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asdfghjmak 2 > P1 L3 > Flashcards

P1 L3 Flashcards

1
Q

What is the central dogma of molecular biology?

A

It states that information cannot be transferred back from protein to nucleic acid and that Information can only be passed from nucleic acid to nucleic acid/protein

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2
Q

What is the role of RNA polymerase in transcription?

A

RNA polymerase uses DNA as a template to synthesize RNA.

DNA ->RNA

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3
Q

What is transcription?

A

Synthesis of mRNA, copy of DNA

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4
Q

What is ribosomal translation?

A

The conversion of RNA into the specific protein sequence

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5
Q

What is important to note about the secondary RNA structure

A

The pairing of the bases is different.
The loop forms the unpaired region
The helix with the loop is called a hairpin.

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6
Q

Describe the initiation of transcription

A

Initiated at promoters

RNA synthesis is carried out by the RNA polymerase.
5‘ -> 3’
The sigma factors are only needed for initiation here because they recognise the promoters.
It interacts with the promoter

No primer is necessary and no free -OH end.
errors not corrected

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7
Q

How is the promoter constructed?

A

2 regions
-The short AT-rich region (-10 region) -> 10 base pairs upstream of the transcription start site

  • The -35 sequence which is 35 base pairs above/upstream of the start site.
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8
Q

define upstream

A

closer to 5’ end of RNA

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9
Q

What are the properties of the promoter?

A

The sigma factors recognise the specific promoter sequences.

Only one DNA strand is transcribed for each gene.
The genes are on both DNAs but at different locations.

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10
Q

Where does the alfa subunit bind to the promoter and what is its function?

A

The alfa subunit binds at the -35 region and stabilises the binding of the RNA polymerase to the DNA

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11
Q

What are the steps of transcription

A

1) The RNA polymerase binds the sigma factor
2) The RNA polymerase holoenzyme recognises the promoter sequences
3) The DNA double helix opens and RNA synthesis normally starts opposite A or G (+1 side)
4) The sigma factor drops
5) The RNA polymerase (helicase) develops the DNA double helix
6) RNA synthesis continues up to the terminator

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12
Q

Which are the 3 main channels of RNA polymerase

A

-the nucleotide entry channel
-active site channel
-exit channel

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13
Q

How is the TEC constructed?

A

Transcription elongation complex.
The RNA polymerase opens the DNA double helix and forms the ‘transcription bubble’.

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14
Q

What is the significance of the transcription bubble formed during transcription?

A

It is where the DNA double helix unwinds for RNA synthesis.

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15
Q

How is transcription terminated?
(bacteria)

A

There are 2 terminators:
-Intrinsic (Rho-independent)
-Rho-dependent

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16
Q

how does the intrinsic terminator function?

A

It is Rho-independent and consists of 2 complementary parts

The inverted repeating unit forms a hairpin.

The A’s of the template are ‘stretched’ so that a series of U’s are synthesised into the RNA.

These A-U base pairs in the DNA-RNA hybrid are less stable.

It forms a hairpin structure that destabilizes the DNA-RNA hybrid.

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17
Q

Describe the Rho-dependent terminator

A

ATP-dependent
Rho is a DNA-RNA helicase -> separates/unwinds the RNA-DNA duplex
The Rho protein forms a ring (with 6 identical subunits) around the RNA at the rut site
The ring moves slowly along the RNA 5‘ -> 3’

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18
Q

Why does the Rho protein move so slowly along the RNA?

A

Because it might otherwise encounter the RNA polymerase which occasionally pauses.
and once it does transcription stops

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19
Q

What happens when RNA polymerase reaches a terminator sequence?

A

Transcription stops, and RNA synthesis is terminated.

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20
Q

What is the start codon in mRNA?

A

AUG

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21
Q

How is a gene that codes for proteins structured?

A

The coding region begins at the start codon (ATG sequence) and ends at the stop codon.
This region, that encodes protein, is called open reading frames (ORFs)

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22
Q

What are the components of protein translation?

A

The ribosomes need a signal to initiate transcription -> The ribsome binding site is located upstream of the start codon. Further ahead is the ‘transcription start’ and the promoter.
at the very opposite end, by the stop codon, is the transcription terminator

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23
Q

Properties of the operon

A

Collection of genes that are read/transcribed by the promoter.
Proteins that are responsible for the same functionare usually encoded by the same operon.
It has only one transcription terminator.
mRNA -> polycistronic RNA

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24
Q

What is located upstream of the start codon?

A

The transcription start and the promoter

25
Q

What is the significance of polycistronic mRNA in bacteria?

A

It allows multiple proteins to be encoded and translated from a single mRNA molecule.

26
Q

What is the role of tRNA in protein synthesis?

A

tRNA transfers amino acids to the ribosome during translation.

