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Molecular Cell Biology > Complete review for molecular cell biology midterm 2 (Lectures 8) > Flashcards

Complete review for molecular cell biology midterm 2 (Lectures 8) Flashcards

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1
Q

What is a tRNA?

A

Non-coding RNA that has an associated amino acid on its 3’ end, displays complementarity with itself, leading to intramolecular binding and has an anticodon sequence that is complementary to a codon sequence on an mRNA.

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2
Q

What is the wobble base of tRNA?

A

This is the last base in which the anticodon can have complementarity with the codon. The first two must be a perfect match but the last can vary as, it will still match the correct amino acid.

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3
Q

What two things does a tRNA need to recognize?

A

The codon to base pair with and it’s amino acid, by virtue of being recognized by tRNA synthetase.

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4
Q

What is tRNA synthetase?

A

tRNA synthetases link each amino acid to its appropriate tRNA molecule. There is one synthetase for every tRNA (that binds a certain amino acid). The tRNA makes specific contacts with tRNA synthetase.

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5
Q

How does tRNA synthetase make a charged tRNA?

A

By virtue of an ATP dependent reaction forming an AMP bond of high energy which will be critical for the formation of the peptide bond later.

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6
Q

Amino acids are added to what terminal end of a growing polypeptide chain?

A

C-terminal end

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7
Q

Draw the mechanism of a growing peptide showing only: the peptidyl tRNA, the aminoacyl tRNA, the growing chain.

A

Refer to notes.

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8
Q

Describe eukaryotic ribosomes.

A

Ribosomes are either free or bound to the ER. They translate mRNAs. Composed of a large and a small subunit. (as well as other proteins like peptidyl transferase). Has three sites, E site, P site and A site.

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9
Q

mRNA mainly interacts with which subunit?

A

The small subunit.

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10
Q

What proteins are directly involved in translation initation?

A

eIF2, eIF4E, eIF4G, PABP, additional eIFs, (small and large ribosomal subunit),

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11
Q

What is the initiator tRNA?

A

met-tRNAi

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12
Q

What is peculiar of met-tRNAi?

A

It can bind to the small ribosomal subunit without the presence of the large subunit. It binds to the P site rather than the A site, like most tRNAs.

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13
Q

What does eIF2 do?

A

Mediates the binding of initiator tRNA to the ribosome (small unit) in a GTP dependent manner.

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14
Q

What does eIF4E do?

A

Binds to the 5’ cap (7-methyl guanosine)

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15
Q

What does eIF4G do?

A

Binds to both eIF4E and PABP and links the 5’ and 3’ ends of the mRNA allowing for recruitment of initiator tRNA.

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16
Q

What does PABP do?

A

Bind to poly-A tail on 3’ end of mRNA.

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17
Q

Why is the looping of the 5’ and 3’ ends necessary?

A

Allows translation apparatus to ascertain that both ends are intact.

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18
Q

What is the start codon?

A

AUG

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19
Q

How does the small ribosomal subunit, along with the initiator tRNA, move along the mRNA towards to start sequence?

A

The additional eIFs function as ATP-dependent helicases to facilitate its movement.

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20
Q

What dissociates when the start sequence is reached?

A

eIF2 and the additional eIFs.

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21
Q

What does the dissociation of eIFs following recognition of the AUG sequence allow?

A

For the large ribosomal subunit to bind.

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22
Q

Draw the complete translational initiation mechanism up until the association of the large ribosomal subunit. Clearly annotate all proteins (at least the first time they appear), when they are added, what they do and when they dissociate.

A

Refer to notes.

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23
Q

What are the four steps of translation?

A

Step 1 - tRNA enters the A site
Step 2 - peptide bond formation
Step 3 - translocation of large subunit
Step 4 - translocation of small subunit. Ejection of tRNA from E-site.

24
Q

Draw the translation mechanism very crudely, clearly showing all four steps.

A

Refer to notes.

25
Q

What are the different stop codons?

A

UAA- You are away
UGA- You go away
UAG- You are gone

26
Q

What do stop codons encode?

A

No amino acids.

27
Q

Stop codons mark the end of translation, which site in the ribosome do they affect?

A

The A site.

28
Q

What are eRF1 and eRF3?

A

Eukaryotic release factors that, when the ribosome’s A site reaches the stop codon sequence, allows them to enter. They catalyze the addition of water causing the polypeptide to come off the tRNA and be released.

29
Q

Draw the mechanism of termination.

