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medical sciences
biochemistry

Questions and Answers of Biochemistry

Te average human chromosome contains about 1 × 108 bp of DNA.(a) If each base pair has a mass of about 660 daltons and there are about 2 g of protein (histones plus nonhistones) per gram of DNA, how
Forming nucleosomes and wrapping them into a 30-nm ﬁber provide part of the compaction of DNA in chromatin. If the ﬁber contains about six nucleosomes per 10 nm of length, what is the approximate
Huntington's disease is an inherited neurological ailment with a variable age of onset (see Chapter 22). A protein called huntingtin has a sequence of repeated glutamine residues, all encoded by CAG.
A sample of chromatin was partially digested by the enzyme Staphylococcal nuclease. The DNA fragments from this digestion were puriï¬ed and resolved on a polyacrylamide gel. A set of
Describe an experimental approach to determining the processivity of a DNA polymerase (i.e., the number of nucleotides incorporated per chain per polymerase binding event).
The 3′-exonuclease activity of E. coli DNA polymerase I was found to show no discrimination between correctly and incorrectly base-paired nucleotides at the 3′ -terminus; properly and improperly
2′, 3′-Dideoxyinosine has been approved as an anti-HIV drug. Propose a mechanism by which it might block the growth of the HIV virus.
What information would you need to tell whether the leading and lagging strands in yeast are replicated with equal ﬁdelity?
It takes 40 minutes to completely replicate the E. coli chromosome, even in an optimally nourished cell. However, bacterial cells can divide as frequently as every 20 minutes. How can cells divide
5-Bromouracil (BU) resembles thymine suﬃciently that BU base-pairs readily with adenine in a DNA helix, and it can readily substitute for thy-mine in DNA replication. However, its electron
The oxidation of a DNA-guanine residue to 8-oxoguanine (8-oxoG) is mutagenic, because 8-oxoG pairs readily with adenine in the next round of replication. Show a pathway beginning with the oxidation
In mammalian cells, genes that are expressed in a particular cell are reported to undergo replication during the ﬁrst half of S phase and genes not ex-pressed in that cell are replicated in the
DNA precursor imbalances are mutagenic. For example, if dGTP accumulates, it can compete with dATP for incorporation opposite dTMP in the template, leading to a transition mutation. Investigators
Bacteriophage T4 has a linear double-stranded DNA genome, yet mapping many mutations, as shown in Figure 22.11, generates a circular linkage map. How might you explain this discrepancy?
Match each enzyme name in the left column with the correct descriptive phrase in the right column.a. Topoisomerase II .................... i. Catalyzes most nucleotide
Adenylate cyclase, which synthesizes cyclic AMP from ATP, requires two metal ions, and the enzyme has the same constellation of amino acid residues in the active site as does DNA polymerase I. In
A mixture of four α-[32P]-labeled ribonucleoside triphosphates was added to permeabilized bacterial cells undergoing DNA replication in the presence of an RNA polymerase inhibitor, and incorporation
Deoxyadenylate residues in DNA undergo deamination fairly readily, as do deoxycytidylate residues. (a) What is the product of dAMP deamination? (b) Te deamination product is known to base-pair with
Te E. coli chromosome is 1.28 mm long. Under optimal conditions, the chromosome is replicated in 40 minutes.(a) What is the distance traversed by one replication fork in 1 minute?(b) If replicating
DNA ligase has the ability to relax super-coiled circular DNA in the presence of AMP but not in its absence. (a) What is the mechanism of this reaction, and why does it depend on AMP? (b) How could
Suppose that a replicative DNA polymerase had its 3′ exonuclease site 1.5 nm from the polymerase site, rather than the 3.0 nm seen in Klenow fragment. How would this change aﬀect the ﬁdelity of
Although DNA polymerases require both a template and a primer, the following single-stranded polynucleotide was found to serve as a substrate for DNA polymerase in the absence of any additional
Predict whether a dam methylasc deficiency would increase, decrease, or have no effect on spontaneous mutation rates, and explain the basis for your prediction.
In what ways can insertion of a transposon affect the expression of genes in the neighborhood of the insertion site?
Briefly explain how integration of a retroviral genome could activate transcription of genes adjacent to the integration site.
Outline a pathway for mutagenesis, comparable to that shown on page 711, resulting from a mut M gene mutation.
There is evidence that some oxidative damage to DNA occurs at the nucleotide level, with oxidation of a nucleotide, followed by incorporation of the damaged nucleotide into DNA. (a) Describe a
Consider the Meselson-Wcigle experiment. Which established that recombination occurs via breaking and joining of DNA strands. For the experiment outlined in the text, construct a graph showing the
For each DNA repair process in column I. list all characteristics from column II that correctly describe that process.I(a) Nucleotide excision repair(b) Photorcactivation(c) Base excision repair(d)
Foe each of the following characteristics, list all of the bases to which they apply(a) A signal that identifies a parental DNA strand in the Mut H, L, S mismatch correction system (b) Most likely to
Deficiencies in the activity of either dUTPase or DNA ligase stimulate recombination. Why?
