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BMS242 Cell and Molecular > L8 - RNA Transcription > Flashcards

L8 - RNA Transcription Flashcards

1
Q

What is transcription

A

The process of RNA synthesis from a DNA template

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2
Q

Transcription is known as the

A

Central DOGMA of biology

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3
Q

What is mRNA

A

Messenger RNA which codes for proteins

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4
Q

What is the % of total RNA made up by mRNA

A

3-5%

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5
Q

What is t-RNA?
How many families?
What is found on each t-RNA?

A

Transfer RNA involved with translation,
49 families of tRNAs
Each carrys an amino acid and an anti-codon loop

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6
Q

What is rRNA

How many types

A

Ribosomal RNA - four main types

The main consituent

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7
Q

What are the functions served by non-coding RNAs

A

Structural and enzymatic roles within the cell

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8
Q

What are the four main differences seen in the primary structure of mRNA when compared to DNA

A

1) Ribose instead of deoxyribose
2) Uracil instead of thymine
3) Synthesised as a single strand
4) Very unstable

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9
Q

As being synthesised as a single strand what tends to happen to RNA

A

Folds on itself

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10
Q

What is the difference between ribose and deoxyribose

A

Ribose have an OH instead of a H at the 2’ position

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11
Q

What is the main base pairing in RNA?

What is another example of base pairing which can occur

A

A-U C-G

Also non Watson-Crick base pairing e.g. G-U

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12
Q

What secondary structures are common in RNA

A

Semi-loop secondary strucutres

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13
Q

What is meant by the tertiary strucuture

A

The folding of a molecule in three dimensions

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14
Q

What is RNA pol I involved with

A

Synthesis of rRNA

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15
Q

What is RNA pol II involved with

A

Transcription of protein encoding genes

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16
Q

What is RNA pol III involved with

A

tRNA - small nuclear RNA - 5s RNA

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17
Q

What direction is RNA always synthesised in

A

5’ –> 3’

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18
Q

What are 5 ways that RNA transcription differs from the replication of DNA

A

Multiple RNA polymerases bind to the same gene
No primer required
Only one strand is required as a template
Transcript does not remain bound to the template
Higher error rate than DNA replication

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19
Q

Where can genes be found

A

Can be on either side of the DNA

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20
Q

What is the template described as being

A

Anti-sense

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21
Q

What strand are genes found

A

The sense strand (but this can be either one of the strands of DNA

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22
Q

Unwinding how many basepairs leads to creation of supercoiling

A

10bp

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23
Q

What enzyme helps to overcome supercoiling, how

A

Topoisomerases

Release supercoils and allow pol2 progression

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24
Q

What are the four general TF elements

A

BRE TATA INR DPE

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25
Q

What protein binds to the TATA box

A

TATA binding protein

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26
Q

What general TF bindis to INR and DPE

A

TFIID

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27
Q

Where is the TATA box found in relation to the start of the gene

A

At the start of the gene

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28
Q

Where is BRE found in relation to the start of the gene

A

35 bp upstream

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29
Q

Where is INR found in relation to the start of the gene

A

30 bp upstream

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30
Q

Where is DPE found in relation to the start of the gene

A

30 bp downstream

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31
Q

What is the large complex called (this binds to other TFS

A

Mediator

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32
Q

What does an activator bind to

A

Enhancer element and the mediator complex

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33
Q

What two proteins are required to bind to the transcription initiation complex for transcritpion to begin

A

Chromatin remodelling factors and histone modifying enzymes

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34
Q

What are the three processing stages of RNA

A

Splicing of introns
5’ capping
Poly A tailing

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35
Q

What does intron splicing ahcieve

A

Elimination of non coding regions of mRNAs from the primary transcript to generate more mature mRNA for protein synthesis

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36
Q

What is 5’ capping nesc for

A

Stabilitiy and aids in the binding of the mRNA to the ribosome

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37
Q

What is poly A tailing required for

A

Part of the termination process (add of a poly A tail) mRNA stability
Also helps with nuclear export and translocation

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38
Q

What is splicing specific to

A

Eukaryotic mRNA

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39
Q

What can vary regarding splicing

A

Some mRNAs can be spliced in more than one way this gives rise to splice variants

