Fundamentals of Biochemistry

Donald Voet, Judith G. Voet, Charlotte W. Pratt

Chapter 26

Transcription and RNA Processing - all with Video Answers

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Chapter Questions

Problem 1

The antibiotic cordycepin inhibits bacterial RNA synthesis.
(a) Of which nucleoside is cordycepin a derivative?
(b) Explain cordycepin's mechanism of action.

Shazia Naz

Shazia Naz

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Problem 2

The bacterial enzyme polynucleotide phosphorylase (PNPase) is a $3^{\prime} \rightarrow 5^{\prime}$ exoribonuclease that degrades mRNA.
(a) The enzyme catalyzes a phosphorolysis reaction, as does glycogen phosphorylase (Section $16-1$ ), rather than hydrolysis. Write an equation for the mRNA phosphorolysis reaction.
(b) In vitro, PNPase also catalyzes the reverse of the phosphorolysis reaction. What does this reaction accomplish and how does it differ from the reaction carried out by RNA polymerase?
(c) PNPase includes a binding site for long ribonucleotides, which may promote the enzyme's processivity. Why would this be an advantage for the primary activity of PNPase in vivo?

Shazia Naz

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Problem 3

Design a six-residue nucleic acid probe that would hybridize with the greatest number of $E .$ coli gene promoters.

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Problem 4

Why does promoter efficiency tend to decrease with the number of $G \cdot C$ base pairs in the -10 region of a prokaryotic gene?

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Problem 5

Many bacterial genes with related functions are arranged in operons, sets of contiguous genes that are under the control of a single promoter and are transcribed together. (a) What is the advantage of this arrangement? (b) How might eukaryotic cells, which do not contain operons, ensure the simultaneous transcription of different genes?

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Problem 6

A eukaryotic ribosome contains four different rRNA molecules and $\sim 82$ different proteins. Why does a cell contain many more copies of the rRNA genes than the ribosomal protein genes?

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Problem 7

Replication of many RNA viruses depends on RNA polymerase. The antiviral drug ribavirin does not inhibit the polymerase but instead increases its error rate. Explain how this affects the virus.

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Problem 8

Collisions between DNA polymerase and a slower-moving RNA polymerase using the same template strand may be responsible for the observation that leading strand synthesis in bacteria is discontinuous in vivo. Draw a diagram to show how DNA synthesis that has been halted after the DNA polymerase-RNA polymerase collision can resume using the RNA transcript as a primer.

Hailey Tomashek

Hailey Tomashek

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Problem 9

Predict the effect of the antibiotic bicyclomycin, an antibiotic that inhibits Rho, on gene expression in $E$. coli.

Shazia Naz

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Problem 10

Certain $E$. coli bacteriophages encode a protein called $Q$, which binds to RNAP shortly after transcription initiation but before $\sigma^{70}$ is released. Q increases the rate of transcription and renders RNAP resistant to Rho-dependent termination.
(a) Explain how Q could enhance expression of bacteriophage genes.
(b) Explain why the effect of $Q$ depends on its ability to interact with specific DNA sequences, not just RNAP.

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Problem 11

Design an oligonucleotide-based affinity chromatography system for purifying mature mRNAs from eukaryotic cell lysates.

Rabeya Zahid

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Problem 12

A eukaryotic cell carrying out transcription and RNA processing is incubated with $^{32}$ P-labeled ATP. Where will the radioactive isotope appear in mature mRNA if the ATP is labeled at the (a) $\alpha$ position,
(b) $\beta$ position, and
(c) $\gamma$ position?

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Problem 13

Compare DNA polymerase, RNA polymerase, poly(A) polymerase, and CCA-adding polymerase with respect to requirement for a primer, template, and substrates.

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Problem 14

Explain why the active site of poly(A) polymerase is much narrower than that of DNA and RNA polymerases.

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Problem 15

Explain why the $O^{2}$ -methylation of ribose residues protects rRNA from RNases.

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Problem 16

The $5^{\prime}$ end of some bacterial regulatory RNAs are linked to the $3^{\prime}$ OH group of the adenosine residue of $\mathrm{NAD}^{+}$. Propose a biological function for the modification and explain how the activity of the modified RNA might reflect the cell's overall metabolic activity

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Problem 17

Would you expect spliceosome-catalyzed intron removal to be reversible in a highly purified in vitro system and in vivo? Explain.

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Problem 18

Introns in eukaryotic protein-coding genes may be quite large, but almost none are smaller than about 65 bp. What is the reason for this minimum intron size?

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Problem 19

In what ways do histone gene transcripts differ from transcripts of other vertebrate protein-coding genes?

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Problem 20

$N^{6}$ methylation of adenosine residues is one of the most common mRNA modifications. (a) Draw the structure of the modified base. (b) Would you expect the modification to alter the RNA's ability to form stem-loop structures?

Shazia Naz

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Problem 21

Infection with certain viruses inhibits snRNA processing in eukaryotic cells. Explain why this favors the expression of viral genes in the host cell.

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Problem 22

Draw a diagram, including exons and introns, of a gene that encodes both membrane-bound and soluble forms of a protein. Explain how one gene can code for two different forms of a protein.

Rabeya Zahid

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Problem 23

Indicate the -10 region, the -35 region, and the initiating nucleotide on the sense strand of the $E .$ coli tRNA $^{\text {Tyr }}$ promoter.

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Problem 24

Diagram the likely secondary structure of an RNA with the sequence
$$\text{5'-UGCUGCCAUCUCUUUUCCUCUCUAUGCGAGGAUUUGGACUGGCAGCG3'}$$

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Problem 25

Explain why inserting 5 bp of DNA at the -50 position of $a$ eukaryotic gene decreases the rate of RNA polymerase II transcription initiation to a greater extent than inserting 10 bp at the same site.

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Problem 26

The RNA polymerase from bacteriophage T7 differs structurally from prokaryotic and eukaryotic RNAPs and is extremely specific for its own promoter. Why do these properties make T7 RNAP useful in experiments with recombinant DNA?

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Problem 27

TFIIB appears to interact with proteins that bind to sequences at the $3^{\prime}$ end of genes. Explain how this interaction could enhance transcription of a gene.

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Problem 28

Human cells contain a protein that binds to the $5^{\prime}$ triphosphate groups of RNA. Explain why this protein would be part of the defense against viral infection.

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Problem 29

If an enhancer is placed on one plasmid and its corresponding promoter is placed on a second plasmid that is catenated (linked) with the first, initiation is almost as efficient as when the enhancer and promoter are on the same plasmid. However, initiation does not occur when the two plasmids are unlinked. Explain.

Shazia Naz

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Problem 30

Why aren't primary rRNA transcripts present in wild-type $E$. coli?

Shazia Naz

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