Chapter 1-Biologists explore life from the microscopic to the global scale

• 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

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 • 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.
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 • 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.

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 • 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.

Chapter 2:
 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.
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 Two oxygen atoms can form a molecule by sharing two pairs of valence electrons.
 These atoms have formed a double covalent bond.
 The attraction of an atom for the shared electrons of a covalent bond is called its electronegativity.
 Strongly electronegative atoms attempt to pull the shared electrons toward themselves.
 If electrons in a covalent bond are shared equally, then this is a nonpolar covalent bond.
 A covalent bond between two atoms of the same element is always nonpolar.
 A covalent bond between atoms that have similar electronegativities is also nonpolar.
 Because carbon and hydrogen do not differ greatly in electronegativities, the bonds of CH4 are nonpolar.
 When two atoms that differ in electronegativity bond, they do not share the electron pair equally and form a polar covalent bond.
 The bonds between oxygen and hydrogen in water are polar covalent because oxygen has a much higher electronegativity than does
hydrogen.
 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.
 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.
 For example, sodium, with one valence electron in its third shell, transfers this electron to chlorine, with 7 valence electrons in its third shell.
 Now, sodium has a full valence shell (the second) and chlorine has a full valence shell (the third).
 After the transfer, both atoms are no longer neutral, but have charges and are called ions.
Hydrogen bondsform when a hydrogen atom already covalently bonded to a strongly electronegative atom is
attracted to another strongly electronegative atom.
 Molecules or atoms in close proximity can be attracted by these fleeting charge differences, creating van der Waals interactions.
 While individual bonds (ionic, hydrogen, van der Waals) are weak and temporary, collectively they are strong and play important biological
roles.
 About 25 of the 92 natural elements are known to be essential for life.
 Four elements—carbon (C), oxygen (O), hydrogen (H), and nitrogen (N)—make up 96% of living matter.
 Most of the remaining 4% of an organism’s weight consists of phosphorus (P), sulfur (S), calcium (Ca), and potassium (K).
 Trace elementsare required by an organism but only in minute quantities.
 Also, radioactive tracers can be used with imaging instruments to monitor chemical processes in the body.
 While useful in research and medicine, the energy emitted in radioactive decay is hazardous to life.
 This energy can destroy molecules within living cells.
 The severity of damage depends on the type and amount of radiation that the organism absorbs.
 The chemical behavior of an atom depends mostly on the number of electrons in its outermost shell, the valence shell.
 Electrons in the valence shell are known as valence electrons.
 Lithium has one valence electron; neon has eight.
 Atoms with the same number of valence electrons have similar chemical behaviors.
 An atom with a completed valence shell, like neon, is nonreactive.
 Atoms with incomplete valence shells can interact with each other by sharing or transferring valence electrons.
 These interactions typically result in the atoms remaining close together, held by attractions called chemical bonds.
 The strongest chemical bonds are covalent bonds and ionic bonds.
 A covalent bond is formed by the sharing of a pair of valence electrons by two atoms.
 If two atoms come close enough that their unshared orbitals overlap, they will share their newly paired electrons. Each atom can count both
electrons toward its goal of filling the valence shell.
 For example, if two hydrogen atoms come close enough that their 1s orbitals overlap, then they can share a pair of electrons, with each atom
contributing one.
 Two or more atoms held together by covalent bonds constitute a molecule.
 We can abbreviate the structure of the molecule by substituting a line for each pair of shared electrons, drawing the structural formula.

Chapter 3:
 The pH scale, ranging from 1 to 14, compresses the range of concentrations by employing logarithms.
 pH = − log [H+] or [H+] = 10−pH
 In a neutral solution, [H+] = 10−7 M, and the pH = 7.
 Values for pH decline as [H+] increase.
 While the pH scale is based on [H+], values for [OH−] can be easily calculated from the product relationship.
 The pH of a neutral solution is 7.
 Acidic solutions have pH values less than 7, and basic solutions have pH values greater than 7.
 Most biological fluids have pH values in the range of 6 to 8.
 However, the human stomach has strongly acidic digestive juice with a pH of about 2.
 Each pH unit represents a tenfold difference in H+ and OH− concentrations.
 A small change in pH actually indicates a substantial change in H+ and OH− concentrations.
 The chemical processes in the cell can be disrupted by changes to the H+ and OH− concentrations away from their normal values, usually near
pH 7.
 To maintain cellular pH values at a constant level, biological fluids have buffers.
 Buffers resist changes to the pH of a solution when H+ or OH− is added to the solution.
 Buffers accept hydrogen ions from the solution when they are in excess and donate hydrogen ions when they have been depleted.
 Buffers typically consist of a weak acid and its corresponding base.
 One important buffer in human blood and other biological solutions is carbonic acid, which dissociates to yield a bicarbonate ion and a
hydrogen ion.
 The chemical equilibrium between carbonic acid and bicarbonate acts as a pH regulator. The equilibrium shifts left or right as other metabolic
processes add or remove H+ from the solution.
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 An acid is a substance that increases the hydrogen ion concentration in a solution.
 When hydrochloric acid is added to water, hydrogen ions dissociate from chloride ions: HCl -> H+ + Cl−
 Addition of an acid makes a solution more acidic.
 Any substance that reduces the hydrogen ion concentration in a solution is a base.
 Some bases reduce the H+ concentration directly by accepting hydrogen ions.
 Ammonia (NH3) acts as a base when the nitrogen’s unshared electron pair attracts a hydrogen ion from the solution, creating an ammonium
ion (NH4+).
 NH3 + H+ <=> NH4+
 Other bases reduce H+ indirectly by dissociating to OH−, which then combines with H+ to form water.
 NaOH -> Na+ + OH− OH− + H+ -> H2O
 Solutions with more OH− than H+ are basic solutions.
 Solutions with more H+ than OH− are acidic solutions.
 Solutions in which concentrations of OH− and H+ are equal are neutral solutions.
 Some acids and bases (HCl and NaOH) are strong acids or bases.
 These molecules dissociate completely in water.
 Other acids and bases (NH3) are weak acids or bases.
 For these molecules, the binding and release of hydrogen ions are reversible.
 At equilibrium, there will be a fixed ratio of products to reactants.
 Carbonic acid (H2CO3) is a weak acid:
 H2CO3 <=> HCO3− + H+
 At equilibrium, 1% of the H2CO3 molecules will be dissociated.
 In any solution, the product of the H+ and OH− concentrations is constant at 10−14.
 To maintain cellular pH values at a constant level, biological fluids have buffers.
 Buffers resist changes to the pH of a solution when H+ or OH− is added to the solution.
 Buffers accept hydrogen ions from the solution when they are in excess and donate hydrogen ions when they have been depleted.
 Buffers typically consist of a weak acid and its corresponding base.
 One important buffer in human blood and other biological solutions is carbonic acid, which dissociates to yield a bicarbonate ion and a
hydrogen ion.
 The chemical equilibrium between carbonic acid and bicarbonate acts as a pH regulator. The equilibrium shifts left or right as other metabolic
processes add or remove H+ from the solution
In a water molecule, two hydrogen atoms form single polar covalent bonds with an oxygen atom.

• Because oxygen is more electronegative than hydrogen, the region around the oxygen atom has a partial negative charge.
• The regions near the two hydrogen atoms have a partial positive charge.
• A water molecule is a polar molecule in which opposite ends of the molecule have opposite charges.
• Water has a variety of unusual properties because of the attraction between polar water molecules.
• The slightly negative regions of one water molecule are attracted to the slightly positive regions of nearby water molecules, forming
hydrogen bonds.
• Each water molecule can form hydrogen bonds with up to four neighbors.
• The hydrogen bonds joining water molecules are weak, about 1/20 as strong as covalent bonds.
• They form, break, and reform with great frequency. Each hydrogen bond lasts only a few trillionths of a second.
• At any instant, a substantial percentage of all water molecules are bonded to their neighbors, creating a high level of structure.
• Collectively, hydrogen bonds hold water together, a phenomenon called cohesion.
• Cohesion among water molecules plays a key role in the transport of water and dissolved nutrients against gravity in plants.
• Water molecules move from the roots to the leaves of a plant through water-conducting vessels.
• As water molecules evaporate from a leaf, other water molecules from vessels in the leaf replace them.
• Hydrogen bonds cause water molecules leaving the vessels to tug on molecules farther down.
• This upward pull is transmitted down to the roots.
• Adhesion,clinging of one substance to another, contributes too, as water adheres to the wall of the vessels.
• Surface tension,a measure of the force necessary to stretch or break the surface of a liquid, is related to cohesion.
• Water has a greater surface tension than most other liquids because hydrogen bonds among surface water molecules resist stretching
or breaking the surface.
• Water behaves as if covered by an invisible film.
• Some animals can stand, walk, or run on water without breaking the surface.

 While there are several ways to measure heat energy, one convenient unit is the calorie (cal).
 One calorie is the amount of heat energy necessary to raise the temperature of one g of water by 1°C.
 A calorie is released when 1 g of water cools by 1°C.
 In many biological processes, the kilocalorie (kcal) is more convenient.
 A kilocalorie is the amount of heat energy necessary to raise the temperature of 1000 g of water by 1°C.
 Another common energy unit, the joule (J), is equivalent to 0.239 cal.
 Water stabilizes temperature because it has a high specific heat.

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 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.
 By definition, the specific heat of water is 1 cal per gram per degree Celsius or 1 cal/g/°C.
 Water has a high specific heat compared to other substances.
 For example, ethyl alcohol has a specific heat of 0.6 cal/g/°C.
 The specific heat of iron is 1/10 that of water.
 Water resists changes in temperature because of its high specific heat.
 In other words, water absorbs or releases a relatively large quantity of heat for each degree of temperature change.

 Water’s high specific heat is due to hydrogen bonding.

 Each dissolved ion is surrounded by a sphere of water molecules, a hydration shell.

 Eventually, water dissolves all the ions, resulting in a solution with two solutes: sodium and chloride ions.
 Polar molecules are also soluble in water because they form hydrogen bonds with water.
 Even large molecules, like proteins, can dissolve in water if they have ionic and polar regions.
 Any substance that has an affinity for water is hydrophilic (water-loving).
 These substances are dominated by ionic or polar bonds.
 Some hydrophilic substances do not dissolve because their molecules are too large.
 For example, cotton is hydrophilic because cellulose, its major constituent, has numerous polar covalent bonds. However, its giant cellulose
molecules are too large to dissolve in water.
 Water molecules form hydrogen bonds with the cellulose fibers of cotton, allowing you to dry yourself with your cotton towel as the water is
pulled into the towel.
 Substances that have no affinity for water are hydrophobic (water-fearing).
 These substances are nonionic and have nonpolar covalent bonds.
 Because there are no consistent regions with partial or full charges, water molecules cannot form hydrogen bonds with hydrophobic
molecules.
 Oils such as vegetable oil are hydrophobic because the dominant bonds, carbon-carbon and carbon-hydrogen, share electrons equally.
 Hydrophobic molecules are major ingredients of cell membranes.

Chapter 4:

· The components of organic molecules that are most commonly involved in chemical reactions are known as functional
groups.

· If we consider hydrocarbons to be the simplest organic molecules, 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.

· The number and arrangement of functional groups help give each molecule its unique properties.

· As an example, the basic structure of testosterone (a male sex hormone) and estradiol (a female sex hormone) is the
same.

· Both are steroids with four fused carbon rings, but they differ in the functional groups attached to the rings.

· These functional groups interact with different targets in the body.

· There are six functional groups that are most important to the chemistry of life: hydroxyl, carbonyl, carboxyl, amino,
sulfhydryl, and phosphate groups.

· All are hydrophilic and increase the solubility of organic compounds in water.

· In a hydroxyl group (—OH), a hydrogen atom forms a polar covalent bond with an oxygen atom, which forms a polar
covalent bond to the carbon skeleton.

· Because of these polar covalent bonds, hydroxyl groups increase the solubility of organic molecules.

· Organic compounds with hydroxyl groups are alcohols, and their names typically end in -ol.

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· A carbonyl group (>CO) consists of an oxygen atom joined to the carbon skeleton by a double bond.

· If the carbonyl group is on the end of the skeleton, the compound is an aldehyde.

· If the carbonyl group is within the carbon skeleton, then the compound is a ketone.

· Isomers with aldehydes versus ketones have different properties.

· 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.

· Compounds with carboxyl groups are carboxylic acids.

· 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+).

· An amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and the carbon skeleton.

· Organic compounds with amino groups are amines.

· The amino group acts as a base because the amino group can pick up a hydrogen ion (H+) from the solution.

· Amino acids, the building blocks of proteins, have amino and carboxyl groups.

· A sulfhydryl group (—SH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone.

· This group resembles a hydroxyl group in shape.

· Organic molecules with sulfhydryl groups are thiols.

· Two sulfhydryl groups can interact to help stabilize the structure of proteins.

· A phosphate group (—OPO32−) consists of a phosphorus atom bound to four oxygen atoms (three with single bonds and
one with a double bond).

· A phosphate group connects to the carbon backbone via one of its oxygen atoms.

· Phosphate groups are anions with two negative charges, as two protons have dissociated from the oxygen atoms.

· One function of phosphate groups is to transfer energy between organic molecules.

· Adenosine triphosphate, or ATP, is the primary energy-transferring molecule in living cells.

These are the chemical elements of life.

· Living matter consists mainly of carbon, oxygen, hydrogen, and nitrogen, with smaller amounts of sulfur and
phosphorus.

· These elements are linked by strong covalent bonds.

· Carbon, with its four covalent bonds, is the basic building block in molecular architecture.

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· 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.

Chapter 5:

• Proteins account for more than 50% of the dry mass of most cells. They are instrumental in almost everything that an organism does.
• Protein functions include structural support, storage, transport, cellular signaling, movement, and defense against foreign substances.
• Most important, protein enzymes function as catalysts in cells, regulating metabolism by selectively accelerating chemical reactions
without being consumed.
• Humans have tens of thousands of different proteins, each with a specific structure and function.
• Proteins are the most structurally complex molecules known.
• Each type of protein has a complex three-dimensional shape or conformation.
• All protein polymers are constructed from the same set of 20 amino acid monomers.
• Polymers of proteins are called polypeptides.
• A protein consists of one or more polypeptides folded and coiled into a specific conformation.

Amino acids are the monomers from which proteins are constructed.

• Amino acidsare organic molecules with both carboxyl and amino groups.
• At the center of an amino acid is an asymmetric carbon atom called the alpha carbon.
• Four components are attached to the alpha carbon: a hydrogen atom, a carboxyl group, an amino group, and a variable R group (or
side chain).
• Different R groups characterize the 20 different amino acids.
• R groups may be as simple as a hydrogen atom (as in the amino acid glycine), or it may be a carbon skeleton with various functional
groups attached (as in glutamine).
• The physical and chemical properties of the R group determine the unique characteristics of a particular amino acid.
• One group of amino acids has hydrophobic R groups.
• Another group of amino acids has polar R groups that are hydrophilic.
• A third group of amino acids includes those with functional groups that are charged (ionized) at cellular pH.
• Some acidic R groups are negative in charge due to the presence of a carboxyl group.
• Basic R groups have amino groups that are positive in charge.
• Note that all amino acids have carboxyl and amino groups. The terms acidic and basic in this context refer only to these groups in the
R groups.
• 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.
• The resulting covalent bond is called a peptide bond.
• Repeating the process over and over creates a polypeptide chain.
• 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).
• Polypeptides range in size from a few monomers to thousands.
• Each polypeptide has a unique linear sequence of amino acids.

The four major classes of macromolecules are carbohydrates, lipids, proteins, and nucleic acids.

Concept 5.2 Carbohydrates serve as fuel and building material

• Carbohydratesinclude sugars and their polymers.

• The simplest carbohydrates are monosaccharides, or simple sugars.
• Disaccharides, or double sugars, consist of two monosaccharides joined by a condensation reaction.
• Polysaccharides are polymers of many monosaccharides.

Sugars, the smallest carbohydrates, serve as fuel and a source of carbon.

• Monosaccharidesgenerally have molecular formulas that are some multiple of the unit CH2O.
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 • For example, glucose has the formula C6H12O6.
• Monosaccharides have a carbonyl group (>C=O) and multiple hydroxyl groups (—OH).
• Depending on the location of the carbonyl group, the sugar is an aldose or a ketose.
• Most names for sugars end in -ose.
• Glucose, an aldose, and fructose, a ketose, are structural isomers.
• Monosaccharides are also classified by the number of carbons in the carbon skeleton.
• Glucose and other six-carbon sugars are hexoses.
• Five-carbon backbones are pentoses; three-carbon sugars are trioses.
• Monosaccharides may also exist as enantiomers.
• For example, glucose and galactose, both six-carbon aldoses, differ in the spatial arrangement of their parts around asymmetrical
carbons.
• Monosaccharides, particularly glucose, are a major fuel for cellular work.
• They also function as the raw material for the synthesis of other monomers, such as amino acids and fatty acids.
• While often drawn as a linear skeleton, monosaccharides in aqueous solutions form rings.
• Two monosaccharides can join with a glycosidic linkage to form a disaccharide via dehydration.
• Maltose, malt sugar, is formed by joining two glucose molecules.
• Sucrose, table sugar, is formed by joining glucose and fructose. Sucrose is the major transport form of sugars in plants.
• Lactose, milk sugar, is formed by joining glucose and galactose.

Polysaccharides, the polymers of sugars, have storage and structural roles.

• Polysaccharidesare polymers of hundreds to thousands of monosaccharides joined by glycosidic linkages.

