Zomerdijk class

Question 1

House keeping genes

Answer 1

Expressed in all cells

Question 2

Transient bubble

Answer 2

DNA bubble formed in RNA polymerase

Question 3

What percentage of the genome are coding sequences

Answer 3

Less than 2%

Question 4

What percentage of the genome are Non-coding sequences

Answer 4

98%

Question 5

RNA polymerase II targets

Answer 5

transcribes all coding genes, snoRNA, miRNA, siRNA, LncRNA, snRNA

Question 6

General Transcription Factors

Answer 6

Required for transcribing every gene

Question 7

TFIID

Answer 7

Made up of 2 subunits: TBP and TAF (11 subunits).
TBP - Recognises TATA box in promoter
TAF - recognise DNA sequences near transcription start. Regulates DNA-binding by TBP

Question 8

TFIIB

Answer 8

Recognises BRE element in promoters. Helps accurately position RNA pol.

Question 9

TFIIF

Answer 9

3 subunits
Recruits RNA pol and stabilises RNA pol interaction with TBP and TFIIB.
Helps attract TFIIE and TFIIH

Question 10

TFIIE

Answer 10

2 subunits
Attracts and regulates TFIIH

Question 11

TFIIH

Answer 11

9 subunits
Unwinds DNA at transcription start point.
Phosphorylates Ser5 of the RNA pol CTD (C-terminal domain)
Releases RNA pol from the promoter.

Question 12

Capping proteins

Answer 12

Recruited by the phosphorylated CTD, allowing for the capping proteins to get near the newly transcribed RNA.
Attaches to the 5 prime end of mRNA.
Protects mRNA from degradation.

Question 13

Splicing proteins

Answer 13

Recruited by the phosphorylated CTD, allowing splicing proteins to be near the newly transcribed RNA.

Question 14

Transcription coupled repair

Answer 14

DNA helicase subunits of TFIIH help in nucleotide excision repair.

Question 15

Cis-regulatory sequences

Answer 15

Enhancers/Silencers
Modulate levels of promoter initiation.
Orientation independent.
Location is variable.

Question 16

TF Activation Domain

Answer 16

Recruit chromatin remodling enzymes, recruit co-activators/co-repressors, recruit general transcriptional machinery.

Question 17

TF Regulatory Domain

Answer 17

Involved in dimerisation.
Helps in Nuclear transport.
Auto-inhibition - negatively regulates other domains.

Question 18

TF DNA Binding Domain

Answer 18

Sequence specific recognition.
Asparagine can form H-bonds with DNA nucleotides.

Question 19

Palindromic sequences

Answer 19

Can be read the same way in reverse.

Question 20

Homodimer

Answer 20

Dimer of two of the same Transcription Factors.

Question 21

Heterodimer

Answer 21

Dimer of two different Transcription Factors.

Question 22

Inhibitory Factor

Answer 22

Can dimerise with transcription factors, but does not have a DNA binding domain or an activation domain. Therefore preventing the TF dimerised with it from recognising DNA binding sites.

Question 23

Cooperative binding

Answer 23

Transcription factors may have weak binding on their own, but together they have much stronger binding and increased specificity.
EXAMPLE: NFAT and AP1

Question 24

Enhanceosome

Answer 24

Multiple TFs assemble together into a macromolecular complex at enhancer sequences.
This complex helps stabilise TFs.

Question 25

Synergistic TFs

Answer 25

Multiple TF can work synergistically, where transcription can increase 10 fold from 2 TFs binding at the same time, rather than just adding together their individual effects on transcription

Question 26

DNA looping

Answer 26

Allows enhancers to help modulate the assembly of transcription machinery at the promoter.

Question 27

Topologically associated domain (loop)

Answer 27

Loop formed where enhancers are moved close to the promoter region.
Bound by Cohesin and CTCF.

Question 28

Transcriptional condensates

Answer 28

Formed by TFs and Co-activators in a DNA loop. Spanning the enhancers and promoter.

Question 29

Histone chaperone

Answer 29

Pull off histones from the DNA. Opening the DNA by removing nucleosomes and exposing it to TFs. Recruited by TF.

Some chaperones change the structure of the nucleosome, causing conf changes where the DNA is more exposed.

Question 30

Histone-modifying enzyme

Answer 30

Enzymes that modify histones, destabilising the compact forms of chromatin and attracting TFs.

Question 31

TF activators

Answer 31

Protein Synthesis
Ligand Binding
Covalent modification (Phosphorylation of TF)
Addition of subunit
Removal of inhibitor
Stimulation by Nuclear entry
Release from membrane

Question 32

Introns

Answer 32

Non-coding sequences

Question 33

Exons

Answer 33

Coding sequences

Question 34

Why must Introns be removed?

Answer 34

They may contain stop codons that would end translation prematurely.
They may shift the translation reading frame of downstream exons.
If splicing is inhibited in cells, they die because they can’t make new proteins.

Question 35

Spliceosome

Answer 35

RNA-protein complex that catalyzes the splicing of introns.
Has about 300 proteins and 5 smallRNAs
Composed pf 5 different snRNPs

Question 36

aSpiceosome snRNPs

Answer 36

Composed of a small nuclear RNA and protein factors
Types
- U1
- U2
- U4 + U6
- U5
- U6 + U4 + U5

Question 37

Intron recognition

Answer 37

Splice site consensus sequences recognised.
- GU at the 5’ end
- AG at the 3’ end
If either were to be changed, splicing would be inhibited

Question 38

Recognition of Splice Sites

Question 39

RNA Polymerase I

Answer 39

rRNA 28S, 18S, 5.8S