18. Transcriptional Circuits in Prokaryotes and Eukaryotes

Question 1

What is the Transcriptome? (3pts)

Answer 1

1. Transcriptome= segment that is transcribed.
2. Most of the eukaryotic genome is never transcribed. Only about 50% of the prokaryotic genome is transcribed.
3. Only a fraction of the transcriptose is transcribed at any one time.

Question 2

Decribe Gene 1 (abundant transcript)?

Answer 2

Gives rise too many different RNA molecules. If the gene is expressed in every cell this is called a housekeeping gene.

Question 3

Describe Gene 2 (rare transcript)?

Answer 3

Not expressed or expressed at very low levels

Question 4

Describe gene 3 (no transcript)?

Answer 4

Tissue-specific e.g globin.

Question 5

Describe an inducible gene (2pts)

Answer 5

1. Gene becomes abundant in response to a stimulus therefore is converted form a rare transcript to an abundant transcript.
2. called an inducible gene as its expression can be induced by different stimuli

Question 6

Describe RNA polymerase (2pts)

Answer 6

1. Promotors recruit RNA polymerase to a DNA template.

2. RNA polymerase can only move one way.

Question 7

Describe enhancers? (3pts)

Answer 7

1. Enhancers are sequences of DNA that are not immediately adjacent to where transcription starts that act to enhance the binding of RNA polymerase to a promoter.
2. Enhancer can reside in the 5 prime, 3 prime or within an intron.
3. Like promoters, enhancers contain DNA sequences that are very strong binding sites for specificity factors or transcription factors.

Question 8

Describe the recruitment of RNA polymerase to promotors? (4pts)

Answer 8

1. Neither prokaryotic nor eukaryotic RNA polymerase make stable contact with DNA.
2. Recognition of promoters is mediated by imitation factors.
3. Prokaryotes= Sigma factor
4. Eukaryotes- TFII basal transcriptional machinery.
5. Once stably recruited to DNA, RNA polymerase is able to convert from a closed complex to an open complex.

Question 9

Describe the Tata box? (2pts)

Answer 9

1. Tata box= needed to recruit general transcription factors and then RNA polymerase
2. Tata box binding factors= TBP recognises the TATA box.

Question 10

Describe Regulatory transcription factors? (5pts)

Answer 10

1. Regulatory transcription factors= mediate regulatory change
2. The ability of sigma factor and TF11 to recruit RNA polymerases to promoters are generic- i.e they happen at every promoter. This does not account for the ability to vary the level of transcription from a promoter.
3. Regulatory transcription factors mediate regulatory changes.
4. In both prokaryotes and eukaryotes, regulatory transcription factors function to dramatically alter the level of recruitment of RNA polymerase and its ability to imitate transcription.
5. In eukaryotes regulatory transcription factors can influence local chromatin structure.

Question 11

Describe the Lac operon? (3pts)

Answer 11

1. Lac operon= a prokaryotic paradigm for the regulation of transcription
2. Lac ZYA= genes needed to utilise lactose as a carbon source.
3. If cells are in the presence of lactose and glucose they will not utilise lactose and the lac operon gene will be silenced.

Question 12

Low levels of glucose? (3pts)

Answer 12

1. Low levels of glucose
2. Bacteria will utilise lactose if present.
3. Cap protein is only active under low glucose. It will bind to the promoter of the lac operon.

Question 13

Absence of Lactose? (3pts)

Answer 13

1. Absence of lactose
2. The lac repressor will bind to the DNA sequence in the promoter
3. The lac repressor prevents functioning.

Question 14

Cells in the presence of lactose? (3pts)

Answer 14

1. Cells are in the presence of lactose
2. Lactose binds to protein therefore it is released from binding DNA.
3. Genes are expressed and will utilise lactose as a source of energy.

Question 15

Describe how regulatory factors recognise their target sequences?

Answer 15

Regulatory factors recognise their target sequences by interacting with the DNA. They do not have to unwind the DNA double helix to see their target therefore an intact DNA molecule can present information to the cell.

Question 16

Describe a regulatory element?

