Chapter Summary, Questions Answers - Regulation of Gene Expression

CHAPTER SUMMARY

Gene expression results in the production of a functional gene product (either RNA or protein) through the processes of replication, transcription, and translation (Figure 32.19). Genes can be either constitutive (always expressed, housekeeping genes) or regulated (expressed only under certain conditions in all cells or in a subset of cells). The ability to appropriately express (positive regulation) or repress (negative regulation) genes is essential in all organisms. Regulation of gene expression occurs primarily at the level of transcription in both prokaryotes and eukaryotes and is mediated through the binding of trans-acting proteins to cis-acting regulatory elements on the DNA. In eukaryotes, regulation also occurs through modifications to the DNA as well as through posttranscriptional a nd posttranslational events. In prokaryotes, such as E. coli, the coordinate regulation of genes whose protein products are required for a particular process is achieved through operons (groups of genes sequentially arranged on the chromosome along with the regulatory elements that determine their transcription). The lac operon contains the Z, Y, and A structural genes, the protein products of which are needed for the catabolism of lactose. It is subject to negative and positive regulation. When glucose is available, the operon is repressed by the binding of t h e repressor protein (the product of the lacI gene) to the operator, thus preventing transcription. When only lactose is present, the operon is induced by an isomer of lactose (allolactose) that binds the repressor protein, preventing it from binding to the operator. In addition, cyclic AMP binds the catabolite-activator protein (CAP), and the complex binds the DNA at the CAP site. This increases promoter efficiency and results in the expression of the structural genes through the production of a polycistronic messenger RNA (mRNA). When both glucose and lactose are present, glucose prevents formation of cAMP and transcription of these genes is negligible. The trp operon contains genes needed for the synthesis of tryptophan (Trp), and, like the lac operon, it is regulated by negative control. Unlike the lac operon, it is also regulated by attenuation, in which mRNA synthesis that escaped repression by Trp is terminated before completion. Transcription of ribosomal RNA and transfer RNA is selectively inhibited in prokaryotes by the stringent response to amino acid starvation. Translation is also a site of prokaryotic gene regulation: Excess ribosomal proteins bind the Shine-Dalgarno sequence on their own polycistronic mRNA, preventing ribosomes from binding. Gene regulation is more complex in eukaryotes. Operons typically are not present, but coordinate regulation of the transcription of genes located on different chromosomes can be achieved through the binding of trans-acting proteins to cis-acting elements. In multicellular organisms, hormones can cause coordinated regulation, either through the binding of the hormone receptor–hormone complex to the DNA (as with steroid hormones) or through the binding of a protein that is activated in response to a second messenger (as with glucagon). In each case, binding to DNA is mediated through structural motifs such as the zinc finger. Co- and posttranscriptional regulation is also seen in eukaryotes and includes splice-site choice, polyA-site choice, mRNA editing, and variations in mRNA stability as seen with transferrin receptor synthesis and with RNA interference. Regulation at the translational level can be caused by the phosphorylation and inhibition of eukaryotic initiation factor, eIF-2. Gene expression in eukaryotes is also influenced by availability of DNA to the transcriptional apparatus, the amount of DNA, and the arrangement of the DNA. Epigenetic changes to histone proteins and DNA also influence gene expression.

Figure 32.19 Summary of key concepts for the regulation of gene expression. GRE = glucocorticoid-response element; ppGpp = polyphosphorylated guanosine; r-protein = ribosomal protein; SD sequence = Shine-Dalgarno sequence; RNAi = RNA interference; eIF-2 = eukaryotic initiation factor 2. 

Study Questions
Choose the one best answer.

32.1 Which of the following mutations is most likely to result in reduced expression of the lac operon?

A. cyA^- (no adenylyl cyclase made)

B. i^– (no repressor protein made)

C. Oc (operator cannot bind repressor protein)

D. One resulting in functionally impaired glucose transport

Correct answer = A. In the absence of glucose, adenylyl cyclase makes cyclic AMP, which forms a complex with the catabolite activator protein (CAP). The cAMP–CAP complex binds the CAP site on the DNA, causing RNA polymerase to bind more efficiently to the lac operon promoter, thereby increasing expression of the operon. With cyA^- mutations, adenylyl cyclase is not made, and so the operon is unable to be turned on even when glucose is absent and lactose is present. The absence of a repressor protein or decreased ability of the repressor to bind the operator results in constitutive (constant) expression of the lac operon.

