Identifying Photosynthetic Reactants and Products

Photosynthesizing plants take in CO₂, water, and light energy, producing O₂ and carbohydrates. The overall reaction is

6 CO₂ + 12 H₂O + light →C₆H₁₂O₆ + 6 O₂ + 6 H₂O

The oxygen atoms in the O₂ produced by photosynthesis come from water, not from CO₂.

The Two Pathways of Photosynthesis: An Overview

In plants, photosynthesis takes place in chloroplasts.

In the light reactions of photosynthesis, electron transport and photophosphorylation produce ATP and reduce NADP+ to NADPH + H+.

ATP and NADPH + H+ are needed for the reactions that fix and reduce CO₂ in the Calvin–Benson cycle, forming carbohydrates.

The Interactions of Light and Pigments

Light energy comes in packets called photons, but it also has wavelike properties.

Absorption of a photon puts a pigment molecule in an excited state that has more energy than its ground state.

Pigments absorb light in the visible spectrum

Each compound has a characteristic absorption spectrum. An action spectrum reveals the biological effectiveness of different wavelengths of light. The absorption spectrum of the plant pigment chlorophyll a correlates well with the action spectrum for photosynthesis.

Chlorophylls and accessory pigments form antenna systems for absorption of light energy.

An excited pigment molecule may lose its energy by fluorescence or by transferring it to another pigment molecule.

Electron Transport, Reductions, and Photophosphorylation

Noncyclic electron transport uses two photosystems (I and II) and produces ATP, NADPH + H+, and O₂. Photosystem II uses P680 chlorophyll, from which light-excited electrons are passed to a redox chain that drives chemiosmotic ATP production.

Light-driven oxidation of water releases O₂ and passes electrons from water to the P680 chlorophyll. Photosystem I passes electrons from P700 chlorophyll to another redox chain and then to NADP+, forming NADPH + H+.

Cyclic electron transport uses P700 chlorophyll and produces only ATP. Its operation maintains the proper balance of ATP and NADPH + H+ in the chloroplast.

Chemiosmosis is the mechanism of ATP production in photophosphorylation. Electron transport pumps protons from the stroma into the thylakoids. Diffusion of the protons back to the stroma via ATP synthase channels drives ATP formation.

Making Carbohydrate from CO₂: The Calvin–Benson Cycle

The Calvin–Benson cycle makes sugar from CO₂. This pathway was elucidated through the use of radioactive tracers.

The Calvin–Benson cycle consists of three phases: fixation of CO₂, reduction and carbohydrate production, and regeneration of RuBP. RuBP is the initial CO₂ acceptor, and 3PG is the first stable product of CO₂ fixation. The enzyme rubisco catalyzes the reaction of CO₂ and RuBP to form 3PG.

Photorespiration and Its Consequences

The enzyme rubisco can catalyze a reaction between O2 and RuBP in addition to the reaction between CO₂ and RuBP. This reaction with O₂ is called photorespiration and significantly reduces the efficiency of photosynthesis. The reactions that constitute photorespiration are distributed over three organelles: chloroplasts, peroxisomes, and mitochondria.

At high temperatures and low CO₂ concentrations, the oxygenase function of rubisco is favored.

C4 plants bypass photorespiration with special chemical reactions and specialized leaf anatomy. In C4 plants, PEP carboxylase in chloroplasts of the mesophyll cells initially fixes CO₂ in a four-carbon compound, which then diffuses into bundle sheath cells, where its decarboxylation produces locally high concentrations of CO₂.

CAM plants operate much like C4 plants but their initial CO₂ fixation by PEP carboxylase is temporally separated from the Calvin–Benson cycle, rather than spatially separated as in C4 plants.

Metabolic Pathways in Plants

Photosynthesis and respiration are linked through the Calvin–Benson cycle, the citric acid cycle and glycolysis.

To survive, a plant must photosynthesize more than it respires.

Energy and Electrons from Glucose

- Metabolic pathways occur in small steps, each catalyzed by a specific enzyme. They are often compartmentalized.

- When glucose burns, energy is released as heat and light. The same equation applies to the metabolism of glucose by cells but the reaction is accomplished in many separate steps so that the energy can be captured in ATP.

- Oxidation is the loss of electrons; reduction is the gain of electrons. As a material is oxidized, the electrons it loses are transferred to another material, which is thereby reduced. Such redox reactions transfer large amounts of energy.

- The coenzyme NAD is a key electron carrier in biological redox reactions. It exists in two forms, one oxidized (NAD+) and the other reduced (NADH + H+).

- Glycolysis operates in the presence or absence of O₂. Under aerobic conditions cellular respiration continues the process of breaking down glucose. Under anaerobic conditions fermentation occurs.

- Cellular respiration consists of three pathways: pyruvate oxidation, the citric acid cycle and the respiratory chain.

- Pyruvate oxidation and the citric acid cycle produce CO₂ and hydrogen atoms carried by NADH and FADH2. The respiratory chain combines these hydrogens with O₂, releasing enough energy for the synthesis of ATP.

- In eukaryotes, glycolysis and fermentation take place in the cytoplasm outside of the mitochondria; pyruvate oxidation, the citric acid cycle, and the respiratory chain operate in association with mitochondria. In prokaryotes, glycolysis, fermentation, and the citric acid cycle take place in the cytoplasm and pyruvate oxidation and the respiratory chain operate in association with the plasma membrane.

Glycolysis: From Glucose to Pyruvate

- Glycolysis is a pathway of ten enzyme-catalyzed reactions located in the cytoplasm. Glycolysis provides starting materials for both cellular respiration and fermentation.

- The energy-investing reactions of glycolysis use two ATPs per glucose molecule and eventually yield two G3P molecules. In the energy-harvesting reactions, two NADH molecules are produced and four ATP molecules are generated by substrate-level phosphorylation. Two pyruvate molecules are produced for each glucose molecule.

Pyruvate Oxidation

- The pyruvate dehydrogenase complex catalyzes three reactions: (1) Pyruvate is oxidized to an acetyl group, releasing one CO₂ molecule and considerable energy. (2) Some of this energy is captured when NAD+ is reduced to NADH + H+. (3) The remaining energy is captured when the acetyl group is combined with coenzyme A, yielding acetyl CoA.

The Citric Acid Cycle

- The energy in acetyl CoA drives the reaction of acetate with oxaloacetate to produce citrate. The citric acid cycle is a series of reactions in which citrate is oxidized and oxaloacetate regenerated (hence a “cycle”). It produces 2 CO₂, 1 FADH2, 3 NADH, and 1 ATP for each acetyl CoA.

The Respiratory Chain: Electrons, Proton Pumping,and ATP Production

- NADH and FADH2 from glycolysis, pyruvate oxidation and the citric acid cycle are oxidized by the respiratory chain regenerating NAD+ and FAD. Most of the enzymes and other electron carriers of the chain are part of the inner mitochondrial membrane.

Oxygen (O₂) is the final acceptor of electrons and protons forming water (H₂O).

- The chemiosmotic mechanism couples proton transport to oxidative phosphorylation. As the electrons move along the respiratory chain, protons are pumped out of the mitochondrial matrix, establishing a gradient of both proton concentration and electric charge — the proton-motive force.

- The proton-motive force causes protons to diffuse back into the mitochondrial matrix through the membrane channel protein ATP synthase, which couples that diffusion to the production of ATP. Several key experiments demonstrate that chemiosmosis produces ATP.

