8.1 - 8.3

Question 1

what does RNA pol I transcribe

Answer 1

rRNA

Question 1

what does RNA pol II transcribe

Answer 1

mRNA, miRNA, snRNA

Question 2

what does RNA pol III transcribe

Answer 2

tRNA

Question 3

what are the similarities between prokaryotic and eukaryotic polymerase

Question 4

what are the differences between prokaryotic and eukaryotic polymerase

Question 5

what is the function of the clamp structure in RNA pol II

Answer 5

clamp domain swings over the cleft between the jaws of the polymerase during formation of the transcribing complex, trapping the template DNA strand and transcript

Question 6

list eukaryotic promoter elements

Answer 6

1. TATA box
2. initiator
3. CpG islands
4. BRE and DPE (in combination with TATA or Inr)

Question 7

what is CpG island

Answer 7

stretch of 20-50 CG nucleotides located approx. 100 bp upstream from transcription start site

Question 8

what is the first element to bind to promoter DNA

Answer 8

TFIID: TATA-binding protein (TBP) and TATA-associated factors (TAFs)

Question 9

what happens after TFIID binds

Answer 9

TFIIA and TFIIB come along and bend the DNA (this is essential)

Question 10

what happens after DNA is bent

Answer 10

RNA pol II comes along with CTD and TFIIF forming core PIC

Question 11

before ATP, is the PIC closed or open

Answer 11

closed

Question 12

after ATP, is the PIC closed or open

Answer 12

open

Question 13

CTD must be ____________ for elongation to begin

Answer 13

FULLY PHOSPHORYLATED

Question 14

what is the first step in the formation of the pre-initation complex (PIC)

Answer 14

TATA-binding protein binds to the minor groove of DNA

Question 15

what is happening in a mutated region where transcription is completely abolished

Answer 15

there is a mutation in the TATA box region

Question 16

what does DNase I footprinting tell us

Answer 16

reveals the region of a DNA sequence where a transcription factor binds

defines the regions where proteins are being bound

Question 17

what does gel electrophoresis tell us

Answer 17

if the DNA is free or if there is a protein bound (the slower moving one will be the one with the protein bound)

Question 18

all transcription factors that function as activators have what

Answer 18

a DNA binding domain and an activator domain

Question 19

what are the 3 common structures of DNA binding domains

Answer 19

helix-turn-helix
zinc fingers
leucine zipper
coiled-coil

Question 20

where do the majority of DNA binding domains bind

Answer 20

in the MAJOR GROOVE

Question 21

what is cooperative binding

Answer 21

the cooperative binding of two transcription factors to neighboring sites (strengthens binding)

Question 22

what is the DNA recognition code

Answer 22

the edge of each base pair contains a distinctive pattern of hydrogen bond donors, hydrogen bond acceptors and methyl groups

Question 23

why do majority of transcription factors bind to major groove

Answer 23

from the major groove, each base pair has a distinct pattern that is recognizable but this is not the case from the minor groove

Question 24

what is a homeodomain

Answer 24

binds DNA through 3 helix structures (recognition helix) and the major groove