CH 33 to 40

Suppose that a single-strand circular DNA with the base composition 30% A, 20% T, 15% C, and 35% G serves as the template for the synthesis of a complementary strand by DNA polymerase. (a) Give the base composition of the complementary strand. (b) Give the overall base composition of the resulting double-helical DNA

(a) 30% T, 20% A, 15% G, 35% C (b) 25% A, 25% T, 25% C, 25% G. The base composition of the double strand is the average of that of the two single strands

6. For each of the following, identify it as a feature of eukaryotic (E) or prokaryotic (P) gene transcription. (a) The ends of mRNA are modified. (b) Transcription and translation are coupled. (c) There are three RNA polymerases involved. (d) There are three promoter elements involved. (e) The resulting mRNA is spliced.

(a) E; (b) P; (c) E; (d) P; (e) E

You are given two solutions containing different purified DNAs. One is from the bacterium P. aeruginosa and has a GC composition of 68%, whereas the other is from a mammal and has a G C composition of 42.5%. (a) You measure the absorbance of ultraviolet light of each solution as a function of increasing temperature. Which solution will yield the higher Tm value and why? (b) After melting the two solutions, mixing them together, and allowing them to cool, what would you expect to happen? (c) Would appreciable amounts of bacterial DNA be found associated in a helix with mammalian DNA? Explain.

(a) The bacterial DNA solution has the higher Tm value because it has the higher GC content and is therefore more stable to the thermal-induced separation of its strands because GC base pairs are more stable than AT base pairs. (b) The complementary DNA strands from each species will anneal to form Watson-Crick double helices as the solution cools. (c) No; each strand will find its partner because the perfect match between the linear arrays of the bases of complementary strands is far more stable than the mostly imperfect matches in duplexes composed of one strand of bacterial and one strand of mammalian DNA would be.

Which of the following answers completes the sentence correctly? The wobble hypothesis (a) accounts for the conformational looseness of the amino acid acceptor stem of tRNAs that allows sufficient flexibility for the peptidyl-tRNA and aminoacyltRNA to be brought together for peptide-bond formation. (b) accounts for the ability of some anticodons to recognize more than one codon. (c) explains the occasional errors made by the aminoacyl-tRNA synthetases. (d) explains the oscillation of the peptidyl-tRNAs between the A and P sites on the ribosome. (e) assumes steric freedom in the pairing of the first (5′) nucleotide of the codon and the third (3′) nucleotide of the anticodon.

(b) accounts for the ability of some anticodons to recognize more than one codon.

Which of the following statements about DNA molecules that are topoisomers are Correct? (a) They are bound to topoisomerases. (b) They differ from one another topologically only in that they have different linking numbers. (c) They may be separated from one another by electrophoresis. (d) They have identical molecular weights. (e) They are topological or spatial isomers.

. b, c, d, e. Answer (a) is not correct because the DNA topoisomer need not necessarily be bound by a topoisomerase.

p lac repressor

.contains a specific binding sequence for RNA polymerase .is the lac promoter

o

.contains a specific binding sequence for the .is the lac operator

y and a

.encodes a galactoside permease .encodes thiogalactoside transacetylase

z

.encodes a protein that binds allolactose .encodes -galactosidase

I

.encodes a protein that interferes with the activation of RNA polymerase .encodes a protein that binds allolactose .is a regulatory gene .encodes the lac repressor

. Explain the forces that stabilize the double helix.

1. the ds helix is stabilized by the hydrophobic effect (interactions) 2. adjacent base pairs attract one another through van der Waals forces

[CH 33] List the important features of the Watson-Crick DNA double helix including its dimensions. Relate the base pairing of adenine with thymine and of cytosine with guanine to the duplex structure of DNA and to the replication of the helix. Explain the molecular determinants of the specific base pairs in DNA

1.two antiparallel (3'⇾5' and 5'⇾3') DNA strands are coiled in a right-handed manner around the same axis 2. the DNA backbone of the two the DNA strands are oriented on the outside, and the bases are oriented towards the inside of the double helix 3.each base in one strand pairs through hydrogen bonds with a unique base from the complementary strand. 4. allowed base pairs: (A double bond T) and (C Triple bond G)

Haploid human DNA has 3 x10^6 kilobase pairs (a kilobase pair, abbreviated kb, is 1000 base pairs). What is the total length of human haploid DNA in centimeters?

102 cm. The math is as follows: (3*10^6 kb * 10^3 bases/kb* 3.4A/base*106-8cm/A)= 102cm

The duplication of the ends of linear, duplex DNA in humans presents a problem to the replicative machinery of a cell. Describe this problem, its cause, and the way the cell overcomes it.

: Because DNA polymerases extend their growing polynucleotide chains only in the 5'⟶3'direction and because the two strands of the parental DNA duplex are antiparallel, removal of the RNA primer that is paired with the 3'end of the parental template DNA would leave an overhanging 3′DNA strand with no means of having its complement synthesized. Ordinary DNA polymerases are unable to initiate DNA chains de novo. Each round of replication would consequently shorten the DNA because a portion could not be copied. To circumvent this problem, human DNA chromosomes have a segment of repeating G-rich DNA (telomeres) at their ends. In addition, a special enzyme, telomerase, which is an RNA-dependent DNA polymerase (reverse transcriptase) that carries its own RNA template, can extend the uncompleted end at each round of replication. The RNA template renews the repeating telomere sequence so that the DNA is not shortened.

Why are helicases required during DNA replicaton? Is ATP required for their action?

: Duplex B-DNA is a stable molecule at physiological temperature and helicases are required to unwind the two strands of the helix so that each can serve as a template for DNA polymerases. Because DNA is so stable, energy is required in the form of ATP hydrolysis to drive helicase action.

Which of the following statements about the subunit of RNA polymerase are correct? (a) It enables the enzyme to transcribe asymmetrically. (b) It confers on the core enzyme the ability to initiate transcription at promoters. (c) It decreases the affinity of RNA polymerase for regions of DNA that lack promoter sequences. (d) It facilitates the termination of transcription by recognizing hairpins in the transcript.

: a, b, c. The subunit recognizes promoter sites, decreases the affinity of the enzyme for regions of DNA lacking promoter sequences, and facilitates the specific, oriented initiation of transcription. Orienting the binding of the enzyme to the DNA results in only one of the two DNA strands functioning as a template for RNA transcription; that is, it gives rise to asymmetric transcription.

