Regulation of Gene Expression

How does the binding of the trp corepressor to the trp repressor alter repressor function and transcription? What about the binding of the lac inducer to the lac repressor?

Describe the binding of RNA polymerase, repressors, and activators to the lac operon when both lactose and glucose are scarce. What is the effect of these scarcities on transcription of the lac operon?

A certain mutation in E.coli changes the lac operon so that the active repressor cannot bind. How would this affect the cell’s production of beta-galactosidase?

(a) What is the independent variable in the graph? (b) What is the dependent variable? (c) What was the control treatment in this experiment? Label it on the diagram.

Do the data suggest that any of these possible control elements are actual control elements? Explain.

(a) Did deletion of any of the possible control elements cause a reduction in reporter gene expression? If so, which one (s), and how can you tell? (b) If loss of a control element causes a reduction in gene expression, what must be the normal role of that control element? Provide a biological explanation for how the loss of such a control element could lead to a reduction in gene expression.

(a) Did deletion of any of the possible control elements cause an increase in reporter gene expression relative to the control? If so, which one (s), and how can you tell? (b) If loss of a control element causes an increase in gene expression, what must be the normal role of that control element? Provide a biological explanation for how the loss of such a control element could lead to an increase in gene expression.

In general, what are the effects of histone acetylation and DNA methylation on gene expression?

Speculate about whether the same enzyme could methylate both a histone and a DNA base (See Concept 5.3)

Compare the roles of general and specific transcription factors in regulating gene expression.

Once mRNA encoding a particular protein reaches the cytoplasm, what are four mechanisms that can regulate the amount of the protein that is active in the cell?

Suppose you compared the nucleotide sequences of the distal control elements in the enhancers of three genes that are expressed only in muscle cells. What would you expect to find? Why?

Compare miRNAs and siRNAs, including their functions.

Suppose the mRNA being degraded in Figure 18.14 coded for a protein that promotes cell division in a multi-cellular organism. What would happen if a mutation disabled the gene for the miRNA that triggers this degradation?

Inactivation of one of the X chromosomes in female mammals involves IncRNA called XIST RNA, mentioned in this section and in Concept 15.2. Describe transcription and binding of XIST RNA, then suggest a model for how it initiates Barr body formation.

As you learned in Chapter 12, mitosis gives rise to two daughter cells that are genetically identical to the parent cell. Yet you, the product of many mitotic divisions, are not composed of identical, zygote-like cells. Why?

Explain how the signaling molecules released by an embryonic cell can induce changes in a neighboring cell without entering the cell. (See Figures 11.15 and 11.16.)

How do fruit fly maternal effect genes determine the polarity of the egg and the embryo?

In Figure 18.17b, the lower cell is synthesizing signaling molecules, whereas the upper cell is expressing receptors for these molecules. In terms of gene regulation and cytoplasmic determinants, explain how these cells came to synthesize different molecules.

Cancer-promoting mutations are likely to have different effects on the activity of proteins encoded by protooncogenes than they do on proteins encoded by tumour suppressor genes. Explain.

Under what circumstances is cancer considered to have a hereditary component?

The p53 protein can activate genes involved in apoptosis. Review Concept 11.5, and discuss how mutations in genes coding for proteins that function in apoptosis could contribute to cancer.

Cell differentiation always involves

(A)    transcription of the myoD gene.

(B)    the movement of cells.

(C)    the production of tissue-specific factors

(D)    the selection loss of certain genes from the genome.

Muscle cells differ from nerve cells mainly because they

(A)    express different genes

(B)     contains different genes.

(C)     use different genetic codes.

(D)    have unique ribosomes.

The functioning of enhancers is an example of

(A)    a eukaryotic equivalent of prokaryotic promoter functioning.

(B)    transcriptional control of gene expression

(C)    the stimulation of translation by initiation factors.

(D)    post-translational control activates certain proteins.

Cell differentiation always involves

(A)    transcription of the myoD gene.

(B)    the movement of cells.

(C)    the production of tissue-specific factors

(D)    the selection loss of certain genes from the genome.

Which of the following is an example of post-transcriptional control of gene expression?

(A)     the addition of methyl group to cytosine bases of DNA

(B)    the binding of transcription factors to a promoter

(C)    the removal of introns and alternative splicing of exons

(D)    gene amplification contributing to cancer

What would occur if the repressor of an inducible operon were mutated so it could not bind the operator?

