MCC_Exam 1

Use your knowledge of amino acid characteristics to order the peptides below according to the net charge contributed by their side chains at physiological pH (~pH 7). Each peptide contains eight amino acids. Use the single-letter amino acid designations to generate your list, placing the most negatively charged peptide on the left and the most positively charged peptide on the right. In addition, for each peptide, list the total number of positive and negative charges. Remember that, at neutral pH, the amino terminus carries a positive charge and the carboxyl terminus carries a negative charge. A. YGAKKRA B. ARRKSTRK C. DERKQNST D. DDAEIYSA E. NQSTYEEG

(D) This peptide has 4 negative charges and one positive charge. The peptide in (E) has 3 negative charges and one positive charge. The peptide in (C) has 3 negative charges and 3 positive charges. The peptide in (A) has 4 positive charges and one negative charge. The peptide in (B) has 6 positive charges and one negative charge.

You have two purified samples of protein Y: the wild-type (nonmutated) protein and a mutant version with a single amino acid substitution. When washed through the same gel-filtration column, mutant protein Y runs through the column more slowly than the normal protein. Which of the following changes in the mutant protein is most likely to explain this result? (a) the loss of a binding site on the mutant-protein surface through which protein Y normally forms dimers (b) a change that results in the mutant protein acquiring an overall positive instead of a negative charge (c) a change that results in the mutant protein being larger than the wild-type protein (d) a change that results in the mutant protein having a slightly different shape from the wild-type protein

(a) Dimers formed by a normal protein will run through the gel-filtration column faster than a mutant protein Y monomer. Choice (b) is unlikely, because gel-filtration columns separate proteins on the basis of size, not charge or affinity for small molecules. Choice (c) is unlikely, because if the mutant protein were larger than normal it would be less able to enter the porous beads and would run through the column faster than the normal protein. Choice (d) is unlikely, because a small change in shape without a change in size would be unlikely to have a major effect on the behavior of a protein in a gel-filtration column.

The three-dimensional coordinates of atoms within a folded protein are determined experimentally. After researchers obtain a protein's structural details, they can use different techniques to highlight particular aspects of the structure. What visual model best displays a protein's secondary structures (α helices and β sheets)? (a) ribbon (b) space-filling (c) backbone (d) wire

(a) Space-filling and wire models illustrate all atoms, which makes it difficult to see the secondary structure. Backbone models are better but not as good as the ribbon models, which are stylized and make it easy for even the untrained eye to see secondary structures.

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. Oxygen is toxic to certain prokaryotic organisms. B. Mitochondria are thought to have evolved from anaerobic bacteria. C. Photosynthetic bacteria contain chloroplasts.

(a) True (b) False. Mitochondria use oxygen to generate energy and are thought to have evolved from aerobic bacteria. (c) False. Photosynthetic bacteria have enzyme systems similar to those found in chloroplasts, which allow them to harvest light energy to fix carbon dioxide.

Larger molecules have hydrogen-bonding networks that contribute to specific, high-affinity binding. Smaller molecules such as urea can also form these networks. How many hydrogen bonds can urea (Figure Q2-36) form if dissolved in water?

(a) Urea can form at least six hydrogen bonds in water: two from the oxygen atom and one from each hydrogen atom.

To study how proteins fold, scientists must be able to purify the protein of interest, use solvents to denature the folded protein, and observe the process of refolding at successive time points. What is the effect of the solvents used in the denaturation process? (a) The solvents break all covalent interactions. (b) The solvents break all noncovalent interactions. (c) The solvents break some of the noncovalent interactions, resulting in a misfolded protein. (d) The solvents create a new protein conformation.

(b) In the case of choice (b), the polypeptide is completely unfolded, allowing the complete refolding to be observed. Detergents do not break the covalent bonds of the polypeptide backbone [choice (a)]. Mild detergents that do not break all noncovalent interactions within a protein would not lead to misfolding but instead to partial unfolding [choice (c)]. Proteins fold into only one single, correct conformation. Denaturation followed by renaturation of a protein does not generate a new protein fold [choice (d)].

Which of the following statements is true with respect to this in vitro replication system? (a) There will be only one leading strand and one lagging strand produced using this template. (b) The leading and lagging strands compose one half of each newly synthesized DNA strand. (c) The DNA replication machinery can assemble at multiple places on this plasmid. (d) One daughter DNA molecule will be slightly shorter than the other.

(b) Leading and lagging strands are synthesized bidirectionally from the replication origin, and are joined together by DNA ligase where the two replication forks meet at the termination site. Choice (a) is not correct, because this answer implies that the replication fork is not bidirectional and that replication continues around the plasmid until the process makes it back to the origin of replication. Choice (c) is incorrect because the origin is a specialized sequence where initiator proteins bind and open the DNA so that the DNA replication machinery can assemble. Choice (d) is incorrect because the daughter DNA molecules will be same size as the original plasmid (and each other).

You wish to explore how mutations in specific genes affecting sugar metabolism might alter tooth development. Which organism is likely to provide the best model system for your studies, and why? (a) horses (b) mice (c) E. coli (d) Arabidopsis

(b) Mice are likely to provide the best model system. Mice have teeth and have long been used as a model organism. Mice reproduce relatively rapidly and the extensive scientific community that works with mice has developed techniques to facilitate genetic manipulations. E. coli (a bacterium) and Arabidopsis (a plant) do not have teeth. Horses like sugar and have big teeth, but they would not be a good model organism. There is not an extensive scientific community working on the molecular and biochemical mechanisms of cell behaviors in horses; they are expensive and have a long reproduction time, which makes genetic studies costly and slow; and tools for genetic manipulation (other than traditional breeding) have not been developed.

Studies conducted with a lysozyme mutant that contains an Asp!Asn change at position 52 and a Glu!Gln change at position 35 exhibited almost a complete loss in enzymatic activity. What is the most likely explanation for the decrease in enzyme activity in the mutant? (a) increased affinity for substrate (b) absence of negative charges in the active site (c) change in the active-site scaffold (d) larger amino acids in the active site decreases the affinity for substrate

(b) The negatively charged amino acids aspartic acid and glutamic acid are required to attack the sugar bonds being cleaved by lysozyme. Replacing these with side chains that are the same length and are polar, but uncharged, would most probably affect only the catalysis, not the binding of substrate or the stability of the protein.

You are studying a biochemical pathway that requires ATP as an energy source. To your dismay, the reactions soon stop, partly because the ATP is rapidly used up and partly because an excess of ADP builds up and inhibits the enzymes involved. You are about to give up when the following table from a biochemistry textbook catches your eye. Which of the following reagents are most likely to revitalize your reaction? (a) a vast excess of A TP (b) glucose 6-phosphate and enzyme D (c) creatine phosphate and enzyme A (d) pyrophosphate

(c) An excess of ATP will initially restore the reactions, but as ATP is hydrolyzed, ADP will build up and inhibit the enzymes again. Pyrophosphate does not look like ATP and is therefore unlikely to be used by the enzymes as an alternative energy source. Pyrophosphate + enzyme D will just heat things up. What you need is a high-energy source of phosphate that can convert ADP back to ATP. Because the ΔG° of the reaction ATP + creatine -> ADP + creatine phosphate catalyzed by enzyme A is greater than zero, the addition of creatine phosphate and enzyme A can be used to form ATP from ADP, regenerating the ATP while also forming creatine as a waste product.

Which of the following statements is true? (a) Disulfide bonds are formed by the cross-linking of methionine residues. (b) Disulfide bonds are formed mainly in proteins that are retained within the cytosol. (c) Disulfide bonds stabilize but do not change a protein's final conformation. (d) Agents such as mercaptoethanol can break disulfide bonds through oxidation.

(c) Choice (a) is incorrect, because S-S bonds are formed between cysteines. Choice (b) is incorrect, because disulfide bonds are formed mainly in extracellular proteins. Choice (d) is incorrect; the bonds are broken by mercaptoethanol, but by reduction not by oxidation.

Fully folded proteins typically have polar side chains on their surfaces, where electrostatic attractions and hydrogen bonds can form between the polar group on the amino acid and the polar molecules in the solvent. In contrast, some proteins have a polar side chain in their hydrophobic interior. Which of the following would not occur to help accommodate an internal, polar side chain? (a) A hydrogen bond forms between two polar side chains. (b) A hydrogen bond forms between a polar side chain and the protein backbone. (c) A hydrogen bond forms between a polar side chain and an aromatic side chain. (d) Hydrogen bonds form between polar side chains and a buried water molecule.

(c) Choices (a), (b), and (d) are all common mechanisms employed to accommodate buried polar amino acids. Choice (c) is not likely to accomplish this because aromatic side chains are nonpolar, hydrophobic residues and will not interact favorably with a polar, hydrophilic side chain.

Scientists learned that cell death is a normal and even important part of life by studying the development of the nematode worm C. elegans. What was the most important feature of C. elegans for the study of programmed cell death? (a) The nematode is smaller and simpler than the fruit fly. (b) 70% of C. elegans genes have homologs in humans. (c) The developmental pathway of each cell in the adult worm was known. (d) Its genome was partially sequenced.

(c) This is the best answer because it was the prior developmental studies tracing cell lineages from the egg to the adult that allowed scientists to identify the precise time and location of cells that were being targeted for cell death. It was observed that this cell death was a normal and necessary part of the developmental pathway in the worm. Programmed cell death has since become known to be an important process in all multicellular eukaryotic organisms.

Most types of molecules in the cell have asymmetric (chiral) carbons. Consequently there is the potential to have two different molecules that look much the same but are mirror images of each other and therefore not equivalent. These special types of isomer are called stereoisomers. Which of the four carbons circled in Figure Q2-51 is the asymmetric carbon that determines whether the amino acid (threonine in this case) is a ᴅ or an ʟ stereoisomer?

(c) Two of the carbon atoms of threonine are asymmetric (numbered 2 and 3 in Figure Q2-51) but by convention it is the α-carbon (number 3) that determines whether the amino acid is the ᴅ or ʟ isomer.

Although all protein structures are unique, there are common structural building blocks that are referred to as regular secondary structures. Some proteins have α helices, some have β sheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements? (a) specific amino acid sequences (b) side-chain interactions (c) the hydrophobic-core interactions (d) hydrogen bonds along the protein backbone

(d) Choices (a), (b), and (c) are factors that contribute to the uniqueness of proteins, but because the protein backbone is a repeating, identical unit, interactions between backbone atoms are something that all proteins can have in common.

The Ras protein is a GTPase that functions in many growth-factor signaling pathways. In its active form, with GTP bound, it transmits a downstream signal that leads to cell proliferation; in its inactive form, with GDP bound, the signal is not transmitted. Mutations in the gene for Ras are found in many cancers. Of the choices below, which alteration of Ras activity is most likely to contribute to the uncontrolled growth of cancer cells? (a) a change that prevents Ras from being made (b) a change that increases the affinity of Ras for GDP (c) a change that decreases the affinity of Ras for GTP (d) a change that decreases the rate of hydrolysis of GTP by Ras

(d) Ras is a proto-oncogene. When it is active, it promotes cell growth. Choice (d) is the only option that would lead to an increase in Ras activity. Choices (a), (b), and (c) would decrease its activity.

The protein structure in Figure Q4-28 contains four α helices arranged in a bundle. Label each helix by number (1 to 4) starting from the N-terminus and going to the C-terminus, both of which are labeled. List the six possible pairings of these helices, and indicate within each pair whether the helices are parallel or antiparallel.

1,2 antiparallel 1,3 parallel 1,4 antiparallel 2,3 antiparallel 2,4 parallel 3,4 antiparallel

Circle the appropriate cell type in which the listed structure or molecule can be found. 1.animal 2.plant 3.bacterial DNA nucleus plasma membrane chloroplast cell wall lysosome mitochondrion Golgi appartus

1,2,3 1,2 1,2,3 2,3 2,3 1,2 1,2 1,2

Given the sequence of one strand of a DNA helix (below), provide the sequence of the complementary strand and label the 5′ and 3′ ends. 5′-GCATTCGTGGGTAG-3′

5′-CTACCCACGAATGC-3′

For some proteins, small molecules are integral to their structure and function. Enzymes can synthesize some of these small molecules, whereas others, called vitamins, must be ingested in the food we eat. Which of the following molecules is not classified as a vitamin but does require the ingestion of a vitamin for its production? (a) retinal (b) biotin (c) zinc (d) heme

A

Evolutionary biologists have always used a broad range of modern organisms to infer the characteristics that ancestral organisms may have possessed. Genomic sequences are now available for an increasing number of species, and scientists studying evolutionary processes can take advantage of this enormous amount of data to bring evolution into the arena of molecular studies. By aligning the sequences of homologous genes and looking for regions of similarity and where changes have occurred, it is possible to infer the sequence of the ancestral gene. A. What term is used to describe the changes in gene sequences that have occurred? How can we use what we know about this process to construct a time line showing when various sequence changes occurred and when they led to the modern sequences that we know today? B. It is possible to express an ancestral gene sequence in modern organisms and subsequently compare the function of its product with that of the modern protein. Why might this approach give misleading conclusions?

A. Changes in gene sequence occur through mutation. Mutations accumulate over time, occurring independently and at different sites in each gene lineage. Homologous genes that diverged recently will differ only slightly; genes that diverged long ago will differ more. Knowing the average mutation rate, you can estimate the time that has elapsed since the different versions of the gene diverged. By seeing how closely the various members of the family of homologous genes resemble one another, you can draw up a family tree, showing the sequence of lineage splits that lead from the ancestral gene to its many modern descendants. Suppose this family tree shows that family members A and B diverged from one another long ago, but that C diverged from B more recently; and suppose that at a certain site in the gene, A and B have the same sequence but C is different. Then, it is likely that the sequence of A and B is ancestral, while that of C reflects a recent mutation that has occurred in the lineage of C alone. B. Although an inferred ancestral sequence can be reconstructed and the protein expressed, you would be placing an inferred, ancient protein in the context of a modern cell. If there are important interacting partners for the modern protein, there is a chance they may not recognize the ancestral protein, and therefore any information about its function may be inaccurate.

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. Plants do not require a cytoskeleton because they have a cell wall that lends structure and support to the cell. B. The cytoskeleton is used as a transportation grid for the efficient, directional movement of cytosolic components. C. Thermal energy promotes random movement of proteins, vesicles, and small molecules in the cytosol.

A. False. Although plant cells do have a cell wall that lends structure and support, they still need a cytoskeleton, which also helps with connections between cells and the transport of vesicles inside the cell. B. True C. True

Indicate whether the statements below are true or false. If a statement is false, explain why it is false. A. The chemistry of life is carried out and coordinated primarily by the action of small molecules. B. Carbon-based compounds make up the vast majority of molecules found in cells. C. The chemical reactions in living systems are loosely regulated, allowing for a wide range of products and more rapid evolution.

A. False. Although small molecules are important in many processes, the chemical reactions in living systems are regulated by the coordinated action of large polymeric molecules. B. True. C. False. The chemical reactions in living systems are very tightly controlled, ensuring that events occur at the proper time and at the proper location inside the cell.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Homologous recombination cannot occur in prokaryotic cells, because they are haploid, and therefore have no extra copy of the chromosome to use as a template for repair. B. The first step in repair requires a nuclease to remove a stretch of base pairs from the 5′ end of each strand at the site of the break. C. The 3′ overhang "invades" the homologous DNA duplex, which can be used as a primer for the repair DNA polymerase. D. The DNA template used to repair the broken strand is the homologous chromosome inherited from the other parent.

A. False. Homologous recombination also occurs in prokaryotic cells, and typically occurs very shortly after DNA replication, when the newly replicated duplexes are in close proximity. B. True. C. True. D. False. Although it is called homologous recombination, this is not a process that depends on the proximity of parental homologs. When used as a mechanism for DNA repair, homologous recombination uses the sister chromatids in an undamaged, newly replicated (homologous) DNA helix as a template.

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. With respect to cellular respiration, the only organelles used by animal cells are mitochondria, while plant cells use both mitochondria and chloroplasts. B. The number of mitochondria inside a cell remains constant over the life of the cell.

A. False. In plants, only mitochondria perform cellular respiration (using oxygen to break down organic molecules to produce carbon dioxide) just as in animal cells. Chloroplasts perform photosynthesis in which water molecules are split to generate oxygen and fix carbon dioxide molecules. B. False. Mitochondria have their own division cycle and their numbers change based on the rate of division.

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. Primitive plant, animal, and fungal cells probably acquired mitochondria after they diverged from a common ancestor. B. Protozoans are single-celled eukaryotes with cell morphologies and behaviors that can be as complex as those of some multicellular organisms. C. The first eukaryotic cells on Earth must have been aerobic; otherwise, they would not have been able to survive when the planet's atmosphere became oxygen-rich.

A. False. The mitochondria in modern plant, animal, and fungal cells are very similar, implying that these lines diverged after the mitochondrion was acquired by the ancestral eukaryote.B. True. C. False. The first eukaryotic cells likely contained a nucleus but no mitochondria. These ancestral eukaryotes subsequently adapted to survive in a world filled with oxygen by engulfing primitive aerobic prokaryotic cells.

The antibiotic streptomycin inhibits protein synthesis in bacteria. If this antibiotic is added to a culture of animal cells, protein synthesis in the cytosol continues normally. However, over time, the population of mitochondria in the cell becomes depleted. Specifically, it is observed that the protein-synthesis machinery inside the mitochondria is inhibited. A. Explain this observation based on what you know about the origins of the modern eukaryote. B. What do you expect to observe if, in a new experiment, animal cells are treated with diphtheria toxin, a compound that is known to block cytosolic protein synthesis but does not have any impact on bacterial growth?

A. If the mitochondria originated from an ancient aerobic bacterium that was engulfed by an ancient eukaryote, as postulated, it is possible that an antibiotic that inhibits protein synthesis in bacteria could also block that process in mitochondria. B. We would expect that although cytosolic protein synthesis would stop, mitochondrial protein synthesis should still occur normally (at least for a little while). This result would lend further support to the idea that mitochondria are derived from a noneukaryotic organism. If this were not the case, these compounds would be expected to affect protein synthesis at both locations.

Homologous recombination is initiated by double-strand breaks (DSBs) in a chromosome. DSBs arise from DNA damage caused by harmful chemicals or by radiation (for example, X-rays). During meiosis, the specialized cell division that produces gametes (sperm and eggs) for sexual reproduction, the cells intentionally cause DSBs so as to stimulate crossover homologous recombination. If there is not at least one occurrence of crossing-over within each pair of homologous chromosomes during meiosis, those noncrossover chromosomes will not segregate properly. A. Consider the copy of Chromosome 3 that you received from your mother. Is it identical to the Chromosome 3 that she received from her mother (her maternal chromosome) or identical to the Chromosome 3 she received from her father (her paternal chromosome), or neither? Explain. B. Starting with the representation in Figure Q6-43 of the double-stranded maternal and paternal chromosomes found in your mother, draw two possible chromosomes you may have received from your mother. C. What does this indicate about your resemblance to your grandfather and grandmother?

A. Neither. The copy of Chromosome 3 you received from your mother is a hybrid of the ones she received from her mother and her father. B. See Figure A6-43. The correct answers include any chromosome in which a portion matches the information from the paternal chromosome and the remainder matches the information from the maternal chromosome. C. As a result of extensive crossing-over, you resemble both your grandmother and your grandfather. If there were no crossing-over, you might have a much stronger resemblance to one than the other.

You are studying a newly identified chromatin-remodeling complex, which you call NICRC. You decide to run an in vitro experiment to characterize the activity of the purified complex. Your molecular toolbox includes: (1) a 400-base-pair DNA molecule that has a single recognition site for the restriction endonuclease EcoRI, an enzyme that cleaves internal sites on double-stranded DNA (dsDNA); (2) purified EcoRI enzyme; (3) purified DNase I, a DNA endonuclease that will cleave dsDNA at nonspecific sites if they are exposed; and (4) core octamer histones. You are able to assemble core nucleosomes on this DNA template and test for NICRC activity. Figure Q5-60A illustrates the DNA template used and indicates both the location of the EcoRI cleavage site and the size of the DNA fragments that are produced when it cuts. Figure Q5-60B illustrates how the DNA molecules in your experiment looked after separation according to size by using gel electrophoresis. Your experiment had a total of six samples, each of which was treated according to the legend below the gel. The sizes of the DNA fragments observed are indicated on the left side of the gel. A. Explain the results in lanes 1-4 and why it is important to have this information before you begin to test your remodeling complex. B. What can you conclude about your purified remodeling complex from the results in lanes 5 and 6?

A. Sample 1 confirms the location of the EcoRI restriction site and shows what those fragments should look like when separated on the gel. The cleavage is the readout that will tell us whether the remodeling complex is working. Sample 2 demonstrates that DNA that is not assembled into nucleosomes can be cut into many small fragments by DNaseI. That is why we do not see discrete bands. Sample 3 demonstrates that when nucleosomes are assembled on the DNA, DNase I cuts only in one place, presumably in the linker region between two assembled nucleosomes. Sample 4 demonstrates that EcoRI cannot access its cleavage site when nucleosomes are assembled over it. B. True. C. False. Histones have a higher number of lysines and arginines than most proteins. These amino acids are positively charged and help to increase the nonspecific affinity between the histones and the negatively charged phosphates in the DNA backbone. D. False. When cells enter mitosis, the interphase chromosomes undergo at least one more level of packaging, which facilitates the segregation of sister chromatids. B. Sample 5 demonstrates that our purified complex is working. It must be moving the nucleosomes, providing access for EcoRI, such that it can now cleave at its restriction site, which was not possible in the absence of NICRC. Sample 6 shows that NICRC will function only if ATP is available as an energy source for the remodeling process.

A. On a DNA strand that is being synthesized, which end is growing—the 3′ end, the 5′ end, or both ends? Explain your answer. B. On a DNA strand that is being used as a template, where is the copying occurring relative to the replication origin—3′ of the origin, 5′, or both?

A. The 3′ end. DNA polymerase can add nucleotides only to the 3′-OH end of a nucleic acid chain. B. Both, as a result of the bidirectional nature of chromosomal replication.

Figure Q4-30 shows a fatty-acid-binding protein from two different angles. Apart from its two short α helices, its structural elements are extended strands that form a curved β sheet, which is called a β barrel. A. Draw arrows on the six top strands in panel (A) (those running horizontally) to determine whether the β barrel is made up of parallel or antiparallel strands. B. Look at panel (B) and predict the relative distribution of polar and nonpolar side chains (inside the barrel or outside the barrel) and explain your answer.

A. The strands form an antiparallel β sheet. B. The prediction is that nonpolar side chains are on the inside of the barrel, and polar side chains are distributed to the outside of the barrel. The outside of the barrel is completely exposed to the aqueous solvent and it is stabilized by solvent-protein hydrogen bonds. And, although the barrel seems open and accessible to solvent molecules, this protein binds fatty acids and would most probably do that by enclosing them inside the barrel, away from the aqueous solvent and close to nonpolar amino acid side chains lining the inside of the barrel.

When double-stranded DNA is heated, the two strands separate into single strands in a process called melting or denaturation. The temperature at which half of the duplex DNA molecules are intact and half have melted is defined as the Tm. A. Do you think Tm is a constant, or can it depend on other small molecules in the solution? Do you think high salt concentrations increase, decrease, or have no effect on Tm? B. Under standard conditions, the expected melting temperature in degrees Celsius can be calculated from the equation Tm = 59.9 + [0.41 × %(G + C)] - (675/length of duplex). Does the Tm increase or decrease if there are more G + C (and thus fewer A + T) base pairs? Does the Tm increase or decrease as the length of DNA increases? Why? C. Calculate the predicted Tm for a stretch of double helix that is 100 nucleotides long and contains 50% G + C content.