For each of the following steps of translation, give the cofactor involved and the number of high-energy phosphate bonds consumed. (a) amino acid activation (b) formation of the 70S initiation complex (c) delivery of aminoacyl-tRNA to the ribosome (d) formation of a peptide bond (e) translocation

Ans: (a) ATP, 2 (b) GTP, 1 (c) GTP, 1 (d) none (e) GTP, 1. With regard to the answer for (d), the formation of a peptide bond per se does not require a cofactor. The energy for the exergonic reaction is supplied by the activated aminoacyl-tRNA.

10. What is the minimum number of contiguous nucleotides in mRNA that can serve as a codon? Explain.

Ans: Three contiguous nucleotides is the minimum that can serve as a codon. There are four kinds of nucleotides in mRNA. A codon consisting of only two nucleotides (either of which could be any of the four possible nucleotides) allows only 16 possible combinations (4 x4 16). This would not be sufficient to specify all 20 of the amino acids. A codon consisting of three nucleotides, however, allows 64 possible combinations (4 x 4 x4 64), more than enough to specify the 20 amino acids.

DNA polymerase activity requires (a) a template (b) a primer with a free 5′hydroxyl group (c) dATP, dCTP, dGTP and dTTP (which is the same as TTP). (d) ATP (e) Mg2+

Ans: a, c, and e. a template, dATP, dCTP, dGTP and dTTP (which is the same as TTP) and Mg2+ . Answer (b) is incorrect because, although the enzyme requires a primer, the nature of its 5′-end is irrelevant since dNMP residues are added to its 3′-end. A primer with a 3′-OH is required. Answer (d) is not correct because the enzyme uses dNTP and not NTP molecules, where N means A, C, G, T, or U. Note that dTTP is used interchangeably with TTP.

9. Which of the following are characteristics or functions of tRNA? (a) It contains a codon. (b) It contains an anticodon. (c) It can become covalently attached to an amino acid. (d) It interacts with mRNA to stimulate transcription. (e) It can have any of a number of different sequences. (f) It serves as an adaptor between the information in mRNA and an individual amino acid.

Ans: b, c, e, and f. Answer (d) is incorrect because the interaction of tRNA with mRNA takes place during translation, not transcription

The text states that RNA polymerases backtrack for proofreading. Why would this be energetically unfavorable? What is the error rate of RNA synthesis?

Backtracking involves breaking hydrogen bonds between an RNA-DNA base pair, but if the base pair is Incorrect there will often be fewer hydrogen bonds to break. The text states that the final error rate is between one mistake in 104 and one in 105 nucleotides added. Compare this to the DNA error rate (after various Corrective processes have been applied, including mismatch repair) of one in 109-1010.

1) involved in replication (2) requires a primer and a template (3) involved in DNA repair (5) removes the primer and fills in gaps during replication

DNA polymerase I

1) involved in replication (2) requires a primer and a template (4) makes most of the DNA phosphodiester bonds during replication

DNA polymerase III

When E. coli is added to a culture containing both lactose and glucose, which of the sugars is metabolized preferentially? What is the mechanism underlying this selectivity?

Glucose is metabolized preferentially because it results in a decrease in the synthesis of cAMP by adenylate cyclase. The lack of cAMP prevents the formation of the cAMP-CAP complex, which is necessary for the efficient transcription of the lac operon and other catabolite-repressible operons.

Which of the following statements about the poly(A) tails that are found on most eukaryotic mRNAs are Correct? (a) They are added as preformed polyriboadenylate segments to the 3′ ends of mRNAprecursors by an RNA ligase activity. (b) They are encoded by stretches of polydeoxythymidylate in the template strand of the gene. (c) They are added by RNA polymerase II in a template-independent reaction using ATP as the sole nucleotide substrate. (d) They are added by poly(A) polymerase using dATP as the sole nucleotide substrate. (e) They are cleaved from eukaryotic mRNAs by a sequence-specific endoribonuclease that recognizes the RNA sequence AAUAAA.

None of the statements is correct. Poly(A) polymerase uses ATP, not dATP, to add a stretch of A residues to the 3′-hydroxyl formed by the cleavage of an mRNA precursor by a specific ribonuclease that recognizes the upstream sequence AAUAAA within particular mRNA sequence contexts.

15. How many errors would be expected to occur in a 1000-amino acid protein given an error frequency of 10-3?

One error would be expected. An value of 10-3 means 1 error per 1000 amino acids.

DNA replication is Escherichia coli begins at a unique site called the:

Oric

In contrast to prokaryotes, eukaryotes have multiple RNA polymerases. Which eukaryotic RNA polymerase is involved in synthesis of pre-mRNAs? RNA polymerase I RNA polymerase II RNA polymerase III RNA polymerase I and II RNA polymerase II and III

RNA polymerase II

What functions are the caps and tails of mRNAs thought to perform?

The 5′caps are thought to contribute to the stability and efficiency of translation of the mRNA. The poly(A) tails probably perform the same functions, albeit by different, unknown mechanisms

Give two reasons why eukaryotes must use multiple origins of replication (in contrast to prokaryotes, which usually use one).

The great amount of genomic DNA in eukaryotes (6 x109 bp in a human) requires that polymerases start at multiple sites in order to complete the DNA synthesis in a biologically relevant period of time. In addition, the genome of eukaryotes comprises multiple separate DNA molecules—23 pairs of chromosomes in a human, so sites must be provided on each molecule. The first requirement accounts for the vast majority of the ~30,000 origins in a human cell.

Many antibiotics act by inhibiting protein synthesis. How can some of these be used in humans to counteract microbial infections without causing toxic side effects due to the inhibition of eukaryotic protein synthesis?

The inhibition of the prokaryotic translation and not that of the eukaryote can result from differences between their respective ribosomes. Some antibiotics interact with the RNA components that are unique to bacterial ribosomes and, consequently, can inhibit bacterial growth without affecting the human cells.

About 5% of the total bacterial protein is EF-Tu. Explain why this protein is so abundant.

The large amounts of EF-Tu in the cell bind essentially all of the aminoacyl-tRNAs and protect these activated complexes from hydrolysis.

What is the sequence of the mRNA that will be synthesized from a template strand of DNA having the following sequence? . . .ACGTTACCTAGTTGC. . .

