L11 Molecular Biology of the Gene and Gene Expression

Question 1

Almost all human genes possess a set of similar characteristics. Which of the following are common characteristics of genes?

a) Promoter
b) Transcription ‘start’ and ‘stop’ signals
c) Exons and introns
d) Upstream regulatory regions
e) All of the above?

Answer 1

e) All of the above

Question 2

Not all genes are expressed in all cells, all the time. How does a cell control which genes are expressed or not?

Answer 2

• Gene expression is driven by RNA polymerase II
• Transcription factors bind in and around the promoter region.
• Activators bind to enhancer sequences on DNA to significantly increase expression

Question 3

Which enzyme drives gene expression?

Answer 3

RNA polymerase II

Question 4

Where do transcription factors bind?

Answer 4

Promoter region of the gene

Question 5

Where to activators bind on a gene to fine tune and enhance it’s expression?

Answer 5

Upstream enhancer sequence

Question 6

How many types of RNA polymerase are there?

Answer 6

3

Type I, II, and III

Question 7

Which RNA polymerase is responsible for the production of the large ribosomal RNA?

Answer 7

RNA polymerase I

Question 8

Which RNA polymerase is responsible for the production of mRNA?

Answer 8

RNA polymerase II

Question 9

Which RNA polymerase is responsible for the production of tRNA and the small ribosomal RNA molecules?

Answer 9

RNA polymerase III

Question 10

What is the role of RNA polymerase I?

Answer 10

Production of large ribosomal RNA

Question 11

What is the role of RNA polymerase II?

Answer 11

Production of mRNA

Question 12

What is the role of RNA polymerase III?

Answer 12

Production of tRNA and the small ribosomal RNA moleules

Question 13

At which stage of DNA replication does the creation of mRNA, tRNA and rRNA take place? Which enzyme is responsible for producing these molecules?

Answer 13

During transcription RNA polymerase produces these molecules.

There are 3 types of RNA polymerase.

Question 14

__1__ molecules collide randomly with DNA in the __2__ and bind with specific DNA sequences called __3__ (i.e. the __4__ sequence or __5__ box).

The RNA polymerase then opens up a short length of the DNA double helix, exposing a specific section of DNA on each strand.

One strand acts as a __6__ for base pairing with the incoming __7__.

Answer 14

1) RNA polymerase
2) nucleus
3) promoters
4) TATA
5) TATA
6) template
7) RNA nucleotides

Question 15

__1__ switch genes off in two ways:

1. They may bind next to __2__, thus blocking its function, or;
2. Their binding site may __3__ that of the __4__, preventing it from binding in the first place.

Answer 15

1) Transcriptional repressors
2) transcriptional activators
3) overlap
4) activators

Question 16

Wilm’s tumour protein (WT1) is an example of a transcriptional [activator / repressor]. In the developing kidney, WT1 binds to the __2__ region of the EGR-1 gene (a transcriptional activator), switching __3__ expression.

Mutation of the gene that encodes WT1 can lead to uncontrolled expression of EGR-1 and can lead to development of kidney tumours early in life.

In this respect, the WT1 gene is considered to be a tumour suppressor gene.

Answer 16

1) repressor
2) promoter
3) off

Question 17

What happens at the 5’ end of the mRNA molecule during transcription?

Answer 17

5’ end is capped by addition of methylated G nucleotide by removal of a phosphate by a phosphatase, addition of a GMP via a guananyl transferase, and the addition of a methyl group via a methyl transferase.

Question 18

What happens at the 3’ end of the mRNA molecule during transcription?

Answer 18

The 3’ end is cleaved at a specific site and a poly-A tail of up to 200 nucleotides is added by poly-A polymerase.

Question 19

Are all of the codons that are transcribed into mRNA used?

Answer 19

No. There are coding regions (exons) and non-coding regions (introns). The introns are spliced out of the sequence.

Question 20

What is the translational start codon?

Answer 20

AUG

This codes for methionine.

Question 21

What are the translational stop codons?

Answer 21

UAA
UAG
UGA

Question 22

What are the 3 stages of translation?

Answer 22

1) Initiation
2) Elongation
3) Termination

Question 23

How is the half-life of mRNA related to the control of gene expression?

Answer 23

In cytoplasm, mRNA associates with ribosomes which translate the RNA sequence into a polypeptide chain (protein)

Many ribosomes attach to each mRNA (multiple bubbles)

In time mRNA is degraded (half-life)

The half-life of mRNA is a way in which the cell can regulate gene expression levels

Question 24

What is EGR-1?

Answer 24

A transcriptional activator (promotes gene transcription)

Question 25

Which transcriptional repressor switches off EGR-1 in the kidneys?

Answer 25

Wilms Tumour Protein

Question 26

In which direction does nucleic acid synthesis occur?

Answer 26

5’ to 3’

Nucleotides are only able to be added to the 3’ end.

Question 27

Where does translation take place?

Answer 27

On the ribosomes, mRNA provides the template

Question 28

What provides the template for genetic translation?

Answer 28

mRNA

Question 29

How is genetic translation initiated?

Answer 29

An initiator tRNA carrying methionine associates with a small ribosomal unit in association with eukaryotic initiation factor 2 (eIF2).

This small ribosomal unit-tRNA complex recognises the 5’ end of a mRNA (capped with eIF4E and eIF4G) and scans along the mRNA for a start codon. This allows the large subunit to bind, initiating translation.

Question 30

There are three binding sites within the ribosome, these are the __1__ site, the __2__ site, and the __3__ site.

Answer 30

1) E
2) P
3) A

Question 31

What are the 4 stages of translation elongation?

Answer 31

1) An aminoacyl – tRNA binds to the A site and the tRNA molecule at the E site is released
2) Carboxyl end of the polypeptide chain is uncoupled from the tRNA in the P site and joined by a peptide bond to the amino acid attached to the new tRNA molecule in the A site via a peptide transferase enzyme.
3) Large ribosomal sub unit steps one codon along the mRNA
4) Small ribosomal subunit steps one codon along so that the new peptidyl –tRNA in the A site moves to the P site as and the tRNA that occupied the P site of the ribosome moves 1 codon along the mRNA molecule and becomes the new E –site. This generates a new A site.

Question 32

What mnemonic is helpful for remembering the order of the binding sites in translation elongation?

Answer 32

APE

The elongation APE?

APEs have long arms?

Question 33

Which molecules drive elongation?

Answer 33

Elongation factors EF1 and EF2

Question 34

How is translation terminated?

Answer 34

When the ribosome encounters a stop codon (UAA, UAG, UGA), cytoplasmic release factors bind to the stop codon and free the carboxyl end of the growing polypeptide chain.

Question 35

What is splicing?

Answer 35

A genetic sequence contains sections of coding and non-coding sequences. The coding sequences are called exons and the non-coding sequences are called introns. Introns are spliced out of the sequence by enzymes, and the exons are joined together to form a continuous chain.

Splicing can take place in different ways to produce different ISOFORMS