Questions and Answers of Fundamentals Of Biochemistry

For the RNA sequence AUUGGCAUCCGAUAA, draw the secondary structure that maximizes its base pairing.
Protamines are small proteins that take the place of histones during spermatogenesis in vertebrates. What amino acids are likely to be abundant in protamines?
Why are the most commonly observed conformations of the ribose ring those in which either atom C2′ or atom C3′ is out of the plane of the other four ring atoms?
At Na+ concentrations >5 M, the Tm of DNA decreases with increasing [Na+]. Explain this behavior. Consider the solvation requirements of Na+.
Polyoma virus DNA can be separated by sedimentation in an ultracentrifuge at neutral pH into three components that have sedimentation coefficients of 20, 16, and 14.5S and that are known as Types I,
A bacterial chromosome consists of a protein–DNA complex in which its single DNA molecule appears to be supercoiled. However, in contrast to the case with naked circular duplex DNA, the light
Approximately how many Okazaki fragments are synthesized in the replication of the E. coli chromosome?
Why are there no Pol I mutants that completely lack 5′ → 3′ exonuclease activity?
E. coli oriC is rich in A · T base pairs. Why is this advantageous?
Explain why DNA gyrase is required for efficient unwinding of DNA by helicase at the replication fork.
Why is the observed mutation rate of E. coli 10–8 to 10–10 per base pair replicated, even though the error rates of Pol I and Pol III are 10–6 to 10–7 per base pair replicated?
How does a eukaryotic cell distinguish the end of a broken chromosome from the end of an intact linear chromosome?
Give the name of the enzyme that catalyzes each of the following reactions:(a) Makes a DNA strand from a DNA template(b) Makes a DNA strand from an RNA template(c) Makes an RNA strand from a DNA
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
In eukaryotic cells, a specific triphosphatase cleaves deoxy-8-oxoguanosine triphosphate (oxo-dGTP) to oxo-dGMP + PPi. What is the advantage of this reaction?
Under cellular conditions, dATP can be oxidized to its 2-hydroxy form, which is a substrate for an enzyme that converts 2-OH-dATP to 2-OH-dAMP + PPi. Explain why compounds that inhibit the activity
Explain why mutations are more likely to occur on the lagging strand than on the leading strand in eukaryotes.
What type of repair system would cells most likely use to repair DNA with a deaminated adenine?
Ribonucleotides are erroneously incorporated into newly synthesized DNA as a result of incomplete primer removal or misincorporation by DNA polymerase. What types of enzymes would be required to
Explain why interstrand DNA cross-links are much more mutagenic than intrastrand cross-links.
A DNA template strand containing a thymine dimer can be replicated by DNA polymerase η. Does pol η fix the damaged DNA?
Two approaches for correcting single-gene defects are gene therapy such as is discussed and the CRISPR–Cas9 system. Explain why the CRISPR–Cas9 approach can potentially provide more complete
The 3′ → 5′ exonuclease activity of Pol I excises only unpaired 3′-terminal nucleotides from DNA, whereas this enzyme’s pyrophosphorolysis activity removes only properly paired
To put the E. coli replication system on a human scale, let us imagine that the 20-Å-diameter B-DNA was expanded to 1 m in diameter. If everything were proportionally expanded, then each DNA
Deinococcus radiodurans, which the Guinness Book of World Records has dubbed the world’s toughest bacterium, can tolerate doses of ionizing radiation ∼3000-fold greater than those that are lethal
A composite transposon integrated in a circular plasmid occasionally transposes the DNA comprising the original plasmid rather than the transposon’s central region. Explain how this is possible.
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.
Explain why the active site of poly(A) polymerase is much narrower than that of DNA and RNA polymerases.
The 5′ end of some bacterial regulatory RNAs are linked to the 3′- OH group of the adenosine residue of NAD+. Propose a biological function for the modification and explain how the activity of
Infection with certain viruses inhibits snRNA processing in eukaryotic cells. Explain why this favors the expression of viral genes in the host cell.
Diagram the likely secondary structure of an RNA with the sequence 5′-UGCUGCCAUCUCUUUUCCUCUCUAUGCGAGGAUUUGGACUGGCAGCG-3′
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
Why aren’t primary rRNA transcripts present in wild-type E. coli?
In the genetic code used by mitochondria in many species, UGA codes for tryptophan rather than a Stop signal. How does mitochondrial translation terminate?
IleRS uses a double-sieve mechanism to accurately produce IletRNA Ile and prevent the synthesis of Val-tRNAIle. Which other pairs of amino acids differ in structure by a single carbon and might have
In eukaryotes, the primary rRNA transcript is a 45S rRNA that includes the sequences of the 18S, 5.8S, and 28S rRNAs separated by short spacers. What is the advantage of this operon-like arrangement
Explain why the translation of a given mRNA can be inhibited by a segment of its complementary sequence, a so-called antisense RNA.