• Some polysaccharides serve for storage and are hydrolyzed as sugars are needed.
• Other polysaccharides serve as building materials for the cell or the whole organism.
• Starchis a storage polysaccharide composed entirely of glucose monomers.
• Most of these monomers are joined by 1–4 linkages (number 1 carbon to number 4 carbon) between the glucose molecules.
• The simplest form of starch, amylose, is unbranched and forms a helix.
• Branched forms such as amylopectin are more complex.
• Plants store surplus glucose as starch granules within plastids, including chloroplasts, and withdraw it as needed for energy or carbon.
• Animals that feed on plants, especially parts rich in starch, have digestive enzymes that can hydrolyze starch to glucose.
• Animals store glucose in a polysaccharide called glycogen.
• Glycogen is highly branched like amylopectin.
• Humans and other vertebrates store a day’s supply of glycogen in the liver and muscles.
• Celluloseis a major component of the tough wall of plant cells.
• Plants produce almost one hundred billion tons of cellulose per year. It is the most abundant organic compound on Earth.
• Like starch, cellulose is a polymer of glucose. However, the glycosidic linkages in these two polymers differ.
• The difference is based on the fact that there are actually two slightly different ring structures for glucose.
• 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.
• Starch is a polysaccharide of alpha glucose monomers.
• Cellulose is a polysaccharide of beta glucose monomers, 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 polymers built with alpha glucose form helical structures, polymers built with beta glucose form straight structures.
• The straight structures built with beta glucose allow H atoms on one strand to form hydrogen bonds with OH groups on other strands.
• In plant cell walls, parallel cellulose molecules held together in this way are grouped into units called microfibrils, which form strong
building materials for plants (and for humans, as lumber).
• The enzymes that digest starch by hydrolyzing its alpha linkages cannot hydrolyze the beta linkages in cellulose.
• Cellulose in human food passes through the digestive tract and is eliminated in feces as “insoluble fiber.”
• As it travels through the digestive tract, cellulose abrades the intestinal walls and stimulates the secretion of mucus, aiding in the
passage of food.
• Some microbes can digest cellulose to its glucose monomers through the use of cellulase enzymes.
• Many eukaryotic herbivores, from cows to termites, have symbiotic relationships with cellulolytic microbes, providing the microbe
and the host animal access to a rich source of energy.
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 • Some fungi can also digest cellulose.
• Another important structural polysaccharide is chitin, used in the exoskeletons of arthropods (including insects, spiders, and
crustaceans).
• Chitin is similar to cellulose, except that it contains a nitrogen-containing appendage on each glucose monomer.
• Pure chitin is leathery but can be hardened by the addition of calcium carbonate.
• Chitin also provides structural support for the cell walls of many fungi.

Concept 5.3 Lipids are a diverse group of hydrophobic molecules

• Unlike other macromolecules, lipids do not form polymers.

• The unifying feature of lipids is that they all have little or no affinity for water.
• This is because they consist mostly of hydrocarbons, which form nonpolar covalent bonds.
• Lipids are highly diverse in form and function.

Fats store large amounts of energy.

• Although fats are not strictly polymers, they are large molecules assembled from smaller molecules by dehydration reactions.
• A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids.
• Glycerolis a three-carbon alcohol with a hydroxyl group attached to each carbon.
• A fatty acid consists of a carboxyl group attached to a long carbon skeleton, often 16 to 18 carbons long.
• The many nonpolar C—H bonds in the long hydrocarbon skeleton make fats hydrophobic.
• Fats separate from water because the water molecules hydrogen bond to one another and exclude the fats.
• In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride.
• The three fatty acids in a fat can be the same or different.
• Fatty acids may vary in length (number of carbons) and in the number and locations of double bonds.
• If the fatty acid has no carbon-carbon double bonds, then the molecule is a saturated fatty acid, saturated with hydrogens at every
possible position.
• If the fatty acid has one or more carbon-carbon double bonds formed by the removal of hydrogen atoms from the carbon skeleton,
then the molecule is an unsaturated fatty acid.
• A saturated fatty acid is a straight chain, but an unsaturated fatty acid has a kink wherever there is a double bond.
• Fats made from saturated fatty acids are saturated fats.
• Most animal fats are saturated.
• Saturated fats are solid at room temperature.
• Fats made from unsaturated fatty acids are unsaturated fats.
• Plant and fish fats are liquid at room temperature and are known as oils.
• The kinks caused by the double bonds prevent the molecules from packing tightly enough to solidify at room temperature.
• The phrase “hydrogenated vegetable oils” on food labels means that unsaturated fats have been synthetically converted to saturated
fats by the addition of hydrogen.
• Peanut butter and margarine are hydrogenated to prevent lipids from separating out as oil.
• A diet rich in saturated fats may contribute to cardiovascular disease (atherosclerosis) through plaque deposits.
• The process of hydrogenating vegetable oils produces saturated fats and also unsaturated fats with trans double bonds. These trans fat
molecules contribute more than saturated fats to atherosclerosis.
• The major function of fats is energy storage.
• A gram of fat stores more than twice as much energy as a gram of a polysaccharide such as starch.
• Because plants are immobile, they can function with bulky energy storage in the form of starch. Plants use oils when dispersal and
compact storage is important, as in seeds.
• Animals must carry their energy stores with them and benefit from having a more compact fuel reservoir of fat.
• 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.
• Adipose tissue also functions to cushion vital organs, such as the kidneys.
• A layer of fat can also function as insulation.
• This subcutaneous layer is especially thick in whales, seals, and most other marine mammals.

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Phospholipids are major components of cell membranes.

• Phospholipidshave two fatty acids attached to glycerol and a phosphate group at the third position.
• The phosphate group carries a negative charge.
• Additional smaller groups may be attached to the phosphate group to form a variety of phospholipids.
• The interaction of phospholipids with water is complex.
• The fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head.
• When phospholipids are added to water, they self-assemble into assemblages with the hydrophobic tails pointing toward the interior.
• This type of structure is called a micelle.
• Phospholipids are arranged as a bilayer at the surface of a cell.
• Again, the hydrophilic heads are on the outside of the bilayer, in contact with the aqueous solution, and the hydrophobic tails point
toward the interior of the bilayer.
• The phospholipid bilayer forms a barrier between the cell and the external environment.
• Phospholipids are the major component of all cell membranes.

Steroids include cholesterol and certain hormones.

• Steroidsare lipids with a carbon skeleton consisting of four fused rings.

• Different steroids are created by varying functional groups attached to the rings.
• Cholesterol,an important steroid, is a component in animal cell membranes.
• Cholesterol is also the precursor from which all other steroids are synthesized.
• Many of these other steroids are hormones, including the vertebrate sex hormones.
• While cholesterol is an essential molecule in animals, high levels of cholesterol in the blood may contribute to cardiovascular disease.
• Both saturated fats and trans fats exert their negative impact on health by affecting cholesterol levels.

Amino acids are the monomers from which proteins are constructed.

• Amino acidsare organic molecules with both carboxyl and amino groups.
• At the center of an amino acid is an asymmetric carbon atom called the alpha carbon.
• Four components are attached to the alpha carbon: a hydrogen atom, a carboxyl group, an amino group, and a variable R group (or
side chain).
• Different R groups characterize the 20 different amino acids.
• R groups may be as simple as a hydrogen atom (as in the amino acid glycine), or it may be a carbon skeleton with various functional
groups attached (as in glutamine).
• The physical and chemical properties of the R group determine the unique characteristics of a particular amino acid.
• One group of amino acids has hydrophobic R groups.
• Another group of amino acids has polar R groups that are hydrophilic.
• A third group of amino acids includes those with functional groups that are charged (ionized) at cellular pH.
• Some acidic R groups are negative in charge due to the presence of a carboxyl group.
• Basic R groups have amino groups that are positive in charge.
• Note that all amino acids have carboxyl and amino groups. The terms acidic and basic in this context refer only to these groups in the
R groups.
• 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.
• The resulting covalent bond is called a peptide bond.
• Repeating the process over and over creates a polypeptide chain.
• 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).
• Polypeptides range in size from a few monomers to thousands.
• Each polypeptide has a unique linear sequence of amino acids.

The amino acid sequence of a polypeptide can be determined.

• Frederick Sanger and his colleagues at Cambridge University determined the amino acid sequence of insulin in the 1950s.
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 • Sanger used protein-digesting enzymes and other catalysts to hydrolyze the insulin at specific places.
• The fragments were then separated by a technique called chromatography.
• Hydrolysis by another agent broke the polypeptide at different sites, yielding a second group of fragments.
• Sanger used chemical methods to determine the sequence of amino acids in the small fragments.
• He then searched for overlapping regions among the pieces obtained by hydrolyzing with the different agents.
• After years of effort, Sanger was able to reconstruct the complete primary structure of insulin.
• Most of the steps in sequencing a polypeptide have since been automated.

Protein conformation determines protein function.

• A functional protein consists of one or more polypeptides that have been twisted, folded, and coiled into a unique shape.
• It is the order of amino acids that determines what the three-dimensional conformation of the protein will be.
• A protein’s specific conformation determines its function.
• When a cell synthesizes a polypeptide, the chain generally folds spontaneously to assume the functional conformation for that protein.
• The folding is reinforced by a variety of bonds between parts of the chain, which in turn depend on the sequence of amino acids.
• Many proteins are globular, while others are fibrous in shape.
• In almost every case, the function of a protein depends on its ability to recognize and bind to some other molecule.
• For example, an antibody binds to a particular foreign substance.
• An enzyme recognizes and binds to a specific substrate, facilitating a chemical reaction.
• Natural signal molecules called endorphins bind to specific receptor proteins on the surface of brain cells in humans, producing
euphoria and relieving pain.
• Morphine, heroin, and other opiate drugs mimic endorphins because they are similar in shape and can bind to the brain’s endorphin
receptors.
• The function of a protein is an emergent property resulting from its specific molecular order.
• Three levels of structure—primary, secondary, and tertiary structures—organize the folding within a single polypeptide.
• Quaternary structure arises when two or more polypeptides join to form a protein.
• The primary structure of a protein is its unique sequence of amino acids.
• Lysozyme, an enzyme that attacks bacteria, consists of 129 amino acids.
• The precise primary structure of a protein is determined by inherited genetic information.
• Even a slight change in primary structure can affect a protein’s conformation and ability to function.
• The substitution of one amino acid (valine) for the normal one (glutamic acid) at a particular position in the primary structure of
hemoglobin, the protein that carries oxygen in red blood cells, can cause sickle-cell disease, an inherited blood disorder.
• The abnormal hemoglobins crystallize, deforming the red blood cells into a sickle shape and clogging capillaries.
• Most proteins have segments of their polypeptide chains repeatedly coiled or folded.
• These coils and folds are referred to as secondary structure and result from hydrogen bonds between the repeating constituents of the
polypeptide backbone.
• The weakly positive hydrogen atom attached to the nitrogen atom has an affinity for the oxygen atom of a nearby peptide bond.
• Each hydrogen bond is weak, but the sum of many hydrogen bonds stabilizes the structure of part of the protein.
• Typical secondary structures are coils (an alpha helix) or folds (beta pleated sheets).
• The structural properties of silk are due to beta pleated sheets.
• The presence of so many hydrogen bonds makes each silk fiber stronger than a steel strand of the same weight.
• Tertiary structureis determined by interactions among various R groups.
• These interactions include hydrogen bonds between polar and/or charged areas, ionic bonds between charged R groups, and
hydrophobic interactions and van der Waals interactions among hydrophobic R groups.
• While these three interactions are relatively weak, 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.
• Quaternary structureresults from the aggregation of two or more polypeptide subunits.
• Collagen is a fibrous protein of three polypeptides that are supercoiled like a rope.
• This provides structural strength for collagen’s role in connective tissue.
• Hemoglobin is a globular protein with quaternary structure.
• It consists of four polypeptide subunits: two alpha and two beta chains.
• Both types of subunits consist primarily of alpha-helical secondary structure.
• Each subunit has a nonpeptide heme component with an iron atom that binds oxygen.
• What are the key factors determining protein conformation?
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 • 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.
• The folding occurs as the protein is being synthesized within the cell.
• However, protein conformation also depends on the physical and chemical conditions of the protein’s environment.
• Alterations in pH, salt concentration, temperature, or other factors can unravel or denature a protein.
• These forces disrupt the hydrogen bonds, ionic bonds, and disulfide bridges that maintain the protein’s shape.
• Most proteins become denatured if the are transferred to an organic solvent. The polypeptide chain refolds so that its hydrophobic
regions face outward, toward the solvent.
• Denaturation can also be caused by heat, which disrupts the weak interactions that stabilize conformation.
• This explains why extremely high fevers can be fatal. Proteins in the blood become denatured by the high body temperatures.
• Some proteins can return to their functional shape after denaturation, but others cannot, especially in the crowded environment of the
cell.
• Biochemists now know the amino acid sequences of more than 875,000 proteins and the 3D shapes of about 7,000.
• Nevertheless, it is still difficult to predict the conformation of a protein from its primary structure alone.
• Most proteins appear to undergo several intermediate stages before reaching their “mature” configuration.
• The folding of many proteins is assisted by chaperonins or chaperone proteins.
• Chaperonins do not specify the final structure of a polypeptide but rather work to segregate and protect the polypeptide while it folds
spontaneously.
• At present, scientists use X-ray crystallography to determine protein conformation.
• This technique requires the formation of a crystal of the protein being studied.
• 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.
• Nuclear magnetic resonance (NMR) spectroscopy has recently been applied to this problem.
• This method does not require protein crystallization.

Chapter 6:

 Chemical reactions can be classified as either exergonic or endergonic based on free energy.
 An exergonic reaction proceeds with a net release of free energy; DGis negative.
 The magnitude of DGfor an exergonic reaction is the maximum amount of work the reaction can perform.
 The greater the decrease in free energy, the greater the amount of work that can be done.
 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, 686 kcal of energy are made available to do work in the cell.
 The products have 686 kcal less free energy than the reactants.
 An endergonic reaction is one that absorbs free energy from its surroundings.
 Endergonic reactions store energy in molecules; DGis positive.
 Endergonic reactions are nonspontaneous, and the magnitude of DGis the quantity of energy required to drive the reaction.
 If cellular respiration releases 686 kcal, then photosynthesis, the reverse reaction, must require an equivalent investment of energy.
 For the conversion of carbon dioxide and water to sugar, DG= +686 kcal/mol.
 Photosynthesis is strongly endergonic, powered by the absorption of light energy.
 Reactions in a closed system eventually reach equilibrium and can do no work.
 A cell that has reached metabolic equilibrium has a DG= 0 and is dead!
 Metabolic disequilibrium is one of the defining features of life.
 Cells maintain disequilibrium because they are open systems. The constant flow of materials into and out of the cell keeps metabolic
pathways from ever reaching equilibrium.
 A cell continues to do work throughout its life.
 A catabolic process in a cell releases free energy in a series of reactions, not in a single step.
 Some reversible reactions of respiration are constantly “pulled” in one direction, as the product of one reaction does not accumulate but
becomes the reactant in the next step.
 Sunlight provides a daily source of free energy for photosynthetic organisms.

 Nonphotosynthetic organisms depend on a transfer of free energy from photosynthetic organisms in the form of organic molecules.

 Energy transfers and transformations make the universe more disordered due to this loss of usable energy.
 Entropyis a quantity used as a measure of disorder or randomness.

 The more random a collection of matter, the greater its entropy.

 Free energy can be thought of as a measure of the stability of a system.

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 Systems that are high in free energy—compressed springs, separated charges, organic polymers—are unstable and tend to move toward a
more stable state, one with less free energy.
 Systems that tend to change spontaneously are those that have high enthalpy, low entropy, or both.
 In any spontaneous process, the free energy of a system decreases.
 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, the system must either give up enthalpy (decrease in H), give up order (increase in S), or both.
 DGmust be negative for a process to be spontaneous.
 Every spontaneous process is characterized by a decrease in the free energy of the system.
 Processes that have a positive or zero DG are never spontaneous.
 The greater the decrease in free energy, the more work a spontaneous process can perform.
 Nature runs “downhill.”
 A system at equilibrium is at maximum stability.
 In a chemical reaction at equilibrium, the rates of forward and backward reactions are equal, and there is no change in the concentration of
products or reactants.
 At equilibrium DG= 0, and the system can do no work.
 A process is spontaneous and can perform work only when it is moving toward equilibrium.
 Movements away from equilibrium are nonspontaneous and require the addition of energy from an outside energy source (the surroundings).
 Chemical reactions can be classified as either exergonic or endergonic based on free energy.
 An exergonic reaction proceeds with a net release of free energy; DGis negative.
 The magnitude of DGfor an exergonic reaction is the maximum amount of work the reaction can perform.

 The greater the decrease in free energy, the greater the amount of work that can be done.

 Thermodynamicsis the study of energy transformations.

 In this field, the term system refers to the matter under study and the surroundings include everything outside the system.
 A closed system, approximated by liquid in a thermos, is isolated from its surroundings.
 In an open system, energy and matter can be transferred between the system and its surroundings.
 Organisms are open systems.
 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 first law of thermodynamics states that energy can be transferred and transformed, but it cannot be created or destroyed.
 The first law is also known as the principle of conservation of energy.
 Plants do not produce energy; they transform light energy to chemical energy.
 During every transfer or transformation of energy, some energy is converted to heat, which is the energy associated with the random
movement of atoms and molecules.
 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.
 If temperature is uniform, as in a living cell, heat can only be used to warm the organism.
 Energy transfers and transformations make the universe more disordered due to this loss of usable energy.
 Entropyis a quantity used as a measure of disorder or randomness.
 The more random a collection of matter, the greater its entropy.
 The second law of thermodynamics states that every energy transfer or transformation increases the entropy of the universe.
 While order can increase locally, there is an unstoppable trend toward randomization of the universe.
 Much of the increased entropy of the universe takes the form of increasing heat, which is the energy of random molecular motion.
 In most energy transformations, ordered forms of energy are converted at least partly to heat.
 Automobiles convert only 25% of the energy in gasoline into motion; the rest is lost as heat.
 Living cells unavoidably convert organized forms of energy to heat.
 For a process to occur on its own, without outside help in the form of energy input, it must increase the entropy of the universe.
 The word spontaneous describes a process that can occur without an input of energy.
 Spontaneous processes need not occur quickly.
 Some spontaneous processes are instantaneous, such as an explosion. Some are very slow, such as the rusting of an old car.
 Another way to state the second law of thermodynamics is for a process to occur spontaneously, it must increase the entropy of the universe.