The mRNA sequence will be ...GCAACUAGGUAACGU..., written in the 5'to 3′ direction.

Identify the post-transcriptional modifications of tRNA precursor processing. What modifications are made to the bases?

The modifications are cleavage of the 5- and 3′ ends of the tRNA, removal of a 14- nucleotide intron, and addition of a CCA to the 3′-end. The modification to the base shown on Figure 38.2 is the conversion of uracil to pseudouracil.

What is the sequence of the polypeptide that would be encoded by the DNA sequence ACGTTACCTAGTTGC? Assume that the reading frame starts with the 5′ nucleotide given. The genetic code is given on page 709 of the text.

The sequence of the polypeptide would be Ala-Thr-Arg. The reading frame is set by the nucleotide at the 5′ end of the mRNA transcript; the fourth codon of the mRNA transcript is UAA, which is a translation termination codon.

14. Explain why tRNA molecules must have both unique and common structural features.

Transfer RNAs need common features for their interactions with ribosomes and elongation factors but unique features for their interactions with the activating enzymes.

20. Assuming that each nucleotide in the left column is in the first position of an anticodon, with which nucleotide or nucleotides in the right column could it pair during a codon-anticodon interaction if each of the nucleotides on the right is in the third position (3'position) of a codon? (a) adenosine (1) adenosine (b) cytidine (2) cytidine (c) guanosine (3) guanosine (d) inosine (4) uridine (e) uridine

a) 4 (b) 3 (c) 2, 4 (d) 1, 2, 4 (e) 1, 3.

12. The following is a partial list of mRNA codons and the amino acids they encode: AGU serine AGC serine; AAU asparagine AAC asparagine; AUG methionine AUA isoleucine From this list, which of the following statements are correct? (a) The genetic code is degenerate. (b) The alteration of a single nucleotide in the DNA directing the synthesis of these codons could lead to the substitution of a serine for an asparagine in a polypeptide. (c) The alteration of a single nucleotide in the DNA directing the synthesis of these codons would necessarily lead to an amino acid substitution in the encoded polypeptide. (d) A tRNA with the anticodon ACU would be bound by a ribosome in the presence of one of these codons.

a, b, and d. Answer (a) is correct because both AGU and AGC specify serine; since more than one codon can specify the same amino acids, the genetic code is said to be degenerate. Answer (b) is correct because the alteration of a single nucleotide in the DNA could change a codon on the mRNA transcript from AGU, which specifies serine, to AAU, which specifies asparagine. Answer (d) is correct because the anticodon ACU would base-pair with the codon AGU. Answer (c) is not correct because the alteration of a single nucleotide in the DNA could result in another codon that specifies the same amino acid; for example, a codon changed from AGU to AGC would continue to specify serine

Which of the following statements about DNA polymerases are correct, (a) They add deoxyribonucleotide units to the 3′-hydroxyl of a primer. (b) They use the template strand to help determine which deoxyribonucleotide unit to add to the growing DNA chain. (c) They contain a 3′→ 5′nuclease that cleaves phosphodiester bonds of mis-incorporated deoxyribonucleotides. (d) They check the size of an incoming deoxyribonucleotide triphosphate (dNTP) to help ensure that the correct, complementary choice is made. (e) They bind one complementary dNTP and add a second complementary dNTP to initiate a new DNA chain.

a, b, c, d

The topological features of circular DNA may affect which of the following? (a) the electrophoretic mobility of the DNA (b) the sedimentation properties of the DNA (c) its affinities toward proteins that bind to the DNA (d) the susceptibility of the strands of the DNA to unwinding (e) the susceptibility of the DNA to the action of DNA ligase

a, b, c, d. In regard to answer (e), supercoiling is ordinarily a property of covalently closed circular DNA—that is, of DNA in which there are no discontinuities in either strand of the helix. Hence, these molecules are not substrates for DNA ligase, because they lack ends.

9. Which of the following are required for the DNA-dependent RNA polymerase reaction to produce a unique RNA transcript? (a) ATP (g) RNA (b) CTP (h) Mg2+ (c) GTP (i) promoter sequence (d) dTTP (j) operator sequence (e) UTP (k) terminator sequence (f) DNA

a, b, c, e, f, h, i, and k. Answer (f) is correct because DNA is needed to serve as the template. Answers (k) and (i) are correct because the promoter and terminator sequences are needed to specify the precise start and stop points, respectively, for the transcription

An important key to understanding the structure and function of DNA was the observation that the amount of A equaled the amount of T and the amount of G equaled the amount of C. This important observation was made by: a. Erwin Chargaff. b. Watson and Crick. c. Rosalind Franklin. d. Maurice Wilkins. e. Meselson and Stahl.

a. Erwin Chargaff. Correct. Chargaff's rules are that A = T (Double bond) and G = C.(Triple bond)

13. Which of the following statements about functional tRNAs are correct? (a) They contain many modified nucleotides. (b) About half their nucleotides are in base-paired helical regions. (c) They contain fewer than 100 ribonucleotides. (d) Their anticodons and amino acid accepting regions are within 5 Å of each other. (e) They consist of two helical stems that are joined by loops to form a U-shaped structure. (f) They have a terminal AAC sequence at their amino acid accepting end.

a, b, c. The molecules consist of two helical stems, each of which is made of two stacked helical segments. However, the molecules are L-shaped, and the anticodon and amino acid accepting regions are some 80 Å from each other. Functional tRNAs have a CCA sequence, not an AAC sequence at their 3′termini

Which of the following statements about topoisomerases are correct? (a) They alter the linking numbers of topoisomers. (b) They break and reseal phosphodiester bonds. (c) They require NAD+ as a cofactor to supply the energy to drive the conversion of a supercoiled molecule to its relaxed form. (d) They form covalent intermediates with their DNA substrates. (e) They can, in the case of a particular type of topoisomerase, use ATP to form negatively supercoiled DNA from relaxed DNA in E. coli.

a, b, d, e. Although all topoisomerases break and reseal phosphodiester bonds, an external energy source is not always required. Relieving the torsional stress in a negatively supercoiled DNA molecule by relaxing it with topoisomerase I is exergonic and requires no energy input, whereas introducing negative supercoils with DNA gyrase is endergonic and must be coupled to ATP hydrolysis. The particular catalytic mechanisms of given topoisomerases determine whether they are coupled to ATP hydrolysis.