Fermentation: ATP from Glucose, without O₂

- Many organisms and some cells live without O₂, deriving all their energy from glycolysis and fermentation. Together, these pathways partly oxidize glucose and generate energy-containing products such as lactic acid or ethanol.

Contrasting Energy Yields

- For each molecule of glucose used, fermentation yields 2 molecules of ATP. In contrast, glycolysis operating with pyruvate oxidation, the citric acid cycle, and the respiratory chain yields up to 36 molecules of ATP per molecule of glucose.

Relationships between Metabolic Pathways

- Catabolic pathways feed into the energy-harvesting metabolic pathways. Polysaccharides are broken down into glucose, which enters glycolysis. Glycerol from fats also enters glycolysis and acetyl CoA from fatty acid degradation enters the citric acid cycle. Proteins enter glycolysis and the citric acid cycle via amino acids.

- Anabolic pathways use intermediate components of energyharvesting pathways to synthesize fats, amino acids, and other essential building blocks.

Regulating Energy Pathways

- The rates of glycolysis and the citric acid cycle are increased or decreased by the actions of ATP, ADP, NAD+, or NADH + H+ on allosteric enzymes.

- Inhibition of the glycolytic enzyme phosphofructokinase by abundant ATP from cellular respiration slows down glycolysis.

ADP activates this enzyme, speeding up glycolysis. The citric acid cycle enzyme isocitrate dehydrogenase is inhibited by ATP and NADH and activated by ADP and NAD+.

Cells: The Basic Units of Life

- All cells come from preexisting cells and have certain processes, types of molecules, and structures in common.

- The first cells may have arisen from aggregates of macromolecules in bubbles.

- To maintain adequate exchanges with its environment, a cell’s surface area must be large compared with its volume.

- Cells can be visualized by various methods using microscopes.

- All cells are surrounded by a plasma membrane.

- All prokaryotic cells have a plasma membrane, a nucleoid region with DNA, and a cytoplasm that contains ribosomes, water, and dissolved proteins and small molecules.

- Some prokaryotes have additional protective structures: cell wall, outer membrane, and capsule. Some prokaryotes contain photosynthetic membranes or mesosomes, and some have flagellaor pili.

- Like prokaryotic cells, eukaryotic cells have a plasma membrane, cytoplasm, and ribosomes. However, eukaryotic cells are larger and contain many membrane-enclosed organelles.

- The membranes that envelop organelles in the eukaryotic cell are partial barriers, ensuring that the chemical composition of the interior of the organelle differs from that of the surrounding cytoplasm.

- Organelles can be isolated by cell fractionation.

- The nucleus is usually the largest organelle in a cell. It is surrounded by a double membrane, the nuclear envelope, which disassembles during cell division. Within the nucleus, the nucleolus is the source of the ribosomes found in the cytoplasm. Nuclear pores have a complex structure.

- The nucleus contains most of the cell’s DNA, which associates with protein to form chromatin. Chromatin is diffuse throughout the nucleus until just before cell division when it condenses to form chromosomes.

- The endomembrane system is made up of a series of interrelated compartments enclosed by membranes.

- The rough endoplasmic reticulum has attached ribosomes that synthesize proteins. The smooth endoplasmic reticulum lacks ribosomes and is associated with the synthesis of lipids.

- The Golgi apparatus receives materials from the rough ER by means of vesicles that fuse with its cis region. Vesicles originating from the trans region of the Golgi contain proteins targeted to different cellular locations. Some of these vesicles fuse with the plasma membrane and release their contents outside the cell.

- Lysosomes contain many digestive enzymes. Lysosomes fuse with the phagosomes produced by phagocytosis to form secondary lysosomes in which engulfed materials are digested. Undigested materials are secreted from the cell when the secondary lysosome fuses with the plasma membrane.

- Mitochondria are enclosed by an outer membrane and an inner membrane that folds inward to form cristae. Mitochondria contain the proteins needed for cellular respiration.

- The cells of photosynthetic eukaryotes contain chloroplasts. These organelles are enclosed by double membranes and contain an internal system of thylakoids organized as grana.

- Thylakoids within chloroplasts contain the chlorophyll and proteins that harvest light energy for photosynthesis.

- Both mitochondria and chloroplasts contain their own DNA and ribosomes and are capable of making some of their own proteins.

- The endosymbiosis theory of the evolutionary origin of mitochondria and chloroplasts states that these organelles originated when larger prokaryotes engulfed, but did not digest, smaller prokaryotes. Mutual benefits permitted this symbiotic relationship to be maintained, allowing the smaller cells to evolve into the eukaryotic organelles observed today.

- Peroxisomes and glyoxysomes contain special enzymes andcarry out specialized chemical reactions inside the cell.

- Vacuoles are prominent in many plant cells and consist of a membrane-enclosed compartment full of water and dissolved substances. By taking in water, vacuoles enlarge and provide the pressure needed to stretch the cell wall and provide structural support for the plant.

- The cytoskeleton within the cytoplasm of eukaryotic cellsprovides shape, strength, and movement. It consists of three interacting types of protein fibers.

- Microfilaments consist of two chains of actin units that together form a double helix. Microfilaments strengthen cellular structures and provide the movement in animal cell division, cytoplasmic streaming and pseudopod extension. Microfilaments may be found as individual fibers, bundles of fibers, or networks of fibers joined by linking proteins.

- Intermediate filaments are formed of keratins and are organized into tough, ropelike structures that hold organelles in place within the celland add strength to cell attachments in multicellular organisms.

- Microtubules are composed of dimers of the protein tubulin.

They can lengthen and shorten by adding and losing tubulin dimers. They are involved in the structure and function of cilia and flagella, both of which have a characteristic “9 + 2” pattern of microtubules.

- The movements of cilia and flagella result from the binding of the motor protein dynein to the microtubules. Dynein and another motor protein, kinesin, also bind to microtubules to move organelles through the cell.

- Centrioles, made up of triplets of microtubules, are involved in the distribution of chromosomes during cell division.

- Materials external to the plasma membrane provide protection, support, and attachment for cells in multicellular systems.

- The cell walls of plants consist principally of cellulose. They are pierced by plasmodesmata that join the cytoplasm of adjacent cells.

- In multicellular animals, the extracellular matrix consists of different kinds of proteins, including proteoglycans. In bone and cartilage, the protein collagen predominates.

Chromosomes, Cell Cycle and Cell Division

Cell division is necessary for the reproduction, growth and repair of an organism.

Cell division must be initiated by a reproductive signal. Cell division consists of three steps: replication of the genetic material (DNA), segregation of the two DNA molecules to separate portions of the cell, and cytokinesis, or division of the cytoplasm.

In prokaryotes, cellular DNA is a single molecule or chromosome. Prokaryotes reproduce by cell fission.

In eukaryotes, cells divide by either mitosis or meiosis.

The mitotic cell cycle has two main phases: interphase (during which cells are not dividing) and mitosis (when cells are dividing).

During most of the cell cycle, the cell is in interphase, which is divided into three subphases: S, G1, and G2. DNA is replicated during the S phase.

Cyclin-Cdk complexes regulate the passage of cells through checkpoints in the cell cycle. The most important one is the R point in G1, which determines whether the rest of the cycle will proceed.

In addition to the internal cyclin-Cdk complexes, controls external to the cell, such as growth factors and hormones, can also stimulate the cell to begin a division cycle.

A eukaryotic chromosome contains a DNA molecule bound to proteins in a complex called chromatin. At mitosis, the replicated chromatids are held together at the centromere. Each chromatid consists of one double-stranded DNA molecule.