 Living systems create ordered structures from less ordered starting materials.

Metabolism, the intersecting set of chemical pathways characteristic of life, is a choreographed interplay of
thousands of different kinds of cellular molecules.

 Structures within the cell help bring order to metabolic pathways.

 A team of enzymes for several steps of a metabolic pathway may be assembled as a multienzyme complex.
 The product from the first reaction can then pass quickly to the next enzyme until the final product is released.
 Some enzymes and enzyme complexes have fixed locations within the cells as structural components of particular membranes.

 Others are confined within membrane-enclosed eukaryotic organelles.

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 • In many cases, the molecules that naturally regulate enzyme activity behave like reversible noncompetitive inhibitors.
• Regulatory molecules often bind weakly to an allosteric site, a specific receptor on the enzyme away from the active site.
• Binding by these molecules can either inhibit or stimulate enzyme activity.
• Most allosterically regulated enzymes are constructed of two or more polypeptide chains.
• Each subunit has its own active site.
• Allosteric sites are often located where subunits join.
• The binding of an activator stabilizes the conformation that has functional active sites, while the binding of an inhibitor stabilizes the
inactive form of the enzyme.
• As the chemical conditions in the cell shift, the pattern of allosteric regulation may shift as well.
• By binding to key enzymes, reactants and products of ATP hydrolysis may play a major role in balancing the flow of traffic between
anabolic and catabolic pathways.
• For example, ATP binds to several catabolic enzymes allosterically, inhibiting their activity by lowering their affinity for substrate.
• ADP functions as an activator of the same enzymes.
• ATP and ADP also affect key enzymes in anabolic pathways.
• In this way, allosteric enzymes control the rates of key reactions in metabolic pathways.
• In enzymes with multiple catalytic subunits, binding by a substrate to one active site stabilizes favorable conformational changes at all
other subunits, a process called cooperativity.
• This mechanism amplifies the response of enzymes to substrates, priming the enzyme to accept additional substrates.
• 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 product acts as an inhibitor of an enzyme in the pathway.
• Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed.
•  Heat would speed up reactions, but it would also denature proteins and kill cells.
•  Enzymes speed reactions by lowering EA.
•  The transition state can then be reached even at moderate temperatures.
•  Enzymes do not change DG.
•  They hasten reactions that would occur eventually.
•  Because enzymes are so selective, they determine which chemical processes will occur at any time.

By binding to key enzymes, reactants and products of ATP hydrolysis may play a major role in balancing the
flow of traffic between anabolic and catabolic pathways.

 If inhibitors attach to the enzyme by covalent bonds, inhibition may be irreversible.

 If inhibitors bind by weak bonds, inhibition may be reversible.

As the substrate enters the active site, interactions between the substrate and the amino acids of the protein
causes the enzyme to change shape slightly, leading to a tighter induced fit that brings chemical groups in
position to catalyze the reaction.

Chapter 7:

• The discovery and early study of cells progressed with the invention of microscopes in 1590 and their improvement in the 17th
century.
• In a light microscope (LM), visible light passes through the specimen and then through glass lenses.
• The lenses refract light such that the image is magnified into the eye or onto a video screen.
• Microscopes vary in magnification and resolving power.
• Magnificationis the ratio of an object’s image to its real size.
• Resolving poweris a measure of image clarity.
• It is the minimum distance two points can be separated and still be distinguished as two separate points.
• Resolution is limited by the shortest wavelength of the radiation used for imaging.
• The minimum resolution of a light microscope is about 200 nanometers (nm), the size of a small bacterium.
• Light microscopes can magnify effectively to about 1,000 times the size of the actual specimen.
• At higher magnifications, the image blurs.

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• Techniques developed in the 20th century have enhanced contrast and enabled particular cell components to be stained or labeled so
they stand out.
• While a light microscope can resolve individual cells, it cannot resolve much of the internal anatomy, especially the organelles.
• To resolve smaller structures, we use an electron microscope (EM), which focuses a beam of electrons through the specimen or onto
its surface.
• Because resolution is inversely related to wavelength used, electron microscopes (whose electron beams have shorter wavelengths
than visible light) have finer resolution.
• Theoretically, the resolution of a modern EM could reach 0.002 nanometer (nm), but the practical limit is closer to about 2 nm.
• Transmission electron microscopes (TEMs)are used mainly to study the internal ultrastructure of cells.
• A TEM aims an electron beam through a thin section of the specimen.
• The image is focused and magnified by electromagnets.
• To enhance contrast, the thin sections are stained with atoms of heavy metals.
• Scanning electron microscopes (SEMs)are useful for studying surface structures.
• The sample surface is covered with a thin film of gold.
• The beam excites electrons on the surface of the sample.
• These secondary electrons are collected and focused on a screen.
• The result is an image of the topography of the specimen.
• The SEM has great depth of field, resulting in an image that seems three-dimensional.
• Electron microscopes reveal organelles that are impossible to resolve with the light microscope.
• However, electron microscopes can only be used on dead cells.
• Light microscopes do not have as high a resolution, but they can be used to study live cells.
• Microscopes are major tools in cytology, the study of cell structures.
• Cytology combined with biochemistry, the study of molecules and chemical processes in metabolism, to produce modern cell biology.
• 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, a machine that can spin at up to 130,000 revolutions per minute and apply forces of
more than 1 million times gravity (1,000,000 g).
• Fractionation begins with homogenization, gently disrupting the cell.
• The homogenate is spun in a centrifuge to separate heavier pieces into the pellet while lighter particles remain in the supernatant.
• As the process is repeated at higher speeds and for longer durations, smaller and smaller organelles can be collected in subsequent
pellets.
• Cell fractionation prepares isolates of specific cell components.
• This enables the functions of these organelles to be determined, especially by the reactions or processes catalyzed by their proteins.
• For example, one cellular fraction was enriched in enzymes that function in cellular respiration.
• Electron microscopy revealed that this fraction is rich in mitochondria.
• This evidence helped cell biologists determine that mitochondria are the site of cellular respiration.
• Cytology and biochemistry complement each other in correlating cellular structure and function.
• All cells are surrounded by a plasma membrane.
• The semifluid substance within the membrane is the cytosol, containing the organelles.
• All cells contain chromosomes that have genes in the form of DNA.
• All cells also have ribosomes, tiny organelles that make proteins using the instructions contained in genes.
• A major difference between prokaryotic and eukaryotic cells is the location of chromosomes.
• In a eukaryotic cell, chromosomes are contained in a membrane-enclosed organelle, the nucleus.
• In a prokaryotic cell, the DNA is concentrated in the nucleoid without a membrane separating it from the rest of the cell.
• In eukaryote cells, the chromosomes are contained within a membranous nuclear envelope.
• The region between the nucleus and the plasma membrane is the cytoplasm.
• All the material within the plasma membrane of a prokaryotic cell is cytoplasm.
• Within the cytoplasm of a eukaryotic cell are a variety of membrane-bound organelles of specialized form and function.
• These membrane-bound organelles are absent in prokaryotes.
• Eukaryotic cells are generally much bigger than prokaryotic cells.
• The logistics of carrying out metabolism set limits on cell size.
• At the lower limit, the smallest bacteria, mycoplasmas, are between 0.1 to 1.0 micron.
• Most bacteria are 1–10 microns in diameter.
• Eukaryotic cells are typically 10–100 microns in diameter.

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 • Metabolic requirements also set an upper limit to the size of a single cell.
• As a cell increases in size, its volume increases faster than its surface area.
• Smaller objects have a greater ratio of surface area to volume.
• The plasma membrane functions as a selective barrier that allows the passage of oxygen, nutrients, and wastes for the whole volume
of the cell.
• The volume of cytoplasm determines the need for this exchange.
• Rates of chemical exchange across the plasma membrane may be inadequate to maintain a cell with a very large cytoplasm.
• The need for a surface sufficiently large to accommodate the volume explains the microscopic size of most cells.
• Larger organisms do not generally have larger cells than smaller organisms—simply more cells.
• Cells that exchange a lot of material with their surroundings, such as intestinal cells, may have long, thin projections from the cell
surface called microvilli. Microvilli increase surface area without significantly increasing cell volume.

Concept 6.3 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.

• Additional genes are located in mitochondria and chloroplasts.
• The nucleus averages about 5 microns in diameter.
• The nucleus is separated from the cytoplasm by a double membrane called the nuclear envelope.
• The two membranes of the nuclear envelope are separated by 20–40 nm.
• The envelope is perforated by pores that are about 100 nm in diameter.
• At the lip of each pore, the inner and outer membranes of the nuclear envelope are fused to form a continuous membrane.
• A protein structure called a pore complex lines each pore, regulating the passage of certain large macromolecules and particles.
• The nuclear side of the envelope is lined by the nuclear lamina, a network of protein filaments that maintains the shape of the
nucleus.
• There is evidence that a framework of fibers called the nuclear matrix extends through the nuclear interior.
• Within the nucleus, the DNA and associated proteins are organized into discrete units called chromosomes, structures that carry the
genetic information.
• Each chromosome is made up of fibrous material called chromatin, a complex of proteins and DNA.
• Stained chromatin appears through light microscopes and electron microscopes as a diffuse mass.
• As the cell prepares to divide, the chromatin fibers coil up and condense, becoming thick enough to be recognized as the familiar
chromosomes.
• Each eukaryotic species has a characteristic number of chromosomes.
• A typical human cell has 46 chromosomes.
• A human sex cell (egg or sperm) has only 23 chromosomes.
• In the nucleus is a region of densely stained fibers and granules adjoining chromatin, the nucleolus.
• In the nucleolus, ribosomal RNA (rRNA) is synthesized and assembled with proteins from the cytoplasm to form ribosomal subunits.
• The subunits pass through the nuclear pores to the cytoplasm, where they combine to form ribosomes.
• The nucleus directs protein synthesis by synthesizing messenger RNA (mRNA).
• 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 build a cell’s proteins.

• Ribosomes,containing rRNA and protein, are the organelles that carry out protein synthesis.
• Cell types that synthesize large quantities of proteins (e.g., pancreas cells) have large numbers of ribosomes and prominent nucleoli.
• Some ribosomes, free ribosomes, are suspended in the cytosol and synthesize proteins that function within the cytosol.
• Other ribosomes, bound ribosomes, are attached to the outside of the endoplasmic reticulum or nuclear envelope.
• These synthesize proteins that are either included in membranes or exported from the cell.
• Ribosomes can shift between roles depending on the polypeptides they are synthesizing.

Concept 6.4 The endomembrane system regulates protein traffic and performs metabolic functions in the cell

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 • Many of the internal membranes in a eukaryotic cell are part of the endomembrane system.
• These membranes are either directly continuous or connected via transfer of vesicles, sacs of membrane.
• In spite of these connections, these membranes are diverse in function and structure.
• The thickness, 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.
• The endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and the
plasma membrane.

The endoplasmic reticulum manufactures membranes and performs many other biosynthetic functions.

• The endoplasmic reticulum (ER) accounts for half the membranes in a eukaryotic cell.
• The ER includes membranous tubules and internal, fluid-filled spaces called cisternae.
• The ER membrane is continuous with the nuclear envelope, and the cisternal space of the ER is continuous with the space between the
two membranes of the nuclear envelope.
• There are two connected regions of ER that differ in structure and function.
• Smooth ERlooks smooth because it lacks ribosomes.
• Rough ERlooks rough because ribosomes (bound ribosomes) are attached to the outside, including the outside of the nuclear
envelope.
• The smooth ER is rich in enzymes and plays a role in a variety of metabolic processes.
• Enzymes of smooth ER synthesize lipids, including oils, phospholipids, and steroids.
• These include the sex hormones of vertebrates and adrenal steroids.
• In the smooth ER of the liver, enzymes help detoxify poisons and drugs such as alcohol and barbiturates.
• Frequent use of these drugs leads to the proliferation of smooth ER in liver cells, increasing the rate of detoxification.
• This increases tolerance to the target and other drugs, so higher doses are required to achieve the same effect.
• Smooth ER stores calcium ions.
• Muscle cells have a specialized smooth ER that pumps calcium ions from the cytosol and stores them in its cisternal space.
• When a nerve impulse stimulates a muscle cell, calcium ions rush from the ER into the cytosol, triggering contraction.
• Enzymes then pump the calcium back, readying the cell for the next stimulation.
• Rough ER is especially abundant in cells that secrete proteins.
• As a polypeptide is synthesized on a ribosome attached to rough ER, it is threaded into the cisternal space through a pore formed by a
protein complex in the ER membrane.
• As it enters the cisternal space, the new protein folds into its native conformation.
• Most secretory polypeptides are glycoproteins, proteins to which a carbohydrate is attached.
• Secretory proteins are packaged in transport vesicles that carry them to their next stage.
• Rough ER is also a membrane factory.
• Membrane-bound proteins are synthesized directly into the membrane.
• Enzymes in the rough ER also synthesize phospholipids from precursors in the cytosol.
• As the ER membrane expands, membrane can be transferred as transport vesicles to other components of the endomembrane system.

The Golgi apparatus is the shipping and receiving center for cell products.

• Many transport vesicles from the ER travel to the Golgi apparatus for modification of their contents.
• The Golgi is a center of manufacturing, warehousing, sorting, and shipping.
• The Golgi apparatus is especially extensive in cells specialized for secretion.
• The Golgi apparatus consists of flattened membranous sacs—cisternae—looking like a stack of pita bread.
• The membrane of each cisterna separates its internal space from the cytosol.
• One side of the Golgi, the cis side, is located near the ER. The cis face receives material by fusing with transport vesicles from the ER.
• The other side, the trans side, buds off vesicles that travel to other sites.
• During their transit from the cis to the trans side, products from the ER are usually modified.
• The Golgi can also manufacture its own macromolecules, including pectin and other noncellulose polysaccharides.
• The Golgi apparatus is a very dynamic structure.
• According to the cisternal maturation model, the cisternae of the Golgi progress from the cis to the trans face, carrying and modifying
their protein cargo as they move.
• Finally, the Golgi sorts and packages materials into transport vesicles.
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 • Molecular identification tags are added to products to aid in sorting.
• Products are tagged with identifiers such as phosphate groups. These act like ZIP codes on mailing labels to identify the product’s
final destination.

Lysosomes are digestive compartments.

• A lysosome is a membrane-bound sac of hydrolytic enzymes that an animal cell uses to digest macromolecules.
• Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids.
• These enzymes work best at pH 5.
• Proteins in the lysosomal membrane pump hydrogen ions from the cytosol into the lumen of the lysosomes.
• 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.
• However, massive rupture of many lysosomes can destroy a cell by autodigestion.
• Lysosomal enzymes and membrane are synthesized by rough ER and then transferred to the Golgi apparatus for further modification.
• Proteins on the inner surface of the lysosomal membrane are spared by digestion by their three-dimensional conformations, which
protect vulnerable bonds from hydrolysis.
• Lysosomes carry out intracellular digestion in a variety of circumstances.
• Amoebaseat by engulfing smaller organisms by phagocytosis.
• The food vacuole formed by phagocytosis fuses with a lysosome, whose enzymes digest the food.
• As the polymers are digested, monomers pass to the cytosol to become nutrients for the cell.
• Lysosomes can play a role in recycling of the cell’s organelles and macromolecules.
• This recycling, or autophagy, renews the cell.
• During autophagy, a damaged organelle or region of cytosol becomes surrounded by membrane.
• A lysosome fuses with the resulting vesicle, digesting the macromolecules and returning the organic monomers to the cytosol for
reuse.
• The lysosomes play a critical role in the programmed destruction of cells in multicellular organisms.
• This process plays an important role in development.
• The hands of human embryos are webbed until lysosomes digest the cells in the tissue between the fingers.
• This important process is called programmed cell death, or apoptosis.

Vacuoles have diverse functions in cell maintenance.

• Vesicles and vacuoles (larger versions) are membrane-bound sacs with varied functions.
• Food vacuolesare formed by phagocytosis and fuse with lysosomes.
• Contractile vacuoles,found in freshwater protists, pump excess water out of the cell to maintain the appropriate concentration of salts.
• A large central vacuole is found in many mature plant cells.
• The membrane surrounding the central vacuole, the tonoplast, is selective in its transport of solutes into the central vacuole.
• The functions of the central vacuole include stockpiling proteins or inorganic ions, disposing of metabolic byproducts, holding
pigments, and storing defensive compounds that defend the plant against herbivores.
• Because of the large vacuole, the cytosol occupies only a thin layer between the plasma membrane and the tonoplast. The presence of
a large vacuole increases surface area to volume ratio for the cell.

Concept 6.5 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.
• Mitochondriaare the sites of cellular respiration, generating ATP from the catabolism of sugars, fats, and other fuels in the presence
of oxygen.
• Chloroplasts,found in plants and algae, are the sites of photosynthesis.
• They convert solar energy to chemical energy and synthesize new organic compounds such as sugars from CO2 and H2O.
• Mitochondria and chloroplasts are not part of the endomembrane system.
• In contrast to organelles of the endomembrane system, each mitochondrion or chloroplast has two membranes separating the
innermost space from the cytosol.

