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MCB > MCB4 - Transcription and Translation > Flashcards

MCB4 - Transcription and Translation Flashcards

1
Q

Define transcription.

A

Process of copying one strand of DNA into complementary RNA sequence by enzyme RNA polymerase.

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2
Q

Give examples of types of functional RNA

A

tRNA - transfer RNA for transfer of amino acids in translation
rRNA - ribosomal RNA for production of ribosomes
snRNA - small nuclear RNA involved with processing of pre-mRNA molecules

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3
Q

What is the transcription factor binding site and its purpose.

A

Specific sequences that allow transcription factors to bind to and aid modulation of gene expression. Dispersed through promoters (before TSS) and Enhancers (downstream from TSS)

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4
Q

Define upstream and downstream in relative to DNA molecule.

A

Upstream is prior to transcription start site. Downstream is further down after transcription start site.

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5
Q

Define and discuss TATA

A

TATA box is region at approximately -10 upstream from transcription start site. Contains majority T and A bases.

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6
Q

What is basal transcription complex.

A

Minimum complex of proteins required for initiation of transcription.

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7
Q

Why does RNA polymerase not require a primer for mRNA production.

A

RNA polymerase stabilises the first nucleotide in a DNA sequence allowing the RNA to be produced with no seeding point.

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8
Q

Discuss difference between enhancer and promoter.

A

Enhancer - sequences of DNA which enhance rate of transcription and do not need to be near transcription start site.
Promoter - sequence of DNA initiating transcription, upstream of the transcription start site where transcription factors and RNA polymerase can bind to.

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9
Q

Discuss order in which transcription factors are recruited.

A

TFIID complex contains proteins such as TATA binding proteins (TBP) and TBP accessory factors (TAFs) and binds to TATA site on DNA.
DNA partially unwinds allowing increased contact with bases.
TFIIA and TFIIB bind to TFIID allowing RNA polymerase to bind to TFIIB.
RNA polymerase binds with TFIIF attached to it.
More transcription factors bind (TFIIE, TFIIH, TFIIJ).
TFIIH promotes further unwinding of DNA double helix facilitating RNA synthesis.
RNA polymerase becomes phosphorylation activating transcription at basal level.
Further transcription factors involved which alter chromatin structure modulating gene expression.

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10
Q

How are nucleotides recruited during transcription.

A

Nucleotide enter through intake hole in RNA polymerase which are then matched to DNA in complementary manner.

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11
Q

What are the two processing steps which occur to pre-mRNA

A

Splicing and capping.

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12
Q

Which cap is added to each end of nascent mRNA

A

5’ cap and poly A tail to 3’ end

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13
Q

What three enzymes are involved in RNA capping and in what order. Where do they come from.

A

Phosphatase.
Guanyl transferase.
Methyl transferase.
Enzymes are associated with C terminal domain of RNA polymerase II

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14
Q

What is the cap added to the 5’ end of the mRNA.

A

7-methylguanosine (m7-G)

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15
Q

Discuss process of 5’ capping.

A

Phosphate removed from 5’ end of mRNA by phosphatase. GMP added via 5’ to 5’ linkage by guanyl transferase. Methyl group added to guanosine by methyl transferase.

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16
Q

What charge is present on the 5’ cap of processed mRNA and why is it useful.

A

Positive charge which aids identification and binding by eIFs.

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17
Q

Why is capping necessary.

A

Protects mRNA from degradation. Helps efficient splicing. Aids translation process. Aids exportation out of nucleus of the mRNA.

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18
Q

What is a snRNP.

A

Small nuclear ribonuclear protein

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19
Q

Discuss general function of splicing.

A

Removal of introns which are non coding DNA sections.

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20
Q

What are the sequences on either side of intron.

A

5’ sequence is AGGU

3’ sequence is AGG

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21
Q

Discuss process of splicing of introns.

A

Branch point binding protein (BBP) binds to branch point site with helper protein U2AF at 3’ branch site. Various RNA and protein complexes are involved in the following steps. U1 snRNP binds to 5’ splice site by forming base pairs. U2 snRNP binds to branch site by displacing BBP + U2AF. U4+U6 complex binds to U1 forming intron loop called a lariat structure. U5 holds the two ends together to form the lariat. Adenin base in intron attacks 5’ splice site cutting the lariat. Ends of exons are joined together.

22
Q

What is the CstF and how is it involved in cleavage of pre-mRNA.

A

Cleavage stimulation factor. Binds to GU rich element within the mRNA.

23
Q

What is CPSF and what is it’s role in polyadenylation and cleavage.

A

Cleavage and polyadenylation specific factor which binds to the consensus sequence AAUAAA

24
Q

How do CstF and CPSF aid cleavage of mRNA.