40
Q

Give an example of splice variation

A

COX3 in the brain is a splice varaint of COX1

Thought to be the target of paracetamol

41
Q

What are the three sites of importantce during mRNA splicing

A

Splice donor site
Branch site
Splice acceptor site

42
Q

What is the process of splicing (describe)

A

2’ OH branch site A attacks the phosphodiester bond on donor site G
Cleavage occurs at the donor site
Lariat formation
3’ OH of donor site G attacks the phosphodiester bond on the acceptor site G freeing the lariat
Lariat is the degraded

43
Q

What is responsible for splicing

A

Spliceosome

44
Q

WHat is the spliceosome

A

Nuclear complex made of about 150 proteins and SnRP

45
Q

What is SnRNP

A

Small nuclear RNA and proteins

46
Q

Three functions of the spiceosome

A

Recognition of 5’ donor and branch sites
Bring the sites together
Catlayse the RNA cleavage

47
Q

What type of RNAs contain a 5’ cap

A

All eukaryotic

48
Q

When is the 5’ cap added to the mRNA

A

When the mRNA is around 20-40 nucleotides long (early during synthesis)

49
Q

What is the function of thr 5’ cap

A

Prevention of degredation of the 5’ end

50
Q

What modification is made to to a base when it is 5’ capped

A

Guanine is methylated

51
Q

Three enzymes involved in the formation of the 5’ cap

A

RNA triphosphatase
Guanylyl transferase
Methyl transferase

52
Q

What is the function of RNA triphosphatase

A

Removal of Pi from the 5’ end

53
Q

What is the function of guanylyl transferase

A

Linkage of guanine by 3 pi

54
Q

What is unusual about the linkage of G in cap formatio n

A

By 5’ –> 5’

55
Q

What is the function of methyl transferase

A

Addition of a methyl group to guanine

56
Q

What is the poly A signal

A

AAUAAA

57
Q

Desicribe how poly adenylation occurs to the mRNA

A

Cleavage site is 30-40 nucleotides downstream of the poly A signal
At the poly A signal CSTF and CPSF bind
RNA is then cleaved + release of CstF
PAP then binds to the 5’ end - poly A binding proteins bind to adenine residues
Removal of SPSF and PAP – more poly A binding protein binds

58
Q

What is CSTF

A

Cleavage stimulating factor

59
Q

What is CPSF

A

Cleavage and polyadenylation specific factor

60
Q

What is CTD

A

Pol 2 C’ terminal domain

61
Q

What is significant about viruses when it comes to protein synthesis

A

Viruses break the central dogma of DNA–>RNA–>Protein whereby reverse transcriptase enzymes can make DNA from RNA

62
Q

mRNA accounts for the majority of RNA, T or F

A

F – RNA only accounts for between 3-5% of all RNA

63
Q

How many families of tRNAs are there

A

49

64
Q

What is the role of tRNA

A

tRNA participates in translation where its bound amino acid is added to the growing polypeptide chain when the tRNAs anticodon loop binds to the complimentary codon on the mature mRNA strand

65
Q

Describe the role of rRNAs

A

Ribosomal RNAs are a major constituent of ribosomes. They are very large and very abundant and catalyse protein synthesis

66
Q

What is significant about non-coding RNAs

A

Non-coding RNAs serve structural and enzymatic functions, acting more like proteins

67
Q

What is meant by the primary sequence of RNA

A

The polyribonucleotide sequence

68
Q

What are the key differences between RNA and DNA

A

RNA replaces thymine with uracil. RNA is also synthesised as a single strand and thus is unstable and rapidly degraded. Finally RNA contains a ribose sugar backbone instead of a deoxyribose sugar. The difference is an -OH group replaces the H bonded to the 2’ carbon in the sugar ring

69
Q

What is meant by the secondary structure of RNAs

A

Secondary RNA structure refers to the base pairing that occurs within a single RNA strand.