During interphase, the DNA in chromatin is wound around cores of histones to form nucleosomes. DNA folds over and over again, packing itself within the nucleus. During mitosis or meiosis, it folds even more.

After DNA is replicated during the S phase, the first sign of mitosis is the separation of the replicated centrosomes which initiate microtubule formation for the spindle.

Mitosis can be divided into several phases, called prophase, prometaphase, metaphase, anaphase and telophase.

During prophase, the chromosomes condense and appear as paired chromatids and the spindle forms.

During prometaphase, the chromosomes move toward the middle of the spindle. In metaphase, they gather at the middle of the cell with their centromeres on the equatorial plate. At the end of metaphase, the centromeres holding the sister chromatids together separate, and during anaphase, each chromatid, now called the daughter chromosome, migrates to its pole along the microtubule track.

Cohesin holds sister chromatids together from the time they are formed in DNA replication until the onset of anaphase. Separin hydrolyzes cohesin when an inhibitory subunit, securin, is hydrolyzed.

During telophase, the chromosomes become less condensed. The nuclear envelopes and nucleoli re-form, thus producing two nuclei whose chromosomes are identical to each other and to those of the cell that began the cycle.

Nuclear division is usually followed by cytokinesis. Animalcell cytoplasm usually divides by a furrowing of the plasma membrane, caused by the contraction of cytoplasmic microfilaments.In plant cells, cytokinesis is accomplished by vesicle fusion and the synthesis of new cell wall material.

The cell cycle can repeat itself many times, forming a clone ofgenetically identical cells.

Asexual reproduction produces a new organism that is genetically identical to the parent. Any genetic variety is the result of mutations.

In sexual reproduction, two haploid gametes—one from each parent—unite in fertilization to form a genetically unique diploid zygote.

In sexually reproducing organisms, certain cells in the adult undergo meiosis, a process by which a diploid cell produces haploid gametes. Each gamete contains a random selection of one of each pair of homologous chromosomes from the parent.

The number, shapes and sizes of the chromosomes constitute the karyotype of an organism.

Meiosis reduces the chromosome number from diploid to haploid, ensures that each haploid cell contains one member of each chromosome pair, and results in genetically diverse products. It consists of two nuclear divisions.

During prophase I of the first meiotic division, homologous chromosomes pair up with each other, and material may be exchanged between the two homologs by crossing over. In metaphase I, the paired homologs line up at the equatorial plate.

In anaphase I, entire chromosomes, each with two chromatids, migrate to the poles. By the end of meiosis I, there are two nuclei, each with the haploid number of chromosomes.

In meiosis II, the sister chromatids separate. No DNA replication precedes this division, which in other aspects is similar to mitosis. The result of meiosis is four cells, each with a haploid chromosome content.

Both crossing over during prophase I and the random selection of which homolog of a pair migrates to which pole during anaphase I ensure that the genetic composition of each haploid gamete is different from that of the parent cell and from that of the other gametes. The more chromosome pairs there are in a diploid cell, the greater the diversity of chromosome combinations generated by meiosis.

In nondisjunction, one member of a homologous pair of chromosomes fails to separate from the other and both go to the same pole. Pairs of homologous chromosomes may also fail to stick together when they should. These events may lead to one gamete with an extra chromosome and another lacking that chromosome.

The union of a gamete with an abnormal chromosome number with a normal haploid gamete at fertilization results in aneuploidy and genetic abnormalities that are invariably harmful or lethal to the organism.

Polyploid organisms can have difficulty in cell division. Natural and artificially produced polyploids underlie modern agriculture.

Cells may die by necrosis, or they may self-destruct by apoptosis, a genetically programmed series of events that includes the detachment of the cell from its neighbors and the fragmentation of its nuclear DNA.

The Foundations of Genetics

Although it had long been known that both parents contribute to the character traits of their offspring, before Mendel’s time it was believed that, once they were brought together, the units of inheritance blended and could never be separated. Although Gregor Mendel’s work was meticulous and well documented, his discoveries, reported in the 1860s, were ignored until decades later.

Mendel’s Experiments and the Laws of Inheritance

Mendel used the garden pea for his studies because the plants were easily cultivated and crossed and because they showed numerous characters (such as seed shape) with clearly different traits (spherical or wrinkled). In a monohybrid cross, the offspring of the first generation (F1) showed only one of the two parental traits. Mendel proposed that the trait observed in the F1 was dominant and the other was recessive.

When the F1 offspring were self-pollinated, the resulting F2 generation showed a 3:1 phenotypic ratio, with the recessive phenotype present in one-fourth of the offspring. This reappearance of the recessive phenotype refuted the blending theory.

Because some alleles are dominant and some are recessive, the same phenotype can result from different genotypes. Homozygous genotypes have two copies of the same allele; heterozygous genotypes have two different alleles. Heterozygous genotypes yield phenotypes that show the dominant trait.

On the basis of many crosses using different characters, Mendel proposed his first law: that the units of inheritance (now known as genes) are particulate, that there are two alleles of each gene in each parent, and that during gamete formation the two alleles segregate from each other.

Geneticists who followed Mendel showed that genes are carried on chromosomes and that alleles are segregated during meiosis I.

Using a test cross, Mendel was able to determine whether a plant showing the dominant phenotype was homozygous or heterozygous. The appearance of the recessive phenotype in half of the offspring of such a cross indicates that the parent is heterozygous.

From studies of the inheritance of two characters using dihybrid crosses, Mendel concluded that alleles of different genes assort independently.

We can predict the results of hybrid crosses either by using a Punnett square or by calculating probabilities. To determine the joint probability of independent events, we multiply the individual probabilities. To determine the probability of an event that can occur in two or more different ways, we add the individual probabilities.

The analysis of pedigrees can trace Mendelian inheritance patterns in humans.

Alleles and Their Interactions

- New alleles arise by mutation, and many genes have multiple alleles.

- Dominance is sometimes not complete, since both alleles in a heterozygous organism may be expressed in the phenotype.

- In epistasis, the products of different genes interact to produce a phenotype.

- Environmental variables such as temperature, nutrition and light affect gene action.

- In some cases, the phenotype is the result of the effects of several genes and the environment and inheritance is quantitative.

Genes and Chromosomes

- Each chromosome carries many genes. Genes located on the same chromosome are said to be linked, and they are often inherited together.

- Linked genes can recombine by crossing over in prophase I of meiosis. The result is recombinant gametes which have new combinations of linked genes because of the exchange.

- The distance between two genes on a chromosome is proportional to the frequency of crossing over between them. Genetic maps are based on recombinant frequencies.

Sex Determination and Sex-Linked Inheritance

- Sex chromosomes carry genes that determine whether the organism will produce male or female gametes. The specific functions of X and Y chromosomes differ among species.

- In fruit flies and mammals, the X chromosome carries many genes, but the Y chromosome has only a few. Males have only one allele for X-linked genes, so rare alleles show up phenotypically more often in males than in females.

Non-Nuclear Inheritance

- Cytoplasmic organelles such as plastids and mitochondria contain some heritable genes.

- Cytoplasmic organelle genes are generally inherited only from the mother because male gametes contribute only their nucleus to the zygote at fertilization.

One Gene, One Polypeptide

- Genes are expressed in the phenotype as polypeptides (proteins).

- Beadle and Tatum’s experiments with the bread mold Neurospora resulted in several mutant strains, each lacking a specific enzyme in a biochemical pathway. Their results led to the one-gene, one-polypeptide hypothesis.

- Certain hereditary diseases in humans had been found to be caused by the absence of certain enzymes. These observations supported the one-gene, one-polypeptide hypothesis.