A

Following the binding of these proteins, additional factors are recruited which cleaves RNA from RNA polymerase.

25
Q

What is the function of PAP in polyadenylation.

A

Poly A polymerase adds ~200 A nucleotides with no template to create the poly A tail.

26
Q

What is the role of poly-A binding proteins

A

Determines the exact length of the poly A tail

27
Q

When is the mRNA exported out of the nucleus into the cytosol.

A

Following successful processing - cleavage, splicing , polyadenylation, capping.

28
Q

Define translation.

A

Process by which nucleotide sequence in mRNA drives the incorporation of amino acids into a protein by a ribosome.

29
Q

What is the start codon and its amino acid.

A

AUG - methionine

30
Q

Discuss the various points on a mRNA as it is about to be translated.

A 
5’cap 
5’ untranslated region (UTR) 
Start codon
Coding DNA sequence (CDS) 
Stop codon 
3’ UTR 
Poly A tail
31
Q

What happens to the 5’ and 3’ UTR

A

Can form a secondary structure which can regulate translation by stabilising the mRNA. Does this by forming base pairs.

32
Q

How many nucleotides code for a amino acid.

A

3 bases form a codon which codes for an amino acid

33
Q

Discuss the structure of tRNA

A

Transfer RNA is in a clover leaf shape. 3’ end forms acceptor arm where amino acid is attached to. One more loop. Second loop forms anticodon loop which is complementary to the codon on the mRNA. Another loop. 5’ forms base pairs with acceptor arm.

34
Q

What is the order for loops in tRNA.

A

Amino acid loop. TUC arm. Anticodon loop. D arm loop.

35
Q

What are the three steps involved in translation.

A

Initiation. Elongation. Termination.

36
Q

Discuss process of initiation in translation.

A

Pre-initiation complex formed which assembles on 5’ cap of mRNA - includes 40S subunit, eIFs complexed with GTP and initiator tRNA with methionine. mRNA scanned until AUG is reached. eIFs hydrolysis GTP which allows 60S subunit to be recruited.

37
Q

Discuss elongation in translation.

A

t-Met located in peptidyl site with following empty site referred to as aminoacyl site. Incoming tRNA goes to aminoacyl site. tRNA must match codon with its anticodon. When match occurs, it is bound by eEF1 which is complexed to GTP. Peptidyltransferase reaction occurs forming bond between peptide and new amino acid. Empty tRNA is ejected from ribosome and ribosome moves to next codon
Process repeats creating polypeptide chain.

38
Q

Discuss termination in translation.

A

eRF1 and eRF3 recognise stop codon on mRNA. Cleavage of bond between polypeptide chain and tRNA is stimulated which causes the polypeptide to be released and the ribosome to detach by becoming disassembled.

39
Q

Define homozygous vs heterozygous.

A

Homozygous is two same alleles. Heterozygous is two different alleles.

40
Q

Define an allele.

A

Different version of a gene.

41
Q

Define difference between genotype and phenotype.

A

Genotype is genetic make up . Phenotype is physical trait expressed.

42
Q

Give examples of gene mutations.

A

Deletion, silent, substitution and insertion.

43
Q

Define a frame shift.

A

When insertion or deletion causes a shift in frame of the reading of the codons.

44
Q

Difference between nonsense and missense mutations.

A

Missense is when a different Amino acid is coded for.

Nonsense is when a premature stop codon is coded for.

45
Q

Do intron variations have an effect on protein structure.

A

Sometimes can if frame shift occurs.
If intron splice site is affected then splicing may be affected.
Can have no effect is a silent mutation occurs.

46
Q

What is a silent mutation.

A

If mutation occurs within intron and has no effect then is silent.
Change in nucleotide but same amino acid coded for can also be considered as a silent mutation.

47
Q

Give examples of chromosomal mutations.

A

Deletion. Inversion. Translocation. Duplication. Recombination.

48
Q

Discuss colloquial variant nomenclature.

A

Uses single letter amino acid code. Discusses changes in code. Uses del for deletion.

49
Q

Discuss problems with colloquial variant nomenclature.

A

Can’t determine between amino acid vs. DNA sequence change.
Intrinsic mutations can’t be determined if amino acid change doesn’t occur.
Uses single letter amino acid code which also coded for nucleotides

50
Q

Which society published guidelines for naming of variants

A

Human genome variation society

51
Q

What is g. And c. At the start of standard mutation nomenclature.

A

G presents genomic sequence.

C represents coding DNA sequence.

52
Q

Define the variations: 36+2C>T and 37-2G>A

A

2 nucleotides downstream from 36th position change from C to T.
2 nucleotides upstream from 37th position change from G to A.

MCB (13 decks)

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