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 • Their membrane proteins are not made by the ER, but rather by free ribosomes in the cytosol and by ribosomes within the organelles
themselves.
• Both organelles have small quantities of DNA that direct the synthesis of the polypeptides produced by these internal ribosomes.
• Mitochondria and chloroplasts grow and reproduce as semiautonomous organelles.
• Almost all eukaryotic cells have mitochondria.
• There may be one very large mitochondrion or hundreds to thousands of individual mitochondria.
• The number of mitochondria is correlated with aerobic metabolic activity.
• A typical mitochondrion is 1–10 microns long.
• Mitochondria are quite dynamic: moving, changing shape, and dividing.
• Mitochondria have a smooth outer membrane and a convoluted inner membrane with infoldings called cristae.
• The inner membrane divides the mitochondrion into two internal compartments.
• The first is the intermembrane space, a narrow region between the inner and outer membranes.
• The inner membrane encloses the mitochondrial matrix, a fluid-filled space with DNA, ribosomes, and enzymes.
• Some of the metabolic steps of cellular respiration are catalyzed by enzymes in the matrix.
• The cristae present a large surface area for the enzymes that synthesize ATP.
• The chloroplast is one of several members of a generalized class of plant structures called plastids.
• Amyloplasts are colorless plastids that store starch in roots and tubers.
• Chromoplasts store pigments for fruits and flowers.
• Chloroplasts contain the green pigment chlorophyll as well as enzymes and other molecules that function in the photosynthetic
production of sugar.
• Chloroplasts measure about 2 microns × 5 microns and are found in leaves and other green organs of plants and algae.
• The contents of the chloroplast are separated from the cytosol by an envelope consisting of two membranes separated by a narrow
intermembrane space.
• Inside the innermost membrane is a fluid-filled space, the stroma, in which float membranous sacs, the thylakoids.
• The stroma contains DNA, ribosomes, and enzymes.
• The thylakoids are flattened sacs that play a critical role in converting light to chemical energy. In some regions, thylakoids are
stacked like poker chips into grana.
• The membranes of the chloroplast divide the chloroplast into three compartments: the intermembrane space, the stroma, and the
thylakoid space.
• Like mitochondria, chloroplasts are dynamic structures.
• Their shape is plastic, and they can reproduce themselves by pinching in two.
• Mitochondria and chloroplasts are mobile and move around the cell along tracks of the cytoskeleton.

Peroxisomes generate and degrade H2O2 in performing various metabolic functions.

• Peroxisomes contain enzymes that transfer hydrogen from various substrates to oxygen.
• An intermediate product of this process is hydrogen peroxide (H2O2), a poison.
• The peroxisome contains an enzyme that converts H2O2 to water.
• Some peroxisomes break fatty acids down to smaller molecules that are transported to mitochondria as fuel for cellular respiration.
• Peroxisomes in the liver detoxify alcohol and other harmful compounds.
• Specialized peroxisomes, glyoxysomes, convert the fatty acids in seeds to sugars, which the seedling can use as a source of energy and
carbon until it is capable of photosynthesis.
• Peroxisomes are bound by a single membrane.
• They form not from the endomembrane system, but by incorporation of proteins and lipids from the cytosol.
• They split in two when they reach a certain size.

Concept 6.6 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.

• The cytoskeleton organizes the structures and activities of the cell.

The cytoskeleton provides support, motility, and regulation.

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• The cytoskeleton provides mechanical support and maintains cell shape.
• The cytoskeleton provides anchorage for many organelles and cytosolic enzymes.
• The cytoskeleton is dynamic and can be dismantled in one part and reassembled in another to change the shape of the cell.
• The cytoskeleton also plays a major role in cell motility, including changes in cell location and limited movements of parts of the cell.
• The cytoskeleton interacts with motor proteins to produce motility.
• 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.
• The same mechanism causes muscle cells to contract.
• Inside the cell, vesicles can travel along “monorails” provided by the cytoskeleton.
• The cytoskeleton manipulates the plasma membrane to form food vacuoles during phagocytosis.
• Cytoplasmic streaming in plant cells is caused by the cytoskeleton.
• Recently, evidence suggests that the cytoskeleton may play a role in the regulation of biochemical activities in the cell.
• There are three main types of fibers making up the cytoskeleton: microtubules, microfilaments, and intermediate filaments.
• Microtubules,the thickest fibers, are hollow rods about 25 microns in diameter and 200 nm to 25 microns in length.
• Microtubule fibers are constructed of the globular protein tubulin.
• Each tubulin molecule is a dimer consisting of two subunits.
• A microtubule changes in length by adding or removing tubulin dimers.
• Microtubules shape and support the cell and serve as tracks to guide motor proteins carrying organelles to their destination.
• Microtubules are also responsible for the separation of chromosomes during cell division.
• In many cells, microtubules grow out from a centrosome near the nucleus.
• These microtubules resist compression to the cell.
• In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring.
• Before a cell divides, the centrioles replicate.
• A specialized arrangement of microtubules is responsible for the beating of cilia and flagella.
• Many unicellular eukaryotic organisms are propelled through water by cilia and flagella.
• Cilia or flagella can extend from cells within a tissue layer, beating to move fluid over the surface of the tissue.
• For example, cilia lining the windpipe sweep mucus carrying trapped debris out of the lungs.
• Cilia usually occur in large numbers on the cell surface.
• They are about 0.25 microns in diameter and 2–20 microns long.
• There are usually just one or a few flagella per cell.
• Flagella are the same width as cilia, but 10–200 microns long.
• Cilia and flagella differ in their beating patterns.
• A flagellum has an undulatory movement that generates force in the same direction as the flagellum’s axis.
• Cilia move more like oars with alternating power and recovery strokes that generate force perpendicular to the cilium’s axis.
• In spite of their differences, both cilia and flagella have the same ultrastructure.
• Both have a core of microtubules sheathed by the plasma membrane.
• Nine doublets of microtubules are arranged in a ring around a pair at the center. This “9 + 2” pattern is found in nearly all eukaryotic
cilia and flagella.
• Flexible “wheels” of proteins connect outer doublets to each other and to the two central microtubules.
• The outer doublets are also connected by motor proteins.
• The cilium or flagellum is anchored in the cell by a basal body, whose structure is identical to a centriole.
• The bending of cilia and flagella is driven by the arms of a motor protein, dynein.
• Addition and removal of a phosphate group causes conformation changes in dynein.
• Dynein arms alternately grab, move, and release the outer microtubules.
• Protein cross-links limit sliding. As a result, the forces exerted by the dynein arms cause the doublets to curve, bending the cilium or
flagellum.
• Microfilamentsare solid rods about 7 nm in diameter.
• Each microfilament is built as a twisted double chain of actin subunits.
• Microfilaments can form structural networks due to their ability to branch.
• The structural role of microfilaments in the cytoskeleton is to bear tension, resisting pulling forces within the cell.

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 • They form a three-dimensional network just inside the plasma membrane to help support the cell’s shape, giving the cell cortex the
semisolid consistency of a gel.
• Microfilaments are important in cell motility, especially as part of the contractile apparatus of muscle cells.
• In muscle cells, thousands of actin filaments are arranged parallel to one another.
• Thicker filaments composed of myosin interdigitate with the thinner actin fibers.
• Myosin molecules act as motor proteins, walking along the actin filaments to shorten the cell.
• In other cells, actin-myosin aggregates are less organized but still cause localized contraction.
• A contracting belt of microfilaments divides the cytoplasm of animal cells during cell division.
• Localized contraction brought about by actin and myosin also drives amoeboid movement.
• Pseudopodia,cellular extensions, extend and contract through the reversible assembly and contraction of actin subunits into
microfilaments.
• Microfilaments assemble into networks that convert sol to gel.
• According to a widely accepted model, filaments near the cell’s trailing edge interact with myosin, causing contraction.
• The contraction forces the interior fluid into the pseudopodium, where the actin network has been weakened.
• The pseudopodium extends until the actin reassembles into a network.
• In plant cells, actin-myosin interactions and sol-gel transformations drive cytoplasmic streaming.
• This creates a circular flow of cytoplasm in the cell, speeding the distribution of materials within the cell.
• Intermediate filamentsrange in diameter from 8–12 nanometers, larger than microfilaments but smaller than microtubules.
• Intermediate filaments are a diverse class of cytoskeletal units, built from a family of proteins called keratins.
• Intermediate filaments are specialized for bearing tension.
• Intermediate filaments are more permanent fixtures of the cytoskeleton than are the other two classes.
• They reinforce cell shape and fix organelle location.

Concept 6.7 Extracellular components and connections between cells help coordinate cellular activities

Plant cells are encased by cell walls.

• The cell wall, found in prokaryotes, fungi, and some protists, has multiple functions.
• In plants, the cell wall protects the cell, maintains its shape, and prevents excessive uptake of water.
• It also supports the plant against the force of gravity.
• The thickness and chemical composition of cell walls differs from species to species and among cell types within a plant.
• The basic design consists of microfibrils of cellulose embedded in a matrix of proteins and other polysaccharides. This is the basic
design of steel-reinforced concrete or fiberglass.
• A mature cell wall consists of a primary cell wall, a middle lamella with sticky polysaccharides that holds cells together, and layers
of secondary cell wall.
• Plant cell walls are perforated by channels between adjacent cells called plasmodesmata.

The extracellular matrix (ECM) of animal cells functions in support, adhesion, movement, and regulation.

• Though lacking cell walls, animal cells do have an elaborate extracellular matrix (ECM).
• The primary constituents of the extracellular matrix are glycoproteins, especially collagen fibers, embedded in a network of
glycoprotein proteoglycans.
• In many cells, fibronectins in the ECM connect to integrins, intrinsic membrane proteins that span the membrane and bind on their
cytoplasmic side to proteins attached to microfilaments of the cytoskeleton.
• The interconnections from the ECM to the cytoskeleton via the fibronectin-integrin link permit the integration of changes inside and
outside the cell.
• The ECM can regulate cell behavior.
• Embryonic cells migrate along specific pathways by matching the orientation of their microfilaments to the “grain” of fibers in the
extracellular matrix.
• The extracellular matrix can influence the activity of genes in the nucleus via a combination of chemical and mechanical signaling
pathways.
• This may coordinate the behavior of all the cells within a tissue.

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Intercellular junctions help integrate cells into higher levels of structure and function.

• Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact.
• Plant cells are perforated with plasmodesmata, channels allowing cytosol to pass between cells.
• Water and small solutes can pass freely from cell to cell.
• In certain circumstances, proteins and RNA can be exchanged.
• Animals have 3 main types of intercellular links: tight junctions, desmosomes, and gap junctions.
• In tight junctions, membranes of adjacent cells are fused, forming continuous belts around cells.
• This prevents leakage of extracellular fluid.
• Desmosomes(or anchoring junctions) fasten cells together into strong sheets, much like rivets.
• Intermediate filaments of keratin reinforce desmosomes.
• Gap junctions(or communicating junctions) provide cytoplasmic channels between adjacent cells.
• Special membrane proteins surround these pores.
• Ions, sugars, amino acids, and other small molecules can pass.
• In embryos, gap junctions facilitate chemical communication during development.

Chapter 8:

 First, not all membranes were alike. Membranes differ in thickness, appearance when stained, and percentage of proteins.
 Membranes with different functions differ in chemical composition and structure.
 Second, measurements showed that membrane proteins are not very soluble in water.
 Membrane proteins are amphipathic, with hydrophobic and hydrophilic regions.
 If membrane proteins were at the membrane surface, their hydrophobic regions would be in contact with water.
 In 1972, S. J. Singer and G. Nicolson presented a revised model that proposed that the membrane proteins are dispersed and individually
inserted into the phospholipid bilayer.
 In this fluid mosaic model, the hydrophilic regions of proteins and phospholipids are in maximum contact with water, and the hydrophobic
regions are in a nonaqueous environment within the membrane.
 A specialized preparation technique, freeze-fracture, splits a membrane along the middle of the phospholipid bilayer.

 When a freeze-fracture preparation is viewed with an electron microscope, protein particles are interspersed in a smooth matrix, supporting
the fluid mosaic model.

 Other proteins never move and are anchored to the cytoskeleton.

 Membrane fluidity is influenced by temperature. As temperatures cool, membranes switch from a fluid state to a solid state as the
phospholipids pack more closely.
 Membrane fluidity is also influenced by its components. 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.
 The steroid cholesterol is wedged between phospholipid molecules in the plasma membrane of animal cells.
 At warm temperatures (such as 37°C), cholesterol restrains the movement of phospholipids and reduces fluidity.
 At cool temperatures, it maintains fluidity by preventing tight packing.
 Thus, cholesterol acts as a “temperature buffer” for the membrane, resisting changes in membrane fluidity as temperature changes.
 To work properly with active enzymes and appropriate permeability, membranes must be about as fluid as salad oil.
 Cells can alter the lipid composition of membranes to compensate for changes in fluidity caused by changing temperatures.
 For example, cold-adapted organisms such as winter wheat increase the percentage of unsaturated phospholipids in their membranes in the
autumn.

 This prevents membranes from solidifying during winter.

• A membrane is a collage of different proteins embedded in the fluid matrix of the lipid bilayer.
• Proteins determine most of the membrane’s specific functions.
• The plasma membrane and the membranes of the various organelles each have unique collections of proteins.
• There are two major populations of membrane proteins.
• Peripheral proteinsare not embedded in the lipid bilayer at all.
• Instead, they are loosely bound to the surface of the protein, often connected to integral proteins.
• Integral proteinspenetrate the hydrophobic core of the lipid bilayer, often completely spanning the membrane (as transmembrane
proteins).
• The hydrophobic regions embedded in the membrane’s core consist of stretches of nonpolar amino acids, often coiled into alpha
helices.
• Where integral proteins are in contact with the aqueous environment, they have hydrophilic regions of amino acids.
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 • On the cytoplasmic side of the membrane, some membrane proteins connect to the cytoskeleton.
• On the exterior side of the membrane, some membrane proteins attach to the fibers of the extracellular matrix.
• The proteins of the plasma membrane have six major functions:
• Transport of specific solutes into or out of cells.
• Enzymatic activity, sometimes catalyzing one of a number of steps of a metabolic pathway.
• Signal transduction, relaying hormonal messages to the cell.
• Cell-cell recognition, allowing other proteins to attach two adjacent cells together.
• Intercellular joining of adjacent cells with gap or tight junctions.
• Attachment to the cytoskeleton and extracellular matrix,maintaining cell shape and stabilizing the location of certain membrane
proteins.

• Differences in the relative concentration of dissolved materials in two solutions can lead to the movement of ions from one to the
other.
• The solution with the higher concentration of solutes is hypertonic relative to the other solution.
• The solution with the lower concentration of solutes is hypotonic relative to the other solution.
• These are comparative terms.
• Tap water is hypertonic compared to distilled water but hypotonic compared to seawater.
• Solutions with equal solute concentrations are isotonic.
• Imagine that two sugar solutions differing in concentration are separated by a membrane that will allow water through, but not sugar.
• The hypertonic solution has a lower water concentration than the hypotonic solution.
• More of the water molecules in the hypertonic solution are bound up in hydration shells around the sugar molecules, leaving fewer
unbound water molecules.
• Unbound water molecules will move from the hypotonic solution, where they are abundant, to the hypertonic solution, where they are
rarer. Net movement of water continues until the solutions are isotonic.
• The diffusion of water across a selectively permeable membrane is called osmosis.
• The direction of osmosis is determined only by a difference in total solute concentration.
• The kinds of solutes in the solutions do not matter.
• This makes sense because the total solute concentration is an indicator of the abundance of bound water molecules (and, therefore, of
free water molecules).
• When two solutions are isotonic, water molecules move at equal rates from one to the other, with no net osmosis.
• The movement of water by osmosis is crucial to living organisms.

Cell survival depends on balancing water uptake and loss.

• 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.
• Water molecules move across the membrane but at the same rate in both directions.
• The volume of the cell is stable.
• The same cell in a hypertonic environment will lose water, shrivel, and probably die.
• A cell in a hypotonic solution will gain water, swell, and burst.
• For organisms living in an isotonic environment (for example, many marine invertebrates), osmosis is not a problem.
• The cells of most land animals are bathed in extracellular fluid that is isotonic to the cells.
• Organisms without rigid walls have osmotic problems in either a hypertonic or hypotonic environment and must have adaptations for
osmoregulation, the control of water balance, to maintain their internal environment.
• For example, Paramecium, a protist, is hypertonic to the pond water in which it lives.
• In spite of a cell membrane that is less permeable to water than other cells, water still continually enters the Paramecium cell.
• To solve this problem, Paramecium cells have a specialized organelle, the contractile vacuole, which functions as a bilge pump to
force water out of the cell.
• The cells of plants, prokaryotes, fungi, and some protists have walls that contribute to the cell’s water balance.
• A plant cell in a hypotonic solution will swell until the elastic cell wall opposes further uptake.
• At this point the cell is turgid (very firm), a healthy state for most plant cells.
• Turgid cells contribute to the mechanical support of the plant.
• If a plant cell and its surroundings are isotonic, there is no movement of water into the cell. The cell becomes flaccid (limp), and the
plant may wilt.

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 • The cell wall provides no advantages when a plant cell is immersed in a hypertonic solution. As the plant cell loses water, its volume
shrinks. Eventually, the plasma membrane pulls away from the wall. This plasmolysis is usually lethal.

Specific proteins facilitate passive transport of water and selected solutes.