The ribosome can transfer any peptidyl group from the P-site tRNA to any aminoacyl group on the A-site RNA, but the rate may vary with the identities of those groups. Propose an explanation why the
Mitochondrial ribosomes manufacture 13 proteins, all of which are components of the oxidative phosphorylation machinery. Propose an explanation why the peptide exit tunnel of the mitoribosome is
The peptidyl transferase activity of the ribosome does not require an additional source of free energy. Is the reaction catalyzed by glutamylcysteine synthetase (Problem 19) also exergonic?Data from
One cause of the neurodegenerative disease amyotropic lateral sclerosis (ALS) is the expansion of the repeating hexanucleotide sequence GGGGCC in the noncoding region of a gene. By unknown
The flu virus maximizes the use of its limited (13.5 kb) genome by using alternative translation initiation sites, overlapping reading frames, and ribosomal frameshifting. For example, part of the
Explain why a minimum of 32 tRNAs are required to translate the “standard” genetic code.
Predict whether loss of the following E. coli genes would be lethal or not:(a) dnaB(b) polA(c) ssb(d) recA.
Would you expect spliceosome-catalyzed intron removal to be reversible in a highly purified in vitro system and in vivo? Explain.
In what ways do histone gene transcripts differ from transcripts of other vertebrate protein-coding genes?
N6 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
How many different types of macromolecules must be minimally contained in a cell-free protein synthesizing system from E. coli? Count each type of ribosomal component as a different macromolecule.
Under conditions of nutrient starvation, bacteria produce a protein that binds to the 3′ end of 16S rRNA. What is the result of this interaction and why is it beneficial to the cell?
An antibiotic named fixmycin, which you have isolated from a fungus growing on ripe passion fruit, is effective in curing several types of sexually transmitted diseases. In characterizing
The fusion of cancer cells with normal cells often suppresses the expression of the tumorigenic phenotype. Explain.
Why is transcriptionally active chromatin ∼10 times more susceptible to cleavage by DNase I than transcriptionally silent chromatin?
Describe the appearance of a Drosophila embryo, in which the knirps gene protein-coding sequence has been replaced by lacZ, following incubation in a solution of X-gal.
Why do E. coli cells with a defective lacZ gene fail to show galactoside permease activity after the addition of lactose in the absence of glucose?
Explain why inactivation of the O1 sequence of the lac operator almost completely abolishes repression of the lac operon.
The marine alga Ostreococcus tauri has an unusually high gene density for a eukaryote: ∼8000 genes in an ∼13,000-kb genome. Assuming that intergene distances are negligible, what is the average
In addition to SNPs, humans exhibit copy-number polymorphisms (CNPs), which result from relatively large deletions or insertions of certain segments of the genome. One study showed that individuals
Use the information in Table 11-1 to estimate the half-life, in years, of a phosphodiester bond in DNA.Table 11-1 Enzyme Carbonic anhydrase Chorismate mutase Triose phosphate isomerase
Infection with the influenza virus interferes with the normal expression of genes in the host cell. The viral protein M1 binds to histones electrostatically.(a) Would increasing the salt
The NS1 protein in the H3N2 strain of the influenza virus has a C-terminal sequence of –KMARTARSKV (using one-letter amino acid abbreviations). The N-terminus of histone H3 has the sequence
A high rate of base-substitution mutations can result from a polymerase’s tendency to incorporate a mispaired nucleotide or from its poor ability to incorporate the correct nucleotide. Use the
The E. coli genome contains 1009 Chi sequences. Do these sequences occur at random, and, if not, how much more or less frequently than random do they occur?
The pathways outlined in this chapter include steps that involve cleavage of a nucleoside triphosphate. Which of these reactions is/are phosphoryl group transfer?
The pathways outlined in this chapter include steps that involve cleavage of a nucleoside triphosphate. Which of these cleavage reactions is/are not phosphoryl group transfer?
The net equation for oxidative phosphorylation can be written asWrite an analogous equation for the light reactions of photosynthesis. 2 NADH + 2H+ + O 2 HO + 2 NAD+
Green sulfur bacteria use H2S as an electron donor for photosynthesis. Write an equation that describes photosynthesis in these organisms.
The “red tide” is a massive proliferation of certain algal species that causes seawater to become visibly red. Describe the spectral characteristics of the dominant photosynthetic pigments in the
How many moles of ATP could theoretically be synthesized under standard conditions using the energy of the photons in Problem 5?Problem 5Calculate the energy of one mole of photons of red light (λ =
The three electron-transporting complexes of the thylakoid membrane can be called plastocyanin–ferredoxin oxidoreductase, plastoquinone– plastocyanin oxidoreductase, and water–plastoquinone
H218O is added to a suspension of chloroplasts capable of photosynthesis. Where does the label appear when the suspension is exposed to sunlight?