DNA, RNA, and the Flow of Information

- RNA differs from DNA in three ways: It is single-stranded, its sugar molecule is ribose rather than deoxyribose and its fourth base is uracil rather than thymine.

- The central dogma of molecular biology is DNA→RNA→protein.

- A gene is expressed in two steps: first, DNA is transcribed to RNA; then RNA is translated into protein.

- Some viruses are exceptions to the central dogma. Some viruses exclude DNA altogether, going directly from RNA to protein. In retroviruses, the central dogma is reversed: RNA→DNA.

Transcription: DNA-Directed RNA Synthesis

- RNA is transcribed from a DNA template after the bases of DNA are exposed by unwinding of the double helix.

- In a given gene, only one of the two strands of DNA (the template strand) acts as a template for transcription.

- RNA polymerase catalyzes transcription from the template strand of DNA.

- The initiation of transcription requires that RNA polymerase recognize and bind tightly to a promoter sequence on the DNA.

- RNA elongates in a 5′-to-3′direction, antiparallel to the template DNA. Special sequences and protein helpers terminate transcription.

- In prokaryotes, translation begins before transcription of the mRNA is completed. In eukaryotes, transcription occurs in the nucleus and translation occurs in the cytoplasm.

The Genetic Code

- The genetic code consists of triplets of nucleotide bases (codons). There are four bases, so there are 64 possible codons.

- One mRNA codon indicates the starting point of translation and codes for methionine. Three stop codons indicate the end of translation. The other 60 codons code only for particular amino acids.

- Because there are only 20 different amino acids, the genetic code is redundant; that is, there is more than one codon for certain amino acids. But the code is not ambiguous: A single codon does not encode more than one amino acid.

- Test-tube experiments led to the assignment of amino acids to codons.

Preparation for Translation: Linking RNAs, Amino Acids and Ribosomes

- In translation, amino acids are linked in an order specified by the codons in mRNA. This task is achieved by transfer RNAs (tRNAs), which bind to specific amino acids. Each tRNA species has an anticodon complementary to an mRNA codon. _ A family of activating enzymes attaches specific amino acids to their appropriate tRNAs, forming charged tRNAs.

- The mRNA meets the charged tRNAs at a ribosome.

- The small subunit of the ribosome checks to determine whether the tRNA anticodon and mRNA codon have formed hydrogen bonds.

Translation: RNA-Directed Polypeptide Synthesis

- An initiation complex consisting of a charged tRNA and a small ribosomal subunit bound to mRNA triggers the beginning of translation.

- Polypeptides grow from the N terminus toward the C terminus. The ribosome moves along the mRNA one codon at a time in the 5′-to-3′direction.

- The presence of a stop codon in the A site of the ribosome terminates translation.

Regulation of Translation

- Some antibiotics and bacterial toxins work by blocking events in translation.

- In a polysome, more than one ribosome moves along the mRNA at one time.

Posttranslational Events

- Signals contained in the amino acid sequences of proteins direct them to their cellular destinations.

- Protein synthesis begins on free ribosomes in the cytoplasm. Those proteins destined for the nucleus and other organelles are completed there. These proteins have signals that allow them to bind to and enter their destined organelles.

- Proteins destined for the ER, Golgi apparatus, lysosomes, and outside the cell complete their synthesis on the surface of the ER.

They enter the ER by the interaction of a hydrophobic signal sequence with a channel in the membrane.

- Modifications of proteins after translation include proteolysis, glycosylation, and phosphorylation.

Mutations: Heritable Changes in Genes

- Mutations in DNA are often expressed as abnormal proteins. However, the result may not be easily observable phenotypic changes. Some mutations are detectable only under certain conditions.

- Point mutations (silent, missense, nonsense or frame-shift) result from alterations in single base pairs of DNA.

- Chromosomal mutations (deletions, duplications, inversions, or translocations) involve large regions of a chromosome.

- Mutations can be spontaneous or induced. Spontaneous mutations occur because of instabilities in DNA or chromosomes.

Induced mutations occur when a mutagen damages DNA.

The Introduction to Theory of Evolution

- Darwin developed his theory of evolution by natural selection by carefully observing nature, especially during his voyage around the world on the Beagle.

- Darwin based this theory on well-known facts and some key inferences.

- Modern genetics has discovered the mechanisms of inheritance which Darwin did not understand.

- Darwin had no examples of the action of natural selection, so he based his arguments on artificial selection.

- For a population to evolve, its members must possess heritable genetic variation, which is the raw material on which agents of evolution act.

- A single individual has only some of the alleles found in the population of which it is a member.

- Considerable genetic variation characterizes most natural populations.

- Allele frequencies measure the amount of genetic variation in a population. Biologists estimate allele frequencies by measuring a sample of individuals from a population. The sum of all allele frequencies at a locus is equal to 1.

- Genotype frequencies show how a population’s genetic variation is distributed among its members. Populations that have the same allele frequencies may nonetheless have different genotype frequencies.

- Several conditions are required for a population to be at Hardy–Weinberg equilibrium: mating is random, the population is very large, there is no migration, there is no mutation, and natural selection is not acting on the population.

- In a population at Hardy–Weinberg equilibrium, allele frequencies remain the same from generation to generation. In addition, genotype frequencies will remain in the proportions p2 + 2pq + q2 = 1.

- Biologists can determine whether an agent of evolution is acting on a population by comparing the genotype frequencies of that population with Hardy–Weinberg expectations.

- Changes in the genetic structure of populations are caused by several evolutionary agents: mutation, gene flow, genetic drift, nonrandom mating and natural selection.

- The origin of genetic variation is mutation. Most mutations are harmful or neutral to their bearers but some are advantageous, particularly if the environment changes.

- Movement of individuals or gametes from one population to another, followed by reproduction in the new location, produces gene flow. Gene flow may add new alleles to a population or may change the frequencies of alleles already present.

- The random loss of alleles, known as genetic drift, produces changes in allele frequencies, which may be especially dramatic in small populations. Organisms that normally have large populations may pass through occasional periods (bottlenecks) when only a small number of individuals survive.

- New populations established by a few founding immigrants also have gene frequencies that differ from those in the parent population.

- If individuals mate more often with other individuals of a certain genotype than would be expected on a random basis—that is, when mating is not random—genotype frequencies differ from Hardy–Weinberg expectations.

- Self-fertilization, an extreme form of nonrandom mating, reduces the frequencies of heterozygous individuals below Hardy–Weinberg expectations without changing allele frequencies.

- Natural selection is the only agent of evolution that adapts populations to their environments.

- The reproductive contribution of a phenotype to subsequent generations relative to the contributions of other phenotypes is

its fitness. The fitness of a phenotype is determined by the average rates of survival and reproduction of individuals with that phenotype.

- Stabilizing selection reduces variation and preserves the average characteristics of a population.

- Directional selection changes a character by favoring individuals that vary in one direction from the population mean. If directional selection operates over many generations, an evolutionary trend may result.

- Disruptive selection changes a character by favoring individuals that vary in both directions from the population mean.

- Sexually selected traits may evolve because females prefer tomate with males having those traits.

- Possessing resistance to toxic chemicals may involve tradeoffs, such as reduced reproductive output.

- Sexually selected traits may result in higher parasite loads and mortality rates in males.

- Genetic drift, stabilizing selection, and directional selection all tend to reduce genetic variation, but most populations are genetically highly variable.

- Sexual recombination increases the evolutionary potential of populations, but it does not influence the frequencies of alleles.