Suppose that you want to study retroviral integration mechanisms by determining the nucleotide sequence at the integration site several dozen nucleotides on each side of the viral-cellular DNA
Identify and briefly describe three of the processes by which deamination of DNA-cytosine residues by AID could lead to mutagenesis.
Outline an experimental approach to determining the average chain growth rate for transcription in vivo. Chain growth rate is the number of nucleotides polymerized per minute per RNA chain.
Estimate the time needed for E. coli RNA polymerase at 37oC to transcribe the entire gene for a 50-kilodalton protein. What assumption or assumptions must be made for this estimate to be accurate?
Describe how RNA polymerase backtracking could function to increase the fidelity of transcription.
As discussed in the text, promoters were originally identified as consensus sequences upstream from transcriptional start sites. What additional evidence might support the assignment of these
In this chapter and elsewhere, we have described two types of ultracen-trifugation experiments - sucrose - gradient centrifugation and equilibrium density - gradient centrifugation. Briefly discuss
About 98% of the E. coli genome codes for proteins, yet mRNA, the template for protein synthesis, comprises only about 2% of the total RNA in the cell. Explain this apparent discrepancy.
Outline an experimental approach to determining the average RNA chain growth rate during transcription of a cloned gene in vitro.
Measurements of RNA chain growth rates are often led astray by the phenomenon of pausing, in which an RNA polymerase molecule stops transcription when it reaches certain sites, for intervals that may
Suppose you want to study the transcription in vitro of one particular gene in a DNA molecule that contains several genes and promoters. Without adding specific regulatory proteins, how might you
The tac promoter, an artificial promoter made from portions of the trp and lacUV5 promoters, has been introduced into a plasmid. It is a hybrid of the lac and trp (tryptophan) promoters, containing
Explain the basis for the following statement: Transcription of two genes on a plasmid can occur without the concomitant action of a topoisomerase, but only if those two genes are oriented in
Some years ago, it was suggested that the function of the poly (A) tail on a eukaryotic message may be to "ticket" the message. That is, each time the message is used, one or more residues are
For the original detection of DNA-RNA hybrid molecules, the DNA-RNA hybrid was detected in a CsCl equilibrium gradient. Why are RNA and DNA-RNA hybrids denser than double-stranded DNA?
Shown below is an R loop prepared for electron microscopy by annealing a purified eukaryotic messenger RNA with DNA from a genomic clone containing the full-length gene corresponding to the mRNA.(a)
A random-sequence polyribonucleotide produced by polynucleotide phosphorylase, with CDP and ADP in a 5:1 molar ratio stimulated the incorporation of proline, histidine, threonine, glutamine,
Suppose that the probability of making a mistake in translation at each translational step is a small number, δ. Show that the probability, p, that a given protein molecule, containing n residues,
Assume that the translational error frequency, δ, is 1 × 10-4. (a) Calculate the probability of making a perfect protein of 100 residues. (b) Repeat for a 1000-residue protein.
An important validation of the genetic code occurred when George Streisinger determined the amino acid sequence of bacteriophage T4 lysozyme and of mutants induced by proﬂavin, a dye with a planar
In another such analysis, the Streisinger group found that the altered amino acid sequence in the affected part of the double mutation involved addition of one amino acid, as shown below. Explain how
Assuming that glucose is metabolized to CO2 as an energy source, how many amino acid residues can be incorporated into a protein molecule for each glucose consumed by a cell? Is this a maximum or
Compare and contrast the metabolic pathways leading to thymine in DNA and thymine as a modified base in tRNA.
The genetic code is thought to have evolved to maximize genetic stability by minimizing the effect on protein function of most substitution mutations (single-base changes). We will use the six
The following polynucleotide was synthesized and used as a template for peptide synthesis in a cell-free system from E. coli... AUAUAUAUAUAUAU ...What polypeptide would you expect to be produced?
Suppression of a nonsense mutation involves a change in nucleotide sequence of a tRNA molecule.(a) What part of the tRNA molecule is changed?(b) How might this affect translation globally within a
Suppose that a gene underwent a mutation that changed a GAA codon to UAA. (a) Name the amino acid encoded by the original triplet. (b) Identify a tRNA anticodon that could translate the nonsense UAA
When polynucleotides are synthesized with repeating triplets of nucleotide residues, one, two, or three different polypeptide chains will be produced in cell-free synthesis.(a) Explain why these
Although the Shine-Dalgarno sequences vary considerably in different genes, they include examples like GAGGGG that could serve as code-in this case, for Glu-Gly. Does this imply that the sequence
According to wobble rules, what codons should be recognized by the following anti-codons? What amino acid residues do these correspond to?(a) 5′ - ICC - 3′(b) 5′ - GCU -3′
In the early days of ribosome research, before the exact role of ribosomes was clear, a researcher made the following observation. She could find, in sedimentation experiments on bacterial lysates,
The E site may not require codon recognition. Why?
