Chapter 17 - Control of Gene Regulation in Eukaryotes

Question 1

Eukaryotic structural genes each have their own __ and are transcribed __.

Answer 1

Promoter; independently

Question 2

__ mRNA: each mRNA codes for a single polypeptide.

__ mRNA: each mRNA codes for 2 or more polypeptides and is only found in __.

Answer 2

monocistronic

polycistronic; prokaryotes

Question 3

Transcription in eukaryotes requires unwinding of DNA from __; basically changing from __ to __.

Answer 3

nucleosomes; heterochromatin; euchromatin

Question 4

Eukaryotes have much more transcriptional __ and __ than their prokaryotic counterparts.

Of the two, eukaryotes have more __ than __.

Answer 4

activators; repressors

activators; repressors

Question 5

__ __ complex binds to DNA and repositions nucleosomes to expose a transcription factor binding site. __ is the energy source.

Answer 5

Chromatin remodeling

ATP

Question 6

This experiment is used to “probe” chromatin structure; it can detect changes in chromatin and determine areas that are transcriptionally active.

Answer 6

DNAse I Hypersensitivity

Question 7

DNA located ~ 1000 bp upstream of a promoter of transcriptionally __ genes is hypersensitive to cleavage by __ _. This indicates that chromatin is more loosely associated (relaxed) with __.

Answer 7

active; DNAse I

nucleosomes

Question 8

One way in which chromatin is relaxed is via histone __. Histones have positively charged “__” that interact with negatively charged __. __ transferases transfer __ groups to __ and __ (AAs found in histones) and neutralize their charge to relax the chromatin.

Answer 8

acetylation.

tails; phosphates

Acetyl; acetyl; arginine; lysine

Question 9

T or F: Histone acetylation makes DNA more resistant to degradation by DNAse I.

Answer 9

False: it makes it hypersensitive

Question 10

In general; high levels of DNA methylation are correlated with __ transcription.

Answer 10

repressed.

Question 11

__ of cytosine at the 5th position is an important mechanism for controlling transcription. __ usually occurs in p islands: areas where __ cytosine is followed by __ which repress gene expression. This is found in inactive genes such as the inactive __ chromosome of mammalian females.

Answer 11

methylation
Methylation; CpG; methylated; guanine
X

Question 12

__ changes are usually due to methylation; and some of these changes can be passed to progeny.

Answer 12

epigenetics

Question 13

__ transcription factors assemble as part of the BAS. Together they bind to the __ promoter.

Answer 13

General; core

Question 14

Transcriptional __ enhance the rate of transcription by stimulating or stabilizing the BTA. They bind to either a __ promoter (upstream of the __ promoter) or to an __.

Answer 14

Activators

regulatory; core; enhancer

Question 15

Transcriptional activators have 2 functional __: (1) one __ binds to a specific DNA sequence - either an __ or a __ promoter; (2) the other __ interacts directly with the __ of the BTA, or it interacts with a __.

Answer 15

domains; domain;
enhancer; regulatory;
domain; mediator; coactivator

Question 16

GAL4 is a __ __ that regulates transcription of several yeast genes involved in galactose metabolism.

Answer 16

transcriptional activator

Question 17

Why is GAL4 (yeast transcriptional activator for several genes involved in galactose metabolism) widely used in molecular biology research?

Answer 17

Most other eukaryotes don’t have a homologous transcription factor (a transcription factor that equates to GAL4).

Question 18

The element that GAL4 (yeast transcriptional activator) binds to is called UASg (g is a subscript G) which stands for __ __ __ for ‘G’AL4.

Answer 18

‘U’pstream ‘A’ctivator ‘S’equence (for ‘G’AL4)

Question 19

GAL4 is regulated by __.
In the absence of galactose, __ binds to GAL4 and prevents transcription.
In the presence of galactose, __ binds to galactose causing __ changes and preventing it from binding to GAL4.

Answer 19

GAL₈₀

GAL₈₀
GAL₈₀; allosteric

Question 20

__ - the element to which GAL4 binds, is located 1000s of bp away from the galactose genes it regulates which makes it look like an __ sequence.

Answer 20

UASg; enhancer

Question 21

Most enhancers interact with many genes. One potential problem is you don’t want them interacting with an unintended target; this issue is resolved by __ __(aka __ elements).

Answer 21

insulator elements; boundary.

Question 22

If an __ lies between and enhancer and a promoter, it blocks the action of the enhancer.

Answer 22

insulator

Question 23

For Eukaryotes, thermal stress activates ~20 heat shock genes dispersed throughout the genome (opposite of operons) in a coordinated manner with the help of __ elements.

Answer 23

response

Question 24

Genes that require coordinated transcription (e.g. heat shock) share common regulatory elements called __ elements.
One gene can have a multiple __ elements enabling transcription / activation of a single gene in response to various stimuli.

