RNA

Question 1

types of RNA (5) and associated rna polymerase

Answer 1

II
- mRNA: messenger - amino acid sequences
- rRNA - ribosomal - ribosomal proteins, make up ribosomes
- miRNA - micro - non-coding, regulate gene expression

III
- tRNA : transfer - brings aminos to ribosome during translation
- snRNA - small nuclear, with proteins, form complexes for processing (splicing)

Question 2

how are rna pols isolated

Question 3

enhancers

Answer 3

bound by transcription factors
regulate gene expression

Question 4

elements that regulate gene expression

Answer 4

• TATA box: promoter sequence
• CpG island promoter
• Enhancer

Question 5

Core promoter elements

Answer 5

help initiate transcription
- site for binding

Question 6

core promoter element vs proximal promoter elements

Answer 6

Core: site for binding
proximal: regulation of expression

Question 7

Tata box binding protein

Answer 7

c-terminal binds to TATA
- bends double helix
- aids in uncoiling so RNApol can bind

Question 8

gene specific transcription factor binding elements

Answer 8

• Activate transcription
• can repress it
• Recruited in certain situations
  ‘Regulatory”

Question 9

general transcription factors (TFII)

Answer 9

Always needed for rna ii
Bind DNA or other proteins
“housekeeping”

Question 10

preinitiation complex (PIC)

Answer 10

Composed of
- TFIIs
- Mediator
- RNA pol ii

Question 11

formation of pic

Answer 11

1. TFIID recruited
   - TAFs bind elements on promoter
2. TFIIB recruited
   - binds TBP
3. TFIIB binds RNAPII and TFIIF
4. TFIIE and TFIIH bind
   - H brings 2 helicases and 1 kinase

Question 12

TFIIs

Answer 12

TFIID: TBP and TBP-associated factors (TAFs)
TFIIB
TFIIF
TFIIE: 2 subunits
TFIIH: 10 subunits

Question 13

Describe the effects the following would have on
transcription of mRNA and tRNA genes.
a. Loss of TBP

Answer 13

TBP binds to TATA box AND binds TFIIB

No TBP = no complex

Question 14

Describe the effects the following would have on
transcription of mRNA and tRNA genes.

b. Loss of TFIIB

Answer 14

TFIIB binds to TBP, then allows RNA pol, TFIIF, TFIIE, TFIIH to bind

No TFIIB = only TFIID = no function

Question 15

Describe the effects the following would have on
transcription of mRNA and tRNA genes.

c. Loss of TFIID

Answer 15

TFIID = TBP and TAFS

No TFIID = no binding to dna = no complex

Question 16

mediator in PIC

Answer 16

20 subunits
flexible
stimulated transcription

binds RNAPII and TFs

Question 17

what could be an advantage to using weak interactions to hold together complimentary dna strands and the PIC

Answer 17

Allows them to easily come apart when needed

recycle pic components
replicate dna

Question 18

To make DNA and RNA, phosphodiester bonds are
formed between which two chemical groups on the
deoxyribose sugar? (select all that apply)
1. H 2 O
2. 5’ hydroxyl group
3. 3’ hydroxyl group
4. 5’ phosphate
5. 3’ phosphate
6. pyrophosphate

Answer 18

3. 3’ Hydroxyl group
4. 5’ phosphate

Question 19

transcriptional activators

Answer 19

• interact w mediated and TFs
• mod chromatin structure

Question 20

transcriptional repressors

Answer 20

1. competitive dna binding
   - binding site overlaps (downstream) binding site for activator = activator can’t bind
2. masking activation surface
   - repressor binding site downstream
   - binds to activator (inhibits)
3. direct interaction w TFs
   - binds so activator can’t

Question 21

how do transcriptional repressors work

Answer 21

recruit histone deacetyltransferases
- affects chromatin remodelling

Question 22

overview of mrna processing

Answer 22

1. 5’ capping after transcription
2. cleavage at polyA site via endonuclease (remove junk after site)
3. polyadenylation (add poly a tail to site)
4. splicing

Question 23

what doe sit mean that mRNA processing occurs co-transcriptionally

Answer 23

The processing of mrna happens while transcription is occuring

Question 24

c terminal domain (CTD) of rnapolii

Answer 24

a coordinator of mrna processing

bidning site for modifications

Question 25

What is the role of Cet1 and is its spatial distribution consistent with that function? - peaks at TSS - climbs back slightly after processing - lower than TFIIB

Answer 25

At beginning before/during start = 5' end = 5' capping

Question 26

What is the role of Pcf11 and is its special distribution consistent with that function? - Starts low - peaks after poly a site

Answer 26

At poly a site = cleavage

Question 27

how does CTD phosphorylation cycle regulate transcriptional processing

Answer 27

different patterns of phosphorylation recruit different factors The enzymes bind to the residues of phosphorylation areas

Question 28

You discover a new protein and show it is important for transcription termination and can bind the RNAPII-CTD. Based on what you know about the RNAPII-CTD phosphorylation cycle, which CTD modification state is this new protein likely to recognize and bind? What do you expect to see if you remove the kinases and phosphatases responsible for depositing or removing that the relevant modifications?

Answer 28

- recognize the dephosphorylation of Ser2 - Ser2 stays phosphorylated - protein can't bind - termination can't occur

Question 29

ctd phosphorylation patterns

Answer 29

Initiation: - CDK7 : Ser5 Ser7 Elongation: - CDK9: Ser2 - Ser 5 and Ser 7 dephosphorylated Near termination - Fcp1 dephosphorylates Ser2-P

Question 30

how are locations of exons and introns determined

Answer 30

- comparing the genomic sequence (has introns) with a global mRNA sequence (only has exons) - look at seq before and after splice sites - predict where splice sites are - highest frequency of 5' GU and 3' AG

Question 31

Describe the effect the following would have on splicing 1. A deletion mutation removing the section highlighted in yellow (splice site between exon 1 and intron)

Answer 31

There would be no splicing between exon 1 and intron, but it would splice between intron and exon 2 Intron would not be removed

Question 32

Describe the effect the following would have on splicing 2. Changing all the adenines in the section highlighted in yellow to guanine (splice site between exon 1 and intron, AGGUAAGUA)

Answer 32

--> GGGUGGGUG

Question 33

dna repair - photoreactivation

Answer 33

uv induced thymine dimers repaired via photoreactivation light used by enzymjes to break bonds that form cyclobutane ring

Question 34

dna repair - nucleotide excision repair of thymine dimers

Answer 34

dmamged dna unwound by helicase cleaved on either side of dimer gap filled by pol

Question 35

dna repair - base excision

Answer 35

uracil paired with guanine by accident bond between uracil and deoxyribose cleaved leaves sugar w no base dna chain cleaved gap filled