A. Tm depends on the identity and concentration of other molecules in the solution. High salt concentrations are more effective at shielding the two negatively charged sugar-phosphate backbones in the double helix from each other, so the two strands repel each other less strongly. Thus, a high salt concentration stabilizes the duplex and increases the melting temperature. B. The Tm increases as the proportion of G + C bases increases and as the length increases. The thermal energy required for melting depends on how many hydrogen bonds between the strands must be broken. Each G-C base pair contributes three hydrogen bonds, whereas an A-T base pair contributes only two. C. Inserting values into the equation in part B gives Tm = 59.9 + (0.41 × 50) - (675/100) = 73.65°C, which is about twice the normal temperature of the human body and nearly too hot to touch.

Drawn below are segments of β sheets, which are rigid pleated structures held together by hydrogen bonds between the peptide backbones of adjacent strands (Figure Q4-31). The amino acid side chains attached to the α-carbons are omitted for clarity. For panel (A) and for panel (B), indicate whether the structure is parallel or antiparallel. B. Draw the hydrogen bonds as dashed lines (||||||).

A. (A) is parallel and (B) is antiparallel B. See Figure A4-31.

A. If 0.5 mole of glucose weighs 90g, what is the molecular mass of glucose? B. What is the concentration, in grams per liter (g/L), of a 0.25 M solution of glucose? C. How many molecules are there in 1 mole of glucose?

A. 180 daltons. A mole of a substance has a mass equivalent to its molecular weight expressed in grams. B. 45 g/L C. 6 x 10^23

A. How many carbon atoms does the molecule represented in Figure Q2-50 have? B. How many hydrogen atoms does it have? C. What type of molecule is it?

A. 20 B. 31 C. A fatty acid

A. Define a gene B. Consider two different species of yeast that have similar genome sizes. It it likely that they contain the same number of genes? A similar number of chromosomes?

A. A gene is a segment of DNA that stores the information required to specify the particular sequence found in a protein (or, in some cases, the sequence of a structural or catalytic RNA). B. A similar genome size indicates relatively little about the number of genes and virtually nothing about the number of chromosomes. For example, the commonly studied yeasts Saccharomyces cerevisiae (Sc) and Schizosaccharomyces pombe (Sp) are separated by roughly 400 million years of evolution, and both have a genome of 14 million base pairs. Yet Sc has 6500 genes packaged into 16 chromosomes and Sp has 4800 genes in 3 chromosomes.

For each process (A-D), circle the simplest model organism from the list of three that would be best used for investigation: A. programmed cell death B. chloroplast function C. immunology D. development of a multi cellar tissue

A. C. elegans B. Arabidopsis C. mouse D. Drosophilia

Eukaryotic cells have their DNA molecules inside their nuclei. However, to package all the DNA into such a small volume requires the cell to use specialized proteins called histones. Histones have amino acid sequences enriched for lysines and arginines. A. What problem might a cell face in trying to package DNA into a small volume without histones, and how do these special packaging proteins alleviate the problem? B. Lysine side chains are substrates for enzymes called acetylases. A diagram of an acetylated lysine side chain is shown in Figure Q2-72. How do you think the acetylation of lysines in histone proteins will affect the ability of a histone to perform its role (refer to your answer in part A)?

A. DNA is a nucleic acid polymer in which each monomer has a negatively charged phosphate group. The negative charges will naturally repel each other, so in order to wrap the high density of negative charges into a small space, positively charged molecules must be present. Histones accomplish this because they are rich in lysines and arginines, which are positively charged in solution at pH 7. B. A histone with acetylated lysine residues will not be as good at packaging the DNA. The addition of the acetyl group to the terminal amino on the lysine side chain lowers the histone's net positive charge, which makes it less effective at buffering the negative charges on the DNA backbone.

True of False. If False, explain: A. A disaccharide consists of a sugar covalently linked to another molecule such as an amino acid or a nucleotide. B. The hydroxyl groups on monosaccharides are reaction hot spots and can be replaced by other functional groups to produce derivatives of the original sugar. C. The presence of double bonds in the hydrocarbon tail of a fatty acid does not greatly influence its structure.

A. False. A disaccharide consists of two sugar molecules that undergo a condensation reaction to form a covalent bond (known as a glycosidic linkage). B. True. C. False. The presence of a double bond in the hydrocarbon chain of a fatty acid causes a kink in the chain, decreasing its flexibility and packing with neighboring hydrocarbon chains.

Indicate whether the following statements about enzymes are true or false. If a statement is false, explain why it is false. A. Enzymes alter the equilibrium point of a reaction. substrate concentration Km Figure Q3-53 3-54 Protein E can bind to two different proteins, S and I. The binding reactions are rate of reaction B. Vmax can be determined by measuring the amount of product accumulated late in the reaction. C. Competitive inhibitors bind irreversibly to the enzyme active site, lowering Vmax.

A. False. An enzyme catalyzes its reaction in both directions, lowering the energy of activation for both the forward and reverse reactions. Enzymes do not affect the free energy of the reactants and products are the same, and thus they do not affect the reaction equilibrium. B False. Initial reaction velocities are measured to determine Vmax. C. False. Competitive inhibitors bind reversibly to an enzyme's active site.

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. The terms "prokaryote" and "bacterium" are synonyms. B. Prokaryotes can adopt several different basic shapes, including spherical, rod-shaped, and spiral. C. Some prokaryotes have cell walls surrounding the plasma membrane.

A. False. Archaea make up a class of prokaryotic organisms that are significantly different from bacteria. B. True. C. True.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Collagen is a protein that participates in both the cytoskeleton and the extracellular matrix. B. Collagen fibers and elastin fibers serve similar functions, which is expected because the structure of these two types of fibers is quite similar. C. The assembly of both collagen and elastin fibers requires the formation of disulfide bonds.

A. False. Collagen is not used inside the cell; it is secreted and incorporated into the existing collagen fibers in the extracellular matrix. B. False. Collagen fibers and elastin fibers are very different in structure and function. Collagen fibers are highly organized, triple-strand coiled-coils that provide strength to hold tissue together. Elastin molecules are linked together in a loose network with disulfide bonds; this allows the fibers (and tissues) to stretch without tearing. C. True.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. DNA molecules, like proteins, consist of a single, long polymeric chain that is assembled from small monomeric subunits. B. The polarity of a DNA strand results from the polarity of the nucleotide subunits. C. There are five different nucleotides that become incorporated into a DNA strand. D. Hydrogen bonds between each nucleotide hold individual DNA strands together.

A. False. DNA is double-stranded. It is actually made of two polymers that are complementary in sequence. B. True. C. False. There are four different nucleotides that are used to make a DNA polymer: adenine, thymine, guanine, and cytosine. A fifth nucleotide, uracil, is found exclusively in RNA molecules, replacing thymine nucleotides in the DNA sequence. D. False. Nucleotides are linked covalently through phosphodiester bonds. Hydrogen-bonding between nucleotides from opposite strands holds the DNA molecule together.

Which of the following statements are true or false? If a statement is false, explain why it is false. A. Enzymes lower the free energy released by the reaction that they facilitate. B. Enzymes lower the activation energy for a specific reaction. C. Enzymes increase the probability that any given reactant molecule will be converted to product. D. Enzymes increase the average energy of reactant molecules.

A. False. Enzymes do not affect the initial energy of the reactants nor the final energy of the products after the reaction is complete, which are the values that determine the change in free energy of a reaction. B. True. C. True. D. False. By lowering the energy of activation, enzymes increase the number of molecules in a population that can overcome the activation barrier.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. When two macromolecules form a complex, the free energy of the system increases because there is a net increase in the amount of order in the cell. B. Sequential pathways can help drive unfavorable reactions by siphoning off the products into the next energetically favorable reaction in the series. C. The cytosol is densely packed with molecules, creating what is more an aqueous gel than a solution. D. The diffusion rates for smaller molecules in the cytosol are much lower than what is observed for the same molecules in water.

A. False. Even nonspecific interactions between macromolecules can be favorable if there is a large number of water molecules and ions displaced at the interaction interface. This would lead to an overall increase in disorder, even though the two larger molecules become associated and more ordered. B. True. C. True. D. False. Small molecules diffuse through the cytosol nearly as rapidly as they diffuse in water.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Feedback inhibition is defined as a mechanism of down-regulating enzyme activity by the accumulation of a product earlier in the pathway. B. If an enzyme's allosteric binding site is occupied, the enzyme may adopt an alternative conformation that is not optimal for catalysis. C. Protein phosphorylation is another way to alter the conformation of an enzyme and serves exclusively as a mechanism to increase enzyme activity. D. GTP-binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the "off" conformation.

A. False. Feedback inhibition occurs when an enzyme acting early in a metabolic pathway is inhibited by the accumulation of a product late in the pathway. The inhibitory product binds to a site on the enzyme that lowers its catalytic activity. B. True. C. False. Although phosphorylation of a protein can change its conformation, this modification may be either as a positive or a negative regulator of enzyme activity, depending on the protein in question. D. True.

Indicate whether the statements below are true or false. If a statement is false, explain why it is false. A. Any covalently bonded H atom can participate in a hydrogen bond if it comes in close proximity with an oxygen atom that forms part of a water molecule. B. Protons are constantly moving between water molecules, which means there is an overall equilibrium between hydroxyl ions and hydronium ions in aqueous solutions. C. A strong base is defined as a molecule that can readily remove protons from water.

A. False. Hydrogen atoms that are covalently bonded to carbon atoms do not participate in hydrogen bonds because these hydrogens have almost no net positive charge. B. True C. True.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Photosynthetic organisms release only O2 into the atmosphere, while nonphotosynthetic organisms release only CO2. B. The cycling of carbon through the biosphere first requires the incorporation of inorganic CO2 into organic molecules. C. The oxidation of one molecule is always coupled to the reduction of a second molecule. D. During cellular respiration, carbon-containing molecules become successively more oxidized until they reach their most oxidized form, as CO2.

A. False. Plants, as well as photosynthetic algae and bacteria, perform both photosynthesis and respiration. This means that photosynthetic organisms release both O2 and CO2 into the atmosphere. B. True. C. True. This forms the basis for redox pairs. D. True.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. The amino acids in the interior of a protein do not interact with the ligand and do not play a role in selective binding. B. Antibodies are Y-shaped and are composed of six different polypeptide chains. C. ATPases generate ATP for the cell. D. Hexokinase recognizes and phosphorylates only one of the glucose stereoisomers.

A. False. The interior amino acids form a structural scaffold that maintains the specific orientation for those that directly interact with the ligand. Changes to these interior amino acids can change the protein shape and render it nonfunctional. B. False. Although antibodies are Y-shaped, they are composed of four, not six, polypeptide chains. There are two heavy chains and two light chains. C. False. ATPases hydrolyze ATP; they do not produce it. These enzymes enable the cell to harness the chemical energy stored in the high-energy phosphate bonds. D. True.

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. The nucleus of an animal cell is round, small, and difficult to distinguish using light microscopy. B. The presence of the plasma membrane can be inferred by the well-defined boundary of the cell. C. The cytosol is fairly empty, containing a limited number of organelles, which allows room for rapid movement via diffusion.

A. False. The nucleus is one of the largest organelles and is the easiest organelle to discern within a typical cell B. True C. False. The cytosol is actually brimming with individual proteins, protein fibers, extended membrane systems, transport vesicles, and small molecules. And although cellular components do move by diffusion, the rate of movement is limited by the space available and the size of the component in question

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Generally, the total number of nonpolar amino acids has a greater effect on protein structure than the exact order of amino acids in a polypeptide chain. B. The "polypeptide backbone" refers to all atoms in a polypeptide chain, except for those that form the peptide bonds. C. The chemical properties of amino acid side chains include charged, uncharged polar, and nonpolar. D. The relative distribution of polar and nonpolar amino acids in a folded protein is determined largely by hydrophobic interactions, which favor the clustering of nonpolar side chains in the interior.

A. False. The order in which amino acids are linked is unique for each protein and is the most important factor in determining overall protein structure. B. False. Peptide bonds are planar amide bonds that are central to the polypeptide backbone formation. The atoms in the amino acid side chains are not considered to be part of the backbone. C. True. D. True.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. The repair polymerase is the enzyme that proofreads the newly synthesized strands to ensure the accuracy of DNA replication. B. There is a single enzyme that degrades the RNA primers and lays down the corresponding DNA sequence behind it. C. DNA ligase is required to seal the sugar-phosphate backbone between all the DNA fragments on the lagging strand. D. The repair polymerase does not require the aid of the sliding clamp, because it is only synthesizing DNA over very short stretches.

A. False. The repair polymerase is used to fill in the spaces left vacant after the RNA primers are degraded. B. False. This is a two-step process that requires two different enzymes. First, a nuclease removes the RNA primers. Then, the repair polymerase fills in the complementary DNA sequence. C. True. D. True.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. The second law of thermodynamics states that the total amount of energy in the Universe does not change. B. The ultimate source of energy for living systems is chlorophyll. C. CO2 gas is fixed in a series of reactions that are light-dependent. D. H2 is the most stable and abundant form of hydrogen in the environment.

A. False. The second law of thermodynamics states that components of any system move toward greater disorder. It is the first law of thermodynamics that states that energy is neither created nor destroyed. B. False. The ultimate source of energy for living organisms is sunlight. C. False. The fixation of carbon from CO2 occurs independently of light. D. False. The most stable form of hydrogen is H2O.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. When DNA is being replicated inside a cell, local heating occurs, allowing the two strands to separate. B. DNA replication origins are typically rich in G-C base pairs. C. Meselson and Stahl ruled out the dispersive model for DNA replication. D. DNA replication is a bidirectional process that is initiated at multiple locations along chromosomes in eukaryotic cells.

A. False. The two strands do need to separate for replication to occur, but this is accomplished by the binding of initiator proteins at the origin of replication. B. False. DNA replication origins are typically rich in A-T base pairs, which are held together by only two hydrogen bonds (instead of three for C-G base pairs), making it easier to separate the strands at these sites. C. True. D. True.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Comparing the relative number of chromosome pairs is a good way to determine whether two species are closely related. B. Chromosomes exist at different levels of condensation, depending on the stage of the cell cycle. C. Eukaryotic chromosomes contain many different sites where DNA replication can be initiated. D. The telomere is a specialized DNA sequence where microtubules from the mitotic spindle attach to the chromosome so that duplicate copies move to opposite ends of the dividing cell.

A. False. There are several examples of closely related species that have a drastically different number of chromosome pairs. Two related species of deer—Chinese and Indian muntjac—have 23 and 3, respectively. B. True. C. True. D. False. The telomere is a specialized DNA sequence, but not for the attachment of spindle microtubules. Telomeres form special caps that stabilize the ends of linear chromosomes.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Van der Waals interactions and hydrophobic interactions are two ways to describe the same type of weak forces that help proteins fold. B. A large number of noncovalent interactions is required to hold two regions of a polypeptide chain together in a stable conformation. C. A single polypeptide tends to adopt 3-4 different conformations, which all have equivalent free-energy values (G).

A. False. Van der Waals attractions are weakly attractive forces that occur between all atoms. Hydrophobic interactions are only observed between nonpolar molecules in the context of an aqueous solution. B. True. C. False. There is a single, final fold for every polypeptide. The fold adopted is the "best" conformation, for which the free energy (G) of the molecule is at a minimum.

Indicate whether the statements below are true or false. If a statement is false, explain why it is false. A. "Nonpolar interactions" is simply another way of saying "van der Waals attractions." B. Condensation reactions occur in the synthesis of all the macromolecules found in cells. C. All proteins and RNAs pass through many unstable conformations as they are folded, finally settling on one single, preferred conformation.

A. False. Van der Waals attractions describe the general attractive forces between all atoms. The contact distance between any two nonbonded atoms is the sum of the van der Waals radii. Nonpolar interactions are based on the exclusion of hydrophobic molecules from a hydrophilic environment. B. True. C. True.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. The histone proteins that constitute the core nucleosome include tetramers of histones H2A, H2B, H3, and H4. B. Linker histones help compact genomic DNA by influencing the path of the DNA after it has wrapped about the nucleosome core. C. Histone proteins have a lower-than-average number of lysines and arginines in their polypeptide chains. D. Interphase chromosomes represent a physical state of the chromatin with the highest order of packaging.

A. False. When the core nucleosome is analyzed, it is revealed that there are H2A/H2B tetramers and H3/H4 tetramers in solution. Each of the tetramers has two subunits of the respective histone proteins.B. True. C. False. Histones have a higher number of lysines and arginines than most proteins. These amino acids are positively charged and help to increase the nonspecific affinity between the histones and the negatively charged phosphates in the DNA backbone. D. False. When cells enter mitosis, the interphase chromosomes undergo at least one more level of packaging, which facilitates the segregation of sister chromatids.

A. You are measuring the effect of temperature on the rate of an enzyme- catalyzed reaction. If you plot reaction rate against temperature, which of the graphs in Figure Q3-57 would you expect your plot to resemble? B. Explain why temperature has this effect.

A. Graph 1 B. By increasing thermal motion, increasing the temperature increases the number of collisions of sufficient energy to overcome the activation energy. An increase in temperature will thus increase the reaction rate initially. However, enzymes are proteins and are held together by noncovalent interactions, so at very high temperatures the enzyme will begin to denature and the reaction rate will fall.

For each polypeptide sequence listed, choose from the options given below to indicate which secondary structure the sequence is most likely to form upon folding. The nonpolar amino acids are italicized. A. Leu-Gly-Val-Leu-Ser-Leu-Phe-Ser-Gly-Leu-Met-Trp-Phe-Phe-Trp-Ile B. Leu-Leu-Gln-Ser-Ile-Ala-Ser-V al-Leu-Gln-Ser-Leu-Leu-Cys-Ala-Ile C. Thr-Leu-Asn-Ile-Ser-Phe-Gln-Met-Glu-Leu-Asp-Val-Ser-Ile-Arg-Trp amphipathic α helix hydrophilic β sheet amphipathic β sheet hydrophobic α helix hydrophilic α helix

A. Hydrophobic α helix. Nearly all of the amino acid side chains in this sequence are nonpolar or hydrophobic, which favors the only hydrophobic option given in the list.B. Amphipathic α helix. In an ideal α helix, there are 3.6 residues per complete turn. Thus, an amphipathic helix with one hydrophobic side and one hydrophilic side will have, minimally, nonpolar side chains (N) repeating every third then next fourth amino acid: NxxNxxxNxxNxxxN. Polar side chains (P) will have the same pattern but shifted relative to the nonpolar side chains; for example, xxPxxxPxxPxxxPxxP . C. Amphipathic β sheet. Because of the zigzag-like structure of a β sheet, a sequence with alternating nonpolar and polar side chains may form an amphipathic β sheet that is hydrophobic on one side and hydrophilic on the other.

A. How can nucleosome core particles be isolated from chromatin? B. What molecular components were identified after this treatment was complete? C. What portion of the nucleosome was destroyed/removed during this treatment and what function does it normally serve?

A. In a test tube, the nucleosome core particle can be released from chromatin by treatment with a nuclease that degrades the exposed, linker DNA, but not the DNA wrapped around the nucleosome core. B. The core nucleosome was revealed to contain two molecules of the histones H2A, H2B, H3, and H4, as well as a 147-base-pair (bp) fragment of DNA. C. Nuclease treatment degrades linker DNA, which can be up to 80 bp in length. This region of DNA is typically bound to linker histones (H1), which are involved in higher-level packing of the chromatin.

Consider the reaction X!Y in a cell at 37°C. At equilibrium, the concentrations of X and Y are 50 μM and 5 μM, respectively. Use this information and the equations below to answer questions A-E. ΔG° = -0.616 ln Keq ΔG = ΔG° + 0.616 ln [Y]/[X] Recall that the natural log of a number z will have a negative value when z < 1, positive when z > 1, and 0 when z = 1. A. What is the value of Keq for this reaction? B. Is the standard free-energy change of this reaction positive or negative? Is the reaction X!Y an energetically favorable or unfavorable reaction under standard conditions? C. What is the value of the standard free energy? Refer to Table 3-1 in the textbook or use a calculator. D. Imagine circumstances in which the concentration of X is 1000 μM and that of Y is 1 μM. Is conversion of X to Y favorable? Will it happen quickly? E. Imagine starting conditions in which the reaction X!Y is unfavorable, yet the cell needs to produce more Y. Describe two ways in which this may be accomplished.

A. Keq = [Y]/[X] = 5 μM/50 μM = 0.1 B. The standard free-energy change, ΔG°, is positive because Keq is less than 1. Under standard conditions (equal concentrations of X and Y), the reaction X!Y is unfavorable. C. ΔG° = -0.616 ln Keq = -0.616 ln 0.1 = (-0.616) (-2.3) = 1.4 kcal/mole. D. Yes, the conversion is favorable because the value of [Y]/[X] is less than the equilibrium value. However, the speed of the reaction cannot be determined from the free-energy difference. For example, combustion of this piece of paper is a highly favorable reaction, yet it will not happen in our lifetime without a catalyst. E. The cell may directly couple the unfavorable reaction to a second, energetically favorable reaction whose negative ΔG has a value larger than the positive ΔG of the X!Y reaction; the coupled reaction will have a ΔG equal to the sum of the component reactions. Alternatively, more X will be converted to Y if the concentration of Y drops; this may happen if Y is converted to Z in a second reaction or if Y is exported from the cell or compartment where the X!Y reaction occurs.

You have made a collection of mutant fruit flies that are defective in various aspects of DNA repair. You test each mutant for its hypersensitivity to three DNA-damaging agents: sunlight, nitrous acid (which causes deamination of cytosine), and formic acid (which causes depurination). The results are summarized in Table Q6-55, where a "yes" indicates that the mutant is more sensitive than a normal fly, and blanks indicate normal sensitivity. A. Which mutant is most likely to be defective in the DNA repair polymerase? B. What aspect of repair is most likely to be affected in the other mutants?

A. Mr Self-destruct is more likely than the other mutants to be defective in the DNA repair polymerase because Mr Self-destruct is defective in the repair of all three kinds of DNA damage. The repair pathways for all three kinds of damage are similar in the later steps, including a requirement for the DNA repair polymerase. B. The other mutants are specific for a particular type of damage. Thus, the mutations are likely to be in genes required for the first stage of repair—the recognition and excision of the damaged bases. Dracula and Mole are likely to be defective in the recognition or excision of thymidine dimers; Faust is likely to be defective in the recognition or excision of U-G mismatched base pairs; and Marguerite is likely to be defective in the recognition or excision of abasic sites.

Indicate whether the molecules below are inorganic (I) or organic (O). A. glucose B. ethanol C. sodium chloride D. water E. cholesterol F. adenosine G. calcium H. glycine I. oxygen J. iron K. phospholipid

A. O B. O C. I D. I E. O F. O G. I H. O I. I J. I K. O

During DNA replication in a bacterium, a C is accidentally incorporated instead of an A into one newly synthesized DNA strand. Imagine that this error was not corrected and that it has no effect on the ability of the progeny to grow and reproduce. A. After this original bacterium has divided once, what proportion of its progeny would you expect to contain the mutation? B. What proportion of its progeny would you expect to contain the mutation after three more rounds of DNA replication and cell division?