• 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.
• The passive movement of molecules down their concentration gradient via transport proteins is called facilitated diffusion.
• Two types of transport proteins facilitate the movement of molecules or ions across membranes: channel proteins and carrier proteins.
• Some channel proteins simply provide hydrophilic corridors for the passage of specific molecules or ions.
• For example, water channel proteins, aquaporins, greatly facilitate the diffusion of water.
• Manyion channels function as gated channels. These channels open or close depending on the presence or absence of a chemical or
physical stimulus.
• If chemical, the stimulus is a substance other than the one to be transported.
• For example, stimulation of a receiving neuron by specific neurotransmitters opens gated channels to allow sodium ions into the cell.
• When the neurotransmitters are not present, the channels are closed.
• 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.
• These shape changes may be triggered by the binding and release of the transported molecule.
• In certain inherited diseases, specific transport systems may be defective or absent.
• 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.
• An individual with cystinuria develops painful kidney stones as amino acids accumulate and crystallize in the kidneys.

Chapter 9:

Redox reactions release energy when electrons move closer to electronegative atoms.

• Catabolic pathways transfer the electrons stored in food molecules, releasing energy that is used to synthesize ATP.
• Reactions that result in the transfer of one or more electrons from one reactant to another are oxidation-reduction reactions, or redox
reactions.
• The loss of electrons is called oxidation.
• The addition of electrons is called reduction.
• The formation of table salt from sodium and chloride is a redox reaction.
• Na + Cl àNa+ + Cl−
• Here sodium is oxidized and chlorine is reduced (its charge drops from 0 to −1).
• More generally: Xe− + Y àX + Ye−
• X, the electron donor, is the reducing agent and reduces Y.
• Y, the electron recipient, is the oxidizing agent and oxidizes X.
• Redox reactions require both a donor and acceptor.
• 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 the combustion of methane to form water and carbon dioxide, the nonpolar covalent bonds of methane (C—H) and oxygen (O=O)
are converted to polar covalent bonds (C=O and O—H).
• When methane reacts with oxygen to form carbon dioxide, electrons end up farther away from the carbon atom and closer to their new
covalent partners, the oxygen atoms, which are very electronegative.
• In effect, the carbon atom has partially “lost” its shared electrons. Thus, methane has been oxidized.
• The two atoms of the oxygen molecule share their electrons equally. When oxygen reacts with the hydrogen from methane to form
water, the electrons of the covalent bonds are drawn closer to the oxygen.
• In effect, each oxygen atom has partially “gained” electrons, and so the oxygen molecule has been reduced.
• Oxygen is very electronegative, and is one of the most potent of all oxidizing agents.
• Energy must be added to pull an electron away from an atom.
• 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.
• A redox reaction that relocates electrons closer to oxygen, such as the burning of methane, releases chemical energy that can do work.
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 • During glycolysis, glucose, a six carbon-sugar, is split into two three-carbon sugars.
• These smaller sugars are oxidized and rearranged to form two molecules of pyruvate, the ionized form of pyruvic acid.
• Each of the ten steps in glycolysis is catalyzed by a specific enzyme.
• These steps can be divided into two phases: an energy investment phase and an energy payoff phase.
• In the energy investment phase, the cell invests ATP to provide activation energy by phosphorylating glucose.
• This requires 2 ATP per glucose.
• In the energy payoff phase, ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by electrons released
by the oxidation of glucose.
• The net yield from glycolysis is 2 ATP and 2 NADH per glucose.
• No CO2 is produced during glycolysis.
• Glycolysis can occur whether O2 is present or not.
• More than three-quarters of the original energy in glucose is still present in the two molecules of pyruvate.
• If oxygen is present, pyruvate enters the mitochondrion where enzymes of the citric acid cycle complete the oxidation of the organic
fuel to carbon dioxide.
• After pyruvate enters the mitochondrion via active transport, it is converted to a compound called acetyl coenzyme A or acetyl CoA.
• This step is accomplished by a multienzyme complex that catalyzes three reactions:
• A carboxyl group is removed as CO2.
• The remaining two-carbon fragment is oxidized to form acetate. An enzyme transfers the pair of electrons to NAD+ to form NADH.
• Acetate combines with coenzyme A to form the very reactive molecule acetyl CoA.
• Acetyl CoA is now ready to feed its acetyl group into the citric acid cycle for further oxidation.
• The citric acid cycle is also called the Krebs cycle in honor of Hans Krebs, who was largely responsible for elucidating its pathways in
the 1930s.
• The citric acid cycle oxidizes organic fuel derived from pyruvate.
• The citric acid cycle has eight steps, each catalyzed by a specific enzyme.
• The acetyl group of acetyl CoA joins the cycle by combining with the compound oxaloacetate, forming citrate.
• The next seven steps decompose the citrate back to oxaloacetate. It is the regeneration of oxaloacetate that makes this process a cycle.
• Three CO2 molecules are released, including the one released during the conversion of pyruvate to acetyl CoA.
• The cycle generates one ATP per turn by substrate-level phosphorylation.
• A GTP molecule is formed by substrate-level phosphorylation.
• The GTP is then used to synthesize an ATP, the only ATP generated directly by the citric acid cycle.
• Most of the chemical energy is transferred to NAD+ and FAD during the redox reactions.
• The reduced coenzymes NADH and FADH2 then transfer high-energy electrons to the electron transport chain.
• Each cycle produces one ATP by substrate-level phosphorylation, three NADH, and one FADH2 per acetyl CoA.

 NADH and FADH2 account for the vast majority of the energy extracted from the food.
 These reduced coenzymes link glycolysis and the citric acid cycle to oxidative phosphorylation, which uses energy released by the electron
transport chain to power ATP synthesis.
 The electron transport chain is a collection of molecules embedded in the cristae, the folded inner membrane of the mitochondrion.
 The folding of the cristae increases its surface area, providing space for thousands of copies of the chain in each mitochondrion.
 Most components of the chain are proteins bound to prosthetic groups, nonprotein components essential for catalysis.
 Electrons drop in free energy as they pass down the electron transport chain.
 During electron transport along the chain, electron carriers alternate between reduced and oxidized states as they accept and donate electrons.
 Each component of the chain becomes reduced when it accepts electrons from its “uphill” neighbor, which is less electronegative.
 It then returns to its oxidized form as it passes electrons to its more electronegative “downhill” neighbor.
 Electrons carried by NADH are transferred to the first molecule in the electron transport chain, a flavoprotein.
 The electrons continue along the chain that includes several cytochrome proteins and one lipid carrier.
 The prosthetic group of each cytochrome is a heme group with an iron atom that accepts and donates electrons.
 The last cytochrome of the chain, cyt a3, passes its electrons to oxygen, which is very electronegative.
 Each oxygen atom also picks up a pair of hydrogen ions from the aqueous solution to form water.
 For every two electron carriers (four electrons), one O2 molecule is reduced to two molecules of water.
 The electrons carried by FADH2 have lower free energy and are added at a lower energy level than those carried by NADH.
 The electron transport chain provides about one-third less energy for ATP synthesis when the electron donor is FADH2 rather than NADH.
 The electron transport chain generates no ATP directly.
 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.
 How does the mitochondrion couple electron transport and energy release to ATP synthesis?
 The answer is a mechanism called chemiosmosis.
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 A protein complex, ATP synthase, in the cristae actually makes ATP from ADP and Pi.
 ATP uses the energy of an existing proton gradient to power ATP synthesis.
 The proton gradient develops between the intermembrane space and the matrix.
 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 protons pass back to the matrix through a channel in ATP synthase, using the exergonic flow of H+ to drive the phosphorylation of ADP.
 Thus, the energy stored in a H+ gradient across a membrane couples the redox reactions of the electron transport chain to ATP synthesis.
 From studying the structure of ATP synthase, scientists have learned how the flow of H+ through this large enzyme powers ATP generation.
 ATP synthase is a multisubunit complex with four main parts, each made up of multiple polypeptides:
 A rotor in the inner mitochondrial membrane.
 A knob that protrudes into the mitochondrial matrix.
 An internal rod extending from the rotor into the knob.
 A stator, anchored next to the rotor, which holds the knob stationary.
 Protons flow down a narrow space between the stator and rotor, causing the rotor and its attached rod to rotate.
 The spinning rod causes conformational changes in the stationary knob, activating three catalytic sites in the knob where ADP and inorganic
phosphate combine to make 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.
 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.
 The H+ has a tendency to diffuse down its gradient.
 The ATP synthase molecules are the only place that H+ can diffuse back to the matrix.
 The exergonic flow of H+ is used by the enzyme to generate ATP.
 This coupling of the redox reactions of the electron transport chain to ATP synthesis is called chemiosmosis.
 How does the electron transport chain pump protons?
 Certain members of the electron transport chain accept and release H+ along with electrons.
 At certain steps along the chain, electron transfers cause H+ to be taken up and released into the surrounding solution.
 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.
 The H+ gradient that results is the proton-motive force.
 The gradient has the capacity to do work.
 Chemiosmosis is an energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular
work.
 In mitochondria, the energy for proton gradient formation comes from exergonic redox reactions, and ATP synthesis is the work performed.
 Chemiosmosis in chloroplasts also generates ATP, but light drives the electron flow down an electron transport chain and H+ gradient
formation.
 Prokaryotes generate H+ gradients across their plasma membrane.

 They can use this proton-motive force not only to generate ATP, but also to pump nutrients and waste products across the membrane and to
rotate their flagella.

 The inner membrane of the mitochondrion is the site of electron transport and chemiosmosis, processes that together constitute oxidative
phosphorylation.
 Oxidative phosphorylation produces almost 90% of the ATP generated by respiration.
 Some ATP is also formed directly during glycolysis and the citric acid cycle by substrate-level phosphorylation.
 Here an enzyme transfers a phosphate group from an organic substrate to ADP, forming ATP.
 For each molecule of glucose degraded to carbon dioxide and water by respiration, the cell makes up to 38 ATP, each with 7.3 kcal/mol of
free energy.
 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.

 The quantity of energy in ATP is more appropriate for the level of work required in the cell.

Chapter 10:

 The thylakoids convert light energy into the chemical energy of ATP and NADPH.
 Light is a form of electromagnetic radiation.
 Like other forms of electromagnetic energy, light travels in rhythmic waves.
 The distance between crests of electromagnetic waves is called the wavelength.
 Wavelengths of electromagnetic radiation range from less than a nanometer (gamma rays) to more than a kilometer (radio waves).
 The entire range of electromagnetic radiation is the electromagnetic spectrum.
 The most important segment for life is a narrow band between 380 to 750 nm, the band of visible light.
 While light travels as a wave, many of its properties are those of a discrete particle, the photon.
 Photons are not tangible objects, but they do have fixed quantities of energy.
 The amount of energy packaged in a photon is inversely related to its wavelength.
 Photons with shorter wavelengths pack more energy.

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 While the sun radiates a full electromagnetic spectrum, the atmosphere selectively screens out most wavelengths, permitting only visible light
to pass in significant quantities.
 Visible light is the radiation that drives photosynthesis.
 When light meets matter, it may be reflected, transmitted, or absorbed.
 Different pigments absorb photons of different wavelengths, and the wavelengths that are absorbed disappear.
 A leaf looks green because chlorophyll, the dominant pigment, absorbs red and blue light, while transmitting and reflecting green light.
 A spectrophotometer measures the ability of a pigment to absorb various wavelengths of light.
 It beams narrow wavelengths of light through a solution containing the pigment and measures the fraction of light transmitted at each
wavelength.
 An absorption spectrum plots a pigment’s light absorption versus wavelength.

 The light reaction can perform work with those wavelengths of light that are absorbed.

 There are about half a million chloroplasts per square millimeter of leaf surface.
 The color of a leaf comes from chlorophyll, the green pigment in the chloroplasts.
 Chlorophyll plays an important role in the absorption of light energy during photosynthesis.
 Chloroplasts are found mainly in mesophyll cells forming the tissues in the interior of the leaf.
 O2 exits and CO2 enters the leaf through microscopic pores called stomata in the leaf.
 Veins deliver water from the roots and carry off sugar from mesophyll cells to nonphotosynthetic areas of the plant.
 A typical mesophyll cell has 30–40 chloroplasts, each about 2–4 microns by 4–7 microns long.
 Each chloroplast has two membranes around a central aqueous space, the stroma.
 In the stroma is an elaborate system of interconnected membranous sacs, the thylakoids.
 The interior of the thylakoids forms another compartment, the thylakoid space.
 Thylakoids may be stacked into columns called grana.
 Chlorophyll is located in the thylakoids.
 Photosynthetic prokaryotes lack chloroplasts.

 Their photosynthetic membranes arise from infolded regions of the plasma membranes, folded in a manner similar to the thylakoid
membranes of chloroplasts.

 In the thylakoid membrane, chlorophyll is organized along with proteins and smaller organic molecules into photosystems.
 A photosystem is composed of a reaction center surrounded by a light-harvesting complex.
 Each light-harvesting complex consists of pigment molecules (which may include chlorophyll a, chlorophyll b, and carotenoid molecules)
bound to particular proteins.
 Together, these light-harvesting complexes act like light-gathering “antenna complexes” for the reaction center.
 When any antenna molecule absorbs a photon, it is transmitted from molecule to molecule until it reaches a particular chlorophyll a molecule,
the reaction center.
 At the reaction center is a primary electron acceptor, which accepts an excited electron from the reaction center chlorophyll a.
 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 photosystem—reaction-center chlorophyll and primary electron acceptor surrounded by an antenna complex—functions in the
chloroplast as a light-harvesting unit.
 There are two types of photosystems in the thylakoid membrane.
 Photosystem I (PS I)has a reaction center chlorophyll a that has an absorption peak at 700 nm.
 Photosystem II (PS II)has a reaction center chlorophyll a that has an absorption peak at 680 nm.
 The differences between these reaction centers (and their absorption spectra) lie not in the chlorophyll molecules, but in the proteins
associated with each reaction center.

 These two photosystems work together to use light energy to generate ATP and NADPH.

 The light reactions (photo) convert solar energy to chemical energy.

 The Calvin cycle (synthesis) uses energy from the light reactions to incorporate CO2 from the atmosphere into sugar.
 In the light reactions, light energy absorbed by chlorophyll in the thylakoids drives the transfer of electrons and hydrogen from water to
NADP+ (nicotinamide adenine dinucleotide phosphate), forming NADPH.
 NADPH, an electron acceptor, provides reducing power via energized electrons to the Calvin cycle.
 Water is split in the process, and O2 is released as a by-product.
 The light reaction also generates ATP using chemiosmosis, in a process called photophosphorylation.
 Thus light energy is initially converted to chemical energy in the form of two compounds: NADPH and ATP.
 The Calvin cycle is named for Melvin Calvin who, with his colleagues, worked out many of its steps in the 1940s.
 The cycle begins with the incorporation of CO2 into organic molecules, a process known as carbon fixation.
 The fixed carbon is reduced with electrons provided by NADPH.
 ATP from the light reactions also powers parts of the Calvin cycle.
 Thus, it is the Calvin cycle that makes sugar, 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, because none of the steps requires light
directly.
 Nevertheless, the Calvin cycle in most plants occurs during daylight, because that is when the light reactions can provide the NADPH and
ATP the Calvin cycle requires.
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 While the light reactions occur at the thylakoids, the Calvin cycle occurs in the stroma.

• One of the major problems facing terrestrial plants is dehydration.

• At times, solutions to this problem require tradeoffs with other metabolic processes, especially photosynthesis.
• The stomata are not only the major route for gas exchange (CO2 in and O2 out), but also for the evaporative loss of water.
• On hot, dry days, plants close their stomata to conserve water. This causes problems for photosynthesis.
• In most plants (C3 plants), initial fixation of CO2 occurs via rubisco, forming a three-carbon compound, 3-phosphoglycerate.
• C3 plants include rice, wheat, and soybeans.
• When their stomata partially close on a hot, dry day, CO2 levels drop as CO2 is consumed in the Calvin cycle.
• At the same time, O2 levels rise as the light reaction converts light to chemical energy.
• While rubisco normally accepts CO2, when the O2:CO2 ratio increases (on a hot, dry day with closed stomata), rubisco can add O2 to
RuBP.
• When rubisco adds O2 to RuBP, RuBP splits into a three-carbon piece and a two-carbon piece in a process called photorespiration.
• The two-carbon fragment is exported from the chloroplast and degraded to CO2 by mitochondria and peroxisomes.
• Unlike normal respiration, this process produces no ATP.
• In fact, photorespiration consumes ATP.
• Unlike photosynthesis, photorespiration does not produce organic molecules.
• In fact, photorespiration decreases photosynthetic output by siphoning organic material from the Calvin cycle.
• A hypothesis for the existence of photorespiration is that it is evolutionary baggage.
• When rubisco first evolved, the atmosphere had far less O2 and more CO2 than it does today.
• The inability of the active site of rubisco to exclude O2 would have made little difference.
• Today it does make a difference.
• Photorespiration can drain away as much as 50% of the carbon fixed by the Calvin cycle on a hot, dry day.
• Certain plant species have evolved alternate modes of carbon fixation to minimize photorespiration.
• C4 plantsfirst fix CO2 in a four-carbon compound.
• Several thousand plants, including sugarcane and corn, use this pathway.
• A unique leaf anatomy is correlated with the mechanism of C4 photosynthesis.
• In C4 plants, there are two distinct types of photosynthetic cells: bundle-sheath cells and mesophyll cells.
• Bundle-sheath cellsare arranged into tightly packed sheaths around the veins of the leaf.
• Mesophyll cellsare more loosely arranged cells located between the bundle sheath and the leaf surface.
• The Calvin cycle is confined to the chloroplasts of the bundle-sheath cells.
• However, the cycle is preceded by the incorporation of CO2 into organic molecules in the mesophyll.
• The key enzyme, phosphoenolpyruvate carboxylase, adds CO2 to phosphoenolpyruvate (PEP) to form oxaloacetate.
• PEP carboxylasehas a very high affinity for CO2 and can fix CO2 efficiently when rubisco cannot (i.e., on hot, dry days when the
stomata are closed).
• The mesophyll cells pump these four-carbon compounds into bundle-sheath cells.
• The bundle-sheath cells strip a carbon from the four-carbon compound as CO2, and return the three-carbon remainder to the mesophyll
cells.
• The bundle-sheath cells then use rubisco to start the Calvin cycle with an abundant supply of CO2.
• In effect, the mesophyll cells pump CO2 into the bundle-sheath cells, keeping CO2 levels high enough for rubisco to accept CO2 and
not O2.
• C4 photosynthesis minimizes photorespiration and enhances sugar production.
• C4 plants thrive in hot regions with intense sunlight.
• A second strategy to minimize photorespiration is found in succulent plants, cacti, pineapples, and several other plant families.
• These plants are known as CAM plants for crassulacean acid metabolism.
• They open their stomata during the night and close them during the day.
• Temperatures are typically lower at night, and humidity is higher.
• During the night, these plants fix CO2 into a variety of organic acids in mesophyll cells.
• During the day, the light reactions supply ATP and NADPH to the Calvin cycle, and CO2 is released from the organic acids.
• Both C4 and CAM plants add CO2 into organic intermediates before it enters the Calvin cycle.
• In C4 plants, carbon fixation and the Calvin cycle are spatially separated.
• In CAM plants, carbon fixation and the Calvin cycle are temporally separated.
• Both eventually use the Calvin cycle to make sugar from carbon dioxide.

