eukaryotic gene expression

Question 1

what is the primary purpose of gene control in multicellular organisms?

Answer 1

the execution of precise developmental programs
- so that the proper genes are expressed in the proper cells at the proper times (during embryologic development and cellular differentiation)

Question 2

what is another name for epigenetic regulation?

Answer 2

chromatin-mediated regulation

Question 3

where does transcription in eukaryotes take place?

Answer 3

on DNA that is wrapped in chromatin

Question 4

what does the pioneer transcription factor required for?

Answer 4

unwinding and opening up DNA

Question 5

Heterochromatin and how its packed

Answer 5

• regions of chromosomes that are more intensely stained (densely packed)

Question 6

what is heterochromatin rich in?

Answer 6

rich in repetitive DNA (transposons), centromeres and telomeres

Question 7

what type of genes are found in heterochromatin

Answer 7

Inactive genes

Question 8

Euchromatin

Answer 8

lightly strained chromosome regions

Question 9

what type of genes are found in euchromatin?

Answer 9

Active genes

Question 10

IMPORTANT
What does RNA polymerase I transcribe?

Answer 10

Pre-RNA (28S, 18S, 5.8S rRNAs)

Question 11

IMPORTANT
What is the function of RNA polymerase I

Answer 11

Ribosome components, protein synthesis

Question 12

IMPORTANT
what does RNA polymerase II transcribe? what are their functions?

Answer 12

mRNA (encodes proteins)
snRNAs (RNA splicing)
siRNAs (Chromatin-mediated repression, translation control)
miRNAs (translation control)

Question 13

IMPORTANT
what does RNA polymerase III transcribe? what are their functions?

Answer 13

• tRNAs (protein synthesis)
• 5S rRNA (ribosome component, protein
  synthesis)
• snRNA U6 (RNA splicing)
• 7S RNA (signal recognition particle for insertion of polypeptides into the endoplasmic reticulum)
• other small stable RNAs (various functions, unknown for many)

Question 14

how many polypeptides are in RNA pol II? What are they called?

Answer 14

• 12
• RPB1-RPB12

Question 15

true or false? all eukaryotic RNA polymerases share a very low level of homology with the yeast RNA pol II

Answer 15

false. - high level of homology

Question 16

the clamp domain in the polymerase _______ accommodates ___ and then is ____ by a bridge

Answer 16

RPB1, DNA, closed

Question 17

how does the synthesized RNA exit?

Answer 17

through a channel

Question 18

eukaryotic RNA pol II contains a unique _______ of its RPB1 subunit

Answer 18

carboxy-terminal domain (CTD)

Question 19

what is the role of CTD

Answer 19

-involved in multiple regulatory interactions
key role in initiation, release, elongation and processing of the synthesized mRNAs

Question 20

what is the amino acid sequence of the CTD?
How many repeats are there? in mammals?

Answer 20

• Tyr-Ser-Pro-Thr-Ser-Pro-Ser (The Sad Player Tried Some Pro Soccer)
• contains 26 repeats
• 52 repeats in mammals

Question 21

How are Ser residues in the CTD phosphorylated?

Answer 21

upon transition from initiation to elongation.

Question 22

In the RNA pol II structure, where does the RNA transcript come in?

Answer 22

in between the wall (on the left) and the clamp domain (on the right)

Question 23

what are the RNA polymerase II transcribed genes regulated by?

Answer 23

1. conserved basal promoter elements, also called CORE PROMOTER SEQUENCES
2. promoter-proximal binding sites for transcriptional activators
3. distal enhancers or repressors
4. chromatin structure

Question 24

where is the core promoter elements BRE and TFIIB located on pol II?

Answer 24

-37 to -32

Question 25

where is the TATA box located on pol II?

Answer 25

-31 to -26

Question 26

where is the Inr (Initiator) located on pol II?

Answer 26

-2 to +4

Question 27

where is the DPE (downstream promoter element) located on pol II?

Answer 27

+28 to +32

Question 28

which 3 elements direct the positioning of the polymerase?

Answer 28

TATA box, Initiator, BRE

Question 29

As the TATA box and Initiator start at a defined point on the coding strand. which TGCA does it bind to?

Answer 29

usually A

Question 30

where is the TATA box prevalent in?

Answer 30

highly transcribed genes

Question 31

Some genes contain an initiator but no TATA box. are initiator elements highly or poorly conserved?

Answer 31

poorly

Question 32

which recognition element does BRE known as?

Answer 32

TFIIB

Question 33

RNA polymerases must recognize the promoter and correctly initiate transcription at a very specific position. BUT THEY CAN NOT DO THIS ALONE. what other factors does this require help form?

Answer 33

- several general pol II transcription factors (GTFs) assemble the pre initiation complex over the core promoter sequence - DNA helicase

Question 34

how does protein kinase help initiation of transcription?

Answer 34

release the polymerase

Question 35

how else do other factors help initiate transcription?

Answer 35

help the polymerase elongate move nucleosomes out of the way

Question 36

what are the pol I GTFs

Answer 36

TFIA, TFIB

Question 37

what are the pol II GTFs

Answer 37

TFIIA, TFIIB, TFIID,TFIIE, TFIIH