A. One-half, or 50%. DNA replication in the original bacterium will create two new DNA molecules, one of which will now carry a mismatched C-T base pair. So one daughter cell of that cell division will carry a completely normal DNA molecule; the other cell will have the molecule with the mutation mispaired to a correct nucleotide. B. One-quarter, or 25%. At the next round of DNA replication and cell division, the bacterium carrying the mismatched C-T will produce and pass on one normal DNA molecule from the undamaged strand containing the T and one mutant DNA molecule with a fully mutant C-G base pair. So at this stage, one out of the four progeny of the original bacterium is mutant. Subsequent cell divisions of these mutant bacteria will give rise only to mutant bacteria, whereas the other bacteria will give rise to normal bacteria. The proportion of progeny containing the mutation will therefore remain at 25%.

A. Sketch three different ways in which three water molecules could be held together by hydrogen-bonding. B. On a sketch of a single water molecule, indicate the distribution of positive and negative charge (using the symbols δ+ and δ-). C. How many hydrogen bonds can a hydrogen atom in a water molecule form? How many hydrogen bonds can the oxygen atom in a water molecule form?

A. See Figure A2-37A. B. See Figure A2-37B. C. Hydrogen can form one; oxygen two.

A. Explain the reason why the cell requires a mechanism for identifying specific sequences of DNA. B. On average, how often would the nucleotide sequence CGATTG be expected to occur in a DNA strand 4000 bases long? Show your work and explain your answer. C. Molecular processes depend upon sequence-specific interactions of proteins with DNA. Recognition sequences can be 4, 5, 6, 7, or even 8 base pairs in length for a single protein. What might be the advantages of a short recognition sequence? What might be the advantage of a longer recognition sequence?

A. Sequence information contains indicators important for the regulation of gene expression and DNA packaging. Examples include sequence indicators for where a gene starts and ends, where transcription begins, and where to assemble specific protein complexes at specialized sequences such as those found in telomeric or centromeric DNA. B. Because 46 (= 4096) different sequences of six nucleotides can occur in DNA, any given sequence of six nucleotides would be expected to occur on average once in a DNA strand 4000 bases long, assuming a random distribution of sequences. C. Short recognition sequences do not have as many sequence-specific contacts (which means they don't bind as tightly to the binding site in question), and they are more likely to be found randomly throughout the genome. Using the same type of calculation from part B, there are 256 possible combinations for a 4-base- pair recognition sequence, which could be found 15-16 times over a 4000-base- pair segment by random chance. This could be useful for proteins that need to bind to a large number of sites with low affinity. If we take the case of the 8-base- pair sequence, there are 65,536 different possible sequences. So, not only do they represent high-affinity binding sites, they are much less likely to be found by random chance.

Meselson and Stahl grew cells in media that contained different isotopes of nitrogen (15N and 14N) so that the DNA molecules produced from these different isotopes could be distinguished by mass. A. Explain how "light" DNA was separated from "heavy" DNA in the Meselson and Stahl experiments. B. Describe the three existing models for DNA replication when these studies were begun, and explain how one of them was ruled out definitively by the experiment you described for part A. C. What experimental result eliminated the dispersive model of DNA replication?

A. The DNA samples collected were placed into centrifuge tubes containing cesium chloride. After high-speed centrifugation for 2 days, the heavy and light DNA products were separated by density.B. The three models were conservative, semiconservative, and dispersive. The conservative model suggested a mechanism by which the original parental strands stayed together after replication and the daughter duplex was made entirely of newly synthesized DNA. The semiconservative model proposed that the two DNA duplexes produced during replication were hybrid molecules, each having one of the parental strands and one of the newly synthesized strands. The dispersive model predicted that the new DNA duplexes each contained segments of parental and daughter strands all along the molecule. The conservative model was ruled out by the density-gradient experiments. C. The dispersive model was ruled out by using heat to denature the DNA duplexes and then comparing the densities of the single-stranded DNA. If the dispersive model had been correct, individual strands should have had an intermediate density. However, this was not the case; only heavy strands and light strands were observed, which convincingly supported the semiconservative model for DNA replication.

The synthesis of DNA in living systems occurs in the 5′-to-3′ direction. However, scientists synthesize short DNA sequences needed for their experiments on an instrument dedicated to this task. A. The chemical synthesis of DNA by this instrument proceeds in the 3′-to-5′ direction. Draw a diagram to show how this is possible and explain the process. B. Although 3′-to-5′ synthesis of DNA is chemically possible, it does not occur in living systems. Why not?

A. The actual chemical reaction in DNA synthesis is the same regardless of whether going in the 5′-to-3′ or in the 3′-to-5′ direction. The most important distinction between these two options is that if DNA is synthesized in the 3′-to-5′ direction, the 5′ end of the elongating strand, rather than the 3′ end, will have a nucleoside triphosphate. B. DNA synthesis from 3′ to 5′ does not allow proofreading. If the last nucleotide added is mispaired and is removed, the last nucleotide on the growing strand is a nucleoside monophosphate and the nucleotide coming in only has a hydroxyl group on the 3′ end. Thus, there is no favorable hydrolysis reaction to drive the addition of new nucleotides.

Your lab director requests that you add new growth medium to the mammalian cell cultures before heading home from the lab on a Friday night. Unfortunately, you need to make fresh medium because all the premixed bottles of medium have been used. One of the ingredients you know you need to add is a mix of the essential amino acids (those that cannot be made by the cells, but are needed in proteins). On the shelf of dry chemicals you find the amino acids you need, and you mix them into your medium, along with all the other necessary nutrients, and replace the old medium with your new medium. On Sunday, you come in to the lab just to check on your cells and find that the cells have not grown. You are sure you made the medium correctly, but on checking you see that somebody wrote a note on the dry mixture of amino acids you used: "Note: this mixture contains only ᴅ-amino acids." A. What is the meaning of the note and how does it explain the lack of cell growth in your culture? B. Are there any organisms that could grow using this mixture? Justify your answer.

A. The note indicates that the mixture contains only one of the two possible stereoisomers (ʟ or ᴅ). Because mammalian cells use only the ʟ stereoisomer, the ᴅ-amino acid mixture could not be used and therefore it is as though no amino acids were added at all. B. Not unless ʟ-amino acids were also mixed in. Certain types of bacteria use ᴅ- amino acids to produce their cell walls, but they would still require ʟ-amino acids for the rest of the proteins they make

Chromatography is frequently used to purify proteins from cellular extracts. There are various strategies that can be used, depending on the tools and reagents available. You are interested in isolating additional proteins that interact with your protein target, but your labmates have used all the purified protein stocks. A. Why would you need purified target protein to do this experiment? B. What other strategies/tools could you use to carry out the affinity chromatography? C. What are the limitations to the method you described in part B that would not be a concern if you could use the purified protein directly?

A. The target protein can be covalently linked to the resin used to make the affinity column. When cell extracts are applied to the column, any proteins that associate with high affinity to your target will be bound until they are eluted in the presence of high-salt buffer. B. You could instead use antibodies specific for your target protein. This is very similar to the first procedure, but instead of your protein being directly linked to the column resin, the antibodies are bound instead. The antibody will bind to your target, which should be bound to any associated proteins in the cell extracts. C. One important limitation to recognize is that the antibodies could block the binding surface typically recognized by the other proteins that would normally bind to your target, reducing the number of binding partners isolated by the affinity chromatography. You would also need to have an antibody that recognizes your target protein that could be attached to the column in the first place.

Coenzyme A can be converted to acetyl CoA, which is an important activated carrier molecule that has a central role in metabolism and can be used to add two carbons in each successive cycle of fatty acid synthesis. A. Identify the location and type of high-energy bond in the acetyl CoA molecule shown in Figure Q3-74. B. How does the bond energy help promote the synthesis of fatty acids? C. What function does the rest of the coenzyme A molecule serve in these reaction pathways?

A. The thioester bond is the high-energy bond, boxed in Figure A3-74. B. The generation of long-chain fatty acids requires the generation of new carbon- carbon bonds and the reduction of carbon-oxygen bonds. The energy stored in the acetyl CoA thioester bond promotes the addition of new carbons to an elongating fatty acid chain, two carbons at a time. However, the high-energy electrons required to reduce the carbonyl bond are derived from a second type of molecule, NADPH. C. The rest of the acetyl CoA molecule provides a specific surface recognized by the enzymes that catalyze reactions in which acetyl CoA is required.

The human genome comprises 23 pairs of chromosomes found in nearly every cell in the body. Answer the quantitative questions below by choosing one of the numbers in the following list: 23 69 >200 46 92 >109 A. How many centromeres are in each cell? What is the main function of the centromere? B. How many telomeres are in each cell? What is their main function? C. How many replication origins are in each cell? What is their main function?

A. There are 46 centromeres per cell, one on each chromosome. The centromeres have a key role in the distribution of chromosomes to daughter cells during mitosis. B. There are 92 telomeres per cell, two on each chromosome. Telomeres serve to protect the ends of chromosomes and to enable complete replication of the DNA of each chromosome all the way to its tips. C. There are far more than 200 replication origins in a human cell, probably about 10,000. These DNA sequences direct the initiation of DNA synthesis needed to replicate chromosomes.

The sequences for three different tripeptides are written out below. Indicate whether you expect to find them in the inner core or on the surface of a cytosolic protein, and explain your answer. A. Serine-Threonine-Tyrosine B. Alanine-Glycine-Leucine C. Proline-Serine-Alanine

A. This tripeptide is made up of entirely polar amino acids, which means it will most likely be found on the surface of the protein, interacting with the aqueous environment of the cytosol. B. True. C. False. There is a single, final fold for every polypeptide. The fold adopted is the B. This peptide is made up of nonpolar amino acids. The side chains are most likely buried in the interior of the protein, which would promote interactions with other hydrophobic side chains and avoid unfavorable interactions with the aqueous environment of the cytosol. C. This peptide is made up of both polar and nonpolar amino acids, and one of the nonpolar amino acids is proline. Proline residues have a restricted degree of conformational freedom because the side chain is covalently linked to the backbone nitrogen as well as the α-carbon. So, a likely scenario is that the proline is at the surface of the protein, providing a structural turn between two secondary structure elements (β strands or α helices), the serine is still close enough to the surface to interact with water, and the alanine is close enough to the interior of the protein to interact with other hydrophobic side chains.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Primase is needed to initiate DNA replication on both the leading strand and the lagging strand. B. The sliding clamp is loaded once on each DNA strand, where it remains associated until replication is complete. C. Telomerase is a DNA polymerase that carries its own RNA molecule to use as a primer at the end of the lagging strand. D. Primase requires a proofreading function that ensures there are no errors in the RNA primers used for DNA replication.

A. True B. False. Although the sliding clamp is only loaded once on the leading strand, the lagging strand needs to unload the clamp once the polymerase reaches the RNA primer from the previous segment and then reload it where a new primer has been synthesized. C. True. D. False. Primase does not have a proofreading function, nor does it need one because the RNA primers are not a permanent part of the DNA. The primers are removed, and a DNA polymerase that does have a proofreading function fills in the remaining gaps.

Indicate whether the statements below are true or false. If a statement is false, explain why it is false. A. Electron shells fill discrete regions around the nucleus of the atom and limit the number of electrons that can occupy a specific orbit. B. H, C, O, and N are the most common elements in biological molecules because they are the most stable. C. Some atoms are more stable when they lose one or two electrons, even though this means they will have a net positive charge.

A. True B. False. H, C, N, and O are the most common elements in biological molecules because their outer shells are unfilled, making them highly reactive. C. True.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Ionizing radiation and oxidative damage can cause DNA double-strand breaks. B. After damaged DNA has been repaired, nicks in the phosphate backbone are maintained as a way to identify the strand that was repaired. C. Depurination of DNA is a rare event that is caused by ultraviolet irradiation. D. Nonhomologous end joining is a mechanism that ensures that DNA double-strand breaks are repaired with a high degree of fidelity to the original DNA sequence.

A. True B. False. It is believed that the nicks are generated during DNA replication as a means of easy identification of the newly synthesized strand but are sealed by DNA ligase shortly after replication is completed. C. False. Depurination occurs constantly in our cells through spontaneous hydrolysis of the bond linking the DNA base to the deoxyribose sugar. D. False. Homologous recombination can repair double-strand breaks without any change in DNA sequence, but nonhomologous end joining always involves a loss of genetic information because the ends are degraded by nucleases before they can be ligated back together.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Each strand of DNA contains all the information needed to create a new double-stranded DNA molecule with the same sequence information. B. All functional DNA sequences inside a cell code for protein products. C. Gene expression is the process of duplicating genes during DNA replication. D. Gene sequences correspond exactly to the respective protein sequences produced from them.

A. True B. False. Some sequences encode only RNA molecules, some bind to specific regulatory proteins, and others are sites where specific chromosomal protein structures are built (for example, centromeric and telomeric DNA). C. False. Gene expression is the process of going from gene sequence to RNA sequence, to protein sequence. D. False. This statement is false for two reasons. First, genes often contain intron sequences. Second, genes always contain nucleotides flanking the protein-coding sequences that are required for the regulation of transcription and translation.

Indicate whether the statements below are true or false. If a statement is false, explain why it is false. A. Electrons are constantly moving around the nucleus of the atom, but they can move only in discrete regions. B. There is no limit to the number of electrons that can occupy the fourth electron shell. C. Atoms with unfilled outer electron shells are especially stable and are therefore less reactive.

A. True B. False. The fourth electron shell has the capacity to hold 18 electrons. C. False. Atoms that have their outer electron shells filled are the most stable and least reactive. Atoms with unfilled outer shells are more reactive because they tend to share or transfer electrons to fill and therefore stabilize the outer shell.

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. Membrane components in the cell are made in the endoplasmic reticulum. B. The Golgi apparatus is made up of a series of membrane-enclosed compartments through which materials destined for secretion must pass. C. Lysosomes are small organelles where fatty acid synthesis occurs.

A. True B. True. C. False. Lysosomes house enzymes that break down nutrients for use by the cell and help recycle materials that cannot be used, which will later be excreted from the cell.

On the basis of the two reactions below, decide which of the following statements are true and which are false. 1: ATP + Y->Y-P + ADP ; ΔG = -100 kcal/mole 2: Y-P + A->B ; ΔG = 50 kcal/mole A. Reaction 1 is favorable because of the large negative ΔG associated with the hydrolysis of ATP. B. Reaction 2 is an example of an unfavorable reaction. C. Reactions 1 and 2 are coupled reactions, and when they take place together, reaction 2 will proceed in the forward direction. D. Reaction 2 can be used to drive reaction 1 in the reverse direction.

A. True B. True. C. True. D. False. This is false for two reasons: (1) reaction 2 is unfavorable, as indicated by the positive free-energy change associated with the reaction; (2) the reverse reaction, although possibly more favorable, will yield the product for reaction 1, not reactants to help drive it forward.

Indicate whether the statements below are true or false. If a statement is false, explain why it is false. A. There are four elements that constitute 99% of all the atoms found in the human body. B. Copper, zinc, and manganese are among 11 nonessential trace elements that contribute less than 0.1% of all the atoms in the human body. C. Approximately 0.9% of the atoms in the human body come from seven essential elements—Na, Mg, K, Ca, P, S, and Cl—all of which form stable ions in aqueous solution.

A. True. B. False. Cu, Zn, and Mn are essential trace elements in the human body. C. False. Na, Mg, K, Ca, and Cl form ions in aqueous solution, but P and S form covalent bonds in order to fill their outer election shells

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. The human genome is roughly 30 times larger than the Arabidopsis genome, but contains approximately the same number of protein-coding genes. B. The variation in genome size among protozoans is larger than that observed across all species of mammals, birds, and reptiles. C. The vast majority of our genome encodes functional RNA molecules or proteins and most of the intervening DNA is nonfunctional.

A. True. B. True. C. False. It is a relatively small proportion of our DNA that encodes RNA and protein molecules. The majority of nonencoding sequences is probably involved in critical regulatory processes.

Consider a description of an enzymatic reaction pathway that begins with the binding of substrate S to enzyme E, and ends with the release of product P from the enzyme. E + S!ES!EP!E + P In many circumstances, Km = [E][S]/[ES] A. What proportion of enzyme molecules is bound to substrate when [S] = Km? B. Recall that when [S] = Km, the reaction rate is 1⁄2Vmax. Does your answer to part A make sense in the light of this rate information?

A. When [S] is substituted for Km in the equation, it becomes clear that [E] = [ES]. Thus, half of the enzyme molecules are free and half are bound to the substrate. B. Yes. If half of the enzyme molecules are bound to the substrate, it makes intuitive sense that the reaction rate is half of the maximum possible rate, or half of the rate observed when all of the enzyme molecules are bound to the substrate.

In an attempt to define the protein domains of protein X, you treat it with a protease and use polyacrylamide gel electrophoresis to analyze the peptides produced. In the past, you have used chymotrypsin to perform this experiment, but the stock of this enzyme has been used up. You find a stock of elastase and decide to use it instead of waiting for a new stock of chymotrypsin to arrive. A. Give two reasons why elastase is a good substitute for chymotrypsin in this assay. B. Why might proteolysis of the same substrate by chymotrypsin or elastase yield different results?

A. You might assume that chymotrypsin and elastase would yield the same results because (1) they are both serine proteases and (2) they have a high degree of structural similarity. B. The slight structural differences of the substrates cause the enzymatic activities of the proteases to differ. As a result, they have different substrate affinities and cleave the bond between a different set of amino acids.

Given what you know about the differences between prokaryotic cells and eukaryotic cells, rate the following things as "good" or "bad" processes to study in the model organism E. coli. A. formation of the endoplasmic reticulum B. DNA replication C. how the actin cytoskeleton contributes to cell shape D. how cells decode their genetic instructions to make proteins E. how mitochondria get distributed to cells during cell division

A. bad B. good C. bad D. good E. bad

A protein chain folds into its stable and unique three-dimensional structure, or conformation, by making many noncovalent bonds between different parts of the chain. Such noncovalent bonds are also critical for interactions with other proteins and cellular molecules. From the list provided, choose the class(es) of amino acids that are most important for the interactions detailed below. A. forming ionic bonds with negatively charged DNA B. forming hydrogen bonds to aid solubility in water C. binding to another water-soluble protein D. localizing an "integral membrane" protein that spans a lipid bilayer E. tightly packing the hydrophobic interior core of a globular protein

A. basic B. uncharged polar C. uncharged polar, basic, and acidic D. non polar E. non polar

Examine the three protein monomers in Figure Q4-38. From the arrangement of complementary binding surfaces, which are indicated by similarly shaped protrusions and indentations, decide whether each monomer could assemble into a defined multimer, a filament, or a sheet.

A. defined multimer with four subunits, called a tetramer B. sheet C. filament

A. In which scientific unit is the strength of a chemical bond usually expressed? B. If 0.5 kilocalories of energy are required to break 6 × 1023 bonds of a particular type, what is the strength of this bond?

A. kcal/mole B. 0.5 kcal/mole

A. What is the pH of pure water? B. What concentration of hydronium ions does a solution of pH 8 contain? C. Complete the following reaction: CH3COOH + H2O ↔ __________. D. Will the reaction in (C) occur more readily (be driven to the right) if the pH of the solution is high?

A. pH 7 B. 10^-8 M C. CH3COO- + H3O+ D. Yes. If the pH is high, then the concentration of hydronium ions will be low. Therefore the rightward reaction, which produces hydronium ions, will be favored.

A. Write out the sequence of amino acids in the following peptide, using the full names of the amino acids Pro-Val-Thr-Gly-Lys-Cys-Glu B. Write the same sequence with the single-letter code for amino acids. C. According to the conventional way of writing the sequence of a peptide or a protein, which is the C-terminal amino acid and which is the N-terminal amino acid in the above peptide?

A. proline-valine-threonine-glycine-lysine-cysteine-glutamic acid (or glutamate) B. PVTGKCE C. C-terminal is glutamic acid (or glutamate); N-terminal is proline

Consider the structure of the DNA double helix. A. You and a friend want to split a double-stranded DNA molecule so you each have half. Is it better to cut the length of DNA in half so each person has a shorter length, or to separate the strands and each take one strand? Explain. B. In the original 1953 publication describing the discovery of the structure of DNA, Watson and Crick wrote, "It has not escaped our notice that the specific pairings we have postulated immediately suggest a possible copying mechanism for the genetic material." What did they mean?

A.It is better to separate the strands and each take a single strand, because all of the information found in the original molecule is preserved in a full-length single strand but not in a half-length double-stranded molecule. B. Watson and Crick meant that the complementary base-pairing of the strands allows a single strand to contain all of the information necessary to direct the synthesis of a new complementary strand.

Alanine

Ala, A, non polar

Genes that have homologs in a variety of species have been discovered through the analysis of genome sequences. In fact, it is not uncommon to find a family of homologous genes encoding proteins that are unmistakably similar in amino acid sequence in organisms as diverse as budding yeast, archaea, plants, and humans. Even more remarkably, many of these proteins can substitute functionally for their homologs in other organisms. Explain what it is about the origins of cells that makes it possible for proteins expressed by homologous genes to be functionally interchangeable in different organisms.

All living beings on Earth (and thus, all cells) are thought to be derived from a common ancestor. Solutions to many of the essential challenges that face a cell (such as the synthesis of proteins, lipids, and DNA) seem to have been achieved in this ancient common ancestor. The ancestral cell therefore possessed sets of proteins to carry out these essential functions. Many of the essential challenges facing modern-day cells are the same as those facing the ancestral cell, and the ancient solutions are often still effective. Thus, it is not uncommon for organisms to use proteins and biochemical pathways inherited from their ancestors. Although these proteins usually show some species-specific diversification, they still retain the basic biochemical characteristics of the ancestral protein. For example, homologous proteins often retain their ability to interact with a specific protein target, even in cells of diverse species. Because the basic biochemical characteristics are retained, homologous proteins are often capable of functionally substituting for one another.

Protein families arise when a protein sequence that generates a stable fold diverges over many generations and acquires new functions. One example of this can be seen in the globin family. Myoglobin is a stable monomeric protein that can help carry oxygen using a heme molecule. Hemoglobin is stable as a tetramer. It also carries oxygen through the use of heme groups, but it is useful over a much more dynamic range of oxygen than myoglobin. The "globin fold" is structurally conserved across these proteins, but the ability to tetramerize arose through genetic drift and natural selection. Provide an explanation for how the globin sequence can change and still produce the same overall fold. Support your explanation by suggesting the location and type of sequence alterations that might have little effect on the overall protein fold, but may favor the formation of a multisubunit protein.

Amino acids that are found on the surface of a folded monomeric protein are the best candidates for mutations. Because they are on the surface of the protein, the side-chain interactions are not important for forming the structural core. If alternative amino acids are polar, they can interact equally well with the aqueous environment. It is likely that the sequence comparisons between myoglobin and the α/β globins will reflect changes of surface residues. Furthermore, we may predict that if the surface amino acids changed from polar amino acids to nonpolar amino acids, this would promote multimerization. Nonpolar residues would interact with each other rather than the polar molecules in the cytosol.

Arginine

Arg, R, positive

You are trying to make a synthetic copy of a particular protein but accidentally join the amino acids together in exactly the reverse order. One of your classmates says the two proteins must be identical, and bets you $20 that your synthetic protein will have exactly the same biological activity as the original. After having read this chapter, you have no hesitation in staking your $20 that it won't. What particular feature of a polypeptide chain makes you sure your $20 is safe and that the project must be done again

As a peptide bond has a distinct chemical polarity, a polypeptide chain also has a distinct polarity (see Figure A2-68). The reversed protein chain cannot make the same noncovalent interactions during folding and thus will not adopt the same three- dimensional structure as the original protein. The activities of these two proteins will definitely be different, because the activity of a protein depends on its three-dimensional structure. It is unlikely that the reverse chain will fold into any well-defined, and hence functionally useful, structure at all, because it has not passed the stringent selective pressures imposed during evolution.