27
Q

What is the typical error rate of RNA polymerase during transcription?

A

approx 10^-5

28
Q

What are exoribonucleases?

A

Enzymes that degrade RNA from 3‘ -> 5’ or from 5‘ -> 3’

29
Q

What are endonucleases?

A

They cleave the RNA molecules from the centre outwards

30
Q

What influences the stability of RNA?

A

This is encoded in its sequence. Highly structured: ribosomal RNA and transfer RNAs are very stable and persist over several cell divisions
Bacterial mRNAs are very unstable

31
Q

Which 3 types of rRNA do bacterial ribosomes have?

A

16S, 23S and 5S

32
Q

How are ribosomal RNAs synthesized?

A

As a long precursor RNA containing all three rRNAs

33
Q

Which sequence is found at the 3’ end of all tRNAs?

A

CCA

34
Q

What are the special codons in the genetic code?
start + stop

A

Start (AUG) and Stop (UAA, UAG, UGA) codons

35
Q

What are the key steps in the central dogma of molecular biology?

A

DNA/RNA replication
Transcription (DNA to RNA)
Translation (mRNA to Protein)
Reverse transcription (RNA to DNA)

36
Q

Define translation

A

messenger RNA is template for protein synthesis

mRNA ->Protein

37
Q

What is the role of codons in translation?

A

Three-pack of nucleotides that decode the mRNA by pairing with the corresponding anticodon of the tRNA.

It has 3 sites: E(exit), P(peptidyl), A(aminoacyl)

38
Q

Role of mRNA in translation

A

encodes protein sequence in ‘codons’

39
Q

Role of tRNA in translation

A

carries specific amino acid, recognises mRNA codons by basepairing

40
Q

Role of ribosome in translation

A

moves along mRNA (5-3) and links amino acids.. has the 3 sites

41
Q

How are peptide bonds formed?

A
  • Formed during the reaction of an amino and a carboxyl group of two amino acids: water is split off and the OH group of a carboxyl group is replaced by an NH2 group
42
Q

What are ribosomes made of? (bacteria)

A

Made up of over 50 different proteins and 3 different RNAs

43
Q

What are the 70s ribosomes made of?

A

Of 2 subunits:
-30S: consists of a 16S rRNA
-50S: consists of a 23S and a 5S rRNA

44
Q

What is the 23S rRNA used for?

A

RNA enzyme -> ribozyme

It is a peptidyltransferase that connects two amino acids

45
Q

What does the aminoacyl-tRNA synthetase do?

A

It joins the tRNA to the amino acid.
Specifically recognises only one amino acid and one type of tRNA. It recognises the structure of the tRNA as well as its anticodon.

46
Q

How is the genetic code structured?

A

With a series of 3 base pairs of codons.

47
Q

Can several codons code for the same amino acid?

A

Yes, there are 64 codons but only 20 amino acids

48
Q

What are the wobble bases?

A

It allows pairing that does not follow Watson-Crick base pair rules
Fundamental for RNA secondary structure and translation
G-U
I-U
I-A
I-C

49
Q

What is the role of hypoxanthine (I) in tRNA?

A

It can base pair with uracil, adenine, and cytosine

50
Q

How is translation initiated?

A

The small ribosomal subunit binds to the mRNA at the start codon. The tRNA binds to the A site. Methionine (amino acid) and amino acid at the A site form peptide bond

Initiator tRNA located in P site of ribosome

51
Q

What does the Shine-Dalgarno sequence do?

A

It is complementary to 16S rRNA and helps in ribosome binding

52
Q

How does the elongation of translation proceed?

A
  1. the ribosome always moves 3 nucleotides along the mRNA (5‘->3’)

The tRNA comes via the A site and binds to the elongation factor EF-Tu. In the process, the now flat-paired previous tRNA is separated.

The elongation factor is cleaved/split to GDP upon hydrolysis of GTP on the EF-Tu.

  1. the EF-G is added and moves the tRNA and mRNA from A to P site
53
Q

What happens during peptide bond formation in translation elongation?

A

The polypeptide is transferred from the tRNA in the P site to the tRNA in the A site

54
Q

How does the termination of translation work?

A

No suitable tRNA for the termination codons.
bind of Release factors -> proteins that are needed that recognise the termination codons and trigger the release of the polypeptides of the tRNA.

55
Q

What are polysomes?

A

Several ribosomes arranged in a chain that translate the same mRNA.

56
Q

How are proteins folded?

A

Chaperones (other proteins) are responsible for this

expression inc during stress

57
Q

How do Gram(-) bacteria move protein across the membrane to the outside?

A

With specialised secretion systems, often including virulence factors

58
Q

What is the role of the Tat secretion pathway?

A

It transports folded proteins and complexes from cytoplasm to periplasm without unfolding

asdfghjmak 2 (8 decks)

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