19. Indicate the possible ways in which different aminoacyl-tRNA synthetases may recognize their corresponding tRNAs. (a) by recognizing the anticodon (b) by recognizing specific base pairs in the acceptor stem (c) by recognizing the 3′CCA sequence of the tRNA (d) by recognizing both the anticodon and acceptor stem region (e) by recognizing extended regions of the L-shaped molecules

a, b, d, e. There are many different ways in which aminoacyl-tRNA synthetases recognize their specific tRNAs. Answer (c) is Incorrect because the 3′CCA sequence is common to all tRNAs and cannot be used to distinguish among them.

Which of the following statements about DNA replication in E. coli are correct? (a) It occurs at a replication fork. (b) It starts at a unique locus on the chromosome. (c) It proceeds with one replication fork per replicating molecule. (d) It is bidirectional. (e) It involves discontinuous synthesis on the leading strand. (f) It uses RNA transiently as a template.

a, b, d. Answer (c) is incorrect because, although not explicitly stated in the text, the replicating E. coli chromosome has two replication forks that synthesize the DNA bidirectionally from the unique oriC origin. Answer (e) is incorrect because only the lagging strand is synthesized discontinuously. Answer (f) is incorrect because RNA serves as a primer and not as a template.

Which of the following statements about DNA polymerase III holoenzyme from E. coli are correct? (a) It elongates a growing DNA chain hundreds of times faster than does DNA polymerase I. (b) It associates with the parental template, adds a few nucleotides to the growing chain, and then dissociates before initiating another synthesis cycle. (c) It maintains a high fidelity of replication, in part, by acting in conjunction with a subunit containing a 3'⟶5' exonuclease activity. (d) When replicating DNA, it is a molecular assembly composed of at least 10 different kinds of subunits.

a, c, d. Answer (b) is incorrect because DNA polymerase III holoenzyme is a highly processive enzyme that synthesizes extensively before dissociating from its template.

9. Which of the following statements about occurrences during translation are correct? (a) The carboxyl group of the growing polypeptide chain is transferred to the amino group of an aminoacyl-tRNA. (b) The carboxyl group of the amino acid on the aminoacyl-tRNA is transferred to the amino group of a peptidyl-tRNA. (c) Peptidyl-tRNA may reside in either the A or the P site. (d) Aminoacyl-tRNAs are shuttled from the A to the P site by EF-G.

a, c. The aminoacyl-tRNA in the A site becomes a peptidyl-tRNA when it receives the carboxyl group of the growing polypeptide chain from the peptidyl-tRNA in the P site. After the free tRNA leaves, the extended polypeptide on its new tRNA is then moved to the P site by EF-G. Answer (d) is Incorrect because transfer RNAs bearing aminoacyl derivatives with free amino groups are never found in the P site.

17 Which of the following statements about the aminoacyl-tRNA synthetase reaction are correct? (a) ATP binds to the synthase. (b) GTP binds to the synthase. (c) The amino acid is attached to the 2′- or 3′-hydroxyl of the nucleotide cofactor (ATP). (d) The amino group of the amino acid is activated. (e) A mixed anhydride bond is formed. (f) An acyl ester bond is formed. (g) An acyl thioester bond is formed. (h) A phosphoamide (P-N) bond is formed.

a, e, f. The carboxyl group of the amino acid is activated in a two-step reaction via the formation of an intermediate containing a mixed anhydride linkage to AMP. The amino acid is ultimately linked by an ester bond to the 2′- or 3′-hydroxyl of the tRNA.

11. Purified duplex DNA molecules can be (a) linear. (b) circular and supercoiled. (c) linear and supercoiled. (d) circular and relaxed, that is, not supercoiled.

a,b,d d. Answer (d) is correct because, if at least one discontinuity exists in the phosphodiester backbone of either chain of a circular duplex molecule, the chains are free to rotate about one another to assume the relaxed circular form.

3. During translation, the mRNA is read in the _____ direction and protein synthesized in the _____ direction. a. 5′-to-3′; amino-to-carboxyl b. 3′-to-5′; carboxyl-to-amino c. 5′-to-3′; carboxyl-to-amino d. 3′-to-5′; amino-to-carboxyl

a. 5′-to-3′; amino-to-carboxyl Correct. The 5' end of the message corresponds to the amino end of the protein and the 3' end of the message to the carboxyl end.

As a sample of DNA is heated, it is said to melt. What is occurring? a. As hydrogen bonds are broken, the two strands separate. b. The DNA is converted from a solid to a liquid state. c. The large polymeric DNA is broken down into smaller pieces as the backbone is partially hydrolyzed. d. The DNA becomes less soluble and precipitates out of solution. e. The glycosidic linkages are broken, causing separation of the bases from the backbone.

a. As hydrogen bonds are broken, the two strands separate. The temperature at which this process is halfway complete is referred to as the Tm or melting temperature.

7. Which of the following is TRUE regarding the relationship of replication and transcription of DNA? a. Replication requires both a template and a primer, while transcription requires only a template. b. Copies of both DNA strands are made during both processes. c. Both utilize the same nucleotides. d. The polymerase for both require a Mn2+ cofactor for activity. e. Both have extensive processes to Correct errors.

a. Replication requires both a template and a primer, while transcription requires only a template. DNA polymerase requires both a template and a primer while the RNA polymerase requires only a template.

18. The G°′of the reaction catalyzed by the aminoacyl-tRNA synthetases is (a) ~0 kcal/mol. (b) <0 kcal/mol. (c) >0 kcal/mol.

a. Since the standard free energy of the hydrolysis of an aminoacyl-tRNA is nearly equal to that of the hydrolysis of ATP, the reaction has a G°′~ 0; that is, it has an equilibrium constant near 1.

[39] 1. The genetic code is said to be degenerate. This means that a. an amino acid may be specified by more than one codon. b. a codon may specify more than one amino acid. c. a codon may code for no amino acid. d. all amino acids are represented by an equal number of codons. e. the third base of the codon is irrelevant in determining the amino acid it codes for.

a. an amino acid may be specified by more than one codon. Correct. Some amino acids may be specified by as many as six codons.

3. Gene regulation in eukaryotes involves reorganization of chromatin structure such that DNA binding is weakened in regions to be transcribed. This is accomplished through a. chemical modification of histone proteins. b. enzymatic degradation of histone proteins. c. release of histone proteins by competition with other nuclear proteins. d. chemical modifications to the DNA that weaken histone association. e. release of histone proteins by DNA helicase.

a. chemical modification of histone proteins. Correct. The acetylation and deacetylation of lysine amino groups on histones are believed involved in regulation of gene expression.