Asparagine

Asn, N, uncharged, polar

Aspartic acid

Asp, D, negative

The amino acid histidine is often found in enzymes. Depending on the pH of its environment, sometimes histidine is neutral and at other times it acquires a proton and becomes positively charged. Consider an enzyme with a histidine side chain that is known to have an important role in the function of the enzyme. It is not clear whether this histidine is required in its protonated or its unprotonated state. To answer this question, you measure enzyme activity over a range of pH, with the results shown in Figure Q2-40. Which form of histidine is necessary for the active enzyme?

Assuming that the change in enzyme activity is due to the change in the protonation state of histidine, the enzyme must require histidine in the protonated, charged state. The enzyme is active only at low, acidic pH, where the proton (or hydronium ion) concentration is high; thus, the loss of a proton from histidine will be disfavored so that histidine is likely to be protonated.

You explain to a friend what you have learned about Avogadro's number. Your friend thinks the number is so large that he doubts there is even a mole of living cells on the Earth. You have recently heard that there are about 50 trillion (5 × If 0.5 mole of glucose weighs 90 g, what is the molecular mass of 1013) human cells in each adult human body and that each human contains more bacterial cells (in the digestive system) than human cells, so you bet your friend $5 that there is more than a mole of cells on Earth. The human population is approximately 7 billion (7 × 109). What calculation can you show your friend to convince him you are right?

Avogadro's number, or 6 × 1023, is the number of atoms (or units) in a mole. If you multiply the number of people on Earth by the number of cells in the human body, then double it to account for the bacteria, you will calculate: (7 × 109) × (1 × 1014) = 7 × 1023. Thus, even when only considering the human population and the associated microbial populations, you can estimate more than a mole of living cells on Earth. You win $5.

For each of the following, indicate whether the individual folded polypeptide chain forms a globular (G) or fibrous (F) protein molecule. A. keratin B. lysozyme C. elastin D. collagen E. hemoglobin F. actin

A—F; B—G; C—F; D—F; E—G; F—G

For each of the pairs A-D in Figure Q3-16, pick the more reduced member of the pair.

A—ii; B—ii; C—i; D—ii. "More reduced" means having more electrons; gain of electrons can result in an increased negative charge or a decreased positive charge and can be due to an increase in the number of hydrogen atoms in a molecule.

Match each biological process with the model organism that is best suited or most specifically useful for its study, based on information provided in your textbook. You may list individual processes more than once. A. cell division B. development (multicellular) C. programmed cell death D. photosynthesis E. immunology _____ A. thaliana (Arabidopsis) _____ M. musculus (mouse) _____ S. pombe _____ C. elegans _____ S. cerevisiae _____ D. rerio (zebrafish) _____ D. melanogaster

B, D B, E A C A B B

Consider an analogy between reaction-coupling and money. In a simple economy, barter provides a means of direct exchange of material goods. For example, the owner of a cow may have excess milk and need eggs, whereas a chicken owner has excess eggs and needs milk. Provided that these two people are in close proximity and can communicate, they may exchange or barter eggs for milk. But in a more complex economy, money serves as a mediator for the exchanges of goods or services. For instance, the cow owner with excess milk may not need other goods until three months from now, or may want goods from someone who does not need milk. In this case, the "energy" from providing milk to the economy can be temporarily "stored" as money, which is a form of "energy" used for many transactions in the economy. Using barter and money as analogies, describe two mechanisms that can serve to drive an unfavorable chemical reaction in the cell

Barter is analogous to the direct coupling of a favorable to an unfavorable reaction by a single enzyme. Money is analogous to the storage of energy from a favorable reaction in the form of high-energy bonds in an activated carrier molecule. Such activated carrier molecules can later be used to drive a huge variety of other unfavorable reactions in the cell, either by being hydrolyzed to provide the needed energy for a reaction or by transferring an activated chemical group to another molecule.

In principle, what would be the minimum number of consecutive nucleotides necessary to correspond to a single amino acid to produce a workable genetic code (it can specifically code for all 20 amino acids)? Assume that each amino acid is encoded by the same number of nucleotides. Explain your reasoning.

Because there are 20 amino acids used in proteins, each amino acid would have to be encoded by a minimum of three nucleotides. For example, a code of two consecutive nucleotides could specify a maximum of 16 (42) different amino acids, excluding stop and start signals. A code of three consecutive nucleotides has 64 (43) different members and thus can easily accommodate the 20 amino acids plus a signal to stop protein synthesis.

Although the biochemical study of reaction rates and free energies is important for understanding each biological reaction individually, these studies do not provide an accurate picture of what is happening to reactants and products inside the cell. Why not?

Chemical reactions inside the cell do not reach a state of equilibrium because both reactants and products are typically used in more than one set of reactions, which means their concentrations are constantly fluctuating. As a result, the forward and reverse reaction rates are almost never identical.

The anhydride formed between a carboxylic acid and a phosphate (Figure Q3- 69A) is a high-energy intermediate for some reactions in which ATP is the energy source. Arsenate can also be incorporated into a similar high-energy intermediate in place of the phosphate (Figure Q3-69B). Figure Q3-69C shows the reaction profiles for the hydrolysis of these two high-energy intermediates. What is the effect of substituting arsenate for phosphate in this reaction? (a) It forms a high-energy intermediate of lower energy. (b) It forms a high-energy intermediate of the same energy. (c) It decreases the stability of the high-energy intermediate. (d) It increases the stability of the high-energy intermediate.

Choice (c) is correct. The activation energy of the arsenate compound is extremely low, as can be seen from the reaction profile, meaning that its high-energy intermediate is very unstable and will be spontaneously hydrolyzed more rapidly than the phosphate compound. In fact, this hydrolysis occurs rapidly without enzyme catalysis, even in cellular conditions. Arsenate is therefore quite deleterious for living organisms.

Which of the following statements is true? (a) Peptide bonds are the only covalent bonds that can link together two amino acids in proteins. (b) The polypeptide backbone is free to rotate about each peptide bond. (c) Nonpolar amino acids tend to be found in the interior of proteins. (d) The sequence of the atoms in the polypeptide backbone varies between different proteins.

Choice (c) is the correct answer. Choice (a) is untrue, because some proteins also contain covalent disulfide bonds (-S-S- bonds) linking two amino acids. Choice (b) is untrue, because the peptide bond is rigid. Choice (d) is untrue, because the sequence of atoms in the polypeptide backbone itself is always the same from protein to protein; it is the order of the amino acid side chains that differs

Protein E can bind to two different proteins, S and I. The binding reactions are described by the following equations and values: E + S -> ES Keq for ES = 10 E + I -> EI Keq for EI = 2 Given the equilibrium constant values, which one of the following statements is true? (a) E binds I more tightly than S. (b) When S is present in excess, no I molecules will bind to E. (c) The binding energy of the ES interaction is greater than that of the EI interaction. (d) Changing an amino acid on the binding surface of I from a basic amino acid to an acidic one will probably make the free energy of association with E more negative.

Choice (c) is true. The binding energy is the standard free energy of the binding reaction, and thus is proportional to ln Keq. As the binding energy increases, the equilibrium constant for the association reaction becomes larger. Choices (a) and (b) are false, because although E binds S more tightly than it does I, some E molecules will still be bound to I molecules. Choice (d) is false; although not enough information is given to be certain, it is more likely that binding would be weakened by this change, making the free energy of association more positive.

You wish to produce a human enzyme, protein A, by introducing its gene into bacteria. The genetically engineered bacteria make large amounts of protein A, but it is in the form of an insoluble aggregate with no enzymatic activity. Which of the following procedures might help you to obtain soluble, enzymatically active protein? Select all options that may be useful. Explain your reasoning. A. Make the bacteria synthesize protein A in smaller amounts. B. Dissolve the protein aggregate in urea, then dilute the solution and gradually remove the urea. C. Treat the insoluble aggregate with a protease. D. Make the bacteria overproduce chaperone proteins in addition to protein A. E. Heat the protein aggregate to denature all proteins, then cool the mixture.

Choices A, B, and D are all worth trying. Some proteins require molecular chaperones if they are to fold properly within the environment of the cell. In the absence of chaperones, a partly folded polypeptide chain has exposed amino acids that can form noncovalent bonds with other regions of the protein itself and with other proteins, thus causing nonspecific aggregation of proteins. A. Because the protein you are expressing in bacteria is being made in large quantities, it is possible that there are not enough chaperone molecules in the bacterium to fold the protein. Expressing the protein at lower levels might increase the amount of properly folded protein. B. Urea should solubilize the protein and completely unfold it. Removing the urea slowly and gradually often allows the protein to refold. Presumably, under less crowded conditions, the protein should be able to refold into its proper conformation. C. Treating the aggregate with a protease, which cleaves peptide bonds, will probably solubilize the protein by trimming it into pieces that do not interact as strongly with one another; however, chopping up the protein will also destroy its enzymatic activity. D. Overexpressing chaperone proteins might increase the amount of properly folded protein. E. Heating can lead to the partial denaturation and aggregation of proteins to form a solid gelatinous mass, as when cooking an egg white, and rarely helps solubilize proteins.

Explain the differences between chromosome painting and the older, more traditional method of staining chromosomes being prepared for karyotyping. Highlight the way in which each method identifies chromosomes by the unique sequences they contain.

Chromosome painting relies on the specificity of DNA complementarity. Because unique sequences for each chromosome are known, short DNA molecules matching a set of these sites can be designed for each chromosome. Each set is labeled with a specific combination of fluorescent dyes and then allowed to hybridize (form base pairs) with the two homologous chromosomes that contain the unique sequences being targeted. Giemsa stain is a nonfluorescent dye that has a high affinity for DNA, and specifically accumulates in regions that are rich in A-T nucleotide pairs. This dye produces a pattern of dark and light bands, which differ for each chromosome on the basis of the distribution of AT-rich regions.

Assume that the average human adult requires 2000 kilocalories per day to sustain all normal processes and maintain a constant weight. If manufactured solar panels could somehow provide power directly to the human body, what size solar panel would be required (in cm2)? Assume there are 10 hours of sunlight per day, and that the usable energy output for a typical solar panel is 850 kJ/ft2 per hour. Note: 1 kcal = 4.184 kJ 1 ft2 = 929.03 cm2

Conversion factors: 1 kcal = 4.184 kJ 1 ft2 = 929.03 cm2 If there are 10 hours of sunlight each day hitting the solar panel, there are 8500 kJ/ft2 produced per day. The average adult human requires 8368 kJ per day; thus, with a conventional solar panel, we would require a surface area of about a square foot, or more precisely in cm2: 8368 kJ/X = 8500 kJ/929.03 cm2 929.03 μltiply 8368/8500 = X Page 16 of 50 X = 914.57 cm2

Cysteine

Cys, C, non polar

Match the type of microscopy on the left with the corresponding description provided below. There is one best match for each. A. confocal B. transmission electron C. fluorescence D. phase-contrast E. scanning electron F. bright-field

D F C A B E

Researchers have isolated a mutant strain of E. coli that carries a temperature- sensitive variant of the enzyme DNA ligase. At the permissive temperature, the mutant cells grow just as well as the wild-type cells. At the nonpermissive temperature, all of the cells in the culture tube die within 2 hours. DNA from mutant cells grown at the nonpermissive temperature for 30 minutes is compared with the DNA isolated from cells grown at the permissive temperature. The results are shown in Figure Q6-33, where DNA molecules have been separated by size by means of electrophoresis (P, permissive; NP, nonpermissive). Explain the appearance of a distinct band with a size of 200 base pairs (bp) in the sample collected at the nonpermissive temperature.

DNA ligase has an important role in DNA replication. After Okazaki fragments are synthesized, they must be ligated (covalently connected) to each other so that they finally form one continuous strand. At the nonpermissive temperature this does not happen, and although there may be a range of fragments, the notable band at 200 base pairs is the typical size of an individual Okazaki fragment.

Each chromosome is a single molecule of __________________ whose extraordinarily long length can be compacted by as much as __________________-fold during __________________ and tenfold more during __________________. This is accomplished by binding to __________________ that help package the DNA in an orderly manner so it can fit in the small space delimited by the __________________. The structure of the DNA-protein complex, called __________________, is highly __________________ over time.

DNA, 1000, interphase, mitosis, proteins, nuclear envelope, chromatin, dynamic

The protozoan Didinium feeds on other organisms by engulfing them. Why are bacteria, in general, unable to feed on other cells in this way?

Didinium engulfs prey by changing its shape, and for this it uses its cytoskeleton. Bacteria have no cytoskeleton and cannot easily change their shape because they are generally surrounded by a tough cell wall.

Use your knowledge of amino acid characteristics to order the peptides below by their degree of polarity. Each peptide contains eight amino acids. Use the single- letter amino acid designations to generate your list, placing the most polar peptide on the left and the most nonpolar peptide on the right. A. SGAKKRAH B. CA TWNGQV C. FWGTSILA D. DDAEIHW A E. SSTAMYRK

E, A, D, B, C

Chemical reactions are reversible; they can proceed in both the forward and reverse directions. If the ΔG° for the reaction Y!X is energetically favorable, how can you explain the fact that not all of the Y molecules will be converted to X molecules?

Even when the forward reaction is highly favorable, it is important to keep in mind that molecules exist as part of a population, and each member of a given population has a varying level of energy per molecule. Statistically speaking, there will always be some molecules that have sufficient energy to reach the energy of activation for the back reaction X!Y, even though the proportion of molecules with this energy will be much lower than that for the forward reaction Y!X. As more and more X molecules are converted to Y molecules, eventually the Y molecules in the mixture outnumber the X molecules to such a large extent that the fluxes in the backward and forward directions become equal; it is here that the reaction reaches its equilibrium point.

T/R: The paramecium is a multicellular microorganism covered with hairlike cilia

F. The paramecium is a single-celled organism

You have been following the recent presidential elections and have heard some candidates disparaging excessive and "unnecessary" federal government expenditures. One particular candidate asks: "Why are we spending millions of dollars studying fruit flies? How can that possibly help us find a cure for cancer?" Use your knowledge of model organisms to explain why studies in D. melanogaster (the fruit fly) are actually an excellent use of research funding.

Funding research on D. melanogaster is a worthwhile investment for several reasons: (1) working with insect animal models is relatively inexpensive; (2) fruit flies have historically proven useful in helping understand eukaryotic chromosome behavior; and (3) many of the genes in Drosophila are highly similar in sequence to the homologous human genes, and thus can be used to study human diseases.

Glutamine

Gln, Q, uncharged, polar

Glutamic acid

Glu, E, negative

Glycine

Gly, G, nonpolar

Fill in the blanks, selecting from the choices below. Light + _________ + _________->_________ + heat + sugars CO, CO2, O2, H2, H2O, N2, NO

H2O, CO2, O2

Histidine

His, H, positive

Match each term related to the structure of nucleic acids (A-I) with one of the descriptions provided. A. base B. glycosidic bond C. nucleoside D. nucleotide E. phosphoanhydride bond F. phosphoester bond G. ribose H. phosphodiester bond I. deoxyribose ____ the linkage between two nucleotides ____ the linkage between the 5′ sugar hydroxyl and a phosphate group ____ the nitrogen-containing aromatic ring ____ five-carbon sugar found in DNA ____ sugar unit linked to a base ____ linkage between the sugar and the base

H—the linkage between two nucleotides F—the linkage between the 5′ sugar hydroxyl and a phosphate group A—the nitrogen-containing aromatic ring I—five-carbon sugar found in DNA C—sugar unit linked to a base B—linkage between the sugar and the base E—linkages between phosphate groups D—sugar linked to a base and a phosphate G—five-carbon sugar found in RNA

Match the general type of biochemical reaction catalyzed in the left column with the class of enzyme listed in the column on the right. ___ removes a phosphate group from a molecule ___ hydrolyzes ATP ___ hydrolyzes bonds between nucleotides ___ adds phosphate groups to molecules ___ catalyzes reactions in which one molecule is oxidized and another is reduced ___ hydrolyzes peptide bonds ___ joins two ends of DNA together ___ catalyzes the synthesis of polymers such as RNA and DNA ___ rearranges bonds within a single molecule A. ATPase B. Polymerase C. ligase D. kinase E. isomerase F. nuclease G. oxide-reductase H. protease I. phosphatase

I A F D G H C B E

Match the basic protein functions in the left column with a specific example of that type of protein in the column on the right. ___ gene regulatory ___ motor ___ storage ___ enzyme ___ transport ___ structural ___ special purpose ___ receptor ___ signal A. insulin B. carboxylase C. rhodopsin D. hemoglobin E. ferritin F. myosin G. green fluorescent protein H. tubulin I. homeodomain proteins

I F E B D H G C A

One way in which an enzyme can lower the activation energy required for a reaction is to bind the substrate(s) and distort its structure so that the substrate more closely resembles the transition state of the reaction. This mechanism will be facilitated if the shape and chemical properties of the enzyme's active site are more complementary to the transition state than to the undistorted substrate; in other words, if the enzyme were to have a higher affinity for the transition state than for the substrate. Knowing this, your friend looked in an organic chemistry textbook to identify a stable chemical that closely resembles the transition state of a reaction that converts X into Y. She generated an antibody against this transition-state analog and mixed the antibody with chemical X. What do you think might happen?

If your friend was lucky, she made a "catalytic antibody" that catalyzed the conversion of X into Y. Such catalytic antibodies have been isolated and shown to catalyze a variety of reactions, but with lower efficiency than genuine enzymes.

Isoleucine

Ile, I, nonpolar

How does cellular specialization serve multicellular organisms and how might a high degree of specialization be detrimental?

In a multicellular organism, the specialization of cells creates a division of labor and each type of cell relies on the activities of other cell types for survival. This cooperation b/t specializes cells is essential for the organism as a whole. If one of these overly specializes cells are removed from the context of the organism, it would not have the capabilities needed to generate offspring and would probably not even live very long.

Using the example of the p53 protein, postulate how different combinations of covalent modifications can lead to a wide variety of protein functions.

In a protein with a complex regulatory protein code, such as p53, the covalent attachment or removal of modifying groups can change the protein's behavior, its activity or stability, its binding partners, or its location within a cell. In the case of p53, there are at least 20 different locations (amino acids) that can be modified through such processes as phosphorylation, ubiquitylation, and acetylation.

Some of the enzymes that oxidize sugars to yield usable cellular energy (for example, ATP) are regulated by phosphorylation. For these enzymes, would you expect the inactive form to be the phosphorylated form or the dephosphorylated form? Explain your answer.

In general, the inactive form is the phosphorylated form. The main purpose of glycolysis and the citric acid cycle is to generate ATP; thus, the enzymes are inactive when the concentration of ATP is high and active when it is low. It makes sense that cells would not want to have to phosphorylate their enzymes to turn them on when ATP levels are already low, because phosphorylation requires ATP.

Most cells in the body of an adult human lack the telomerase enzyme because its gene is turned off and is therefore not expressed. An important step in the conversion of a normal cell into a cancer cell, which circumvents normal growth control, is the resumption of telomerase expression. Explain why telomerase might be necessary for the ability of cancer cells to divide over and over again.

In the absence of telomerase, the life-span of a cell and its progeny cells is limited. With each round of DNA replication, the length of telomeric DNA will shrink, until finally all the telomeric DNA has disappeared. Without telomeres capping the chromosome ends, the ends might be treated like breaks arising from DNA damage, or crucial genetic information might be lost. Cells whose DNA lacks telomeres will stop dividing or die. However, if telomerase is provided to cells, they may be able to divide indefinitely because their telomeres will remain a constant length despite repeated rounds of DNA replication.

Hydrolysis reactions are commonly used inside the cell to split high-energy covalent bonds. For each of the three reactions below, use the ΔG° for each reaction to determine the equilibrium constants (K). Assume that each reaction occurs independently of the other two. ΔG° (kcal/mole) Reaction 1: acetyl-P!actetate + P ; -10.3 Reaction 2: ATP!ADP + P ; -7.3 Reaction 3: glucose 6-P!glucose + P ; -3.3

K can be easily calculated from the standard free-energy values by solving the standard free-energy equation (ΔG° = -1.42 log K) for K (K =10ΔG°/-1.42). Reaction 1: K = 107.25 Reaction 2: K = 105.14 Reaction 3: K = 102.32

Leucine

Leu, L, nonpolar

Lysine

Lys, K, positive

Methionine

Met, M, nonpolar

In general, there is a positive change in free energy associated with reduction reactions, and most of them are coupled with oxidation reactions. The last step in the biosynthesis of cholesterol involves the reduction of a carbon-carbon double bond. What activated carrier molecule is used in this reaction (and generally for the reduction of lipids) and how would this reaction be influenced by the levels of available ATP?

NADPH is the activated carrier used in the final reduction reaction to produce cholesterol. The rate of this reaction will depend upon the concentration of NADPH, the regeneration of which depends upon ATP hydrolysis. If ATP levels are low, then we can expect that the levels of NADPH will be correspondingly low. The rate of cholesterol synthesis will be lower than if the cell is in a high-energy state with abundant levels of ATP, and consequently high levels of NADPH

You have produced a monoclonal antibody that binds to the protein actin. To be sure that the antibody does not cross-react with other proteins, you test your antibody in a western blot assay on whole-cell lysates that have been subjected to electrophoresis under nondenaturing conditions (shown in Figure Q4-37A) and denaturing conditions (shown in Figure Q4-37B). Does the antibody cross-react with other proteins? If so, does this explain the results in the two western blots? If not, how do you explain the difference observed?

No, the antibody does not seem to cross-react with other proteins. In each western blot, there is only one band, indicating that only one protein is bound by the monoclonal antibody. Actin is a protein that forms long filaments. Under the nondenaturing conditions of the first gel (A), the filaments remain intact and, as a multiprotein complex, actin migrates very slowly through the polyacrylamide matrix. In the case where sodium dodecyl sulfate (SDS) is added (denaturing conditions), actin filaments dissociate into monomers. Thus, the band is lower in panel (B) because the monomers have a lower molecular weight and migrate faster through the gel.

If you weigh yourself on a scale one morning, then eat four pounds of food during the day, will you weigh four pounds more the next morning? Why or why not? (Hint: What happens to the atoms from the food you ingested?)

No, you will not weigh four pounds more the next morning because only a small portion of the mass of the food will form components of the body. Much of the mass of food is either released as CO2 and H2O that are breathed out into the atmosphere or converted into materials excreted as waste products.

It is now a routine task to determine the exact order in which individual subunits have been linked together in polynucleotides (DNA) and polypeptides (proteins). However, it remains difficult to determine the arrangement of monomers in a polysaccharide. Explain why this is the case.

Nucleotides and amino acids have an intrinsic directionality, and the mechanism by which monomers are added into a growing polymer is always the same. This yields a linear polymer with the same directionality as the monomers. Polysaccharides are produced by linking monosaccharides together. The monosaccharides can be either added directly or modified to produce various derivatives before addition. Beyond this, there are multiple sites on each monosaccharide where addition can occur, producing highly complex, branched polymers.