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Chapter 11:

The three stages of cell signaling are reception, transduction, and response.

• E. W. Sutherland and his colleagues pioneered our understanding of cell signaling.

• Their work investigated how the animal hormone epinephrine stimulates breakdown of the storage polysaccharide glycogen in liver
and skeletal muscle.
• Breakdown of glycogen releases glucose derivatives that can be used for fuel in glycolysis or released as glucose in the blood for fuel
elsewhere.
• Thus one effect of epinephrine, which is released from the adrenal gland during times of physical or mental stress, is mobilization of
fuel reserves.
• Sutherland’s research team discovered that epinephrine activated a cytosolic enzyme, glycogen phosphorylase.
• However, epinephrine did not activate the phosphorylase directly in vitro but could only act via intact cells.
• Therefore, there must be an intermediate step or steps occurring inside the cell.
• The plasma membrane must be involved in transmitting the epinephrine signal.
• The process involves three stages: reception, transduction, and response.
• In reception, a chemical signal binds to a cellular protein, typically at the cell’s surface or inside the cell.
• In transduction, 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 molecules in the pathway are called relay molecules.
• In response, the transduced signal triggers a specific cellular activity.

 There are three major types of membrane receptors: G-protein-linked receptors, receptor tyrosine kinases, and ion-channel receptors.
 A G-protein-linked receptor consists of a receptor protein associated with a G protein on the cytoplasmic side.
 Seven alpha helices span the membrane.
 G-protein-linked receptors bind many different signal molecules, including yeast mating factors, epinephrine and many other hormones, and
neurotransmitters.
 The G protein acts as an on/off switch.
 If GDP is bound to the G protein, the G protein is inactive.
 When the appropriate signal molecule binds to the extracellular side of the receptor, the G protein binds GTP (instead of GDP) and becomes
active.
 The activated G protein dissociates from the receptor and diffuses along the membrane, where it binds to an enzyme, altering its activity.
 The activated enzyme triggers the next step in a pathway leading to a cellular response.
 The G protein can also act as a GTPase enzyme to hydrolyze GTP to GDP.
 This change turns the G protein off.
 Now inactive, the G protein leaves the enzyme, which returns to its original state.
 The whole system can be shut down quickly when the extracellular signal molecule is no longer present.
 G-protein receptor systems are extremely widespread and diverse in their functions.
 They play important roles during embryonic development.
 Vision and smell in humans depend on these proteins.
 Similarities among G proteins and G-protein-linked receptors of modern organisms suggest that this signaling system evolved very early.
 Several human diseases involve G-protein systems.
 Bacterial infections causing cholera and botulism interfere with G-protein function.
 The tyrosine-kinase receptor system is especially effective when the cell needs to trigger several signal transduction pathways and cellular
responses at once.
 This system helps the cell regulate and coordinate many aspects of cell growth and reproduction.
 The tyrosine-kinase receptor belongs to a major class of plasma membrane receptors that have enzymatic activity.
 A kinase is an enzyme that catalyzes the transfer of phosphate groups.
 The cytoplasmic side of these receptors functions as a tyrosine kinase, transferring a phosphate group from ATP to tyrosine on a substrate
protein.
 An individual tyrosine-kinase receptor consists of several parts:
 An extracellular signal-binding site.
 A single alpha helix spanning the membrane.
 An intracellular tail with several tyrosines.
 The signal molecule binds to an individual receptor.
 Ligands bind to two receptors, causing the two receptors to aggregate and form a dimer.
 This dimerization activates the tyrosine-kinase section of the receptors, each of which then adds phosphate from ATP to the tyrosine tail of
the other polypeptide.
 The fully activated receptor proteins activate a variety of specific relay proteins that bind to specific phosphorylated tyrosine molecules.
 One tyrosine-kinase receptor dimer may activate ten or more different intracellular proteins simultaneously.
 These activated relay proteins trigger many different transduction pathways and responses.
 A ligand-gated ion channel is a type of membrane receptor that can act as a gate when the receptor changes shape.

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 When a signal molecule binds as a ligand to the receptor protein, the gate opens to allow the flow of specific ions, such as Na+ or Ca2+,
through a channel in the receptor.
 Binding by a ligand to the extracellular side changes the protein’s shape and opens the channel.
 When the ligand dissociates from the receptor protein, the channel closes.
 The change in ion concentration within the cell may directly affect the activity of the cell.
 Ligand-gated ion channels are very important in the nervous system.
 For example, neurotransmitter molecules released at a synapse between two neurons bind as ligands to ion channels on the receiving cell,
causing the channels to open.
 Ions flow in and trigger an electrical signal that propagates down the length of the receiving cell.

 Some gated ion channels respond to electrical signals, instead of ligands.

 Hydrophobic messengers include the steroid and thyroid hormones of animals.

 Nitric oxide (NO) is a gas whose small size allows it to pass between membrane phospholipids.
 Testosterone is secreted by the testis and travels through the blood to enter cells throughout the body.
 The cytosol of target cells contains receptor molecules that bind testosterone, activating the receptor.
 These activated proteins enter the nucleus and turn on specific genes that control male sex characteristics.
 How does the activated hormone-receptor complex turn on genes?
 These activated proteins act as transcription factors.
 Transcription factors control which genes are turned on—that is, which genes are transcribed into messenger RNA.
 mRNA molecules leave the nucleus and carry information that directs the synthesis (translation) of specific proteins at the ribosome.

 Other intracellular receptors (such as thyroid hormone receptors) are found in the nucleus and bind to the signal molecules there.

 Many signaling pathways involve small, water-soluble, nonprotein molecules or ions called second messengers.

 These molecules rapidly diffuse throughout the cell.

Chapter 12:

 The mitotic spindle begins to form.

 It is composed of centrosomes and the microtubules that extend from them.

 The mitotic spindle, fibers composed of microtubules and associated proteins, is a major driving force in mitosis.
 As the spindle assembles during prophase, the elements come from partial disassembly of the cytoskeleton.
 The spindle fibers elongate by incorporating more subunits of the protein tubulin.
 Assembly of the spindle microtubules starts in the centrosome.
 The centrosome (microtubule-organizing center) is a nonmembranous organelle that organizes the cell’s microtubules.
 In animal cells, the centrosome has a pair of centrioles at the center, but the centrioles are not essential for cell division.
 During interphase, the single centrosome replicates to form two centrosomes.
 As mitosis starts, the two centrosomes are located near the nucleus.
 As the spindle microtubules grow from them, the centrioles are pushed apart.
 By the end of prometaphase, they are at opposite ends of the cell.
 An aster, a radial array of short microtubules, extends from each centrosome.
 The spindle includes the centrosomes, the spindle microtubules, and the asters.
 Each sister chromatid has a kinetochore of proteins and chromosomal DNA at the centromere.
 The kinetochores of the joined sister chromatids face in opposite directions.
 During prometaphase, some spindle microtubules (called kinetochore microtubules) attach to the kinetochores.
 When a chromosome’s kinetochore is “captured” by microtubules, the chromosome moves toward the pole from which those microtubules
come.
 When microtubules attach to the other pole, this movement stops and a tug-of-war ensues.
 Eventually, the chromosome settles midway between the two poles of the cell, on the metaphase plate.
 Nonkinetochore microtubules from opposite poles overlap and interact with each other.
 By metaphase, the microtubules of the asters have grown and are in contact with the plasma membrane.

 The spindle is now complete.

 An aster, a radial array of short microtubules, extends from each centrosome.

 The spindle includes the centrosomes, the spindle microtubules, and the asters.
 Each sister chromatid has a kinetochore of proteins and chromosomal DNA at the centromere.
 The kinetochores of the joined sister chromatids face in opposite directions.
 During prometaphase, some spindle microtubules (called kinetochore microtubules) attach to the kinetochores.

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 When a chromosome’s kinetochore is “captured” by microtubules, the chromosome moves toward the pole from which those microtubules
come.
 When microtubules attach to the other pole, this movement stops and a tug-of-war ensues.
 Eventually, the chromosome settles midway between the two poles of the cell, on the metaphase plate.
 Nonkinetochore microtubules from opposite poles overlap and interact with each other.
 By metaphase, the microtubules of the asters have grown and are in contact with the plasma membrane.
 The spindle is now complete.
 Anaphase commences when the proteins holding the sister chromatids together are inactivated.
 Once the chromosomes are separate, full-fledged chromosomes, they move toward opposite poles of the cell.
 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.
 Experimental evidence supports the hypothesis that motor proteins on the kinetochore “walk” the attached chromosome along the microtubule
toward the nearest pole.
 Meanwhile, the excess microtubule sections depolymerize at their kinetochore ends.
 What is the function of the nonkinetochore microtubules?
 Nonkinetochore microtubules are responsible for lengthening the cell along the axis defined by the poles.
 These microtubules interdigitate and overlap across the metaphase plate.
 During anaphase, the area of overlap is reduced as motor proteins attached to the microtubules walk them away from one another, using
energy from ATP.

 As microtubules push apart, the microtubules lengthen by the addition of new tubulin monomers to their overlapping ends, allowing
continued overlap.

 Cytokinesis, division of the cytoplasm, is usually well underway by late telophase.

 In animal cells, cytokinesis involves the formation of a cleavage furrow, which pinches the cell in two.

 In plant cells, vesicles derived from the Golgi apparatus produce a cell plate at the middle of the cell.

In animal cells, the centrosome has a pair of centrioles at the center, but the centrioles are not essential for cell
division.

Chapter 13:

• Many steps of meiosis resemble steps in mitosis.

• Both are preceded by the replication of chromosomes.
• However, in meiosis, there are two consecutive cell divisions, meiosis I and meiosis II, resulting in four daughter cells.
• The first division, meiosis I, separates homologous chromosomes.
• The second, meiosis II, separates sister chromatids.
• The four daughter cells have only half as many chromosomes as the parent cell.
• Meiosis I is preceded by interphase, in which the chromosomes are replicated to form sister chromatids.
• These are genetically identical and joined at the centromere.
• The single centrosome is replicated, forming two centrosomes.
• Division in meiosis I occurs in four phases: prophase I, metaphase I, anaphase I, and telophase I.

Prophase I

• Prophase I typically occupies more than 90% of the time required for meiosis.
• During prophase I, the chromosomes begin to condense.
• Homologous chromosomes loosely pair up along their length, precisely aligned gene for gene.
• In crossing over, DNA molecules in nonsister chromatids break at corresponding places and then rejoin the other chromatid.
• In synapsis, a protein structure called the synaptonemal complex forms between homologues, holding them tightly together along their
length.
• As the synaptonemal complex disassembles in late prophase, each chromosome pair becomes visible as a tetrad, or group of four
chromatids.
• Each tetrad has one or more chiasmata, sites where the chromatids of homologous chromosomes have crossed and segments of the
chromatids have been traded.
• Spindle microtubules form from the centrosomes, which have moved to the poles.
• The breakdown of the nuclear envelope and nucleoli take place.
• Kinetochores of each homologue attach to microtubules from one of the poles.
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Metaphase I

• At metaphase I, the tetrads are all arranged at the metaphase plate, with one chromosome facing each pole.
• Microtubules from one pole are attached to the kinetochore of one chromosome of each tetrad, while those from the other pole are
attached to the other.

Anaphase I

• In anaphase I, the homologous chromosomes separate. One chromosome moves toward each pole, guided by the spindle apparatus.
• Sister chromatids remain attached at the centromere and move as a single unit toward the pole.

Telophase I and cytokinesis

• In telophase I, movement of homologous chromosomes continues until there is a haploid set at each pole.
• Each chromosome consists of two sister chromatids.
• Cytokinesis usually occurs simultaneously, by the same mechanisms as mitosis.
• In animal cells, a cleavage furrow forms. In plant cells, a cell plate forms.
• No chromosome replication occurs between the end of meiosis I and the beginning of meiosis II, as the chromosomes are already
replicated.

Meiosis II

• Meiosis II is very similar to mitosis.

• During prophase II, a spindle apparatus forms and attaches to kinetochores of each sister chromatid.
• Spindle fibers from one pole attach to the kinetochore of one sister chromatid, and those of the other pole attach to kinetochore of the
other sister chromatid.
• At metaphase II, the sister chromatids are arranged at the metaphase plate.
• Because of crossing over in meiosis I, the two sister chromatids of each chromosome are no longer genetically identical.
• The kinetochores of sister chromatids attach to microtubules extending from opposite poles.
• At anaphase II, the centomeres of sister chromatids separate and two newly individual chromosomes travel toward opposite poles.
• In telophase II, the chromosomes arrive at opposite poles.
• Nuclei form around the chromosomes, which begin expanding, and cytokinesis separates the cytoplasm.
• At the end of meiosis, there are four haploid daughter cells.

The sister chromatids separate during the second meiosis division, meiosis II.

 Crossing overproduces recombinant chromosomes, which combine genes inherited from each parent.
 Crossing over begins very early in prophase I as homologous chromosomes pair up gene by gene.

 In crossing over, homologous portions of two nonsister chromatids trade places.

Crossing over, by combining DNA inherited from two parents into a single chromosome, is an important source of
genetic variation.

 The random nature of fertilization adds to the genetic variation arising from meiosis.
 Any sperm can fuse with any egg.
 The ovum is one of more than 8 million possible chromosome combinations.
 The successful sperm is one of more than 8 million possibilities.
 The resulting zygote could contain any one of more than 70 trillion possible combinations of chromosomes.
 Crossing over adds even more variation to this.
 Each zygote has a unique genetic identity.
 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.
 Crossing over between homologous chromosomes during prophase I.
 Random fertilization of an ovum by a sperm.

 All three mechanisms reshuffle the various genes carried by individual members of a population.
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 Any cell with two sets of chromosomes is called a diploid cell and has a diploid number of chromosomes, abbreviated as 2n.
 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).
 A gamete with a single chromosome set is haploid, abbreviated as n.
 Any sexually reproducing species has a characteristic haploid and diploid number of chromosomes.

 For humans, the haploid number of chromosomes is 23 (n = 23), and the diploid number is 46 (2n = 46).

 In plants and animals, sperm and ova (unfertilized eggs) transmit genes from one generation to the next.
 After fertilization (fusion of a sperm cell and an ovum), genes from both parents are present in the nucleus of the fertilized egg, or zygote.
 Almost all the DNA in a eukaryotic cell is subdivided into chromosomes in the nucleus.
 Tiny amounts of DNA are also found in mitochondria and chloroplasts.
 Every living species has a characteristic number of chromosomes.
 Humans have 46 chromosomes in almost all of their cells.
 Each chromosome consists of a single DNA molecule associated with various proteins.

 Each chromosome has hundreds or thousands of genes, each at a specific location, its locus.

 Human females have a homologous pair of X chromosomes (XX).

 Human males have an X and a Y chromosome (XY).
 Only small parts of the X and Y are homologous.
 Most of the genes carried on the X chromosome do not have counterparts on the tiny Y.
 The Y chromosome also has genes not present on the X.
 The occurrence of homologous pairs of chromosomes is a consequence of sexual reproduction.
 We inherit one chromosome of each homologous pair from each parent.

 The 46 chromosomes in each somatic cell are two sets of 23, a maternal set (from your mother) and a paternal set (from your father).

Chapter 14:

 Around 1857, Mendel began breeding garden peas to study inheritance.

 Pea plants have several advantages for genetic study.
 Pea plants are available in many varieties with distinct heritable features, or characters, with different variant traits.
 Mendel could strictly control which plants mated with which.
 Each pea plant has male (stamens) and female (carpal) sexual organs.
 In nature, pea plants typically self-fertilize, fertilizing ova with the sperm nuclei from their own pollen.
 However, Mendel could also use pollen from another plant for cross-pollination.
 Mendel tracked only those characters that varied in an “either-or” manner, rather than a “more-or-less” manner.
 For example, he worked with flowers that were either purple or white.
 He avoided traits, such as seed weight, that varied on a continuum.
 Mendel started his experiments with varieties that were true-breeding.
 When true-breeding plants self-pollinate, all their offspring have the same traits.
 In a typical breeding experiment, Mendel would cross-pollinate (hybridize) two contrasting, true-breeding pea varieties.
 The true-breeding parents are the P generation, and their hybrid offspring are the F1 generation.
 Mendel would then allow the F1 hybrids to self-pollinate to produce an F2 generation.