Answer 24

response

response

Question 25

__ splicing of mRNA can also regulate gene expression. An example is __ protein in Drosophila: it's produced in females, but not males. When present, it affects the splice site of pre-mRNA for __ producing a functional protein. Functional __ protein causes female-specific splicing of the __ pre-mRNA.

Answer 25

Alternative sxl tra tra dsx

Question 26

In male Drosophila, the absence of __ protein changes the cascade of events leading to male-specific splicing of __ pre-mRNA (and a ___ protein due to a premature __ codon in exon B). This, in turn, leads to male-specific splicing of __ pre-mRNA.

Answer 26

sxl; tra; nonfunctional; stop dsx

Question 27

Degradation of mRNA usually begins at the _' __. But mRNA stability is much higher in eukaryotes which can lead to large differences in the __ of protein made.

Answer 27

5' cap quantity / amount

Question 28

``` RNA silencing (interference): --RNA is cleaved by __ and unwound to produce --RNAs. These --RNAs combine with __ complex, then bind to complimentary regions of mRNA. The --RNA/__complex cleaves mRNA which leads to __. ```

Answer 28

dsRNA; Dicer; siRNAs siRNAs; RISC siRNA/RISC; degradation

Question 29

Eukaryotic gene regulation: There are factors that bind with the _' __ or the _' __ (rarer) that affect the rate of translation. In addition to the rate of translation, control of gene expression can happen post-translation because newly-synthesized proteins are often __ and require additional processes such as __, __, __, __ (MPGA).

Answer 29

5' UTR; 3' UTR inactive; methylation, phosphorylation, glycosylation; acetylation.

Question 30

Which of the following statements about histone and gene expression is correct? A. In a general sense, highly condensed DNA bound with histone proteins represses gene expression. B. Acetylation involves the addition of acetyl groups to histone proteins, and it usually results in repression of transcription. C. Addition of methyl groups to the tails of histone proteins always results in activation of transcription. D. All statements above are correct

Answer 30

A. In a general sense, highly condensed DNA bound with histone proteins represses gene expression.

Question 31

Yeast cultures are normally grown at 30°C. Suppose you isolate a strain with a temperature sensitive mutation in the Gal₈₀ gene. The Gal₈₀ protein cannot bind to Gal4 when the cells are grown at 30°C. What would you predict would occur when this mutant yeast strain is grown at 30°C in the absence of galactose? A. The Gal4 protein will bind to UASG and stimulate transcription. B. The Gal4 protein will bind to an UAS other than UASG. C. The Gal₈₀ protein will bind to UASG instead of Gal4 D. The Gal₈₀ protein will be degraded. E. You cannot predict the outcome based on the information provided.

Answer 31

A. The Gal4 protein will bind to UASG and stimulate transcription.

Question 32

In eukaryotes, there are a variety of post-transcriptional mechanisms of gene regulation. Which of these mechanisms function in the nucleus? A. Alternative splicing of pre-mRNA B. Increased initiation of translation C. miRNA mediated translational repression D. Addition of phosphate or sugar groups to proteins

Answer 32

A. Alternative splicing of pre-mRNA

Question 33

__ is a form of gene regulation that couples transcription and translation.

Answer 33

Attenuation.

Question 34

Which of the following mutations would probably lead to constitutive (continuous) gene expression? A. The DNA binding domain of a transcriptional activator protein such that it no longer bound to the appropriate enhancer. B. The TATA box sequence in the core promoter sequence that abolishes binding with the TATA box binding protein. C. A repressor protein that could not bind to the operator sequence of the bacterial operon. D. An enhancer sequence that moved it 200 bp upstream from its usual position. E. More than one of the above

Answer 34

C. A repressor protein that could not bind to the operator sequence of the bacterial operon.

Question 35

Which of the following are key differences between the gene organization in eukaryotic and prokaryotic cells? A. Monocistronic mRNA is found exclusively in prokaryotic cells. B. Histone proteins are associated with prokaryotic DNA to form chromatin. C. A small fraction (less than 5%) of the eukaryotic genome is composed of repetitive DNA sequences. D. Only eukaryotic genes are organized into introns and exons. E. All of the above

Answer 35

D. Only eukaryotic genes are organized into introns and exons.

Question 36

Leucine zippers are structural motifs commonly associated with A. Enhancers and promoters B. DNA binding proteins C. Methylases (the enzymes that methylate DNA) D. Prokaryotic sigma factor E. Select this answer if more than one of the choices A-D are correct.

Answer 36

B. DNA binding proteins

Question 37

Recessive mutations in a gene are nearly always __ and are inherited as __ alleles A. Gain-of-function mutations; recessive. B. Loss-of-function mutations; recessive. C. Recessive lethal mutations; dominant. D. Nonsense mutations; dominant. E. None of the above.

Answer 37

B. Loss-of-function mutations; recessive.