a female sex hormone) is the same. However. and phosphate groups. amino. Water resists changes in temperature because of its high specific heat. carbonyl. allowing you to dry yourself with your cotton towel as the water is pulled into the towel. Eventually. water absorbs or releases a relatively large quantity of heat for each degree of temperature change. sulfhydryl.6 cal/g/°C. Each dissolved ion is surrounded by a sphere of water molecules. a hydrogen atom forms a polar covalent bond with an oxygen atom. The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1°C. resulting in a solution with two solutes: sodium and chloride ions. Hydrophobic molecules are major ingredients of cell membranes. share electrons equally. Even large molecules. The number and arrangement of functional groups help give each molecule its unique properties. ethyl alcohol has a specific heat of 0. · · Because of these polar covalent bonds. Because there are no consistent regions with partial or full charges. Page | 7 . For example. Polar molecules are also soluble in water because they form hydrogen bonds with water. · In a hydroxyl group (—OH). These functional groups interact with different targets in the body. but they differ in the functional groups attached to the rings. Any substance that has an affinity for water is hydrophilic (water-loving). Water has a high specific heat compared to other substances. carbon-carbon and carbon-hydrogen. Substances that have no affinity for water are hydrophobic (water-fearing). These substances are dominated by ionic or polar bonds. These substances are nonionic and have nonpolar covalent bonds. Some hydrophilic substances do not dissolve because their molecules are too large. Oils such as vegetable oil are hydrophobic because the dominant bonds. the specific heat of water is 1 cal per gram per degree Celsius or 1 cal/g/°C. For example. · If we consider hydrocarbons to be the simplest organic molecules. · There are six functional groups that are most important to the chemistry of life: hydroxyl. By definition. water dissolves all the ions. cotton is hydrophilic because cellulose. hydroxyl groups increase the solubility of organic molecules. has numerous polar covalent bonds. we can view functional groups as attachments that replace one or more of the hydrogen atoms bonded to the carbon skeleton of the hydrocarbon. · · Each functional group behaves consistently from one organic molecule to another. like proteins. a hydration shell. · As an example.
with its four covalent bonds. · A carboxyl group (—COOH) consists of a carbon atom with a double bond to an oxygen atom and a single bond to the oxygen of a hydroxyl group. If the carbonyl group is within the carbon skeleton. One function of phosphate groups is to transfer energy between organic molecules. Page | 8 . and nitrogen. · Compounds with carboxyl groups are carboxylic acids. · · These elements are linked by strong covalent bonds. · · · · · · · · An amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and the carbon skeleton. Phosphate groups are anions with two negative charges. have amino and carboxyl groups. the building blocks of proteins. is the primary energy-transferring molecule in living cells. · · · · A phosphate group connects to the carbon backbone via one of its oxygen atoms. · Living matter consists mainly of carbon. This group resembles a hydroxyl group in shape. Amino acids. Organic compounds with amino groups are amines. If the carbonyl group is on the end of the skeleton. or ATP. These are the chemical elements of life. · A carboxyl group acts as an acid because the combined electronegativities of the two adjacent oxygen atoms increase the dissociation of hydrogen as an ion (H+). the compound is an aldehyde.· · · · A carbonyl group (>CO) consists of an oxygen atom joined to the carbon skeleton by a double bond. Two sulfhydryl groups can interact to help stabilize the structure of proteins. oxygen. is the basic building block in molecular architecture. A sulfhydryl group (—SH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone. · A phosphate group (—OPO32−) consists of a phosphorus atom bound to four oxygen atoms (three with single bonds and one with a double bond). then the compound is a ketone. The amino group acts as a base because the amino group can pick up a hydrogen ion (H+) from the solution. as two protons have dissociated from the oxygen atoms. Organic molecules with sulfhydryl groups are thiols. Adenosine triphosphate. Carbon. Isomers with aldehydes versus ketones have different properties. hydrogen. with smaller amounts of sulfur and phosphorus.
A third group of amino acids includes those with functional groups that are charged (ionized) at cellular pH. Most important. • • • • • • • • • • • • • • • • • • Amino acidsare organic molecules with both carboxyl and amino groups. an amino group. The simplest carbohydrates are monosaccharides. the smallest carbohydrates. A protein consists of one or more polypeptides folded and coiled into a specific conformation. Polypeptides range in size from a few monomers to thousands. and nucleic acids. Each type of protein has a complex three-dimensional shape or conformation. The physical and chemical properties of the R group determine the unique characteristics of a particular amino acid. regulating metabolism by selectively accelerating chemical reactions without being consumed. At one end is an amino acid with a free amino group (the N-terminus) and at the other is an amino acid with a free carboxyl group (the C-terminus). Four components are attached to the alpha carbon: a hydrogen atom.2 Carbohydrates serve as fuel and building material • • • • Carbohydratesinclude sugars and their polymers. One group of amino acids has hydrophobic R groups. and defense against foreign substances. protein enzymes function as catalysts in cells. They are instrumental in almost everything that an organism does. Sugars. Different R groups characterize the 20 different amino acids. or double sugars. transport. Some acidic R groups are negative in charge due to the presence of a carboxyl group. serve as fuel and a source of carbon. Humans have tens of thousands of different proteins. Basic R groups have amino groups that are positive in charge. lipids. Repeating the process over and over creates a polypeptide chain. and a variable R group (or side chain). The resulting covalent bond is called a peptide bond. Note that all amino acids have carboxyl and amino groups. Another group of amino acids has polar R groups that are hydrophilic. The four major classes of macromolecules are carbohydrates.· The great diversity of organic molecules with their special properties emerges from the unique arrangement of the carbon skeleton and the functional groups attached to the skeleton. or it may be a carbon skeleton with various functional groups attached (as in glutamine). Polysaccharides are polymers of many monosaccharides. Disaccharides. At the center of an amino acid is an asymmetric carbon atom called the alpha carbon. All protein polymers are constructed from the same set of 20 amino acid monomers. Amino acids are joined together when a dehydration reaction removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of another. Each polypeptide has a unique linear sequence of amino acids. Protein functions include structural support. consist of two monosaccharides joined by a condensation reaction. • Monosaccharidesgenerally have molecular formulas that are some multiple of the unit CH2O. a carboxyl group. Page | 9 . storage. proteins. or simple sugars. Chapter 5: • • • • • • • • • Proteins account for more than 50% of the dry mass of most cells. cellular signaling. Proteins are the most structurally complex molecules known. movement. Polymers of proteins are called polypeptides. each with a specific structure and function. R groups may be as simple as a hydrogen atom (as in the amino acid glycine). Concept 5. Amino acids are the monomers from which proteins are constructed. The terms acidic and basic in this context refer only to these groups in the R groups.
parallel cellulose molecules held together in this way are grouped into units called microfibrils. such as amino acids and fatty acids. Sucrose. While polymers built with alpha glucose form helical structures. three-carbon sugars are trioses. polymers built with beta glucose form straight structures. Monosaccharides are also classified by the number of carbons in the carbon skeleton. Monosaccharides may also exist as enantiomers. Maltose. is formed by joining two glucose molecules. Page | 10 . providing the microbe and the host animal access to a rich source of energy. table sugar. Polysaccharides. is formed by joining glucose and fructose. Cellulose is a polysaccharide of beta glucose monomers. a ketose. which form strong building materials for plants (and for humans. These two ring forms differ in whether the hydroxyl group attached to the number 1 carbon is fixed above (beta glucose) or below (alpha glucose) the plane of the ring. Glycogen is highly branched like amylopectin. Celluloseis a major component of the tough wall of plant cells. glucose has the formula C6H12O6. Many eukaryotic herbivores. malt sugar. amylose. In plant cell walls. Glucose. Most of these monomers are joined by 1–4 linkages (number 1 carbon to number 4 carbon) between the glucose molecules. • • • • • • • • • • • • • • • • • • • • • • • • • • • • Polysaccharidesare polymers of hundreds to thousands of monosaccharides joined by glycosidic linkages. Plants store surplus glucose as starch granules within plastids. the glycosidic linkages in these two polymers differ. cellulose abrades the intestinal walls and stimulates the secretion of mucus. It is the most abundant organic compound on Earth. Monosaccharides. and withdraw it as needed for energy or carbon. Most names for sugars end in -ose. Five-carbon backbones are pentoses. the sugar is an aldose or a ketose. differ in the spatial arrangement of their parts around asymmetrical carbons. The enzymes that digest starch by hydrolyzing its alpha linkages cannot hydrolyze the beta linkages in cellulose. The difference is based on the fact that there are actually two slightly different ring structures for glucose. have storage and structural roles. an aldose. They also function as the raw material for the synthesis of other monomers. The straight structures built with beta glucose allow H atoms on one strand to form hydrogen bonds with OH groups on other strands. have digestive enzymes that can hydrolyze starch to glucose. Sucrose is the major transport form of sugars in plants.• • • • • • • • • • • • • • • • • For example. and fructose. the polymers of sugars. Other polysaccharides serve as building materials for the cell or the whole organism. especially parts rich in starch. as lumber). Branched forms such as amylopectin are more complex. Some microbes can digest cellulose to its glucose monomers through the use of cellulase enzymes. making every other glucose monomer upside down with respect to its neighbors. The differing glycosidic links in starch and cellulose give the two molecules distinct three-dimensional shapes. While often drawn as a linear skeleton. cellulose is a polymer of glucose. Two monosaccharides can join with a glycosidic linkage to form a disaccharide via dehydration.” As it travels through the digestive tract. Like starch. aiding in the passage of food. glucose and galactose. Some polysaccharides serve for storage and are hydrolyzed as sugars are needed. Humans and other vertebrates store a day’s supply of glycogen in the liver and muscles. Plants produce almost one hundred billion tons of cellulose per year. Depending on the location of the carbonyl group. Animals that feed on plants. particularly glucose. from cows to termites. Cellulose in human food passes through the digestive tract and is eliminated in feces as “insoluble fiber. However. including chloroplasts. are a major fuel for cellular work. is unbranched and forms a helix. Lactose. Starch is a polysaccharide of alpha glucose monomers. Monosaccharides have a carbonyl group (>C=O) and multiple hydroxyl groups (—OH). Glucose and other six-carbon sugars are hexoses. is formed by joining glucose and galactose. both six-carbon aldoses. have symbiotic relationships with cellulolytic microbes. monosaccharides in aqueous solutions form rings. milk sugar. are structural isomers. For example. Starchis a storage polysaccharide composed entirely of glucose monomers. Animals store glucose in a polysaccharide called glycogen. The simplest form of starch.
The major function of fats is energy storage. The three fatty acids in a fat can be the same or different.3 Lipids are a diverse group of hydrophobic molecules • • • • Unlike other macromolecules. three fatty acids are joined to glycerol by an ester linkage. Chitin is similar to cellulose. Adipose tissue also functions to cushion vital organs. creating a triacylglycerol. The phrase “hydrogenated vegetable oils” on food labels means that unsaturated fats have been synthetically converted to saturated fats by the addition of hydrogen. A diet rich in saturated fats may contribute to cardiovascular disease (atherosclerosis) through plaque deposits. often 16 to 18 carbons long. seals. Fatty acids may vary in length (number of carbons) and in the number and locations of double bonds. The many nonpolar C—H bonds in the long hydrocarbon skeleton make fats hydrophobic. A fatty acid consists of a carboxyl group attached to a long carbon skeleton. Pure chitin is leathery but can be hardened by the addition of calcium carbonate. Fats separate from water because the water molecules hydrogen bond to one another and exclude the fats. Another important structural polysaccharide is chitin. and most other marine mammals. These trans fat molecules contribute more than saturated fats to atherosclerosis. and crustaceans). lipids do not form polymers. which form nonpolar covalent bonds. as in seeds. If the fatty acid has one or more carbon-carbon double bonds formed by the removal of hydrogen atoms from the carbon skeleton. The process of hydrogenating vegetable oils produces saturated fats and also unsaturated fats with trans double bonds. In a fat. or triglyceride. This subcutaneous layer is especially thick in whales. Fats store large amounts of energy. they can function with bulky energy storage in the form of starch. Concept 5. Plant and fish fats are liquid at room temperature and are known as oils. Chitin also provides structural support for the cell walls of many fungi. Lipids are highly diverse in form and function. Saturated fats are solid at room temperature. Glycerolis a three-carbon alcohol with a hydroxyl group attached to each carbon. then the molecule is a saturated fatty acid. saturated with hydrogens at every possible position. • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • Although fats are not strictly polymers. The kinks caused by the double bonds prevent the molecules from packing tightly enough to solidify at room temperature. they are large molecules assembled from smaller molecules by dehydration reactions. except that it contains a nitrogen-containing appendage on each glucose monomer. Humans and other mammals store fats as long-term energy reserves in adipose cells that swell and shrink as fat is deposited or withdrawn from storage. Fats made from saturated fatty acids are saturated fats. Page | 11 . Peanut butter and margarine are hydrogenated to prevent lipids from separating out as oil. Animals must carry their energy stores with them and benefit from having a more compact fuel reservoir of fat. Plants use oils when dispersal and compact storage is important. then the molecule is an unsaturated fatty acid. used in the exoskeletons of arthropods (including insects. Most animal fats are saturated. Because plants are immobile. The unifying feature of lipids is that they all have little or no affinity for water. If the fatty acid has no carbon-carbon double bonds. A layer of fat can also function as insulation. Fats made from unsaturated fatty acids are unsaturated fats.• • • • • Some fungi can also digest cellulose. A saturated fatty acid is a straight chain. A gram of fat stores more than twice as much energy as a gram of a polysaccharide such as starch. This is because they consist mostly of hydrocarbons. spiders. but an unsaturated fatty acid has a kink wherever there is a double bond. A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids. such as the kidneys.
Again. is a component in animal cell membranes. or it may be a carbon skeleton with various functional groups attached (as in glutamine). The resulting covalent bond is called a peptide bond. • • • • • • • • • • • • • • • • • • Amino acidsare organic molecules with both carboxyl and amino groups. Phospholipids are the major component of all cell membranes. The interaction of phospholipids with water is complex. At one end is an amino acid with a free amino group (the N-terminus) and at the other is an amino acid with a free carboxyl group (the C-terminus). Amino acids are the monomers from which proteins are constructed. Different steroids are created by varying functional groups attached to the rings. Each polypeptide has a unique linear sequence of amino acids. Some acidic R groups are negative in charge due to the presence of a carboxyl group. The fatty acid tails are hydrophobic. the hydrophilic heads are on the outside of the bilayer.Phospholipids are major components of cell membranes. Cholesterol is also the precursor from which all other steroids are synthesized. an amino group. Another group of amino acids has polar R groups that are hydrophilic. R groups may be as simple as a hydrogen atom (as in the amino acid glycine). This type of structure is called a micelle. Repeating the process over and over creates a polypeptide chain. they self-assemble into assemblages with the hydrophobic tails pointing toward the interior. Phospholipids are arranged as a bilayer at the surface of a cell. Both saturated fats and trans fats exert their negative impact on health by affecting cholesterol levels. and the hydrophobic tails point toward the interior of the bilayer. One group of amino acids has hydrophobic R groups. but the phosphate group and its attachments form a hydrophilic head. The phospholipid bilayer forms a barrier between the cell and the external environment. The physical and chemical properties of the R group determine the unique characteristics of a particular amino acid. At the center of an amino acid is an asymmetric carbon atom called the alpha carbon. high levels of cholesterol in the blood may contribute to cardiovascular disease. The amino acid sequence of a polypeptide can be determined. including the vertebrate sex hormones. a carboxyl group. Additional smaller groups may be attached to the phosphate group to form a variety of phospholipids. Different R groups characterize the 20 different amino acids. Four components are attached to the alpha carbon: a hydrogen atom. Polypeptides range in size from a few monomers to thousands. Amino acids are joined together when a dehydration reaction removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of another. When phospholipids are added to water. Note that all amino acids have carboxyl and amino groups.an important steroid. in contact with the aqueous solution. While cholesterol is an essential molecule in animals. Cholesterol. • • • • • • • • • • • Phospholipidshave two fatty acids attached to glycerol and a phosphate group at the third position. • • • • • • • Steroidsare lipids with a carbon skeleton consisting of four fused rings. Basic R groups have amino groups that are positive in charge. Page | 12 . The terms acidic and basic in this context refer only to these groups in the R groups. The phosphate group carries a negative charge. Many of these other steroids are hormones. Steroids include cholesterol and certain hormones. and a variable R group (or side chain). • Frederick Sanger and his colleagues at Cambridge University determined the amino acid sequence of insulin in the 1950s. A third group of amino acids includes those with functional groups that are charged (ionized) at cellular pH.
