Exam 1 - Gene expression/ Transcription

Question 1

transcription and translation are found in both

Answer 1

Prokaryotes and eukaryotes

Question 2

compare prokaryotes vs eukaryotes during transcription and translation

Answer 2

prokaryotes are: simultaneous and single location. So both transc. and transl. occur in the same cell so it much more simple

eukaryotes are: sequential and separate location. so transc. will occur in the nucleus and transl. will occur in the cytoplasm

Question 3

what is the anatomy for a eukaryotic DNA and mRNA sequence?

Answer 3

DNA = 1 - regulatory region
2 - promotor region (start)
3 - transcribed region
4 - regulatory region

mRNA= 1 - meG (upside down) 5’ cap
2 - 5’ UTR (untranslated)
3 - AUG (start protein)
4- exons and introns
5 - UAG (stop codon)
6 - 3’ UTR (untranslated)
7 - AAAAAA tail

Question 4

3 steps of Transcription

Answer 4

1 - Initiation
a) promotor binding
b) transcription bubble opens
2 - Elongation
3 - Elimination

Question 5

Transcription : initiation(simple steps)

Answer 5

1 - specific sequences in DNA are recognized by transcription factors (TF)

2 - RNA polymerase II is recruited by a promotor

3 - C-terminal tail of RNA polymerase II is phosphorylated to release TF

Question 6

Transcription: Initiation (detailed version)

Answer 6

1 - TFIID recruited FIRST
a) TATA binding protein recognizes TATA box and this binding distorts the DNA helix
b) binds initiator element (INR) and downstream protein element (DPE) at the same time

2 - TFIIB recruited SECOND
a) binds B recognition element (BRE)

3 - TFIIF stabilizes RNA polymerase

4 - TFIIH has helicase and kinase function
a) helicase: creates transcription bubble
b) kinase: all TFII are released and allow RNA poly II to change shape and begin elongation

Question 7

Initiation promotor elements

Answer 7

TATA box, BRE, DPE, INR

Question 8

Initiation TF

Answer 8

1 - TFIID: recognizes TATA box and other DNA sequences near transcription start point

2 - TFIIB: Recognizes BRE in promotors

3 - TFIIH: enzyme unwinds the helicase function

Question 9

How are eukaryotes turned on or off in transcription

Answer 9

histone density

Question 10

how many RNA poly options in transcription

Answer 10

3

Question 11

what are the three RNA poly options

Answer 11

1 - RNA poly 1: rRNA
2 - RNA poly 2 : all protein coding and noncoding (everything else)
3 - RNA poly 3: tRNA

Question 12

What is the general idea for transcription, what are we starting with and what are we making

Answer 12

DNA —> RNA —> protein

Question 13

DNA —> mRNA occurs in the _______. Since it is still in the nucleus, the mRNA is called ______.

Answer 13

Nucleus

pre-mRNA

Question 14

why do we need RNA polymerase

Answer 14

used to create a sequence that will become mRNA. RNA poly will attach to the promotor region on DNA

Question 15

Transcription Elongation

Answer 15

only one strand of DNA duplex serves as a template strand for the RNA

the RNA sequence is the reverse and compliment of this DNA template

Question 16

Promotor Proximal Pausing in transcription elongation

Answer 16

RNA poly 2 pauses after transcribing 20 - 60 nucleotides

• NELF (negative elongation factor) induces the pause
  - the DRB sensitivity factor will interact with NELF to maintain pause

Question 17

Why do we pause in Promotor Proximal Pausing?

Answer 17

to check to any mistakes, collect instruction, resolve heterochromatin

Question 18

Positive Transcription Elongation Factor B (P - TEFb) transcription factor

Answer 18

releases promotor proximal pausing

a kinase will add phosphate to C terminal of RNA poly 2 - this releases NELF

Question 19

What does FACT do

Answer 19

removes histones - (histone flicker hockey stick)

Question 20

What does NAP do

Answer 20

recycles H2A/H2B dimer

Question 21

what do topoisomerase do

Answer 21

type 1: open 1 DNA strand and unwinds TOP1 and TOP3b

type 2: opens 2 DNA strands and untangles TOP2a and TOP2b

Question 22

What are the three events of Transcription Elimination

Answer 22

1 - RNA trimmed
2 - RNA polyadenylation (poly A tail)
3 - RNA Poly II falls off

Question 23

what are the two models of eukaryotic termination

Answer 23

1 - torpedo: exonuclease XRN2 chews back RNA and kicks off RNA Pol II when the two proteins collide

2 - Allosteric: PolyA tail on mRNA signals RNA Poly II to change shape and fall off

Question 24

what are the two models of prokaryotic termination

Answer 24

1 - Rho protein facilitates
2 - RNA secondary structure (hairpin)