S3: Control of Gene Expression

Question 1

human tissue proteosome

Answer 1

c

Question 2

Describe the liver proteome

Answer 2

• It is in the liver which is the largest internal organ.
• Functions include production of bile, hormones and vitamins, removal of toxic substances, decomposition of RBC, synthesis of plasma proteins and homeostatic regulation of the plasma constituents.
• Cells are parenchymal (hepatocytes and bile ducts cells) and non-parenchymal (sinusoidal endothelial cells, Kupffer cells, and hepatic stellate cells).

Question 3

Describe housekeeping genes

Answer 3

• All the cells in our body have the same DNA but only some are expressed.
• Housekeeping genes are genes that are expressed in all cells.
• These genes are likely to be structural proteins that are essential for all cells in the human body.
• Specific cell types (i.e. different types of cell, hepatocyte, nerve cell, macrophage); are made by expressing a specific set of genes.
• It is for this reason we need to be able to control which genes are turned on and off.

Question 4

How many house keeping genes do we have and give some examples?

Answer 4

• Human protein atlas counts 7319 proteins expressed in all tissues.
• Some examples include RNA polymerase proteins, ribosomal proteins, citric acid cycle proteins (to make energy e.g. enzymes) and cytoskeletal proteins (to maintain cell shape).

Question 5

How can genes be transcribed to different levels?

Answer 5

• Different levels of transcription leads to different levels of protein being made by translation.
• Housekeeping genes are abundantly transcribed.
• Some genes have lower level transcription but can still be housekeeping.
• Some genes are only expressed in tissue specific manner.
• It could also be that the expression of the gene only occurs when induced by external stimuli. these type of genes mean that the transcript is rare or there is none at all (its transcription is supressed). Then upon the stimulus, this suppression is removed and we get abundant transcription of this gene.

Question 6

Give examples of inducible genes and their stimuli

Answer 6

• Cytokine production in immune cells – in response to infection.
• Insulin production in the pancreas – in response to glucose.
• Hormone responsive genes e.g. in response to oestrogen.

Question 7

What mechanism does each cell in our body achieve differential gene expression?

Answer 7

• Regulatory transcription factors.

- Chromatin remodelling.

Question 8

How are genes turned off and on in prokaryotes with E.coli as an example adapting to use lactose as its energy source

Answer 8

• E. coli’s default energy (carbon) source is glucose. If glucose isn’t available, it can still survive by turning on genes that enable it to process other energy sources.
• In order to get our mRNA transcript of the gene(s) we want, we need RNA polymerase. However RNA polymerase isn’t good at binding to the promoter of genes, this is a necessary because if RNA polymerase were good at binding to promoters, then it would bind to all promoters and all genes would start getting transcribed.
• We have made sure that the RNA polymerase can only bind to the promoter when it has help. In this particular case, RNA polymerase needs the CAP protein to bind to the promoter and CAP is only active when glucose levels are low.
• When the CAP protein binds to the DNA, together it forms what we call an “address”. It is an address that tells RNA polymerase it can come and bind and transcribe the gene.
• So RNA polymerase comes in and binds! However we have another level of control, in E.coli, we don’t want to transcribe these genes when JUST glucose is low, we want to transcribe it when glucose is low AND lactose is present and available to use.
• So until lactose is present, we have another protein, the Lac repressor protein, that acts as a red light for RNA polymerase preventing it from transcribing.
• However, when we do get lactose in the environment, lactose will bind to the lac repressor protein and it will fall off. Allowing transcription to take place.
• The lac repressor protein drops off when lactose is present. Now RNA polymerase can move along the DNA in the 5’-3’ direction and copy the lower strand.
• Thus we get our gene expressed! Allowing lactose to be used.

Question 9

How do regulatory factors recognise their target>

Answer 9

• Regulatory factors such as CAP, recognise their target sequences by interacting with the DNA through the major groove.
• The factors recognise specific DNA sequences on the DNA. The proteins look at the base pairs in the major groove to recognise it (the DNA contains binding motifs).
• A very important point is that these proteins do not have to unwind the DNA double helix to recognise and bind to their target. This means that the intact DNA molecule is presenting the information already, to be recognised.

Question 10

What is a typical eukaryotic promoter made of?