Cellular processes are often regulated by unknown mechanisms. In many cases, biologists work backward in an attempt to understand a process in which they are interested. This was the case when Nurse and Hartwell were trying to understand how cell division is controlled in yeast. Describe the process by which they "broke" the system and then supplied the "missing parts" to get the cell cycle running again. What further evidence did they collect to show that human cells and yeast cells regulate the cell cycle using a similar mechanism?

Nurse and Hartwell first treated yeast cells with a chemical mutagen. The mutated population of cells was then grown and observed. Cells that demonstrated defects in cell- cycle regulation (characterized by cell-cycle arrest, larger-than-normal cells, and smaller- than-normal cells) were then isolated. The use of a library of plasmids that each express a normal gene from yeast cells allowed the scientists to identify exactly which gene could be used to "rescue" the mutant, because when the normal gene is expressed again, the cells return to a normal cell cycle. After this big result, the scientists went on to show that the homologous gene from other organisms could also rescue the mutant phenotype. The most exciting result was obtained with the human version of the cdc2 gene, which demonstrated that there are common principles underlying cell-cycle regulation across a large range of eukaryotic organisms.

Silicon is an element that, like carbon, has four vacancies in its outer electron shell and therefore has the same bonding chemistry as carbon. Silicon is not found to any significant degree in the molecules found in living systems, however. Does this difference arise because elemental carbon is more abundant than silicon? What other explanations are there for the preferential selection of carbon over silicon as the basis for the molecules of life?

On the basis of Figure 2-4 in your textbook, silicon is actually more abundant in the Earth's crust than carbon, so this is not likely to be the reason that carbon was used preferentially. Carbon might have been the element of choice in living systems because it is lighter than silicon and forms shorter covalent bonds with other elements. Shorter bonds are typically stronger and more stable.

Describe the mechanism by which heterochromatin can spread, once it has been established in one region of the chromosome.

Once the initial H3 lysine 9 methylation is established on core histone octamers in one region, the modification attracts a specific set of proteins and other histone-methylating enzymes. These enzymes create the same modification on adjacent histone octamers, which continue to recruit more heterochromatin-specific proteins and enzymes, creating a wave of heterochromatin spreading along the chromosome.

As a protein is made, the polypeptide is in an extended conformation, with every amino acid exposed to the aqueous environment. Although both polar and charged side chains can mix readily with water, this is not the case for nonpolar side chains. Explain how hydrophobic interactions may play a role in the early stages of protein folding, and have an influence on the final protein conformation.

One reason that nonpolar groups are excluded from an aqueous environment is that a hydrophobic surface would organize water into a highly structured network of hydrogen bonds, which is energetically unfavorable. So, you would expect that nonpolar amino acids would group together early, forming "hydrophobic pockets," while the polar and charged side chains remain at the interface of the surrounding solution. In the final, folded protein, most of the nonpolar amino acids will remain buried inside the protein. This fold is more stable because nonpolar atoms are prevented from contact with water and remain in contact with each other.

Phenylalanine

Phe, F, nonpolar

Proline

Pro, P, nonpolar

You are digesting a protein 625 amino acids long with the enzymes Factor Xa and thrombin, which are proteases that bind to and cut proteins at particular short sequences of amino acids. You know the amino acid sequence of the protein and so can draw a map of where Factor Xa and thrombin should cut it (Figure Q4-36). You find, however, that treatment with each of these proteases for an hour results in only partial digestion of the protein, as summarized under the figure. List the segments (A-E) of the protein that are most likely to be folded into compact, stable domains.

Segments B and D. To cut the protein chain, Factor Xa and thrombin must bind to their preferred cutting sites. If these sites are folded into the interior of a stable protein domain, it will be much more difficult for the proteases to gain access to them than if they are part of a relatively unstructured part of the chain. Hence, sites that are folded inside a protein domain are protected from cleavage by a protease. From the sizes of the fragments produced by digestion of the protein with Factor Xa, we can conclude that the enzyme does not cut at the sites in regions B or D, although it does cut in region E. From the sizes of the fragments produced by thrombin, we can conclude that this enzyme cuts at the sites in A, C, and E. Therefore, the segments of the protein that are most likely to be folded into compact, stable domains are B and D.

Serine

Ser, S, uncharged, polar

Selenium (Se) is an element required in the human body in trace amounts. Selenium is obtained through the diet and levels of selenium found in food depend greatly on the soil where it is grown. Once ingested and absorbed as selenate, it can become incorporated into a small number of polypeptides. These selenoproteins are formed when selenium replaces an element that is found in two of the twenty "standard" amino acids. Using your knowledge of atomic structure, the periodic table in Figure 2-7, and the structure of amino acids found in Panel 2-5, deduce which two amino acids may be converted to "seleno" amino acids and used to make selenoproteins.

Sulfur is the only element found exclusively in two of the twenty amino acids. This element is located directly above selenium in the periodic table, indicating that these elements have the same number of electrons in their outer shell and both prefer to form bonds with other atoms to fill their outer orbital. If selenium instead of sulfur is incorporated into cysteine or methionine, the altered "seleno" amino acids will be produced (selenocysteine and selenomethionine). We can expect that this substitution will alter the nature of the proteins in which these amino acids are incorporated because selenium is a larger atom than sulfur.

T/F: Cells of different types can have different chemical requirements

T

T/F: The branchlike extensions that sprout from a single nerve cell in a mammalian brain can extend over several hundred micrometers

T

If base pairs were aligned and stacked directly on top of each other, the major and minor grooves would be linear depressions all along the DNA. Explain why this is not the actual conformation of a DNA molecule.

The DNA base pairs are rotated with respect to each other. For a double-stranded DNA molecule with 10 base pairs, a full 360° rotation has occurred. This is referred to as one turn of the helix, and it can be seen in Figure A5-17A in the alignment of the A-T base pair at the bottom with the G-C base pair at the top

Evidence suggests that the replication of DNA packaged into heterochromatin occurs later than the replication of other chromosomal DNA. What is the simplest possible explanation for this phenomenon?

The DNA double helix in heterochromatin may be so tightly packed and condensed that it is inaccessible to the proteins that bind replication origins, including the DNA replication machinery. It may take extra time to remodel the chromatin to make it more accessible to the proteins required to initiate and perform DNA replication.

Employ the principles of evolution discussed in this chapter to explain how the specific features and predatory behaviors of some primitive eukaryotes may have given them a selective advantage over others 1.5 billion years ago.

The Earth's atmosphere became oxygen-rich roughly 1.5 billion years ago. If some primitive predatory eukaryotic cells were similar to modern-day protozoans, they may have been mobile and able to engulf other cells. These characteristics would have been advantageous in the face of a changing atmosphere, and the establishment of a symbiotic relationship with an engulfed aerobe would have been selected for in the eukaryotic cell populations.

The sliding clamp complex encircles the DNA template and binds to DNA polymerase. This helps the polymerase synthesize much longer stretches of DNA without dissociating. While the loading of the clamp only occurs once on the leading strand, it must happen each time a new Okazaki fragment is made on the lagging strand. How does the cell expedite this process?

The cell employs an additional protein in order to make the constant reloading of the sliding clamp on the lagging strand much more efficient. The protein, called the clamp loader, harnesses energy from ATP hydrolysis to lock a sliding clamp complex around the DNA for every successive round of DNA synthesis.

A mismatched base pair causes a distortion in the DNA backbone. If this were the only indication of an error in replication, the overall rate of mutation would be much higher. Explain why.

The distortion in the DNA backbone is insufficient information for the mismatch repair system to identify which base is incorrect and which was originally part of the chromosome when replication began. Without additional marks that identify the difference between the newly synthesized strand and the template strand, the repair would be corrected only 50% of the time by random chance. The error rate (and therefore the mutation rate) would still be less than in a system that lacked the mismatch repair enzymes (1 mistake per 107 base pairs), but greater than the error rate in a system that accurately identifies the newly synthesized strand (1 mistake per 109 base pairs).

Enzymes generally make good drug targets because a specific reaction of interest can be targeted with a high degree of selectivity. Consider the following three drugs and explain why, although reaction-specific, the first two produce side effects, while the third does not. A. Statins inhibit HMG CoA reductase to block intracellular cholesterol synthesis. B. Methotrexate inhibits dihydrofolate reductase, which subsequently leads to blocked DNA replication. C. Gleevec® inhibits BCR, a kinase that is only produced in certain types of leukemia cells.

The first two inhibitors (statins and methotrexate) are blocking reactions that are very important to all cells, not just the cells affected by the illness in question. Thus, drug side effects can be hard to predict, and may be very specific to the patient being treated. In the case of chronic myeloid leukemia (CML), the mutant enzyme is specific to the leukemia cells, and no other cells in the body are affected by this drug. This also means that the usefulness of this drug is limited to those CML patients that have this specific mutation.

The addition of a new deoxynucleotide to a growing DNA chain requires more energy than can be obtained by the hydrolysis of ATP to ADP + Pi. What alternative series of reactions is used, and how does this help overcome the energy barrier for DNA synthesis?

The hydrolysis of ATP to ADP is favorable, with a ΔG between -11 and -13 kcal/mole. However, this is not sufficient to drive the addition of a nucleotide to the end of a growing DNA strand. Instead, two reactions are used. The first reaction converts ATP to a DNA-linked AMP residue when a phosphodiester bond is formed during DNA synthesis; simultaneously, a pyrophosphate molecule (PPi) is released. In the second reaction, the PPi is hydrolyzed to form two molecules of Pi. This second reaction is also favorable, providing roughly another -13 kcal/mole. Adding up the ΔG for the entire process, there will be about -26 kcal/mole to drive the addition of the nucleotide to the growing DNA chain, which is sufficient to drive the reaction strongly in one direction.

The branched diagram in Figure Q3-30 represents several possible reaction pathways that substance X may follow. Each branch point represents two possible reactions, which would give rise to different products. Next to each of these points are values for the uncatalyzed activation energies and catalyzed activation energies (in kcal/mole), respectively. A. Order the final products in the relative amounts you expect them to be produced in the absence of any enzymes (from greatest to least). B. Order the final products in the relative amounts you expect them to be produced when enzymes for each reaction are present. b d cY reaction pathway Figure Q3-29 cY free energy free energy C. Compare your answers for parts A and B. How do you think the uncatalyzed reactions could influence the rates of catalyzed reactions inside the cell?

The lower the activation energy, the larger the number of molecules that have the energy required to overcome the energy barrier. When no enzymes are present, the uncatalyzed activation energies will determine the relative rates at which the substrate undergoes either reaction. A. Following this principle, the relative amounts of products in the absence of the necessary enzymes (from greatest to least) are: C, D, A, B, H, G, E, F. B. In the presence of the enzymes required to catalyze the two different reactions represented by each branch, we should expect to see a different distribution of products: G, H, E, F, A, B, D, C. C. Although we can make these predictions based on activation energies, there are many other factors that determine how fast a certain product will accumulate: reactant concentration, catalytic efficiency of the enzyme in question, and the relative reactivity of the product, to name a few. If a reaction has a very low uncatalyzed activation energy, it could occur spontaneously at a rapid rate, which would decrease the concentration of substrate available for the enzyme-catalyzed reaction. If this is the case, the relative abundances predicted in part B will change.

Because hydrogen bonds hold the two strands of a DNA molecule together, the strands can be separated without breaking any covalent bonds. Every unique DNA molecule "melts" at a different temperature. In this context, Tm (melting temperature) is the point at which two strands separate, or become denatured. Order the DNA sequences listed below according to relative melting temperatures (from lowest Tm to highest Tm). Assume that they all begin as stable double- stranded DNA molecules. Explain your answer. A. GGCGCACC B. TATTGTCT C. GACTCCTG D. CTAACTGG

The order in which the DNA molecules would denature as the temperature increases is: 1—B; 2—D; 3—C; 4—A All the DNA molecules are the same length, so only the A + T and G + C content determines their relative Tm. Molecules with higher G + C content will be more stable than molecules with a high A + T content. This is because there are three hydrogen bonds between each G-C base pair but only two between each A-T base pair. More energy (heat) is required to disrupt a larger number of hydrogen bonds.

Figure Q3-59 illustrates the amount of energy per molecule for a population in a contained, controlled environment. Most molecules will have the average energy of the population, shown in region 1. The number of molecules in the population with enough energy to be converted to product is shown in region 2. The number of molecules with enough energy to react in the presence of enzyme is shown in region 3. Use this information to explain how enzymes catalyze reactions.

The presence of enzyme in the mixture of reactant molecules does not change the energy distribution of the population of molecules. Their average energy will remain the same, and there still will be only a very small proportion of the molecules with high energy. Enzyme catalysis increases the total number of molecules that have sufficient energy to participate in the reaction because the total energy required per molecule that reacts is lowered.

Two college roommates do not agree on the best way to handle the clutter piled up in your dorm room. Roommate 1 explains that chaos is inevitable, so why fight it? Roommate 2 counters that maintaining an organized environment makes life easier in many ways, and that chaos is not inevitable. What law of thermodynamics drives the thinking of Roommate 1? What thermodynamic argument can be used to support Roommate 2?

The second law of thermodynamics supports Roommate 1's view. It is favorable for a system to become less ordered. However, if the energy used to create an ordered environment in the room is accompanied by enough release of heat, the Universe will become more disordered as the room becomes more organized. Thus, while increasing chaos is inevitable, the room—like a cell—can be kept highly organized, by interconverting types of energy.

The cell is able to harvest energy from various processes in order to generate ATP molecules. These ATPs represent a form of stored energy that can be used later to drive other important processes. Explain how the cell can convert the chemical energy stored in ATP to generate mechanical energy, for example changing the shape of a protein.

The terminal phosphate group is typically hydrolyzed and the energy released from this chemical bond is often "reinvested" to generate a new bond that links the phosphate group to a protein. This addition of a phosphate group can cause a change in the protein's conformation. This conformational change is usually associated with change in function or transient interactions with other macromolecules, generating a domino effect within the cell.

Typical folded proteins have a stability ranging from 7 to 15 kcal/mole at 37°C. Stability is a measure of the equilibrium between the folded (F) and unfolded (U) forms of the protein, with the unfolded form having a greater free energy (see Figure Q4-20). For a protein with a stability of 7.1 kcal/mole, calculate the fraction of protein that would be unfolded at equilibrium at 37°C. The equilibrium constant (Keq) is related to the free energy (ΔG°) by the equation Keq = 10-ΔG°/1.42.

The ΔG° of the unfolding reaction is equal to the stability of the protein, 7.1 kcal/mole. At equilibrium, the ratio of unfolded to folded protein is Keq = [U]/[F] = 10-ΔG°/1.42 = 10-7.1/1.42 = 10-5. Thus, one molecule in 100,000 is unfolded.

Knowing that there are 20 different possible amino acids that can be used at each position in a polypeptide, calculate the number of different polypeptides that could theoretically be produced for a protein that is 180 amino acids in length. Do you expect to find all of these possible protein sequences produced in living systems? Explain your answer.

There are 20180 possible sequences for a 180 amino acid polypeptide (20 different possible amino acids for each position). No, we would not expect all of the theoretically possible proteins to be made. A much smaller subset can be expected in living systems because it is not likely that all sequences would lead to a stably folded protein. Natural selection favors the retention of genes that encode proteins with stable conformations.

Use your knowledge of how a new strand of DNA is synthesized to explain why DNA replication must occur in the 5′-to-3′ direction. In other words, what would be the consequences of 3′-to-5′ strand elongation?

There would be several detrimental consequences to 3′-to-5′ strand elongation. One of those most directly linked to the processes of DNA replication involves synthesis of the lagging strand. After the RNA primers are degraded, the DNA segments remaining will have 5′ ends with a single phosphate group. The incoming nucleotide will have a 3′-OH group. Without the energy provided by the release of PPi from the 5′ end, the process of elongation would no longer be energetically favorable.

Avery, MacLeod, and McCarty carried out experiments to identify the class of biological molecule that carries heritable information. Explain how they identified the "transforming principle" that could convert a harmless strain of bacteria to a pathogenic one.

They prepared extracts from the infectious, pathogenic bacterial strain, and separated the different types of macromolecules (RNA, DNA, protein, lipids, and carbohydrates). Each of these materials was incubated separately with the noninfectious strain. The researchers were able to conclude that DNA was the "transforming principle" because it was the only macromolecule isolated from the pathogenic strain that was able to convert the noninfectious strain into an infectious one.

Threonine

Thr, T, uncharged, polar

Tryptophan

Trp, W, nonpolar

Tyrosine

Tyr, Y, uncharged, polar

Enzymes A and B catalyze different reactions, but use the same reactant molecule as a substrate. The graph in Figure Q3-63 presents the reaction rates observed when enzyme A and enzyme B are mixed together in a single test tube containing molecule X. What are the Vmax and the apparent Km values for each enzyme under these conditions? How might these values change for enzyme B if it were analyzed in the absence of enzyme A? Explain your answer.

Under the mixed conditions, enzyme A has a Vmax of 6 and an apparent Km of 1 μM X; enzyme B has a Vmax of 10 and an apparent Km of 3 μM. Because enzyme A has a higher affinity for substrate, it more quickly binds to reactant X and converts it into the product Y, lowering the effective concentration of X reactant available for enzyme B. If enzyme B were tested separately, the Vmax should stay the same, but the Km might be smaller and be a more accurate reflection of the binding affinity of enzyme B for the reactant molecule X.

The deamination of cytosine generates a uracil base. This is a naturally occurring nucleic acid base, and so does not represent a DNA lesion caused by damage due to chemicals or irradiation. Why is this base recognized as "foreign" and why is it important for cells to have a mechanism to recognize and remove uracil when it is found in the DNA duplex?

Uracil is an RNA base and it is recognized as a mutational lesion because, as it is formed from the deamination of cytosine, it will be paired with a guanine in the context of the DNA duplex. Uracil pairs by forming two hydrogen bonds, similar to thymine, and is thus a poor partner for guanine, which forms three hydrogen bonds with cytosine. The mismatch causes a distortion of the DNA backbone, allowing the repair machinery to recognize the uracil as a lesion. Because uracil pairs preferably with adenine (its partner in double-stranded RNA), the deamination of cytosine to uracil is highly mutagenic. If unrepaired, it can result in the transition of a C-G base pair to a T-A base pair.

Valine

Val, V, nonpolar

The relative strengths of covalent bonds and van der Waals interactions remain the same when tested in a vacuum or in water. However, this is not true of hydrogen bonds or ionic bonds, whose bond strengths are lowered considerably in the presence of water. Explain these observations.

We estimate bond strengths by measuring the amount of energy needed to break them. As explained in Panel 2-7 (p.78-79), in an aqueous solution, water can form hydrogen bonds with any polar molecules that are capably of forming hydrogen bonds with each other. This formation of bonds with water takes away from the net energy that would be gained from the molecules forming hydrogen bonds with each other, as they would in a vacuum. Similarly, water forms favorable electrostatic interactions with ions, thereby greatly weakening the ionic bonds that form between positive and negative ions in a vacuum (see Panel 2-7). Thus, for example, solid table salt (NaCl) readily dissociates in water, producing separate Na+ and Cl- ions as it dissolves. In contrast, covalent bonds and van der Waals attractions have an intrinsic bond strength that is independent of the aqueous environment, because changes in water molecule associations are not involved in the formation of these two types of bonds.

In the cytoplasm, materials are organized, separated, and sorted by membranes. Cells exploit the selective permeability of these membranes to partition populations of molecules and generate chemical energy for the cell. Use the principles of the first and second laws of thermodynamics to explain how membranes can be used to produce chemical energy.

When one type of molecule accumulates at a higher concentration on one side of the membrane, the molecules become "organized" by having their movement limited to the space they occupy. The second law of thermodynamics indicates that, if allowed to do so, the molecules would move across the membrane until there is an equal distribution of molecules on either side. The accumulation of molecules on one side of the membrane represents a store of potential energy. The first law of thermodynamics tells us that this energy will not be lost, but rather converted into a different type of energy. First, when the molecules are then allowed to move across the membrane, this potential energy is converted into kinetic energy. The kinetic energy of molecules moving through a protein channel to cross the membrane is often linked to conformational changes in the protein, promoting specific chemical reactions.

Your friend has just returned from a deep-sea mission and claims to have found a new single-celled life-form. He believes this new life-form may not have descended from the common ancestor that all types of life on Earth share. You are convinced that he must be wrong, and you manage to extract DNA from the cells he has discovered. He says that the mere presence of DNA is not enough to prove the point: his cells might have adopted DNA as a useful molecule quite independently of all other known life-forms. What could you do to provide additional evidence to support your argument?

You could use modern technology to discover the sequence of the DNA. If you are right, you would expect to find parts of this sequence that are unmistakably similar to corresponding sequences in other, familiar, living organisms; it would be highly improbable that such similar sequences would have evolved independently. You could, of course, also analyze other features of the chemistry of his cells; for example, do they contain proteins made of the same set of 20 amino acids? This could all be supporting evidence that this newly discovered species arose from the same common ancestral cells as all other life on Earth.

In addition to the extracts and the plasmid DNA, are there any additional materials you should add to this in vitro replication system? Explain your answer.

You will probably add exogenous nucleoside triphosphates to serve as the building blocks needed to make new strands of DNA. Although these monomers will be present in the extracts, they will be present at lower concentrations than are normally found inside the cell. They may also be subject to hydrolysis, and the nucleoside diphosphates that are the products of this hydrolysis are not usable substrates for DNA replication. For both of these reasons, it is important to add excess nucleotides to the reaction mixture for efficient DNA replication to occur.

You fertilize egg cells from a healthy plant with pollen (which contains the male germ cells) that has been treated with DNA-damaging agents. You find that some of the offspring have defective chloroplasts, and that this characteristic can be passed on to future generations. This surprises you at first because you happen to know that the male germ cell in the pollen grain contributes no chloroplasts to the fertilized egg cell and thus to the offspring. What can you deduce from these results?

Your results show that not all of the information required for making a chloroplast is encoded in the chloroplast's own DNA; some, at least, must be encoded in the DNA carried in the nucleus. The reasoning is as follows. Genetic information is carried only in DNA, so the defect in the chloroplasts must be due to a mutation in DNA. But all of the chloroplasts in the offspring (and thus all of the chloroplast DNA) must derive from those in the female egg cell, since chloroplasts only arise from other chloroplasts. Hence, all of the chloroplasts contain undamaged DNA from the female parent's chloroplasts. In all the cells of the offspring, however, half of the nuclear DNA will have come from the male germ-cell nucleus, which combined with the female egg nucleus at fertilization. Since this DNA has been treated with DNA-damaging agents, it must be the source of the heritable chloroplast defect. Thus, some of the information required for making a chloroplast is encoded by the nuclear DNA.

