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genetics - heather > Lecture 1 > Flashcards

Lecture 1 Flashcards

1
Q

Originally people through that DNA directly encoded proteins. Why is this wrong?

A

DNA is too stable to be the intermediate. The unstable intermediate is RNA. DsDNA is converted to RNA- bidirectional.

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2
Q

Death cap mushroom

A

Amanita phalloides- causes death by inhibiting the process of transcription. Produces alpha amanitin- transcription inhibitor.

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3
Q

Why is transcription and translation simpler in prokaryotes?

A

Everything occurs in one compartment.

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4
Q

What 3 things do you need for transcription to occur?

A

DNA template for complementary base pairing
4 ribonuclease triphosphates (ATP, CTP, GTP, UTP)
RNA polymerase

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5
Q

What is one advantage of using RNA polymerase?

A

It does not need a primer

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6
Q

Describe DNA

A 
Deoxyribose 
no OH on 2'
AGCT
Nucleotides joined by phosphodiester bonds
double stranded
secondary structure is a helix
stable
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7
Q

Describe RNA

A 
Ribose
presence of OH on 2'
AGCU
Nucleotides joined by phosphodiester bonds
single stranded
Many secondary structures
Easily degraded
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8
Q

Ribosomal RNA

A

In the cytoplasm.

Role: binding of mRNA & tRNA and protein synthesis.

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9
Q

Messenger RNA

A

In the cytoplasm.

Role: carrier of gene sequence

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10
Q

Transfer RNA

A

In the cytoplasm.

Role: adaptor between mRNA and protein sequences- involved in translation

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11
Q

Mircro RNA

A

In the cytoplasm and nucleus.

Role: regulates transcription and translation

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12
Q

Primary and secondary structure of RNA

A

RNA has a primary structure (A) and a secondary structure (B)

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13
Q

Common RNA secondary structures

A

Tetraloops
Pseudoknots
Stem-loops

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14
Q

RNA polymerase clamp

A

Keeps the polymerase anchored to the DNA. Clamp made up of jaws.
DNA is held sideways with a sharp bed to its left as it exits the polymerase. Bending helps to force the two strands apart.
rNTPs (ribonucleotide triphosphates) enter the active site at the same side that DNA is pulled through, but through a secondary channel. mRNA leaves from the back of the polymerase and the flap ensures that mRNA is retained.

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15
Q

5 Subunits of bacterial RNA polymerase

A

two copies of alpha
single copy of Beta
Single copy of Beta prime
Single copy of omega

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16
Q

What does the core enzyme of Bacterial RNA polymerase catalyse?

A

the elongation of the RNA molecule by the addition of RNA nucleotides

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17
Q

How is the holoenzyme formed

A

The sigma factor joins the core to form the holoenzyme which is capable of binding to a promoter and initiating transcription.

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18
Q

Omega subunit function in bacterial RNA polymerase

A

stabilises the enzyme

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19
Q

Three stages of transcription

A

Initiation
Elongation
Termination

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20
Q

INITIATION

What region does RNA polymerase bind?

A

To the promoter region as directed by the protein-sigma factor.

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21
Q

INITIATION

What does the promoter region determine?

A

Where to start transcription

Which strand of DNA to transcribe

22
Q

INITIATION

Which strand is the template and where does transcription begin?

A

Either strands can be templates
Part of each promoter region is the initiation site where transcription begins. DNA polymerase will open a bubble to start transcribing genes.

23
Q

INITIATION

Describe promoter regions in bacterial DNA.

A

Promoters of all bacterial genes have regions of similarity. These consensus sequences are similar in all genes studied. They are hexameric (6 bases) sequences at -35 and -10 bases upstream of the start of transcription.

24
Q

INITIATION

What is the commonly first transcribed base?

A

Adenine

25
Q

INITIATION

Where does RNA polymerase holoenzyme bind?

A

The RNA polymerase holoenzyme (including the sigma factor) recognises the consensus sequences at -35 and -10 and binds.
The sigma factor recognises and binds to the -35 consensus to anchor the polymerase

26
Q

INITIATION

What is the advantage of the sigma factor?

A

Allows RNA polymerase to bind more tightly with specific connections.

