Chapter Questions
DNA isolated from an organism can be sheared into fragments of uniform size $(\sim 1000 \mathrm{bp})$, heated to separate the strands, then cooled to allow complementary strands to reanneal. The renaturation process can be followed over time. Explain why the renaturation of $E$. coli DNA is a monophasic process, whereas the renaturation of human DNA is biphasic (an initial rapid phase followed by a slower phase).
Explain why the organization of genes in operons facilitates the assignment of functions to previously unidentified ORFs in a bacterial genome.
The genome of Daphnia pulex, a small freshwater crustacean, includes approximately 30,000 genes in $\sim 200,000 \mathrm{kb}$ of DNA. How does the genome compare to that of Drosophila melanogaster, another arthropod, and to that of humans?
The marine alga Ostreococcus tauri has an unusually high gene density for a eukaryote: $\sim 8000$ genes in an $\sim 13,000$ -kb genome. Assuming that intergene distances are negligible, what is the average size of anO. tauri gene? How does this compare to the average gene size in the prokaryote $E .$ coli?
A possible mechanism for the pathology of trinucleotide repeat diseases is aberrant translation, in which all three reading frames are used. Which repeating amino acid residues will result from the translation of transcripts made from repeating DNA sequences of(a) CAG and(b) CTG?
In addition to SNPs, humans exhibit copy-number polymorphisms $(\mathrm{CNPs}),$ which result from relatively large deletions or insertions of certain segments of the genome. One study showed that individuals differed by $11 \mathrm{CNPs}$ with an average length of 465 kb. Calculate the fraction of the human genome represented by copy-number variants.
Explain why inactivation of the $O_{1}$ sequence of the $l a c$ operator almost completely abolishes repression of the lac operon.
Explain why (a) inactivation of the $O_{2}$ or $O_{3}$ sequence of the lac operon causes only a twofold loss in repression, and(b) inactivation of both $O_{2}$ and $O_{3}$ reduces repression $\sim 70$ -fold.
Why do $E$. coli cells with a defective $\operatorname{lacZ}$ gene fail to show galactoside permease activity after the addition of lactose in the absence of glucose?
Describe the probable genetic defect that abolishes the sensitivity of the lac operon to the absence of glucose when other metabolic operons continue to be sensitive to the absence of glucose.
Why can't eukaryotic transcription be regulated by attenuation?
Predict the effect of deleting the leader peptide sequence on regulation of the $t r p$ operon.
Draw the molecular formula of the covalently modified histone side chain of acetyllysine. How does this modification alter the chemical properties of the side chain?
Draw the molecular formulas of the covalently modified histone side chains of methyllysine and methylarginine. How do these modifications alter the chemical properties of the side chains?
Monomethylation of histone Arg residues can be reversed by the action of a peptidylarginine deiminase, which requires water to remove the methyl group along with the imino group of Arg. Draw the structure of the resulting amino acid side chain and identify this nonstandard amino acid.
Is it possible for a transcription enhancer to be located within the protein-coding sequence of a gene? Explain.
Explain why natural selection has favored the instability of RNA.
How many different heavy chain variable regions can theoretically be generated by somatic recombination in humans (ignore junctional flexibility)? If each of these heavy chains could combine with any of the $\sim 2000$ \kappa light chains, how many different immunoglobulins could be produced?
$V / D / J$ recombination frequently yields a gene whose mRNA cannot be successfully translated into an immunoglobulin chain. What aspect of somatic recombination is likely to produce nonproductive gene rearrangement?
Explain what might happen if the activation-induced cytidine deaminase (AID) were activated in a cell other than a B cell.
Why is it disadvantageous for single-celled eukaryotes such as yeast to undergo apoptosis?
During apoptosis, phosphatidylserine (Section 9-1C) undergoes transverse movement (flip-flop). Explain why this could help identify apoptotic cells to phagocytic cells for engulfment and disposal.
In Drosophila, an esc $^{-}$ homozygote develops normally unless its mother is also an $e s c^{-}$ homozygote. Explain.
Describe the appearance of a Drosophila embryo, in which the knirps gene protein-coding sequence has been replaced by $\operatorname{lacZ}$, following incubation in a solution of X-gal.
Red-green color blindness is caused by an X-linked recessive genetic defect. Hence females rarely exhibit the red-green colorblind phenotype but may be carriers of the defective gene. When a narrow beam of red or green light is projected onto some areas of the retina of such a female carrier, she can readily differentiate the two colors, but on other areas she has difficulty in doing so. Explain.
Why is transcriptionally active chromatin $\sim 10$ times more susceptible to cleavage by DNase I than transcriptionally silent chromatin?
Explain why a deficiency of the vitamin folic acid could lead to undermethylation of histones and DNA.
Proliferation and differentiation of $\mathrm{T}$ and $\mathrm{B}$ lymphocytes during an immune response are mediated by signaling that leads to phosphorylation of a protein called I\kappaB. Unphosphorylated I\kappaB binds to and inhibits the transcription factor $\mathrm{NF}$ - $\kappa \mathrm{B}$. Phosphorylated I\kappa $\mathrm{B}$ releases $\mathrm{NF}$ - $\kappa \mathrm{B}$ and is then ubiquitinated and degraded by a proteasome.(a) Explain why this mechanism for activating NF-kB allows rapid changes in gene expression.(b) Explain why directly phosphorylating $\mathrm{NF}$ - $\mathrm{KB}$ might not be an effective mechanism for altering gene expression.(c) A protein produced by Yersinia pestis (the bacterium that causes plague) removes the ubiquitin molecules from I\kappaB. How would this affect the immune response to the Yersinia infection?
Explain why RNAi would be a less efficient mechanism for regulating the expression of specific genes if Dicer hydrolyzed double-stranded RNA every 11 bp rather than every 22 bp.
B cells suppress the expression of all but one heavy chain allele and one light chain allele, a process known as allelic exclusion, by inhibiting the further somatic recombination of heavy and light chain genes after a productive recombination has occurred. Describe the aberrant properties of immunoglobulins produced by a $\mathrm{B}$ cell in which allelic exclusion is defective.
The fusion of cancer cells with normal cells often suppresses the expression of the tumorigenic phenotype. Explain.