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medical sciences
biochemistry
Fundamentals of biochemistry Life at the Molecular Level 4th edition Donald Voet, Judith G. Voet, Charlotte W. Pratt - Solutions
What is the probability that the palindromic symmetry of the trp repressor target DNA sequence (Section 24-4B) is merely accidental?
The E. coli genome contains approximately 4639 kb. (a) How many copies of the 6-bp recognition sequence for the trp repressor would be expected to occur in the E. coli chromosome? (b) Explain why it is advantageous for the trp repressor to be a dimer that recognizes two adjacent 6-bp sequences.
The enzyme ornithine decarboxylase generates a product that has been proposed to play a role in stabilizing compacted DNA. Draw the structure of the ornithine decarboxylase reaction product and explain how it interacts with DNA.
For a linear B-DNA molecule of 50,000 kb, calculate (a) The contour length and (b) The length of the DNA as packaged in nucleosomes with linker histones present.
Calculate the length of the 50,000-bp DNA in a 30-nm fiber.
Most protein-coding genes are present in just one copy per genome. Explain why eukaryotic genomes typically contain dozens of copies of histone genes.
Amino acid residues in proteins are each specified by three contiguous bases. What is the contour length of a segment of B-DNA that encodes a 50-kD protein?
Eukaryotic DNA is typically covalently modified by methylation of certain nucleotide bases. How would the addition of methyl groups affect the packaging of DNA in nucleosomes?
A standard A ˆ™ T base pair is shown in Fig. 24-1. Under certain conditions, an adenine residue in B-DNA can transiently adopt the syn conformation. Draw the resulting A ˆ™ T base pair. Is the helix diameter larger or smaller in this alternate arrangement?In Figure 24.1
A standard G ˆ™ C base pair is shown in Fig. 24-1. Under certain conditions, the guanine residue can transiently adopt the syn conformation. Draw the resulting G ˆ™ C base pair, which has two hydrogen bonds.In Problem 24.1
The ends of eukaryotic chromosomes terminate in a G-rich single- stranded overhang that can fold up on itself to form a fourstranded structure. In this structure, four guanine residues assume a hydrogen-bonded planar arrangement with an overall geometry that can be represented asDraw the complete
Show schematically how a single strand of four repeating TTAGGG sequences can fold to generate a structure with three stacked G quartets linked by TTA loops.
Compounds known as peptide nucleic acids (PNAs) have been developed as nucleic acid-binding probes. A PNA molecule has a polypeptide-like backbone with purine and pyrimidine bases attached as side chains. Draw the PNA backbone resulting from amide bond formation between two molecules of N-(2-
What feature of DNA replication, as shown in Figure, is inconsistent with the known enzymatic properties of DNA polymerases? What observation reconciled this inconsistency?
In the pairs of DNA sequences below, the lower duplex represents a mutagenized daughter duplex. Identify the mutation as a transition, a transversion, an insertion, or a deletion.(a)(b)
What kinds of mutations does 5-bromouracil generate?
Match the compound on the left with the kind of mutation on the right. ____ Acridine orange A. Transition ____ Nitrous acid B. Transversion ____ Ethylnitrosourea C. Insertion or deletion ____ Dimethyl sulfate ____ Ethidium bromide
Match the proteins below with their roles in DNA repair. A. O6-alkylguanine-DNA alkyltransferase B. UvrABC endonuclease C. Uracil-DNA glycosylase D. RecA ____ Removes 7-methyladenine residues from damaged DNA ____ Serves as a sink for methyl residues abstracted from O6-methylguanine residues ____
You transformed a strain of E. coli with a plasmid containing a transposon that includes an ampicillin-resistance gene. To recover the plasmid, you pick a colony from a culture plate containing ampicillin. Much to your surprise, the plasmid you recover is twice the size you expected. You then pick
Describe the roles of the exonuclease activities of Pol I?