Answer 16

A regulatory element is needed to regulate recruitment of RNA polymerase

Question 17

How is transcription regulated? (2pts)

Answer 17

1. Transcription is regulated by the efficiency of recruitment of RNA polymerase II
2. Regulatory factors bind promoter and help recruit general transcriptional factors.

Question 18

Describe steroid hormone signalling? (3pts)

Answer 18

1. The receptor for this steroid hormone is located in the cytoplasm.
2. The steroid binds to the receptor protein and the ligand bond causing a conformational change.
3. The protein translocated into the cell nucleus and binds to the promoter region and so the activation of transcription of those genes will occur.

e.g oestrogen

Question 19

Describe Oestrogen activation? (4pts)

Answer 19

1. Oestrogen will bind to free oestrogen receptor complex in the cytoplasm
2. As a result of this binding this complex will translocate into the nucleus and this complex will start scanning genomic DNA for the oestrogen responsive elements.
3. As a result of this binding, recruitment of general transcription factors to the TATA box occurs.
4. This causes recruitment of RNA polymerase and the start of transcription of genes responding to the presence of oestrogen.

Question 20

How can we target therapeutic drugs?

Answer 20

Interfering with the interactions between regulatory and general transcription factors is a way of targeting therapeutic drugs. For example Tamoxifen is an antagonist of oestrogen-responsive transcription and is used to treat breast cancer.

Question 21

Describe Tissue specific transcription according to the B-globin protein? (2pts)

Answer 21

1. Gata 1 is only expressed in cells that are differentiated into red blood cells therefore we have a high expression of the B-globin gene only in red blood cells because these ones are expressing the Gata-1 transcription factor.
2. Gata 1 is not expressed in other cell types therefore beta-globin is only expressed in red blood cells.

Question 22

Describe Ubiquious factors in the expression of the B-globin gene?

Answer 22

Ubiquitous factors will start inducing the expression of the B-globin gene when the blood cells start to differentiate into red blood cells and will eventually have a high expression in red blood cells due to the presence of Gata-1.

Question 23

Describe regulation of the cell cycle? (2pts)

Answer 23

1. G1 phase- regulated by mitogenic signals. These tell the cell to start cell division.
2. S, G2, M Phase= insensitive to the external environment.

Question 24

What is the key events in the G1/S transition?

Answer 24

The transcriptional activation of genes that encode proteins involved in DNA replication. CDK’s target transcriptional factors.

Question 25

Describe the E2F factor? (4pts)

Answer 25

1. The promoters for G1/S transition genes are activated by the E2F factor.
2. Genes are regulated by tata boxes.
3. The E2F sites bind to the promoter of the gene and are only activated in the s phase.
4. E2F activity is repressed in G0 and early G1 by the product of the Retinoblastoma gene.

Question 26

Describe the Retionoblastoma gene? (3pts)

Answer 26

1. Tumour supressor gene
2. When it is mutated it causes different types of tumours
3. Binds to E2F which creates a complex that causes genes not to be expressed.

Question 27

Describe the effects of the mitogenic stimulus? (3pts)

Answer 27

1. If the cells receives mitogenic stimuli these stimuli activate the CDK- (cyclin-dependant kinase)
2. The CDK will phosphorylate the retinoblastoma protein which means it can no longer bind to EF2.
3. The gene is then released from EF2.

Question 28

What happens if the pRB protein(retinoblastoma protein) inhibits E2F?

Answer 28

pRB (retinoblastoma protein) inhibits E2F from allowing the expression of genes which allow the cells to proceed from the G1 phase to the S phase in the cell cycle. If the cells receive mitogens and are phosphorylated the cells can progress through the cell cycle to the s phase.

Question 29

What happens if the Retinoblastoma protein is not expressed ?

Answer 29

The Retinoblastoma protein cannot bind to E2F and tumours will occur.

Question 30

Describe viral transformation?

Answer 30

Some viruses can transform cells after infecting them and the cells become cancerous. The viruses express viral proteins which compete to bind to the Retinoblastoma protein therefore the Retinoblastoma protein cannot bind to e2F so uncontrolled cell division occurs.