Rather, it generates new combinations of genetic material on which natural selection can act.

- Genetic variation within a population may be maintained by frequency-dependent selection.

- Much genetic variation is maintained geographically.

- Natural selection acts by modifying what already exists.

- Learned traits can spread rapidly via cultural evolution.

- Patterns of long-term evolutionary change can be strongly influenced by events that occur so infrequently or so slowly that they are unlikely to be observed during short-term evolutionary studies. Additional types of evidence must be gathered to understand why evolution in the long term took the particular course it did.

Test questions 1

1. Coenzymes differ from enzymes in that coenzymes are

a. only active outside the cell.

b. polymers of amino acids.

c. smaller, such as vitamins.

d. specific for one reaction.

e. always carriers of high-energy phosphate.

2. Which statement about thermodynamics is true?

a. Free energy is used up in an exergonic reaction.

b. Free energy cannot be used to do work, such as chemical

transformations.

c. The total amount of energy can change after a chemical

transformation.

d. Free energy can be kinetic but not potential energy

e. Entropy tends always to a maximum.

3. In a chemical reaction,

a. the rate depends on the value of G.

b. the rate depends on the activation energy.

c. the entropy change depends on the activation energy.

d. the activation energy depends on the value of G.

e. the change in free energy depends on the activation energy.

4. Which statement about enzymes is not true?

a. They consist of proteins, with or without a nonprotein

part.

b. They change the rate of the catalyzed reaction.

c. They change the value of G of the reaction.

d. They are sensitive to heat.

e. They are sensitive to pH.

5. The active site of an enzyme

a. never changes shape.

b. forms no chemical bonds with substrates.

c. determines, by its structure, the specificity of the enzyme.

d. looks like a lump projecting from the surface of the enzyme.

e. changes G of the reaction.

6. The molecule ATP is

a. a component of most proteins.

b. high in energy because of the presence of adenine (A).

c. required for many energy-producing biochemical reactions.

d. a catalyst.

e. used in some endergonic reactions to provide energy.

7. In an enzyme-catalyzed reaction,

a. a substrate does not change.

b. the rate decreases as substrate concentration increases.

c. the enzyme can be permanently changed.

d. strain may be added to a substrate.

e. the rate is not affected by substrate concentration.

8. Which statement about enzyme inhibitors is not true?

a. A competitive inhibitor binds the active site of the enzyme.

b. An allosteric inhibitor binds a site on the active form of the enzyme.

c. A noncompetitive inhibitor binds a site other than the active site.

d. Noncompetitive inhibition cannot be completely overcome

by the addition of more substrate.

e. Competitive inhibition can be completely overcome by the addition of more substrate.

9. Which statement about feedback inhibition of enzymes is not true?

a. It is exerted through allosteric effects.

b. It is directed at the enzyme that catalyzes the first committed step in a branch of a pathway.

c. It affects the rate of reaction, not the concentration of enzyme.

d. It acts very slowly.

e. It is an example of negative feedback.

10. Which statement about temperature effects is not true?

a. Raising the temperature may reduce the activity of an enzyme.

b. Raising the temperature may increase the activity of an enzyme.

c. Raising the temperature may denature an enzyme.

d. Some enzymes are stable at the boiling point of water.

e. All enzymes have the same optimal temperature.

Test questions 2

1. In noncyclic photosynthetic electron transport, water is used to

a. excite chlorophyll.

b. hydrolyze ATP.

c. reduce chlorophyll.

d. oxidize NADPH.

e. synthesize chlorophyll.

2. Which statement about light is true?

a. An absorption spectrum is a plot of biological effectiveness

versus wavelength.

b. An absorption spectrum may be a good means of identifying

a pigment.

c. Light need not be absorbed to produce a biological effect.

d. A given kind of molecule can occupy any energy level.

e. A pigment loses energy as it absorbs a photon.

3. Which statement about chlorophylls is not true?

a. They absorb light near both ends of the visible spectrum.

b. They can accept energy from other pigments, such as

carotenoids.

c. Excited chlorophyll can either reduce another substance

or fluoresce.

d. Excited chlorophyll may be an oxidizing agent.

e. They contain magnesium.

4. In cyclic electron transport,

a. oxygen gas is released.

b. ATP is formed.

c. water donates electrons and protons.

d. NADPH + H+ forms.

e. CO2 reacts with RuBP.

5. Which of the following does not happen in noncyclic electron

transport?

a. Oxygen gas is released.

b. ATP forms.

c. Water donates electrons and protons.

d. NADPH + H+ forms.

e. CO2 reacts with RuBP.

6. In the chloroplasts,

a. light leads to the pumping of protons out of the thylakoids.

b. ATP forms when protons are pumped into the thylakoids.

c. light causes the stroma to become more basic than the

thylakoids.

d. protons return passively to the stroma through protein

channels.

e. proton pumping requires ATP.

7. Which statement about the Calvin–Benson cycle is not true?

a. CO2 reacts with RuBP to form 3PG.

b. RuBP forms by the metabolism of 3PG.

c. ATP and NADPH + H+ form when 3PG is reduced.

d. The concentration of 3PG rises if the light is switched off.

e. Rubisco catalyzes the reaction of CO2 and RuBP.

8. In C4 photosynthesis,

a. 3PG is the first product of CO2 fixation.

b. rubisco catalyzes the first step in the pathway.

c. four-carbon acids are formed by PEP carboxylase in

bundle sheath cells.

d. photosynthesis continues at lower CO2 levels than in

C3 plants.

e. CO2 released from RuBP is transferred to PEP.

9. Photosynthesis in green plants occurs only during the day.

Respiration in plants occurs

a. only at night.

b. only when there is enough ATP.

c. only during the day.

d. all the time.

e. in the chloroplast after photosynthesis.

10. Photorespiration

a. takes place only in C4 plants.

b. includes reactions carried out in peroxisomes.

c. increases the yield of photosynthesis.

d. is catalyzed by PEP carboxylase.

e. is independent of light intensity.

Test questions 3

1. Which is present in both prokaryotic cells and in eukaryotic

plant cells?

a. Chloroplasts

b. Cell walls

c. Nucleus

d. Mitochondria

e. Microtubules

2. The major factor limiting cell size is the

a. concentration of water in the cytoplasm.

b. need for energy.

c. presence of membranous organelles.

d. ratio of surface area to volume.

e. composition of the plasma membrane.

3. Which statement about mitochondria is not true?

a. Their inner membrane folds to form cristae.

b. They are usually 1 nano-m or smaller in diameter.

c. They are green because they contain chlorophyll.

d. Energy-rich substances from the cytosol are oxidized in them.

e. Much ATP is synthesized in them.

4. Which statement about plastids is true?

a. They are found in prokaryotes.

b. They are surrounded by a single membrane.

c. They are the sites of cellular respiration.

d. They are found in fungi.

e. They are of several types with different functions.

5. If all the lysosomes within a cell suddenly ruptured, what would be the most likely result?

a. The macromolecules in the cytosol would begin to break

down.

b. More proteins would be made.

c. The DNA within mitochondria would break down.

d. The mitochondria and chloroplasts would divide.

e. There would be no change in cell function.

6. The Golgi apparatus

a. is found only in animals.

b. is found in prokaryotes.

c. is the appendage that moves a cell around in its

environment.

d. is a site of rapid ATP production.

e. packages and modifies proteins.