For each of the enzymes and proteins listed below, match the function or feature related to DNA replication in E. coli. A. DNA polymerase I B. DNA polymerase II C. DNA polymerase III D. DNA ligase E. DnaB F. Single-strand binding protein G. Primase H. Tus protein I. DNA gyrase ____ Required for
From the gut of a slug in your garden you have identified a new circular, double-stranded DNA-containing bacteriophage. Electron micrographs of infected bacteria during production of phage progeny reveal the structures shown below (thick lines represent double-stranded DNA and thin lines represent
Which eukaryotic DNA polymerase is most likely responsible for the following activities: (a) Synthesizing the leading strand, (b) Synthesizing the lagging strand, (c) Synthesizing mitochondrial DNA, (d) Initiating DNA replication?
Why does reverse transcription of retroviral DNA require a specific host tRNA for DNA synthesis? What section of the tRNA is most likely to be involved?
When reverse transcriptase is used in the oligo(T)-primed synthesis of double-stranded DNA from a specific cellular mRNA, the aggregate length of the resulting double stranded cDNA is sometimes twice as long as that of the mRNA template. Explain this phenomenon?
In some experimental systems, a newly synthesized RNA primer is transferred from primase to the clamp or clamp loader rather than directly to DNA polymerase. Explain why this would maximize the efficiency of DNA replication.
Why can't a linear duplex DNA, such as that of bacteriophage T7, be fully replicated by just E. coli-encoded proteins?
Telomerase adds six deoxynucleotides to the end of a DNA strand using a built-in RNA template. Explain why the templating region of the RNA includes one and a half repeats of the telomeric sequence (~9 nucleotides).
The base analog 5-bromouracil (5BU),Which sterically resembles thymine, more readily undergoes tautomerization from its keto form to its enol form than does thymine. 5BU can be incorporated into newly synthesized DNA when it pairs with adenine on the template strand. However, the enol form of 5BU
Hydroxylamine (NH2OH) converts cytosine to the compound shown below.With which base does this modified cytosine pair? Does this generate a transition or a transversion mutation?
Oxidative deamination of adenine produces hypoxanthine (the base of inosine), which can base pair with cytosine. (a) If no repair takes place, describe the makeup of the DNA in the two daughter cells following cell division. (b) Describe the makeup of the DNA in the four daughter cells following a
Approximately how many Okazaki fragments are synthesized in the replication of the human genome?
A certain mutant DNA polymerase is error-prone, tending to incorporate C opposite a template A. When such a DNA polymerase replicates a segment of DNA containing an A ∙ T base pair, what will be the DNA composition in the daughter cells after (a) One and (b) Two rounds of cell division? Assume
According to the text, approximately 20,000 of 6.0 billion glycosidic bonds in the DNA of a diploid human cell spontaneously hydrolyze each day. What is the half-life in years of such a bond?
Yeast and some other organisms produce proteins that closely resemble O6-alkylguanine-DNA alkyltransferase but lack a Cys at the active site. (a) Explain why these proteins cannot remove an alkyl group attached to guanine. (b) These proteins do protect cells against DNA alkylation damage. In which
Certain sites in the E. coli chromosome are known as hot spots because they have unusually high rates of point mutations. Many of these sites contain a 5-methylcytosine residue. Explain the existence of such hot spots.
Since mammalian DNA contains roughly 25% thymine residues, why do mammalian cells need a thymine-DNA glycosylase?
Explain why base excision repair, nucleotide excision repair, and mismatch repair-which all require nucleases to excise damaged DNA-require DNA ligase.
In E. coli, all newly synthesized DNA appears to be fragmented (an observation that could be interpreted to mean that the leading strand as well as the lagging strand is synthesized discontinuously). However, in E. coli mutants that are defective in uracil-DNA glycosylase, only about half the newly
Explain why a DNA polymerase that could synthesize DNA in the 3' → 5' direction would have a selective disadvantage even if it had 5' → 3' proofreading activity.
Broken DNA can be repaired by DNA ligase (single-strand breaks) or nonhomologous end-joining (double-strand breaks). Explain why the cell's set of repair enzymes also includes tyrosyl-DNA phosphodiesterases.