Arrange the following molecules in order with respect to their relative levels of oxidation (assign 5 to the most oxidized and 1 to the most reduced). _______ CH2O (formaldehyde) _______ CH4 (methane) _______ CHOOH (formic acid) _______ CH3OH (methanol) _______ CO2 (carbon dioxide)

__3__ CH2O (formaldehyde) __1__ CH4 (methane) __4__ CHOOH (formic acid) __2__ CH3OH (methanol) __5__ CO2 (carbon dioxide)

Because all DNA polymerases synthesize DNA in the 5′-to-3′ direction, and the parental strands are antiparallel, DNA replication is accomplished with the use of two mechanisms: continuous and discontinuous replication. Indicate whether the following items relate to (1) continuous replication, (2) discontinuous replication, or (3) both modes of replication. ______ primase ______ single-strand binding protein ______ sliding clamp ______ RNA primers ______ leading strand ______ lagging strand ______ Okazaki fragments ______ DNA helicase ______ DNA ligase

___3___ primase ___2___ single-strand binding protein ___3___ sliding clamp ___3___ RNA primers ___1___ leading strand ___2___ lagging strand ___2___ Okazaki fragments ___3___ DNA helicase ___2___ DNA ligase

A covalent bond between two atoms is formed as a result of the ______________. (a) sharing of electrons. (b) loss of electrons from both atoms. (c) loss of a proton from one atom. (d) transfer of electrons from one atom to the other.

a

Although covalent bonds are 10-100 times stronger than noncovalent interactions, many biological processes depend upon the number and type of noncovalent interactions between molecules. Which of the noncovalent interactions below will contribute most to the strong and specific binding of two molecules, such as a pair of proteins? (a) electrostatic attractions (b) hydrogen bonds (c) hydrophobic interactions (d) Van der Waals attractions

a

Aromatic carbon compounds such as benzene are planar and very stable. Double- bond character extends around the entire ring, which is why it is often drawn as a hexagon with a circle inside. This characteristic is caused by electron __________. (a) resonance. (b) pairing. (c) partial charge. (d) stacking.

a

By definition, prokaryotic cells do not possess __________. (a) a nucleus. (b) replication machinery. (c) ribosomes. (d) membrane bilayers.

a

Cyclic AMP (cAMP) is a small molecule that associates with its binding site with a high degree of specificity. Which types of noncovalent interactions are the most important for providing the "hand in a glove" binding of cAMP? (a) hydrogen bonds (b) electrostatic interactions (c) van der Waals interactions (d) hydrophobic interactions

a

DNA polymerase catalyzes the joining of a nucleotide to a growing DNA strand. What prevents this enzyme from catalyzing the reverse reaction? (a) hydrolysis of pyrophosphate (PPi) to inorganic phosphate (Pi) + Pi (b) release of PPi from the nucleotide (c) hybridization of the new strand to the template (d) loss of ATP as an energy source

a

Drosophila melanogaster is a/an __________. This type of animal is the most abundant of all animal species, making it an appropriate choice as an experimental model. (a) insect (b) bird (c) amphibian (d) mammal

a

During respiration, energy is retrieved from the high-energy bonds found in certain organic molecules. Which of the following, in addition to energy, are the ultimate products of respiration? (a) CO2, H2O (b) CH3, H2O (c) CH2OH, O2 (d) CO2, O2

a

Each nucleotide in DNA and RNA has an aromatic base. What is the principal force that keeps the bases in a polymer from interacting with water? (a) hydrophobic interactions (b) hydrogen bonds (c) covalent bonds (d) van der Waals interactions

a

Eukaryotic cells are able to trigger the release of material from secretory vesicles to the extracellular space using a process called exocytosis. An example of materials commonly released this way is _____________. (a) hormones. (b) nucleic acids. (c) sugars. (d) cytosolic proteins.

a

For the reaction Y!X at standard conditions with [Y] = 1 M and [X] = 1 M, ΔG is initially a large negative number. As the reaction proceeds, [Y] decreases and [X] increases until the system reaches equilibrium. How do the values of ΔG and ΔG° change as the reaction equilibrates? (a) ΔG becomes less negative and ΔG° stays the same. (b) ΔG becomes positive and ΔG° becomes positive. (c) ΔG stays the same and ΔG° becomes less negative. (d) ΔG reaches zero and ΔG° becomes more negative.

a

Globular proteins fold up into compact, spherical structures that have uneven surfaces. They tend to form multisubunit complexes, which also have a rounded shape. Fibrous proteins, in contrast, span relatively large distances within the cell and in the extracellular space. Which of the proteins below is not classified as a fibrous protein? (a) elastase (b) collagen (c) keratin (d) elastin

a

Instead of studying one or two proteins or protein complexes present in the cell at any given time, we can now look at a snapshot of all proteins being expressed in cells being grown in specific conditions. This large-scale, systematic approach to the study of proteins is called _______________. (a) proteomics. (b) structural biology. (c) systems biology. (d) genomics.

a

Isomerization of glucose 1-phosphate to glucose 6-phosphate is energetically favorable. At 37°C, ΔG° = -1.42 log10K. What is the equilibrium constant for this reaction if ΔG° = -1.74 kcal/mole at 37°C? (a) 16.98 (b) 0.09 (c) -0.09 (d) 0.39

a

Many of the breakthroughs in modern biology came after Watson and Crick published their model of DNA in 1953. However, chromosomes were identified earlier. In what decade did scientists first identify chromosomes? (a) 1880s (b) 1920s (c) 1940s (d) 1780s

a

Many of the mechanisms that cells use for maintenance and reproduction were first studied at the molecular level in bacteria. Which bacterial species had a central role in advancing the field of molecular biology? (a) E. coli (b) D. melanogaster (c) S. pombe (d) C. elegans

a

Methylation and acetylation are common changes made to histone H3, and the specific combination of these changes is sometimes referred to as the "histone code." Which of the following patterns will probably lead to gene silencing? (a) lysine 9 methylation (b) lysine 4 methylation and lysine 9 acetylation (c) lysine 14 acetylation (d) lysine 9 acetylation and lysine 14 acetylation

a

Mitotic chromosomes are _____ times more compact than a DNA molecule in its extended form. (a) 10,000 (b) 100,000 (c) 1000 (d) 100

a

Nonhomologous end joining can result in all but which of the following? (a) the recovery of lost nucleotides on a damaged DNA strand (b) the interruption of gene expression (c) loss of nucleotides at the site of repair (d) translocations of DNA fragments to an entirely different chromosome

a

Oligosaccharides are short sugar polymers that can become covalently linked to proteins and lipids through condensation reactions. These modified proteins and lipids are called glycoproteins and glycolipids, respectively. Within a protein, which of the amino acids (shown in Figure Q2-48) is the most probable target for this type of modification? (a) serine (b) glycine (c) phenylalanine (d) methionine

a

Oxidation is a favorable process in an aerobic environment, which is the reason cells are able to derive energy from the oxidation of macromolecules. Once carbon has been oxidized to _______________, its most stable form, it can only cycle back into the organic portion of the carbon cycle through __________________. (a) CO2, photosynthesis. (b) CH3, combustion. (c) CO2, respiration. (d) CO, reduction.

a

Polypeptides are synthesized from amino acid building blocks. The condensation reaction between the growing polypeptide chain and the next amino acid to be added involves the loss of ________________. (a) a water molecule. (b) an amino group. (c) a carbon atom. (d) a carboxylic acid group.

a

Protein folding can be studied using a solution of purified protein and a denaturant (urea), a solvent that interferes with noncovalent interactions. Which of the following is observed after the denaturant is removed from the protein solution? (a) The polypeptide returns to its original conformation. (b) The polypeptide remains denatured. (c) The polypeptide forms solid aggregates and precipitates out of solution. (d) The polypeptide adopts a new, stable conformation.

a

Proteins can assemble to form large complexes that work coordinately, like moving parts inside a single machine. Which of the following steps in modulating the activity of a complex protein machine is least likely to be directly affected by ATP or GTP hydrolysis? (a) translation of protein components (b) conformational change of protein components (c) complex assembly (d) complex disassembly

a

Several experiments were required to demonstrate how traits are inherited. Which scientist or team of scientists first demonstrated that cells contain some component that can be transferred to a new population of cells and permanently cause changes in the new cells? (a) Griffith (b) Watson and Crick (c) Avery, MacLeod, and McCarty (d) Hershey and Chase

a

Sometimes, chemical damage to DNA can occur just before DNA replication begins, not giving the repair system enough time to correct the error before the DNA is duplicated. This gives rise to mutation. If the cytosine in the sequence TCAT is deaminated and not repaired, which of the following is the point mutation you would observe after this segment has undergone two rounds of DNA replication? (a) TTAT (b) TUA T (c) TGA T (d) TAAT

a

Specific regions of eukaryotic chromosomes contain sequence elements that are absolutely required for the proper transmission of genetic information from a mother cell to each daughter cell. Which of the following is not known to be one of these required elements in eukaryotes? (a) terminators of replication (b) origins of replication (c) telomeres (d) centromeres

a

The DNA from two different species can often be distinguished by a difference in the ______________________. (a) ratio of A + T to G + C. (b) ratio of A + G to C + T. (c) ratio of sugar to phosphate. (d) presence of bases other than A, G, C, and T

a

The amino acids glutamine and glutamic acid are shown in Figure Q2-46. They differ only in the structure of their side chains (circled). At pH 7, glutamic acid can participate in molecular interactions that are not possible for glutamine. What types of interactions are these? (a) ionic bonds (b) hydrogen bonds (c) van der Waals interactions (d) covalent bonds

a

The chromosomes we typically see in images are isolated from mitotic cells. These mitotic chromosomes are in the most highly condensed form. Interphase cells contain chromosomes that are less densely packed and __________________________. (a) occupy discrete territories in the nucleus. (b) share the same nuclear territory as their homolog. (c) are restricted to the nucleolus. (d) are completely tangled with other chromosomes.

a

The classic "beads-on-a-string" structure is the most decondensed chromatin structure possible and is produced experimentally. Which chromatin components are not retained when this structure is generated? a. linker histones b. linker DNA c. nucleosome core particles d. core histones

a

The mitochondrial proteins found in the inner membrane are involved in the conversion of ADP to ATP, a source of energy for the cell. This process consumes which of the following substances? (a) oxygen (b) nitrogen (c) sulfur (d) carbon dioxide

a

The net distance a molecule travels through the cytosol via diffusion is relatively short in comparison with the total distance it may need to travel. This is because movement governed by diffusion alone is a ________________ process that is most effective for the dispersion of small molecules over short distances. (a) slow (b) random (c) regulated (d) complicated

a

The process of generating monoclonal antibodies is labor-intensive and expensive. An alternative is to use polyclonal antibodies. A subpopulation of purified polyclonal antibodies that recognize a particular antigen can be isolated by chromatography. Which type of chromatography is used for this purpose? (a) affinity (b) ion-exchange (c) gel-filtration (d) any of the above

a

The repair of mismatched base pairs or damaged nucleotides in a DNA strand requires a multistep process. Which choice below describes the known sequence of events in this process? (a) DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by repair proteins, the gap is filled by DNA polymerase, and the strand is sealed by DNA ligase. (b) DNA repair polymerase simultaneously removes bases ahead of it and polymerizes the correct sequence behind it as it moves along the template. DNA ligase seals the nicks in the repaired strand. (c) DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by an exonuclease, and the gap is repaired by DNA ligase. (d) A nick in the DNA is recognized, DNA repair proteins switch out the wrong base and insert the correct base, and DNA ligase seals the nick.

a

The study of enzymes also includes an examination of how the activity is regulated. Molecules that can act as competitive inhibitors for a specific reaction are often similar in shape and size to the enzyme's substrate. Which variable(s) used to describe enzyme activity will remain the same in the presence and absence of a competitive inhibitor? (a) Vmax (b) V (c) Vmax and Km (d) Km

a

The synthesis of glutamine from glutamic acid requires the production of an activated intermediate followed by a condensation step that completes the process. Both amino acids are shown in Figure Q3-71. Which molecule is added to glutamic acid in the activation step? (a) phosphate (b) NH3 (c) ATP (d) ADP

a

There are 20100 different possible sequence combinations for a protein chain with 100 amino acids. In addition to the amino acid sequence of the protein, what other factors increase the potential for diversity in these macromolecules? (a) free rotation around single bonds during synthesis (b) noncovalent interactions sampled as protein folds (c) the directionality of amino acids being added (d) the planar nature of the peptide bond

a

What information regarding an enzyme-catalyzed reaction is obtained in a plot of the inverse of the initial velocities against the inverse of the corresponding substrate concentrations? (a) 1/Vmax and 1/Km (b) 1/V and 1/[S] (c) Vmax and Km (d) V and [S]

a

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking helicase were used to make the cell extracts? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading-strand elongation (d) lagging-strand completion

a

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking primase were used to make the cell extracts? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading-strand elongation (d) lagging-strand completion

a

Which of the following best describes the mechanism by which chromatin- remodeling complexes "loosen" the DNA wrapped around the core histones? (a) They use energy derived from ATP hydrolysis to change the relative position of the DNA and the core histone octamer. (b) They chemically modify the DNA, changing the affinity between the histone octamer and the DNA. (c) They remove histone H1 from the linker DNA adjacent to the core histone octamer. (d) They chemically modify core histones to alter the affinity between the histone octamer and the DNA.

a

Which of the following elements is least abundant in living organisms? (a) sulfur (b) carbon (c) oxygen (d) nitrogen

a

Which of the following expressions accurately describes the calculation of pH? (a) pH = -log10[H+] (b) pH = log10[H+] (c) pH = -log2[H+] (d) pH = -log10[OH-]

a

Which of the following factors do not influence the length of a covalent bond? (a) the tendency of atoms to fill the outer electron shells (b) the attractive forces between negatively charged electrons and positively charged nuclei (c) the repulsive forces between the positively charged nuclei (d) the minimization of repulsive forces between the two nuclei by the cloud of shared electrons

a

Which of the following globular proteins is used to form filaments as an intermediate step to assembly into hollow tubes? (a) tubulin (b) actin (c) keratin (d) collagen

a

Which of the following is not a feature commonly observed in α helices? (a) left-handedness (b) one helical turn every 3.6 amino acids (c) cylindrical shape (d) amino acid side chains that point outward

a

Which of the following methods would be the most suitable to assess whether your protein exists as a monomer or in a complex? (a) gel-filtration chromatography (b) gel electrophoresis (c) western blot analysis (d) ion-exchange chromatography

a

Which of the following statements about allostery is true? (a) Allosteric regulators are often products of other chemical reactions in the same biochemical pathway. (b) Allosteric regulation is always used for negative regulation of enzyme activity. (c) Enzymes are the only types of proteins that are subject to allosteric regulation. (d) Binding of allosteric molecules usually locks an enzyme in its current conformation, such that the enzyme cannot adopt a different conformation.

a

Which subatomic particles contribute to the atomic number for any given element? (a) protons (b) protons and neutrons (c) neutrons (d) protons and electrons

a

A pregnant mouse is exposed to high levels of a chemical. Many of the mice in her litter are deformed, but when they are interbred with each other, all their offspring are normal. Which two of the following statements could explain these results? (a) In the deformed mice, somatic cells but not germ cells were mutated. (b) The original mouse's germ cells were mutated. (c) In the deformed mice, germ cells but not somatic cells were mutated. (d) The toxic chemical affects development but is not mutagenic.

a and d

Which statement is NOT true about mutations

a mutation is a result of sexual reproduction

In the first stage of photosynthesis, light energy is converted into what other form of energy? (a) electrical (b) chemical (c) potential (d) kinetic

a or d

Which of the following are examples of isomers? (a) glucose and galactose (b) alanine and glycine (c) adenine and guanine (d) glycogen and cellulose

a) glucose and galactose are both six-carbon sugars and thus both have the formula C6H12O6. They are therefore isomers of each other. Adenine and guanine are bases containing different numbers of nitrogen and oxygen atoms. Glycogen and cellulose are different polymers of glucose. Alanine and glycine are amino acids with quite different side chains: a methyl group and a hydrogen atom, respectively.

which elements form stable but reactive diatomic gases?

a) nitrogen, oxygen

Although there are many distinct prokaryotic species, most have a small range of shapes, sizes, and growth rates. Which of the following characteristics are not observed in prokaryotes? (a) a highly structured cytoplasm (b) endoplasmic reticulum (c) the ability to divide rapidly (d) a cell wall

a,b

There are 20 _________

amino acids

A. thaliana, or Arabidopsis, is a common weed. Biologists have selected it over hundreds of thousands of other flowering plant species to serve as an experimental model organism because __________________. (a) it can withstand extremely cold climates. (b) it can reproduce in 8-10 weeks. (c) it produces thousands of offspring per plant. (d) Both (b) and (c) are true.

b

Because there are four different monomer building blocks that can be used to assemble RNA polymers, the number of possible sequence combinations that can be created for an RNA molecule made of 100 nucleotides is _______. (a) 1004 (b) 4100 (c) 4 × 100 (d) 100/4

b

Both DNA and RNA are synthesized by covalently linking a nucleoside triphosphate to the previous nucleotide, constantly adding to a growing chain. In the case of DNA, the new strand becomes part of a stable helix. The two strands are complementary in sequence and antiparallel in directionality. What is the principal force that holds these two strands together? (a) ionic interactions (b) hydrogen bonds (c) covalent bonds (d) van der Waals interactions

b

Brewer's yeast, apart from being an irreplaceable asset in the brewery and in the bakery, is an experimental organism used to study eukaryotic cells. However, it does have some limitations. Which of the processes below cannot be studied in yeast? (a) DNA replication (b) cell motility (c) exocytosis (d) cell division

b

Caenorhabditis elegans is a nematode. During its development, it produces more than 1000 cells. However, the adult worm has only 959 somatic cells. The process by which 131 cells are specifically targeted for destruction is called ______________. (a) directed cell pruning. (b) programmed cell death. (c) autophagy. (d) necrosis.

b

Carbon 14 is an unstable isotope of carbon that decays very slowly. Compared to the common, stable carbon 12 isotope, carbon 14 has two additional ______________. (a) electrons. (b) neutrons. (c) protons. (d) ions.

b

Catalysts are molecules that lower the activation energy for a given reaction. Cells produce their own catalysts called _____________. (a) proteins. (b) enzymes. (c) cofactors. (d) complexes.

b

Chemical reactions carried out by living systems depend on the ability of some organisms to capture and use atoms from nonliving sources in the environment. The specific subset of these reactions that break down nutrients in food can be described as _____________. (a) metabolic. (b) catabolic. (c) anabolic. (d) biosynthetic.

b

Coiled-coils are typically found in proteins that require an elongated structural framework. Which of the following proteins do you expect to have a coiled-coil domain? (a) insulin (b) collagen (c) myoglobin (d) porin

b

DNA and RNA are different types of nucleic acid polymer. Which of the following is true of DNA but not true of RNA? (a) It contains uracil. (b) It contains thymine. (c) It is single-stranded. (d) It has 5′-to-3′ directionality.

b

DNA polymerases are processive, which means that they remain tightly associated with the template strand while moving rapidly and adding nucleotides to the growing daughter strand. Which piece of the replication machinery accounts for this characteristic? (a) helicase (b) sliding clamp (c) single-strand binding protein (d) primase

b

Determining a protein's sequence, site of covalent modification, or entire three- dimensional structure requires the careful analysis of complex data sets. Which of the data sets below would you have to interpret to solve the structure of a protein by using X-ray crystallography?

b

Enzymes facilitate reactions in living systems. Figure Q3-29 presents an energy diagram for the reaction X!Y. The solid line in the energy diagram represents changes in energy as the reactant is converted to product under standard conditions. The dashed line shows changes observed when the same reaction takes place in the presence of a dedicated enzyme. Which equation below indicates how the presence of an enzyme affects the activation energy of the reaction (catalyzed versus uncatalyzed)? (a) d-c versus b-c (b) d-a versus b-a (c) a + d versus a + b (d) d-c versus b-a

b

Figure Q5-45 clearly depicts the nucleolus, a nuclear structure that looks like a large, dark region when stained. The other dark, speckled regions in this image are the locations of particularly compact chromosomal segments called ____________. (a) euchromatin. (b) heterochromatin. (c) nuclear pores. (d) nucleosomes.

b

Fred Griffith studied two strains of Streptococcus pneumonia, one that causes a lethal infection when injected into mice, and a second that is harmless. He observed that pathogenic bacteria that have been killed by heating can no longer cause an infection. But when these heat-killed bacteria are mixed with live, harmless bacteria, this mixture is capable of infecting and killing a mouse. What did Griffith conclude from this experiment? (a) The infectious strain cannot killed by heating. (b) The heat-killed pathogenic bacteria "transformed" the harmless strain into a lethal one. (c) The harmless strain somehow revived the heat-killed pathogenic bacteria. (d) The mice had lost their immunity to infection with S. pneumoniae.

b

Homologous recombination is an important mechanism in which organisms use a "backup" copy of the DNA as a template to fix double-strand breaks without loss of genetic information. Which of the following is not necessary for homologous recombination to occur? (a) 3′ DNA strand overhangs (b) 5′ DNA strand overhangs (c) a long stretch of sequence similarity (d) nucleases

b

How many replication forks are formed when an origin of replication is opened? (a) 1 (b) 2 (c) 3 (d) 4

b

In somatic cells, if a base is mismatched in one new daughter strand during DNA replication, and is not repaired, what fraction of the DNA duplexes will have a permanent change in the DNA sequence after the second round of DNA replication? (a) 1/2 (b) 1/4 (c) 1/8 (d) 1/16

b

Initiator proteins bind to replication origins and disrupt hydrogen bonds between the two DNA strands being copied. Which of the factors below does not contribute to the relative ease of strand separation by initiator proteins? (a) replication origins are rich in A-T base pairs (b) the reaction can occur at room temperature (c) they only separate a few base pairs at a time (d) once opened, other proteins of the DNA replication machinery bind to the origin

b

Interphase chromosomes are about______ times less compact than mitotic chromosomes, but still are about______ times more compact than a DNA molecule in its extended form. (a) 10, 1000 (b) 20, 500 (c) 5, 2000 (d) 50, 200

b

Mitotic chromosomes were first visualized with the use of very simple tools: a basic light microscope and some dyes. Which of the following characteristics of mitotic chromosomes reflects how they were named? (a) motion (b) color (c) shape (d) location

b

Most eukaryotic cells only express 20-30% of the genes they possess. The formation of heterochromatin maintains the other genes in a transcriptionally silent (unexpressed) state. Which histone modification directs the formation of the most common type of heterochromatin? (a) H3 lysine 4 methylation (b) H3 lysine 9 methylation (c) H3 lysine 14 methylation (d) H3 lysine 27 methylation

b

Oxidation is the process by which oxygen atoms are added to a target molecule. Generally, the atom that is oxidized will experience which of the following with respect to the electrons in its outer shell? (a) a net gain (b) a net loss (c) no change (d) an equal sharing

b

Photosynthesis enables plants to capture the energy from sunlight. In this essential process, plants incorporate the carbon from CO2 into high-energy __________ molecules, which the plant cell mitochondria use to produce ATP. (a) fat (b) sugar (c) protein (d) fiber

b

Proteins bind selectively to small-molecule targets called ligands. The selection of one ligand out of a mixture of possible ligands depends on the number of weak, noncovalent interactions in the protein's ligand-binding site. Where is the binding site typically located in the protein structure? (a) on the surface of the protein (b) inside a cavity on the protein surface (c) buried in the interior of the protein (d) forms on the surface of the protein in the presence of ligand

b

Seed oils are often dehydrogenated and added back into processed foods as partly unsaturated fatty acids. In comparison with the original oil, the new fatty acids have additional double carbon-carbon bonds, replacing what were once single bonds. This process could also be described as _____________. (a) isomerization. (b) oxidation. (c) reduction. (d) protonation.

