Chapter 33 the control of gene expression in eukaryotes

Question 1

why are there different stable cell types

Answer 1

epigonome, differences in chromatin structure and covalent modification of DNA and not that the sequence is different

Question 2

what do transcription factors do?

Answer 2

they interact directly with the transcriptional machinery and indirectly by changing chromatin structure

Question 3

what is a chromatin

Answer 3

the entire complex of a DNA + the associated proteins

Question 4

histone octamer

Answer 4

two units of H2A, H2B, H3 and H4

Question 5

nucleosome core particle

Answer 5

145 bP + histones

Question 6

which histone binds to linker DNA

Answer 6

H1

Question 7

what does DNA form when wrapped around the histone core

Answer 7

a left-handed superhelix

Question 8

what parts of the DNA do the histone core proteins interact with

Answer 8

inner face of DNA especially the phosphodiester backbone and the minor groove

Question 9

why is the DNA wrapped around histone octamer as left-handed superhelix

Answer 9

because the left-handed direction stores negative supercoils, which can be used to underwind DNA when replication or transcription takes place

Question 10

what part of transcription factor promotes transcription and how does it do it?

Answer 10

activation domain by interacting with RNA polymerase II, or by changing local chromatin structure or interacting with proteins that lead to the interaction with RNA polymerase II

Question 11

classes of DNA-binding proteins in transcription factors in eukaryotes

Answer 11

Homeodomains
basic-leucin zipper proteins
cys2his2 zinc finger-domains

Question 12

how can transcription factors for example act indirectly on RNA polymerase II?

Answer 12

through mediators interactions with the activation domains of transcription factors.
mediators faciltate the phorphorylation of the carboxyæ terminal of Polymerase

Question 13

common features between activation domains

Answer 13

1- redundant: a part of it can be deleted without loss of function

2- modular: activate transcription when paired with a variety of DNA -binding domaains

3- act synergestically: acting together much stronger effect than acting alone

Question 14

the opposite of mediators

Answer 14

transcriptional repressors

Question 15

combinatorial control

Answer 15

proteins affecting the patterns of gene expression

Question 16

enhancer

Answer 16

only effective when they are found in cells expressing the regulatory proteins that bind to them

they change the local chromatin structure rather than interacting directly with the RNA polymerase

Question 17

Hypersensitive sites

Answer 17

regions adjacent to genes if transcribed are susceptible to cleavage by DNase 1 if not transccribed resistent to cleavage

Question 18

DNA-methylation causes the ….. of transcription

Answer 18

inhibition

Question 19

Which nukleotide can be methylated and describe the mechanism

Answer 19

cytosin
5-methyl group extends to the major groove and interferes with the binding of proteins that cause the stimulation of trascription

Question 20

hypomethylation

Answer 20

absence of 5-methylcytosine near the start site

Question 21

estrogen binds to and the mode of action

Answer 21

nuclear hormone receptors
Estrogen receptor
consensus sequence AGGTCANNNTGTCCT
binds as a dimer
DNA-binding domain lies at the center and consists of a set of zinc based domains bind to DNA via alpha helices inserted into the major groove.
Ligand binding site towards the carboxyl terminal

Question 22

How does estrogen receptor and related receptors induce the change in gene expression

Answer 22

by attracting coactivators upon the binding of estrogen to the receptor SRC-1 (sterioid receptor coactivator 1)
GRIP-1 (glucocorticoid receptor interacting protein 1 )
NcoA-1 (nuclear hormone receptor coactivator 1)
the belong p160 family

Question 23

Tamoxifin and Estrogen-receptor mediated pathway

Answer 23

blocks the binding of coactivators and inhibits the activation of gene expression
does that by binding to the bindings sites and thus block the normal conformational changes that lead to induce and cause the chromatin structureto change
. helix 12 can not pack into its usual position and therefore, the helix 12 will block the binding of the coactivator

Question 24

histone acetyl-transferases which histone H3

Answer 24

transfer of acetyl from acetyl-CoA to lysin
some coactivators from p160 family can also do that
H3

Question 25

what is a bromodomain

Answer 25

a domain in many eukaryotic regulatory proteins. Bind to peptides containing acetyllysine

Question 26

proteins binding to TATA-box

Answer 26

TAFS (TATA-box-binding protein associated factors)

Question 27

where are bromdomains present?

Answer 27

In TAFs and chromatin remodelling complexes/engines

Question 28

chromatin remodelling complexes how do they work and what do they need?

Answer 28

ATP hydrolysis

they shift the positions of nucleosomes along the DNA and induce other conformational changes

Question 29

how does acetylation work

Answer 29

1- reduced affinity
2- recruiting other components of the transcriptional machinery
3- shifting the positions of nucleosomes
they all activate transcription

Question 30

what removes the acetyl group from histones

and what does this cause

Answer 30

histone deacetylases

the block of transcription by increasing the affinity of the histones for the DNA

Question 31

why is excess of iron damaging

Answer 31

because there are not proteins enough to bind the iron and the iron will therefore be free to form many reactive radicals

Question 32

to what end does the IRP bind to ferritin-mRNA

Answer 32

5’ end

Question 33

to what end does the IRP bind to transferrin-mRNA

Answer 33

3’end