Mechanism of Transcription

Question 1

How is gene expression tightly regulated?

Answer 1

On transcriptional level by turning DNA to RNA synthesis on/off. On post-transcriptional level by regulation of RNA stability/translation.

Question 2

Which RNA polymerase transcribes protein-encoding genes?

Answer 2

RNA polymerase 2

Question 3

What is the structure of RNA pol 2?

Answer 3

Cleft where DNA enters. Jaws which grip the DNA and may open/close to stabilise the complex. DNA will hit wall at the back which will cause conformational change.

Question 4

Where can the TATA box be found?

Answer 4

-35 to -25 nucleotides before the first one copied.

Question 5

What are general transcription factors?

Answer 5

Basic set of proteins needed for activation of transcription. Needed by RNA polymerases.

Question 6

What forms TFIID? What is its function?

Answer 6

Transcription factor is formed from TBP and approx. 10 TAFs. Transcription initiator.

Question 7

What does TFIIB do?

Answer 7

It provides a binding surface for Pol II and is involved in start-site determination.

Question 8

What binds after TFIIB?

Answer 8

TFIIF which is require for accurate initiation and also recruits TFIIE and TFIIH.

Question 9

What is the function of TFIIH?

Answer 9

It binds and catalyses ATP-dependent unwinding of the start site DNA and phosphorylation of C terminal domain of polymerase.

Question 10

What happens during steroid hormone signalling?

Answer 10

Steroid moves into cytoplasm, binds to receptor, moves inside the nucleus and binds to DNA to form the hormone-complex which forms a new protein.

Question 11

What is tamoxifen?

Answer 11

Antagonist as it competes for oestrogen receptor and it is used for breast cancer.

Question 12

What motifs do activation domains have?

Answer 12

No clear common motifs, glutamine-rich and acidic.

Question 13

What motifs do DNA binding domains have?

Answer 13

Zinc finger, homeodomain, helix-loop-helix and leucine zipper.

Question 14

What are zinc finger motifs ?

Answer 14

Zinc bound between 2 cysteine and 2 histidine residues OR could be zinc bound between 4 cysteine residue.

Question 15

What are homeodomains?

Answer 15

3 helices, 3rd helix binds to the groove. Helix-turn-helix motif.

Question 16

What are leucine zippers?

Answer 16

Contains basic region and adjacent alpha-helical zipper dimerization domain.

Question 17

What are some ways in which transcriptional activators/repressors can be recruited?

Answer 17

Ligand binding, protein phosphorylation, addition of second subunit, unmasking, release from membrane.

Question 18

What are enhancers?

Answer 18

Sequences of DNA not immediately adjacent to where transcription starts. Located at both 5’ and 3’ end and even in introns. Work in position and orientation independent manner.

Question 19

What is a mediator?

Answer 19

A modullar complex that transducer both positive and negative regulatory information from specific activators and repressors to the core transcriptional machinery. It does not bind to DNA sequences and it interacts with RNA Pol II via the CTD. Increases the rate of PIC assembly.

Question 20

How can transcriptional repressors work?

Answer 20

Competitive DNA binding, masking the activation surface and by direct interaction with general TFs.

Question 21

What are transcriptional coactivators?

Answer 21

Activators recruit coactivators via their activation domains. They increase the rate of transcription.

Question 22

What are the 2 classes of transcriptional coactivators?

Answer 22

1. Closely associated with basal transcription machinery

2. Modify chromatin structure

Question 23

How do transcriptional corepressors work?

Answer 23

Directly affect the activities of components associated with basal transcription machinery OR modify chromatin structure to reduce accessibility to promoter.

Question 24

Which residues can be modified for histone modifications?

Answer 24

Lysine residues can be acetylated, methylated and ubiquitinated. Arginine and histidine residues can be methylated. Serine and histidine residues can be phosphorylated.

Question 25

What is the histone code?

Answer 25

Type and number of modifications present on histones which specifies a distinct biological outcome. Read by other proteins.

Question 26

What do the bromo and chromo domains recognise?

Answer 26

Bromo domains recognise acetylated groups while chromo domains recognise methylated groups.

Question 27

What are the 3 types of chromatin-modifying coactivators?

Answer 27

HATs, ATP- dependent remodelling complexes and histone arginine methyltransferases.

Question 28

What is the function of HATs?

Answer 28

Destabilize histone-DNA interactions by reducing the positive charge on histones. Contains at least 2 domains, HAT domain and Chromatin binding domain.

Question 29

What is the function of ATP-dependent remodelling complexes?

Answer 29

They use energy derived from ATP hydrolysis to increase accessibility to nucleosomal DNA.

Question 30

What are the histone modifications associated with transcriptional repression?

Answer 30

Deacetylation of lysine residues by histone deacetylases. Methylation of K9/27 on histone H3 by histone lysine methyltransferases.

Question 31

What is epigenetics?

Answer 31

Non-sequence dependence changes to the genome. DNA methylation and histone modifications.