Transcription & RNA processing

Question 1

Where is DNA converted to RNA

Answer 1

In the nucleus DNA is converted to RNA

Question 2

Why must genetic code be copied and transferred out of nucleus

Answer 2

Because the DNA found in nucleus is too big to move out (carried from DNA in nucleus to ribosomes in cytoplasm)

Question 3

Define proteome

Answer 3

All protein in a cell

Question 4

Enzymes that synthesise RNA from DNA are called _____

Answer 4

RNA polymerases (Pol II)

Question 5

RNA is synthesised from which strand of DNA and in what direction

Answer 5

RNA is synthesised from the TEMPLATE (antisense) DNA strand which runs 3’—5’

Question 6

In which direction does RNA polymerase synthesise complementary RNA

Answer 6

RNA is synthesised 5’—3’ as we synthesise RNA from the template strand so complementary base pairing means it’s the right way round 5’—3’ when it’s made (in RNA U instead of T)

Question 7

What are the 5 steps of mRNA synthesis

Answer 7

INITIATION: polymerase binds to gene

ELONGATION: polymerase transcribes gene

TERMINATION: polymerase stops transcribin gene

PROCESSING: pre mRNA—> mature mRNA is formed

EXPORT: mRNA leaves nucleus through nuclear pore to be translated

Question 8

What region initiates transcription that the RNA polymerase binds to at beginning

Answer 8

RNA polymerase binds close to PROMOTER REGION to initiate transcription

Question 9

The promoter acts as a template for assembly of ______. This brings Pol II to gene. Once bound, polymerase can transcribe

Answer 9

The promoter acts as a template for assembly of PREINITIATION COMPLEX. This brings Pol II to gene. Once bound, polymerase can transcribe

Question 10

What are the polymerase positioning elements

Answer 10

• TATA box= initiator

• upstream + downstream elements that bind +ve & -vely acting transcription factors (enhancers + silencers)

Question 11

What happens in elongation stage of transcription

Answer 11

RNA polymerase synthesises complementary RNA in 5’—3’ direction using NTPs ( ribonucleoside triphosphates)

Question 12

List difference between RNA & DNA

Answer 12

• different pentose sugar: deoxyribose in DNA, ribose in RNA

*DNA is double stranded; RNA is single stranded

*DNA has Thymine (T), RNA has Uracil (U)

Question 13

How many bonds between
Thymine and Adenine
Uracil and Adenine

Answer 13

2 bonds between T & A
2 bonds between U & A

Question 14

How many bonds between Guanine and Cytosine

Answer 14

3 bonds between G & C

Question 15

What type of linkages form backbone of both DNA & RNA

Answer 15

PHOSPHODIESTER linkages form backbone of both DNA & RNA

Question 16

Primary mRNA transcript needs to be modified before it’s exported into cytoplasm, explain the 2 caps and their role

Answer 16

5’ cap helps with efficient translation, prevents degradation of unstable mRNA molecule. Also directs pre mRNA splicing

3’ cap helps prevent degradation, assists splicing + nuclear export of mRNA

Question 17

What is the role of poly A and where is it

Answer 17

Poly A is AAAA at 3’ end of RNA it provides the mRNA with stability and prevents degradation.

Question 18

Describe RNA splicing (going from pre mRNA to final mature mRNA)

Answer 18

Cuts out INTRONS (non-coding RNA regions) are spliced out of pre-mRNA leaving the EXONS in the final mature mRNA

Question 19

Define intron

Answer 19

Non coding region

Question 20

Define exon

Answer 20

Coding region

Question 21

Alternative splicing of mRNA forms what?

Answer 21

Alternative splicing forms different ISOFORMS of a protein

I.e. pre-mRNA—> alt splicing—> isoform 1 + isoform 2

These isoforms are fundamentally the same proteins but with slightly different features

Question 22

Describe process of mRNA termination

Answer 22

RNA polymerase reaches TERMINATOR SEQUENCE —> transcription stops, mRNA is released

Question 23

Describe process of mRNA processing

Answer 23

Polyadenylated region (at PolyA tail on 3’ region) is CLEAVED, the rest of mRNA degrades.
Mature mRNA is ready to be released into cytoplasm

Question 24

What is the function of non-coding regions on DNA

Answer 24

Non-coding DNA corresponds to the portions of an organism’s genome that do not code for amino acids (build proteins).

Some non-coding DNA sequences are known to serve functional roles: e.g. regulation of gene expression, while other areas of non-coding DNA have no known function

Question 25

When we want to infer mRNA sequence, we know complementary base pairs line up to form non-template sense (?’) strand (but with U instead of T) from the template antisense (?’) strand

Answer 25

When we want to infer mRNA sequence, we know complementary base pairs line up to form non-template sense (5’) strand (but with U instead of T) from the template antisense (3’) strand

Question 26

Give some examples of Mis-regulated gene expression + disease

Answer 26

• general transcription factors can be mutated = e.g. cMyc-one is commonly amplified oncogene (large number of transcription factors important for development)

• mutated splice sites = e.g. cancer BRCA1 + 2, spinal muscular atrophy (SMN2), atypical cystic fibrosis (CFTR)

• mutated splicing machinery= retinitis pigmentosa, spinal muscular atrophy

Question 27

Where is information that codes for proteome stored

Answer 27

Information to code for proteome is stored in DNA

Question 28

Primary transcripts must be processed by 3 things:

Answer 28

Capping
Splicing
Polyadenylating
— this all forms mature mRNA that can be exported to ribosomes in cytoplasm

Question 29

_____ in transcription factors (activating + inactivating) + splice sites affect gene expression + cause disease

Answer 29

MUTATIONS in transcription factors (activating + inactivating) + splice sites affect gene expression + cause disease

Question 30

What’s the function of preinitiation complex

Answer 30

Regulates transcription + allows polymerase to attach to right part of the gene in order for transcription to be initiated

Question 31

What is the UTR + why is it important

Answer 31

Untranslated region (UTR) they are all the regions before + after stop and start codon
They’re important as it’s where RNA polymerase will bind, it’s where termination factors will bind, where preinitiation complexes bind. I.e. controls all proteins that control transcription but don’t contain any sequence that is translated

Question 32

We read DNA 5’ to 3’. We read RNA 5’ to 3’, why do we need to used 3’ to 5’ to synthesise RNA strand in 5’ to 3’

Answer 32

Because we use the template antisense strand (3’ to 5’) as RNA polymerase can complementary base pair to this strand and therefore form RNA 5’ to 3’ ( so RNA will be a copy of the 5’ to 3’ strand just with U instead of T)

Question 33

What determines alternative splicing and what exons are kept

Answer 33

Different proteins in different cells will determine where the splicing will occur. It requires proteins to bind to splice sites depending on cell. So always different

Question 34

In regards to exon splicing, how many can you splice out but still maintain function of protein

Answer 34

Depends on protein! Depends where functional domains are within the protein.

Question 35

If you get mutations in transcription factors that will affect _____

Answer 35

If you get mutations in transcription factors that will affect TRANSCRIPTION OF THE GENE I.e. transcription factor isn’t moving away after initiated transcription so the patient will be transcribing gene continuously. If this gene regulates growth or cell division= unregulated growth/ cell division = cause cancer

Question 36

Define oncogene

Answer 36

A gene in viruses (v-onc) + mammalian cells (c-onc) that can cause cancer. It results from a mutation of a normal gene