In almost every case. and coiled into a unique shape. Each subunit has a nonpeptide heme component with an iron atom that binds oxygen. When a cell synthesizes a polypeptide. The folding is reinforced by a variety of bonds between parts of the chain. Lysozyme. which in turn depend on the sequence of amino acids. The primary structure of a protein is its unique sequence of amino acids. an inherited blood disorder. A protein’s specific conformation determines its function. Sanger was able to reconstruct the complete primary structure of insulin. Three levels of structure—primary. ionic bonds between charged R groups. The function of a protein is an emergent property resulting from its specific molecular order. He then searched for overlapping regions among the pieces obtained by hydrolyzing with the different agents. The precise primary structure of a protein is determined by inherited genetic information. an antibody binds to a particular foreign substance. and hydrophobic interactions and van der Waals interactions among hydrophobic R groups. Tertiary structureis determined by interactions among various R groups. the protein that carries oxygen in red blood cells. the function of a protein depends on its ability to recognize and bind to some other molecule. while others are fibrous in shape. Hydrolysis by another agent broke the polypeptide at different sites. Natural signal molecules called endorphins bind to specific receptor proteins on the surface of brain cells in humans. For example. Quaternary structureresults from the aggregation of two or more polypeptide subunits. These coils and folds are referred to as secondary structure and result from hydrogen bonds between the repeating constituents of the polypeptide backbone. This provides structural strength for collagen’s role in connective tissue. but the sum of many hydrogen bonds stabilizes the structure of part of the protein. secondary. deforming the red blood cells into a sickle shape and clogging capillaries. Most proteins have segments of their polypeptide chains repeatedly coiled or folded. The weakly positive hydrogen atom attached to the nitrogen atom has an affinity for the oxygen atom of a nearby peptide bond. Even a slight change in primary structure can affect a protein’s conformation and ability to function. An enzyme recognizes and binds to a specific substrate.• • • • • • • Sanger used protein-digesting enzymes and other catalysts to hydrolyze the insulin at specific places. After years of effort. Sanger used chemical methods to determine the sequence of amino acids in the small fragments. Collagen is a fibrous protein of three polypeptides that are supercoiled like a rope. Protein conformation determines protein function. While these three interactions are relatively weak. Quaternary structure arises when two or more polypeptides join to form a protein. • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • A functional protein consists of one or more polypeptides that have been twisted. consists of 129 amino acids. Most of the steps in sequencing a polypeptide have since been automated. facilitating a chemical reaction. Many proteins are globular. folded. the chain generally folds spontaneously to assume the functional conformation for that protein. yielding a second group of fragments. can cause sickle-cell disease. What are the key factors determining protein conformation? Page | 13 . strong covalent bonds called disulfide bridges that form between the sulfhydryl groups (SH) of two cysteine monomers act to rivet parts of the protein together. and tertiary structures—organize the folding within a single polypeptide. It is the order of amino acids that determines what the three-dimensional conformation of the protein will be. The substitution of one amino acid (valine) for the normal one (glutamic acid) at a particular position in the primary structure of hemoglobin. It consists of four polypeptide subunits: two alpha and two beta chains. Both types of subunits consist primarily of alpha-helical secondary structure. Each hydrogen bond is weak. and other opiate drugs mimic endorphins because they are similar in shape and can bind to the brain’s endorphin receptors. an enzyme that attacks bacteria. producing euphoria and relieving pain. heroin. Typical secondary structures are coils (an alpha helix) or folds (beta pleated sheets). The fragments were then separated by a technique called chromatography. Morphine. The abnormal hemoglobins crystallize. The structural properties of silk are due to beta pleated sheets. These interactions include hydrogen bonds between polar and/or charged areas. The presence of so many hydrogen bonds makes each silk fiber stronger than a steel strand of the same weight. Hemoglobin is a globular protein with quaternary structure.
DGis negative. Photosynthesis is strongly endergonic. or other factors can unravel or denature a protein. toward the solvent. The polypeptide chain refolds so that its hydrophobic regions face outward. An exergonic reaction proceeds with a net release of free energy. The folding occurs as the protein is being synthesized within the cell. Page | 14 . Reactions in a closed system eventually reach equilibrium and can do no work. An endergonic reaction is one that absorbs free energy from its surroundings. However. This technique requires the formation of a crystal of the protein being studied. ionic bonds.• • • • • • • • • • • • • • • • • • • Chapter 6: A polypeptide chain of a given amino acid sequence can spontaneously arrange itself into a 3D shape determined and maintained by the interactions responsible for secondary and tertiary structure. then photosynthesis. Endergonic reactions are nonspontaneous. The folding of many proteins is assisted by chaperonins or chaperone proteins. Most proteins become denatured if the are transferred to an organic solvent. A cell continues to do work throughout its life. The constant flow of materials into and out of the cell keeps metabolic pathways from ever reaching equilibrium. Sunlight provides a daily source of free energy for photosynthetic organisms. This method does not require protein crystallization. A catabolic process in a cell releases free energy in a series of reactions. it is still difficult to predict the conformation of a protein from its primary structure alone. Chaperonins do not specify the final structure of a polypeptide but rather work to segregate and protect the polypeptide while it folds spontaneously. Biochemists now know the amino acid sequences of more than 875. Endergonic reactions store energy in molecules. Nevertheless. protein conformation also depends on the physical and chemical conditions of the protein’s environment. For the overall reaction of cellular respiration: C6H12O6 + 6O2 -> 6CO2 + 6H2O DG= −686 kcal/mol For each mole (180 g) of glucose broken down by respiration.000. Nonphotosynthetic organisms depend on a transfer of free energy from photosynthetic organisms in the form of organic molecules.000 proteins and the 3D shapes of about 7. For the conversion of carbon dioxide and water to sugar. and disulfide bridges that maintain the protein’s shape. The more random a collection of matter. powered by the absorption of light energy. The greater the decrease in free energy. Energy transfers and transformations make the universe more disordered due to this loss of usable energy. Most proteins appear to undergo several intermediate stages before reaching their “mature” configuration. and the magnitude of DGis the quantity of energy required to drive the reaction. Entropyis a quantity used as a measure of disorder or randomness. the reverse reaction. Some reversible reactions of respiration are constantly “pulled” in one direction. The pattern of diffraction of an X-ray by the atoms of the crystal can be used to determine the location of the atoms and to build a computer model of its structure. Chemical reactions can be classified as either exergonic or endergonic based on free energy. but others cannot. If cellular respiration releases 686 kcal. salt concentration. the greater the amount of work that can be done. Nuclear magnetic resonance (NMR) spectroscopy has recently been applied to this problem. DGis positive. not in a single step. This explains why extremely high fevers can be fatal. Some proteins can return to their functional shape after denaturation. temperature. DG= +686 kcal/mol. as the product of one reaction does not accumulate but becomes the reactant in the next step. Proteins in the blood become denatured by the high body temperatures. must require an equivalent investment of energy. which disrupts the weak interactions that stabilize conformation. At present. Cells maintain disequilibrium because they are open systems. the greater its entropy. 686 kcal of energy are made available to do work in the cell. A cell that has reached metabolic equilibrium has a DG= 0 and is dead! Metabolic disequilibrium is one of the defining features of life. These forces disrupt the hydrogen bonds. Alterations in pH. The products have 686 kcal less free energy than the reactants. Free energy can be thought of as a measure of the stability of a system. scientists use X-ray crystallography to determine protein conformation. especially in the crowded environment of the cell. The magnitude of DGfor an exergonic reaction is the maximum amount of work the reaction can perform. Denaturation can also be caused by heat.
they transform light energy to chemical energy. is a choreographed interplay of thousands of different kinds of cellular molecules. which is the energy of random molecular motion. The first law of thermodynamics states that energy can be transferred and transformed. the rates of forward and backward reactions are equal. there is an unstoppable trend toward randomization of the universe. give up order (increase in S). and there is no change in the concentration of products or reactants. separated charges. without outside help in the form of energy input. the intersecting set of chemical pathways characteristic of life. DGis negative. Another way to state the second law of thermodynamics is for a process to occur spontaneously. During every transfer or transformation of energy. The greater the decrease in free energy. The product from the first reaction can then pass quickly to the next enzyme until the final product is released. Every spontaneous process is characterized by a decrease in the free energy of the system. energy and matter can be transferred between the system and its surroundings. Automobiles convert only 25% of the energy in gasoline into motion. We can represent this change in free energy from the start of a process until its finish by: DG= Gfinal state − Gstarting state Or DG= DH− TDS For a process to be spontaneous. ordered forms of energy are converted at least partly to heat. the greater its entropy. A team of enzymes for several steps of a metabolic pathway may be assembled as a multienzyme complex. the rest is lost as heat. organic polymers—are unstable and tend to move toward a more stable state. Entropyis a quantity used as a measure of disorder or randomness. Processes that have a positive or zero DG are never spontaneous. Chemical reactions can be classified as either exergonic or endergonic based on free energy. or both. Spontaneous processes need not occur quickly. Organisms are open systems. Systems that tend to change spontaneously are those that have high enthalpy. The magnitude of DGfor an exergonic reaction is the maximum amount of work the reaction can perform. but it cannot be created or destroyed. While order can increase locally. In most energy transformations. Some spontaneous processes are instantaneous. the free energy of a system decreases. The greater the decrease in free energy. Some are very slow. or both. For a process to occur on its own. In an open system. Nature runs “downhill. it must increase the entropy of the universe. In a chemical reaction at equilibrium. At equilibrium DG= 0. the greater the amount of work that can be done. Page | 15 . Living systems create ordered structures from less ordered starting materials. heat can only be used to warm the organism. They absorb energy—light or chemical energy in the form of organic molecules—and release heat and metabolic waste products such as urea or CO2 to their surroundings. The second law of thermodynamics states that every energy transfer or transformation increases the entropy of the universe. DGmust be negative for a process to be spontaneous. In any spontaneous process. Metabolism. such as an explosion. Some enzymes and enzyme complexes have fixed locations within the cells as structural components of particular membranes. the term system refers to the matter under study and the surroundings include everything outside the system. A system can use heat to do work only when there is a temperature difference that results in heat flowing from a warmer location to a cooler one. the more work a spontaneous process can perform. The more random a collection of matter. is isolated from its surroundings.” A system at equilibrium is at maximum stability. Structures within the cell help bring order to metabolic pathways. Thermodynamicsis the study of energy transformations. In this field. The word spontaneous describes a process that can occur without an input of energy. Systems that are high in free energy—compressed springs. which is the energy associated with the random movement of atoms and molecules. Movements away from equilibrium are nonspontaneous and require the addition of energy from an outside energy source (the surroundings). Energy transfers and transformations make the universe more disordered due to this loss of usable energy. Plants do not produce energy. A closed system. as in a living cell. it must increase the entropy of the universe. If temperature is uniform. and the system can do no work. such as the rusting of an old car. An exergonic reaction proceeds with a net release of free energy. some energy is converted to heat. one with less free energy. Others are confined within membrane-enclosed eukaryotic organelles. low entropy. Much of the increased entropy of the universe takes the form of increasing heat. the system must either give up enthalpy (decrease in H). Living cells unavoidably convert organized forms of energy to heat. The first law is also known as the principle of conservation of energy. A process is spontaneous and can perform work only when it is moving toward equilibrium. approximated by liquid in a thermos.
visible light passes through the specimen and then through glass lenses. allosteric enzymes control the rates of key reactions in metabolic pathways. Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed. Enzymes speed reactions by lowering EA. binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits. Resolution is limited by the shortest wavelength of the radiation used for imaging. inhibiting their activity by lowering their affinity for substrate. Microscopes vary in magnification and resolving power. ATP and ADP also affect key enzymes in anabolic pathways. If inhibitors bind by weak bonds. the image blurs. In this way. but it would also denature proteins and kill cells.• • • • • • • • • • • • • • • • • • • • • • • • In many cases. Regulatory molecules often bind weakly to an allosteric site. It is the minimum distance two points can be separated and still be distinguished as two separate points. ADP functions as an activator of the same enzymes. Light microscopes can magnify effectively to about 1. Most allosterically regulated enzymes are constructed of two or more polypeptide chains. The minimum resolution of a light microscope is about 200 nanometers (nm). Magnificationis the ratio of an object’s image to its real size. The transition state can then be reached even at moderate temperatures. Binding by these molecules can either inhibit or stimulate enzyme activity. At higher magnifications. ATP binds to several catabolic enzymes allosterically. they determine which chemical processes will occur at any time.000 times the size of the actual specimen. Chapter 7: • • • • • • • • • • • The discovery and early study of cells progressed with the invention of microscopes in 1590 and their improvement in the 17th century. leading to a tighter induced fit that brings chemical groups in position to catalyze the reaction. the size of a small bacterium. In a light microscope (LM). Heat would speed up reactions. As the substrate enters the active site. reactants and products of ATP hydrolysis may play a major role in balancing the flow of traffic between anabolic and catabolic pathways. By binding to key enzymes. If inhibitors attach to the enzyme by covalent bonds. By binding to key enzymes. They hasten reactions that would occur eventually. the pattern of allosteric regulation may shift as well. a specific receptor on the enzyme away from the active site. Allosteric sites are often located where subunits join. Page | 16 . inhibition may be reversible. a process called cooperativity. Because enzymes are so selective. the molecules that naturally regulate enzyme activity behave like reversible noncompetitive inhibitors. The product acts as an inhibitor of an enzyme in the pathway. inhibition may be irreversible. For example. Resolving poweris a measure of image clarity. priming the enzyme to accept additional substrates. reactants and products of ATP hydrolysis may play a major role in balancing the flow of traffic between anabolic and catabolic pathways. Enzymes do not change DG. This mechanism amplifies the response of enzymes to substrates. Each subunit has its own active site. A common method of metabolic control is feedback inhibition in which an early step in a metabolic pathway is switched off by the pathway’s final product. The binding of an activator stabilizes the conformation that has functional active sites. In enzymes with multiple catalytic subunits. As the chemical conditions in the cell shift. The lenses refract light such that the image is magnified into the eye or onto a video screen. interactions between the substrate and the amino acids of the protein causes the enzyme to change shape slightly. while the binding of an inhibitor stabilizes the inactive form of the enzyme.
the study of molecules and chemical processes in metabolism. The homogenate is spun in a centrifuge to separate heavier pieces into the pellet while lighter particles remain in the supernatant. These membrane-bound organelles are absent in prokaryotes. For example. are between 0. gently disrupting the cell. This enables the functions of these organelles to be determined. electron microscopes can only be used on dead cells. Page | 17 . we use an electron microscope (EM). Electron microscopy revealed that this fraction is rich in mitochondria. the nucleus. At the lower limit. In a prokaryotic cell.002 nanometer (nm). electron microscopes (whose electron beams have shorter wavelengths than visible light) have finer resolution. Cell fractionation prepares isolates of specific cell components. to produce modern cell biology. Cytology and biochemistry complement each other in correlating cellular structure and function. the chromosomes are contained within a membranous nuclear envelope. All the material within the plasma membrane of a prokaryotic cell is cytoplasm. smaller and smaller organelles can be collected in subsequent pellets. The result is an image of the topography of the specimen. In a eukaryotic cell. tiny organelles that make proteins using the instructions contained in genes. containing the organelles. chromosomes are contained in a membrane-enclosed organelle. the resolution of a modern EM could reach 0. All cells also have ribosomes. Eukaryotic cells are typically 10–100 microns in diameter. All cells are surrounded by a plasma membrane. These secondary electrons are collected and focused on a screen. All cells contain chromosomes that have genes in the form of DNA. A major difference between prokaryotic and eukaryotic cells is the location of chromosomes. To enhance contrast.000. To resolve smaller structures. Fractionation begins with homogenization. but the practical limit is closer to about 2 nm.• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • Techniques developed in the 20th century have enhanced contrast and enabled particular cell components to be stained or labeled so they stand out. The beam excites electrons on the surface of the sample. The SEM has great depth of field. The semifluid substance within the membrane is the cytosol. but they can be used to study live cells. it cannot resolve much of the internal anatomy. resulting in an image that seems three-dimensional. Microscopes are major tools in cytology. the DNA is concentrated in the nucleoid without a membrane separating it from the rest of the cell.1 to 1. one cellular fraction was enriched in enzymes that function in cellular respiration. especially the organelles.000 g). the study of cell structures. In eukaryote cells. The logistics of carrying out metabolism set limits on cell size. Light microscopes do not have as high a resolution. the thin sections are stained with atoms of heavy metals. Transmission electron microscopes (TEMs)are used mainly to study the internal ultrastructure of cells. While a light microscope can resolve individual cells. Because resolution is inversely related to wavelength used. a machine that can spin at up to 130. The sample surface is covered with a thin film of gold. mycoplasmas. Electron microscopes reveal organelles that are impossible to resolve with the light microscope. Theoretically. However. A TEM aims an electron beam through a thin section of the specimen. This evidence helped cell biologists determine that mitochondria are the site of cellular respiration. Scanning electron microscopes (SEMs)are useful for studying surface structures. Within the cytoplasm of a eukaryotic cell are a variety of membrane-bound organelles of specialized form and function. The goal of cell fractionation is to separate the major organelles of the cells so their individual functions can be studied. This process is driven by an ultracentrifuge.0 micron. The region between the nucleus and the plasma membrane is the cytoplasm.000 revolutions per minute and apply forces of more than 1 million times gravity (1. The image is focused and magnified by electromagnets. which focuses a beam of electrons through the specimen or onto its surface. Most bacteria are 1–10 microns in diameter. especially by the reactions or processes catalyzed by their proteins. the smallest bacteria. Eukaryotic cells are generally much bigger than prokaryotic cells. Cytology combined with biochemistry. As the process is repeated at higher speeds and for longer durations.