 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.

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, but could be homozygous dominant or heterozygous.
 The answer is to carry out a testcross.
 The mystery individual is bred with a homozygous recessive individual.

 If any of the offspring display the recessive phenotype, the mystery parent must be heterozygous.

 One extreme is the complete dominance characteristic of Mendel’s crosses.

 At the other extreme from complete dominance is codominance, in which two alleles affect the phenotype in separate, distinguishable ways.
 For example, the M, N, and MN blood groups of humans are due to the presence of two specific molecules on the surface of red blood cells.
 People of group M (genotype MM) have one type of molecule on their red blood cells, people of group N (genotype NN) have the other type,
and people of group MN (genotype MN) have both molecules present.
 The MN phenotype is not intermediate between M and N phenotypes but rather exhibits both the M and the N phenotype.
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 Some alleles show incomplete dominance, in which heterozygotes show a distinct intermediate phenotype not seen in homozygotes.
 This is not blending inheritance because the traits are separable (particulate), as shown in further crosses.
 Offspring of a cross between heterozygotes show three phenotypes: each parental and the heterozygote.
 The phenotypic and genotypic ratios are identical: 1:2:1.
 A clear example of incomplete dominance is seen in flower color of snapdragons.
 A cross between a white-flowered plant and a red-flowered plant will produce all pink F1 offspring.
 Self-pollination of the F1 offspring produces 25% white, 25% red, and 50% pink F2 offspring.

 The relative effects of two alleles range from complete dominance of one allele, through incomplete dominance of either allele, to
codominance of both alleles.

 Phenotype depends on environment and genes.

 A person becomes darker if they tan, despite their inherited skin color.
 A single tree may have leaves that vary in size, shape, and greenness, depending on exposure to wind and sun.
 For humans, nutrition influences height, exercise alters build, sun-tanning darkens skin, and experience improves performance on intelligence
tests.
 Even identical twins, who are genetically identical, accumulate phenotypic differences as a result of their unique experiences.
 The relative importance of genes and the environment in influencing human characteristics is a very old and hotly contested debate.
 The product of a genotype is generally not a rigidly defined phenotype, but a range of phenotypic possibilities, the norm of reaction, that are
determined by the environment.
 In some cases, the norm of reaction has no breadth, and a given genotype specifies a particular phenotype (for example, blood type).

 In contrast, a person’s red and white blood cell count varies with factors such as altitude, customary exercise level, and presence of infection.

 However, most genes are pleiotropic, affecting more than one phenotypic character.
 For example, the wide-ranging symptoms of sickle-cell disease are due to a single gene.
 Considering the intricate molecular and cellular interactions responsible for an organism’s development, it is not surprising that a gene can
affect a number of characteristics.
 In epistasis, a gene at one locus alters the phenotypic expression of a gene at a second locus.
 For example, in mice and many other mammals, coat color depends on two genes.

 One, the epistatic gene, determines whether pigment will be deposited in hair or not.

 Cystic fibrosisstrikes one of every 2,500 whites of European descent.

 One in 25 people of European descent is a carrier for this condition.
 The normal allele for this gene codes for a membrane protein that transports Cl− between cells and extracellular fluid.
 If these channels are defective or absent, there are abnormally high extracellular levels of chloride.
 This causes the mucus coats of certain cells to become thicker and stickier than normal.
 This mucus buildup in the pancreas, lungs, digestive tract, and elsewhere causes poor absorption of nutrients, chronic bronchitis, and bacterial
infections.
 Without treatment, affected children die before five, but with treatment, they can live past their late 20s or even 30s.
 Tay-Sachs diseaseis another lethal recessive disorder.
 It is caused by a dysfunctional enzyme that fails to break down specific brain lipids.
 The symptoms begin with seizures, blindness, and degeneration of motor and mental performance a few months after birth.
 Inevitably, the child dies after a few years.
 Among Ashkenazic Jews (those from central Europe), this disease occurs in one of 3,600 births, about 100 times greater than the incidence
among non-Jews or Mediterranean (Sephardic) Jews.
 The most common inherited disease among people of African descent is sickle-cell disease, which affects one of 400 African-Americans.
 Sickle-cell disease is caused by the substitution of a single amino acid in hemoglobin.
 When oxygen levels in the blood of an affected individual are low, sickle-cell hemoglobin aggregate into long rods that deform red blood
cells into a sickle shape.
 This sickling creates a cascade of symptoms, demonstrating the pleiotropic effects of this allele, as sickled cells clump and clog capillaries
throughout the body.
 Doctors can use regular blood transfusions to prevent brain damage and new drugs to prevent or treat other problems.
 At the organismal level, the nonsickle allele is incompletely dominant to the sickle-cell allele.
 Carriers are said to have sickle-cell trait.
 These individuals are usually healthy, although some suffer some symptoms of sickle-cell disease under blood oxygen stress.
 At the molecular level, the two alleles are codominant as both normal and abnormal (sickle-cell) hemoglobins are synthesized.
 About one in ten African-Americans has sickle-cell trait.
 The high frequency of heterozygotes is unusual for an allele with severe detrimental effects in homozygotes.
 Individuals with one sickle-cell allele have increased resistance to malaria, a parasite that spends part of its life cycle in red blood cells.
 In tropical Africa, where malaria is common, the sickle-cell allele is both a boon and a bane.
 Homozygous normal individuals die of malaria and homozygous recessive individuals die of sickle-cell disease, while carriers are relatively
free of both.
 The relatively high frequency of sickle-cell trait in African-Americans is a vestige of their African roots.
 Normally it is relatively unlikely that two carriers of the same rare, harmful allele will meet and mate.
 However, consanguineous matings between close relatives increase the risk.
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 Individuals who share a recent common ancestor are more likely to carry the same recessive alleles.
 Most societies and cultures have laws or taboos forbidding marriages between close relatives.
 Although most harmful alleles are recessive, a number of human disorders are due to dominant alleles.
 For example, achondroplasia, a form of dwarfism, has an incidence of one case in 25,000 people.
 Heterozygous individuals have the dwarf phenotype.
 Those who are not achondroplastic dwarfs, 99.99% of the population, are homozygous recessive for this trait.
 This provides another example of a trait for which the recessive allele is far more prevalent than the dominant allele.
 Lethal dominant alleles are much less common than lethal recessives.
 If a lethal dominant kills an offspring before it can mature and reproduce, the allele will not be passed on to future generations.
 In contrast, a lethal recessive allele can be passed on by heterozygous carriers who have normal phenotypes.
 A lethal dominant allele can escape elimination if it causes death at a relatively advanced age, after the individual has already passed on the
lethal allele to his or her children.
 One example is Huntington’s disease, a degenerative disease of the nervous system.
 The dominant lethal allele has no obvious phenotypic effect until an individual is about 35 to 45 years old.
 The deterioration of the nervous system is irreversible and inevitably fatal.
 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.
 In the United States, this devastating disease afflicts one in 10,000 people.
 Recently, molecular geneticists have used pedigree analysis of affected families to track the Huntington’s allele to a locus near the tip of
chromosome 4.
 This has led to the development of a test that can detect the presence of the Huntington’s allele in an individual’s genome.
 While some diseases are inherited in a simple Mendelian fashion due to alleles at a single locus, many other disorders have a multifactorial
basis.
 These may have a genetic component plus a significant environmental influence.
 Multifactorial disorders include heart disease; diabetes; cancer; alcoholism; and certain mental illnesses, such as schizophrenia and manic-
depressive disorder.
 The genetic component of such disorders is typically polygenic.
 At present, little is understood about the genetic contribution to most multifactorial diseases.

 The best public health strategy is education about relevant environmental factors and promotion of healthy behavior.

Chapter 15:

• Although the anatomical and physiological differences between women and men are numerous, the chromosomal basis of sex is rather
simple.
• In humans and other mammals, there are two varieties of sex chromosomes, X and Y.
• An individual who inherits two X chromosomes usually develops as a female.
• An individual who inherits an X and a Y chromosome usually develops as a male.
• Other animals have different methods of sex determination.
• The X-0 system is found in some insects. Females are XX, males are X.
• In birds, some fishes, and some insects, females are ZW and males are ZZ.
• In bees and ants, females are diploid and males are haploid.
• In the X-Y system, the Y chromosome is much smaller than the X chromosome.
• Only relatively short segments at either end of the Y chromosome are homologous with the corresponding regions of the X
chromosome.
• The X and Y rarely cross over.
• In both testes (XY) and ovaries (XX), the two sex chromosomes segregate during meiosis, and each gamete receives one.
• Each ovum receives an X chromosome.
• Half the sperm cells receive an X chromosome, and half receive a Y chromosome.
• Because of this, each conception has about a fifty-fifty chance of producing a particular sex.
• If a sperm cell bearing an X chromosome fertilizes an ovum, the resulting zygote is female (XX).
• If a sperm cell bearing a Y chromosome fertilizes an ovum, the resulting zygote is male (XY).
• In humans, the anatomical signs of sex first appear when the embryo is about two months old.
• In 1990, a British research team identified a gene on the Y chromosome required for the development of testes.
• They named the gene SRY (sex-determining region of the Y chromosome).
• In individuals with the SRY gene, the generic embryonic gonads develop into testes.
• Activity of the SRY gene triggers a cascade of biochemical, physiological, and anatomical features because it regulates many other
genes.
• Other genes on the Y chromosome are necessary for the production of functional sperm.
• In the absence of these genes, an XY individual is male but does not produce normal sperm.
• In individuals lacking the SRY gene, the generic embryonic gonads develop into ovaries.
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  Nondisjunctionoccurs when problems with the meiotic spindle cause errors in daughter cells.

 This may occur if tetrad chromosomes do not separate properly during meiosis I.

 Alternatively, sister chromatids may fail to separate during meiosis II.

 As a consequence of nondisjunction, one gamete receives two of the same type of chromosome, and another gamete receives no copy.

 Offspring resulting from fertilization of a normal gamete with one produced by nondisjunction will have an abnormal chromosome
number, a condition known as aneuploidy.

Chapter 16:

• Hershey and Chase found that when the bacteria had been infected with T2 phages that contained radiolabeled proteins, most of the
radioactivity was in the supernatant that contained phage particles, not in the pellet with the bacteria.
• When they examined the bacterial cultures with T2 phage that had radiolabeled DNA, most of the radioactivity was in the pellet with
the bacteria.
• 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.
• 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.
• 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.
• By 1947, 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, deoxyribose, and a phosphate group.
• The bases could be adenine (A), thymine (T), guanine (G), or cytosine (C).
• Chargaff noted that the DNA composition varies from species to species.
• In any one species, the four bases are found in characteristic, but not necessarily equal, ratios.
• He also found a peculiar regularity in the ratios of nucleotide bases that are known as Chargaff’s rules.
• In all organisms, the number of adenines was approximately equal to the number of thymines (%T = %A).
• The number of guanines was approximately equal to the number of cytosines (%G = %C).
• Human DNA is 30.9% adenine, 29.4% thymine, 19.9% guanine, and 19.8% cytosine.
• The basis for these rules remained unexplained until the discovery of the double helix.

Watson and Crick discovered the double helix by building models to conform to X-ray data.

• By the beginnings of the 1950s, the race was on to move from the structure of a single DNA strand to the three-dimensional structure
of DNA.
• Among the scientists working on the problem were Linus Pauling in California and Maurice Wilkins and Rosalind Franklin in
London.
• Maurice Wilkins and Rosalind Franklin used X-ray crystallography to study the structure of DNA.
• In this technique, X-rays are diffracted as they passed through aligned fibers of purified DNA.
• The diffraction pattern can be used to deduce the three-dimensional shape of molecules.
• James Watson learned from their research that DNA was helical in shape, and he deduced the width of the helix and the spacing of
nitrogenous bases.
• The width of the helix suggested that it was made up of two strands, contrary to a three-stranded model that Linus Pauling had
recently proposed.
• Watson and his colleague Francis Crick began to work on a model of DNA with two strands, the double helix.
• Using molecular models made of wire, they placed the sugar-phosphate chains on the outside and the nitrogenous bases on the inside
of the double helix.
• This arrangement put the relatively hydrophobic nitrogenous bases in the molecule’s interior.
• The sugar-phosphate chains of each strand are like the side ropes of a rope ladder.
• Pairs of nitrogenous bases, one from each strand, form rungs.
• The ladder forms a twist every ten bases.
• The nitrogenous bases are paired in specific combinations: adenine with thymine and guanine with cytosine.

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• Pairing like nucleotides did not fit the uniform diameter indicated by the X-ray data.
• A purine-purine pair is too wide, and a pyrimidine-pyrimidine pairing is too short.
• Only a pyrimidine-purine pairing produces the 2-nm diameter indicated by the X-ray data.
• In addition, Watson and Crick determined that chemical side groups of the nitrogenous bases would form hydrogen bonds, connecting
the two strands.
• Based on details of their structure, adenine would form two hydrogen bonds only with thymine, and guanine would form three
hydrogen bonds only with cytosine.
• This finding explained Chargaff’s rules.
• The base-pairing rules dictate the combinations of nitrogenous bases that form the “rungs” of DNA.
• However, this does not restrict the sequence of nucleotides along each DNA strand.
• The linear sequence of the four bases can be varied in countless ways.
• Each gene has a unique order of nitrogenous bases.
• In April 1953, Watson and Crick published a succinct, one-page paper in Nature reporting their double helix model of DNA.

 The exergonic hydrolysis of pyrophosphate to two inorganic phosphate molecules drives the polymerization of the nucleotide to the new
strand.

 The strands in the double helix are antiparallel.

 The sugar-phosphate backbones run in opposite directions.

• It takes E. coli 25 minutes to copy each of the 5 million base pairs in its single chromosome and divide to form two identical daughter
cells.
• A human cell can copy its 6 billion base pairs and divide into daughter cells in only a few hours.
• This process is remarkably accurate, with only one error per ten billion nucleotides.
• More than a dozen enzymes and other proteins participate in DNA replication.
• Much more is known about replication in bacteria than in eukaryotes.
• The process appears to be fundamentally similar for prokaryotes and eukaryotes.
• The replication of a DNA molecule begins at special sites, origins of replication.
• In bacteria, this is a specific sequence of nucleotides that is recognized by the replication enzymes.
• These enzymes separate the strands, forming a replication “bubble.”
• Replication proceeds in both directions until the entire molecule is copied.
• In eukaryotes, there may be hundreds or thousands of origin sites per chromosome.
• At the origin sites, the DNA strands separate, forming a replication “bubble” with replication forks at each end.
• The replication bubbles elongate as the DNA is replicated, and eventually fuse.
• DNA polymerasescatalyze the elongation of new DNA at a replication fork.
• As nucleotides align with complementary bases along the template strand, they are added to the growing end of the new strand by the
polymerase.
• The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells.
• In E. coli, two different DNA polymerases are involved in replication: DNA polymerase III and DNA polymerase I.
• In eukaryotes, at least 11 different DNA polymerases have been identified so far.
• Each nucleotide that is added to a growing DNA strand is a nucleoside triphosphate.
• Each has a nitrogenous base, deoxyribose, and a triphosphate tail.
• ATP is a nucleoside triphosphate with ribose instead of deoxyribose.
• Like ATP, the triphosphate monomers used for DNA synthesis are chemically reactive, partly because their triphosphate tails have an
unstable cluster of negative charge.
• As each nucleotide is added to the growing end of a DNA strand, the last two phosphate groups are hydrolyzed to form
pyrophosphate.
• The exergonic hydrolysis of pyrophosphate to two inorganic phosphate molecules drives the polymerization of the nucleotide to the
new strand.
• The strands in the double helix are antiparallel.
• The sugar-phosphate backbones run in opposite directions.
• 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.
• The 5’ à3’ direction of one strand runs counter to the 3’ à5’ direction of the other strand.
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 • DNA polymerases can only add nucleotides to the free 3’ end of a growing DNA strand.
• A new DNA strand can only elongate in the 5’ à3’ direction.
• Along one template strand, DNA polymerase III can synthesize a complementary strand continuously by elongating the new DNA in
the mandatory 5’ à3’ direction.
• The DNA strand made by this mechanism is called the leading strand.
• The other parental strand (5’ à3’ into the fork), the lagging strand, is copied away from the fork.
• Unlike the leading strand, which elongates continuously, the lagging stand is synthesized as a series of short segments called
Okazakifragments.
• Okazakifragments are about 1,000–2,000 nucleotides long in E. coli and 100–200 nucleotides long in eukaryotes.
• Another enzyme, DNA ligase, eventually joins the sugar-phosphate backbones of the Okazaki fragments to form a single DNA strand.
• DNA polymerases cannot initiate synthesis of a polynucleotide.
• They can only add nucleotides to the 3’ end of an existing chain that is base-paired with the template strand.
• The initial nucleotide chain is called a primer.
• In the initiation of the replication of cellular DNA, the primer is a short stretch of RNA with an available 3’ end.
• The primer is 5–10 nucleotides long in eukaryotes.
• Primase,an RNA polymerase, links ribonucleotides that are complementary to the DNA template into the primer.
• RNA polymerases can start an RNA chain from a single template strand.
• After formation of the primer, 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.
• Returning to the original problem at the replication fork, the leading strand requires the formation of only a single primer as the
replication fork continues to separate.
• For synthesis of the lagging strand, each Okazaki fragment must be primed separately.
• Another DNA polymerase, DNA polymerase I, replaces the RNA nucleotides of the primers with DNA versions, adding them one by
one onto the 3’ end of the adjacent Okazaki fragment.
• The primers are converted to DNA before DNA ligase joins the fragments together.
• In addition to primase, DNA polymerases, and DNA ligases, several other proteins have prominent roles in DNA synthesis.
• Helicaseuntwists the double helix and separates the template DNA strands at the replication fork.
• This untwisting causes tighter twisting ahead of the replication fork, and topoisomerase helps relieve this strain.
• Single-strand binding proteinskeep the unpaired template strands apart during replication.
• To summarize, at the replication fork, the leading strand is copied continuously into the fork from a single primer.
• The lagging strand is copied away from the fork in short segments, each requiring a new primer.
• It is conventional and convenient to think of the DNA polymerase molecules as moving along a stationary DNA template.
• In reality, the various proteins involved in DNA replication form a single large complex, a DNA replication “machine.”
• Many protein-protein interactions facilitate the efficiency of this machine.
• For example, helicase works much more rapidly when it is in contact with primase.
• The DNA replication machine is probably stationary during the replication process.
• In eukaryotic cells, multiple copies of the machine may anchor to the nuclear matrix, a framework of fibers extending through the
interior of the nucleus.
• The DNA polymerase molecules “reel in” the parental DNA and “extrude” newly made daughter DNA molecules.