[CH.34] For DNA replication to occur, the two strands of the double helix must be physically separated. This separation is accomplished through the use of a. helicase enzymes. b. topoisomerase enzymes. c. breaking and rejoining of one of the DNA strands. d. single-stranded-binding (SSB) protein. e. primase.

a. helicase enzymes. Correct. The helicase enzymes use the energy of ATP hydrolysis to separate the two strands of DNA.

2. During ribosomal protein synthesis, the growing peptide chain a. is transferred from the tRNA in the P site to the amino acyl tRNA in the A site. b. is transferred from the tRNA in the E site to the amino acyl tRNA in the P site. c. is transferred from the tRNA in the A site to the amino acyl tRNA in the P site. d. is transferred from the tRNA in the P site to the amino acyl tRNA in the E site. e. is transferred from the tRNA in the A site to the amino acyl tRNA in the E site.

a. is transferred from the tRNA in the P site to the amino acyl tRNA in the A site. Correct. Transfer is always from the P site to the A site.

There are five DNA polymerases in E. coli. Which of the following is NOT a function of these enzymes? a. primer formation b. primer removal c. DNA replication d. DNA repair e. exonuclease activity

a. primer formation

The primase enzyme a. synthesizes a short stretch of RNA complementary to a part of the template DNA strand. b. synthesizes a short stretch of DNA that is complementary to a part of the template strand of DNA. c. acts as the recognition site to which DNA polymerases bind to start the replication process. d. replaces the RNA primers used to initiate DNA replication with DNA polymerase. e. ligates the nicks formed by discontinuous replication along the lagging strand.

a. synthesizes a short stretch of RNA complementary to a part of the template DNA strand. Correct. The short segment of RNA serves as the primer to which newly synthesized deoxynucleotides are added at the 3′-end.

EF-Ts

associates with EF-Tu to release a bound nucleoside diphosphate

Which of the following statements is true? (a) RNA polymerase I transcribes a single precursor that encodes 18S, 28S, 5.8S and 5S rRNA. (b) The pre-rRNA is modified by methylation, directed by snoRNAs. (c) Most of the processing steps take place in the nucleolus. (d) The pre-rRNA is cleaved before post-transcriptional modification.

b and c are true. Answer a is false because RNA polymerase I, not RNA polymerase III, encodes 5S rRNA. Answer d is false because the pre-rRNA is modified before it is cleaved.

Which of the following statements about DNA ligase are correct? (a) It forms a phosphodiester bond between a 5′-hydroxyl and a 3′-phosphate in duplex DNA. (b) It requires a cofactor, either NAD_ or ATP, depending on the source of the enzyme, to provide the energy to form the phosphodiester bond. (c) It catalyzes its reaction by a mechanism that involves the formation of a covalently linked enzyme adenylate. (d) It catalyzes its reaction by a mechanism that involves the activation of a DNA phosphate through the formation of a phosphoanhydride bond with AMP. (e) It is involved in DNA replication, repair, and recombination.

b, c, d, e. Answer (a) is incorrect because the enzyme joins a 3′-hydroxyl to a 5′-phosphate.

7. Which of the following statements about translation are correct? (a) Amino acids are added to the amino terminus of the growing polypeptide chain. (b) Amino acids are activated by attachment to tRNA molecules. (c) A specific initiator tRNA along with specific sequences of the mRNA ensures that translation begins at the correct? codon. (d) Peptide bonds form between an aminoacyl-tRNA and a peptidyl-tRNA positioned in the A and P sites, respectively, of the ribosome. (e) Termination involves the binding of a terminator tRNA to a stop codon on the mRNA.

b, c, d. Answer (a) is Incorrect because the incoming activated aminoacyl-tRNA, in the A site of the ribosome, adds its free amino group to the activated carboxyl of the growing polypeptide on a peptidyl-tRNA in the P site. Answer (e) is Incorrect because termination does not involve tRNAs that recognize translation stop codons but rather protein release factors that recognize these and cause peptidyl transferase to donate the growing polypeptide chain to H2O rather than to another aminoacyl-tRNA.

Which of the following statements about release factors are Correct? (a) They recognize terminator tRNAs. (b) They recognize translation stop codons. (c) They cause peptidyl transferase to use H2O as a substrate. (d) There are two proteins in E. coli, each of which recognizes two mRNA triplet sequences.

b, c, d. Each of the two release factors of E. coli recognizes two of the three translation stop codons and interacts with the synthesis machinery such that peptidyl transferase donates the polypeptide chain to H2O and thus terminates synthesis by hydrolyzing the ester linkage of the protein to the tRNA

11. The sequence of a duplex DNA segment in a longer DNA molecule is 5'-ATCGCTTGTTCGGA-3′ 3′-TAGCGAACAAGCCT-5' When this segment serves as a template for E. coli RNA polymerase, it gives rise to a segment of RNA with the sequence 5′-UCCGAACAAGCGAU-3′. Which of the following statements about the DNA segment are correct? (a) The top strand is the coding strand. (b) The bottom strand is the sense strand. (c) The top strand is the template strand. (d) The bottom strand is the antisense strand.

b, c. The sense (bottom) strand of the template DNA has the same sequence as the mRNA.

13. Which of the following statements about eukaryotic translation are correct? (a) A formylmethionyl-tRNA initiates each protein chain. (b) It occurs on ribosomes containing one copy each of the 5S, 5.8S, 18S, and 28S rRNA molecules. (c) The Correct AUG codon for initiation is selected by the base-pairing of a region on the rRNA of the small ribosomal subunit with an mRNA sequence upstream from the translation start site. (d) It is terminated by a release factor that recognizes stop codons and hydrolyzes GTP. (e) It involves proteins that bind to the 5'ends of mRNAs. (f) It can be regulated by protein kinases.

b, d, e, f. Eukaryotic ribosomes usually scan the mRNA from the 5′ end for the first AUG codon, which then serves to initiate the synthesis. Answer (e) is correct because proteins that bind to the cap of the mRNA are involved in the association of the ribosome with the mRNA

In eukaryotes, DNA is present in a chromatin structure. Chromatin is made up of a. DNA that is highly compacted by interaction with itself. b. DNA that is highly ordered by wrapping around histones. c. DNA that is tightly associated with the inner face of the nuclear membrane. . d. DNA that is highly compacted by supercoiling. e. DNA that is highly compacted by compartmentalization in a series of vesicles.

b. DNA that is highly ordered by wrapping around histones. Correct. The wrapping of DNA around histone cores generates structures known as nucleosomes that are the basic units of chromatin.

