S3: Genes - What they are and How we study them?

Question 1

What is the protein the cells expresses called in molecular medicine?

Answer 1

They are called the phenotype.
Cells are defined by the types of protein they make for example:
- RBC: Haemoglobin
- Retinal rod cells: =Rhodopsin
- Skeletal muscle cells: Myosin

Question 2

Describe genes

Answer 2

• Genes are the instruction manuals for out cells to make all the proteins that are necessary for us to function (genotype)
• All genes are present in the cell nucleus but only a small subset are expressed in a particular cell
• Cells therefore turn off ans suppress genes they don’t require
• Genes can be very different in size and there is no correlation between organism complexity and genome size

Question 3

What are house keeping genes?

Answer 3

They are genes that are expressed in all cells and they aren’t suppressed. They code for proteins that are required in many types of cells e.g. structural proteins.

Question 4

What is the central dogma?

Answer 4

The central dogma says that there is a unidirectional flow from DNA to RNA to protein.

Question 5

Does one gene only code one protein?

Answer 5

One gene actually codes one polypeptide. However, alternative splicing can result in a different end protein.

Question 6

Describe structure of a gene

Answer 6

• Gene promoter at the beginning which controls the on/off, where, when and how much protein is made.
• The coding region which is the part that is transcripted to RNA.
• The non coding regions either side of the coding regions are cis-linked control regions. Cis linked means that these are regions physically close to the exons on the DNA strand.
• Trans-regulatory regions can be on different chromosomes.
• Exons are the coding regions for amino acids and retained in mature mRNA
• Introns are non conding regions removed to form mature mRNA
• The transcription unit is the whole region transcribed into RNA

Question 7

How many base pairs are in each haploid ‘genome’ in humans?

Answer 7

3x109 base pairs

Question 8

How many genes in human genome and proportion that codes for proteins?

Answer 8

• Human genome contains 25,000 genes

- Only about 3% of DNA is protein coding sequence (most is intergenic regions of unknown function or regulatory)

Question 9

What are the differences in mutations of introns and expons?

Answer 9

Because the exons code for the amino acids, mutations here are more likely to lead to altered proteins.
However as the majority of our genome is the intergeneic regions, mutations are more likely to occur there. This accounts for the majority of difference in DNA between individuals. We don’t think that this has a massive effect. Whereas a small variant in an exon can completely change a protein.

Question 10

What is the intergenic region?

Answer 10

The inergenic regions is mainly ‘junk’ DNA. It is repetitive DNA from either endogenous retroviruses (that has been inserted) or pseudogenes (genes we no longer use). However, we also find a lot of regulatory function in these regions.

Question 11

Why do genes often cluster together in families i.e. in the same region?

Answer 11

For example globin clusters which tend to be in the same region on the same chromosomes.
This is thought to be because it enables good coordination of gene regulation, so the cis-regulatory regions are near each other.
Or it could reflect evolutionary history, where there was a duplication event which resulted in an extra type of globin that turned out to be useful so remained in the genome.

Question 12

Describe the promotor region and 5’UTR during transcription and translation

Answer 12

Promoters are recognition sequences that lie outside the transcribed region. The promoters recruits RNA polymerase to a DNA template. RNA polymerase will bind asymmetrically and move in one direction (5’ - 3’). Once the promoter recruits the RNA polymerase, the RNA polymerase will unwind the local region of DNA and binds to the lower strand so that as it starts adding bases it is in the 5’-3’ direction.
The 5’UTR is the untranslated region that is transcribed into mature mRNA but not translated (thus does not code for amino acids).

• The 5’UTR is transcribed but the promoter isn’t.

Question 13

What are the 3 types of RNA polymerase in eukaryotes?

Answer 13

RNA polymerase I which is needed to transcribed rRNA genes.
RNA polymerase II which is needed to transcribe mRNA genes.
RNA polymerase III which is needed to transcribe tRNA and other small RNA.

Question 14

How to eukaryotic RNA polymerases recognise promoters?

Answer 14

RNA polymerases contain many subunits and they need help from transcription factors to recognise promoters efficiently.

Question 15

Explain the process of transcription

Answer 15

• When the promoter is activated by a transcription factor, it will recruit RNA polymerase to bind to the beginning of the transcription unit.
• When it first binds, it is in whats called a closed complex (DNA is still double stranded).
• The RNA then helps the DNA strand unwind to an open complex but this is local.
• This enables RNA polymerase to start making the complementary chain to the lower strand. It goes in the direction 5’ - 3’.
• RNA is formed until a STOP signal is reached.
• RNA polymerase then dissociates along with RNA.

Question 16

What is the TATA box?

Answer 16

TATA box is found in the promoter region. It is needed to recruit general transcription factors and thus RNA polymerase.

Question 17

What are the regulatory elements in the promoter region?

Answer 17

The promoter is also made up of lots of other regulatory elements (small sequences that recruit regulatory transcription factors that help RNA polymerase find the gene being transcribed). So these regulatory elements are very important for regulating tissue specificity of gene expression as well as the timing of gene expression. For example, at a specific point a cell receives a signal, there is a signalling cascade resulting in transcription factor binding to these regulatory elements, this allows RNA polymerase to then start transcribing this region.
E.g. steroids, thyroid hormones.

Question 18

What is the role of introns?

Answer 18

They separate exons and are thought to help with splicing. A variant in introns can lead to alternate splicing and a differently folding proteins. Introns are still transcribed and they vary in size and number.

• Some genes have no introns e.g. histones
• Some genes have very large numbers e.g. dystrophin

Question 19

What are the 3 modifications done to RNA to form mature mRNA?

Answer 19

1. It is capped at the 5’ end
2. It is polyadenylated at the 3’ end
3. The introns are removed by splicing.

Question 20

Describe the 5’ capping, polyadenylation at 3’ end

Answer 20

• The 5’ cap is added soon after the RNA polymerase begins transcription. It is a methylated cap that tells the ribosome which end to start translating first (5’ end).
  Transcription goes on to the end.
• When we get to the end of the pre-mRNA, there is a sequence (AAUAAA) that gets cleavage factors to bind. Once they are bound (which is to the 3’ end). It will cut the extra 3’ region of and add a bunch of A’s. The polyadenylate tail is thought to help with the stability of the mRNA and helps prevent degradation before mRNA is translated.
• Splicing occurs last and it removes sequences between exons.

Question 21

What removes the introns during splicing of RNA to form mature mRNA?

Answer 21

The introns are removed by a structure called a spliceosome. This is done by snRNPs (small nuclear ribonucleoproteins).

Question 22

Describe alternative splicing

Answer 22

• The IVSs can be spliced out but we are able to change which exons are put together.
• Therefore, these sequences, coding for amino acids are different and mRNA sequences are different and they have been alternatively spliced.
• These variations of proteins are called isoforms.

Question 23

What are Exon Junction Complexes?

Answer 23

• Once we have mature mRNA, the positions where we now have the exons close together act as binding sites for proteins. this is the exon junction complex.
• These are important because they recruit other proteins that help move the mRNA from the nucleus into the cytoplasm, so it can then be translated into protein by a ribosome.
  The protein these exon junction complexes recruit is called TREX (Transcription Export) complex.