Lecture 18

Question 1

Do transcriptional regulators bind to DNA, RNA, or the protein?

Answer 1

It binds to DNA.

Question 2

What is the quaternary structure of most transcriptional regulatory proteins (specific transcription
factors)?

Answer 2

Contains domains that can interact with DNA (e.g. Zinc fingers) in order to regulate the expression of certain genes

Also contains protein to protein interaction domains

Question 3

What is a common pattern for the sequences that transcriptional regulators bind? How do the pattern of binding sequences and the quaternary structure relate?

Answer 3

Palindromes

Causes DNA to form a loop

Question 4

When a transcriptional regulatory protein binds to DNA, does it bind to the phosphates, the sugars or the bases? Why is this important?

Answer 4

It binds the H-acceptors/donors, other H groups and methyl groups on the bases pairing.

Question 5

Why is the major groove a better binding target for proteins than the minor groove?

Answer 5

The major grove is better because the backbone is further apart so the base pairs are move open. The H -donor/acceptor, other H and methyl groups are similar on the minor grove whereas they are different between each base pair in the major grove.

Question 6

What sort of chemical bonds hold the transcriptional regulatory protein to the DNA?

Answer 6

.

Question 7

What is an enhancer?

Answer 7

An enhancer is a site where the activator binds.

Question 8

What is an activator?

Answer 8

An activator is a protein that increase the likelihood of transcription occurring.

Question 9

What is an mediator?

Answer 9

An mediator is a protein that mediates between proteins/complexes.

Question 10

Is mediator one protein?

Answer 10

A mediator is made up of more than one protein.

Question 11

Give two examples of DNA binding domains found in eukaryotic transcriptional regulators.

Answer 11

Zinc finger and Helix loop helix.

Question 12

What is a zinc finger and why does it have zinc in its name?

Answer 12

A zinc finger is a DNA binding domain that binds to the DNA and recognise sequences. It has zinc in its name as there is a zinc being coordinated by histidine and cysteine.

Question 13

The initial pre‐mRNA transcript is edited to make the mature mRNA. What does this mean? What does the editing? Is this process regulated?

Answer 13

Introns and differen exons are spliced.

Question 14

For a single gene, is this editing of the pre‐mRNA the same in all cells, or different?

Answer 14

No as different exons are spliced out to produce different proteins.

Question 15

Different proteins are produced from the α‐tropomyosin gene in different types of muscle. How is this achieved?

Answer 15

Different pattern of splicing of the pre-mRNA produced by the gene can lead to the production of different proteins.

Question 16

What does a splicing repressor do?

Answer 16

Splicing repressor binds to the pre-mRNA and alters the spliceosome interaction with the pre-mRNA tell it to cut out that particular section. (strong splice border - tends to be left in the sequence - repressor masks sequence)

Question 17

What does a splicing enhancer do?

Answer 17

Splicing enhancer binds to the pre-mRNA and interacting with the spliceosome so that it recognises certain sequences that are normally cut out and prevent it from being cut out. (weak splice borders - spliceosome tends to skip it, cutting it out)

Question 18

What is a miRNA? What is the protein complex that binds it? Do they bind DNA, RNA or protein?

Answer 18

miRNA (microRNA) are ~ 20 bases long and regulate a third of genes. Sequence on the gene is transcribed and modified (dicer + helicase) into short single strands (miRNA). Mature miRNA binds to RISC and targets mRNA and base pairs with it (reverse complementary). If its close to exact complementary -> target mRNA is degraded. It dampens translation of mRNA

Question 19

Given the sequence of a gene, could you figure out the sequence of a miRNA that regulates it?

Answer 19

No

Question 20

Give two examples of posttranscriptional modification, and what it achieves.

Answer 20

Formation of disulphide bridge: increase in stability of protein.
Phosphorylation: activate/deactivate, induces protein-protein interaction
Ubiquitination: adds ubiquitin to target degradation
Glycosylation: stability and folding
SUMOylation: adds SUMO protein, changes what it binds to
Palmitoylation: allows synapse function, attachment of lipid

Question 21

TRUE or FALSE: Majority of regulation is positive.

Answer 21

TRUE

Question 22

TRUE or FALSE: The average transcription factor has around 6 binding sites.

Answer 22

TRUE.

Question 23

What is the basal transcription level in humans?

Answer 23

Low