1.4 Eukaryotic Gene Regulation

Question 1

how many rnap do prokaryotes have

Answer 1

1

Question 2

differentiate between the 3 rnap of eukaryotes, in regards to which genes they transcribe

Answer 2

rnapI: rRNA genes
rnapII: all protein coding genes
rnapIII: tRNA genes

Question 3

transcription initiation in eukaryotes require many proteins named? and what do they do?

Answer 3

general transcription factors. they help position rnap at eukaryotic promoters

Question 4

name is the general transcription factor of prokaryotes (that is apart of rnap)

Answer 4

sigma factor

Question 5

eukaryotic genomes lack _______

Answer 5

operons

Question 6

how many general tf (transcription factors) are involved in rnapII transcription

Answer 6

5: TFIID, TFIIB, TFIIF, TFIIE, TFIIH

Question 7

eukaryotic dna is packaged into __________ which provides an additional mode of __________

Answer 7

chromatin, regulation

Question 8

are gene regulatory proteins also a tf?

Answer 8

yes

Question 9

the _______ acts as an intermediate between regulatory proteins and rnap

Answer 9

mediator

Question 10

t/f can gene regulatory proteins act over very large distances

Answer 10

yes - through dna looping

Question 11

coactivators and corepressors assemble on dna-bound gene regulatory proteins do not bind directly on dna, so where can they bind?

Answer 11

cis reg elements

Question 12

describe the modular design of eukaryotic activator proteins

Answer 12

1. dna binding domain (dbd) which recognizes specific DNA sequences
2. activation domain (ad) which accelerates the freq/rate of transcription
   you can mix and match dbds and ads, as long as the dbd can bind to the target which leads to activation of the tata box

Question 13

how do activator proteins activate transcription

Answer 13

they attract position and modify gen tf, mediator, rnapII
they can do that by either directly acting on these components (attracts them to promoters like prokaryotic activators) or indirectly modifying chromatin structure

Question 14

what is the basic structure of eukaryotic chromatin

Answer 14

nucleosomes

Question 15

describe the structure of nucleosomes

Answer 15

dna wound around a histone octamer (h2a, h2b, h3, and h4)x2
the linker dna (10-80bp) is attached to h1 on one nucleosome, a nucleosome includes ~200 nucleotide pairs on dna and the dna that wraps around the core is approx 1217 bp long

Question 16

how do nucleosomes pack

Answer 16

as compact chromatin fibers in a zigzag or solenoid model

Question 17

when nucleosomes are packed, transcriptional machinery cannot assemble on promoters tightly packed in chromatin, how is this solved?

Answer 17

activator proteins can alter chromatin structure and increase promoter accessibility

Question 18

how many ways can activator proteins alter chromatin

Answer 18

4

Question 19

describe the purpose and process of nucleosome sliding

Answer 19

nucleosome structure can be altered by chromatin remodeling complexes in an atp dependent manner to increase promoter accessibility - it just moves the dna around to show the parts you wanna show

Question 20

nucleosome removal and histone exchange requires cooperation with __________________

Answer 20

histone chaperones

Question 21

describe the 2 methods of altering chromatin through histone chaperones

Answer 21

• remove histones which leads to more space. an optional step is to put an alternate protein using histone chaperone, which binds more loosely to help gen tfs get in there
• an atp dependent chromatin remodeling complex w a histone chaperon brings a histone and changes the prot for an exchange of h2a-h2b dimers which bind more loosely

Question 22

what are the histone code

Answer 22

histone modifying enzymes produce specific patterns of histone modifications

Question 23

what enzymes are involved in the addition of phosphate, acetyl, and methyl groups

Answer 23

phosphorylation: kinase
acetylation: acetyltransferase
methylation: methyltransferase

Question 24

where do histone modifications occur

Answer 24

on specific aa of histone tails (usually on n terminus but c terminus is also possible)

Question 25

which enzymes are nicknamed writers and why

Answer 25

histone modifying enzymes - they make specific modifications to histone tails

Question 26

what can reader proteins do

Answer 26

can recognize specific modifications and provide meaning to the code

Question 27

describe the steps of the human interferon gene regulation

Answer 27

1. activator protein binds to chromatin DNA and attracts a histone acetyltransferase (HAT) 2. HA acetylates lysine 9 of histone H3 and lysine 8 of histone h4 (h3k9 and h4k8) 3. activator protein attracts a histone kinase (hk) 4. hk phosphorylates serine 10 of histone h3 (h3s10). can only occur after acetylation of lysine 9. 5. serine modification (phosphorylation) signals the acetyltransferase to acetylate lysine 14 of histone h3 - the histone code for transcription initiation is written 6. tfIId and chromatin remodeling complex (reads the code) bind to modified histone tails and initiate transcription

Question 28

can you skip steps in the human interferon gene regulation

Answer 28

no

Question 29

unlike prokaryotes, eukaryotic repressor proteins rarely compete with _____ for access to dna

Answer 29

rnap

Question 30

how can eukaryotic repressor proteins inhibit transcription (6)

Answer 30

1. dna competitive binding: repressor with repression domain doesn't allow the activator to bind to the active site bc it's overlapped with where the repressor is 2. masking the activation surface: the activator binds to the binding site but the head (activator surface) is blocked 3. direct interaction with gen tf: repressor can inactivate the gen tf even if on the tata box 4. recruitment of chromatin remodeling complexes: rolls the histone back up to prevent gene expression bc it cannot read it 5. recruitment of histone deacetylases : modify the tails of histone 6. recruitment of histone methyl transferase: modify tails of histone

Question 31

when guided by gene regulatory proteins, histone reader and writer proteins can establish what

Answer 31

a repressive form of chromatin -- the reader keep recruiting writers to write on the following histone tail = chromatin can be stabilized and histone code cna be spread

Question 32

what spreads the histone code along chromatin

Answer 32

reader writer complexes

Question 33

how do reader-writer complexes know to stop spreading the histone code

Answer 33

border sequences

Question 34

what enzyme is attracted by readers to methylate nearby cytosines in dna

Answer 34

dna methylase

Question 35

which nucleotide base is dna methylase doing to methylate

Answer 35

cytosines

Question 36

describe epigenetic inheritance

Answer 36

methylation and further gene expression patterns can be inherited. the whole cell memory is semiconservative as if there are methylated cytosines on one strand then the other would be too

Question 37

what do dna methyl binding proteins do

Answer 37

bind methyl groups and stabilize the structure

Question 38

what does the methylation of cytosines do

Answer 38

blocks tf/rna poly from coming in = transcription repression

Question 39

which of the following would you expect to see at the interferon gene promoter and accompanying histones if an activator protein was present, but histone kinase was inhibition a. acetylated h3k9 and h4k8 b. acetylated h3k9 and h4k8; phosphorylated h3s10 c. a. acetylated h3k9 and h4k8; phosphorylated h3s10; tfiid and chromatin remodeling complex binding d. no histone acetylation of phosphorylation

Answer 39

A. step 3 cannot happen and since you cannot skip steps you won't see the following so it is only at a. there will be some histone acetylation or phosphorylation