32.2 Which of the following is best described as cis acting?

A. Cyclic AMP response element-binding protein

B. Operator

C. Repressor protein

D. Thyroid hormone nuclear receptor

Correct answer = B. The operator is part of the DNA itself, and so is cis acting. The cAMP response element-binding protein, repressor protein, and thyroid hormone nuclear receptor protein are molecules that transit to the DNA, bind, and affect the expression of that DNA and so are trans acting.

32.3 Which of the following is the basis for the intestine-specific expression of apolipoprotein B-48?

A. DNA rearrangement and loss

B. DNA transposition

C. RNA alternative splicing

D. RNA editing

E. RNA interference

Correct answer = D. The production of apolipoprotein (apo) B-48 in the intestine and apoB-100 in liver is the result of RNA editing in the intestine, where a sense codon is changed to a nonsense codon by posttranscriptional deamination of cytosine to uracil. DNA rearrangement and transposition, as well as RNA interference and alternate splicing, do alter gene expression but are not the basis of apoB-48 tissue-specific production.

32.4 Which of the following is most likely to be true in hemochromatosis, a disease of iron accumulation?

A. The mRNA for the transferrin receptor (TfR) is stabilized by the binding of iron regulatory proteins to 3 iron-responsive elements.

B. The mRNA for the transferrin receptor is not bound by iron regulatory proteins and is degraded.

C. The mRNA for apoferritin is not bound by iron regulatory proteins at its 5 iron-responsive element and is translated.

D. The mRNA for apoferritin is bound by iron regulatory proteins and is not translated.

E. Both B and C are correct.

Correct answer = E. When iron levels in the body are high, as is seen with hemochromatosis, there is increased synthesis of the iron-storage molecule, apoferritin, and decreased synthesis of the transferrin receptor (TfR) that mediates iron uptake by cells. These effects are the result of trans-acting iron regulatory proteins binding cis-acting iron-responsive elements, resulting in degradation of the mRNA for TfR, and increased translation of the mRNA for apoferritin.

32.5 Patients with estrogen receptor–positive (hormone responsive) breast cancer may be treated with the drug tamoxifen, which binds the estrogen nuclear receptor without activating it. Which of the following is the most logical outcome of tamoxifen use?

A. Increased acetylation of estrogen-responsive genes

B. Increased growth of estrogen receptor–positive breast cancer cells C. Increased production of cyclic AMP D. Inhibition of the estrogen operon

E. Inhibition of transcription of estrogen-responsive genes

Correct answer = E. Tamoxifen competes with estrogen for binding to the estrogen nuclear receptor. Tamoxifen fails to activate the receptor, preventing its binding to DNA sequences that upregulate expression of estrogen-responsive genes. Tamoxifen, then, blocks the growth-promoting effects of these genes and results in growth inhibition of estrogen-dependent breast cancer cells. Acetylation increases transcription by relaxing the nucleosome. Cyclic AMP is a regulatory signal mediated by cell-surface rather than nuclear receptors. Mammalian cells do not have operons.

32.6 The ZYA region of the lac operon will be maximally expressed if:

A. cyclic AMP levels are low.

B. glucose and lactose are both available.

C. the attenuation stem–loop is able to form.

D. the CAP site is occupied.

Correct answer = D. It is only when glucose is gone, cyclic AMP levels are increased, the cAMP–catabolite activator protein (CAP) complex is bound to the CAP site, and lactose is available that the operon is maximally expressed (induced). If glucose is present, the operon is off as a result of catabolite repression. The lac operon is not regulated by attenuation, a mechanism for decreasing transcription in some operons such as the tryptophan operon.

32.7 X chromosome inactivation is a process by which one of two X chromosomes in human females is condensed and inactivated to prevent overexpression of X-linked genes. What would most likely be true about the degree of DNA methylation and histone acetylation on the inactivated X chromosome?

Cytosines in CG islands would be hypermethylated and histone proteins would be deacetylated. Both conditions are associated with decreased gene expression, and both are important in maintaining X inactivation.