are suspended in the cytosol and synthesize proteins that function within the cytosol. the DNA and associated proteins are organized into discrete units called chromosomes. The nuclear side of the envelope is lined by the nuclear lamina. There is evidence that a framework of fibers called the nuclear matrix extends through the nuclear interior. ribosomal RNA (rRNA) is synthesized and assembled with proteins from the cytoplasm to form ribosomal subunits. becoming thick enough to be recognized as the familiar chromosomes. The two membranes of the nuclear envelope are separated by 20–40 nm. Some ribosomes. Cell types that synthesize large quantities of proteins (e. and wastes for the whole volume of the cell. thin projections from the cell surface called microvilli. A protein structure called a pore complex lines each pore. Each eukaryotic species has a characteristic number of chromosomes. The volume of cytoplasm determines the need for this exchange. regulating the passage of certain large macromolecules and particles. Other ribosomes. The need for a surface sufficiently large to accommodate the volume explains the microscopic size of most cells. may have long. pancreas cells) have large numbers of ribosomes and prominent nucleoli. Ribosomes build a cell’s proteins. a complex of proteins and DNA. A human sex cell (egg or sperm) has only 23 chromosomes. The mRNA travels to the cytoplasm through the nuclear pores and combines with ribosomes to translate its genetic message into the primary structure of a specific polypeptide. • • • • • • Ribosomes. the inner and outer membranes of the nuclear envelope are fused to form a continuous membrane. its volume increases faster than its surface area. The envelope is perforated by pores that are about 100 nm in diameter. bound ribosomes. the nucleolus. The nucleus directs protein synthesis by synthesizing messenger RNA (mRNA). Smaller objects have a greater ratio of surface area to volume. where they combine to form ribosomes. Concept 6. Ribosomes can shift between roles depending on the polypeptides they are synthesizing.• • • • • • • • • Metabolic requirements also set an upper limit to the size of a single cell. The nucleus is separated from the cytoplasm by a double membrane called the nuclear envelope. such as intestinal cells. These synthesize proteins that are either included in membranes or exported from the cell.. Microvilli increase surface area without significantly increasing cell volume. a network of protein filaments that maintains the shape of the nucleus. the chromatin fibers coil up and condense. are the organelles that carry out protein synthesis. Each chromosome is made up of fibrous material called chromatin. Cells that exchange a lot of material with their surroundings. structures that carry the genetic information.3 The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes • • • • • • • • • • • • • • • • • • • • • • The nucleus contains most of the genes in a eukaryotic cell. The subunits pass through the nuclear pores to the cytoplasm. Within the nucleus. Stained chromatin appears through light microscopes and electron microscopes as a diffuse mass. nutrients. Concept 6. The plasma membrane functions as a selective barrier that allows the passage of oxygen. In the nucleolus. As the cell prepares to divide.4 The endomembrane system regulates protein traffic and performs metabolic functions in the cell Page | 18 .g. free ribosomes. The nucleus averages about 5 microns in diameter. Rates of chemical exchange across the plasma membrane may be inadequate to maintain a cell with a very large cytoplasm. At the lip of each pore. are attached to the outside of the endoplasmic reticulum or nuclear envelope. A typical human cell has 46 chromosomes. Larger organisms do not generally have larger cells than smaller organisms—simply more cells.containing rRNA and protein. In the nucleus is a region of densely stained fibers and granules adjoining chromatin. Additional genes are located in mitochondria and chloroplasts. As a cell increases in size.
Finally. Frequent use of these drugs leads to the proliferation of smooth ER in liver cells. The membrane of each cisterna separates its internal space from the cytosol. As the ER membrane expands. warehousing. The Golgi apparatus is the shipping and receiving center for cell products. Smooth ER stores calcium ions. and steroids. There are two connected regions of ER that differ in structure and function. products from the ER are usually modified. The Golgi apparatus is a very dynamic structure. molecular composition and types of chemical reactions carried out by proteins in a given membrane may be modified several times during a membrane’s life. Enzymes of smooth ER synthesize lipids. readying the cell for the next stimulation. Enzymes then pump the calcium back. the cis side. The endomembrane system includes the nuclear envelope. carrying and modifying their protein cargo as they move. vacuoles. These membranes are either directly continuous or connected via transfer of vesicles. so higher doses are required to achieve the same effect. In spite of these connections. The thickness. and the cisternal space of the ER is continuous with the space between the two membranes of the nuclear envelope. The Golgi apparatus is especially extensive in cells specialized for secretion. The other side. The smooth ER is rich in enzymes and plays a role in a variety of metabolic processes. Rough ERlooks rough because ribosomes (bound ribosomes) are attached to the outside. triggering contraction.• • • • • Many of the internal membranes in a eukaryotic cell are part of the endomembrane system. These include the sex hormones of vertebrates and adrenal steroids. Rough ER is especially abundant in cells that secrete proteins. fluid-filled spaces called cisternae. When a nerve impulse stimulates a muscle cell. the cisternae of the Golgi progress from the cis to the trans face. phospholipids. lysosomes. endoplasmic reticulum. increasing the rate of detoxification. the new protein folds into its native conformation. and shipping. This increases tolerance to the target and other drugs. the Golgi sorts and packages materials into transport vesicles. sorting. Secretory proteins are packaged in transport vesicles that carry them to their next stage. and the plasma membrane. In the smooth ER of the liver. including pectin and other noncellulose polysaccharides. sacs of membrane. As it enters the cisternal space. According to the cisternal maturation model. Membrane-bound proteins are synthesized directly into the membrane. The ER includes membranous tubules and internal. Muscle cells have a specialized smooth ER that pumps calcium ions from the cytosol and stores them in its cisternal space. Golgi apparatus. Most secretory polypeptides are glycoproteins. buds off vesicles that travel to other sites. Enzymes in the rough ER also synthesize phospholipids from precursors in the cytosol. Smooth ERlooks smooth because it lacks ribosomes. is located near the ER. The endoplasmic reticulum manufactures membranes and performs many other biosynthetic functions. these membranes are diverse in function and structure. it is threaded into the cisternal space through a pore formed by a protein complex in the ER membrane. • • • • • • • • • • • • Many transport vesicles from the ER travel to the Golgi apparatus for modification of their contents. The Golgi apparatus consists of flattened membranous sacs—cisternae—looking like a stack of pita bread. During their transit from the cis to the trans side. As a polypeptide is synthesized on a ribosome attached to rough ER. One side of the Golgi. enzymes help detoxify poisons and drugs such as alcohol and barbiturates. The Golgi is a center of manufacturing. the trans side. The Golgi can also manufacture its own macromolecules. Page | 19 . including oils. • • • • • • • • • • • • • • • • • • • • • • • • • The endoplasmic reticulum (ER) accounts for half the membranes in a eukaryotic cell. calcium ions rush from the ER into the cytosol. The ER membrane is continuous with the nuclear envelope. proteins to which a carbohydrate is attached. The cis face receives material by fusing with transport vesicles from the ER. membrane can be transferred as transport vesicles to other components of the endomembrane system. Rough ER is also a membrane factory. including the outside of the nuclear envelope.
each mitochondrion or chloroplast has two membranes separating the innermost space from the cytosol. monomers pass to the cytosol to become nutrients for the cell. disposing of metabolic byproducts. Chloroplasts. or apoptosis. pump excess water out of the cell to maintain the appropriate concentration of salts. fats. Lysosomes can play a role in recycling of the cell’s organelles and macromolecules. This recycling. These enzymes work best at pH 5. holding pigments. Mitochondriaare the sites of cellular respiration. Vacuoles have diverse functions in cell maintenance. During autophagy.5 Mitochondria and chloroplasts change energy from one form to another • • • • • • Mitochondria and chloroplasts are the organelles that convert energy to forms that cells can use for work. fats. The food vacuole formed by phagocytosis fuses with a lysosome. Food vacuolesare formed by phagocytosis and fuse with lysosomes. The presence of a large vacuole increases surface area to volume ratio for the cell. generating ATP from the catabolism of sugars. Lysosomes are digestive compartments. and storing defensive compounds that defend the plant against herbivores.found in freshwater protists. Contractile vacuoles. Proteins in the lysosomal membrane pump hydrogen ions from the cytosol into the lumen of the lysosomes. Mitochondria and chloroplasts are not part of the endomembrane system. Products are tagged with identifiers such as phosphate groups. A large central vacuole is found in many mature plant cells. Lysosomes carry out intracellular digestion in a variety of circumstances. Lysosomal enzymes and membrane are synthesized by rough ER and then transferred to the Golgi apparatus for further modification. digesting the macromolecules and returning the organic monomers to the cytosol for reuse. and other fuels in the presence of oxygen. is selective in its transport of solutes into the central vacuole.found in plants and algae. a damaged organelle or region of cytosol becomes surrounded by membrane. Page | 20 . • • • • • • • Vesicles and vacuoles (larger versions) are membrane-bound sacs with varied functions. A lysosome fuses with the resulting vesicle. which protect vulnerable bonds from hydrolysis.• • Molecular identification tags are added to products to aid in sorting. are the sites of photosynthesis. These act like ZIP codes on mailing labels to identify the product’s final destination. and nucleic acids. the tonoplast. Lysosomal enzymes can hydrolyze proteins. or autophagy. The functions of the central vacuole include stockpiling proteins or inorganic ions. Rupture of one or a few lysosomes has little impact on a cell because the lysosomal enzymes are not very active at the neutral pH of the cytosol. The membrane surrounding the central vacuole. renews the cell. They convert solar energy to chemical energy and synthesize new organic compounds such as sugars from CO2 and H2O. As the polymers are digested. The lysosomes play a critical role in the programmed destruction of cells in multicellular organisms. Amoebaseat by engulfing smaller organisms by phagocytosis. massive rupture of many lysosomes can destroy a cell by autodigestion. Proteins on the inner surface of the lysosomal membrane are spared by digestion by their three-dimensional conformations. Concept 6. Because of the large vacuole. This important process is called programmed cell death. • • • • • • • • • • • • • • • • • • • • A lysosome is a membrane-bound sac of hydrolytic enzymes that an animal cell uses to digest macromolecules. In contrast to organelles of the endomembrane system. The hands of human embryos are webbed until lysosomes digest the cells in the tissue between the fingers. the cytosol occupies only a thin layer between the plasma membrane and the tonoplast. This process plays an important role in development. polysaccharides. However. whose enzymes digest the food.
A typical mitochondrion is 1–10 microns long. convert the fatty acids in seeds to sugars. Amyloplasts are colorless plastids that store starch in roots and tubers. There may be one very large mitochondrion or hundreds to thousands of individual mitochondria. Chromoplasts store pigments for fruits and flowers. Concept 6. the stroma. changing shape. Inside the innermost membrane is a fluid-filled space. Peroxisomes generate and degrade H2O2 in performing various metabolic functions. Some of the metabolic steps of cellular respiration are catalyzed by enzymes in the matrix. Mitochondria and chloroplasts are mobile and move around the cell along tracks of the cytoskeleton. Chloroplasts contain the green pigment chlorophyll as well as enzymes and other molecules that function in the photosynthetic production of sugar. In some regions. The inner membrane encloses the mitochondrial matrix.6 The cytoskeleton is a network of fibers that organizes structures and activities in the cell • • The cytoskeleton is a network of fibers extending throughout the cytoplasm. which the seedling can use as a source of energy and carbon until it is capable of photosynthesis. Mitochondria are quite dynamic: moving. but rather by free ribosomes in the cytosol and by ribosomes within the organelles themselves. glyoxysomes. a narrow region between the inner and outer membranes. and they can reproduce themselves by pinching in two. The cristae present a large surface area for the enzymes that synthesize ATP. and regulation. Specialized peroxisomes. Almost all eukaryotic cells have mitochondria. Page | 21 . Peroxisomes in the liver detoxify alcohol and other harmful compounds.• • • • • • • • • • • • • • • • • • • • • • • • • • • Their membrane proteins are not made by the ER. and enzymes. the thylakoids. a fluid-filled space with DNA. Mitochondria and chloroplasts grow and reproduce as semiautonomous organelles. Their shape is plastic. thylakoids are stacked like poker chips into grana. Peroxisomes are bound by a single membrane. and the thylakoid space. The stroma contains DNA. The chloroplast is one of several members of a generalized class of plant structures called plastids. The thylakoids are flattened sacs that play a critical role in converting light to chemical energy. chloroplasts are dynamic structures. The number of mitochondria is correlated with aerobic metabolic activity. ribosomes. but by incorporation of proteins and lipids from the cytosol. motility. They split in two when they reach a certain size. The membranes of the chloroplast divide the chloroplast into three compartments: the intermembrane space. They form not from the endomembrane system. and enzymes. Like mitochondria. The first is the intermembrane space. • • • • • • • • • Peroxisomes contain enzymes that transfer hydrogen from various substrates to oxygen. The cytoskeleton provides support. a poison. Some peroxisomes break fatty acids down to smaller molecules that are transported to mitochondria as fuel for cellular respiration. and dividing. ribosomes. The cytoskeleton organizes the structures and activities of the cell. The contents of the chloroplast are separated from the cytosol by an envelope consisting of two membranes separated by a narrow intermembrane space. the stroma. Both organelles have small quantities of DNA that direct the synthesis of the polypeptides produced by these internal ribosomes. The inner membrane divides the mitochondrion into two internal compartments. The peroxisome contains an enzyme that converts H2O2 to water. in which float membranous sacs. Mitochondria have a smooth outer membrane and a convoluted inner membrane with infoldings called cristae. Chloroplasts measure about 2 microns × 5 microns and are found in leaves and other green organs of plants and algae. An intermediate product of this process is hydrogen peroxide (H2O2).