Answer 10

1. A TATA box.

2. Regulatory element.

Question 11

Describe the TATA box

Answer 11

• The TATA box is found in quite a lot of promoters in eukaryotic cells. It is needed to recruit the general transcription machinery.
• The TATA box facilitates recruitment of general transcription factors, i.e. these proteins recognise the TATA box (proteins that help RNA polymerase to bind).
• The TATA box does this by directly binding TATA box-binding factor (TBP).
• You need lots of other proteins to come in and bind, so TBP and additional proteins are part of the general transcription factors, coming together as a multi-protein complex
• This multi-protein complex acts as an address on the DNA for the stable binding of RNA polymerase II.

Question 12

Describe regulatory elements

Answer 12

• If you have genes that are tissue specific, you need a greater level of control, whether you want them on or off. This is done by the regulatory element, which regulates RNA polymerase.
• Proteins will come in and bind to the regulatory element, once this has happened, it will provide an address for the general transcription machinery to come in and bind to the TATA box, so then RNA polymerase II will be recruited.
• The regulatory element is recognised by regulatory factors that see specific sequence patterns in DNA molecules.

Question 13

Describe sequence of events in transcription initiation using oestrogen as an example

Answer 13

• Promoter region is the starts of the transcription unit.
• The gene is an oestrogen responsive gene, i.e. it will be transcribed when oestrogen is in the environment.
• Oestrogen comes into the cell and then binds to its receptor, causing a conformational change. The oestrogen-oestrogen receptor can then bind to its regulatory element (oestrogen responsive element). It does this through looking at the base sequences in the major groove of DNA.
• Once this has occurred, it allows the recruitment of the general transcription machinery to the TATA box.
  Once these are bound it provides the address for RNA polymerase II to come in. It can now start transcribing the lower strand.

Question 14

Why is understanding the transcription initiation process important?

Answer 14

It allows us to treat certain diseases. Interfering with the interactions between regulatory and general transcription factors is a way of targeting therapeutic drugs.

Question 15

Describe Tamaxifen

Answer 15

• Tamoxifen is a treatment for certain cancers. It is very similar to oestrogen.
• It is an antagonist of the oestrogen receptor, so it binds to the oestrogen receptor but the complex is unable to provide the address for the general transcription factors. As the whole thing is based on very minute details of base sequences.
• Hence there will be no transcription, we have turned off the expression of these genes.

Question 16

What ways do transcription factors regulate transcription?

Answer 16

• Come together as a multi-protein complex to act as an address on DNA for stable binding of RNA.
• The eukaryotic transcription factors also alter chromatin structure by acetylating histones.

Question 17

Decribe beta thalassaemia (as a disease resulting from mutations in the regulatory elements)

Answer 17

• Beta-thalassaemia is a disease caused by mutations in the beta-globin gene. Beta-thalassaemia is not really a disease whereby an aberrant protein is produced, rather you get a reduced amount of beta globin.
  The mutations are preventing the gene being expressed to its proper level.
• There are mutations here in the promoter region, in the introns, by the intron-exon boundaries (meaning there can be incorrect splicing, so the mRNA may not be transported out), as well as the 3’UTR which tells where to add on the polyA tail.
• The main point here, is a gene encompasses the promoter, the UTR’s and the exons and introns.

Question 18

Can a terminally differentiated cell change?

Answer 18

• We have often thought that once a cell is terminally differentiated, it is stable and irreversible. It can no longer change, so a red blood cell is a red blood cell and can’t then become a liver cell.
• In general the less differentiated a cell, the more likely it is to be able to de-differentiate
• There are a few examples where this isn’t the case. Where sub-terminal differentiation is sometimes reversible. Such as in tomato plants and dolly the sheep.

Question 19

Describe how dolly the sheep proved differentiated cells can change

Answer 19

• The cell taken was a somatic cell from the udder (already differentiated). They fused the nucleus with an enucleated ovum of another sheep. Rest of process occurred and we got an entirely new sheep!
• So the somatic cell was able to reprogramme itself, the genes that were being expressed in the mammary cell were wiped clean.
• This shows the genes that weren’t being used were not deleted, they simply were being suppressed. So the cell had to reprogramme itself.