b

Sickle-cell anemia is an example of an inherited disease. Individuals with this disorder have misshapen (sickle-shaped) red blood cells caused by a change in the sequence of the β-globin gene. What is the nature of the change? (a) chromosome loss (b) base-pair change (c) gene duplication (d) base-pair insertion

b

Stepwise condensation of linear DNA happens in five different packing processes. Which of the following four processes has a direct requirement for histone H1? (a) formation of "beads-on-a-string" (b) formation of the 30-nm fiber (c) looping of the 30-nm fiber (d) packing of loops to form interphase chromosomes

b

The DNA duplex consists of two long covalent polymers wrapped around each other many times over their entire length. The separation of the DNA strands for replication causes the strands to be "overwound" in front of the replication fork. How does the cell relieve the torsional stress created along the DNA duplex during replication? (a) Nothing needs to be done because the two strands will be separated after replication is complete. (b) Topoisomerases break the covalent bonds of the backbone allowing the local unwinding of DNA ahead of the replication fork. (c) Helicase unwinds the DNA and rewinds it after replication is complete. (d) DNA repair enzymes remove torsional stress as they replace incorrectly paired bases.

b

The N-terminal tail of histone H3 can be extensively modified, and depending on the number, location, and combination of these modifications, these changes may promote the formation of heterochromatin. What is the result of heterochromatin formation? (a) increase in gene expression (b) gene silencing (c) recruitment of remodeling complexes (d) displacement of histone H1

b

The classic experiments conducted by Meselson and Stahl demonstrated that DNA replication is accomplished by employing a ________________ mechanism. (a) continuous (b) semiconservative (c) dispersive (d) conservative

b

The cytoskeleton provides support, structure, motility, and organization, and it forms tracks to direct organelle and vesicle transport. Which of the cytoskeletal elements listed below is the thickest? (a) actin filaments (b) microtubules (c) intermediate filaments (d) none of the above (all the same thickness)

b

The first task you are assigned in your summer laboratory job is to prepare a concentrated NaOH stock solution. The molecular weight of NaOH is 40. How many grams of solid NaOH will you need to weigh out to obtain a 500 mL solution that has a concentration of 10 M? (a) 800 g (b) 200 g (c) 400 g (d) 160 g

b

The human genome is a diploid genome. However, when germ-line cells produce gametes, these specialized cells are haploid. What is the total number of chromosomes found in each of the gametes (egg or sperm) in your body? (a) 22 (b) 23 (c) 44 (d) 46

b

The information stored in the DNA sequences is used directly as a template to make ___________. (a) lipids. (b) RNA. (c) polypeptides. (d) carbohydrates.

b

The manner in which a gene sequence is related to its respective protein sequence is referred to as the _________ code. (a) protein (b) genetic (c) translational (d) expression

b

The nucleus, an organelle found in eukaryotic cells, confines the __________, keeping them separated from other components of the cell. (a) lysosomes (b) chromosomes (c) peroxisomes (d) ribosomes

b

The phosphorylation of a protein is typically associated with a change in activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in ______________. (a) membrane association. (b) protein degradation. (c) protein secretion. (d) nuclear translocation.

b

The potential energy stored in high-energy bonds is commonly harnessed when the bonds are split by the addition of _______________ in a process called _____________. (a) ATP, phosphorylation. (b) water, hydrolysis. (c) hydroxide, hydration. (d) acetate, acetylation.

b

The second law of thermodynamics states that the disorder in any system is always increasing. In simple terms, you can think about dropping NaCl crystals into a glass of water. The solvation and diffusion of ions is favored because there is an increase in _____________. (a) pH. (b) entropy. (c) ions. (d) stored energy.

b

The variations in the physical characteristics between different proteins are influenced by the overall amino acid compositions, but even more important is the unique amino acid ______________. (a) number. (b) sequence. (c) bond. (d) orientation.

b

Two or three α helices can sometimes wrap around each other to form coiled- coils. The stable wrapping of one helix around another is typically driven by ________________ interactions. (a) hydrophilic (b) hydrophobic (c) van der Waals (d) ionic

b

What is the smallest distance two points can be separated and still resolved using light microscopy? (a) 20 nm (b) 0.2 μm (c) 2 μm (d) 200 μm

b

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking single-strand binding protein were used to make the cell extracts? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading-strand elongation (d) lagging-strand completion

b

When elemental sodium is added to water, the sodium atoms ionize spontaneously. Uncharged Na becomes Na+. This means that the Na atoms have been _____________. (a) protonated. (b) oxidized. (c) hydrogenated. (d) reduced.

b

Which combination of answers best completes the following statement: When atoms are held together by ___________ __________, they are typically referred to as _________. (a) hydrogen bonds, molecules. (b) ionic interactions, salts. (c) ionic interactions, molecules. (d) double bonds, nonpolar.

b

Which of the following choices best describes the role of the lysosome? (a) transport of material to the Golgi (b) clean-up, recycling, and disposal of macromolecules (c) sorting of transport vesicles (d) the storage of excess macromolecules

b

Which of the following is not a chemical modification commonly found on core histone N-terminal tails? (a) methylation (b) hydroxylation (c) phosphorylation (d) acetylation

b

Which of the following is not a feature commonly observed in β sheets? (a) antiparallel regions (b) coiled-coil patterns (c) extended polypeptide backbone (d) parallel regions

b

Which of the following is true for a reaction at equilibrium? (a) ΔG=ΔG° (b) ΔG° + RT ln [X]/[Y] = 0 (c) RT ln [X]/[Y] = 0 (d) ΔG + ΔG° = RT ln [X]/[Y]

b

Which of the following methods would be the most suitable to assess the relative purity of a protein in a sample you have prepared? (a) gel-filtration chromatography (b) gel electrophoresis (c) western blot analysis (d) ion-exchange chromatography

b

Which of the following monomer building blocks is necessary to assemble selectively permeable boundaries around and inside cells? (a) sugars (b) fatty acids (c) amino acids (d) nucleotides

b

Which of the following organelles has both an outer and an inner membrane? (a) endoplasmic reticulum (b) mitochondrion (c) lysosome (d) peroxisome

b

Which of the following statements about sequence proofreading during DNA replication is false? (a) The exonuclease activity is in a different domain of the DNA polymerase. (b) The exonuclease activity cleaves DNA in the 5′-to-3′ direction. (c) The DNA proofreading activity occurs concomitantly with strand elongation. (d) If an incorrect base is added, it is "unpaired" before removal.

b

Which of the following statements is not an accurate statement about thymine dimers? (a) Thymine dimers can cause the DNA replication machinery to stall. (b) Thymine dimers are covalent links between thymidines on opposite DNA strands. (c) Prolonged exposure to sunlight causes thymine dimers to form. (d) Repair proteins recognize thymine dimers as a distortion in the DNA backbone.

b

Which of the following statements would not be true of a favorable binding equilibrium? (a) The free-energy change is negative for the system. (b) The concentration of the complex remains lower than the concentration of the unbound components. (c) The complex dissociation rate is slower than the rate for component association. (d) The binding energy for the association is large and negative.

b

Which statement is NOT true about the events/conclusions from studies during the mid-1800s surrounding the discovery of cells? (a) Cells came to be known as the smallest universal building block of living organisms. (b) Scientists came to the conclusion that new cells can form spontaneously from the remnants of ruptured cells. (c) Light microscopy was essential in demonstrating the commonalities between plant and animal tissues. (d) New cells arise from the growth and division of previously existing cells.

b

Which subatomic particles contribute to the atomic mass for any given element? (a) protons (b) protons and neutrons (c) neutrons (d) protons and electrons

b

Your body extracts energy from the food you ingest by catalyzing reactions that essentially "burn" the food molecules in a stepwise fashion. What is another way to describe this process? (a) reduction (b) oxidation (c) dehydration (d) solvation

b

The variety and arrangement of chemical groups on monomer subunits contribute to the conformation, reactivity, and surface of the macromolecule into which they become incorporated. What type of chemical group is circled on the nucleotide shown in Figure Q2-45? a) pyrophosphate b) phosphoric c) carbonyl d) carboxyl

b) phosphoryl

The human immune system produces __________________ of different immunoglobulins, also called __________________, which enable the immune system to recognize and fight germs by specifically binding one or a few related __________________. The hypervariable structural element that forms the ligand-binding site is comprised of several __________________. Purified antibodies are useful for a variety of experimental purposes, including protein purification using __________________ chromatography.

billions, antibodies, antigens, loops, affinity

Although the chromatin structure of interphase and mitotic chromosomes is very compact, DNA-binding proteins and protein complexes must be able to gain access to the DNA molecule. Chromatin-remodeling complexes provide this access by __________________. (a) recruiting other enzymes. (b) modifying the N-terminal tails of core histones. (c) using the energy of ATP hydrolysis to move nucleosomes. (d) denaturing the DNA by interfering with hydrogen-bonding between base pairs.

c

Antibody production is an indispensible part of our immune response, but it is not the only defense our bodies have. Which of the following is observed during an infection that is not a result of antibody-antigen interactions? (a) B cell proliferation (b) aggregation of viral particles (c) systemic temperature increase (d) antibody secretion

c

At first glance, it may seem that living systems are able to defy the second law of thermodynamics. However, on closer examination, it becomes clear that although cells create organization from raw materials in the environment, they also contribute to disorder in the environment by releasing _____________. (a) water. (b) radiation. (c) heat. (d) proteins.

c

Beside the distortion in the DNA backbone caused by a mismatched base pair, what additional mark is there on eukaryotic DNA to indicate which strand needs to be repaired? (a) a nick in the template strand (b) a chemical modification of the new strand (c) a nick in the new strand (d) a sequence gap in the new strand

c

Chemical reactions that lead to a release of free energy are referred to as "energetically favorable." Another way to describe these reactions is: _____________. (a) uphill. (b) uncatalyzed. (c) spontaneous. (d) activated.

c

Choose the phrase that best completes this sentence: Microtubules ____________ and are required to pull duplicated chromosomes to opposite poles of dividing cells. (a) generate contractile forces (b) are intermediate in thickness (c) can rapidly reorganize (d) are found in especially large numbers in muscle cells

c

DNA replication is considered semiconservative because ____________________________. (a) after many rounds of DNA replication, the original DNA double helix is still intact. (b) each daughter DNA molecule consists of two new strands copied from the parent DNA molecule. (c) each daughter DNA molecule consists of one strand from the parent DNA molecule and one new strand. (d) new DNA strands must be copied from a DNA template.

c

Double covalent bonds are both shorter and stronger than single covalent bonds, but they also limit the geometry of the molecule because they ____________________. (a) create a new arrangement of electron shells. (b) change the reactivity of the bonded atoms. (c) limit the rotation of the bonded atoms. (d) prevent additional bonds from being formed with the bonded atoms.

c

Energy cannot be created or destroyed, but it can be converted into other types of energy. Cells use potential kinetic energy to generate stored chemical energy in the form of activated carrier molecules, which are often employed to join two molecules together in _____________ reactions. (a) oxidation (b) hydrolysis (c) condensation (d) reduction

c

Energy required by the cell is generated in the form of ATP. ATP is hydrolyzed to power many of the cellular processes, increasing the pool of ADP. As the relative amount of ADP molecules increases, they can bind to glycolytic enzymes, which will lead to the production of more ATP. The best way to describe this mechanism of regulation is ___________. (a) feedback inhibition. (b) oxidative phosphorylation. (c) allosteric activation. (d) substrate-level phosphorylation.

c

Even though cellular macromolecules contain a large number of carbon and hydrogen atoms, they are not all spontaneously converted into CO2 and H2O. This absence of spontaneous combustion is due to the fact that biological molecules are relatively __________ and an input of energy is required to reach lower energy states. (a) large (b) polar (c) stable (d) unstable

c

How do changes in histone modifications lead to changes in chromatin structure? (a) They directly lead to changes in the positions of the core histones. (b) They change the affinity between the histone octamer and the DNA. (c) They help recruit other proteins to the chromatin. (d) They cause the histone N-terminal tails to become hyperextended.

c

If the isotope 32S has 16 protons and 16 neutrons, how many protons, neutrons, and electrons will the isotope 35S have, respectively? (a) 16, 20, 15 (b) 16, 19, 15 (c) 16, 19, 16 (d) 16, 19, 17

c

In addition to the repair of DNA double-strand breaks, homologous recombination is a mechanism for generating genetic diversity by swapping segments of parental chromosomes. During which process does swapping occur? (a) DNA replication (b) DNA repair (c) meiosis (d) transposition

c

Mitochondria contain their own genome, are able to duplicate, and actually divide on a different time line from the rest of the cell. Nevertheless, mitochondria cannot function for long when isolated from the cell because they are __________________. (a) viruses. (b) parasites. (c) endosymbionts. (d) anaerobes.

c

Mitochondria perform cellular respiration, a process that uses oxygen, generates carbon dioxide, and produces chemical energy for the cell. Which answer below indicates a correct pairing of material "burned" and the form of energy produced during cellular respiration? (a) fat, ADP (b) sugar, fat (c) sugar, ATP (d) fat, protein

c

Nucleosomes are formed when DNA wraps _____ times around the histone octamer in a ______ coil. (a) 2.0, right-handed (b) 2.5, left-handed (c) 1.7, left-handed (d) 1.3, right-handed

c

Oxidation and reduction states are relatively easy to determine for metal ions, because there is a measurable net charge. In the case of carbon compounds, oxidation and reduction depend on the nature of polar covalent bonds. Which of the following is the best way to describe these types of bond? (a) hydrogen bonds in a nonpolar solution (b) covalent bonds in an aqueous solution (c) unequal sharing of electrons across a covalent bond (d) equal sharing of electrons across a covalent bond

c

Select the option that best completes the following statement: Nonhomologous end joining is a process by which a double-stranded DNA end is joined ___________________. (a) to a similar stretch of sequence on the complementary chromosome. (b) after repairing any mismatches. (c) to the nearest available double-stranded DNA end. (d) after filling in any lost nucleotides, helping to maintain the integrity of the DNA sequence.

c

Several members of the same family were diagnosed with the same kind of cancer when they were unusually young. Which one of the following is the most likely explanation for this phenomenon? It is possible that the individuals with the cancer have _______________________. (a) inherited a cancer-causing gene that suffered a mutation in an ancestor's somatic cells. (b) inherited a mutation in a gene required for DNA synthesis. (c) inherited a mutation in a gene required for mismatch repair. (d) inherited a mutation in a gene required for the synthesis of purine nucleotides.

c

Some prokaryotes can live by utilizing entirely inorganic materials. Which of the following inorganic molecules would you predict to be the predominant building block for fats, sugars, and proteins? (a) O2 (b) N2 (c) CO2 (d) H2

c

Sometimes, chemical damage to DNA can occur just before DNA replication begins, not giving the repair system enough time to correct the error before the DNA is duplicated. This gives rise to mutation. If the adenosine in the sequence TCAT is depurinated and not repaired, which of the following is the point mutation you would observe after this segment has undergone two rounds of DNA replication? (a) TCGT (b) TAT (c) TCT (d) TGTT

c

The biosynthetic pathway for the two amino acids E and H is shown schematically in Figure Q4-60. You are able to show that E inhibits enzyme V, and H inhibits enzyme X. Enzyme T is most likely to be subject to feedback inhibition by __________________ alone. (a) H (b) B (c) C (d) E

c

The chromatin structure in eukaryotic cells is much more complicated than that observed in prokaryotic cells. This is thought to be the reason that DNA replication occurs much faster in prokaryotes. How much faster is it? (a) 2× (b) 5× (c) 10× (d) 100×

c

The core histones are small, basic proteins that have a globular domain at the C- terminus and a long, extended conformation at the N-terminus. Which of the following is not true of the N-terminal "tail" of these histones? (a) It is subject to covalent modifications. (b) It extends out of the nucleosome core. (c) It binds to DNA in a sequence-specific manner. (d) It helps DNA pack tightly.

c

The equilibrium constant (K) for the reaction Y!X can be expressed with respect to the concentrations of the reactant and product molecules. Which of the expressions below shows the correct relationship between K, [Y], and [X]? (a) K = [Y]/[X] (b) K = [Y] * [X] (c) K = [X]/[Y] (d) K = [X] - [Y]

c

The equilibrium constant for complex formation between molecules A and B will depend on their relative concentrations, as well as the rates at which the molecules associate and dissociate. The association rate will be larger than the dissociation rate when complex formation is favorable. The energy that drives this process is referred to as ___________. (a) dissociation energy. (b) association energy. (c) binding energy. (d) releasing energy.

c

The graph in Figure Q3-52 illustrates the relationship between reaction rates and substrate concentration for an enzyme-catalyzed reaction. What does the Km value indicate with respect to enzyme-substrate interactions? (a) the maximum rate of catalysis (b) the number of enzyme active sites (c) the enzyme-substrate binding affinity (d) the equilibrium rate of catalysis

c

The graph in Figure Q3-53 illustrates the change in the rate of an enzyme- catalyzed reaction as the concentration of substrate is increased. Which of the values listed below is used to calculate the enzyme turnover number? (a) 1⁄2Vmax (b) Km (c) Vmax (d) Vmax - Km

c

The process of DNA replication requires that each of the parental DNA strands be used as a ___________________ to produce a duplicate of the opposing strand. (a) catalyst (b) competitor (c) template (d) copy

c

The process of sorting human chromosome pairs by size and morphology is called karyotyping. A modern method employed for karyotyping is called chromosome painting. How are individual chromosomes "painted"? (a) with a laser (b) using fluorescent antibodies (c) using fluorescent DNA molecules (d) using green fluorescent protein

c

The small molecule cyclic AMP (cAMP) takes about 0.2 second to diffuse 10 μm, on average, in a cell. Suppose that cAMP is produced near the plasma membrane on one end of the cell; how long will it take for this cAMP to diffuse through the cytosol and reach the opposite end of a very large cell, on average? Assume that the cell is 200 μm in diameter. (a) 4 seconds (b) 16 seconds (c) 80 seconds (d) 200 seconds

c

What type of macromolecule helps package DNA in eukaryotic chromosomes? (a) lipids (b) carbohydrates (c) proteins (d) RNA

c

When there is a well-established segment of heterochromatin on an interphase chromosome, there is usually a special barrier sequence that prevents the heterochromatin from expanding along the entire chromosome. Gene A, which is normally expressed, has been moved by DNA recombination near an area of heterochromatin. None of the daughter cells produced after this recombination event express gene A, even though its DNA sequence is unchanged. What is the best way to describe what has happened to the function of gene A in these cells? (a) barrier destruction (b) heterochromatization (c) epigenetic inheritance (d) euchromatin depletion

c

When there is an excess of nutrients available in the human body, insulin is released to stimulate the synthesis of glycogen from glucose. This is a specific example of a(n) __________ process, a general process in which larger molecules are made from smaller molecules. (a) metabolic (b) catabolic (c) anabolic (d) biosynthetic

c

Which DNA base pair is represented in Figure Q5-18? (a) A-T (b) T-A (c) G-C (d) C-G

c

Which of the following is not true of molecular chaperones? (a) They assist polypeptide folding by helping the folding process follow the most energetically favorable pathway. (b) They can isolate proteins from other components of the cells until folding is complete. (c) They can interact with unfolded polypeptides in a way that changes the final fold of the protein. (d) They help streamline the protein-folding process by making it a more efficient and reliable process inside the cell.

c

Which of the following mechanisms best describes the manner in which lysozyme lowers the energy required for its substrate to reach its transition-state conformation? (a) by binding two molecules and orienting them in a way that favors a reaction between them (b) by altering the shape of the substrate to mimic the conformation of the transition state (c) by speeding up the rate at which water molecules collide with the substrate (d) by binding irreversibly to the substrate so that it cannot dissociate

c

Which of the following methods used to study proteins is limited to proteins with a molecular mass of 50 kD or less? (a) X-ray crystallography (b) fingerprinting (c) nuclear magnetic resonance (d) mass spectroscopy

c

Which of the following methods would be the most suitable to assess levels of expression of your target protein in different cell types? (a) gel-filtration chromatography (b) gel electrophoresis (c) western blot analysis (d) ion-exchange chromatography

c

Which of the following structural characteristics is not normally observed in a DNA duplex? (a) purine-pyrimidine pairs (b) external sugar-phosphate backbone (c) uniform left-handed twist (d) antiparallel strands

c

Which subatomic particles can vary between isotopes of the same element, without changing the observed chemical properties? (a) electrons (b) protons and neutrons (c) neutrons (d) neutrons and electrons

c

You are a virologist interested in studying the evolution of viral genomes. You are studying two newly isolated viral strains and have sequenced their genomes. You find that the genome of strain 1 contains 25% A, 55% G, 20% C, and 10% T. You report that you have isolated a virus with a single-stranded DNA genome. Based on what evidence can you make this conclusion? (a) single-stranded genomes always have a large percentage of purines (b) using the formula: G - A = C + T (c) Double-stranded genomes have equal amounts of A and T (d) Single-stranded genomes have a higher rate of mutation

c

Zebrafish (Danio rerio) are especially useful in the study of early development because their embryos ______________. (a) are exceptionally large. (b) develop slowly. (c) are transparent. (d) are pigmented.

c

__________ are fairly small organelles that provide a safe place within the cell to carry out certain biochemical reactions that generate harmful, highly reactive oxygen species. These chemicals are both generated and broken down in the same location. (a) Nucleosomes (b) Lysosomes (c) Peroxisomes (d) Endosomes

c

When the polymer X-X-X... is broken down into monomers, it is "phosphorylyzed" rather than hydrolyzed, in the following repeated reaction: X-X-X... + P->X-P + X-X... (reaction 1) Given the ΔG° values of the reactions listed in the following table, what is the expected ratio of X-phosphate (X-P) to free phosphate (P) at equilibrium for reaction 1? (a) 1:106 (b) 1:104 (c) 1:1 (d) 104:1 X-X-X... + H2O -> X + X-X... X + ATP -> X-P + ADP ATP + H2O -> ADP + P DG° = - 4.5 kcal/mole DG° = -2.8 kcal/mole DG° = -7.3 kcal/mole

c. 1:1 b/c the delta G values are additive

Which of the following can be described as the smallest living unit?

cell

In eukaryotic __________________, DNA is complexed with proteins to form __________________. The paternal and maternal copies of human Chromosome 1 are __________________, whereas the paternal copy of Chromosome 1 and the maternal copy of Chromosome 3 are __________________. Cytogeneticists can determine large-scale chromosomal abnormalities by looking at a patient's __________________. Fluorescent molecules can be used to paint a chromosome, by a technique that employs DNA __________________, and thereby to identify each chromosome by microscopy.

chromosomes, chromatin, homologous, non homologous, karyotype, hybridization

A cell's genome________

contains all of a cell's DNA

A chemical reaction is defined as spontaneous if there is a net loss of free energy during the reaction process. However, spontaneous reactions do not always occur rapidly. Favorable biological reactions require ______________ to selectively speed up reactions and meet the demands of the cell. (a) heat (b) ATP (c) ions (d) enzymes

d

Activated carriers are small molecules that can diffuse rapidly and be used to drive biosynthetic reactions in the cell. Their energy is stored in a readily transferable form such as high-energy electrons or chemical groups. Which of the molecules below is the most widely used activated carrier? (a) FADH2 Initial rate of reaction (b) NADH (c) NADPH (d) ATP

d

An (a) sharing of electrons. ionic bond between two atoms is formed as a result of the ______________. (b) loss of electrons from both atoms. (c) loss of a proton from one atom. (d) transfer of electrons from one atom to the other.