Predict the effect of an uncoupler such as dinitrophenol on production of ATP in a chloroplast.
Predict the effect of an uncoupler such as dinitrophenol on production of NADPH in a chloroplast.
Arabidopsis thaliana chloroplasts contain a K+ channel in the thylakoid stromal lamellae. Propose a function for this channel.
Would the activity of the A. thaliana K+ channel described in Problem 21 increase or decrease in response to a rise in pH in the thylakoid lumen?Problem 21Arabidopsis thaliana chloroplasts contain a
For the chloroplasts described in Problem 23, how does the level of 3PG vary after the light is turned off?Problem 23Chloroplasts are illuminated until the levels of the Calvin cycle intermediates
Cyanobacteria contain carboxysomes, which consist of a protein shell that encloses RuBP carboxylase and is permeable to small anions such as HCO−3. Explain why carbonic anhydrase is also a
In an effort to increase the efficiency of photosynthesis in crop plants, researchers have genetically engineered tobacco plants (a model organism) to express cyanobacterial RuBP carboxylase, which
Describe the effects of an increase in oxygen pressure on the dark reactions of photosynthesis.
C4 plants collect CO2 in mesophyll cells, which are close to the leaf surface, then transfer it to bundle-sheath cells, which are rich in RuBP carboxylase and surround the “veins” that deliver
Chlorophyll f, which occurs in some species of cyanobacteria that grow under low illumination, has an absorption maximum of 706 nm, whereas other types of chlorophylls show absorption maxima at
The cyanobacterium Oscillatoria sancta appears reddish-brown when grown under green light but alters its gene expression patterns and becomes blue-green when grown under red light. Explain this
One aspect of climate change is that average nighttime temperatures have increased more than average daytime temperatures have increased. Since the rates of metabolic processes, including
Experiments to address the day-night discrepancy in warming indicate that climate change has inhibited plant growth in warm dry areas more than in cool wet areas. Explain this observation.
If a C3 plant and a C4 plant are placed together in a sealed illuminated box with sufficient moisture, the C4 plant thrives while the C3 plant sickens and eventually dies. Explain.
The action of malic enzyme opposes the action of pyruvate carboxylase.(a) Diagram the substrate cycle formed by these enzymes plus a third enzyme.(b) Write the net equation for converting malate to
Helicobacter pylori, which causes gastric ulcers, does not operate a citric acid cycle but contains many of the citric acid cycle enzymes. H. pylori can convert oxaloacetate to succinate for
The branched-chain α-keto acid dehydrogenase complex, which participates in amino acid catabolism, contains the same three types of enzymes as are in the pyruvate dehydrogenase and the
Malate generated inside the mitochondrion is translocated to the cytosol, where it is a substrate for cytosolic malic enzyme, which catalyzes the following reaction:Explain how the activity of malic
Which compounds would accumulate in an individual with beriberi (caused by thiamine deficiency)?
The archaebacterium Haloarculamarismortui can use acetate (which is converted to acetyl-CoA) as a precursor for carbohydrate synthesis, but it lacks isocitrate lyase and therefore cannot use the
Acetyl-CoA, in addition to providing 2-carbon groups to the citric acid cycle, is also the substrate of enzymes that add acetyl groups to proteins. Histone acetyltransferase adds an acetyl group to
How many ATPs are synthesized for every cytoplasmic NADH that participates in the glycerophosphate shuttle in insect flight muscle?
How many ATPs are synthesized for every cytoplasmic NADH reducing equivalent that is transferred into the matrix via the malate–aspartate shuttle?
Explain why defects in mitochondrial genes often produce symptoms such as lactic acidosis.
Pyocyanin from the bacterium Pseudomonas aeruginosa, which can cause fatal infections, contributes to the production of reactive oxygen species in the mammalian host. What component of the electron
Deficiencies of the components of Complexes I, III, and IV tend to have severe physiological consequences, however, deficiencies of Complex II components tend to have mild effects. Explain.
Vitamin K is the cofactor for an enzyme that post translationally modifies certain proteins. It also functions as an electron carrier in some prokaryotes and may play a similar role in mitochondria.
Cytochrome c may associate with cardiolipin (diphosphatidylglycerol) in the inner mitochondrial membrane. What sort of intermolecular forces are likely to be involved in this association?
For the experimental system described in Problem 17, and assuming all the substrates for oxidative phosphorylation are present in excess, does ATP synthesis increase or decrease with an increase in
Under certain conditions, cytochrome c can trigger apoptosis, or programmed cell death, by activating cytosolic proteins known as caspases.(a) Why doesn’t cytochrome c trigger apoptosis in healthy

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