A specialized arrangement of microtubules is responsible for the beating of cilia and flagella. dynein. Microfilaments can form structural networks due to their ability to branch. both cilia and flagella have the same ultrastructure. Each microfilament is built as a twisted double chain of actin subunits. move. There are three main types of fibers making up the cytoskeleton: microtubules. The cytoskeleton provides anchorage for many organelles and cytosolic enzymes. resisting pulling forces within the cell. bending the cilium or flagellum. and release the outer microtubules. A microtubule changes in length by adding or removing tubulin dimers. Cilia and flagella differ in their beating patterns. Microfilamentsare solid rods about 7 nm in diameter. Cilia or flagella can extend from cells within a tissue layer. Protein cross-links limit sliding. The bending of cilia and flagella is driven by the arms of a motor protein. and intermediate filaments. cilia lining the windpipe sweep mucus carrying trapped debris out of the lungs. Both have a core of microtubules sheathed by the plasma membrane. beating to move fluid over the surface of the tissue. In many cells. whose structure is identical to a centriole. Each tubulin molecule is a dimer consisting of two subunits. the centrioles replicate. Microtubules shape and support the cell and serve as tracks to guide motor proteins carrying organelles to their destination. Nine doublets of microtubules are arranged in a ring around a pair at the center. Page | 22 .25 microns in diameter and 2–20 microns long. vesicles can travel along “monorails” provided by the cytoskeleton.the thickest fibers. Cilia move more like oars with alternating power and recovery strokes that generate force perpendicular to the cilium’s axis. Addition and removal of a phosphate group causes conformation changes in dynein. There are usually just one or a few flagella per cell. A flagellum has an undulatory movement that generates force in the same direction as the flagellum’s axis. each with nine triplets of microtubules arranged in a ring. As a result. Recently. the centrosome has a pair of centrioles.• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • The cytoskeleton provides mechanical support and maintains cell shape. Inside the cell. Before a cell divides. This “9 + 2” pattern is found in nearly all eukaryotic cilia and flagella. Dynein arms alternately grab. They are about 0. are hollow rods about 25 microns in diameter and 200 nm to 25 microns in length. Cytoplasmic streaming in plant cells is caused by the cytoskeleton. The cytoskeleton also plays a major role in cell motility. but 10–200 microns long. The cytoskeleton manipulates the plasma membrane to form food vacuoles during phagocytosis. The cytoskeleton is dynamic and can be dismantled in one part and reassembled in another to change the shape of the cell. These microtubules resist compression to the cell. Microtubule fibers are constructed of the globular protein tubulin. The same mechanism causes muscle cells to contract. The cytoskeleton interacts with motor proteins to produce motility. In spite of their differences. including changes in cell location and limited movements of parts of the cell. microtubules grow out from a centrosome near the nucleus. For example. Microtubules. Many unicellular eukaryotic organisms are propelled through water by cilia and flagella. The cilium or flagellum is anchored in the cell by a basal body. The outer doublets are also connected by motor proteins. The structural role of microfilaments in the cytoskeleton is to bear tension. the forces exerted by the dynein arms cause the doublets to curve. Cytoskeleton elements and motor proteins work together with plasma membrane molecules to move the whole cell along fibers outside the cell. Motor proteins bring about movements of cilia and flagella by gripping cytoskeletal components such as microtubules and moving them past each other. Microtubules are also responsible for the separation of chromosomes during cell division. In animal cells. Flexible “wheels” of proteins connect outer doublets to each other and to the two central microtubules. Cilia usually occur in large numbers on the cell surface. evidence suggests that the cytoskeleton may play a role in the regulation of biochemical activities in the cell. microfilaments. Flagella are the same width as cilia.
giving the cell cortex the semisolid consistency of a gel. In plant cells. Intermediate filaments are specialized for bearing tension. The extracellular matrix (ECM) of animal cells functions in support. Pseudopodia. Intermediate filaments are more permanent fixtures of the cytoskeleton than are the other two classes. and some protists. especially as part of the contractile apparatus of muscle cells. the cell wall protects the cell. causing contraction. This is the basic design of steel-reinforced concrete or fiberglass. Localized contraction brought about by actin and myosin also drives amoeboid movement. In plants. Concept 6.7 Extracellular components and connections between cells help coordinate cellular activities Plant cells are encased by cell walls. has multiple functions. Page | 23 . According to a widely accepted model. maintains its shape. fibronectins in the ECM connect to integrins. In many cells. It also supports the plant against the force of gravity.cellular extensions. thousands of actin filaments are arranged parallel to one another. built from a family of proteins called keratins. extend and contract through the reversible assembly and contraction of actin subunits into microfilaments. Intermediate filaments are a diverse class of cytoskeletal units. found in prokaryotes. The thickness and chemical composition of cell walls differs from species to species and among cell types within a plant. Microfilaments are important in cell motility. and regulation. Myosin molecules act as motor proteins. Embryonic cells migrate along specific pathways by matching the orientation of their microfilaments to the “grain” of fibers in the extracellular matrix. intrinsic membrane proteins that span the membrane and bind on their cytoplasmic side to proteins attached to microfilaments of the cytoskeleton. • • • • • • • The cell wall. The interconnections from the ECM to the cytoskeleton via the fibronectin-integrin link permit the integration of changes inside and outside the cell. movement. speeding the distribution of materials within the cell. In other cells. Plant cell walls are perforated by channels between adjacent cells called plasmodesmata. The contraction forces the interior fluid into the pseudopodium. In muscle cells. a middle lamella with sticky polysaccharides that holds cells together.• • • • • • • • • • • • • • • • • • • • They form a three-dimensional network just inside the plasma membrane to help support the cell’s shape. Intermediate filamentsrange in diameter from 8–12 nanometers. • • • • • • • • Though lacking cell walls. walking along the actin filaments to shorten the cell. larger than microfilaments but smaller than microtubules. filaments near the cell’s trailing edge interact with myosin. where the actin network has been weakened. Microfilaments assemble into networks that convert sol to gel. actin-myosin interactions and sol-gel transformations drive cytoplasmic streaming. Thicker filaments composed of myosin interdigitate with the thinner actin fibers. adhesion. This may coordinate the behavior of all the cells within a tissue. and layers of secondary cell wall. The primary constituents of the extracellular matrix are glycoproteins. especially collagen fibers. This creates a circular flow of cytoplasm in the cell. embedded in a network of glycoprotein proteoglycans. The extracellular matrix can influence the activity of genes in the nucleus via a combination of chemical and mechanical signaling pathways. fungi. The basic design consists of microfibrils of cellulose embedded in a matrix of proteins and other polysaccharides. They reinforce cell shape and fix organelle location. A mature cell wall consists of a primary cell wall. The pseudopodium extends until the actin reassembles into a network. A contracting belt of microfilaments divides the cytoplasm of animal cells during cell division. and prevents excessive uptake of water. The ECM can regulate cell behavior. animal cells do have an elaborate extracellular matrix (ECM). actin-myosin aggregates are less organized but still cause localized contraction.
appearance when stained. channels allowing cytosol to pass between cells. Where integral proteins are in contact with the aqueous environment. J. much like rivets. Instead. often completely spanning the membrane (as transmembrane proteins). The hydrophobic regions embedded in the membrane’s core consist of stretches of nonpolar amino acids. Membrane fluidity is influenced by temperature. Cells can alter the lipid composition of membranes to compensate for changes in fluidity caused by changing temperatures. There are two major populations of membrane proteins. protein particles are interspersed in a smooth matrix. Animals have 3 main types of intercellular links: tight junctions. • • • • • • • • • A membrane is a collage of different proteins embedded in the fluid matrix of the lipid bilayer. Special membrane proteins surround these pores. Singer and G. Membranes differ in thickness. cholesterol restrains the movement of phospholipids and reduces fluidity. it maintains fluidity by preventing tight packing. Page | 24 . This prevents leakage of extracellular fluid. If membrane proteins were at the membrane surface. Integral proteinspenetrate the hydrophobic core of the lipid bilayer. organs. measurements showed that membrane proteins are not very soluble in water. Thus. and the hydrophobic regions are in a nonaqueous environment within the membrane. and communicate through direct physical contact. the hydrophilic regions of proteins and phospholipids are in maximum contact with water. At cool temperatures. In certain circumstances. Intermediate filaments of keratin reinforce desmosomes. not all membranes were alike. Proteins determine most of the membrane’s specific functions. Membranes with different functions differ in chemical composition and structure. gap junctions facilitate chemical communication during development. often connected to integral proteins. resisting changes in membrane fluidity as temperature changes. they are loosely bound to the surface of the protein. Desmosomes(or anchoring junctions) fasten cells together into strong sheets. At warm temperatures (such as 37°C). forming continuous belts around cells. desmosomes. and gap junctions. freeze-fracture. and other small molecules can pass. This prevents membranes from solidifying during winter. membranes switch from a fluid state to a solid state as the phospholipids pack more closely. Plant cells are perforated with plasmodesmata. In this fluid mosaic model. A specialized preparation technique. with hydrophobic and hydrophilic regions. The plasma membrane and the membranes of the various organelles each have unique collections of proteins. Other proteins never move and are anchored to the cytoskeleton. Ions. Membrane fluidity is also influenced by its components. cholesterol acts as a “temperature buffer” for the membrane. First. splits a membrane along the middle of the phospholipid bilayer.Intercellular junctions help integrate cells into higher levels of structure and function. The steroid cholesterol is wedged between phospholipid molecules in the plasma membrane of animal cells. For example. proteins and RNA can be exchanged. Membranes rich in unsaturated fatty acids are more fluid that those dominated by saturated fatty acids because the kinks in the unsaturated fatty acid tails at the locations of the double bonds prevent tight packing. When a freeze-fracture preparation is viewed with an electron microscope. amino acids. interact. As temperatures cool. Second. To work properly with active enzymes and appropriate permeability. Nicolson presented a revised model that proposed that the membrane proteins are dispersed and individually inserted into the phospholipid bilayer. sugars. Membrane proteins are amphipathic. Water and small solutes can pass freely from cell to cell. membranes of adjacent cells are fused. In embryos. In tight junctions. or organ systems often adhere. and percentage of proteins. Peripheral proteinsare not embedded in the lipid bilayer at all. supporting the fluid mosaic model. Gap junctions(or communicating junctions) provide cytoplasmic channels between adjacent cells. In 1972. S. their hydrophobic regions would be in contact with water. often coiled into alpha helices. membranes must be about as fluid as salad oil. • • • • • • • • • • • • • Chapter 8: Neighboring cells in tissues. cold-adapted organisms such as winter wheat increase the percentage of unsaturated phospholipids in their membranes in the autumn. they have hydrophilic regions of amino acids.
leaving fewer unbound water molecules. fungi. The solution with the lower concentration of solutes is hypotonic relative to the other solution. Solutions with equal solute concentrations are isotonic. to maintain their internal environment. to the hypertonic solution. On the exterior side of the membrane. Intercellular joining of adjacent cells with gap or tight junctions.maintaining cell shape and stabilizing the location of certain membrane proteins. and probably die. For example. The same cell in a hypertonic environment will lose water. • • • • • • • • • • • • • • • • An animal cell (or other cell without a cell wall) immersed in an isotonic environment experiences no net movement of water across its plasma membrane. the contractile vacuole. but not sugar. and the plant may wilt. The proteins of the plasma membrane have six major functions: Transport of specific solutes into or out of cells. More of the water molecules in the hypertonic solution are bound up in hydration shells around the sugar molecules. Turgid cells contribute to the mechanical support of the plant. there is no movement of water into the cell. where they are abundant. some membrane proteins connect to the cytoskeleton. relaying hormonal messages to the cell. When two solutions are isotonic. prokaryotes.• • • • • • • • • • • • • • • • • • • • • • • • • On the cytoplasmic side of the membrane. where they are rarer. Signal transduction. Paramecium cells have a specialized organelle. Attachment to the cytoskeleton and extracellular matrix. If a plant cell and its surroundings are isotonic. At this point the cell is turgid (very firm). The diffusion of water across a selectively permeable membrane is called osmosis. water still continually enters the Paramecium cell. This makes sense because the total solute concentration is an indicator of the abundance of bound water molecules (and. A plant cell in a hypotonic solution will swell until the elastic cell wall opposes further uptake. The kinds of solutes in the solutions do not matter. Enzymatic activity. Net movement of water continues until the solutions are isotonic. The cells of plants. and burst. Water molecules move across the membrane but at the same rate in both directions. which functions as a bilge pump to force water out of the cell. Tap water is hypertonic compared to distilled water but hypotonic compared to seawater. many marine invertebrates). The movement of water by osmosis is crucial to living organisms. and some protists have walls that contribute to the cell’s water balance. the control of water balance. is hypertonic to the pond water in which it lives. The solution with the higher concentration of solutes is hypertonic relative to the other solution. of free water molecules). Unbound water molecules will move from the hypotonic solution. The hypertonic solution has a lower water concentration than the hypotonic solution. For organisms living in an isotonic environment (for example. Differences in the relative concentration of dissolved materials in two solutions can lead to the movement of ions from one to the other. The volume of the cell is stable. a healthy state for most plant cells. Page | 25 . A cell in a hypotonic solution will gain water. shrivel. In spite of a cell membrane that is less permeable to water than other cells. The cells of most land animals are bathed in extracellular fluid that is isotonic to the cells. with no net osmosis. osmosis is not a problem. therefore. allowing other proteins to attach two adjacent cells together. swell. Imagine that two sugar solutions differing in concentration are separated by a membrane that will allow water through. Paramecium. The cell becomes flaccid (limp). To solve this problem. Cell-cell recognition. These are comparative terms. a protist. sometimes catalyzing one of a number of steps of a metabolic pathway. water molecules move at equal rates from one to the other. some membrane proteins attach to the fibers of the extracellular matrix. Cell survival depends on balancing water uptake and loss. The direction of osmosis is determined only by a difference in total solute concentration. Organisms without rigid walls have osmotic problems in either a hypertonic or hypotonic environment and must have adaptations for osmoregulation.
Cystinuria is a human disease characterized by the absence of a protein that transports cysteine and other amino acids across the membranes of kidney cells. For example. its volume shrinks. Na + Cl àNa+ + Cl− Here sodium is oxidized and chlorine is reduced (its charge drops from 0 to −1). Redox reactions require both a donor and acceptor. In the combustion of methane to form water and carbon dioxide. the channels are closed. stimulation of a receiving neuron by specific neurotransmitters opens gated channels to allow sodium ions into the cell. For example. the electron recipient. If chemical. An individual with cystinuria develops painful kidney stones as amino acids accumulate and crystallize in the kidneys. releases chemical energy that can do work. the electrons of the covalent bonds are drawn closer to the oxygen. Reactions that result in the transfer of one or more electrons from one reactant to another are oxidation-reduction reactions. aquaporins. Redox reactions also occur when the transfer of electrons is not complete but involves a change in the degree of electron sharing in covalent bonds. In effect. A redox reaction that relocates electrons closer to oxygen. • • • • • • • • • • • • • • Chapter 9: Many polar molecules and ions that are normally impeded by the lipid bilayer of the membrane diffuse passively with the help of transport proteins that span the membrane. such as the burning of methane. When oxygen reacts with the hydrogen from methane to form water. The passive movement of molecules down their concentration gradient via transport proteins is called facilitated diffusion. This plasmolysis is usually lethal. The loss of electrons is called oxidation. Page | 26 . When the neurotransmitters are not present. the electron donor. releasing energy that is used to synthesize ATP. Some channel proteins simply provide hydrophilic corridors for the passage of specific molecules or ions. More generally: Xe− + Y àX + Ye− X. and so the oxygen molecule has been reduced. Y. These channels open or close depending on the presence or absence of a chemical or physical stimulus. Two types of transport proteins facilitate the movement of molecules or ions across membranes: channel proteins and carrier proteins. In certain inherited diseases. electrons end up farther away from the carbon atom and closer to their new covalent partners. the nonpolar covalent bonds of methane (C—H) and oxygen (O=O) are converted to polar covalent bonds (C=O and O—H). the oxygen atoms. and is one of the most potent of all oxidizing agents. When methane reacts with oxygen to form carbon dioxide. is the oxidizing agent and oxidizes X. As the plant cell loses water. Redox reactions release energy when electrons move closer to electronegative atoms. each oxygen atom has partially “gained” electrons.• The cell wall provides no advantages when a plant cell is immersed in a hypertonic solution. Oxygen is very electronegative. • • • • • • • • • • • • • • • • • • • • • • Catabolic pathways transfer the electrons stored in food molecules. is the reducing agent and reduces Y. These shape changes may be triggered by the binding and release of the transported molecule. Some transport proteins do not provide channels but appear to actually translocate the solute-binding site and solute across the membrane as the transport protein changes shape. water channel proteins. Specific proteins facilitate passive transport of water and selected solutes. greatly facilitate the diffusion of water. Manyion channels function as gated channels. Thus. Eventually. specific transport systems may be defective or absent. or redox reactions. The addition of electrons is called reduction. the plasma membrane pulls away from the wall. which are very electronegative. The formation of table salt from sodium and chloride is a redox reaction. The two atoms of the oxygen molecule share their electrons equally. Energy must be added to pull an electron away from an atom. In effect. the stimulus is a substance other than the one to be transported. The more electronegative the atom. the more energy is required to take an electron away from it. An electron loses potential energy when it shifts from a less electronegative atom toward a more electronegative one. the carbon atom has partially “lost” its shared electrons. methane has been oxidized.
