3.9 transcription review

Question 1

how is RNA different than DNA?

Answer 1

• has uracil instead of thymine
• hairpin loop most common structure
• very prone to modifications/processing

Question 2

how is RNA polymerase different than DNA polymerase ?

Answer 2

• no primer needed
• much slower
• can synthesize bases de-novo
• has its own helicase activity

Question 3

what are the 4 basic steps of transcription?

Answer 3

1. initiation
2. elongation
3. termination
4. post-transcriptional modification in eukaryotes

Question 4

how many subunits are bacterial RNA polymerases made of?

Answer 4

6

Question 5

what are the two forms of bacterial RNAP

Answer 5

core (a2bb’w)
Halo (core + sigma)

Question 6

_______ bacterial RNAP can bind to any DNA and start transcribing. ____ binds to core, converts it to holoenzyme, and has specificity

Answer 6

Core
sigma

Question 7

Core RNA is useless until what?

Answer 7

sigma binds

Question 8

promoter regions usually have what two specific regions in them?

Answer 8

-10,-35

Question 9

if you add nucleotides you might not be able to see the __________ and promoters may not be able to bind

Answer 9

-35 and -10 regions

Question 10

every bacteria has how many sigma factors?

Answer 10

multiple

Question 11

steps of transcription initiation in bacteria?

Answer 11

• sigma binds to RNAP
  -RNAP binds to promoter region
  -formation of open complex
• transcription starts
  -initiation ends after first inter-nucleotide bond forms

Question 12

what are some factors that affect transcription initiation?

Answer 12

• promoter strength (how likely will they be recognized)
• dna supercoiling (can. hide or open promoter seq)
  -UP element

Question 13

does RNAP transcribe at a constant rate?

Answer 13

no!! it pauses every ~100 nucleotides

Question 14

what are two ways that RNAP are modulated?

Answer 14

-hairpin pause (hairpin is formed, factors must come relieve it before RNAP can continue)
-backtrack pause (the way is blocked, must backtrack for Gre/Pi to chew away before RNAP can start again)

Question 15

what happens during transcription termination?

Answer 15

• cessation of elongation
• release of transcript from ternary complex
• dissociation of RNAP from complex
  -zipping back of DNA double strands

Question 16

what are the 2 mechanisms of transcription termination?

Answer 16

factor independent and factor dependent

Question 17

_______ is a polycistronic RNA that encodes for multiple gene products

Answer 17

an operon

Question 18

rRNA is transcribed as a ______ transcript

Answer 18

30s

Question 19

you need a 1:1:1 ratio of 16:23:5s rRNA for what to happen?

Answer 19

nuclease processing

Question 20

every tRNA has what?

Answer 20

• G at 5’ end
• ends with CCA

Question 21

bacterial RNAP can bind to _________ on its own but needs ______ for specificity

Answer 21

promoters, sigma

Question 22

bacterial RNAP has very little post-translational modifications except what?

Answer 22

rRNA and tRNA

Question 23

what does eukaryotic RNAP I transcribe?

Answer 23

most rRNA genes

Question 24

what does eukaryotic RNAP II transcribe?

Answer 24

protein coding genes, miRNA genes, some genes for small RNAs

Question 25

what does eukaryotic RNAP III transcribe?

Answer 25

tRNA, 5s RNA

Question 26

which promoters are more well defined: eukaryotic or prokaryotic

Answer 26

prokaryotic

Question 27

_____ are areas of DNA that dont code for a protein

Answer 27

intron

Question 28

_________ help euk RNAP bind to the promoter

Answer 28

general transcription factors

Question 29

______ is a downstream promoter element and is most common when TATA is missing

Answer 29

DPE

Question 30

_____ is the initiator element

Answer 30

Inr

Question 31

_____ is the TFII recognition element

Answer 31

BRE

Question 32

RNAPII cnat bind by itself and needs a what ?

Answer 32

general transcription factor

Question 33

_____ is surrounded by a GC-rich region and is the only upstream promoter with a fixed location

Answer 33

TATA box

Question 34

does eukaryotic RNAP also need to pause?

Answer 34

yes

Question 35

_____ is a TF kinase that phosphorylates CTD of RNAPII to activate elongation

Answer 35

P-TEFb

Question 36

what catalyzes eukaryotic RNAP termination?

Answer 36

Cleavage and polyadenylation complex (CPA) recognizing Poly A signal (this dephosphorylates RNAP)

Question 37

what are some euk RNA modifications?

Answer 37

-5' cap -3' tail -splicing

Question 38

what is a 5' cap and whats its function?

Answer 38

- addition of methylated G7 - protects 5' mRNA - allows for proper ribosome positioning - helps with export to cytoplasm - promotes intron excising

Question 39

what does the Poly-A tail do?

Answer 39

- gives mRNA stability -facilitates export to cytoplasm -helps with ribosome positioning

Question 40

what shows that an RNA is mature?

Answer 40

having a 5'cap, 3' tail, and introns cut out

Question 41

what are the 2 types of splicing?

Answer 41

lariat, transesterification

Question 42

_______ make up spliceosomes that help process nuclear mRNA (introns removed in lariat pattern)

Answer 42

SNRPS

Question 43

_______ can produce a diversity of mRNAs from a single gene by arranging coding sequences

Answer 43

alternative splicing

Question 44

______- is transcribed as a 45S transcript by RNAPI in the nucleus

Answer 44

rRNA

Question 45

______ is processed as a 100nucleotide precursor by RNAPIII and is processed and modified before mature

Answer 45

tRNA

Question 46

RNAP binding at promoters may require ________

Answer 46

transcriptional factors

Question 47

promoters contain ____ elements and sequence for specifying tissue specificity

Answer 47

cis