70
Q

In RNA A pairs with U and C pairs with G however it is possible for unusual base pairing such as G with U, how is this described

A

Non-Watson-Crick pairing

71
Q

The tertiary structure of RNA refers to its interactions with other RNAs, T or F

A

F – tertiary structure is the RNA strands 3D conformation

72
Q

Which RNA polymerase transcribes all protein coding genes

A

RNA Polymerase II

73
Q

Which RNA polymerase transcribes all tRNAs, 5S rRNAs and other snRNAs

A

RNA Polymerase III

74
Q

What is the role of RNA polymerase I

A

Transcribes rRNA genes (28S, 18S and 5.8S)

75
Q

Due to internal folding within the molecule and complimentary base pairing, an RNA molecule appears as a 10th of the length of the corresponding DNA sequence, T or F

A

T

76
Q

How is transcription different from DNA replication

A

Multiple RNA polymerases bind to the same gene, no primers are needed, only one strand of DNA is used as the template and polymerase only moves in one direction. Finally the transcript doesn’t remain bound to the template as in semi-conservative replication

77
Q

What can be said about the error rate in transcription

A

Its much higher than DNA replication

78
Q

Genes can be on either the sense or antisense stands of the DNA but not both, T or F

A

T

79
Q

The RNA molecule produced in transcription will have the same sequence as the DNA sequence that codes for that gene, T or F

A

F – it will have the opposite sequence to the template strand

80
Q

Polymerase action causes an uncoiling of the DNA that provides a force on the upstream DNA, how is this tension relived

A

Topoisomerases release the tension by either making single or double stranded breaks in the DNA upstream hence removing some of the coils from the superhelix

81
Q

Give an example of a promoter sequence to which a general transcription factor binds to

A

TATA box – consisting of a TATAA/TAA/T sequence that lies 30 base pairs upstream of the coding sequence

82
Q

General transcription factors are required for all gene transcription, how do they act

A

They act to guide RNA polymerase and bind to the promoter sequence

83
Q

Specific transcription factors bind close to the promoter region, T or F

A

F – they bind far away

84
Q

Recall the structure of a mature mRNA from start to finish

A

Methyl guanosine cap –> 5’ UTR –> START –> Coding Sequence –> 3’ UTR –> PolyA Tail

85
Q

Which regions of pre-RNA are spliced out but only in eukaryotes

A

Introns

86
Q

Splicing is specific to eukaryotic transcription, T or F

A

T

87
Q

How can splicing explain how the same gene can produce different proteins when translated

A

The mRNA transcript can be spliced in different ways which accounts for differences in the proteins produced

88
Q

Explain how splicing occurs

A

The 2’ OH of an adenine branch site attacks the phosphodiester bond on guanine donor site. Cleavage at the donor site results in the formation of lariat. Next a 3’ OH in the guanine donor site attacks phosphodiester bond on a guanine acceptor site freeing the lariat which is then degraded

89
Q

What is the name given to the machinery that carries our RNA splicing and what does it consist of

A

Spliceosome – a nuclear complex made up of about 150 proteins and 5 RNAs

90
Q

What is meant by SnRNPs and what do they consist of

A

Small nuclear ribonucleo proteins are structures that make up the spliceosome apparatus. They consist of small nuclear RNAs and proteins

91
Q

What are the three functions of snRNAs

A

Recognise 5’ donor and branch sites, bring sites together and catalyse cleavage

92
Q

Describe the synthesis of the 5’ cap in eukaryotes

A

The 5’ cap is present in all eukaryotic mature mRNAs. Its consists of a methyl guanosine trisphosphate cap added to the first nucleotide. The 5’-5’ linkage is unusual and provides stability to the mRNA. The 5’ cap is also required for binding of the eukaryotic initiation factors. The 5’ cap is added when the mRNA is around 20-40 nucleotides long and begins to emerge from RNA polymerase

93
Q

Which end of the mRNA strand is polyadenylated

A

3’ end

94
Q

What is the purpose of the polyA tail

A

The polyA tail serves as a signal to stop translation

95
Q

Explain RNA polymerases role in synthesising the polyA tail

A

RNA polymerase contains a tail that is highly phosphorylated. The negative charge of these phosphates resembles the RNA backbone negative charge. This serves as a docking point for RNA binding proteins which bind to particular RNA sequences known as polyA signals (AAUAAA). Cleavage stimulating factor (Cstf) and cleavage/polyadenylation specific facto (CPSF) jumps off polymerase II when this sequence is detected and bind to the polyA signal and cleave the RNA. This allows PolyA polymerase to synthesise a polyA tail

96
Q

PolyA tails can be up to 200 residues in length, T or F

A

T

BMS242 Cell and Molecular (26 decks)

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