7. Which organelle is not surrounded by one or more membranes?

a. Ribosome

b. Chloroplast

c. Mitochondrion

d. Peroxisome

e. Vacuole

8. The cytoskeleton consists of

a. cilia, flagella and microfilaments.

b. cilia, microtubules and microfilaments.

c. internal cell walls.

d. microtubules, intermediate filaments and microfilaments.

e. calcified microtubules.

9. Microfilaments

a. are composed of polysaccharides.

b. are composed of actin.

c. provide the motive force for cilia and flagella.

d. make up the spindle that aids the movement of chromosomes.

e. maintain the position of the chloroplast in the cell.

10. Which statement about the plant cell wall is not true?

a. Its principal chemical components are polysaccharides.

b. It lies outside the plasma membrane.

c. It provides support for the cell.

d. It completely isolates adjacent cells from one another.

e. It is semirigid.

Test questions 4

1. Which statement about eukaryotic chromosomes is not true?

a. They sometimes consist of two chromatids.

b. They sometimes consist of a single chromatid.

c. They normally possess a single centromere.

d. They consist of proteins.

e. They are clearly visible as defined bodies under the light microscope.

2. Nucleosomes

a. are made of chromosomes.

b. consist entirely of DNA.

c. consist of DNA wound around a histone core.

d. are present only during mitosis.

e. are present only during prophase.

3. Which statement about the cell cycle is not true?

a. It consists of mitosis and interphase.

b. The cell’s DNA replicates during G1.

c. A cell can remain in G1 for weeks or much longer.

d. Proteins are formed throughout all subphases of interphase.

e. Histones are synthesized primarily during S phase.

4. Which statement about mitosis is not true?

a. A single nucleus gives rise to two identical daughter nuclei.

b. The daughter nuclei are genetically identical to the parent nucleus.

c. The centromeres separate at the onset of anaphase.

d. Homologous chromosomes synapse in prophase.

e. Mitotic centers organize the microtubules of the spindle

fibers.

5. Which statement about cytokinesis is true?

a. In animals, a cell plate forms.

b. In plants, it is initiated by furrowing of the membrane.

c. It generally immediately follows mitosis.

d. In plant cells, actin and myosin play an important part.

e. It is the division of the nucleus.

6. Apoptosis

a. occurs in all cells.

b. involves the cell membrane dissolving.

c. does not occur in an embryo.

d. involves a series of programmed events for cell death.

e. is not involved with cancer.

7. In meiosis,

a. meiosis II reduces the chromosome number from diploid to haploid.

b. DNA replicates between meiosis I and II.

c. the chromatids that make up a chromosome in meiosis II are identical.

d. each chromosome in prophase I consists of four chromatids.

e. homologous chromosomes separate from one another in anaphase I.

8. In meiosis,

a. a single nucleus gives rise to two daughter nuclei.

b. the daughter nuclei are genetically identical to the parent nucleus.

c. the centromeres separate at the onset of anaphase I.

d. homologous chromosomes synapse in prophase I.

e. no spindle forms.

9. A plant has a diploid chromosome number of 12. An egg cell of the plant has 5 chromosomes. The most probable

explanation of this is

a. normal mitosis.

b. normal meiosis.

c. nondisjunction in meiosis I.

d. nondisjunction in meiosis I and II.

e. nondisjunction in mitosis.

10. The number of daughter chromosomes in a human cell in anaphase II of meiosis is

a. 2.

b. 23.

c. 46.

d. 69.

e. 92.

Test questions 5

1. In a simple Mendelian monohybrid cross, tall plants were crossed with short plants and the F1 were crossed among themselves. What fraction of the F2 generation are both tall and heterozygous?

a. 1 ⁄8

b. 1⁄4

c. 1⁄3

d. 2⁄3

e. 1⁄2

2. The phenotype of an individual

a. depends at least in part on the genotype.

b. is either homozygous or heterozygous.

c. determines the genotype.

d. is the genetic constitution of the organism.

e. is either monohybrid or dihybrid.

3. The ABO blood groups in humans are determined by a multiple allelic system where IA and IB are codominant and dominant to IO. A newborn infant is type A. The mother is type O. Possible genotypes of the father are:

a. A, B or AB

b. A, B or O

c. O only

d. A or AB

e. A or O

4. Which statement about an individual that is homozygous for an allele is not true?

a. Each of its cells possesses two copies of that allele.

b. Each of its gametes contains one copy of that allele.

c. It is true-breeding with respect to that allele.

d. Its parents were necessarily homozygous for that allele.

e. It can pass that allele to its offspring.

5. Which statement about a test cross is not true?

a. It tests whether an unknown individual is homozygous or heterozygous.

b. The test individual is crossed with a homozygous recessive individual.

c. If the test individual is heterozygous, the progeny will have a 1:1 ratio.

d. If the test individual is homozygous, the progeny will have a 3:1 ratio.

e. Test cross results are consistent with Mendel’s model of inheritance.

6. Linked genes

a. must be immediately adjacent to one another on a chromosome.

b. have alleles that assort independently of one another.

c. never show crossing over.

d. are on the same chromosome.

e. always have multiple alleles.

7. In the F2 generation of a dihybrid cross

a. 4 phenotypes appear in the ratio 9:3:3:1 if the loci are linked.

b. 4 phenotypes appear in the ratio 9:3:3:1 if the loci are unlinked.

c. 2 phenotypes appear in the ratio 3:1 if the loci are unlinked.

d. 3 phenotypes appear in the ratio 1:2:1 if the loci are unlinked.

e. 2 phenotypes appear in the ratio 1:1 whether or not the loci are linked.

8. The sex of a human is determined by

a. ploidy, the male being haploid.

b. the Y chromosome.

c. X and Y chromosomes, the male being XY.

d. the number of X chromosomes, the male being XO.

e. Z and W chromosomes, the male being ZZ.

9. In epistasis

a. nothing changes from generation to generation.

b. one gene alters the effect of another.

c. a portion of a chromosome is deleted.

d. a portion of a chromosome is inverted.

e. the behavior of two genes is entirely independent.

10. In humans, spotted teeth is caused by a dominant sexlinked gene. A man with spotted teeth whose mother had normal teeth marries a woman with normal teeth. Therefore, a. all of their daughters will have normal teeth.

b. all of their daughters will have spotted teeth.

c. all of their children will have spotted teeth.

d. half of their sons will have spotted teeth.

e. none of their sons will have spotted teeth.

Test questions 6

1. Which of the following is not a difference between RNA andDNA?

a. RNA has uracil; DNA has thymine.

b. RNA has ribose; DNA has deoxyribose.

c. RNA has five bases; DNA has four.

d. RNA is a single polynucleotide strand; DNA is a double

strand.

e. RNA is relatively smaller than human chromosomal DNA.

2. Normally, Neurospora can synthesize all 20 amino acids. A certain strain of this mold cannot grow in simple growth medium but grows only when the amino acid leucine is added to the medium. This strain is

a. dependent on leucine for energy.

b. mutated in the synthesis of all proteins.

c. mutated in the synthesis of all 20 amino acids

d. mutated in the synthesis of leucine.

e. mutated in the syntheses of 19 of the 20 amino acids.

3. An mRNA has the sequence 5′-AUGAAAUCCUAG-3′. What is the template DNA strand for this sequence?

a. 5′-TACTTTAGGATC-3′

b. 5′-ATGAAATCCTAG-3′

c. 5′-GATCCTAAAGTA-3′

d. 5′-TACAAATCCTAG-3′

e. 5′-CTAGGATTTCAT-3′

4. The adapters that allow translation of the four-letter nucleic acid language into the 20 letter protein language are called

a. aminoacyl tRNA synthetases.

b. transfer RNAs.

c. ribosomal RNAs.

d. messenger RNAs.

e. ribosomes.