The citric acid cycle is also called the Krebs cycle in honor of Hans Krebs. the cell invests ATP to provide activation energy by phosphorylating glucose. The next seven steps decompose the citrate back to oxaloacetate. Each oxygen atom also picks up a pair of hydrogen ions from the aqueous solution to form water. ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by electrons released by the oxidation of glucose. The folding of the cristae increases its surface area. Its function is to break the large free energy drop from food to oxygen into a series of smaller steps that release energy in manageable amounts. The last cytochrome of the chain. the folded inner membrane of the mitochondrion. The prosthetic group of each cytochrome is a heme group with an iron atom that accepts and donates electrons. Page | 27 . The remaining two-carbon fragment is oxidized to form acetate. the only ATP generated directly by the citric acid cycle. providing space for thousands of copies of the chain in each mitochondrion. If oxygen is present. The cycle generates one ATP per turn by substrate-level phosphorylation. forming citrate. Acetate combines with coenzyme A to form the very reactive molecule acetyl CoA.• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • During glycolysis. Three CO2 molecules are released. The electron transport chain provides about one-third less energy for ATP synthesis when the electron donor is FADH2 rather than NADH. Each component of the chain becomes reduced when it accepts electrons from its “uphill” neighbor. Glycolysis can occur whether O2 is present or not. In the energy investment phase. who was largely responsible for elucidating its pathways in the 1930s. which is very electronegative. More than three-quarters of the original energy in glucose is still present in the two molecules of pyruvate. The electron transport chain is a collection of molecules embedded in the cristae. one O2 molecule is reduced to two molecules of water. a flavoprotein. it is converted to a compound called acetyl coenzyme A or acetyl CoA. The net yield from glycolysis is 2 ATP and 2 NADH per glucose. Electrons drop in free energy as they pass down the electron transport chain. Each cycle produces one ATP by substrate-level phosphorylation. Acetyl CoA is now ready to feed its acetyl group into the citric acid cycle for further oxidation. The electrons continue along the chain that includes several cytochrome proteins and one lipid carrier. No CO2 is produced during glycolysis. including the one released during the conversion of pyruvate to acetyl CoA. nonprotein components essential for catalysis. The electron transport chain generates no ATP directly. the ionized form of pyruvic acid. a six carbon-sugar. These smaller sugars are oxidized and rearranged to form two molecules of pyruvate. These reduced coenzymes link glycolysis and the citric acid cycle to oxidative phosphorylation. An enzyme transfers the pair of electrons to NAD+ to form NADH. Electrons carried by NADH are transferred to the first molecule in the electron transport chain. A GTP molecule is formed by substrate-level phosphorylation. Each of the ten steps in glycolysis is catalyzed by a specific enzyme. After pyruvate enters the mitochondrion via active transport. glucose. How does the mitochondrion couple electron transport and energy release to ATP synthesis? The answer is a mechanism called chemiosmosis. The citric acid cycle oxidizes organic fuel derived from pyruvate. cyt a3. It then returns to its oxidized form as it passes electrons to its more electronegative “downhill” neighbor. For every two electron carriers (four electrons). During electron transport along the chain. NADH and FADH2 account for the vast majority of the energy extracted from the food. The citric acid cycle has eight steps. passes its electrons to oxygen. Most of the chemical energy is transferred to NAD+ and FAD during the redox reactions. and one FADH2 per acetyl CoA. These steps can be divided into two phases: an energy investment phase and an energy payoff phase. which uses energy released by the electron transport chain to power ATP synthesis. pyruvate enters the mitochondrion where enzymes of the citric acid cycle complete the oxidation of the organic fuel to carbon dioxide. The reduced coenzymes NADH and FADH2 then transfer high-energy electrons to the electron transport chain. The acetyl group of acetyl CoA joins the cycle by combining with the compound oxaloacetate. It is the regeneration of oxaloacetate that makes this process a cycle. The GTP is then used to synthesize an ATP. three NADH. Most components of the chain are proteins bound to prosthetic groups. electron carriers alternate between reduced and oxidized states as they accept and donate electrons. which is less electronegative. This step is accomplished by a multienzyme complex that catalyzes three reactions: A carboxyl group is removed as CO2. This requires 2 ATP per glucose. each catalyzed by a specific enzyme. In the energy payoff phase. The electrons carried by FADH2 have lower free energy and are added at a lower energy level than those carried by NADH. is split into two three-carbon sugars.
causing the rotor and its attached rod to rotate. The most important segment for life is a narrow band between 380 to 750 nm. ATP uses the energy of an existing proton gradient to power ATP synthesis. Photons with shorter wavelengths pack more energy. The gradient has the capacity to do work. A knob that protrudes into the mitochondrial matrix. but light drives the electron flow down an electron transport chain and H+ gradient formation. the band of visible light. processes that together constitute oxidative phosphorylation. The amount of energy packaged in a photon is inversely related to its wavelength. The quantity of energy in ATP is more appropriate for the level of work required in the cell. ATP synthase is a multisubunit complex with four main parts. In mitochondria. From studying the structure of ATP synthase. Respiration uses the small steps in the respiratory pathway to break the large denomination of energy contained in glucose into the small change of ATP. At certain steps along the chain. The entire range of electromagnetic radiation is the electromagnetic spectrum. Here an enzyme transfers a phosphate group from an organic substrate to ADP. The H+ has a tendency to diffuse down its gradient. The proton gradient develops between the intermembrane space and the matrix. scientists have learned how the flow of H+ through this large enzyme powers ATP generation. The spinning rod causes conformational changes in the stationary knob. The proton gradient is produced by the movement of electrons along the electron transport chain. The chain is an energy converter that uses the exergonic flow of electrons to pump H+ from the matrix into the intermembrane space. the cell makes up to 38 ATP. Chemiosmosis is an energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular work. While light travels as a wave. Photons are not tangible objects. each made up of multiple polypeptides: A rotor in the inner mitochondrial membrane. activating three catalytic sites in the knob where ADP and inorganic phosphate combine to make ATP. A stator. Page | 28 . The electron carriers are spatially arranged in the membrane in such a way that protons are accepted from the mitochondrial matrix and deposited in the intermembrane space. which holds the knob stationary. the energy stored in a H+ gradient across a membrane couples the redox reactions of the electron transport chain to ATP synthesis. How does the electron transport chain pump protons? Certain members of the electron transport chain accept and release H+ along with electrons. For each molecule of glucose degraded to carbon dioxide and water by respiration. but also to pump nutrients and waste products across the membrane and to rotate their flagella. and ATP synthesis is the work performed. Oxidative phosphorylation produces almost 90% of the ATP generated by respiration. in the cristae actually makes ATP from ADP and Pi. The H+ gradient that results is the proton-motive force. Light is a form of electromagnetic radiation. ATP synthase. using the exergonic flow of H+ to drive the phosphorylation of ADP. The distance between crests of electromagnetic waves is called the wavelength. This coupling of the redox reactions of the electron transport chain to ATP synthesis is called chemiosmosis. Like other forms of electromagnetic energy. The ETC is an energy converter that uses the exergonic flow of electrons to pump H+ across the membrane from the mitochondrial matrix to the intermembrane space. Chapter 10: The thylakoids convert light energy into the chemical energy of ATP and NADPH. each with 7. light travels in rhythmic waves. the energy for proton gradient formation comes from exergonic redox reactions. anchored next to the rotor. The protons pass back to the matrix through a channel in ATP synthase. Some ATP is also formed directly during glycolysis and the citric acid cycle by substrate-level phosphorylation. An internal rod extending from the rotor into the knob.3 kcal/mol of free energy. A protein complex. The exergonic flow of H+ is used by the enzyme to generate ATP. Wavelengths of electromagnetic radiation range from less than a nanometer (gamma rays) to more than a kilometer (radio waves). The ATP synthase molecules are the only place that H+ can diffuse back to the matrix. Chemiosmosis in chloroplasts also generates ATP. many of its properties are those of a discrete particle. Protons flow down a narrow space between the stator and rotor. They can use this proton-motive force not only to generate ATP. How does the inner mitochondrial membrane generate and maintain the H+ gradient that drives ATP synthesis in the ATP synthase protein complex? Creating the H+ gradient is the function of the electron transport chain. but they do have fixed quantities of energy. forming ATP. Thus. electron transfers cause H+ to be taken up and released into the surrounding solution. The inner membrane of the mitochondrion is the site of electron transport and chemiosmosis. Prokaryotes generate H+ gradients across their plasma membrane. the photon.
the Calvin cycle in most plants occurs during daylight. Their photosynthetic membranes arise from infolded regions of the plasma membranes. but only with the help of ATP and NADPH from the light reactions. The metabolic steps of the Calvin cycle are sometimes referred to as the light-independent reactions. Page | 29 . in a process called photophosphorylation. which accepts an excited electron from the reaction center chlorophyll a. An absorption spectrum plots a pigment’s light absorption versus wavelength. the stroma. In the light reactions. There are two types of photosystems in the thylakoid membrane. the thylakoid space. transmitted. and carotenoid molecules) bound to particular proteins. The fixed carbon is reduced with electrons provided by NADPH. it may be reflected. At the reaction center is a primary electron acceptor. Thus. folded in a manner similar to the thylakoid membranes of chloroplasts. Together. There are about half a million chloroplasts per square millimeter of leaf surface. A spectrophotometer measures the ability of a pigment to absorb various wavelengths of light. while transmitting and reflecting green light. these light-harvesting complexes act like light-gathering “antenna complexes” for the reaction center. it is transmitted from molecule to molecule until it reaches a particular chlorophyll a molecule. Chlorophyll is located in the thylakoids. In the stroma is an elaborate system of interconnected membranous sacs. Different pigments absorb photons of different wavelengths. Chloroplasts are found mainly in mesophyll cells forming the tissues in the interior of the leaf. chlorophyll is organized along with proteins and smaller organic molecules into photosystems. an electron acceptor. forming NADPH. Veins deliver water from the roots and carry off sugar from mesophyll cells to nonphotosynthetic areas of the plant. The Calvin cycle is named for Melvin Calvin who. The solar-powered transfer of an electron from a special chlorophyll a molecule to the primary electron acceptor is the first step of the light reactions. each about 2–4 microns by 4–7 microns long. the reaction center. The cycle begins with the incorporation of CO2 into organic molecules. O2 exits and CO2 enters the leaf through microscopic pores called stomata in the leaf. with his colleagues. Nevertheless. and O2 is released as a by-product. Photosystem I (PS I)has a reaction center chlorophyll a that has an absorption peak at 700 nm. a process known as carbon fixation. While the sun radiates a full electromagnetic spectrum. the dominant pigment. Thylakoids may be stacked into columns called grana. The color of a leaf comes from chlorophyll. Each light-harvesting complex consists of pigment molecules (which may include chlorophyll a. Each photosystem—reaction-center chlorophyll and primary electron acceptor surrounded by an antenna complex—functions in the chloroplast as a light-harvesting unit. When light meets matter. Thus light energy is initially converted to chemical energy in the form of two compounds: NADPH and ATP. In the thylakoid membrane. permitting only visible light to pass in significant quantities. When any antenna molecule absorbs a photon. it is the Calvin cycle that makes sugar. Visible light is the radiation that drives photosynthesis. Photosynthetic prokaryotes lack chloroplasts. provides reducing power via energized electrons to the Calvin cycle. The differences between these reaction centers (and their absorption spectra) lie not in the chlorophyll molecules. It beams narrow wavelengths of light through a solution containing the pigment and measures the fraction of light transmitted at each wavelength. ATP from the light reactions also powers parts of the Calvin cycle. the atmosphere selectively screens out most wavelengths. but in the proteins associated with each reaction center. The light reactions (photo) convert solar energy to chemical energy. NADPH. chlorophyll b. A photosystem is composed of a reaction center surrounded by a light-harvesting complex. the thylakoids. Water is split in the process. The interior of the thylakoids forms another compartment. The light reaction can perform work with those wavelengths of light that are absorbed. Photosystem II (PS II)has a reaction center chlorophyll a that has an absorption peak at 680 nm. because that is when the light reactions can provide the NADPH and ATP the Calvin cycle requires. The light reaction also generates ATP using chemiosmosis. because none of the steps requires light directly. light energy absorbed by chlorophyll in the thylakoids drives the transfer of electrons and hydrogen from water to NADP+ (nicotinamide adenine dinucleotide phosphate). A typical mesophyll cell has 30–40 chloroplasts. the green pigment in the chloroplasts. A leaf looks green because chlorophyll. Each chloroplast has two membranes around a central aqueous space. absorbs red and blue light. worked out many of its steps in the 1940s. Chlorophyll plays an important role in the absorption of light energy during photosynthesis. or absorbed. The Calvin cycle (synthesis) uses energy from the light reactions to incorporate CO2 from the atmosphere into sugar. and the wavelengths that are absorbed disappear. These two photosystems work together to use light energy to generate ATP and NADPH.
Page | 30 . C4 photosynthesis minimizes photorespiration and enhances sugar production. In fact. rubisco can add O2 to RuBP. The Calvin cycle is confined to the chloroplasts of the bundle-sheath cells. photorespiration does not produce organic molecules. Bundle-sheath cellsare arranged into tightly packed sheaths around the veins of the leaf. CO2 levels drop as CO2 is consumed in the Calvin cycle. In C4 plants. dry days when the stomata are closed). The stomata are not only the major route for gas exchange (CO2 in and O2 out). photorespiration decreases photosynthetic output by siphoning organic material from the Calvin cycle. this process produces no ATP. Photorespiration can drain away as much as 50% of the carbon fixed by the Calvin cycle on a hot. pineapples. and CO2 is released from the organic acids. PEP carboxylasehas a very high affinity for CO2 and can fix CO2 efficiently when rubisco cannot (i. these plants fix CO2 into a variety of organic acids in mesophyll cells. They open their stomata during the night and close them during the day. These plants are known as CAM plants for crassulacean acid metabolism. The two-carbon fragment is exported from the chloroplast and degraded to CO2 by mitochondria and peroxisomes. phosphoenolpyruvate carboxylase. C4 plants thrive in hot regions with intense sunlight. C3 plants include rice. cacti. Unlike photosynthesis. on hot. Both C4 and CAM plants add CO2 into organic intermediates before it enters the Calvin cycle. The mesophyll cells pump these four-carbon compounds into bundle-sheath cells. and humidity is higher. In most plants (C3 plants). keeping CO2 levels high enough for rubisco to accept CO2 and not O2. This causes problems for photosynthesis. and several other plant families. dry day with closed stomata). During the day. wheat. dry days. but also for the evaporative loss of water. O2 levels rise as the light reaction converts light to chemical energy. RuBP splits into a three-carbon piece and a two-carbon piece in a process called photorespiration. C4 plantsfirst fix CO2 in a four-carbon compound. When their stomata partially close on a hot. Temperatures are typically lower at night. Several thousand plants. A second strategy to minimize photorespiration is found in succulent plants. dry day. 3-phosphoglycerate. The inability of the active site of rubisco to exclude O2 would have made little difference. Unlike normal respiration. plants close their stomata to conserve water. the light reactions supply ATP and NADPH to the Calvin cycle. When rubisco first evolved. • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • One of the major problems facing terrestrial plants is dehydration. the Calvin cycle occurs in the stroma. In C4 plants. and return the three-carbon remainder to the mesophyll cells. In CAM plants. During the night. In fact. At the same time. Today it does make a difference. The key enzyme. the mesophyll cells pump CO2 into the bundle-sheath cells. solutions to this problem require tradeoffs with other metabolic processes. The bundle-sheath cells then use rubisco to start the Calvin cycle with an abundant supply of CO2. carbon fixation and the Calvin cycle are spatially separated.e. adds CO2 to phosphoenolpyruvate (PEP) to form oxaloacetate. dry day. when the O2:CO2 ratio increases (on a hot. Certain plant species have evolved alternate modes of carbon fixation to minimize photorespiration. initial fixation of CO2 occurs via rubisco. and soybeans.. including sugarcane and corn. While the light reactions occur at the thylakoids. In effect. the cycle is preceded by the incorporation of CO2 into organic molecules in the mesophyll. carbon fixation and the Calvin cycle are temporally separated. use this pathway. At times. forming a three-carbon compound. However. A unique leaf anatomy is correlated with the mechanism of C4 photosynthesis. there are two distinct types of photosynthetic cells: bundle-sheath cells and mesophyll cells. The bundle-sheath cells strip a carbon from the four-carbon compound as CO2. When rubisco adds O2 to RuBP. A hypothesis for the existence of photorespiration is that it is evolutionary baggage. especially photosynthesis. On hot. the atmosphere had far less O2 and more CO2 than it does today. Both eventually use the Calvin cycle to make sugar from carbon dioxide. photorespiration consumes ATP. Mesophyll cellsare more loosely arranged cells located between the bundle sheath and the leaf surface. While rubisco normally accepts CO2.