Enzymes proofread DNA during its replication and repair damage in existing DNA.

• Mistakes during the initial pairing of template nucleotides and complementary nucleotides occur at a rate of one error per 100,000
base pairs.
• DNA polymerase proofreads each new nucleotide against the template nucleotide as soon as it is added.
• If there is an incorrect pairing, the enzyme removes the wrong nucleotide and then resumes synthesis.
• The final error rate is only one per ten billion nucleotides.
• DNA molecules are constantly subject to potentially harmful chemical and physical agents.
• Reactive chemicals, radioactive emissions, X-rays, and ultraviolet light can change nucleotides in ways that can affect encoded genetic
information.
• DNA bases may undergo spontaneous chemical changes under normal cellular conditions.
• Mismatched nucleotides that are missed by DNA polymerase or mutations that occur after DNA synthesis is completed can often be
repaired.
• Each cell continually monitors and repairs its genetic material, with 100 repair enzymes known in E. coli and more than 130 repair
enzymes identified in humans.
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 • In mismatch repair, special enzymes fix incorrectly paired nucleotides.
• A hereditary defect in one of these enzymes is associated with a form of colon cancer.
• In nucleotide excision repair, a nuclease cuts out a segment of a damaged strand.
• DNA polymerase and ligase fill in the gap.
• The importance of the proper functioning of repair enzymes is clear from the inherited disorder xeroderma pigmentosum.
• These individuals are hypersensitive to sunlight.
• Ultraviolet light can produce thymine dimers between adjacent thymine nucleotides.
• This buckles the DNA double helix and interferes with DNA replication.
• In individuals with this disorder, mutations in their skin cells are left uncorrected and cause skin cancer.

The ends of DNA molecules are replicated by a special mechanism.

• Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes.
• The usual replication machinery provides no way to complete the 5’ ends of daughter DNA strands.
• Repeated rounds of replication produce shorter and shorter DNA molecules.
• Prokaryotes do not have this problem because they have circular DNA molecules without ends.
• The ends of eukaryotic chromosomal DNA molecules, the telomeres, have special nucleotide sequences.
• Telomeres do not contain genes. Instead, the DNA typically consists of multiple repetitions of one short nucleotide sequence.
• In human telomeres, this sequence is typically TTAGGG, repeated between 100 and 1,000 times.
• Telomeres protect genes from being eroded through multiple rounds of DNA replication.
• Telomeric DNA tends to be shorter in dividing somatic cells of older individuals and in cultured cells that have divided many times.
• It is possible that the shortening of telomeres is somehow connected with the aging process of certain tissues and perhaps to aging in
general.
• 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.
• Eukaryotic cells have evolved a mechanism to restore shortened telomeres in germ cells, which give rise to gametes.
• If the chromosomes of germ cells became shorter with every cell cycle, essential genes would eventually be lost.
• An enzyme called telomerase catalyzes the lengthening of telomeres in eukaryotic germ cells, restoring their original length.
• Telomerase uses a short molecule of RNA as a template to extend the 3’ end of the telomere.
• There is now room for primase and DNA polymerase to extend the 5’ end.
• It does not repair the 3’-end “overhang,” but it does lengthen the telomere.
• Telomerase is not present in most cells of multicellular organisms.
• Therefore, the DNA of dividing somatic cells and cultured cells tends to become shorter.
• Telomere length may be a limiting factor in the life span of certain tissues and of the organism.
• Normal shortening of telomeres may protect organisms from cancer by limiting the number of divisions that somatic cells can
undergo.
• Cells from large tumors often have unusually short telomeres, because they have gone through many cell divisions.
• Active telomerase has been found in some cancerous somatic cells.
• This overcomes the progressive shortening that would eventually lead to self-destruction of the cancer.
• Immortal strains of cultured cells are capable of unlimited cell division.
• Telomerase may provide a useful target for cancer diagnosis and chemotherapy.
•  Like ATP, the triphosphate monomers used for DNA synthesis are chemically reactive, partly because their triphosphate tails have
an unstable cluster of negative charge.
•  As each nucleotide is added to the growing end of a DNA strand, the last two phosphate groups are hydrolyzed to form
pyrophosphate.
•  The exergonic hydrolysis of pyrophosphate to two inorganic phosphate molecules drives the polymerization of the nucleotide to
the new strand.

Chapter 17:

 During transcription, 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, it provides a template
for assembling a sequence of RNA nucleotides.
 Transcription of many genes produces a messenger RNA (mRNA) molecule.
 During translation, there is a change of language.
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 The site of translation is the ribosome, complex particles that facilitate the orderly assembly of amino acids into polypeptide chains.
 Why can’t proteins be translated directly from DNA?
 The use of an RNA intermediate provides protection for DNA and its genetic information.
 Using an RNA intermediate allows more copies of a protein to be made simultaneously, since many RNA transcripts can be made from one
gene.
 Also, each gene transcript can be translated repeatedly.
 The basic mechanics of transcription and translation are similar in eukaryotes and prokaryotes.
 Because bacteria lack nuclei, their DNA is not segregated from ribosomes and other protein-synthesizing equipment.
 This allows the coupling of transcription and translation.
 Ribosomes attach to the leading end of an mRNA molecule while transcription is still in progress.
 In a eukaryotic cell, transcription occurs in the nucleus, and translation occurs at ribosomes in the cytoplasm.
 The transcription of a protein-coding eukaryotic gene results in pre-mRNA.
 The initial RNA transcript of any gene is called a primary transcript.
 RNA processingyields the finished mRNA.
 To summarize, genes program protein synthesis via genetic messages in the form of messenger RNA.

 The molecular chain of command in a cell is DNA àRNA àprotein.

 The interpreter is transfer RNA (tRNA), which transfers amino acids from the cytoplasmic pool to a ribosome.
 A cell has all 20 amino acids available in its cytoplasm, either by synthesizing them from scratch or by taking them up from the surrounding
solution.
 The ribosome adds each amino acid carried by tRNA to the growing end of the polypeptide chain.
 During translation, each type of tRNA links an mRNA codon with the appropriate amino acid.
 Each tRNA arriving at the ribosome carries a specific amino acid at one end and has a specific nucleotide triplet, an anticodon, at the other.

 The anticodon base-pairs with a complementary codon on mRNA.

 Each ribosome is made up of a large and a small subunit.

 The subunits are composed of proteins and ribosomal RNA (rRNA), the most abundant RNA in the cell.
 In eukaryotes, the subunits are made in the nucleolus.

 After rRNA genes are transcribed to rRNA in the nucleus, the rRNA and proteins are assembled to form the subunits with proteins from the
cytoplasm.

• The Mendelian concept of a gene views it as a discrete unit of inheritance that affects phenotype.
• Morgan and his colleagues assigned genes to specific loci on chromosomes.
• We can also view a gene as a specific nucleotide sequence along a region of a DNA molecule.
• We can define a gene functionally as a DNA sequence that codes for a specific polypeptide chain.
• All these definitions are useful in certain contexts.
• Even the one gene–one polypeptide definition must be refined and applied selectively.
• Most eukaryotic genes contain large introns that have no corresponding segments in polypeptides.
• Promoters and other regulatory regions of DNA are not transcribed either, but they must be present for transcription to occur.
• Our molecular definition must also include the various types of RNA that are not translated into polypeptides, such as rRNA, tRNA,
and other RNAs.
• 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.

Chapter 18:

 When an E. coli cell must make tryptophan for itself, all the enzymes are synthesized at one time.
 The switch is a segment of DNA called an operator.
 The operator, located between the promoter and the enzyme-coding genes, controls the access of RNA polymerase to the genes.
 The operator, the promoter, and the genes they control constitute an operon.
 By itself, an operon is on and RNA polymerase can bind to the promoter and transcribe the genes.
 However, if a repressor protein, a product of a regulatory gene, binds to the operator, it can prevent transcription of the operon’s genes.
 Each repressor protein recognizes and binds only to the operator of a certain operon.
 Regulatory genes are transcribed continuously at low rates.
 Binding by the repressor to the operator is reversible.
 The number of active repressor molecules available determines the on or off mode of the operator.
 Repressors contain allosteric sites that change shape depending on the binding of other molecules.
 In the case of the trp, or tryptophan, operon, when concentrations of tryptophan in the cell are high, some tryptophan molecules bind as a
corepressor to the repressor protein.
 This activates the repressor and turns the operon off.

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 At low levels of tryptophan, most of the repressors are inactive, and the operon is transcribed.
 The trp operon is an example of a repressible operon, one that is inhibited when a specific small molecule binds allosterically to a regulatory
protein.
 In contrast, an inducible operon is stimulated when a specific small molecule interacts with a regulatory protein.
 In inducible operons, the regulatory protein is active (inhibitory) as synthesized, and the operon is off.
 Allosteric binding by an inducer molecule makes the regulatory protein inactive, and the operon is turned on.
 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).
 In the absence of lactose, this operon is off, as an active repressor binds to the operator and prevents transcription.
 Lactose metabolism begins with hydrolysis of lactose into its component monosaccharides, glucose and galactose.
 This reaction is catalyzed by the enzyme ß-galactosidase.
 Only a few molecules of this enzyme are present in an E. coli cell grown in the absence of lactose.
 If lactose is added to the bacterium’s environment, the number of ß-galactosidase increases by a thousandfold within 15 minutes.
 The gene for ß-galactosidase is part of the lac operon, which includes two other genes coding for enzymes that function in lactose
metabolism.
 The regulatory gene, lacI, located outside the operon, codes for an allosteric repressor protein that can switch off the lac operon by binding to
the operator.
 Unlike the trp operon, the lac repressor is active all by itself, binding to the operator and switching the lac operon off.
 An inducer inactivates the repressor.
 When lactose is present in the cell, allolactose, an isomer of lactose, binds to the repressor.
 This inactivates the repressor, and the lac operon can be transcribed.
 Repressible enzymes generally function in anabolic pathways, synthesizing end products from raw materials.
 When the end product is present in sufficient quantities, the cell can allocate its resources to other uses.
 Inducible enzymes usually function in catabolic pathways, digesting nutrients to simpler molecules.
 By producing the appropriate enzymes only when the nutrient is available, the cell avoids making proteins that have nothing to do.
 Both repressible and inducible operons demonstrate negative control because active repressors switch off the active form of the repressor
protein.
 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, the degree of transcription depends on the concentrations of other
substrates.

 During transposition, the transposable element moves from one location to another in a cell’s genome.
 In bacteria, the movement may be within the chromosome, from a plasmid to a chromosome (or vice versa), or between plasmids.
 Transposable elements may move by a “copy and paste” mechanism, in which the transposable element replicates at its original site, and the
copy inserts elsewhere.
 In other words, the transposable element is added at a new site without being lost from the old site.
 Most transposable elements can move to many alternative locations in the DNA, potentially moving genes to a site where genes of that sort
have never before existed.
 The simplest transposable elements, called insertion sequences, exist only in bacteria.
 An insertion sequence contains a single gene that codes for transposase, an enzyme that catalyzes movement of the insertion sequence from
one site to another within the genome.
 The insertion sequence consists of the transposase gene, flanked by a pair of inverted repeat sequences.
 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 transposase enzyme recognizes the inverted repeats as the edges of the transposable element.
 Transposase cuts the transposable elements from its initial site and inserts it into the target site.
 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.
 Insertion sequences account for 1.5% of the E. coli genome, but a mutation in a particular gene by transposition is rare, occurring about once
in every 10 million generations.
 This is about the same rate as spontaneous mutations from external factors.
 Transposable elements longer and more complex than insertion sequences, called transposons, also move about in the bacterial genome.
 In addition to the DNA required for transposition, transposons include extra genes that “go along for the ride,” such as genes for antibiotic
resistance.
 In some bacterial transposons, the extra genes are sandwiched between two insertion sequences.
 While insertion sequences may not benefit bacteria in any specific way, transposons may help bacteria adapt to new environments.
 For example, a single R plasmid may carry several genes for resistance to different antibiotics.
 This is explained by transposons, which can add a gene for antibiotic resistance to a plasmid already carrying genes for resistance to other
antibiotics.
 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.
 In an antibiotic-rich environment, natural selection factors bacterial clones that have built up R plasmids with multiple antibiotic resistance
through a series of transpositions.

 Transposable elements are also important components of eukaryotic genomes.

 Transformationis the alteration of a bacterial cell’s genotype by the uptake of naked, foreign DNA from the surrounding environment.
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 For example, harmless Streptococcus pneumoniae bacteria can be transformed to pneumonia-causing cells.
 This occurs when a live nonpathogenic cell takes up a piece of DNA that happens to include the allele for pathogenicity from dead, broken-
open pathogenic cells.
 The foreign allele replaces the native allele in the bacterial chromosome by genetic recombination.
 The resulting cell is now recombinant, with DNA derived from two different cells.
 Years after transformation was discovered in laboratory cultures, most biologists believed that the process was too rare and haphazard to play
an important role in natural bacterial populations.
 Researchers have since learned that many bacterial species have surface proteins that are specialized for the uptake of naked DNA.
 These proteins recognize and transport DNA from closely related bacterial species into the cell, which can then incorporate the foreign DNA
into the genome.
 While E. coli lacks this specialized mechanism, it can be induced to take up small pieces of DNA if cultured in a medium with a relatively
high concentration of calcium ions.

 In biotechnology, this technique has been used to introduce foreign DNA into E. coli.

Transductionoccurs when a phage carries bacterial genes from one host cell to another as a result of aberrations
in the phage reproductive cycle.

 Sometimes known as bacterial “sex,” conjugation transfers genetic material between two bacterial cells that are temporarily joined.
 The transfer is one-way. One cell (“male”) donates DNA and its “mate” (“female”) receives the genes.
 A sex pilus from the male initially joins the two cells and creates a cytoplasmic mating bridge between cells.

 “Maleness,” the ability to form a sex pilus and donate DNA, results from an F (for fertility) factor as a section of the bacterial chromosome
or as a plasmid.

 The capsid is the protein shell enclosing the viral genome.

 Capsids are built of a large number of protein subunits called capsomeres.
 The number of different kinds of proteins making up the capsid is usually small.
 The capsid of the tobacco mosaic virus has more than 1,000 copies of the same protein.
 Adenoviruses have 252 identical proteins arranged into a polyhedral capsid—as an icosahedron.

 Some viruses have accessory structures to help them infect their hosts.

 A genetic element that can replicate either as part of the bacterial chromosome or independently of it is called an episome.
 Episomes such as the F plasmid can undergo reversible incorporation into the cell’s chromosome.

 Temperate viruses are also episomes.

 Retroviruses(class VI) have the most complicated life cycles.

 These carry an enzyme called reverse transcriptase that transcribes DNA from an RNA template.
 This provides RNA àDNA information flow.
 The newly made DNA is inserted as a provirus into a chromosome in the animal cell.
 The host’s RNA polymerase transcribes the viral DNA into more RNA molecules.
 These can function both as mRNA for the synthesis of viral proteins and as genomes for new virus particles released from the cell.

 Human immunodeficiency virus (HIV), the virus that causes AIDS (acquired immunodeficiency syndrome) is a retrovirus.

 When an F+ and F− cell meet, the F+ cell passes a copy of the F plasmid to the F− cell, converting it.
 The plasmid form of the F factor can become integrated into the bacterial chromosome.
 A cell with the F factor built into its chromosome is called an Hfr cell (for High frequency of recombination).
 Hfr cells function as males during conjugation.
 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.

 Random movements almost always disrupt conjugation long before an entire copy of the Hfr chromosome can be passed to the F− cell.

 While phages are the best understood of all viruses, some of them are also among the most complex.
 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.
 In the lytic cycle, the phage reproductive cycle culminates in the death of the host.
 In the last stage, the bacterium lyses (breaks open) and releases the phages produced within the cell to infect others.
 Each of these phages can infect a healthy cell.
 Virulent phagesreproduce only by a lytic cycle.
 While phages have the potential to wipe out a bacterial colony in just hours, bacteria have defenses against phages.

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 Natural selection favors bacterial mutants with receptor sites that are no longer recognized by a particular type of phage.
 Bacteria produce restriction endonucleases, or restriction enzymes, that recognize and cut up foreign DNA, including certain phage DNA.
 Chemical modifications to the bacteria’s own DNA prevent its destruction by restriction nucleases.
 Natural selection also favors phage mutants that are resistant to restriction enzymes.
 In the lysogenic cycle, the phage genome replicates without destroying the host cell.

 Temperate phages,like phage lambda, use both lytic and lysogenic cycles.

 Each type of virus can infect and parasitize only a limited range of host cells, called its host range.

 This host specificity depends on the evolution of recognition systems by the virus.

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