5. At a certain location in a gene, the nontemplate strand of DNA has the sequence GAA. Amutation alters the triplet to GAG. This type of mutation is called

a. silent.

b. missense.

c. nonsense.

d. frame-shift.

e. translocation.

6. Transcription

a. produces only mRNA.

b. requires ribosomes.

c. requires tRNAs.

d. produces RNA growing from the 5′end to the 3′end.

e. takes place only in eukaryotes.

7. Which statement about translation is not true?

a. It is RNA-directed polypeptide synthesis.

b. An mRNA molecule can be translated by only one ribosome at a time.

c. The same genetic code operates in almost all organisms and organelles.

d. Any ribosome can be used in the translation of any mRNA.

e. There are both start and stop codons.

8. Which statement is not true?

a. Transfer RNA functions in translation.

b. Ribosomal RNA functions in translation.

c. RNAs are produced in transcription.

d. Messenger RNAs are produced on ribosomes.

e. DNA codes for mRNA, tRNA, and rRNA.

9. The genetic code

a. is different for prokaryotes and eukaryotes.

b. has changed during the course of recent evolution.

c. has 64 codons that code for amino acids.

d. is degenerate.

e. is ambiguous.

10. A mutation that results in the codon UAG where there had been UGG is

a. a nonsense mutation.

b. a missense mutation.

c. a frame-shift mutation.

d. a large-scale mutation.

e. unlikely to have a significant effect.

Test questions 7

1. The two major components of Darwin’s theory of evolutionare that

a. evolution is a fact and mutations are the agent of evolution.

b. evolution is a fact and natural selection is the agent of evolution.

c. species cannot change into other species, but natural

selection can modify them.

d. species cannot change into other species but mutations

can modify them.

e. evolution is a hypothesis, and genetic drift is the agent of

evolution.

2. To ground his theory, Charles Darwin

a. developed a comprehensive theory of inheritance.

b. described several evolutionary changes and identified the

agents that caused them.

c. used patterns of domestication to show how his theory

differed from those patterns.

d. assembled a broad base of supporting information from

many fields.

e. developed a mathematical model of evolutionary change.

3. The phenotype of an organism is

a. the type specimen of its species in a museum.

b. its genetic constitution, which governs its traits.

c. the chronological expression of its genes.

d. the physical expression of its genotype.

e. the form it achieves as an adult.

4. The appropriate unit for defining and measuring geneticvariation is the

a. cell.

b. individual.

c. population.

d. community.

e. ecosystem.

5. Which statement about allele frequencies is not true?

a. The sum of any set of allele frequencies is always 1.

b. If there are two alleles at a locus and we know the frequency

of one of them, we can obtain the frequency of

the other by subtraction.

c. If an allele is missing from a population, its frequency is 0.

d. If two populations have the same gene pool for a locus, they will have the same proportion of homozygotes at that locus.

e. If there is only one allele at a locus, its frequency is 1.

6. In a population at Hardy–Weinberg equilibrium in which the frequency of A alleles (p) is 0.3, the expected frequency of Aa individuals is

a. 0.21.

b. 0.42.

c. 0.63.

d. 0.18.

e. 0.36.

7. Natural selection that preserves existing allele frequencies is called

a. unidirectional selection.

b. bidirectional selection.

c. prevalent selection.

d. stabilizing selection.

e. preserving selection.

8. The fitness of a genotype is determined by the

a. average rates of survival and reproduction of individuals with that genotype.

b. individuals that have the highest rates of both survival and reproduction.

c. individuals that have the highest rates of survival.

d. individuals that have the highest rates of reproduction.

e. average reproductive rate of individuals with that genotype.

9. Laboratory selection experiments with fruit flies have demonstrated that

a. bristle number is not genetically controlled.

b. bristle number is not genetically controlled but changes in bristle number are caused by the environment in which the fly is raised.

c. bristle number is genetically controlled but there is little variation on which natural selection can act.

d. bristle number is genetically controlled but selection cannot result in flies having more bristles than any individual in the original population had.

e. bristle number is genetically controlled, and selection can result in flies having more bristles than any individual in the original population had.

10. Disruptive selection maintains a bimodal distribution of bill size in the West African seedcracker because

a. bills of intermediate shapes are difficult to form.

b. the two major food sources of the finches differ markedly in size and hardness.

c. males use their large bills in displays.

d. migrants introduce different bill sizes into the population each year.

e. older birds need larger bills than younger birds.

11. A population is said to be polymorphic for a locus if it has at least

a. three different alleles at that locus.

b. two different alleles at that locus.

c. two genotypes for that locus.

d. three genotypes for that locus.

e. two alleles for that locus, the rarest of which is more common than expected by mutation alone.

Test questions 8

1. The role of oxygen gas in our cells is to

a. catalyze reactions in glycolysis.

b. produce CO₂.

c. form ATP.

d. accept electrons from the electron transport chain.

e. react with glucose to split water.

2. Oxidation and reduction

a. entail the gain or loss of proteins.

b. are defined as the loss of electrons.

c. are both endergonic reactions.

d. always occur together.

e. proceed only under aerobic conditions.

3. NAD+ is

a. a type of organelle.

b. a protein.

c. present only in mitochondria.

d. a part of ATP.

e. formed in the reaction that produces ethanol.

4. Glycolysis

a. takes place in the mitochondrion.

b. produces no ATP.

c. has no connection with the respiratory chain.

d. is the same thing as fermentation.

e. reduces two molecules of NAD+ for every glucose

molecule processed.

5. Fermentation

a. takes place in the mitochondrion.

b. takes place in all animal cells.

c. does not require O2.

d. requires lactic acid.

e. prevents glycolysis.

6. Which statement about pyruvate is not true?

a. It is the end product of glycolysis.

b. It becomes reduced during fermentation.

c. It is a precursor of acetyl CoA.

d. It is a protein.

e. It contains three carbon atoms.

7. The citric acid cycle

a. takes place in the mitochondrion.

b. produces no ATP.

c. has no connection with the respiratory chain.

d. is the same thing as fermentation.

e. reduces two NAD+ for every glucose processed.

8. The electron transport chain

a. operates in the mitochondrial matrix.

b. uses proteins embedded within a membrane.

c. always leads to the production of ATP.

d. regenerates reduced coenzymes.

e. operates simultaneously with fermentation.

9. Compared to anaerobic metabolism, aerobic breakdown ofglucose produces

a. more ATP.

b. pyruvate.

c. fewer protons for pumping in mitochondria.

d. less CO2.

e. more oxidized coenzymes.

10. Which statement about oxidative phosphorylation is not true?

a. It is the formation of ATP by the respiratory chain.

b. It is brought about by the chemiosmotic mechanism.

c. It requires aerobic conditions.

d. In eukaryotes, it takes place in mitochondria.

e. Its functions can be served equally well by fermentation.

For Discussion -1

1. How is it possible for endergonic reactions to proceed in organisms?

2. Consider two proteins: One is an enzyme dissolved in the cytosol, the other is an ion channel in a membrane. Contrast the structures of two proteins, indicating at least two important differences.

3. Plot free energy versus the course of an endergonic reaction and that of an exergonic reaction. Include the activation energy

in both plots. Label Ea and G on both graphs.

4. Consider an enzyme that is subject to allosteric regulation. If a competitive inhibitor (not an allosteric inhibitor) is added to a solution of such an enzyme, the ratio of enzyme molecules in the active form to those in the inactive form increases.