In transduction. Page | 31 . The whole system can be shut down quickly when the extracellular signal molecule is no longer present. The activated enzyme triggers the next step in a pathway leading to a cellular response. However. A G-protein-linked receptor consists of a receptor protein associated with a G protein on the cytoplasmic side. and response. If GDP is bound to the G protein. Similarities among G proteins and G-protein-linked receptors of modern organisms suggest that this signaling system evolved very early. The molecules in the pathway are called relay molecules. Sutherland’s research team discovered that epinephrine activated a cytosolic enzyme. the G protein binds GTP (instead of GDP) and becomes active. Ligands bind to two receptors. Now inactive. transduction. each of which then adds phosphate from ATP to the tyrosine tail of the other polypeptide. transduction. and neurotransmitters. This change turns the G protein off. Sutherland and his colleagues pioneered our understanding of cell signaling. epinephrine and many other hormones. A single alpha helix spanning the membrane. A kinase is an enzyme that catalyzes the transfer of phosphate groups. the G protein leaves the enzyme. Bacterial infections causing cholera and botulism interfere with G-protein function. One tyrosine-kinase receptor dimer may activate ten or more different intracellular proteins simultaneously. glycogen phosphorylase. Several human diseases involve G-protein systems. They play important roles during embryonic development. The process involves three stages: reception. The activated G protein dissociates from the receptor and diffuses along the membrane. These activated relay proteins trigger many different transduction pathways and responses. An individual tyrosine-kinase receptor consists of several parts: An extracellular signal-binding site. The fully activated receptor proteins activate a variety of specific relay proteins that bind to specific phosphorylated tyrosine molecules. is mobilization of fuel reserves. This system helps the cell regulate and coordinate many aspects of cell growth and reproduction. When the appropriate signal molecule binds to the extracellular side of the receptor. which returns to its original state. The tyrosine-kinase receptor belongs to a major class of plasma membrane receptors that have enzymatic activity. W. In reception. An intracellular tail with several tyrosines. Vision and smell in humans depend on these proteins. G-protein-linked receptors bind many different signal molecules. the transduced signal triggers a specific cellular activity. Breakdown of glycogen releases glucose derivatives that can be used for fuel in glycolysis or released as glucose in the blood for fuel elsewhere. transferring a phosphate group from ATP to tyrosine on a substrate protein. G-protein receptor systems are extremely widespread and diverse in their functions. The plasma membrane must be involved in transmitting the epinephrine signal. Seven alpha helices span the membrane. Therefore. This dimerization activates the tyrosine-kinase section of the receptors. epinephrine did not activate the phosphorylase directly in vitro but could only act via intact cells. receptor tyrosine kinases. There are three major types of membrane receptors: G-protein-linked receptors. the G protein is inactive. which is released from the adrenal gland during times of physical or mental stress. and response. The G protein acts as an on/off switch. a chemical signal binds to a cellular protein. In response. causing the two receptors to aggregate and form a dimer. typically at the cell’s surface or inside the cell. and ion-channel receptors.Chapter 11: The three stages of cell signaling are reception. Their work investigated how the animal hormone epinephrine stimulates breakdown of the storage polysaccharide glycogen in liver and skeletal muscle. The tyrosine-kinase receptor system is especially effective when the cell needs to trigger several signal transduction pathways and cellular responses at once. including yeast mating factors. Thus one effect of epinephrine. binding leads to a change in the receptor that triggers a series of changes in a series of different molecules along a signal-transduction pathway. The G protein can also act as a GTPase enzyme to hydrolyze GTP to GDP. where it binds to an enzyme. A ligand-gated ion channel is a type of membrane receptor that can act as a gate when the receptor changes shape. The cytoplasmic side of these receptors functions as a tyrosine kinase. altering its activity. • • • • • • • • • • • • E. there must be an intermediate step or steps occurring inside the cell. The signal molecule binds to an individual receptor.
When the ligand dissociates from the receptor protein. Assembly of the spindle microtubules starts in the centrosome. Nonkinetochore microtubules from opposite poles overlap and interact with each other. The centrosome (microtubule-organizing center) is a nonmembranous organelle that organizes the cell’s microtubules. extends from each centrosome. Nitric oxide (NO) is a gas whose small size allows it to pass between membrane phospholipids. through a channel in the receptor. Many signaling pathways involve small. the chromosome moves toward the pole from which those microtubules come. the spindle microtubules. extends from each centrosome. The spindle fibers elongate by incorporating more subunits of the protein tubulin. neurotransmitter molecules released at a synapse between two neurons bind as ligands to ion channels on the receiving cell. the single centrosome replicates to form two centrosomes. By the end of prometaphase. The spindle includes the centrosomes. mRNA molecules leave the nucleus and carry information that directs the synthesis (translation) of specific proteins at the ribosome. Transcription factors control which genes are turned on—that is. activating the receptor. Ions flow in and trigger an electrical signal that propagates down the length of the receiving cell. The cytosol of target cells contains receptor molecules that bind testosterone. The spindle is now complete. the centrioles are pushed apart. a radial array of short microtubules. and the asters. Some gated ion channels respond to electrical signals. the microtubules of the asters have grown and are in contact with the plasma membrane. Binding by a ligand to the extracellular side changes the protein’s shape and opens the channel. How does the activated hormone-receptor complex turn on genes? These activated proteins act as transcription factors. The mitotic spindle. When a signal molecule binds as a ligand to the receptor protein. Testosterone is secreted by the testis and travels through the blood to enter cells throughout the body. Ligand-gated ion channels are very important in the nervous system. The spindle includes the centrosomes. Each sister chromatid has a kinetochore of proteins and chromosomal DNA at the centromere. a radial array of short microtubules. As the spindle microtubules grow from them. and the asters. The kinetochores of the joined sister chromatids face in opposite directions. As mitosis starts. These molecules rapidly diffuse throughout the cell. water-soluble. instead of ligands. When microtubules attach to the other pole. During interphase. such as Na+ or Ca2+. but the centrioles are not essential for cell division. is a major driving force in mitosis. Hydrophobic messengers include the steroid and thyroid hormones of animals. In animal cells. Other intracellular receptors (such as thyroid hormone receptors) are found in the nucleus and bind to the signal molecules there. The kinetochores of the joined sister chromatids face in opposite directions. It is composed of centrosomes and the microtubules that extend from them. For example. Eventually. Page | 32 . causing the channels to open. As the spindle assembles during prophase. Each sister chromatid has a kinetochore of proteins and chromosomal DNA at the centromere. During prometaphase. the spindle microtubules. An aster. The change in ion concentration within the cell may directly affect the activity of the cell. the gate opens to allow the flow of specific ions. During prometaphase. By metaphase. which genes are transcribed into messenger RNA. they are at opposite ends of the cell. on the metaphase plate. this movement stops and a tug-of-war ensues. some spindle microtubules (called kinetochore microtubules) attach to the kinetochores. fibers composed of microtubules and associated proteins. the chromosome settles midway between the two poles of the cell. the elements come from partial disassembly of the cytoskeleton. When a chromosome’s kinetochore is “captured” by microtubules. Chapter 12: The mitotic spindle begins to form. the centrosome has a pair of centrioles at the center. An aster. some spindle microtubules (called kinetochore microtubules) attach to the kinetochores. These activated proteins enter the nucleus and turn on specific genes that control male sex characteristics. the channel closes. nonprotein molecules or ions called second messengers. the two centrosomes are located near the nucleus.
Each tetrad has one or more chiasmata. the area of overlap is reduced as motor proteins attached to the microtubules walk them away from one another. on the metaphase plate. metaphase I. The spindle is now complete. the chromosomes begin to condense. As microtubules push apart. meiosis I and meiosis II. anaphase I. there are two consecutive cell divisions. forming two centrosomes. Nonkinetochore microtubules from opposite poles overlap and interact with each other. cytokinesis involves the formation of a cleavage furrow. holding them tightly together along their length. These are genetically identical and joined at the centromere. the microtubules of the asters have grown and are in contact with the plasma membrane. full-fledged chromosomes. division of the cytoplasm. Spindle microtubules form from the centrosomes. In plant cells. During anaphase. and telophase I. Meiosis I is preceded by interphase. What is the function of the nonkinetochore microtubules? Nonkinetochore microtubules are responsible for lengthening the cell along the axis defined by the poles. allowing continued overlap. The breakdown of the nuclear envelope and nucleoli take place. Kinetochores of each homologue attach to microtubules from one of the poles. Chapter 13: • • • • • • • • • • Many steps of meiosis resemble steps in mitosis. is usually well underway by late telophase. the chromosome settles midway between the two poles of the cell. Cytokinesis. When a chromosome’s kinetochore is “captured” by microtubules. When microtubules attach to the other pole. Experimental evidence supports the hypothesis that motor proteins on the kinetochore “walk” the attached chromosome along the microtubule toward the nearest pole. they move toward opposite poles of the cell. The four daughter cells have only half as many chromosomes as the parent cell. this movement stops and a tug-of-war ensues. the chromosome moves toward the pole from which those microtubules come. but the centrioles are not essential for cell division. By metaphase. each chromosome pair becomes visible as a tetrad. Homologous chromosomes loosely pair up along their length. Anaphase commences when the proteins holding the sister chromatids together are inactivated. Meanwhile. resulting in four daughter cells. a protein structure called the synaptonemal complex forms between homologues. Both are preceded by the replication of chromosomes. In animal cells. precisely aligned gene for gene. In crossing over. DNA molecules in nonsister chromatids break at corresponding places and then rejoin the other chromatid. These microtubules interdigitate and overlap across the metaphase plate. Eventually. As the synaptonemal complex disassembles in late prophase. separates sister chromatids. Prophase I • • • • • • • • • • Prophase I typically occupies more than 90% of the time required for meiosis. meiosis I. separates homologous chromosomes. The first division. In synapsis. The second. Division in meiosis I occurs in four phases: prophase I. the centrosome has a pair of centrioles at the center. in meiosis. or group of four chromatids. However. The single centrosome is replicated. vesicles derived from the Golgi apparatus produce a cell plate at the middle of the cell. Once the chromosomes are separate. which pinches the cell in two. the microtubules lengthen by the addition of new tubulin monomers to their overlapping ends. How do the kinetochore microtubules function into the poleward movement of chromosomes? One hypothesis is that the chromosomes are “reeled in” by the shortening of microtubules at the spindle poles. which have moved to the poles. sites where the chromatids of homologous chromosomes have crossed and segments of the chromatids have been traded. In animal cells. meiosis II. During prophase I. Page | 33 . in which the chromosomes are replicated to form sister chromatids. the excess microtubule sections depolymerize at their kinetochore ends. using energy from ATP.
Cytokinesis usually occurs simultaneously. Telophase I and cytokinesis • • • • • Meiosis II In telophase I. the sister chromatids are arranged at the metaphase plate. • • • • • • • • • • Meiosis II is very similar to mitosis. the two sister chromatids of each chromosome are no longer genetically identical. All three mechanisms reshuffle the various genes carried by individual members of a population. No chromosome replication occurs between the end of meiosis I and the beginning of meiosis II. Sister chromatids remain attached at the centromere and move as a single unit toward the pole. guided by the spindle apparatus. Crossing overproduces recombinant chromosomes. the chromosomes arrive at opposite poles. At metaphase II. Crossing over between homologous chromosomes during prophase I. a cleavage furrow forms. movement of homologous chromosomes continues until there is a haploid set at each pole. During prophase II. a spindle apparatus forms and attaches to kinetochores of each sister chromatid. the homologous chromosomes separate. Page | 34 . The resulting zygote could contain any one of more than 70 trillion possible combinations of chromosomes. Any sperm can fuse with any egg. Spindle fibers from one pole attach to the kinetochore of one sister chromatid. by combining DNA inherited from two parents into a single chromosome. homologous portions of two nonsister chromatids trade places. In telophase II. with one chromosome facing each pole. is an important source of genetic variation. Crossing over. The three sources of genetic variability in a sexually reproducing organism are: Independent assortment of homologous chromosomes during meiosis I and of nonidentical sister chromatids during meiosis II. and cytokinesis separates the cytoplasm. Nuclei form around the chromosomes. At the end of meiosis. meiosis II. which begin expanding. The random nature of fertilization adds to the genetic variation arising from meiosis. as the chromosomes are already replicated. while those from the other pole are attached to the other.Metaphase I • • At metaphase I. Crossing over begins very early in prophase I as homologous chromosomes pair up gene by gene. The kinetochores of sister chromatids attach to microtubules extending from opposite poles. the tetrads are all arranged at the metaphase plate. by the same mechanisms as mitosis. The sister chromatids separate during the second meiosis division. the centomeres of sister chromatids separate and two newly individual chromosomes travel toward opposite poles. In plant cells. The successful sperm is one of more than 8 million possibilities. Because of crossing over in meiosis I. Crossing over adds even more variation to this. there are four haploid daughter cells. which combine genes inherited from each parent. Microtubules from one pole are attached to the kinetochore of one chromosome of each tetrad. a cell plate forms. One chromosome moves toward each pole. Random fertilization of an ovum by a sperm. Each zygote has a unique genetic identity. At anaphase II. Anaphase I • • In anaphase I. In animal cells. The ovum is one of more than 8 million possible chromosome combinations. In crossing over. and those of the other pole attach to kinetochore of the other sister chromatid. Each chromosome consists of two sister chromatids.
Humans have 46 chromosomes in almost all of their cells. or characters. At the other extreme from complete dominance is codominance. distinguishable ways. or zygote. For example. sperm and ova (unfertilized eggs) transmit genes from one generation to the next. that varied on a continuum. In plants and animals. Pea plants are available in many varieties with distinct heritable features. However. The occurrence of homologous pairs of chromosomes is a consequence of sexual reproduction. a maternal set (from your mother) and a paternal set (from your father). genes from both parents are present in the nucleus of the fertilized egg. For example. Each chromosome consists of a single DNA molecule associated with various proteins. the M. N. Almost all the DNA in a eukaryotic cell is subdivided into chromosomes in the nucleus. In a typical breeding experiment. The Y chromosome also has genes not present on the X. We inherit one chromosome of each homologous pair from each parent. Chapter 14: Around 1857. The mystery individual is bred with a homozygous recessive individual. When true-breeding plants self-pollinate. Any cell with two sets of chromosomes is called a diploid cell and has a diploid number of chromosomes. A gamete with a single chromosome set is haploid. and people of group MN (genotype MN) have both molecules present. the mystery parent must be heterozygous. After fertilization (fusion of a sperm cell and an ovum). The 46 chromosomes in each somatic cell are two sets of 23. Tiny amounts of DNA are also found in mitochondria and chloroplasts. Mendel started his experiments with varieties that were true-breeding. In nature. The true-breeding parents are the P generation. but could be homozygous dominant or heterozygous. Only small parts of the X and Y are homologous. Sperm cells or ova (gametes) have only one set of chromosomes—22 autosomes and an X (in an ovum) and 22 autosomes and an X or a Y (in a sperm cell). The MN phenotype is not intermediate between M and N phenotypes but rather exhibits both the M and the N phenotype. He avoided traits. Human females have a homologous pair of X chromosomes (XX). pea plants typically self-fertilize. Most of the genes carried on the X chromosome do not have counterparts on the tiny Y. Mendel would then allow the F1 hybrids to self-pollinate to produce an F2 generation. the haploid number of chromosomes is 23 (n = 23). Mendel tracked only those characters that varied in an “either-or” manner. each at a specific location. Each chromosome has hundreds or thousands of genes. If any of the offspring display the recessive phenotype. One extreme is the complete dominance characteristic of Mendel’s crosses. people of group N (genotype NN) have the other type. The answer is to carry out a testcross. It was mainly Mendel’s quantitative analysis of F2 plants that revealed two fundamental principles of heredity: the law of segregation and the law of independent assortment. People of group M (genotype MM) have one type of molecule on their red blood cells. abbreviated as 2n. true-breeding pea varieties. Mutation ultimate source of variation How can we tell the genotype of an individual with the dominant phenotype? The organism must have one dominant allele. and MN blood groups of humans are due to the presence of two specific molecules on the surface of red blood cells. abbreviated as n. Human males have an X and a Y chromosome (XY). its locus. and the diploid number is 46 (2n = 46). with different variant traits. such as seed weight. and their hybrid offspring are the F1 generation. Mendel would cross-pollinate (hybridize) two contrasting. Any sexually reproducing species has a characteristic haploid and diploid number of chromosomes. Each pea plant has male (stamens) and female (carpal) sexual organs. Mendel began breeding garden peas to study inheritance. in which two alleles affect the phenotype in separate. all their offspring have the same traits. he worked with flowers that were either purple or white. rather than a “more-or-less” manner. Page | 35 . Every living species has a characteristic number of chromosomes. Mendel could strictly control which plants mated with which. fertilizing ova with the sperm nuclei from their own pollen. Pea plants have several advantages for genetic study. Mendel could also use pollen from another plant for cross-pollination. For humans.