d

Avogadro's number, calculated from the atomic weight of hydrogen, tells us how many atoms or molecules are in a mole. The resulting base for all calculations of moles and molarity (how many molecules are present when you weigh out a substance or measure from a stock solution) is the following: 1 g of hydrogen atoms = 6 × 1023 hydrogen atoms = 1 mole of hydrogen Sulfur has a molecular weight of 32. How many moles and atoms are there in 120 grams of sulfur? (a) 3.75 and 6 × 1023 (b) 32 and 6 × 1023 (c) 1.75 and 1.05 ×1024 (d) 3.75 and 2.25 × 1024

d

Biologists cannot possibly study all living species. Instead, they try to understand cell behavior by studying a select subset of them. Which of the following characteristics are useful in an organism chosen for use as a model in laboratory studies? (a) amenability to genetic manipulation (b) ability to grow under controlled conditions (c) rapid rate of reproduction (d) all of the above

d

Cell biologists employ targeted fluorescent dyes or modified fluorescent proteins in both standard fluorescence microscopy and confocal microscopy to observe specific details in the cell. Even though fluorescence permits better visualization, the resolving power is essentially the same as that of a standard light microscope because the resolving power of a microscope is limited by the __________ of light. (a) absorption (b) intensity (c) filtering (d) wavelength

d

Cells require one particular monosaccharide as a starting material to synthesize nucleotide building blocks. Which of the monosaccharides below fills this important role? (a) glucose (b) fructose (c) ribulose (d) ribose

d

Chloroplasts are found only in eukaryotic cells that carry out photosynthesis: plants and algae. Plants and algae appear green as a result of the presence of chlorophyll. Where is chlorophyll located in the chloroplast? (a) in the first, outer membrane (b) in the space between the first and second membranes (c) in the second, inner membrane (d) in the third, innermost membrane

d

Choose the answer that best fits the following statement: Cholesterol is an essential component of biological membranes. Although it is much smaller than the typical phospholipids and glycolipids in the membrane, it is a(n) _________________ molecule, having both hydrophilic and hydrophobic regions. (a) polar (b) oxygen-containing (c) hydrophobic (d) amphipathic

d

Despite the differences between eukaryotic and prokaryotic cells, prokaryotes have proteins that are distantly related to eukaryotic actin filaments and microtubules. What is likely to be the most ancient function of the cytoskeleton? (a) cell motility (b) vesicle transport (c) membrane support (d) cell division

d

Even though DNA polymerase has a proofreading function, it still introduces errors in the newly synthesized strand at a rate of 1 per 107 nucleotides. To what degree does the mismatch repair system decrease the error rate arising from DNA replication? (a) 2-fold (b) 5-fold (c) 10-fold (d) 100-fold

d

Figure Q3-28 is an energy diagram for the reaction X!Y. Which equation below provides the correct calculation for the amount of free-energy change when X is converted to Y? (a) a + b - c (b) a-b (c) a-c (d) c-a

d

Hershey and Chase used radiolabeled macromolecules to identify the material that contains heritable information. What radioactive material was used to track DNA during this experiment? (a) 3H (b) 14C (c) 35S (d) 32P

d

How does the total number of replication origins in bacterial cells compare with the number of origins in human cells? (a) 1 versus 100 (b) 5 versus 500 (c) 10 versus 1000 (d) 1 versus 10,000

d

Human beings with the inherited disease xeroderma pigmentosum have serious problems with lesions on their skin and often develop skin cancer with repeated exposure to sunlight. What type of DNA damage is not being recognized in the cells of these individuals? (a) chemical damage (b) X-ray irradiation damage (c) mismatched bases (d) ultraviolet irradiation damage

d

If proteins A and B have complementary surfaces, they may interact to form the dimeric complex AB. Which of the following is the correct way to calculate the equilibrium constant for the association between A and B? (a) kon/koff = K (b) K = [A][B]/[AB] (c) K = [AB]/[A][B] (d) (a) and (c)

d

If the genome of the bacterium E. coli requires about 20 minutes to replicate itself, how can the genome of the fruit fly Drosophila be replicated in only 3 minutes? (a) The Drosophila genome is smaller than the E. coli genome. (b) Eukaryotic DNA polymerase synthesizes DNA at a much faster rate than prokaryotic DNA polymerase. (c) The nuclear membrane keeps the Drosophila DNA concentrated in one place in the cell, which increases the rate of polymerization. (d) Drosophila DNA contains more origins of replication than E. coli DNA.

d

In a DNA double helix, _____________________. (a) the two DNA strands are identical. (b) purines pair with purines. (c) thymine pairs with cytosine. (d) the two DNA strands run antiparallel.

d

In the 1940s, proteins were thought to be the more likely molecules to house genetic information. What was the primary reason that DNA was not originally believed to be the genetic material? (a) DNA has a high density of negative charges. (b) Nucleotides were known to be a source of chemical energy for the cell. (c) Both protein and nucleic acids were found to be components of chromosomes. (d) DNA was found to contain only four different chemical building blocks.

d

In the case of a simple conversion reaction such as X!Y, which value of ΔG° is associated with a larger concentration of X than Y at equilibrium? (Hint: How is ΔG° related to K?) (a) ΔG°=-5 (b) ΔG°=-1 (c) ΔG° = 0 (d) ΔG° = 1

d

Lysozyme is an enzyme that specifically recognizes bacterial polysaccharides, which renders it an effective antibacterial agent. Into what classification of enzymes does lysozyme fall? (a) isomerase (b) protease (c) nuclease (d) hydrolase

d

Macromolecules in the cell can often interact transiently as a result of noncovalent interactions. These weak interactions also produce stable, highly specific interactions between molecules. Which of the factors below is the most significant in determining whether the interaction will be transient or stable? (a) the size of each molecule (b) the concentration of each molecule (c) the rate of synthesis (d) surface complementarity between molecules

d

Many types of cells have stores of lipids in their cytoplasm, usually seen as fat droplets. What is the lipid most commonly found in these droplets? (a) cholesterol (b) palmitic acid (c) isoprene (d) triacylglycerol

d

Molecular chaperones can work by creating an "isolation chamber." What is the purpose of this chamber? (a) The chamber acts as a garbage disposal, degrading improperly folded proteins so that they do not interact with properly folded proteins. (b) This chamber is used to increase the local protein concentration, which will help speed up the folding process. (c) This chamber serves to transport unfolded proteins out of the cell. (d) This chamber serves to protect unfolded proteins from interacting with other proteins in the cytosol, until protein folding is completed.

d

Motor proteins use the energy in ATP to transport organelles, rearrange elements of the cytoskeleton during cell migration, and move chromosomes during cell division. Which of the following mechanisms is sufficient to ensure the unidirectional movement of a motor protein along its substrate? (a) A conformational change is coupled to the release of a phosphate (Pi). (b) The substrate on which the motor moves has a conformational polarity. (c) A conformational change is coupled to the binding of ADP. (d) A conformational change is linked to ATP hydrolysis.

d

NADH and NADPH are activated carrier molecules that function in completely different metabolic reactions. Both carry two additional ________ and one additional _____________. This combination can also be referred to as a hydride ion. (a) protons, electron. (b) electrons, phosphate. (c) hydrogens, electron. (d) electrons, proton.

d

Polar covalent bonds are formed when the electrons in the bond are not shared equally between the two nuclei. Which one of these molecules contains polar bonds? (a) molecular oxygen (b) methane (c) propane (d) water

d

Prokaryotic cells are able to evolve very fast, which helps them to rapidly adapt to new food sources and develop resistance to antibiotics. Which of the options below lists the three main characteristics that support the rapid evolution of prokaryotic populations? (a) microscopic, motile, anaerobic (b) aerobic, motile, rapid growth (c) no organelles, cell wall, can exchange DNA (d) large population, rapid growth, can exchange DNA

d

Protein structures have several different levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. Consider the definitions below and select the one that best fits the term "protein domain." (a) a small cluster of α helices and β sheets (b) the tertiary structure of a substrate-binding pocket (c) a complex of more than one polypeptide chain (d) a protein segment that folds independently

d

Recombination has occurred between the chromosome segments shown in Figure Q6-61. The genes A and B, and the recessive alleles a and b, are used as markers on the maternal and paternal chromosomes, respectively. After alignment and homologous recombination, the specific arrangements of A, B, a, and b have changed. Which of the choices below correctly indicates the gene combination from the replication products of the maternal chromosome? (a) AB and aB (b) ab and Ab (c) AB and Ab (d) aB and Ab

d

Select the answer that best completes the following statement: Chemical reactions in living systems occur in an ____________ environment, within a narrow range of temperatures. (a) optimal (b) organic (c) extracellular (d) aqueous

d

Several experiments were required to demonstrate how traits are inherited. Which scientist or team of scientists obtained definitive results demonstrating that DNA is the genetic molecule? (a) Griffith (b) Watson (c) Crick (d) Hershey and Chase

d

Telomeres serve as caps at the ends of linear chromosomes. Which of the following is not true regarding the replication of telomeric sequences? (a) The lagging-strand telomeres are not completely replicated by DNA polymerase. (b) Telomeres are made of repeating sequences. (c) Additional repeated sequences are added to the template strand. (d) The leading strand doubles back on itself to form a primer for the lagging strand.

d

The __________ __________ is made up of two concentric membranes and is continuous with the membrane of the endoplasmic reticulum. (a) plasma membrane (b) Golgi network (c) mitochondrial membrane (d) nuclear envelope

d

The cell constantly exchanges materials by bringing nutrients in from the external environment and shuttling unwanted by-products back out. Which term describes the process by which external materials are captured inside vesicles and brought into the cell? (a) degradation (b) exocytosis (c) phagocytosis (d) endocytosis

d

The complete set of information found in a given organism's DNA is called its ____________. (a) genetic code. (b) coding sequence. (c) gene. (d) genome.

d

The correct folding of proteins is necessary to maintain healthy cells and tissues. Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer's disease, Huntington's disease, and Creutzfeldt-Jakob disease (the specific faulty protein is different for each disease). What is the ultimate fate of these disease-causing, unfolded proteins? (a) They are degraded. (b) They bind a different target protein. (c) They form structured filaments. (d) They form protein aggregates.

d

The energy used by the cell to generate specific biological molecules and highly ordered structures is stored in the form of _____________. (a) Brownian motion. (b) heat. (c) light waves. (d) chemical bonds.

d

The events listed below are all necessary for homologous recombination to occur properly: A. Holliday junction cut and ligated B. strand invasion C. DNA synthesis D. DNA ligation E. double-strand break F. nucleases create uneven strands

d

The human genome is divided into linear segments and packaged into structures called chromosomes. What is the total number of chromosomes found in each of the somatic cells in your body? (a) 22 (b) 23 (c) 44 (d) 46

d

The inactivation of one X chromosome is established by the directed spreading of heterochromatin. The silent state of this chromosome is _______________ in the subsequent cell divisions. (a) completed (b) switched (c) erased (d) maintained

d

The maximum velocity (Vmax) of an enzymatic reaction is an important piece of information regarding how the enzyme works. What series of measurements can be taken in order to infer the maximum velocity of an enzyme-catalyzed reaction? (a) the rate of substrate consumption after the system reaches equilibrium, for several reactant concentrations (b) the rate of product consumption shortly after mixing the enzyme and substrate (c) the rate of substrate consumption at high levels of enzyme concentration (d) the rate of substrate consumption shortly after mixing the enzyme and substrate, for several substrate concentrations

d

The octameric histone core is composed of four different histone proteins, assembled in a stepwise manner. Once the core octamer has been formed, DNA wraps around it to form a nucleosome core particle. Which of the following histone proteins does not form part of the octameric core? (a) H4 (b) H2A (c) H3 (d) H1

d

The pH of an aqueous solution is an indication of the concentration of available protons. However, you should not expect to find lone protons in solution; rather, the proton is added to a water molecule to form a(n) ______________ ion. (a) hydroxide (b) ammonium (c) chloride (d) hydronium

d

The study of enzyme kinetics is usually performed with purified components and requires the characterization of several aspects of the reaction, including the rate of association with the substrate, the rate of catalysis, and _____________. (a) the enzyme's structure. (b) the optimal pH of the reaction. (c) the subcellular localization of the enzyme. (d) the regulation of the enzyme activity.

d

The synthesis of glutamine from glutamic acid requires the production of an activated intermediate followed by a condensation step that completes the process. Both amino acids are shown in Figure Q3-72. In the condensation step, _______________ is displaced by ________________. (a) OH, NH3. (b) ADP, NH2. (c) ATP, NH3. (d) phosphate, NH3.

d

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking DNA ligase were used to make the cell extracts? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading-strand elongation (d) lagging-strand completion

d

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking the exonuclease activity of DNA polymerase were used to make the cell extracts? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading-strand elongation (d) lagging-strand completion

d

What unit of length would you generally use to measure a typical plant or animal cell? (a) centimeters (b) nanometers (c) millimeters (d) micrometers

d

Which diagram accurately represents the directionality of DNA strands at one side of a replication fork?

d

Which of the following DNA strands can form a DNA duplex by pairing with itself at each position? (a) 5′-AAGCCGAA-3′ (b) 5′-AAGCCGTT-3′ (c) 5′-AAGCGCAA-3′ (d) 5′-AAGCGCTT-3′

d

Which of the following characteristics would not support the idea that the ancestral eukaryote was a predator cell that captured and consumed other cells? (a) dynamic cytoskeleton (b) large cell size (c) ability to move (d) rigid membrane

d

Which of the following chemical groups is not used to construct a DNA molecule? (a) five-carbon sugar (b) phosphate (c) nitrogen-containing base (d) six-carbon sugar

d

Which of the following questions would not be answered by using karyotyping? (a) Is the individual genetically female or male? (b) Do any of the chromosomes contain pieces that belong to other chromosomes? (c) Does the individual have an extra chromosome? (d) Do any chromosomes contain point mutations?

d

Which of the following statements about the newly synthesized strand of a human chromosome is true? (a) It was synthesized from a single origin solely by continuous DNA synthesis. (b) It was synthesized from a single origin by a mixture of continuous and discontinuous DNA synthesis. (c) It was synthesized from multiple origins solely by discontinuous DNA synthesis. (d) It was synthesized from multiple origins by a mixture of continuous and discontinuous DNA synthesis.

d

Which of the following statements correctly explains what it means for DNA replication to be bidirectional? (a) The replication fork can open or close, depending on the conditions. (b) The DNA replication machinery can move in either direction on the template strand. (c) Replication-fork movement can switch directions when the fork converges on another replication fork. (d) The replication forks formed at the origin move in opposite directions.

d

Which pair of values best fills in the blanks in this statement: On average, eukaryotic cells are __________ times longer and have _________ times more volume than prokaryotic cells. (a) 5, 100 (b) 10, 200 (c) 10, 100 (d) 10, 1000

d

You are examining the DNA sequences that code for the enzyme phosphofructokinase in skinks and Komodo dragons. You notice that the coding sequence that actually directs the sequence of amino acids in the enzyme is very similar in the two organisms but that the surrounding sequences vary quite a bit. What is the most likely explanation for this? (a) Coding sequences are repaired more efficiently. (b) Coding sequences are replicated more accurately. (c) Coding sequences are packaged more tightly in the chromosomes to protect them from DNA damage. (d) Mutations in coding sequences are more likely to be deleterious to the organism than mutations in noncoding sequences.

d

You have a concentrated stock solution of 10 M NaOH and want to use it to produce a 150 mL solution of 3 M NaOH. What volume of water and stock solutions will you measure out to make this new solution? (a) 135 mL of water, 15 mL of NaOH stock (b) 115 mL of water, 35 mL of NaOH stock (c) 100 mL of water, 50 mL of NaOH stock (d) 105 mL of water, 45 mL of NaOH stock

d

You have discovered an "Exo-" mutant form of DNA polymerase in which the 3′- to-5′ exonuclease function has been destroyed but the ability to join nucleotides together is unchanged. Which of the following properties do you expect the mutant polymerase to have? (a) It will polymerize in both the 5′-to-3′ direction and the 3′-to-5′ direction. (b) It will polymerize more slowly than the normal Exo+ polymerase. (c) It will fall off the template more frequently than the normal Exo+ polymerase. (d) It will be more likely to generate mismatched base pairs.

d

ΔG measures the change of free energy in a system as it converts reactant (Y) into product (X). When [Y] =[X], ΔG is equal to _____________. (a) ΔG°+RT (b) RT (c) ln [X]/[Y] (d) ΔG°

d

ΔG° indicates the change in the standard free energy as a reactant is converted to product. Given what you know about these values, which reaction below is the most favorable? (a) ADP + Pi!ATP ΔG° = +7.3 kcal/mole (b) glucose 1-phosphate ! glucose 6-phosphate ΔG° = -1.7 kcal/mole (c) glucose + fructose!sucrose ΔG° = +5.5 kcal/mole (d) glucose!CO2 + H2O ΔG° = -686 kcal/mole

d

β Sheets can participate in the formation of amyloid fibers, which are insoluble protein aggregates. What drives the formation of amyloid fibers? (a) denaturation of proteins containing β sheets (b) extension of β sheets into much longer β strands (c) formation of biofilms by infectious bacteria (d) β-sheet stabilization of abnormally folded proteins

d

A molecule of bacterial DNA introduced into a yeast cell is imported into the nucleus but fails to replicate with the yeast DNA. Where do you think the block to replication arises? Choose the protein or protein complex below that is most probably responsible for the failure to replicate bacterial DNA. Give an explanation for your answer. (a) primase (b) helicase (c) DNA polymerase (d) initiator proteins

d. DNA from all organisms is chemically identical except for the sequence of nucleotides. The proteins listed in choices (a) to (c) can act on any DNA regardless of its sequence. In contrast, the initiator proteins recognize specific DNA sequences at the origins of replication. These sequences differ between bacteria and yeast.

For each of the following sentences, choose one of the options enclosed in square brackets to make a correct statement about nucleosomes. A. Nucleosomes are present in [prokaryotic/eukaryotic] chromosomes, but not in [prokaryotic/eukaryotic] chromosomes. B. A nucleosome contains two molecules each of histones [H1 and H2A/H2A and H2B] as well as of histones H3 and H4. C. A nucleosome core particle contains a core of histone with DNA wrapped around it approximately [twice/three times/four times]. D. Nucleosomes are aided in their formation by the high proportion of [acidic/basic/polar] amino acids in histone proteins. E. Nucleosome formation compacts the DNA into approximately [one- third/one-hundredth/one-thousandth] of its original length.

eukaryotic, prokaryotic H2A and H2B twice basic one-third

The process of change and selection over the course of many generations is the basis of

evolution

What elements are chemically inert?

helium, neon

Interphase chromosomes contain both darkly staining __________________ and more lightly staining __________________. Genes that are being transcribed are thought to be packaged in a __________________ condensed type of euchromatin. Nucleosome core particles are separated from each other by stretches of __________________ DNA. A string of nucleosomes coils up with the help of __________________ to form the more compact structure of the __________________. A __________________ model describes the structure of the 30-nm fiber. The 30 nm chromatin fiber is further compacted by the formation of __________________ that emanate from a central __________________.

heterochromatin, euchromatin, less, linker, histone H1, 30-nm fiber, zigzag, loops, axis

Any substance that will bind to a protein is known as its __________________. Enzymes bind their __________________ at the __________________. The enzyme hexokinase is so specific that it reacts with only one of the two __________________ of glucose. Enzymes catalyze a chemical reaction by lowering the __________________, because they provide conditions favorable for the formation of a __________________ intermediate called the __________________. Once the reaction is completed, the enzyme releases the __________________ of the reaction.

ligand, substrates, inhibitors, active site, isomers, activation energy, high-energy, transition state, products

which elements will form ions with a net charge of +2 in solution?

magnesium, calcium

Cells can be very diverse. They come in various sizes, ranging from bacterial cells such ad Lactobacillus, which is a few______________________ in length, to larger cells such as a frog's egg, which has a diameter of about one _____________. Despite the diversity, cells resemble each other to an astonishing degree in their chemistry. For example, the same 20 __________ are used to make proteins. Similarly, the genetic information of all cells is stored in their __________________. Although __________________ contain the same types of molecules as cells, their inability to reproduce themselves by their own efforts means that they are not considered living matter.

micrometers, millimeter, aa (amino acids), DNA, viruses

Eukaryotic cells are bigger and more elaborate than prokaryotic cells. By definition, all eukaryotic cells have a __________________, usually the most prominent organelle. Another organelle found in essentially all eukaryotic cells is the __________________, which generates the chemical energy for the cell. In contrast, the __________________ is a type of organelle found only in the cells of plants and algae, and performs photosynthesis. If we were to strip away the plasma membrane from a eukaryotic cell and remove all of its membrane-enclosed organelles, we would be left with the __________________, which contains many long, fine filaments of protein that are responsible for cell shape and structure and thereby form the cell's __________________.

nucleus, mitochondrion, chloroplast, cytosol

Proteins are ______________ built from amino acids, which each have an amino group and a _____________ group attached to the central _______________. There are twenty possible _______________ that differ in structure and are generally referred to as "R." In solutions of neutral pH, amino acids are _______________, carrying both a positive and negative charge. When a protein is made, amino acids are linked together through _______________, which are formed by condensation reactions between the carboxyl end of the last amino acid and the ___________________ end of the next amino acid to be added to the growing chain.

polypeptides, carboxyl, alpha-carbon, side chains, ionized, peptide bonds, amino

Cell-free extracts from S-strain cells of S. pneumoniae were fractionated to __________________ DNA, RNA, protein, and other cell components. Each fraction was then mixed with __________________ cells of S. pneumoniae. Its ability to change these into cells with __________________ properties resembling the __________________ cells was tested by injecting the mixture into mice. Only the fraction containing __________________ was able to __________________ the __________________ cells to __________________ (or __________________ ) cells that could kill mice.

purify, R-strain, pathogenic, S-strain, DNA, transform, R-strain, pathogenic, S-strain

By definition, catalysis allows a reaction to occur more __________________. Chemical reactions occur only when there is a loss of __________________ energy. Enzymes act more __________________ than other catalysts. A catalyst decreases the __________________ energy of a reaction.

rapidly, free, selectively, activation

The flow of genetic information is controlled by a series of biochemical reactions that result in the production of proteins, each with its own specific order of amino acids. Choose the correct series of biochemical reactions form the options:

replication, transcription, translation

Whereas ionic bonds form a(n) __________________, covalent bonds between atoms form a(n) __________________. These covalent bonds have a characteristic bond __________________ and become stronger and more rigid when two electrons are shared in a(n) __________________. Equal sharing of electrons yields a(n) __________________ covalent bond. If one atom participating in the bond has a stronger affinity for the electron, this produces a partial negative charge on one atom and a partial positive charge on the other. These __________________ covalent bonds should not be confused with the weaker __________________ bonds that are critical for the three-dimensional structure of biological molecules and for interactions between these molecules.

salt, molecule, length, double bond, non polar, polar, noncovalent

The α helices and β sheets are examples of protein __________________ structure. A protein such as hemoglobin, which is composed of more than one protein __________________, has __________________ structure. A protein's amino acid sequence is known as its __________________ structure. A protein __________________ is the modular unit from which many larger single-chain proteins are constructed. The three-dimensional conformation of a protein is its __________________ structure.

secondary, subunit, quaternary, primary, domain, tertiary

which elements will form ions with a new charge of +1 in solution?

sodium, potassium

A newly synthesized protein generally folds up into a __________________ conformation. All the information required to determine a protein's conformation is contained in its amino acid __________________. On being heated, a protein molecule will become __________________ as a result of breakage of __________________ bonds. On removal of urea, an unfolded protein can become __________________. The final folded conformation adopted by a protein is that of __________________ energy.

stable, sequence, denatured, non covalent, renatured, lowest

Selection the option that best finishes the following statement: "Evolution is a process _________".

that can be understood based on the principles of mutation and selection