Karp's Cell and Molecular Biology: Concepts and Experiments

Janet Iwasa, Wallace Marshall

Chapter 12

Control of Gene Expression - all with Video Answers

Educators

Chapter Questions

Problem 1

Methylation of $\mathrm{K} 9 \text { of histone } \mathrm{H} 3 \text { (by an enzyme } \mathrm{SUV} 39 \mathrm{H} 1)$ is associated with heterochromatinization and gene silencing. It has been reported that methylation of $\mathrm{H} 3$ by other enzymes can lead to transcriptional activation. How can methylation lead to opposite effects?

Sana Riaz

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Problem 2

How many copies of each type of core histone would it take to wrap the entire human genome into nucleosomes? How has evolution solved the problem of producing such a large number of proteins in a relatively short period of time?

Sana Riaz

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Problem 3

Suppose you discovered a temperature-sensitive mutant whose nucleus failed to accumulate certain nuclear proteins at an elevated (restrictive) temperature but continued to accumulate other nuclear proteins. What conclusions might you draw about nuclear localization and the nature of this mutation?

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Problem 4

Humans born with three $X$ chromosomes but no Y chromosomes often develop into females of normal appearance. How many Barr bodies would you expect the cells of these women to have? Why?

Bryan Valdivia

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Problem 5

Suppose that $X$ -inactivation were not a random process, but always led to the inactivation of the X chromosome derived from the father. What effect would you expect this to have on the phenotype of females?

Bryan Valdivia

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Problem 6

The chromosomes shown in Figure $12.22 b$ were labeled by incubating the preparation with DNA fragments known to be specific for each of the chromosomes. Suppose one of the chromosomes in the field contained regions having two different colors. What might you conclude about this chromosome?

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Problem 7

What advantage might be gained by having transcripts synthesized and processed in certain regions of the nucleus rather than randomly throughout the nucleoplasm? (See Quantitative Tutorial Video).

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Problem 8

Compare and contrast the effect of a deletion in the operator of the lactose operon with one in the operator of the tryptophan operon.

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Problem 9

If you were to find a mutant of $E .$ coli that produced continuous polypeptide chains containing both $\beta$ -galactosidase and galactoside permease (encoded by the $y$ gene), how might you explain how this happened?

Sana Riaz

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Problem 10

You suspect that a new hormone you are testing functions to stimulate myosin synthesis by acting at the transcriptional level. What type of experimental evidence would support this contention?

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Problem 11

Suppose you had conducted a series of experiments in which you had transplanted nuclei from several different adult tissues into an activated, enucleated mouse egg and found that the egg did not develop past the blastocyst stage. Could you conclude that the transplanted nucleus had lost genes that were required for postblastula development? Why or why not? What does this type of experiment tell you more generally about interpreting negative results?

Sana Riaz

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Problem 12

It was noted on page 493 that DNA footprinting allows isolation of DNA sequences that bind specific transcription factors. Describe an experimental protocol to identify transcription factors that bind to an isolated DNA sequence. (You might consider the techniques discussed in Section $18.11 .$.)

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Problem 13

How do you explain why enhancers can be moved around within the DNA without affecting their activity, whereas the TATA box can only operate at one specific site?

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Problem 14

Suppose that you are working with a cell that exhibits a very low level of protein synthesis, and you suspect the cells are subject to a global translational-control inhibitor. What experiment might you perform to determine whether this is the case?

Sana Riaz

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Problem 15

The signal sequences that direct the translocation of proteins into the endoplasmic reticulum are cleaved by a signal peptidase, whereas the NLSs and NESs required for movement of a protein into or out of the nucleus remain as part of that protein. Consider a protein such as hnRNPA1, which is involved in the export of mRNA to the cytoplasm. Why is it important that the transport signal sequences for this protein remain as part of the protein, whereas the signal sequence for ER proteins can be cleaved?

Sana Riaz

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Problem 16

When methylated DNA is introduced into cultured mammalian cells, it is generally transcribed for a period before it becomes repressed. Why would you expect this type of delay before inhibition of transcription would occur?

Sana Riaz

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Problem 17

Suppose you had isolated a new transcription factor and wanted to know which genes this protein might regulate. Is there any way that you could use a cDNA microarray of the type shown in Figure 12.35 to approach this question? (Note: The microarray of Figure 12.35 contains the DNA of protein-coding regions, unlike that of Figure 12.46 .

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Problem 18

Although several different mammalian species have been cloned, the efficiency of this process is extremely low. Often tens or even hundreds of oocytes must be implanted with donor nuclei to obtain one healthy live birth. Many researchers believe the difficulties with cloning reside in the epigenetic modifications, such as DNA and histone methylation, that occur within various cells during an individual's life. How do you suspect such modifications might affect the success of an experiment such as that depicted in Figure $12.32 ?$

Sana Riaz

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Problem 19

A study in a British medical journal found there was a correlation in telomere length between fathers and their daughters and between mothers and both their sons and daughters but not between fathers and their sons. How can you explain this finding?

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Problem 20

Some scientific reports are best described as correlations, in that they report on two events or conditions that tend to accompany one another. Correlations are often interpreted as evidence of a causal relationship between the two events or conditions. Other scientific reports involve experimental intervention and generally make a stronger case for a causal relationship. Pick one scientific conclusion that is put forth in this chapter that is based on both types of evidence. Which type of report do you find more convincing?

Sana Riaz

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