4. Which of the following is NOT true regarding the differences between gene transcription in eukaryotes and prokaryotes? a. Most eukaryotes use multiple transcription factors rather than single transcription factors. b. Most eukaryotes have regulatory sites that are close to their promoters. c. Prokaryotic transcription factors usually interact directly with RNA polymerase while eukaryotic transcription factors do not. d. Most prokaryotes transcribe multiple genes under the regulation of a single operon. e. Eukaryotic transcription factors promote remodeling of the chromatin while prokaryotic transcription factors do not.

b. Most eukaryotes have regulatory sites that are close to their promoters. Correct. This statement is false. Most eukaryotes have regulatory sites that are FAR from their promoters, while prokaryotes have transcription-factor binding sites that are close to their promoters.

Which of the following is NOT seen in the editing of RNA in eukaryotes? a. modification of sequences b. adding a poly(A) tail to the 5′ end c. splicing together of the exons d. methylation of certain residues e. adding a 5′ methylguanylate cap

b. adding a poly(A) tail to the 5′ end Correct. A 5'-poly(A) tail is NOT observed. A poly(A) tail is added to the 3' end of mRNAs, not to the 5' end.

7. The enzymes responsible for attaching amino acids to tRNAs are the _____. There are at least 20 different enzymes for the 20 _____. a. aminoacyl tRNA synthetases; codons b. aminoacyl tRNA synthetases; amino acids c. ribosomes; codons d. ribosomes; amino acids e. elongation factors; amino acids

b. aminoacyl tRNA synthetases; amino acids Correct.

The process wherein two separated DNA strands reunite to form a double helix is called a. freezing. b. annealing. c. supercoiling. d. ligation. e. recombination.

b. annealing. The annealing process occurs spontaneously when the temperature is lowered below the Tm.

The catabolite activator protein (CAP) is also involved in regulation of transcription of certain prokaryotic genes. It functions by a. binding to DNA in the region of promoter sites and recruiting RNA polymerase there. b. forming a complex with cAMP which binds to DNA in the region of promoter sites and recruiting RNA polymerase there. c. binding to RNA polymerase forming a complex which enhances the activity of the polymerase although the CAP is not in contact with DNA. d. forming a complex with cAMP which binds to DNA in the region of promotor sites and blocks RNA polymerase access there. . e. binding to RNA polymerase forming a complex that inhibits RNA polymerase activity. .

b. forming a complex with cAMP which binds to DNA in the region of promoter sites and recruiting RNA polymerase there. Correct. The CAP binds to DNA and exerts its effects on transcription only when cAMP is bound to it.

5. The major interaction stabilizing the double helical structure of DNA is a. the favorable charge-charge interactions between the two strands. b. hydrogen bonds between bases on the two strands. c. hydrogen bonding between the backbone components of the two strands. d. van der Waals interactions between the stacked bases of the double helix. e. covalent bonds that crosslink the two strands.

b. hydrogen bonds between bases on the two strands. Correct. Hydrogen bonds not only stabilize the interaction between the two strands; they are key to understanding the replication of DNA.

2. One of the benefits of the degeneracy of the genetic code is that a. it conserves on material, as the same codon can be used over and over in different genes. b. it lessens the chance of deleterious mutations. c. it makes possible the use of a nonoverlapping, unpunctuated code. d. it allows for the tRNA to proofread the mRNA sequence and Correct any mistakes. e. it ensures that methionine will be used only at the start of translation.

b. it lessens the chance of deleterious mutations. Correct. Not only does it decrease the chances of making a premature stop codon, the fact that similar codons often code for identical or similar amino acids means than not all mutations will result in a drastically altered protein.

. DNA replication is Escherichia coli begins at a unique site called the: a. origin of responsiveness. b. origin of replication. (Oric) c. replication origination site. d. oriDNA. e. start site.

b. origin of replication. (oric) Correct.

IF1

binds to the 30S ribosomal subunit, cycles on and off the ribosome, prevents the combination of the 50S and 30S subunits

IF3

binds to the 30S ribosomal subunit, cycles on and off the ribosome, prevents the combination of the 50S and 30S subunits

IF2 the P site

binds to the 30S ribosomal subunit; delivers fMet-tRNAf Met to the P site,) cycles on and off the ribosome, binds GTP

The prokaryotic RNA polymerase holoenzyme has an α2 β β' σ subunit structure. Which of the following statements is TRUE regarding this enzyme? a. The holoenzyme is required in all steps of transcription. b. Although present throughout the transcription process, the σ subunit is required for recognition of promotor sites but not for elongation steps in RNA synthesis. c. The σ subunit is only involved in initiation of transcription and dissociates from the enzyme after RNA synthesis begins. d. The β, β′, and σ subunits are involved in initiation of transcription and dissociate from the α2 subunits after RNA synthesis begins. e. The α2 and σ subunits are involved in initiation of transcription and dissociate from the β and β′ subunits after RNA synthesis begins.

c. The σ subunit is only involved in initiation of transcription and dissociates from the enzyme after RNA synthesis begins. Correct. After initiation of transcription has occurred the σ subunit dissociates from the core enzyme (α2 β β'), which can carry out the elongation process without the σ subunit.

[37] Gene regulation in eukaryotes is much more complex than in prokaryotes. Which of the following does NOT contribute to this added complexity? a. Eukaryotic genes are generally not organized into operons. b. Different cell types express different genes. c. There are significant differences in the genetic code between prokaryotes and eukaryotes. d. DNA packing and organization into chromatin are insignificant. e. The relative size of eukaryotic genomes is immaterial.

c. There are significant differences in the genetic code between prokaryotes and eukaryotes. Correct. The genetic code is the same in prokaryotes and eukaryotes.

