Transcription Circuits

Question 1

What is the transcriptome?

Answer 1

The segment that is transcribed

Question 2

Summarise the different types of transcript(3)

Answer 2

• Abundant transcript- If on in every cell this is called a HOUSEKEEPING gene (e.g. glycolytic enzymes). Essential for cell function eg RNA Pol II
• Rare Transcript- Inducible gene. When given hormone it transcribes.
• No transcript- Tissue specific eg globin. Expressed in one type but not in another.

Question 3

What is the role of promotors?

Answer 3

· The sequence immediately 5’ to the region to be transcribed is called a “promoter”
• Promoters recruit RNA polymerase to a DNA template

Question 4

How is recognition of promotors mediated in prokaryotes and eukaryotes?

Answer 4

– Predominantly “Sigma factor” for prokaryotes

– The TFII basal transcriptional machinery for eukaryotes

Question 5

What are the prokaryotic promotors?

Answer 5

· Sigma factor recognises the -35 and -10 motifs common to prokaryotic promoters and enables RNA polymerase to make stable contacts with DNA

Question 6

What are alternative names for the -10 and -35 regions?(2)

Answer 6

10 region is the Pribnow region -35- consensus sequence- most likely to find

Question 7

What are the eukaryotic promotors?

Answer 7

1.TATA box need to recruit general transcription factors and then RNA polymerase. It is the consensus region for recognition2. TATA binding factor= TBP

Question 8

What are regulatory transcriptition factors?(3)

Answer 8

1. In both prokaryotes and eukaryotes they function to dramatically alter the level of recruitment of RNA polymerase and/or its ability to initiate transcription
2. in eukaryotes they can influence local chromatin structure
3. They do not have to unwind the DNA double helix to see their target so an intact DNA molecule can present info to the cell.

Question 9

What is lac operon in prokaryotes?

Answer 9

Lac Operon codes for three genes- ZYA- required for using lactose for source of energy. Promotor responds to the presence of lactose

Question 10

Describe the state of lac ZYA in the presence of glucose and no lactose(2)

Answer 10

1. In the presence of glucose and lactose they will promote use of glucose. More energy can be made from glucose
2. No transcription of thelacoperon occurs because thelacrepressor remains bound to the operator and prevents transcription by RNA polymerase

Question 11

Describe the state of lac ZYA in the presence of lactose and no glucose(2)

Answer 11

Strong transcription of thelacoperon occurs.1. Thelacrepressor is released from the operator.
CAP( Catabolite activator protein ) is active and bound to the DNA.

2. CAP helps RNA polymerase bind to the promoter, permitting high levels of transcription

Question 12

Name some eukaryotic triggers of transcription switches

Answer 12

Immune stress, cAMP, Oestrogen

Question 13

Describe how hormones interact with promotor regions (6)

Answer 13

1. The cytoplasm contains receptors for the hormone.

2 .Steroid hormone bind to receptor protein

3. A change in the shape of protein.
4. The protein translocate to the cytoplasm.
5. In the nucleus, the protein scans and bind to the promotor region.
6. Recruits binding factors and transcription occurs.”

Question 14

What is GATA-1?

Answer 14

– GATA-1 are tissue specific factor- only expressed in RBCs- it binds to promotor region to recruit RNA polymerase II

Question 15

What happens when RBCs differentiate to start expression of B-globin?

Answer 15

– As RBCs differentiate- NF1, CP1, Sp1 are ubiquitous factors- they start producing the expression of B globin.

Question 16

How are transitions through the cell cycle regulated?(5)

Answer 16

1. The promoters for G1/S transition genes are activated by a factor called E2F. Acts as dimers and bind to specific DNA sequence.
2. E2F activity is repressed in G0 and early G1 by the product of the Retinoblastoma gene (pRB)
3. E2F binds to DNA but cant recruit RNA polymerase because pRb is attached to them
4. When mitogenic stimulus is added pRb are phosphorylated and their shapes change and unbind from E2F.