A

Refer to notes.

30
Q

What are polyribosomes?

A

Multiple proteins translate an mRNA transcript at once.

31
Q

What is unc54?

A

Mutation that causes uncoordinated movement.

32
Q

What is the unc54-r293 mutant transcript?

A

Premature stop codon near the 3’ end of the mRNA, should result in a truncated protein but mRNA is degraded instead.

33
Q

How were SMG mutants discovered?

A

Did a genetic screen in which worms were mutagenized and suppressors of the phenotype were selected for.

34
Q

What do SMG mutants do?

A

Suppress unc54-r293 but not other unc54 mutants (which are not caused by the same premature stop codon).

35
Q

Why does an SMG mutant not complement the unc54-r293 mutant?

A

Because these are double mutants. SMG1, unc54-r293 double mutants have normal movement.

36
Q

Why do SMG1, unc54-r293 double mutants have normal movement?

A

Unc54 mRNA is now stable, truncated protein has partial activity.

37
Q

What is SURF composed of?

A

SMG1, eRF1, eRF3 and UPF1.

38
Q

What does SURF do?

A

Forms a bridge between the ribosome and the downstream EJC. Which, triggers the phosphorylation of UPF1 by SMG1, causing the dissociation of eRF1 and 3 and triggers degradation of the mRNA.

39
Q

What does SMG6 do?

A

Recognizes Upf1-P and cleaves mRNA, exposing 5’ and 3’ end for general pathway of mRNA degradation.

40
Q

How come mRNA degradation doesn’t always occur?

A

Generally ribosome when translating will displace the EJC of normally spliced and non-mutated mRNA. However, if a nonsense mutation causes a premature stop codon, the EJC will be dowstream of the stop codon. This allows for the eRF1 and 3 to associate in the SURF complex for mRNA degradation of nonsense mediated decay.

41
Q

What parts of proteins can fold immediately after leaving the ribosome?

A

Protein domains, which can fold independently of the polypeptide.

42
Q

What do chaperones do, generally?

A

Also called hsp proteins (heat shock proteins). Generally require ATP energy, recognize exposed hydrophobic sequences.

43
Q

Describe the hsp83 chaperone protein.

A

Gene is constitutively expressed and upregulated under heat and other stress conditions. Null alleles are homozygous lethal.

44
Q

Describe the experiment in which hsp83 heterozygote mutants were crossed with wildtype flies.

A

Cross results in hsp83/wild type flies. These still bear deranged phenotypes. Phenotypes are exarcerbated by increased temperature.

45
Q

What did the genetic cross with the wildtype and mutant hsp83 flies show?

A

Wild type drosophila actually carry random mutations that affect protein folding. hsp83 chaperone folds these proteins, masking the mutant phenotype. Heterozygote hsp83 flies do not have enough hsp83 to fold these aberrant proteins, leads to mutant phenotype. High temperature exacerbates this.

46
Q

What are the different avenues that a newly synthesized protein can take. (based on mutant or not)

A

1-fold correctly without assistance
2-fold correctly with the help of a chaperone
3-incompletely folded and digested by proteasome
4-become a protein aggregate and cause disease

47
Q

How do protein aggregates form?

A

Exposed hydrophobic sequences interact together as a means to sequester these sequences, and form aggregates.

48
Q

What are the different components of the proteasome cap?

A

Ubiquitin receptor, ubiquitin hydrolase, unfoldase ring.

49
Q

What does the ubiquitin receptor do?

A

Key to binding ubiquitinated protein to proteasome.

50
Q

What does ubiquitin hydrolase do?

A

Cleaves poly-u and allows for protein to be threaded through cap.

51
Q

What does the unfoldase ring do?

A

Protein complex similar to mcm, allows for protein to enter core of proteasome. Hexamer of AAA protein which, using ATP dependent pathway undergoes a conformational change to form a strained ring that pulls on protein to be degraded.

52
Q

What are the different components of the proteasome?

A

2 x 19S cap and 20S core

53
Q

What is the proteasome core?

A

Contains proteases to digest proteins.

54
Q

How are unfolded proteins recognizedd?

A

By specifc E3 ubiquitin ligases.

55
Q

How can ubiquitin ligases controlled?

A

By phosphorylation, association/dissociation of subunits.

56
Q

How can proteins be regulated for proteasome degradation.

A

Phosphorylation, masking/unmasking.

Molecular Cell Biology (9 decks)

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