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Flow Of Genetic Information > Transcription > Flashcards

Transcription Flashcards

1
Q

What types of RNA are there?

A

rRNA (ribosomal RNA)
tRNA (transfer RNA)
Non-coding RNA
mRNA (messenger)

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2
Q

What is rRNA?

A

Ribosome RNA that forms basic structure of the ribosome also catalyses protein synthesis

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3
Q

What is tRNA?

A

Transfer RNA is an adaptor between mRNA and amino acids. Carries amino acids when acetylation.

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4
Q

How big is a replication bubble?

A

12-14bp long

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5
Q

What are the 3 main steps of transcription?

A

Recognition/initiation
Elongation
Termination

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6
Q

What are the types transcriptional controls in prokaryotes genes?

A

Constitutive genes
Regulated genes
Operons

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7
Q

What is a constitutive gene?

A

Transcribed continually also known as house keeping genes

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8
Q

What are regulated genes?

A

Switches on enzymes genes which are need in certain circumstances

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9
Q

What are operons?

A

Genes encoding for the same protein pathway located adjacent to each other. Transcribed into polycistronic mRNA

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10
Q

What is polycistronic mRNA?

A

A length of mRNA which has no introns but encodes multiple Proteins

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11
Q

What are bacterial promoters?

A

Site of transcription initiation in DNA. In bacteria it’s known as the Prinbow box.

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12
Q

What is the prinbow box?

A

Promoter in bacterial DNA that polymerase binds to. Can be found at -10 and at -35 as well. It’s code is TATAAT it’s asymmetric so polymerase knows which way to move.

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13
Q

What is down mutation in respect to promoters?

A

Reduces promoter efficiency

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14
Q

What is an up mutation in respect to promoters?

A

It’s a mutation that causes a positive effect and increase in promotion

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15
Q

What subunits are in RNA polymerase in prokaryotes?

A

Is a holoenzyme that constists of 2xalpha a beta and beta’ which is the core enzyme and a sigma factor as well.

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16
Q

What ions does DNA polymerase contain to have an affinity for negative DNA?

A

It contains mg2+ and Zn2+ that cause the high affinity

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17
Q

What is important about the sigma subunit of a polymerase?

A

It causes the polymerase to bind at certain promoters. Creates control. But not all polymerases need them only 1/3 have them.

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18
Q

Name three alternative sigma subunits?

A

Sigma 70- general use
Sigma 32- high temp
Sigma 54- presence if nitrogen

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19
Q

What is a negative transcription regulator?

A

Transcriptional repressor

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20
Q

What is a positive transcription regulator?

A

Transcriptional activators

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21
Q

What is the control of lac repressor?

A

Lac repressor would bind to the operator site l that overlaps transcription start site preventing transcription. When allolactose binds a conformational change occurs removing lac repressor from DNA.

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22
Q

What is the lac repressor?

A

It’s a repressor that is a tetramer (made of two dimers). Each dimer binds to one operator site.

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23
Q

How does the lac repressor work?

A

Forms a loop in DNA preventing binding to an operator site.

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24
Q

Types of intrinsic terminators?

A

A run of A and T bases

A palindromic sequence

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25
Q

How does AT rich regions cause termination?

A

Due to weak bonding causes RNA and DNA to split

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26
Q

How does palindromic sequences cause termination?

A

Forms stem and loop pausing polymerase to pause. RNA DNA hybrid unravels.

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27
Q

What does the Rho protein cause?

A

Rho protein binds to RNA and moves along once it catches up with polymerase. Once caught up cause RNA DNA separation.

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28
Q

What are 3 levels of transcriptional control in eukaryotes?

A

Binding of polymerase (TFs)
Histones/chromatin remodelling
DNA methylation

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29
Q

What is the eukaryotic polymerase?

A

Polymerase 3

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30
Q

What is Polymerase 3?

A

A structure with 12 subunits, but needs transcription factors otherwise can’t initiate transcription

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31
Q

How do transcriptional activators help?

A

Are promoters that Bind polymerase 3 help regulate specificity of tissues

32
Q

Where do transcription factors bind?

A

They bind in the major groove

33
Q

What is the core promoter in eukaryotes?

A

TATA box

34
Q

How does initiation of DNA synthesis occur in eukaryotes?

A

Polymerase 2 binds promoter separates DNA allowing it to bind to the TATA box.

35
Q

What is PIC?

A

Pre-initiation complex

36
Q

What makes up the PIC?

A

Tf2- A,B,D,E,F,H

37
Q

How does elongation of transcription occur?

A

The C terminal of polymerase is phosphorylated causing conformational change tightening it’s grip. Elongation factors associate to help process RNA- increase elongation rates

38
Q

What are two parts of TATA promoter?

A

Imitator (INR)

downstream promoter element

39
Q

What sequence does Downstream promoter element (DPE) have?

