Nucleic acids 4- Gene organisation and transcription II

Question 1

How many types of RNA polymerase do bacteria have

Answer 1

1

Question 2

Describe transcription in bacteria

Answer 2

A subunit of RNA polymerase, a sigma factor, binds to the TATAAA (Prinbow box) region of the promoter. The gene is then then transcribed when the sigma factor is released. Sigma factor rebinds to the RNA polymerase at the end of transcription.

Question 3

How do sigma factors spot the prinbow box

Answer 3

Although the bases are on the inside of the DNA double helix- each base presents unique features on the outside of the DNA double helix- allowing the sigma factor to find the promoter sequence without having to separate the entwined DNA strands.

Question 4

Why is the fact that bacteria only have one version of RNA polymerase important.

Answer 4

Antibiotics can be developed which target bacterial RNA polymerase only.

Question 5

What is the initial RNA produced from the gene called

Answer 5

The initial RNA produced from a gene is known as a
“primary transcript” or “Pre- mRNA” or “heterogenous
nuclear RNA” ( hn RNA)

Question 6

What is the difference between exons and introns

Answer 6

Segments of the gene which contain sequences that form part
of the final RNA are called “exons”
Introns” are sequences in the gene which are transcribed
but are edited out of the final mRNA

Question 7

What is the sequence of bases at the splice donor site

Answer 7

AGGU

Question 8

What is the sequence of bases at the splice acceptor site

Answer 8

Pyr15NCAG

Question 9

What are the start and end base sequences of an intron

Answer 9

GU and AG

Question 10

What are the molecules responsible for splicing

Answer 10

snRNPs
U1,U2,U4,U5 AND U6
U1 binds to the splice donor site by complementary base pairing
U5 binds to the splice donor site by complementary base pairing.
The others bind to the middle region of the intron
These molecules form the core of the spliceosome.

Question 11

How does the spliceosome function

Answer 11

The splice donor sequence is cleaved- between AG and GU- phosphodiester link is broken.
G then loops back and looks for A residue (branch point) in the intron- where a phosphodiester bond forms between the 5’ phosphate of G and the 2’OH group of A. The phosphodiester bond between the “G” at the end of the intron and the next exon is then cleaved and the intron removed as a “lariat” structure
The lariat structure is then degraded.

Question 12

How are the remaining exons joined together.

Answer 12

RNA ligase joins the remaining exons together (phosphodiester bonds formed).

Question 13

What is the advantage of having introns and exons

Answer 13

The transcripts of many eukaryotic genes can be spliced in many different ways, each producing a distinct protein. This is known as alternative splicing and it allows the same gene to produce a variety of different proteins.
This gives an advantage to eukaryotes in evolution- novel proteins can be created by joining exons from different genes- creating new genes with different functions- allowing better adaptation to the environment.

Question 14

Describe the post-translational modification of mRNA

Answer 14

RNA capping- Guanine bearing a methyl group is attached to the 5’ end of mRNA by a 5’-5’- triphosphate bridge.
Polyadenylation- Polyadenylation is the addition of a poly A tail to
the pre-mRNA
The poly A tail is added one base at a time
The poly A tail is added 11-30 bases downstream
of the sequence AAUAAA, which is found in all mRNA’s
Enzyme cuts RNA at AAUAAA sequence, a second enzyme then a series of repeated A nucleotides to the cut end.

Question 15

What is the importance of the cap.

Answer 15

Proteins which transport the mRNA to the ribosomes recognise this cap and bind to it.

Question 16

What is the importance of the tail

Answer 16

Increases the stability of the mRNA molecule- preventing its degradation in the cytoplasm.
Also- it is possible that the length of the tail decreases every time it is translated- shows use of the protein and how well it is translated. Cap and tail signal the start and end of the molecule- hence showing whether the full mRNA molecule has been transcribed before translation has begun.

Question 17

How does polio interfere with the cap

Answer 17

Polio removes the cap- hence mRNA molecule is no longer recognised by the ribosome- no translation of host cell protein- only viral protein synthesised.
Polio virus can invade the nervous system, and cause total paralysis in a matter of hours.- nerve cells only make viral proteins- no neurotransmitter.

The virus enters the body through the mouth and multiplies in the intestine. Initial symptoms are fever, fatigue, headache, vomiting, stiffness in the neck and pain in the limbs.

Question 18

What is a mutation

Answer 18

A mutation is a heritable change in the sequence

of a gene.

Question 19

Describe the different percentages of mutations that occur in different regions of the gene.

Answer 19

13% of cases feature mutations in gene promoters- difficulty of RNA polymerase binding
6 % feature mutations of the polyadenylation sequence- AAUAA.
~ 1.2 % feature mutations of RNA capping
33% feature mutations in splice donor / acceptor sequences
the remaining 47% of cases involve mutations that alter the structure / function of the protein being produced.

Question 20

What is Thalassaemia

Answer 20

Thalassaemia is an inherited disorder in which there is an imbalance in the relative amount of globin chains.
Imbalance- not enough beta or alpha- precipitation of the globin- cannot bind to Oxygen.
Thalassaemia is very common in:
The Mediterranean
S.E. Asia
China
Several types of b-Thalassemia feature splice site mutations
in the b-Globin gene

Question 21

Why is the mutation for Thalassaemia passed on to offspring

Answer 21

provides a degree of resistance against malaria- host red blood cells not ideal for the malarial parasite.

Question 22

What treatments are given to sufferers of Thalassaemia

Answer 22

Treatment for patients with thalassemia major includes chronic blood transfusion therapy, iron chelation, splenectomy, and allogeneic hematopoietic transplantation.[ Body sees it as anaemia- tries to make more red blood cells- which do not function. Skull tries to make red blood cells.

Question 23

What are the symptoms of Thalassaemia

Answer 23

Iron Overload (Hemosiderosis) elevated GI absorption of iron due to chronic anaemia results in: hepatic fibrosis & cirrhosis (by age 5 years)  darkening of skin (iron-stimulated melanin production) cardiomyopathy (arrhythmias, congestive heart failure, recurrent pericarditis) 
endocrinopathies (diabetes mellitus, secondary hypopituitarism, hypoparathyroidism, hypothyroidism

Question 24

Describe the potential role of RNA splicing in treating patients with DMD

Answer 24

Mutation in dystrophin gene and exons- premature translation of exons- faulty dystrophin.
Shorter, functional forms of dystrophin can be made by alternative splicing- where mutated exons ae not incorporated into the final mRNA molecule.
Therapies are in clinical trials (eteplirsen).