(A)    irreversible binding of the repressor to the promoter

(B)    reduced transcription of the operon’s genes

(C)     building of a substrate for the pathway controlled by the operon

(D)     continuous transcription of the operon’s gene

Absence of bicoid mRNA from a Drosophila egg leads to the absence of anterior larval body parts and mirror-image duplication of posterior parts. This is evidence that the product of the bicoid gene

(A)    normally leads to the formation of head structures.

(B)    normally leads to formation of tail structures.

(C)    is transcribed in the early embryo.

(D)    is a protein present in all head structures.

Which of the following statements about the DNA in one of your brain cells is true?

(A)    Most of the DNA codes for protein.

(B)    The majority of genes are likely to be transcribed.

(C)    It is the same as the DNA in one of your liver cells.

(D)    Each gene lies immediately adjacent to an enhancer.

Within a cell, the amount of protein made using a given mRNA molecule depends partly on

(A)    the degree of DNA methylation.

(B)    the rate at which the mRNA is degraded.

(C)    the number of introns present in the mRNA.

(D)    the types of ribosomes present in the cytoplasm.

Proto-oncogene can change into oncogenes that cause cancer. Which of the following best explains the presence of these potential time bombs in eukaryotic cells?

(A)    Proto-oncogenes first arose from viral infections.

(B)    Proto-oncogenes are mutant versions of normal genes.

(C)    Proto-oncogenes are genetic “ junk.”

(D)    Proto-oncogenes normally help regulate cell division. 

The diagram below five genes, including their enhancers, from the genome of a certain species. Imagine that pink, blue, green, black, grey and dark blue activator proteins exist that can bind to the approximately colour-coded control elements in the enhancers of these genes. 

(a)    Draw an X above enhancer elements (of all the genes) that would have activators bound in a cell where only gene five is transcribed. Identify which coloured activators would be present. 

(b)    Draw a dot above all enhancer elements that would have activators bound in a cell where the green, blue, and yellow activators are present. Identify which gene(s) would be transcribed.

(c)    Imagine that genes 1, 2, and 4 codes for nerve-specific proteins, and genes 3 and 5 are skin-specific. Identify which activators would have to be present in each cell type to ensure transcription of the appropriate genes.

DNA sequences can act as "tape measures of evolution” (see Concept 5.6). Scientists analyzing the human genome sequence were surprised to find that some of the regions of the human genome are mostly highly conserved (similar to comparable regions in other species) don't code for proteins. Propose a possible explanation for this observation. 

Prostrate cells usually require testosterone and other androgens to survive. But some prostate cancer cells thrive despite treatments that eliminate androgens. One hypothesis is that estrogen, often considered a female hormone, may be activating genes normally controlled by androgen in these cancer cells. Describe one or more experiments to test this hypothesis. (See Figure 11.9 to review the action of these steroid hormones).

Trace amounts of dioxin were present in Agent Orange, a defoliant sprayed on vegetation during the Vietnam War. Animal tests suggest that dioxin can cause birth defects, cancer, liver and thymus damage, and immune system suppression, sometimes leading to death. But the animal tests are equivocal; a hamster is not affected by a dose that can kill a guinea pig. Dioxin acts like a steroid hormone, entering a cell and binding to a cytoplasmic receptor that then binds the cell’s DNA.  

1. Discuss how this mechanism might help explain the variety of dioxin’s effects on different body systems and in different animals. 
2. Discuss how you might determine whether a type of type of illness is related to dioxin exposure. Next, discuss how you might determine whether a particular individual became ill as a result of exposure to dioxin. Which would be more difficult to demonstrate?Why?

In a short essay (100-150words), discuss how the processes shown in Figure 18.2 are examples of feedback mechanisms regulating biological systems in bacterial cells.

The flashlight fish has an organ under its eyethat emits light, which servers to startle predators and attract prey, and allows the fish to communicate with other fish. Some species can rotate the organ inside and then out, so the light appears to flash on and off. The light is actually emitted by bacteria (of the genus Vibrio) that live in the organ in a mutualistic relationship with the fish. (The bacteria receive nutrients from the fish). The bacteria must multiply until they reach a certain density in the organ (a "quorum"; see Chapter 11.1), at which point they all begin emitting light at the same time. There is a group of six or so genes, called lux genes, whose gene products are necessary for light formation. Given that these bacterial genes are regulated together, propose a hypothesis for how the genes are organized and regulated.