E. coli DNA polymerase V has the ability to bypass thymine dimers. However, Pol V tends to incorporate G rather than A opposite the damaged T bases. Would you expect Pol V to be more or less processive than Pol III? Explain.
Predict whether loss of the following E. coli genes would be lethal or not: (a) DnaB (which encodes DnaB), (b) PolA (which encodes Pol I), (c) Ssb, (d) RecA.
During bacterial conjugation, two cells of the same or similar species make close contact and transfer genetic information. In the donor cell, an endonuclease nicks the DNA so that a single strand can enter the recipient cell. Explain why the stable incorporation of the transferred DNA requires
You have discovered a drug that inhibits the activity of inorganic pyrophosphatase. What effect would this drug have on DNA synthesis?
Why is it necessary to use only the Klenow fragment, rather than intact E. coli Pol I, in DNA sequencing reactions (Section 3-4C)?
The three DNA base pairs that fit within the active site of DNA polymerase have a conformation similar to that of A-DNA rather than the usual B-DNA. Why is it important for DNA polymerase to accommodate an A-type helix?
A reaction mixture contains DNA polymerase, the four dNTPs, and one of the DNA molecules whose structure is represented below. Which reaction mixtures generate PPi?
The prokaryotic RNA polymerase holoenzyme contains the core enzyme and a σ factor. What is the function of the core enzyme? What are its limitations in terms of enzymatic activity? What is the role of the σ factor?
The mRNA capping reaction involves cleavage of a methylated guanosine triphosphate to release its pyrophosphate. You wish to measure RNA chain initiation rates in isolated nuclei. Which of the isotopes shown below would you use? Explain. What assumptions are necessary to use this experimental
What is the role of SXL and U2AF in generating alternatively spliced tra mRNA transcripts in the Drosophila sex-determination pathway?
Describe the primer you would use to initiate reverse transcriptase-catalyzed synthesis of DNA that is complementary to a eukaryotic mRNA molecule?
What evidence suggests that newly transcribed RNA is not wound around its template DNA?
You are interested in discerning the role of σ factors in prokaryotic transcription, using asystem of purified core polymerase, a DNA template, a σ factor, and labeled nucleotides(32pppN). The incorporation of 32P into RNA at 2 different core enzyme concentrations (10-10 M and
Distinguish between enhancers and promoters?
You have discovered a novel eukaryotic RNA polymerase. To study this enzyme, you have developed an in vitro assay with an inhibitor of RNA chain elongation, 3′-deoxy-5′[α-32P] CTP. You are surprised by the fact that no 32P is found in the transcribed RNA! What does this result tell you about
Indicate whether the posttranscriptional modifications listed below occur in prokaryotes or in eukaryotes. (a) 5′ Cap (b) Polyadenylation (c) Methylation of nucleotide residues (d) Endonucleolytic cleavage (e) Splicing
The antibiotic cordycepin inhibits bacterial RNA synthesis.(a) Of which nucleoside is cordycepin a derivative? (b) Explain cordycepin's mechanism of action.
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
Predict the effect of the antibiotic bicyclomycin, an antibiotic that inhibits Rho, on gene expression in E. coli.
Certain E. coli bacteriophages encode a protein called Q, which binds to RNAP shortly after transcription initiation, before σ70 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
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?
TFIIB appears to interact with proteins that bind to sequences at the 3' end of genes. Explain how this interaction could enhance transcription of a gene.
Design an oligonucleotide-based affinity chromatography system for purifying mature mRNAs from eukaryotic cell lysates.
Human cells contain a protein that binds to the 5' triphosphate groups of RNA. Explain why this protein would be part of the defense against viral infection.
A eukaryotic cell carrying out transcription and RNA processing is incubated with 32P-labeled ATP. Where will the radioactive isotope appear in mature mRNA if the ATP is labeled at the (a) α position, (b) β position, and (c) γ position?
Compare DNA polymerase, RNA polymerase, poly(A) polymerase, and CCA-adding polymerase with respect to requirement for a primer, template, and substrates.