Explain this observation.

5. If you were presented with a radioactively labeled substance, what experiments would you perform to determine whether it enters cells by simple diffusion or active transport?

For Discussion-2

1. Both photosynthetic electron transport and the Calvin– Benson cycle stop in the dark. Which specific reaction stops

first? Which stops next? Continue answering the question “Which stops next?” until you have explained why both pathways have stopped.

2. In what principal ways are the reactions of electron transport in photosynthesis similar to the respiratory chain and oxidative phosphorylation discussed in previous Chapter ? Differentiate between cyclic and noncyclic electron transport in terms of (1) the products and (2) the source of electrons for the reductionof oxidized chlorophyll.

3. The development of what two experimental techniques made it possible to elucidate the Calvin–Benson cycle? How were these techniques used in the investigation?

4. If water labeled with 18O is added to a suspension of photosynthesizing chloroplasts, which of the following compounds will first become labeled with 18O: ATP, NADPH, O2, or 3PG? If water labeled with 3H is added to a suspension of photosynthesizing chloroplasts, which of the same compounds will first become radioactive? If CO2 labeled with 14C is added to a suspension of photosynthesizing chloroplasts, which of those compounds will first become radioactive?

5. The Viking lander was sent to Mars in 1976 to detect signs of life. Explain the rationale behind the following experiments this unmanned probe performed:

a. A scoop of dirt was inserted into a container and 14CO2 was added. After a while during the Martian day, the 14CO2 was removed and the dirt was heated to high temperatures. Scientists monitoring the experiment back on the Earth looked for the release of 14CO2 as a sign of life.

b. The experiment in (a) was performed, except that the dirt was heated to high temperature for 30 minutes and then allowed to cool to Martian temperature right after scooping and before the 14CO2 was added. If experiment (a) released 14CO2, then this experiment should not release it, if living things were present.

For Discussion- 3

1. Trace the sequence of chemical changes that occurs in mammalian brain tissue when the oxygen supply is cut off. The first change is that the cytochrome c oxidase system becomes totally reduced, because electrons can still flow from cytochrome c but there is no oxygen to accept electrons from cytochrome c oxidase. What are the remaining steps?

2. Trace the sequence of chemical changes that occurs in mammalian muscle tissue when the oxygen supply is cut off. (The first change is the same as that in Question 1.)

3. Some cells that use the citric acid cycle and the respiratory chain can also thrive by using fermentation under anaerobic conditions. Given the lower yield of ATP (per molecule of glucose) in fermentation, why can these cells function so efficiently under anaerobic conditions?

4. Describe the mechanisms by which the rates of glycolysis and aerobic respiration are kept in balance with one another.

5. You eat a hamburger that has polysaccharides, proteins and lipids. Using your knowledge of the integration of biochemical pathways, explain how the amino acids in the proteins and glucose in the polysaccharides can end up as fats.

For Discussion - 4

1. Which organelles and other structures are found in both plant and animal cells? Which are found in plant but not animal cells? In animal but not plant cells? Discuss these differences in relation to the activities of plants and animals.

2. Through how many membranes would a molecule have to pass in going from the interior of a chloroplast to the interior of a mitochondrion? From the interior of a lysosome to the outside of a cell? From one ribosome to another?

3. How does the possession of double membranes by chloroplasts and mitochondria relate to the endosymbiosis theory of the origins of these organelles? What other evidence supports the theory?

4. Compare the extracellular matrix of the animal cell with the plant cell wall with respect to composition of the fibrous and nonfibrous components, rigidity and presence of cytoplasmic “bridges.”

5. Plastids and mitochondria may have arisen via endosymbiosis. Propose a hypothesis for the origin of the cell nucleus.

For Discussion - 5

1. How does a nucleus in the G2 phase of the cell cycle differ from one in the G1 phase?

2. Compare the roles of cohesins and condensin in mitosis, meiosis I and meiosis II.

3. Compare and contrast mitosis (and subsequent cytokinesis) in animals and plants.

4. Suggest two ways in which, with the help of a microscope, one might determine the relative duration of the various phases of mitosis.

5. Contrast mitotic prophase and prophase I of meiosis. Contrast mitotic anaphase and anaphase I of meiosis.

6. Compare the sequence of events in the mitotic cell cycle with the sequence in programmed cell death.

For Discussion-6

1. The genetic code is described as degenerate. What does this mean? How is it possible that a point mutation, consisting of the replacement of a single nitrogenous base in DNA by a different base, might not result in an error in protein production?

2. Har Gobind Khorana at the University of Wisconsin synthesized artificial mRNAs such as poly CA (CACA…) and poly CAA (CAACAACAA…). He found that poly CA codes for a polypeptide consisting of threonine (Thr) and histidine (His), in alternation (His–Thr– His–Thr…). There are two possible codons in poly CA, CAC and ACA. One of these must code for histidine and the other for threonine—but which is which? The answer comes from results with poly CAA, which produces three different polypeptides: poly Thr, poly Gln (glutamine) and poly Asn (asparagine). (An artificial messenger can be read, inefficiently, beginning with any point in the chain; there is no specific initiator region.) Thus poly CAA can be read as a polymer of CAA, of ACA, or of AAC. Compare the results of the poly CA and poly CAA experiments and determine which codon codes for threonine and which for histidine.

3. Look back at Question 2. Using the genetic code as a guide, deduce what results Khorana would have obtained had he used poly UG and poly UGG as artificial messengers. In fact, very few such artificial messengers would have given useful results. For an example of what could happen, consider poly CG and poly CGG. If poly CG were the messenger, a mixed polypeptide of arginine and alanine (Arg–Ala–Ala– Arg . . .) would be obtained; poly CGG would give three polypeptides: poly Arg, poly Ala, and poly Gly (glycine). Can any codons be determined from only these data? Explain.

4. Errors in transcription occur about 100,000 times as often as do errors in DNA replication. Why can this high rate be tolerated in RNA synthesis but not in DNA synthesis?

For Discussion-7

1. During the past 50 years, more than 200 species of insects that attack crop plants have become highly resistant to DDT and other pesticides. Using your recently acquired knowledge of evolutionary processes, explain the rapid and widespread evolution of resistance. Propose ways of using pesticides that would slow down the rate of evolution of resistance. Now that use of DDT has been banned in the United States, what do you expect to happen to levels of resistance to DDT among insect populations? Justify your answer.

2. In what ways does artificial selection by humans differ from natural selection in nature? Was Darwin wise to base so much of his argument for natural selection on the results of artificial selection?

3. In nature, mating among individuals in a population is never truly random, immigration and emigration are common, and natural selection is seldom totally absent. Why then, does it make sense to use the Hardy–Weinberg equilibrium, which is based on assumptions known generally to be false? Can you think of other models in science that are based on false assumptions? How are such models used?

4. As far as we know, natural selection cannot adapt organisms to future events. Yet many organisms appear to respond to natural events before they happen. For example, many mammals go into hibernation while it is still quite warm. Similarly, many birds leave the temperate zone for their southern wintering grounds long before winter has arrived. How can such “anticipatory” behaviors evolve?

5. Populations of most of the thousands of species that have been introduced to areas where they were previously not found, including those that have become pests, began with a few individuals. They should therefore have begun with much less genetic variation than the parent populations have. If genetic variation is advantageous, why have so many of these species been successful in their new environments?

6. The flavors of many crop plants have been enhanced by artificial selection that has removed the bad-tasting chemicals with which they defended themselves in the wild. What problems do growing crop plants with reduced chemical defenses pose for modern agriculture?