In E. coli, the lac operon is turned on by a. a derivative of lactose (allolactose) binding to the gene for a regulatory protein which when produced binds to the operator of the lac operon and initiates its transcription. b. a derivative of lactose (allolactose) binding to a regulatory protein which is bound to the operator of the lac operon which can only be transcribed when the lactose-regulatory protein complex is bound to the operator. c. a derivative of lactose (allolactose) binding to a regulatory protein which is bound to the operator of the lac operon and resulting in the release of the regulatory protein from the operon. d. a derivative of lactose (allolactose) binding to the operator of the lac operon and causing release of the regulatory protein from the operon. e. a derivative of lactose (allolactose) binding to the gene for a structural protein, which when produced binds to the regulator of the lac operon and initiates its transcription.

c. a derivative of lactose (allolactose) binding to a regulatory protein which is bound to the operator of the lac operon and resulting in the release of the regulatory protein from the operon. Correct. Binding of allolactose to the regulatory protein causes its release from the operator of the lac operon such that transcription can occur.

3. During protein synthesis, which of the following is NOT an energy-requiring step? a. formation of amino acyl tRNAs b. delivery of amino acyl tRNAs to the ribosome c. formation of the peptide bond d. translocation of the mRNA and tRNA within the ribosome e. dissociation of the 70S ribosome after translation termination.

c. formation of the peptide bond Correct. No energy input is required for this step. It is a spontaneous process in which an ester bond is replaced by a stronger peptide (amide) bond.

During RNA synthesis, the coding strand: a. is complimentary to the RNA transcript. b. has the same sequence as the RNA transcript. c. is also referred to as the sense strand. d. is also referred to as the template strand. e. is also referred to as the plus strand.

c. is also referred to as the sense strand. Correct.

4. The difference between a nucleoside and a nucleotide is that a. they contain different sugars b. the bases are attached to the sugars at different carbons c. one contains phosphate attached via an ester linkage d. one is used to synthesize DNA and the other, RNA. e. one contains a purine and the other a pyrimidine base

c. one contains phosphate attached via an ester linkage Correct. Nucleotides are phosphate esters of nucleosides.

During transcription, separation of the DNA strands is necessary. This involves: a. separation of the DNA into single stranded stem-loops. b. separation of long segments of the DNA corresponding to genes. c. separation in only a small segment of DNA at a time. d. separation of the DNA strands one base pair at a time. e. separation of the DNA with association of single-stranded-binding proteins.

c. separation in only a small segment of DNA at a time. Correct. The "transcription bubble" is only about 17 base pairs in length.

6. Which of the following is NOT true of tRNA? a. tRNA contains an amino acid attachment site. b. tRNA stands for transfer RNA. c. tRNA contains a codon. d. tRNA contains unusual bases. e. tRNA is L-shaped.

c. tRNA contains a codon. Correct.

DNA is more resistant to hydrolysis than RNA. What feature of DNA is responsible for this characteristic? a. the difference in base composition between DNA and RNA b. the difference in the backbone linkages in DNA and RNA c. the absence of a 2′-hydroxyl group in deoxyribose d. the difference in glycosidic linkages between DNA and RNA e. the shorter length of RNA polymers relative to those of DNA

c. the absence of a 2′-hydroxyl group in deoxyribose Correct. The presence of a 2'-hydroxyl group in RNA is responsible for its greater susceptibility to hydrolysis. The 2'-OH can attack the 3'-phosphate, leading to hydrolytic cleavage of the phosphodiester bond.

[CH 36] 1. Which of the following is NOT a difference between DNA and RNA synthesis? a. the nature of the nucleotide used b. the need for a primer c. the direction of synthesis d. the presence of discrete termination signals e. the simultaneous coding from both strands of DNA.

c. the direction of synthesis Correct. Synthesis of both DNA and RNA proceeds in the 5' 3' direction. In each case, the template strand is read in the 3' to 5' direction.

3. Which of the following accounts for the increased rate of DNA synthesis necessary for replication in eukaryotic cells as compared to that in prokaryotes? a. the use of different chemistry by the DNA polymerase enzymes b. the lack of need for a proofreading mechanism to Correct errors c. the presence of multiple origins at which replication can take place at the same time d. the ability to replicate in both the 5′ to 3′ and 3′ to 5′ directions e. the presence of telomere DNA

c. the presence of multiple origins at which replication can take place at the same time Correct. Prokaryotic DNA has a single origin of replication while eukaryotic DNA contains many. About 30,000 origins of replication are estimated in human DNA.

4. Termination of protein synthesis occurs when a stop or termination codon is in the A site. This occurs because a. the stop codons recognize specific termination tRNAs that do not have amino acids attached to them. b. as the stop codon moves from the A site to the P site the tRNA containing the newly synthesized protein is released. c. these codons are recognized by specific proteins which also release the newly synthesized protein chain from the ribosome. d. there are no tRNAs that base pair with stop codons, so translation stalls and the ribosome dissociates. e. EF-G binds to the empty A-site and pushes the P-site tRNA with attached peptide out of the ribosome.

c. these codons are recognized by specific proteins which also release the newly synthesized protein chain from the ribosome. Correct. These proteins are known as release factors.

CAP binding site

contains a binding sequence for the

8. Which of the following is NOT found in a eukaryotic ribosome? a. α helices b. β sheets c. RNA duplexes d. DNA duplexes e. catalytic RNA

d. DNA duplexes Correct.

The filling of the gaps between the fragments of the lagging strand after the removal of the multiple RNA primers is achieved by: a. DNA polymerase I. b. DNA polymerase III. c. DNA ligase. d. DNA polymerase I and DNA ligase. e. DNA polymerase III and DNA ligase.

d. DNA polymerase I and DNA ligase. Correct.

4. During attachment of an amino acid to its tRNA, how is ATP required? a. The free energy of hydrolysis of ATP is used to provide the energy necessary to link the free amino acid to the tRNA. b. The ATP forms an adenylate-tRNA complex that is activated in such a way that the adenylate can be displaced by the amino acid. c. The ATP phosphorylates the 3′-OH of the tRNA that is activated in such a way that the phosphate can be displaced by the amino acid. d. The ATP forms an amino acyl adenylate that transfers the activated amino acid to the tRNA. e. The ATP phosphorylates the carboxyl terminal of the amino acid that transfers the activated amino acid to the tRNA.

d. The ATP forms an amino acyl adenylate that transfers the activated amino acid to the tRNA. Correct. The amino acyl adenylate represents an activated form of the amino acid, capable of transferring it to the tRNA.