The bacterial enzyme polynucleotide phosphorylase (PNPase) is a 3 → S 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,
Explain why the O2'-methylation of ribose residues protects rRNA from RNases.
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?
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.
Indicate the -10 region, the -35 region, and the initiating nucleotide on the sense strand of the E. coli tRNATyr promoter shown below.
Why does promoter efficiency tend to decrease with the number of G ∙ C base pairs in the - 10 region of a prokaryotic gene?
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.
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
A eukaryotic ribosome contains four different rRNA molecules and ~ 82 different proteins. Why does a cell contain many more copies of the rRNA genes than the ribosomal protein genes?
Why is the genetic code degenerate?
Which of the following amino acids are likely to be linked to only one species of tRNA? What are their anticodons? (a) Phe (b) Leu (c) His
Reticulocyte (immature red blood cell) lysates can be made devoid of mRNA by ribonuclease treatment followed by inactivation and removal of the ribonuclease. These lysates are now capable of synthesizing protein when mRNA, GTP, and aminoacyl-tRNAs are added. How could you use this system to
Match each of the functions on the left with the appropriate prokaryotic protein on the right. ____ Binds fMet-tRNA and GTP....................................... A. RF-1 ____ Binds aminoacyl-tRNA and GTP. ................................ B. RF-2 ____ Recognizes Stop codons.
How could you show that the inhibition of protein synthesis in a bacterial cell extract bypuromycin is not irreversible?
You have isolated a temperature-sensitive mutant E. coli. At 34°C, the growth rate is nearly normal but is reduced 10-fold at 37°C. You eventually discover that EF-Tu·GDP binding to the ribosome is two-fold higher in the mutant at 37°C. What aspect of translation is affected by the mutation?
Which amino acid substitutions might occur in E. coli opal suppressors that arise by singlebase mutations?
The error rates of translation in some rapidly growing E. coli strains is as high as 2 percent. What is the percentage of correctly translated protein in such bacteria (assume the protein has 100 residues)? How can these bacteria do so well?
Distinguish between eukaryotic and prokaryotic polypeptide initiation, elongation, and termination?
What is the adaptive significance of posttranslational cleavage of proteins such as collagen and various hormones?
Proteins destined for membranes or secretion have a stretch of N-terminal hydrophobic amino acids called a signal sequence. What function does this sequence serve?
How many amino acid copolymers can be specified by polynucleotides consisting of two alternating nucleotides? What are the sequences of these polypeptides?
Predict the effect on protein structure and function of an A⋅T to G⋅C transition in the first codon position for lysine?
Identify the polypeptide encoded by the DNA sequence below, in which the lower strand serves as the template for mRNA synthesis?
Describe how nucleotide substitutions at different positions in codons affect the characteristics of the encoded amino acids?
What two reactions are carried out by aminoacyl-tRNA synthetases?
Could a single nucleotide deletion restore the function of a protein- coding gene interrupted by the insertion of a 4-nt sequence? Explain.
The enzyme thiouridylase converts certain tRNA uridine residues to 2-thiouridine. Draw the structure of this modified nucleotide.
Some mutations that do not alter the identity of the encoded amino acid lead to diminished production of the protein. How does the mutation affect translation?
Draw the structures of an I ∙ U wobble pair and an I ∙ C wobble pair.
Explain the significance of the observation that peptides such as fMet-Leu-Phe "activate" the phagocytotic (particle-engulfing) functions of mammalian leukocytes (white blood cells).
Explain why prokaryotic ribosomes can translate a circular mRNA molecule, whereas eukaryotic ribosomes normally cannot, even in the presence of the required cofactors.
Eukaryotic initiation factor eIF2B is a guanine nucleotide exchange factor. Explain why eIF2B would enhance the activity of eIF2.
EF-Tu binds all aminoacyl-tRNAs with approximately equal affinity so that it can deliver them to the ribosome with the same efficiency. Based on the experimentally determined binding constants for EF-Tu and correctly charged and mischarged aminoacyl- tRNAs (see table), explain how the tRNA-EF-Tu
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