The transitions to the different phases are regulated by cyclins and CDKs.

Question 17

What does mutations in pRB mean and what is the role of viral oncogenes in cancers?(2)

Answer 17

1. Mutations mean lack of pRB so cells are always activated.
2. Viral oncogenes express proteins that compete for binding of the pRb so cells are constantly transcribed because E2F is free.

Question 18

What are enhancers?(3)

Answer 18

→They are sequences of DNA (not immediately adjacent to where transcription starts)

→act to enhance the recruitment of RNA polymerase to a promoter.

→They can reside in the 5’, 3’ or even the introns. They are very strong binding sites for specificity factors.

Question 19

The recognition of promoters is mediated by initiation factors. What are these factors in prokaryotes?

Answer 19

→It is the sigma factor, which recognises the -35 and -10 motifs common to prokaryotic promoters.

Question 20

The recognition of promoters is mediated by initiation factors.

What are these factors in eukaryotes?

Answer 20

It is the TF2 basal transcriptional machinery (TF2A, TF2B, etc.).

Question 21

List the known transcriptional switch in prokaryotes (1) and eukaryotes (3).

Answer 21

→PROKARYOTES: - the lac operon

→EUKARYOTES: - oestrogen-responsive transcription - tissue-specific translation (beta-globin) - a complex regulatory circuit (cell cycle)

Question 22

how does the lac operon work?(5)

Answer 22

E.coli prefer using glucose as an energy source, but when glucose is absent they can use lactose instead.

→The Lac Z gene codes for an enzyme that cleaves the lactose into simpler sugars.

→Lac Y codes an enzyme that is used for the absorption of lactose.

→When there is no lactose available then the cell will not transcribe the Lac genes because it is energetically expensive.

The lac repressor protein binds to the promoter region before the start site, the RNA polymerase will not be able to transcribe the genes as the repressor is blocking the RNA from moving forward.
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Question 23

what are inducible genes?

Answer 23

genes which are transcribed in response to stimuli.

Question 24

what do position and orientation independent mean?

Answer 24

→Position independent means that the enhancer can be cut out and be put in another place and it will still work.

→orientation independent so the enhancer can be reinserted backwards and it will still function properly.

Question 25

what are the steps in estrogen controlled protein synthesis?(5)

Answer 25

→Estrogen like all steroid hormones is lipid soluble so it crosses the cell membrane via diffusion and enters the cytoplasm.

→Estrogen binds to a receptor called ERα to form a hormone-receptor complex. This complex is now a transcription factor.

→The active transcription factor diffuses into the nucleus via the nuclear pore.

→ In the nucleus the transcription factor scans the DNA until it finds an estrogen responsive DNA sequence and binds the DNA promoter, upstream of RNA polymerase.

→This binding stimulates RNA polymerase to transcribe genes and so stimulates protein synthesis.

Question 26

what are ubiquitous factors?

Answer 26

transcription factors that are expressed in all cell types

Question 27

give an example of tissue specific transcription(6)

Answer 27

→Beta globin is only expressed in red blood cells, the promoter region contains different sequences that binds to many different transcription factors to activate the RNA pol II.

→In the beta globin gene there is an enhancer which is at the 3’ end of the gene (downstream).

→There are ubiquitous factors (TFs that are expressed in all cell types)

→The binding of these are not sufficient to determine tissue specific expression.

→GATA 1 is a TF expressed in cells that will be erythrocytes.
→it binds to the promoter regions and enhancers to activate the transcription of the tissue specific genes.

Question 28

what does retinoblastoma do?(3)

Answer 28

→G1 retinoblastoma prevents E2F from binding and activating transcription to produce proteins for the S phase.

→If a mitogenic signal occurs, it activates the CDKs which phosphorylates the retinoblastoma which changes shape and releases the E2F.

→it is then free to bind to the E2F sites on the DNA.