Chapter 17: Control of Gene Expression in Eukaryotes

Question 1

differences between eukaryotic gene regulation and bacterial gene regulation

Answer 1

• many bacterial and archaeal genes are organized into operon and are transcribed into a single molecule; most eukaryotic genes have their own promoters that are transcribed separately
• chromatin structure affects gene expression in eukaryotic cells; DNA must unwind from the histone proteins before transcription can take place
• the presence of the nuclear membrane is eukaryotic cells separates transcription and translation in time and space

Question 2

transcription and translation location in eukaryotes

Answer 2

transcription - the nucleus
translation - the cytoplasm

Question 3

transcription and translation location in prokaryotes

Answer 3

simultaneously occur in the cytoplasm

Question 4

modification of chromatin structure

Answer 4

chromatin structure must change before transcription so that DNA becomes more accessible to transcription machinery
- chromatin is tightly coiled around the octamers, making it difficult for proteins to bind to it

Question 5

DNase I hypersensitive sites

Answer 5

regions around genes become highly sensitive to the action of DNase I
- frequently develop 1000 nucleotides upstream of the transcription start site

Question 6

three processes that affect gene regulation by altering chromatin structure

Answer 6

1. chromatin remodeling
2. modification of histone proteins
3. DNA methylation

Question 7

chromatin-remodeling complexes

Answer 7

protiens that alter chromatin structure without altering the chemical structure of the histones directly
- bind to particular sites on DNA and reposition the nucleosome, allowing other transcription factors and RNA polymerase to bind to promoters and initiate transcription

Question 8

two domains of histones in the octamer core

Answer 8

1. a globular domain that associates with other histones and the DNA
2. a positively charged tail domain that interacts with the negatively charged phosphate groups on the DNA

Question 9

histone code

Answer 9

tails of histone proteins are modified by the addition or removal of phosphate groups, methyl groups, or acetyl groups
- encode information that affects how genes are expressed

Question 10

methylation of histones

Answer 10

• the addition of CH3 to the tails of histone proteins
• can bring about the activation or repression of transcription

Question 11

histone methyltransferases

Answer 11

add methyl groups to specific amino acids of histones

Question 12

histone demethylases

Answer 12

remove methyl groups from histones

Question 13

acetylation of histones

Answer 13

addition of acetyl groups (CH3CO) to histones
- usually stimulates transcription
- destabilizes chromatin structure, allowing transcription to take place

Question 14

acetyltransferase enzymes

Answer 14

enzymes that add acetyl groups to histone proteins

Question 15

deacetylase enzymes

Answer 15

enzymes that strip acetyl groups from histones and restore chromatin structure, repressing transcription

Question 16

DNA methylation

Answer 16

• methylation of cytosine bases
• most common on cytosine bases adjacent to guanine nucleotides
• associated with the repression of transcription

Question 17

transcription factors

Answer 17

proteins that bind to specific DNA sequences and regulate transcription

Question 18

cofactors

Answer 18

proteins recruited by transcription factors that stimulate or repress transcription

Question 19

general transcription factors

Answer 19

transcription factors that bind to the core promoter and are part of the basal transcription apparatus
- required for the initiation of transcription

Question 20

basal transcription apparatus

Answer 20

the complex of RNA polymerase, transcription factors, and other proteins that assemble to carry out transcription
- binds to a core promoter and is capable of minimal levels of transcription

Question 21

enhancer

Answer 21

DNA sequence stimulating transcription a distance away from the promoter
- abundant in eukaryotes

Question 22

insulator

Answer 22

DNA sequence that blocks or insulates the effect of enhancers in a position dependent manner
- if one lies between an enhancer and promoter, it blocks the action of the enhancer

Question 23

mediator

Answer 23

complex of proteins that interacts with RNA polymerase
- component of the basal transcription apparatus

Question 24

super-enhancer

Answer 24

number of enhancers clustered together
- able to stimulate levels of transcription higher than regular enhancers are

Question 25

silencers

Answer 25

sequences that have an inhibitory effect on the transcription of distant genes

Question 26

heat-shock proteins

Answer 26

proteins that help prevent damage by stressors like extreme hear

Question 27

response elements

Answer 27

regulatory sequences that typically contain the same consensus sequence at varying distances from the gene being regulated
- binding sites for transcription factors, which bind to the response elements and elevate transcription

Question 28

exonic/intronic splicing enhancers and splicing silencers

Answer 28

additional sequences that promote or repress the use of particular splice sites during the process of RNA splicing, resulting in alternative splicing outcomes
- proteins or ribonucleoprotien particles bind to these sites

Question 29

SR proteins

Answer 29

group of proteins involved in splice-site selection that has two protein domains:
1. an RNA binding region
2. alternating serine and arginine amino acids
SR proteins bind to splicing enhancers on the pre-mRNA and stimulate the attachment of small nuclear ribonucleoprotiens (snRNPs) , which then commit the site to splicing

Question 30

ribonucleases

Answer 30

enzymes that specifically break down RNA

Question 31

poly(A) binding proteins (PABPs)

Answer 31

bind to the poly(A) tail and contribute to its stability enhancing effect

Question 32

RNA silencing

Answer 32

RNA interference; small RNA molecules are diced and produce a silencing complex

Question 33

post translational protein modification

Answer 33

• selective cleavage and trimming of amino acids from the ends
• acetylation
• addition of phosphate groups, methyl groups, carboxyl groups, carbohydrates, or ubiquitin