What is the minumum number of tRNA molecules that a cell must contain in order to translate all 61 sense codons?
The active form of lactose repressor binds to the operator with a dissociation constant of 10-13 M for the reaction R + O ⇆ RO. About 10 molecules per E. coli cell suffice to keep the operon turned
What type of mutation of the lac repressor might be both constitutive and Trans dominant?
It has been proposed that thiogalactoside transacetylase (LacA in the lactose operon) plays a role in detoxification-ridding the cell of potentially toxic β-galactosides by acetylating them to
Riboswitches are generally considered to have been discovered in about 2002. But a comparable regulatory process was described much earlier, when Nomura et al. ( Proc. Natl. Acad. Sci. USA 77:7084
Not long ago investigators were surprised to learn that more than 95% of a mammalian genome is transcribed even though less than 2% encodes proteins. What kind of evidence could be used to determine
What do studies on attenuation tell us about mechanisms of transcription termination in bacteria?
In eukaryotic transcription what is the function of a histone chaperone? Of a chromatin remodeling complex, Of Mediator
Why does histone deacetylase action tend to repress transcription?
Refer to Figure 26.16, which shows the distribution of histone H2A.Z on nucleosomes near a transcription start site. What experimental technique would have been used to generate the data for this
5-Azacytidine is a reagent that suppresses DNA methylation through its conversion to 5-azadeoxycytidine triphosphate. Outline a metabolic pathway leading from Aza-C to Aza-dCTP.
Briefly explain why CpG islands might have come to be underrepresented in eukaryotic genomes.
Explain how a gene knockdown reagent, such as RNAi or a morpholino, could interfere with expression of a gene without affecting the rate of transcription of the target gene.
Briefly explain how heme regulates the expression of globin genes in cells that synthesize hemoglobin.
Suppose you want to study the transcription in vitro of one particular gene in a DNA molecule that contains several genes and promoters. Without adding specific regulatory proteins, how might you
For some time it was not clear whether lac repressor inhibits lac operon transcription by inhibiting the binding of RNA polymerase to its promoter or by allowing transcription initiation but blocking
Why would phage λ need to synthesize more cI repressor during establishment of lysogeny, early in infection, rather than in maintenance of the lysogenic state?
Repressors are inactivated either by interaction with a small-molecule inducer or by proteolytic cleavage. Why is it advantageous for a repressor like the lac repressor to be inactivated by binding
Partial diploid forms of E. coli were created, each of which contained a complete lactose operon at its normal chromosomal site and the regulatory sequences only (lacI, P, lacO) on a plasmid. Predict
What is the most compelling evidence that mitochondria and chloroplasts represent descendents of symbiotic bacteria that lived inside of ancient eukaryotic cells?
What is the relationship between mutation and genetic variation in a population of organisms? Of what significance is it to evolution?
Distinguish between enthalpy and energy. Under what conditions are they equivalent?
What does it mean when q and w are positive?
When crystalline urea is dissolved in water, the temperature of the solution drops precipitously. Does the enthalpy of the system increase or decrease? Explain.
List and define the four major thermodynamic state functions.
Which of the following pairs of states has higher entropy?
Rationalize the temperature dependence of Gibbs free energy changes when both the enthalpy and entropy terms are positive values or when they are both negative values.
Hydrogen gas combines spontaneously with oxygen gas to form water 2 H2 + O2 → 2 H2O Which term, enthalpy or entropy, predominates in the equation for the Gibbs free energy? How are the surroundings
In what critical ways was the atmosphere of the primitive earth different than the earth's current atmosphere?
Based on your reading in this chapter, suggest simple criteria for a reasonable definition of life.
The breakdown of glucose to pyruvate utilizes the free energy of 2 ATP molecules; however, the synthesis of glucose from pyruvate requires 4 ATP. Using the basic ideas of thermodynamics presented in
What is the rationale and significance of the Miller and Urey experiments?
Examine the reaction shown below for the condensation and hydrolysis of lactose (two covalently linked sugars, a disaccharide). Circle the functional groups that will form water during the
The condensation of two functional groups can result in the formation of another common functional group, which can be referred to as a compound functional group. Examine the functional groups in
Give the principal distinguishing feature(s) of each pair of terms: (a) Prokaryote and eukaryote (b) Cytosol and cytoplasm (c) Endoplasmic reticulum and cytoskeleton
Identify the circled functional groups and linkages in the compound below.
Label the following statements true or false: (a) A reaction is said to be spontaneous when it can proceed in either the forward or reverse direction. (b) A spontaneous process always happens very

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