a person’s red and white blood cell count varies with factors such as altitude. although some suffer some symptoms of sickle-cell disease under blood oxygen stress. and elsewhere causes poor absorption of nutrients. there are abnormally high extracellular levels of chloride. Carriers are said to have sickle-cell trait. blindness. The high frequency of heterozygotes is unusual for an allele with severe detrimental effects in homozygotes. The most common inherited disease among people of African descent is sickle-cell disease. Among Ashkenazic Jews (those from central Europe). where malaria is common. This causes the mucus coats of certain cells to become thicker and stickier than normal. A cross between a white-flowered plant and a red-flowered plant will produce all pink F1 offspring. Individuals with one sickle-cell allele have increased resistance to malaria. sickle-cell hemoglobin aggregate into long rods that deform red blood cells into a sickle shape. Considering the intricate molecular and cellular interactions responsible for an organism’s development. Doctors can use regular blood transfusions to prevent brain damage and new drugs to prevent or treat other problems. The phenotypic and genotypic ratios are identical: 1:2:1. A clear example of incomplete dominance is seen in flower color of snapdragons. In tropical Africa. These individuals are usually healthy. Cystic fibrosisstrikes one of every 2. Normally it is relatively unlikely that two carriers of the same rare. A single tree may have leaves that vary in size. blood type). and bacterial infections. The symptoms begin with seizures. to codominance of both alleles. Homozygous normal individuals die of malaria and homozygous recessive individuals die of sickle-cell disease. sun-tanning darkens skin. digestive tract. For example. Offspring of a cross between heterozygotes show three phenotypes: each parental and the heterozygote. It is caused by a dysfunctional enzyme that fails to break down specific brain lipids. that are determined by the environment. the wide-ranging symptoms of sickle-cell disease are due to a single gene. accumulate phenotypic differences as a result of their unique experiences. the nonsickle allele is incompletely dominant to the sickle-cell allele. in mice and many other mammals. In some cases. and 50% pink F2 offspring. Without treatment. as sickled cells clump and clog capillaries throughout the body. Some alleles show incomplete dominance. the sickle-cell allele is both a boon and a bane. and degeneration of motor and mental performance a few months after birth. About one in ten African-Americans has sickle-cell trait. most genes are pleiotropic. coat color depends on two genes. Tay-Sachs diseaseis another lethal recessive disorder. the norm of reaction. This sickling creates a cascade of symptoms. This mucus buildup in the pancreas. who are genetically identical. customary exercise level. 25% red. the child dies after a few years. but a range of phenotypic possibilities. it is not surprising that a gene can affect a number of characteristics. This is not blending inheritance because the traits are separable (particulate). the epistatic gene. The normal allele for this gene codes for a membrane protein that transports Cl− between cells and extracellular fluid. exercise alters build. Phenotype depends on environment and genes. However. Page | 36 . determines whether pigment will be deposited in hair or not. while carriers are relatively free of both. about 100 times greater than the incidence among non-Jews or Mediterranean (Sephardic) Jews. The relative importance of genes and the environment in influencing human characteristics is a very old and hotly contested debate. The relative effects of two alleles range from complete dominance of one allele. When oxygen levels in the blood of an affected individual are low. For example. through incomplete dominance of either allele. as shown in further crosses. they can live past their late 20s or even 30s. and experience improves performance on intelligence tests. At the molecular level. demonstrating the pleiotropic effects of this allele. depending on exposure to wind and sun. The product of a genotype is generally not a rigidly defined phenotype. For humans. which affects one of 400 African-Americans. At the organismal level. despite their inherited skin color. harmful allele will meet and mate.500 whites of European descent. consanguineous matings between close relatives increase the risk. chronic bronchitis. affecting more than one phenotypic character. shape. in which heterozygotes show a distinct intermediate phenotype not seen in homozygotes. and presence of infection. the norm of reaction has no breadth. Even identical twins. nutrition influences height. One in 25 people of European descent is a carrier for this condition. One. but with treatment. the two alleles are codominant as both normal and abnormal (sickle-cell) hemoglobins are synthesized. A person becomes darker if they tan. a gene at one locus alters the phenotypic expression of a gene at a second locus.600 births. this disease occurs in one of 3. If these channels are defective or absent. lungs. In epistasis. However. In contrast. a parasite that spends part of its life cycle in red blood cells. Sickle-cell disease is caused by the substitution of a single amino acid in hemoglobin. Self-pollination of the F1 offspring produces 25% white. Inevitably. affected children die before five. and a given genotype specifies a particular phenotype (for example. The relatively high frequency of sickle-cell trait in African-Americans is a vestige of their African roots. and greenness.
the resulting zygote is female (XX). the generic embryonic gonads develop into testes. alcoholism. such as schizophrenia and manicdepressive disorder. little is understood about the genetic contribution to most multifactorial diseases. The X-0 system is found in some insects. In individuals lacking the SRY gene.000 people. and anatomical features because it regulates many other genes. Each ovum receives an X chromosome. the anatomical signs of sex first appear when the embryo is about two months old. many other disorders have a multifactorial basis. Although most harmful alleles are recessive. The genetic component of such disorders is typically polygenic. a degenerative disease of the nervous system. and half receive a Y chromosome. In contrast. The X and Y rarely cross over. X and Y. The dominant lethal allele has no obvious phenotypic effect until an individual is about 35 to 45 years old. achondroplasia. Other genes on the Y chromosome are necessary for the production of functional sperm.99% of the population. In both testes (XY) and ovaries (XX). Chapter 15: • • • • • • • • • • • • • • • • • • • • • • • • • Although the anatomical and physiological differences between women and men are numerous. In humans. Most societies and cultures have laws or taboos forbidding marriages between close relatives. Activity of the SRY gene triggers a cascade of biochemical. Recently. In bees and ants. a British research team identified a gene on the Y chromosome required for the development of testes. A lethal dominant allele can escape elimination if it causes death at a relatively advanced age. Multifactorial disorders include heart disease. Page | 37 . diabetes. males are X. has an incidence of one case in 25. and some insects. This has led to the development of a test that can detect the presence of the Huntington’s allele in an individual’s genome. 99. a lethal recessive allele can be passed on by heterozygous carriers who have normal phenotypes. Females are XX. This provides another example of a trait for which the recessive allele is far more prevalent than the dominant allele. and each gamete receives one. They named the gene SRY (sex-determining region of the Y chromosome). The best public health strategy is education about relevant environmental factors and promotion of healthy behavior. One example is Huntington’s disease. At present. a number of human disorders are due to dominant alleles. each conception has about a fifty-fifty chance of producing a particular sex. Only relatively short segments at either end of the Y chromosome are homologous with the corresponding regions of the X chromosome. the generic embryonic gonads develop into ovaries. Lethal dominant alleles are much less common than lethal recessives. the chromosomal basis of sex is rather simple. Other animals have different methods of sex determination. Those who are not achondroplastic dwarfs. females are diploid and males are haploid. In the X-Y system. females are ZW and males are ZZ. some fishes. An individual who inherits two X chromosomes usually develops as a female. this devastating disease afflicts one in 10. Heterozygous individuals have the dwarf phenotype. For example.000 people. are homozygous recessive for this trait. If a sperm cell bearing an X chromosome fertilizes an ovum. The deterioration of the nervous system is irreversible and inevitably fatal. In birds. physiological. the allele will not be passed on to future generations. Because of this. These may have a genetic component plus a significant environmental influence. Half the sperm cells receive an X chromosome. molecular geneticists have used pedigree analysis of affected families to track the Huntington’s allele to a locus near the tip of chromosome 4. In the United States. the two sex chromosomes segregate during meiosis. An individual who inherits an X and a Y chromosome usually develops as a male. Any child born to a parent who has the allele for Huntington’s disease has a 50% chance of inheriting the disease and the disorder. If a sperm cell bearing a Y chromosome fertilizes an ovum. after the individual has already passed on the lethal allele to his or her children. and certain mental illnesses. In the absence of these genes. If a lethal dominant kills an offspring before it can mature and reproduce. In humans and other mammals. While some diseases are inherited in a simple Mendelian fashion due to alleles at a single locus. a form of dwarfism. there are two varieties of sex chromosomes. Individuals who share a recent common ancestor are more likely to carry the same recessive alleles. In individuals with the SRY gene. In 1990. the Y chromosome is much smaller than the X chromosome. an XY individual is male but does not produce normal sperm. the resulting zygote is male (XY). cancer.
In this technique. ratios. most of the radioactivity was in the supernatant that contained phage particles. 29. As a consequence of nondisjunction. Watson and Crick discovered the double helix by building models to conform to X-ray data. • • • • • • • • • • • • • • By the beginnings of the 1950s. not in the pellet with the bacteria. X-rays are diffracted as they passed through aligned fibers of purified DNA. Maurice Wilkins and Rosalind Franklin used X-ray crystallography to study the structure of DNA. 19. This may occur if tetrad chromosomes do not separate properly during meiosis I. The width of the helix suggested that it was made up of two strands. guanine (G). Erwin Chargaff had developed a series of rules based on a survey of DNA composition in organisms. He already knew that DNA was a polymer of nucleotides consisting of a nitrogenous base. Nondisjunctionoccurs when problems with the meiotic spindle cause errors in daughter cells. deoxyribose. Human DNA is 30. Offspring resulting from fertilization of a normal gamete with one produced by nondisjunction will have an abnormal chromosome number. one gamete receives two of the same type of chromosome. the four bases are found in characteristic. In any one species. By 1947. Page | 38 . form rungs. Chargaff noted that the DNA composition varies from species to species. a condition known as aneuploidy. The diffraction pattern can be used to deduce the three-dimensional shape of molecules. He also found a peculiar regularity in the ratios of nucleotide bases that are known as Chargaff’s rules. The bases could be adenine (A). The number of guanines was approximately equal to the number of cytosines (%G = %C).9% adenine. the number of adenines was approximately equal to the number of thymines (%T = %A). thymine (T). The basis for these rules remained unexplained until the discovery of the double helix. the race was on to move from the structure of a single DNA strand to the three-dimensional structure of DNA. they placed the sugar-phosphate chains on the outside and the nitrogenous bases on the inside of the double helix. and a phosphate group.9% guanine. the double helix. Using molecular models made of wire. one from each strand. James Watson learned from their research that DNA was helical in shape. Among the scientists working on the problem were Linus Pauling in California and Maurice Wilkins and Rosalind Franklin in London. Similar circumstantial evidence came from the observation that diploid sets of chromosomes have twice as much DNA as the haploid sets in gametes of the same organism. and he deduced the width of the helix and the spacing of nitrogenous bases. This arrangement put the relatively hydrophobic nitrogenous bases in the molecule’s interior. and another gamete receives no copy. The ladder forms a twist every ten bases. Watson and his colleague Francis Crick began to work on a model of DNA with two strands. The nitrogenous bases are paired in specific combinations: adenine with thymine and guanine with cytosine. Chapter 16: • • • • • • • • • • • • • • • Hershey and Chase found that when the bacteria had been infected with T2 phages that contained radiolabeled proteins. Pairs of nitrogenous bases. and 19. contrary to a three-stranded model that Linus Pauling had recently proposed. The sugar-phosphate chains of each strand are like the side ropes of a rope ladder. When they examined the bacterial cultures with T2 phage that had radiolabeled DNA. most of the radioactivity was in the pellet with the bacteria. In all organisms.4% thymine. Hershey and Chase concluded that the injected DNA of the phage provides the genetic information that makes the infected cells produce new viral DNA and proteins to assemble into new viruses. Alternatively.8% cytosine. or cytosine (C). The fact that cells double the amount of DNA in a cell prior to mitosis and then distribute the DNA equally to each daughter cell provided some circumstantial evidence that DNA was the genetic material in eukaryotes. but not necessarily equal. sister chromatids may fail to separate during meiosis II.
Each has a nitrogenous base. at least 11 different DNA polymerases have been identified so far. Each gene has a unique order of nitrogenous bases. the triphosphate monomers used for DNA synthesis are chemically reactive. Much more is known about replication in bacteria than in eukaryotes. The 5’ à3’ direction of one strand runs counter to the 3’ à5’ direction of the other strand. ATP is a nucleoside triphosphate with ribose instead of deoxyribose. This process is remarkably accurate. More than a dozen enzymes and other proteins participate in DNA replication. Watson and Crick determined that chemical side groups of the nitrogenous bases would form hydrogen bonds. connecting the two strands. with only one error per ten billion nucleotides. The sugar-phosphate backbones run in opposite directions. At the origin sites. and eventually fuse. The exergonic hydrolysis of pyrophosphate to two inorganic phosphate molecules drives the polymerization of the nucleotide to the new strand. The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells. there may be hundreds or thousands of origin sites per chromosome. the DNA strands separate. In eukaryotes. Watson and Crick published a succinct. As nucleotides align with complementary bases along the template strand. However. In E. and a triphosphate tail. In addition. origins of replication. coli. Page | 39 . These enzymes separate the strands. The process appears to be fundamentally similar for prokaryotes and eukaryotes. The exergonic hydrolysis of pyrophosphate to two inorganic phosphate molecules drives the polymerization of the nucleotide to the new strand. • • • • • • • • • • • • • • • • • • • • • • • • • • • • It takes E.” Replication proceeds in both directions until the entire molecule is copied. The strands in the double helix are antiparallel. Each nucleotide that is added to a growing DNA strand is a nucleoside triphosphate. A human cell can copy its 6 billion base pairs and divide into daughter cells in only a few hours. DNA polymerasescatalyze the elongation of new DNA at a replication fork. this is a specific sequence of nucleotides that is recognized by the replication enzymes.• • • • • • • • • • • Pairing like nucleotides did not fit the uniform diameter indicated by the X-ray data. coli 25 minutes to copy each of the 5 million base pairs in its single chromosome and divide to form two identical daughter cells. forming a replication “bubble” with replication forks at each end. As each nucleotide is added to the growing end of a DNA strand. Each DNA strand has a 3’ end with a free hydroxyl group attached to deoxyribose and a 5’ end with a free phosphate group attached to deoxyribose. forming a replication “bubble. two different DNA polymerases are involved in replication: DNA polymerase III and DNA polymerase I. Like ATP. partly because their triphosphate tails have an unstable cluster of negative charge. The sugar-phosphate backbones run in opposite directions. one-page paper in Nature reporting their double helix model of DNA. The replication bubbles elongate as the DNA is replicated. and guanine would form three hydrogen bonds only with cytosine. Based on details of their structure. deoxyribose. In eukaryotes. adenine would form two hydrogen bonds only with thymine. A purine-purine pair is too wide. This finding explained Chargaff’s rules. and a pyrimidine-pyrimidine pairing is too short. In April 1953. The linear sequence of the four bases can be varied in countless ways. this does not restrict the sequence of nucleotides along each DNA strand. In bacteria. The replication of a DNA molecule begins at special sites. The strands in the double helix are antiparallel. The base-pairing rules dictate the combinations of nitrogenous bases that form the “rungs” of DNA. the last two phosphate groups are hydrolyzed to form pyrophosphate. Only a pyrimidine-purine pairing produces the 2-nm diameter indicated by the X-ray data. they are added to the growing end of the new strand by the polymerase.
and ultraviolet light can change nucleotides in ways that can affect encoded genetic information. Okazakifragments are about 1. DNA polymerases cannot initiate synthesis of a polynucleotide. Each cell continually monitors and repairs its genetic material. The DNA polymerase molecules “reel in” the parental DNA and “extrude” newly made daughter DNA molecules. Primase. In addition to primase. The lagging strand is copied away from the fork in short segments. Unlike the leading strand. In eukaryotic cells. For synthesis of the lagging strand. The final error rate is only one per ten billion nucleotides. The other parental strand (5’ à3’ into the fork). If there is an incorrect pairing. Helicaseuntwists the double helix and separates the template DNA strands at the replication fork. DNA bases may undergo spontaneous chemical changes under normal cellular conditions. the leading strand requires the formation of only a single primer as the replication fork continues to separate. It is conventional and convenient to think of the DNA polymerase molecules as moving along a stationary DNA template. DNA molecules are constantly subject to potentially harmful chemical and physical agents. • • • • • • • • • Mistakes during the initial pairing of template nucleotides and complementary nucleotides occur at a rate of one error per 100. DNA pol III adds a deoxyribonucleotide to the 3’ end of the RNA primer and continues adding DNA nucleotides to the growing DNA strand according to the base-pairing rules. Mismatched nucleotides that are missed by DNA polymerase or mutations that occur after DNA synthesis is completed can often be repaired. each requiring a new primer. eventually joins the sugar-phosphate backbones of the Okazaki fragments to form a single DNA strand. which elongates continuously. In reality. To summarize. the lagging strand. The DNA strand made by this mechanism is called the leading strand. Page | 40 . is copied away from the fork. Another DNA polymerase. the enzyme removes the wrong nucleotide and then resumes synthesis. DNA polymerases. Reactive chemicals. the primer is a short stretch of RNA with an available 3’ end. RNA polymerases can start an RNA chain from a single template strand.000 nucleotides long in E. each Okazaki fragment must be primed separately. links ribonucleotides that are complementary to the DNA template into the primer. X-rays. In the initiation of the replication of cellular DNA. The primer is 5–10 nucleotides long in eukaryotes. DNA polymerase proofreads each new nucleotide against the template nucleotide as soon as it is added. The initial nucleotide chain is called a primer. a DNA replication “machine. Enzymes proofread DNA during its replication and repair damage in existing DNA. After formation of the primer. A new DNA strand can only elongate in the 5’ à3’ direction. The DNA replication machine is probably stationary during the replication process. and topoisomerase helps relieve this strain. coli and more than 130 repair enzymes identified in humans.000–2. radioactive emissions.000 base pairs. the leading strand is copied continuously into the fork from a single primer. multiple copies of the machine may anchor to the nuclear matrix.• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • DNA polymerases can only add nucleotides to the free 3’ end of a growing DNA strand. Returning to the original problem at the replication fork. Another enzyme. with 100 repair enzymes known in E. at the replication fork. several other proteins have prominent roles in DNA synthesis. For example. adding them one by one onto the 3’ end of the adjacent Okazaki fragment. Along one template strand.” Many protein-protein interactions facilitate the efficiency of this machine. helicase works much more rapidly when it is in contact with primase. the various proteins involved in DNA replication form a single large complex. Single-strand binding proteinskeep the unpaired template strands apart during replication. They can only add nucleotides to the 3’ end of an existing chain that is base-paired with the template strand. DNA ligase. a framework of fibers extending through the interior of the nucleus. replaces the RNA nucleotides of the primers with DNA versions.an RNA polymerase. coli and 100–200 nucleotides long in eukaryotes. the lagging stand is synthesized as a series of short segments called Okazakifragments. DNA polymerase I. This untwisting causes tighter twisting ahead of the replication fork. DNA polymerase III can synthesize a complementary strand continuously by elongating the new DNA in the mandatory 5’ à3’ direction. The primers are converted to DNA before DNA ligase joins the fragments together. and DNA ligases.
