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B1omed - Molecular biology > Module 7 - From RNA to protein > Flashcards

Module 7 - From RNA to protein Flashcards

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1
Q

Wobble position in tRNAs: what is it and what does it allow for?

A

The third position in tRNA anticodon bonding, unlike the stringent (strict) pairing in the first two positions, allows for looser base pairing (including unconventional bonds) that are weaker than normal bonding

The Wobble’s loose base pairing allows one amino acid to be coded for by several codons.

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2
Q

Chemical modifications in tRNAs before leaving the nucleus: how often does it occur and what are two examples?

A

After transcription, many tRNAs (~10%) undergo chemical modifications

Methylation of guanine (turning NH₂ that bonds with cytosine into NC₂H₆)

Deamination of adenine/guanine into inosine to allow for wobble-base pairing

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3
Q

Prokaryotic wobble bonding:
U binds with -
A binds with -
G binds with -
C binds with -

A

Prokaryotic wobble bonding:
* Adenine, guanine, and inosine
* Uracil and inosine
* Cytosine and uracil
* Guanine and inosine

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4
Q

Eukaryotic wobble bonding:
U binds with -
A binds with -
G binds with -
C binds with -

A

Eukaryotic wobble bonding:
* Adenine, guanine, and inosine
* Uracil
* Cytosine
* Guanine and inosine

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5
Q

Why are there differences between EWB and PWB?

A

The differences in wobble base-pairing interactions between bacteria and eucaryotes presumably result from subtle structural differences between bacterial and eukaryotic ribosomes

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6
Q

The process of linking an amino acid to its tRNA

A

ATP is broken down into AMP + P₂ to supply the reaction of binding the amino acid and AMP, forming an adenylated amino acid

This adenylated amino acid then replaces the hydrogen on the hydroxyl on the sugar end of the tRNA molecule, forming an ester linkage

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7
Q

Why do tRNA amino acids have extremely high accuracy?

The first part of tRNA proofreading

A

The correct amino acid has the highest affinity for the active-site pocket of its synthetase active site, this is the initial check of accuracy as larger amino acids will simply not fit

However, accurate discrimination between two similar amino acids, such as isoleucine and valine
(which differ by only a methyl group) can be challenging so there is a secondary check

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8
Q

Why do tRNA amino acids have extremely high accuracy?

The second part of tRNA proofreading

A

When tRNA binds the synthetase, it tries to force the amino acid into a second pocket in the synthetase, the precise dimensions of which exclude the correct amino acid but allow access to closely related amino acids. If an amino acid enters this editing pocket, it is hydrolyzed from the AMP (or from the tRNA itself if the aminoacyl-tRNA bond has already formed) and is released from the enzyme.

This hydrolytic editing, which is analogous to exonucleolytic proofreading by DNA polymerase, raises the overall accuracy of tRNA charging to
approximately one mistake in 40,000 couplings

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9
Q

The Nirenberg-Matthaei experiment: breaking the genetic code

A

Labelled amino acids added along with poly-uracil tRNAs (UUU) into a bacterial extract that was ready for translation

It was found that, after isolating polypeptides, only phenylalanine made a labelled polypeptide: the tRNA code of UUU codes for phenylalanine

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10
Q

Stop codons

A

UAA, UGA, UAG

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11
Q

The structure of tRNA and the function of each part

A

Anticodon arm: contains the anticodon of the tRNA

Acceptor arm: binds to an amino acid

T-loop: stability of the tertiary structure

D-loop: acts as a recognition site for aminoacyl-tRNA synthetase, an enzyme involved in the aminoacylation of the tRNA molecule

V-loop: recognition of the tRNA

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12
Q

Prokaryotic ribosomes

A

Made of a large subunit (50s - 23s rRNA, 5s rRNA, and 31 proteins) and a small subunit (30s - 16s rRNA and 21 proteins)

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13
Q

Eukaryotic ribosomes

A

Made of a large subunit (60s - 28s rRNA, 5.8s rRNA, 6s rRNAand ~49 proteins) and a small subunit (40s - 18s rRNA and 33 proteins)

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14
Q

What does the s stand for in ribosome size?

