Transcription

Question 1

Explain the concept of wobbling taking G:C as an example

Answer 1

Compared to a C:G base pair, the wobble T:G is shifted up so that the bases wobble. Only two hydrogen bonds.

Question 2

Taumerisation

Answer 2

Taumerization is that the ring in the bases has two different forms, of which one can form an alternate (incorrect) base pair. This equilibrium between the two forms can lead to incorrect base pairing and translation of the genetic code.

Question 3

DNAP, Induced fit

Answer 3

DNA-Polymerase has a clamp that closes at correct base-pairing, giving a tighter active seat and reaction speed.

Question 4

The two roles of K-acetylation by HATs

Answer 4

Catalyses the reaction of acetylation of lysine.
Makes DNA recognisable by bromo-domains.

Question 5

A complex that runs acetylation

Answer 5

SAGA

Question 6

What domain of what protein recognizes acetylated lysine

Answer 6

Bromo-domains of co-activators, which has it because it’s a catalytic subunit that catalyzes hyperacetylation of histones near the promotor region. Co-activators are a type of translational co-regulator to increase the rate of transcription, which means that if the co-activator has this domain, it can then make it accessible for the transcription factors

Question 7

Methylated lysine is recognizes by what domain?

Answer 7

Chromo-shadow-domains

Question 8

H3K9 methylation results in gene silencing, how?

Answer 8

HP1 has chromo-shadow-domain and also binds H3K9 HTM (histone methyl transferase) to methylate another nucleosome
to create a binding site for the chromo domain
of the next HP1.
HP1 proteins associate with each other as well, through their chromo-shadow domains.
HP1 binding spreads the chromatin leading to its condensation into heterochromatin.
H2K27me3 is recognized by the polycomb complex.

Question 9

RNAPII CTD

Answer 9

RNAPII CTD is the RNAPII’s C-terminal domain, involved in initiation of DNA transcription. Contains a repeat sequence of hepta-peptides with a consensus of YSPTSPS

Question 10

CTD phosphorylation on Ser5

Answer 10

Is done by the Cyclin H-Cdk7 cyklin-kinase of TFIIH

Question 11

Mediator (RNAPII initiation)

Answer 11

A huge multi-protein complex that interacts with the activation domains of the transcription factors together with the RNAP

Question 12

What is the role of Mediator in the activation of transcription by RNAPII?

Answer 12

Conducts the activation signals from activators (transcription factors for example TFIID) bound to their response elements (specific DNA sequences) of the promotor (enhancers, TATA box for example) to the RNAP. It only plays a part during initiation

Question 13

Why does mediator detach from RNAPII after initiation?

Answer 13

To make RNAPII available for further transcription initiation and does so when CTD is phosphorylated by TFIIH.

Question 14

At which stage of mRNA synthesis does the CAP attachment to pre-mRNA occur

Answer 14

During transcription, when pre-mRNA is about 25 bases long

Question 15

CAP

Answer 15

Catabolite Activator Protein

Question 16

Cap formation is done by?

Answer 16

The capping enzyme attaches CAP during transcription, RNA at about 25 bases long

Question 17

What are the roles of the Cap?

Answer 17

Protecting RNA from degradation
Recruits complexes involved with RNA processing, export and translation
Marks RNA as “self”

Question 18

Spliceosome

Answer 18

Complex that splices introns from pre-mRNA

Question 19

(pro) How are introns recognised in pre-mRNA?

Answer 19

By base pairing U1 and U2 which then recroute the rest of compex

Question 20

Branching A in intron is defined how?

Answer 20

By jutting out when base-pairing U2:RNA

Question 21

SF1/BBP and U2AF at splicing

Answer 21

U2AF promotes binding of U1 and U2

Question 22

Intron recognition in high eucaryotes

Answer 22

Are super long and hard to define, so exons are

Question 23

mRNA poly-adenylation

Answer 23

Poly-A-Polymerase (PAP) creates the poly-A tail after mRNA release from RNAP.

Question 24

Signal of nuclear mRNA poly-adenylation

Answer 24

AAUAA

Question 25

EJCs

Answer 25

Exon Junction Comlpexes

Question 26

EJCs role in mRNA transport to cytoplasm

Answer 26

EJC forms where introns where, has Aly, acting as a bridge to RNA transporter Tap-15

Question 27

Dbp5 helicase role in RNA transportation to cytoplasm

Answer 27

Hydrolysis of it stops RNA from “slipping” back, Browninan Ratchet model

Question 28

TATA? No! Inr and DPE sequence recognition

Answer 28

Inr (Initiator) interacts with TAF1 and TAF2 and DPE (Downstream Promoter Element) interacts with TAF6 and TAF9

Question 29

ISWI function

Answer 29

Organize the nucleosome by imposing regular and proper spacing between Nucleosomes (NSes) that lead to chromatin organization and condensation

Question 30

SWI function

Answer 30

Roll NSes on DNA to open the binding sites for TFs

Question 31

SWR1 function

Answer 31

Modulate histone composition in NSes. They replace the H2A histone with its promotor-boundry-specific H2A.Z variant, which is easily evicted from the chromatin by SWI machines

Question 32

(euc) Repressors

Answer 32

Bind at or near the promotor and lock the access of RNAP to it

Question 33

trigger loop

Answer 33

closes over active site of RNAP at correct (WC) base pairing