A

AGAC- recognised by TF2 allowing pre initiation complex to bind

40
Q

Where is downstream promoter element located?

A

+28-+32

41
Q

TFs can have multiple binding domains?

A

DNA activation domains

DNA inhibition domain

42
Q

Types of binding domains?

A

Zinc fingers
Helix-turn-helix
Basic binding domain

43
Q

What are zinc fingers?

A

Zinc fingers are a loop of 23 amino acids. That act as transcription repressor or activators
Zinc doesn’t directly interact with DNA

44
Q

What are helix turn helix proteins?

A

Proteins made of 60 amino acids, made of 3 helices. One lays in major groove other two point put away from DNA

45
Q

What is an example of a basic binding domain?

A

Leucine zippers

46
Q

Why can’t basic binding domains bind?

A

As they are basic they must be dimers to bind.

47
Q

How do Transcription factor domains work?

A
  • through direct interaction with PIC

- through recruitment of co activators

48
Q

How are histones made?

A

They’re made of 2 domains globular and the tail

49
Q

What is an HAT?

A

Histone acetylases

50
Q

How does a histone acetylase work?

A

It acetylates the N-terminal lysine of histones neutralising the +ve charge. This causes it to open up allowing TFs and RNA pol 2 to get to DNA.

51
Q

What are inhibitory domains?

A

Region of TFs involved in repressing transcription. Binds DNA and blocks TFs with activator domains from binding.

52
Q

How do inhibitory domains work?

A

By binding to the PIC

Or through co-repressor

53
Q

How do co-repressors work?

A

They alter chromatin structure HDATs histone deacetylases. They remove acetyl groups from lysine restoring +ve charge closing chromatin down.

54
Q

What things occur in post-transcriptional processing?

A
  • addition of a 5’ cap
  • 3’ processing and polyadenylation
  • splicing
  • transport
55
Q

Why is there the addition of a 5’ cap to mRNA?

A

For protection and to mark it as mRNA

56
Q

Why is the end of mRNA polyadenylated?

A

Marks the end of mRNA and for protection

57
Q

How does splicing occur?

A

By 2 transesterfication reactions

58
Q

What is the mechanism of splicing?

A

1) cleavage at 5’-hydroxyl group of branch point attacks 5’splice site intron folds back in itself binding between A and G.
2) 3’ OH of exon attacks 3’ splice site. ligase rejoins exons

59
Q

What is the spliceosome?

A

Splicing complex that assembles comprise of 5xRNA and 150 proteins

60
Q

What are the classes of RNA splicing?

A

Nuclear pre-mRNA splicing
Group 2 self splicing introns
Group 1 self splicing introns

61
Q

What is a self splicing intron?

A

Two transesterfication reactions encoded by the intron making it a ribozyme. And removing it from DNA

62
Q

What proteins help splice site selection?

A

S-R proteins, they bind Exonic splicing enhancers (ESEs). They recruit splicing machinery to nearby splice sites

63
Q

What it alternate splicing?

A

This is the fact that RNA can be spliced in different ways to result in different proteins from the genes.

64
Q

What was the first gene known to have alternate splicing?

A

Calcitonin and calcitonin gene related peptide

65
Q

How many exons are in calcitonin gene?

A

6

66
Q

What Exon’s does each protein use in the calcitonin/calcitonin gene related peptide?

A

Calcitonin- 1,2,3,4

Calcitonin gene related peptide- 1,2,3,5,6

67
Q

What is RNA editing?

A

Is process by which information changes of mRNA, like mutations but on purpose.

68
Q

Example of RNA editing?

A

Apoliprotein-B contains a CAA codon that in intestine changes to a UAA (stop codon). This means in the liver it codes for cholesterol and triglyceride uptake where as in intestine it’s for dietary lipid uptake.

69
Q

What is the genetic disorder thalassemia?

A

A disorder where there is decreased production of one globin chain found in haemaglobin.

70
Q

What is the 5’ cap?

A

7-methyl-guanosine

71
Q

When is RNA capped?

A

As soon as it exits RNA polymerases exit tunnel

72
Q

What is the mechanism of 5’ capping?

A

1) RNA triphosphotase removed gamma phosphate at 5’ end
2) guanylyltransferase removes gamma and beta phosphate of GTP. GMP is then added to RNA in reverse
3) methyltransferase add methyl group in 7th position of guanine

73
Q

Poly-A binding proteins do what?

A

They bind it the poly-A tail and help to stabilise the RNA, transcription, nuclear export and localisation in the body

74
Q

Example of the effect of Poly-A tails?

A

BDNF-brain derived neurotrophic factor. Produced in cell body with two isoforms (long poly A and short). Ones with long tails are transported to extremities short are not.

75
Q

How is RNA transported out of the nucleus?

A

REF proteins that bound at exon junctions during splicing remain attached. They’re targeted by transport proteins and help to export mRNA 5’ side first.

Flow Of Genetic Information (4 decks)

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