A

Svedberg: a measure of the sedimentation rate of suspended particles centrifuged under standard conditions, giving a shape and size

This explains why the breakdown of the ribosome doesn’t explain its s size: there are complex shapes as well as size in rRNA so it’s folded smaller from bigger subunits

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15
Q

Shine Dalgarno sequences: what are they?

A

Sections of mRNA that interact with the 16s rRNA of the small subunit of the ribosome to signal where initiation should start

Called Kozak sequences in eukaryotes

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16
Q

Roles of the small subunit in ribosomes

A

Allows a binding spot for mRNA, including binding to the initiation site so that translation can begin at the correct point

17
Q

Role of the large subunit in ribosomes

A

Does the protein synthesising, forming peptide bonds between amino acids

18
Q

The four binding sites in ribosomes

A

The mRNA binding site: where the mRNA will bind

Aminoacyl (A) site: where the codon is read and the anticodon will bind to, bringing an amino acid

Peptide (P) site: where the polypeptide is held

Exit (E) site: where tRNAs give their chain to the tRNA in the P site then detach from the ribosome to bond with another amino acid

19
Q

Initiation factors for translation: what are the three, and what is the initiating tRNA?

A
  • IF1 – Blocks A site to tRNAᶦ-met, inhibiting premature 30S and 50S interaction
  • IF2 – tags tRNAi and regulates entry into ribosome
  • IF3 – Inhibits premature 30S-50S interaction, stabilises free 30S, and acts as an accuracy check for tRNAi-met binding

The initiating tRNA is tRNAᶦ-met which carries methionine: the starting amino acid for most polypeptide chains

20
Q

The first two steps in elongation

A

In the first step, the current polypeptide chain is initially attached to the tRNA attached to the P site and the tRNA with the anticodon for the next codon binds to the A site.

In the second next step, the ester bond between the tRNA and the amino acid attached to it in the chain is broken and a peptide bond is formed between the amino acid connected to the tRNA in the P site and A site simultaneously. This is done by peptidyl transferase

21
Q

The last two steps in elongation

A

In step free, the large subunit of the ribosome moves along the mRNA, causing the tRNA with the polypeptide to enter the P site and the empty tRNA to enter the E site where it is released back into the cytoplasm to bind with another amino acid.

In step four, more conformational changes occur, causing the small subunit to move across the mRNA and open up the next codon for reading.

This process is repeated until a stop codon is reached

22
Q

How tRNAs bind to ribosomes

A

In prokaryotes, EF-Tu binds to both a tRNA and a GTP and it then guides the tRNA to the correct spot on the ribosome and checks that the amino acid is correct

After doing these things, GDP leaves to have phosphate added and EF-Tu binds to another tRNA and GTP

23
Q

How translocation occurs

A

EF-G uses GTP to push the tRNA in the A site to the P site, freeing the A site for the next tRNA and moving both subunits across the mRNA (?)

24
Q

Elongation factors and their effects

A

EF-Tu: mediates aminoacyl-tRNA entry to
ribosome

EF-G: mediates translocation

25
Q

Three release factors and what they react with

A

RF1 - UAA/AUG

RF2 - UAA/UGA

RF3 - Helps RF1/RF2 in binding to the ribosome, acting as a GTPase

These factors will be attached to a GTP

26
Q

Termination of translation

A

Once a stop codon is reached, a release factor will interact with the ribosome and then hydrolyse the polypeptide from the tRNA and then the tRNA and release factor will be released from the ribosome and the ribosome’s subunits will be dissociated from one another

This process uses energy from GTP attached to the RF

27
Q

The role of GTP in translation

A

Provides energy as ATP is converted to ADP

Initiation: addition of the small subunit

Elongation: addition of aminoacyl tRNA by EF-Tu and translocation by EF-G

Termination: Release of chain and ribosome dissociation

B1omed - Molecular biology (13 decks)

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