[38] 1. Many eukaryotic genes are divided into mosaics of exons and introns with only the exon portions containing the coding sequence for a protein. Which of the following is TRUE? a. The introns are transcribed, spliced and translated with the exons. b. The introns are neither transcribed, spliced nor translated. c. The introns are transcribed and spliced, but translated separately. d. The introns are transcribed and spliced out before translation. e. The introns are transcribed, spliced, translated, and removed post translation.

d. The introns are transcribed and spliced out before translation. Correct. They are transcribed onto a pre-mRNA but spliced out to form the mature mRNA before it leaves the nucleus.

The structural genes in an operon a. are all co-transcribed as a single mRNA when the operator is bound by the regulator. b. are transcribed individually as separate mRNAs when an operator is bound by the regulator. c. are transcribed individually when the regulator molecule is bound at the operator for each gene. d. are all cotranscribed as a single mRNA when the operator is not bound by the regulator. a single mRNA. e. are transcribed individually as separate mRNAs when an operator is not bound by the regulator.

d. are all cotranscribed as a single mRNA when the operator is not bound by the regulator. Correct. When an operator is not bound by the regulator, all genes within that operon are cotranscribed as a single mRNA.

[CH 40] Initiation of protein synthesis involves GTP hydrolysis associated with what step? a. dissociation of the 70S ribosome into 30S and 50S subunits such mRNA and formyl-methionine tRNAf can bind b. binding of IF2(GTP) to formyl-methionine tRNAf c. binding of the mRNA and formyl-methionine tRNAf to the 30S subunit of the ribosome d. binding of the 50S subunit to the 30S subunit with bound mRNA and formyl-methionine tRNAf e. peptide bond formation between formyl-methionine and the next amino acid coded for by the mRNA

d. binding of the 50S subunit to the 30S subunit with bound mRNA and formyl-methionine tRNAf Correct. The hydrolysis of GTP at this step leads to the release of protein initiation factors allowing the 50S subunit to bind to form the 70S ribosome.

4. During the replication of prokaryotic DNA, a. both strands are simultaneously synthesized in a continuous manner. b. one strand is synthesized in a continuous manner and the other is synthesized by reverse transcription. c. both stands are simultaneously synthesized in short pieces which are later joined by DNA ligase. d. one strand is synthesized continuously and the other is synthesized in short segments. e. both strands are synthesized continuously, but the lagging strand is synthesized only after the leading strand has been completely replicated.

d. one strand is synthesized continuously and the other is synthesized in short segments. Correct. The leading strand is synthesized in a continuous fashion and the lagging strand is made in short pieces known as Okazaki fragments.

Which of the following is found in DNA but not in RNA? a. guanosine triphosphate b. purine c. ribose d. thymine e. uracil

d. thymine

8. If glucose is scarce, but lactose is available, the lac operon will act to increase the levels of these proteins. a. galactosidepermease and allolactose b. inducer and galactosidetransacetylase c. β-galactosidase and allolactose d. β-galactosidase and galactosidepermease Correct. e. β-galactosidase and inducer

d. β-galactosidase and galactosidepermease Correct.

EF-Tu

delivers aminoacyl-tRNA to the A site , cycles on and off the ribosome, binds GTP, is involved in the hydrolysis of GTP to GDP

5. If the anticodon of an alanyl-tRNA is IGC (inosine-guanine-cytosine), to which of the following codons would it bind? a. GCU only b. GCC only c. GCU or GCC only d. GCU or GCA only e. GCU, GCC, or GCA

e. GCU, GCC, or GCA Correct. Wobble base pairing is allowed in the third position of the codon. Therefore, IGC could recognize GCU, GCC or GCA.

5. Which of the three eukaryotic RNA polymerases can be found in the nucleoplasm? a. RNA polymerase I b. RNA polymerase II c. RNA polymerase III d. RNA polymerase I and RNA polymerase II . e. RNA polymerase II and RNA polymerase III

e. RNA polymerase II and RNA polymerase III Correct.

5. Which of the following is TRUE of the tRNA binding sites of the ribosome? a. The E site stands for the "entry" site. b. The P site stands for the "polypeptide channel site." c. The A site stands for the "active site." d. The active site is located between the E and P sites. e. The A site is closer to the 3' end of the mRNA molecule being translated than the P site.

e. The A site is closer to the 3' end of the mRNA molecule being translated than the P site. Correct.

6. Proteins destined for excretion from the cell are ultimately synthesized on ribosomes located: a. at the cell membrane. b. on the Golgi. synthesized in this organelle. c. in the cytoplasm. d. on the smooth endoplasmic reticulum. synthesized in this organelle. e. on the rough endoplasmic reticulum.

e. on the rough endoplasmic reticulum. Correct.

peptidyl transferase

forms the peptide bond, hydrolyzes peptidyl-tRNA

primase

is an RNA polymerase

leading strand replication in association with dnaA

is synthesized continuously

replication fork

is the locus of DNA unwinding

oriC of replication fork movement

is the locus of DNA unwinding, binds dnaA, dnaB, and dnaC proteins, is the point of initiation of synthesis

DNA ligase

joins lagging strand pieces to each other, uses NAD to form phosphodiester bonds

EF-G

moves the peptidyl-tRNA from the A to; , cycles on and off the ribosome, binds GTP, is involved in the hydrolysis of GTP to GDP

e subunit of DNA polymerase III

performs "proofreading" on most of the DNA synthesized

Which of the following is released during the addition of deoxyribonucleotides to the nascent DNA chain? dNTP pyrophosphate (PPi) ATP Okazaki fragments AMP

pyrophosphate (PPi)

RF1

recognizes stop codons, cycles on and off the ribosome, modifies the peptidyl transferase reaction

RF2

recognizes stop codons, cycles on and off the ribosome, modifies the peptidyl transferase reaction

DNA gyrase

relieves positive supercoiling, hydrolyzes ATP to reduce the linking

single-strand binding protein (ssb)

stabilizes unwound DNA

Okazaki fragment and dnaC proteins

synthesis direction is opposite that, ) is synthesized continuously

DNA polymerase I number of DNA

synthesis direction is opposite that, fills in gaps where RNA existed, contains a 5'⟶3'exonuclease that removes RNA primers

lagging strand

synthesis direction is opposite that, is synthesized discontinuously

DNA polymerase III holoenzyme

synthesizes most of DNA

DnaB helicase

unwinds strands at the origin of