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CHEM141 > DNA Transcription And Translation > Flashcards

DNA Transcription And Translation Flashcards

1
Q

How does amplification happen in protein synthesis?

A

1-2 copies of gene in a cell

Several copies of same RNA can be made

Several protein molecules are then made from each RNA

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2
Q

Why is the 3D shape of RNA hugely varied?

A

Because RNA is usually single stranded, forming a wide variety of shapes

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3
Q

What difference is there between RNA polymerase and DNA polymerase?

A

RNA polymerase can initiate RNA chain growth without a primer

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4
Q

What is the non-coding strand also known as?

A

The template strand

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5
Q

What is transcription the process of?

A

DNA —> RNA

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6
Q

What do mRNAs do?

A

Code for proteins

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7
Q

What do rRNAs do?

A

Form the core of the ribosome’s structure and catalyse protein synthesis

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8
Q

What do miRNAs do?

A

Regulate gene expression

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9
Q

What do tRNAs do?

A

Serve as adaptors between mRNA and amino acids during protein synthesis

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10
Q

What important promoter region is present in bacteria and eukaryotes?

A

TATA box

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11
Q

What’s the reason for having 2 promoter regions in bacterial DNA?

A

Second promoter region - 35BP away from start site - gives directionality of synthesis

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12
Q

In which strand does the promoter sequence lie in?

A

Promoter sequence sits in the coding strand

RNA polymerase then reads the opposite - template - strand to create RNA chain homologous in sequence to coding strand

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13
Q

What’s the key difference between eukaryotic and prokaryotic systems with respect to RNA?

A

There are multiple RNA polymerase in eukaryotic systems

Bacteria have 1 RNA polymerase

Eukaryotes have 3

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14
Q

What genes do the 3 different RNA polymerases transcribe in eukaryotes?

A

RNA Poly l - most rRNA genes

RNA Poly ll - all protein-coding genes, miRNA genes, plus genes for other non-coding RNAs

RNA lll - tRNA genes

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15
Q

What RNA polymerase variant synthesises mRNA?

A

RNA polymerase ll

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16
Q

What further complexes transcription in eukaryotes?

A

Larger number of accessory proteins needed for RNA polymerase

Much more elaborate control of transcription mechanism - JUNK DNA

Chromatin packing consideration is needed

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17
Q

Where does translation occur?

A

In cytoplasm

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18
Q

Where does transcription occur?

A

In nucleus

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19
Q

How far up stream is the TATA box in eukaryotes/prokaryotes?

A

Eu - 25 nucelotides

Pro - 10 nucelotides

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20
Q

Why are phosphates added to RNA polymerase ll in transcription?

A

Phosphates are added to RNA-Pll to disengage from transcription factors so transcription can begin

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21
Q

What’s the reason for the 90˚ kink that happens at TATA box?

A

Partial unwind of DNA which leads to recognition

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22
Q

How is a RNA molecule post-transcriptionally processed to form mRNA?

A

Capping factors are attached to 5’ end early in synthesis - after 25 nucleotides

Polyadenylation factors added to 3’ end

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23
Q

Why is mRNA capped and polyadenylated?

A

Increases stability

Aid export from nucleus to cytoplasm

Protein synthesis machinery can check mRNA to ensure it is fully intact - both sites must be present

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24
Q

What splices introns out?

A

Spliceosome - key component is some catalytic RNA

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25
Q

When does splicing begin?

A

Splicing occurs after capping and whilst mRNA continues to grow.

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26
Q

When does splicing cease?

A

Either just before or just after polyadenylation occurs

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27
Q

Why is splicing not a wasteful process?

A

Because mRNA transcripts can be spliced in different ways to produce different proteins

(Alternative splicing)

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28
Q

What does alternative splicing explain?

A

That we have 100,000 proteins but only 24,000 genes

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29
Q

What do transcription regulators control?

A

They control how often transcription is initiated

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30
Q

Where do transcription regulating proteins bind?

A

Usually at the major groove

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31
Q

How many interactions are formed between TRPs and the DNA sequence?

A

10 - 20

(Strong net force)

32
Q

What are synthetic polyamides and what is their purpose?

A

They are molecules capable of recognising and binding to specific base pairs

Anticancer agents

33
Q

Where are synthetic polyamides capable of binding?

A

Capable of minor groove binding

34
Q

What functional group are present in synthetic polyamides?

A

Heterocyclic rings

35
Q

What is the MoA of synthetic polyamides?

A

Molecule attaches to DNA like a clamp - each arm binds to one DNA strand each

Bind where transcription factor usually would

36
Q

What are the potential uses of short oligonucleotides?

A

Antiviral and anticancer potential

37
Q

What are the benefits of hurt short oligonucleotides?

A

Highly specific - low doses result in fewer side effects than conventional protein inhibition

38
Q

What are the disadvantages of short oligonucleotides?

