Eukaryotic Gene Regulation

Question 1

How does histone modification affect gene regulation?

Answer 1

When methylated, histones are positively charged, chromatin is condensed, no promoter access- transcription is repressed.
When acetylated, histones become neutral, chromatin opens, allowing promoter access and transcription.

Question 2

What enzyme catalyses the acetylation of histones?

Answer 2

Histone Acetyltransferse (HA).

Question 3

What enzyme catalyses the methylation of histones?

Answer 3

Histone Deacetylase (HDAC).

Question 4

How does DNA methylation of CpG islands regulate gene expression?

Answer 4

Cis regulatory elements cannot bind the trans regulatory proteins when CpG islands are methylated.

Question 5

What happens when a CpG island has been methylated?

Answer 5

Transcription factor cannot bind. Methyl-CpG binding protein can bind. Recruits HDAC, which methylates histones and causes chromatin condensation.

Question 6

Which binding proteins are used by RNA polymerase I?

Answer 6

Upstream binding factor and selectivity factor.

Question 7

How does RNA polymerase III transcribe different RNAs?

Answer 7

Using different accessory proteins.

Question 8

Which transcription factors are used by RNA polymerase III to produce 5S rRNA?

Answer 8

TFIIIA, TFIIIB and TFIIIC.

Question 9

Which transcription factors are used by RNA polymerase III to produce tRNA?

Answer 9

TFIIIB and TFIIIC.

Question 10

Which transcription factors are used by RNA polymerase III to produce U6 snRNP?

Answer 10

Oct1/PBP (bind upstream of the TATA box) and TFIIIB.

Question 11

Which transcription factors are required for transcription initiation in RNA polymerase II?

Answer 11

1. TBP binds TATA box, kinking DNA. TFIIA binds.
2. TFIIB binds, recruits TFIIF which carries RNAPII.
3. TFIIE binds, holding the DNA and polymerase in place in the pre-initiation complex.
4. TFIIH binds, forming the transcription initiation complex.

Question 12

How does activator binding affect gene regulation?

Answer 12

Activators bind to specific sites upstream/downstream of the promoter. Allows mediator binding- modulates TFIIH activity. Transcription starts.

Question 13

Where is the Gal pathway found and what does it control?

Answer 13

In yeast. Controls the transcription of genes needed the convert galactose to glucose for use in glycolysis.

Question 14

What is the Gal4 binding site (UAS)?

Answer 14

An enhancer sequence found in each Gal gene. When gal4 binds, the nearby gal gene is transcriptionally active.

Question 15

How does Gal4 binding result in different levels of gene regulation in different gal genes?

Answer 15

Each Gal gene has different numbers of Gal4 binding sites, giving different levels of transcription depending on the polymerase’s affinity for the promoter.

Question 16

What happens in the Gal pathway when there is no galactose present?

Answer 16

Gal80 binds to Gal4 that is bound to UAS. Causes repression of the nearby Gal gene, as the mediator can no longer bind to Gal4.

Question 17

What happens in the Gal pathway when galactose is present?

Answer 17

Gal3 binds galactose and undergoes a conformational change. Gal3 has increased affinity for Gal80- binds Gal80 and carries it to the cytoplasm. Stops binding of Gal80 to Gal4. Gal4 becomes available for mediator binding. Transcription of nearby Gal gene occurs.

Question 18

How is miRNA produced?

Answer 18

Transcribed by RNAPII to form pri-miRNA which is cleaved by DROSHA to form pre-miRNA. Exported to the cytosol by exportin-5. Cleaved by Dicer, which cleaves a stem loop, forming two miRNAs.

Question 19

What is the miRISC complex?

Answer 19

A complex formed when various proteins bind to miRNA.

Question 20

What happens if the miRISC complex is partly complementary to mRNA?

Answer 20

The mRNA is blocked, no ribosome access, no translation.

Question 21

What happens if the miRISC complex if exactly complementary to mRNA?

Answer 21

Recruits RNases, mRNA degradation, no translation.

Question 22

How does lin-4 in C.elegans block protein synthesis?

Answer 22

lin-4 is an miRNA with some complementarity to lin-14, binding to lin-14 when there is a high concentration of lin-4. Binding of lin-4 to lin-14 blocks protein synthesis.

Question 23

How does lin-4 bind to lin-14 in C.elegans?

Answer 23

By complementary base pairing to 7 complementary elements in the lin-14 mRNA 3’ UTR.

Question 24

How can miRNAs decrease gene expression?

Answer 24

By inhibiting translation or causing direct degradation of the mRNA transcript.