• • • • • • • • • In mismatch repair. Prokaryotes do not have this problem because they have circular DNA molecules without ends. Repeated rounds of replication produce shorter and shorter DNA molecules. the DNA of dividing somatic cells and cultured cells tends to become shorter. In human telomeres. Normal shortening of telomeres may protect organisms from cancer by limiting the number of divisions that somatic cells can undergo. repeated between 100 and 1. have special nucleotide sequences. Telomeres protect genes from being eroded through multiple rounds of DNA replication. Page | 41 . An enzyme called telomerase catalyzes the lengthening of telomeres in eukaryotic germ cells. there is a change of language. If the chromosomes of germ cells became shorter with every cell cycle. which give rise to gametes. essential genes would eventually be lost. partly because their triphosphate tails have an unstable cluster of negative charge. a nuclease cuts out a segment of a damaged strand. The exergonic hydrolysis of pyrophosphate to two inorganic phosphate molecules drives the polymerization of the nucleotide to the new strand. This overcomes the progressive shortening that would eventually lead to self-destruction of the cancer. Instead. because they have gone through many cell divisions. the DNA typically consists of multiple repetitions of one short nucleotide sequence. There is now room for primase and DNA polymerase to extend the 5’ end. Active telomerase has been found in some cancerous somatic cells. Telomerase is not present in most cells of multicellular organisms. During translation. The ends of eukaryotic chromosomal DNA molecules. Immortal strains of cultured cells are capable of unlimited cell division. the last two phosphate groups are hydrolyzed to form pyrophosphate. It does not repair the 3’-end “overhang. the triphosphate monomers used for DNA synthesis are chemically reactive. The usual replication machinery provides no way to complete the 5’ ends of daughter DNA strands. Like ATP. Ultraviolet light can produce thymine dimers between adjacent thymine nucleotides. the telomeres. Telomeric DNA tends to be shorter in dividing somatic cells of older individuals and in cultured cells that have divided many times. mutations in their skin cells are left uncorrected and cause skin cancer.” but it does lengthen the telomere. The importance of the proper functioning of repair enzymes is clear from the inherited disorder xeroderma pigmentosum. special enzymes fix incorrectly paired nucleotides. Telomeres do not contain genes. Telomerase may provide a useful target for cancer diagnosis and chemotherapy. In individuals with this disorder. Telomeric DNA and specific proteins associated with it also prevents the staggered ends of the daughter molecule from activating the cell’s system for monitoring DNA damage. it provides a template for assembling a sequence of RNA nucleotides.000 times. Telomerase uses a short molecule of RNA as a template to extend the 3’ end of the telomere. These individuals are hypersensitive to sunlight. Transcription of many genes produces a messenger RNA (mRNA) molecule. This buckles the DNA double helix and interferes with DNA replication. Telomere length may be a limiting factor in the life span of certain tissues and of the organism. • • • • • • • • • • • • • • • • • • • • • • • • • • • • • Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes. In nucleotide excision repair. Therefore. DNA polymerase and ligase fill in the gap. A hereditary defect in one of these enzymes is associated with a form of colon cancer. this sequence is typically TTAGGG. Chapter 17: During transcription. As each nucleotide is added to the growing end of a DNA strand. Cells from large tumors often have unusually short telomeres. It is possible that the shortening of telomeres is somehow connected with the aging process of certain tissues and perhaps to aging in general. a DNA strand provides a template for the synthesis of a complementary RNA strand. Just as a DNA strand provides a template for the synthesis of each new complementary strand during DNA replication. The ends of DNA molecules are replicated by a special mechanism. restoring their original length. Eukaryotic cells have evolved a mechanism to restore shortened telomeres in germ cells.
A cell has all 20 amino acids available in its cytoplasm. Binding by the repressor to the operator is reversible. when concentrations of tryptophan in the cell are high. Morgan and his colleagues assigned genes to specific loci on chromosomes. it can prevent transcription of the operon’s genes. the promoter. Each ribosome is made up of a large and a small subunit. The molecular chain of command in a cell is DNA àRNA àprotein. The switch is a segment of DNA called an operator. but they must be present for transcription to occur. Chapter 18: When an E. and translation occurs at ribosomes in the cytoplasm. binds to the operator. transcription occurs in the nucleus. • • • • • • • • • • The Mendelian concept of a gene views it as a discrete unit of inheritance that affects phenotype. either by synthesizing them from scratch or by taking them up from the surrounding solution. This allows the coupling of transcription and translation. the subunits are made in the nucleolus. and the genes they control constitute an operon. since many RNA transcripts can be made from one gene. all the enzymes are synthesized at one time. Page | 42 . Because bacteria lack nuclei. Even the one gene–one polypeptide definition must be refined and applied selectively. The transcription of a protein-coding eukaryotic gene results in pre-mRNA. Also. After rRNA genes are transcribed to rRNA in the nucleus. each type of tRNA links an mRNA codon with the appropriate amino acid. This is our definition of a gene: A gene is a region of DNA whose final product is either a polypeptide or an RNA molecule. The ribosome adds each amino acid carried by tRNA to the growing end of the polypeptide chain. the rRNA and proteins are assembled to form the subunits with proteins from the cytoplasm. coli cell must make tryptophan for itself. The number of active repressor molecules available determines the on or off mode of the operator. an anticodon. The operator. The basic mechanics of transcription and translation are similar in eukaryotes and prokaryotes. We can also view a gene as a specific nucleotide sequence along a region of a DNA molecule. operon. Most eukaryotic genes contain large introns that have no corresponding segments in polypeptides. During translation. This activates the repressor and turns the operon off. In eukaryotes. Promoters and other regulatory regions of DNA are not transcribed either. All these definitions are useful in certain contexts. Ribosomes attach to the leading end of an mRNA molecule while transcription is still in progress. genes program protein synthesis via genetic messages in the form of messenger RNA. In a eukaryotic cell. Repressors contain allosteric sites that change shape depending on the binding of other molecules. some tryptophan molecules bind as a corepressor to the repressor protein. Each tRNA arriving at the ribosome carries a specific amino acid at one end and has a specific nucleotide triplet. The anticodon base-pairs with a complementary codon on mRNA. To summarize. controls the access of RNA polymerase to the genes. Our molecular definition must also include the various types of RNA that are not translated into polypeptides. a product of a regulatory gene. The site of translation is the ribosome. However. Using an RNA intermediate allows more copies of a protein to be made simultaneously. such as rRNA. complex particles that facilitate the orderly assembly of amino acids into polypeptide chains. By itself. located between the promoter and the enzyme-coding genes. Each repressor protein recognizes and binds only to the operator of a certain operon. the most abundant RNA in the cell. if a repressor protein. RNA processingyields the finished mRNA. tRNA. We can define a gene functionally as a DNA sequence that codes for a specific polypeptide chain. and other RNAs. Why can’t proteins be translated directly from DNA? The use of an RNA intermediate provides protection for DNA and its genetic information. The initial RNA transcript of any gene is called a primary transcript. The operator. The subunits are composed of proteins and ribosomal RNA (rRNA). The interpreter is transfer RNA (tRNA). at the other. each gene transcript can be translated repeatedly. an operon is on and RNA polymerase can bind to the promoter and transcribe the genes. or tryptophan. their DNA is not segregated from ribosomes and other protein-synthesizing equipment. In the case of the trp. which transfers amino acids from the cytoplasmic pool to a ribosome. Regulatory genes are transcribed continuously at low rates.
In bacteria. Transposase cuts the transposable elements from its initial site and inserts it into the target site. the extra genes are sandwiched between two insertion sequences. natural selection factors bacterial clones that have built up R plasmids with multiple antibiotic resistance through a series of transpositions. flanked by a pair of inverted repeat sequences. The transposase enzyme recognizes the inverted repeats as the edges of the transposable element. Positive gene control occurs when an activator molecule interacts directly with the genome to switch transcription on. Even if the lac operon is turned on by the presence of allolactose. in which the transposable element replicates at its original site. this operon is off. This inactivates the repressor. The 20 to 40 nucleotides of the inverted repeat on one side are repeated in reverse along the opposite DNA strand at the other end of the transposable element. the lac repressor is active all by itself. an isomer of lactose. Lactose metabolism begins with hydrolysis of lactose into its component monosaccharides. potentially moving genes to a site where genes of that sort have never before existed. and the operon is transcribed. The regulatory gene. or between plasmids. In contrast. a single R plasmid may carry several genes for resistance to different antibiotics. Insertion sequences account for 1. foreign DNA from the surrounding environment. transposons may help bacteria adapt to new environments. In other words. called insertion sequences. The trp operon is an example of a repressible operon. lacI. the regulatory protein is active (inhibitory) as synthesized. also move about in the bacterial genome. Transformationis the alteration of a bacterial cell’s genotype by the uptake of naked. The simplest transposable elements. and the lac operon can be transcribed. glucose and galactose. called transposons. When lactose is present in the cell. codes for an allosteric repressor protein that can switch off the lac operon by binding to the operator. This is explained by transposons. By producing the appropriate enzymes only when the nutrient is available. binding to the operator and switching the lac operon off. While insertion sequences may not benefit bacteria in any specific way. Transposable elements longer and more complex than insertion sequences. occurring about once in every 10 million generations.” such as genes for antibiotic resistance. exist only in bacteria. During transposition. digesting nutrients to simpler molecules. coli cell grown in the absence of lactose. which can add a gene for antibiotic resistance to a plasmid already carrying genes for resistance to other antibiotics. the movement may be within the chromosome. In the absence of lactose. Most transposable elements can move to many alternative locations in the DNA. but a mutation in a particular gene by transposition is rare. the degree of transcription depends on the concentrations of other substrates. Allosteric binding by an inducer molecule makes the regulatory protein inactive. one that is inhibited when a specific small molecule binds allosterically to a regulatory protein. The gene for ß-galactosidase is part of the lac operon. the transposable element is added at a new site without being lost from the old site. Repressible enzymes generally function in anabolic pathways. binds to the repressor. an inducible operon is stimulated when a specific small molecule interacts with a regulatory protein. the cell avoids making proteins that have nothing to do. This reaction is catalyzed by the enzyme ß-galactosidase. The insertion sequence consists of the transposase gene. and the operon is turned on.5% of the E. This is about the same rate as spontaneous mutations from external factors. An insertion sequence contains a single gene that codes for transposase. coli genome. In inducible operons. Only a few molecules of this enzyme are present in an E. The transmission of this composite plasmid to other bacterial cells by cell division or conjugation can spread resistance to a variety of antibiotics throughout a bacterial population. from a plasmid to a chromosome (or vice versa). If lactose is added to the bacterium’s environment. and the operon is off. In some bacterial transposons. Page | 43 . At low levels of tryptophan. synthesizing end products from raw materials. Unlike the trp operon. The lac operon contains a series of genes that code for enzymes that play a major role in the hydrolysis and metabolism of lactose (milk sugar). as an active repressor binds to the operator and prevents transcription. allolactose. the number of ß-galactosidase increases by a thousandfold within 15 minutes. Transposable elements are also important components of eukaryotic genomes. the cell can allocate its resources to other uses. When the end product is present in sufficient quantities. For example. Both repressible and inducible operons demonstrate negative control because active repressors switch off the active form of the repressor protein. the transposable element moves from one location to another in a cell’s genome. Transposable elements may move by a “copy and paste” mechanism. an enzyme that catalyzes movement of the insertion sequence from one site to another within the genome. An inducer inactivates the repressor. transposons include extra genes that “go along for the ride. which includes two other genes coding for enzymes that function in lactose metabolism. In addition to the DNA required for transposition. Inducible enzymes usually function in catabolic pathways. and the copy inserts elsewhere. In an antibiotic-rich environment. Insertion sequences cause mutations when they happen to land within the coding sequence of a gene or within a DNA region that regulates gene expression. located outside the operon. most of the repressors are inactive.
Page | 44 . This provides RNA àDNA information flow. the F+ cell passes a copy of the F plasmid to the F− cell. While phages are the best understood of all viruses. A cell with the F factor built into its chromosome is called an Hfr cell (for High frequency of recombination). most biologists believed that the process was too rare and haphazard to play an important role in natural bacterial populations. “Maleness. coli lacks this specialized mechanism. In the lytic cycle.” conjugation transfers genetic material between two bacterial cells that are temporarily joined. coli. The Hfr cell initiates DNA replication at a point on the F factor DNA and begins to transfer the DNA copy from that point to its F− partner. Researchers have since learned that many bacterial species have surface proteins that are specialized for the uptake of naked DNA. The capsid of the tobacco mosaic virus has more than 1.” the ability to form a sex pilus and donate DNA.000 copies of the same protein. The capsid is the protein shell enclosing the viral genome. For example. Years after transformation was discovered in laboratory cultures. These proteins recognize and transport DNA from closely related bacterial species into the cell. In the last stage. Virulent phagesreproduce only by a lytic cycle. bacteria have defenses against phages. this technique has been used to introduce foreign DNA into E. These can function both as mRNA for the synthesis of viral proteins and as genomes for new virus particles released from the cell. Transductionoccurs when a phage carries bacterial genes from one host cell to another as a result of aberrations in the phage reproductive cycle. Temperate viruses are also episomes. results from an F (for fertility) factor as a section of the bacterial chromosome or as a plasmid. Adenoviruses have 252 identical proteins arranged into a polyhedral capsid—as an icosahedron. which can then incorporate the foreign DNA into the genome. the virus that causes AIDS (acquired immunodeficiency syndrome) is a retrovirus. Research on phages led to the discovery that some double-stranded DNA viruses can reproduce by two alternative mechanisms: the lytic cycle and the lysogenic cycle. the phage reproductive cycle culminates in the death of the host. In biotechnology. Sometimes known as bacterial “sex. Retroviruses(class VI) have the most complicated life cycles. with DNA derived from two different cells. The resulting cell is now recombinant. The number of different kinds of proteins making up the capsid is usually small. Some viruses have accessory structures to help them infect their hosts. Hfr cells function as males during conjugation. While phages have the potential to wipe out a bacterial colony in just hours. it can be induced to take up small pieces of DNA if cultured in a medium with a relatively high concentration of calcium ions. The transfer is one-way. Each of these phages can infect a healthy cell. Random movements almost always disrupt conjugation long before an entire copy of the Hfr chromosome can be passed to the F− cell. The newly made DNA is inserted as a provirus into a chromosome in the animal cell. Episomes such as the F plasmid can undergo reversible incorporation into the cell’s chromosome. These carry an enzyme called reverse transcriptase that transcribes DNA from an RNA template. the bacterium lyses (breaks open) and releases the phages produced within the cell to infect others. When an F+ and F− cell meet. brokenopen pathogenic cells. One cell (“male”) donates DNA and its “mate” (“female”) receives the genes. This occurs when a live nonpathogenic cell takes up a piece of DNA that happens to include the allele for pathogenicity from dead. harmless Streptococcus pneumoniae bacteria can be transformed to pneumonia-causing cells. Capsids are built of a large number of protein subunits called capsomeres. A sex pilus from the male initially joins the two cells and creates a cytoplasmic mating bridge between cells. some of them are also among the most complex. A genetic element that can replicate either as part of the bacterial chromosome or independently of it is called an episome. While E. The plasmid form of the F factor can become integrated into the bacterial chromosome. The foreign allele replaces the native allele in the bacterial chromosome by genetic recombination. converting it. Human immunodeficiency virus (HIV). The host’s RNA polymerase transcribes the viral DNA into more RNA molecules.
like phage lambda. the phage genome replicates without destroying the host cell. Each type of virus can infect and parasitize only a limited range of host cells. Natural selection favors bacterial mutants with receptor sites that are no longer recognized by a particular type of phage. Bacteria produce restriction endonucleases. called its host range. use both lytic and lysogenic cycles. Temperate phages. Natural selection also favors phage mutants that are resistant to restriction enzymes. This host specificity depends on the evolution of recognition systems by the virus. including certain phage DNA. In the lysogenic cycle. Page | 45 . or restriction enzymes. Chemical modifications to the bacteria’s own DNA prevent its destruction by restriction nucleases. that recognize and cut up foreign DNA.
This action might not be possible to undo. Are you sure you want to continue?
We've moved you to where you read on your other device.
Get the full title to continue listening from where you left off, or restart the preview.