A

Section of mRNA chosen must be exposed - poor absorption and susceptible to metabolism

39
Q

What do short oligonucleotides do?

A

They are used to block coded messages carried by mRNA

40
Q

What is redundant coding?

A

Where multiple codons code for the same amino acid

41
Q

What are the 3 stop codons?

A

UAA

UAG

UGA

42
Q

What is always the start codon?

A

AUG - methionine

43
Q

Since all proteins start with AUG, do all proteins start with methionine?

A

No, Methionine is post-translationally removed if necessary

44
Q

Where do tRNAs vary at?

A

At the anticodon and are attached to an amino acid

45
Q

How long are tRNAs roughly?

A

≈ 80 nucleotides long

46
Q

How many segments do tRNAs consist of?

A

4 short segments form double helical sections

Clover leaf shape

47
Q

What are the 2 unusual bases which tRNAs contain?

A

Dihydrouridine (D)

Pseudouridine (Ψ)

48
Q

When are D and Ψ created?

A

They are created by chemical modification post-transcriptionally

49
Q

Why is the anticodon region important in tRNAs?

A

Because it is the region that binds to mRNA

50
Q

How does redundant coding relate to tRNA?

A

Some aa have more than one tRNA it can attach to

Some tRNAs are made so they require accurate base pairing only at first two positions

51
Q

How are tRNAs charged with amino acids?

A

Each amino acid is linked to it own aminoacyl-tRNA synthase protein.

The synthase recognises the correct tRNA for its amino acid.

This process is called charging and forms high energy bonds

52
Q

What happens after charging?

A

The tRNA anticodon forms base pairs with the codon on the mRNA

53
Q

What is the combined mass of the large and small subunit of ribosomes?

A

10^6 daltons

Standard protein is ≈ 30,000 daltons

54
Q

What way do ribosomes read mRNA?

A

5’ —> 3’ manner - synthesised from N-terminus to C-terminus

Uses 5’ - cap as signal

55
Q

Why is charging important?

A

Because tRNA can’t bind mRNA without being charged first by correct amino acid

56
Q

How many RNA molecules are in ribosomes?

A

4

57
Q

What’s the purpose of the small ribosomal subunit?

A

Matches the tRNA to the codon in mRNA

58
Q

What’s the purpose of the large ribosomal subunit?

A

Catalyses the formation of the peptide bonds during polypeptide chain growth

59
Q

What’s the rate of decoding in eukaryotes?

A

2 amino acids per second

60
Q

What’re the 3 site in ribosomes?

A

A site - Aminoacyl-tRNA site

P site - Peptidyl-tRNA site

E site - Exit site

61
Q

What’s important to remember about the 3 factors of ribosomes?

A

Only 2 sites are ever filled at anytime one time

62
Q

What’s the benefit of polyribosomoes?

A

Many ribosomes can read the same mRNA strand at once

Amplified

63
Q

What do initiation factors do?

A

They help the small subunit locate the starting point of mRNA

5’ cap is recognised by small subunit

64
Q

What happens once 5’ cap has been recognised?

A

Small subunit and initiation factors move along mRNA until start codon is reached

65
Q

What happens once AUG has been reached?

A

Translation initiation factors dissociate

Large subunit binds - forms around mRNA and tRNA

Translation begins

66
Q

What is the first step once translation begins?

A

The correct charged tRNA enters in the A site and binds to the mRNA for long enough for the mechanism to work

Large subunit catalyses the first peptide bond

Trial and error - slow

67
Q

What happens once first peptide bond is formed?

A

New peptide bond is in A site which is then translocated into the P site - middle

The process continues

68
Q

How does the growing peptide chain move from the A site to the P site?

A

The large subunit translocates across to move peptide chain into the P site

The small subunit also then translocate to get back into standard position

The previous tRNA is now in the E site and is ejected

69
Q

What happens in the final phase of protein synthesis?

A

The binding of release factor to an A-site bearing a stop codon terminates translation

70
Q

What does binding of the release factor do?

A

It alters the activity of the peptidyl transferase in the ribosome, catalysing the addition of water instead of an amino acid

This frees up the carboxyl-end of the peptide

71
Q

What is tetrecycline’s specific effect?

A

Blocks binding of aminoacyl-tRNA to A site of ribosome

72
Q

What’re the specific effects of streptomycin?

A

Prevents the transition from initiation complex to chain elongation

Also causes miscoding

73
Q

What’s chloramphenicol’s specific effect?

A

Blocks the peptidyl transferase reaction on ribosomes

74
Q

What’s the specific effects of cycloheximide?

A

Blocks translocation reaction on ribosomes

75
Q

What’s the specific effect of rifamycin?

A

Blocks initiation of transcription by binding to RNA polymerase

CHEM141 (12 decks)

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