27
Q

INITIATION

How do the sigma and beta prime factor work together?

A

They separate the two strands to make a bubble.

28
Q

INITIATION

Where does RNA polymerase start to unwind the DNA?

A

At the Pribnow box (-10) and melting continues forward to cover the start site.

29
Q

INITIATION

RNA polymerase holoenzyme slides along DNA but what happens when it recognises the promoter of a gene?

A

Promoter of gene is recognised through a sigma factor and the polymerase binds tightly to the DNA

30
Q

INITIATION

What happens once the holoenzyme has bound to the active site?

A

The RNA polymerase holoenzyme and DNA undergo a series of conformational changes that consist of opening the DNA up and positioning it in the enzyme’s active site and then tightening the grip of the enzyme around it so it does not become detached before transcription is finished.

31
Q

ELONGATION

How does synthesis start?

A

Opening of the double helix. DNA unwinds 10 base pairs at a time.

32
Q

ELONGATION

What direction does RNA polymerase read the template strand?

A

3’ to 5’ direction

33
Q

ELONGATION

What direction are the nucleotides added?

A

5’ to 3’ direction

34
Q

ELONGATION

What molecules are used as substrates?

A

Ribonucleoside triphosphates

Two phosphate froups are removed from each substrate molecule to release energy to drive the polymerase reaction

35
Q

ELONGATION

What links the nucleotides together in a chain?

A

Phosphodiester bonds

36
Q

ELONGATION

What happens once the mRNA has begun to be synthesised?

A

The sigma factor is released from the holoenzyme and RNA polymerase moves down the chain in a more efficient manner.

37
Q

ELONGATION

When does RNA polymerase unwind DNA?

A

As it moves along the DNA it makes a transcription bubble.

38
Q

ELONGATION

How does polymerase make sure the mRNA are correct matches?

A

Proof reading function

39
Q

ELONGATION

How quickly do mutations occur?

A

Mutations occur in mRNA at a rate of 10^4 to 10^5 bases, this is not detrimental as many copies of RNA are made and RNA has a short lifespan so is not as harmful as DNA mutations

40
Q

TERMINATION

What specifies termination of transcription?

A

Particular base sequences

41
Q

TERMINATION

When must transcription stop?

A

Once the coding sequence has been transcribed into mRNA

42
Q

TERMINATION

When must the RNA polymerase be released?

A

The RNA polymerase releases the growing chain when it encounters a termination signal. The terminator is transcribed and all of the sequence appears in the mRNA.

43
Q

TERMINATION

What can termination signals occur as?

A

Formation of a stem and loop secondary structure through H bonding between Gs and Cs
Protein binding - Rho dependent terminators

44
Q

TERMINATION

How does the hairpin structure form?

A

The inverted repeat sequence of the terminator sequence means that the synthesised RNA molecule will pair to itself and form a hairpin.

45
Q

TERMINATION

What is the purpose of the hairpin structure?

A

Formation of the hairpin helps to pull the transcript away from the RNA polymerase active site. The RNA chain is released. The hairpin is stable so its formation is thermodynamically favoured

46
Q

TERMINATION

Intrinsic terminators

A

G-C rich stem followed by a run of A’s in the template strand. This produced a run of U residues in the transcript.

47
Q

TERMINATION

Run of U’s

A

A=U pairing has only 2 hydrogen bonds which is weaker than the bonds in the stem loop so it becomes increasingly difficult for RNA-DNA hybrid to stay attached and the RNA gets released.

48
Q

TERMINATION

Flap structure

A

The stem loop structure comes into contact with the flap, movement of the flap contributes towards the breakage of the RNA-DNA hybrid and the ultimate termination of the chain.

49
Q

TERMINATION

Protein binding- Rho dependent termination

A

The Rho protein will attach to the transcript and move along the RNA towards the polymerase, but will never catch the polymerase. Polymerase stalls at the termination site and Rho catches up and breaks the base pairs between the DNA and RNA (helicase enzyme) which stops transcription

50
Q

Why must transcription be controlled?

A

Not all proteins are needed all the time

Controlling transcription avoids energy waste

genetics - heather (8 decks)

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