Exam 2: Gene Regulation in Eukaryotes

Question 1

prokaryote genes vs. # eukaryote genes

Answer 1

prokaryotes have ~500-5000 genes

eukaryotes have ~6000-30,000 genes

Question 2

how does genetic control begin?

Answer 2

with a promotor (both prokaryotes and eukaryotes)

promotor longer in eukaryotes

Question 3

how is promotor strength determined?

Answer 3

binding affinity of the promotor

Question 4

transcription factor

Answer 4

any protein that affects transcription (regulates gene expression)

Question 5

how do transcription factors work?

Answer 5

bind a target site in DNA or bind another TF or both

Question 6

what are TF DNA-binding sites called?

Answer 6

enhancers

Question 7

can the same protein act as an activator or repressor in different circumstances?

Answer 7

yes

TFs can also act simultaneously in two places side by side on DNA

Question 8

TF binding sites can be…

Answer 8

near promotors they regular

far away from promotors they regulate

upstream or downstream of transcription unit they control

Question 9

can TF binding sites be in introns?

Answer 9

yes

Question 10

two ways TF regulate genes

Answer 10

direct effects on the transcription complex

spreading effects on chromatin geometry

Question 11

cis regulation sites

Answer 11

sites in DNA close to a gene, which code for TF binding sites

Question 12

trans regulation sites

Answer 12

site in DNA far away from a gene, which code for TF proteins

Question 13

what does trans mean

Answer 13

gene that codes for it is found somewhere else

it could be anywhere in the genome

Question 14

what kind of effects do changes in the cis/trans part of the regulatory system have?

Answer 14

phenotypic effects

Question 15

CRM

Answer 15

cis regulatory module/enhancer

cluster of TF binding sites

Question 16

effects of CRM

Answer 16

converge on the promotor

Question 17

what is a CRM

Answer 17

small region of DNA (500bp) with 5-15 binding sites for TFs

Question 18

how long are the individual TF binding sites in a CRM

Answer 18

6-10 bases long

Question 19

are CRMs on the same DNA as the gene they regulate?

Answer 19

yes, but they can be distant from the gene if they’re on the same dsDNA strand

Question 20

are genes controlled by a single CRM or multiple CRMs?

Answer 20

either

Question 21

why is on-off control of the same gene from different CRMs needed?

Answer 21

b/c many genes get used in more than one place

Question 22

interactions between TFs that control genes by CRM

Answer 22

combinatorial control

cumulative effects

competitive binding

Question 23

how do TFs bind dsDNA?

Answer 23

in the major groove they recognize target base sequences and bind to them

they dimerize and bind to palindromes in the major groove

Question 24

DNA palindrome

Answer 24

5’ GAATTC 3’

3 ‘CTTAAG 5’

Question 25

mammals have how many TF proteins?

Answer 25

2500

it takes a lot of genes to control a lot of genes

Question 26

does each TF have its own transcription unit?

Answer 26

yes

Question 27

leucine zipper

Answer 27

two crossed helices holding DNA

Question 28

how far away can control sites in DNA be from the gene they control?

Answer 28

up to 30,000 bases away and sometimes even farther