Control of gene expression in eukaryotes part 2

Question 1

Define the Helix-turn- Helix motif

Answer 1

1. Present in RDBPs of both euk and prok.
2. Contains C-terminal DNA binding domain (alpha helix) rick in R and K amino acids
3. Interacts primarily with the major groove

Question 2

Define the “Homeodomain” motif

Answer 2

1. improvement of the Helix-turn-Helix
2. Instead of two alpha helices, it has three.
3. Helix 3 interacts with major groove, flexible portion of Helix 1 interacts with minor groove

Question 3

Define the Zinc Finger

Answer 3

1. Consists of a loop containing zinc, 2 B sheets, and one alpha helix
2. Contacts mainly through guanine-R interactions
3. Major groove generally requires 3 zinc fingers for proper binding

Question 4

What is an example of a B-sheet RDBP?

Answer 4

TATA binding protein

Question 5

What is an example of a protruding loop RDBP?

Answer 5

p53

Question 6

Define the leucine zipper dimerization motif

Answer 6

• consists of 8-10 regularly spaced leucines in an amphipathic helix.
• dimerizes with another to form RDBP
• example is the c1 protein

Question 7

Define the Helix-Loop-Helix motif

Answer 7

• performs dimerization

- made of two alpha helices, and one loop

Question 8

Three important consequences of dimerization for eukaryotes

Answer 8

• It allows the simultaneous recognition of two regulatory motifs on the DNA. The two
  motifs will be identical in the case of homodimers and will be different in the case
  of heterodimers.
• It increases the variety of regulatory sites in the genome.
• It allows the regulation of a large number of genes while requiring only a limited
  number of RDBPs through a combinatorial control.

Question 9

What is the role of truncated HLH proteins?

Answer 9

Participate in sequestering other HLH proteins, since they themsleves dont possess a DNA-interaction protein

Question 10

Give an example of a truncated HLH protein

Answer 10

Id protein

Question 11

Define the modular nature of RDBPs

Answer 11

The DNA binding piece and the activation domain piece can be switched in and out

Question 12

Name four ways that RDBPs can be regulated?

Answer 12

Unmasking, Release from membrane, synthesis, phosphorylation

Question 13

Can a single RDBP influence the expression of multiple genes?

Answer 13

Yes.

Question 14

Define synergy

Answer 14

Great output than sum of the parts

Question 15

What are six ways that RDBPs can reduce transcriptional activity

Answer 15

1. competitive DNA binding between repressor and activator
2. Masking activation surface
3. Competitive direct interaction with the general transcription factors
4. Recruitment of histone deacetylases
5. Recruitment of CRCs
6. Recruitment of methyl transferases

Question 16

cytosine methylation is carried out by what protein?

Answer 16

DNA-methyl-transferases

Question 17

Define de novo methyl-transfereases

Answer 17

Put initial methylation pattern at specific sequences

Question 18

Define maintainance methyltransferases

Answer 18

Responsible for methylating a newly synthesized strand that is connected to a previously methylated strand

Question 19

What is thought to be an important step in demethylation?

Answer 19

transformtion of 5-mC into 5-hmC

Question 20

Where is cytosine methylation often found?

Answer 20

in CpG islands

Question 21

How can methylation of CpG islands really inhibt expression of the gene?

Answer 21

Methylation of CpGs can bring over 5meC-binding proteins, that then recruit CRCs and histone deacetylases

Question 22

What is imprinting?

Answer 22

Soon after egg and sperm meet, most of the epigenetic tags that activate and silence genes are stripped from the DNA. However, in mammals, imprinted genes keep their epigenetic tags. Imprinted genes begin the process of development with epigenetic tags in place.

Question 23

Remember, there is this weird example where methyloation can actually activate a gene because the insulator element is methylated

Answer 23

ok