Transcription, RNA Processing and Control of Gene Expression

Question 1

What are three important differences between RNA and DNA?

Answer 1

1) RNA is single-stranded
2) RNA has uracil instead of thymine
3) RNA contains ribose instead of deoxyribose

Question 2

What are the nucleotide donors for RNA?

Answer 2

ATP, GTP, UTP, CTP

Question 3

Which polymerase is associated with rRNAs?

Answer 3

mainly Pol I, some Pol III

Question 4

Which polymerase is associated with tRNAs?

Answer 4

Pol III

Question 5

Which polymerase is associated with mRNAs?

Answer 5

Pol II

Question 6

How does alpha-amanitin work?

Answer 6

Death cap mushroom

- potent inhibitor of Pol II, which blocks synthesis of mRNAs

Question 7

Which type of RNA is the most abundant?

Answer 7

rRNA

Question 8

How can rifampicin kill certain bacteria but have low toxicity against humans?

Answer 8

It is a potent inhibitor of RNA polymerase found in bacteria, therefore do not affect eukaryotic Pol II

Question 9

What are the three modifications needed in order for mRNA to leave the nucleus?

Answer 9

In this specific order:
1) 5' methylguanosine cap
2) splicing, leaving only exons
3) poly-A tail
These processes mark the mRNA 'mature' and ready for transport out of the nucleus

Question 10

Which disease is result of incorrect splicing, caused by a mutation in the gene that altered the nucleotide sequence at the first exon/intron boundary resulting in the destruction of the consensus sequence required for correct splicing?

Answer 10

Beta-thalassemia

Question 11

Which disease is a result of a mutation that caused a single base change in the 5’ splice donor site of one particular intron leading to defective splicing and production of a truncated protein that lacks one exon, which gets rapidly degraded?

Answer 11

Phyenylketouria (PKU)

Question 12

Which type of histone modification acetylates lysine residues in histones and what does it result?

Answer 12

HATs (histone acetyltransferases)

• loosens up the DNA/histone modification
• facilitates transcription

Question 13

Which type of histone modification deacetylates lysine residues in histones and what does it result?

Answer 13

HDACs (histone deacetyltransferases)

• tightens up DNA/histone modification
• inhibits transcription

Question 14

In which base does DNA methylation occur?

Answer 14

cytosine

Question 15

What are large protein complexes that use the energy from ATP hydrolysis to change nucleosome structure temporarily to pack DNA more tightly to the histone core or unpack so the DNA is more accessible?

Answer 15

chromatin remodeling complexes

Question 16

Where do DNA-binding proteins bind to regulate transcription?

Answer 16

major groove

Question 17

Example of a helix-turn-helix protein

Answer 17

homeobox proteins

Question 18

What an example of zinc finger proteins?

Answer 18

glucocorticoid receptor

Question 19

What’s an example of leucine zipper proteins?

Answer 19

Fos and Jun

Question 20

Where are cortisol receptors normally hang out at?

Answer 20

cytoplasm

Question 21

The glucocorticoid receptor enters the nucleus as what structure once its’s been activated by its ligand cortisol?

Answer 21

homodimer

Question 22

Once the homodimer glucocorticoid receptor have formed, how does it regulate transcription once it enters the nucleus?

Answer 22

It is a zinc finger protein and binds to DNA at GRE (glucocorticoid responseive element) region and recruits HAT to facilitate transcription

Question 23

Which cellular compartment are thyroid hormone receptors found?

Answer 23

nucleus

Question 24

How does the thyroid hormone receptor act as a repressor?

Answer 24

• the receptor exist as a heterodimer (thyroid hormone receptor + retinoid X receptor)
• in the absence of thyroid hormone, the receptor recruits HDAC that represses transcription

Question 25

How does PKA regulate transcription?

Answer 25

1) cytoplasm - cAMP levels rise due to glucagon signal. this activates PKA
2) activated PKA enters the nucleus and phosphorylates CREB
3) phosphorylated CREB binds to CRE (located in DNA)
4) the complex recruits CBP that also binds
5) CBP recruits EP300
6) the whole complex has the same function as HAT and regulates transciption