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601 - Exam 2 > 3.12 Translation > Flashcards

3.12 Translation Flashcards

1
Q

Central dogma

A

DNA to RNA to protein

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2
Q

Genetic code is __. Why?

A

degenerate
More than 1 codon for many AA

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3
Q

Wobble base is what position?

A

3rd

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4
Q

What are the “non-sense codons”?

A

UAA
UAG
UGA

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5
Q

Start codon for bacteria and eukaryotes

A

Bacteria = FMet
Eukaryotes = Met

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6
Q

Define wobble base rule

A

a tRNA that recognizes a Pu at the 3rd position of the codon can recognizes the other Pu and vice versa w/ Py

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7
Q

Inosine (hypoxanthine + ribose) can pair with what bases?

A

A, C or U

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8
Q

5 overview steps for translation

A
  1. Charging of tRNA with AA by tRNA synthetases
  2. Initiation
  3. Elongation
  4. Termination
  5. Post-translational processing
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9
Q

The charging of tRNA to have AA attached to it is done by what enzyme?

A

tRNA synthetase

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10
Q

How many ATP are used to charge tRNA?

A

2

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11
Q

What site does charged initiator tRNA go to?

A

P site
(all others enter A site)

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12
Q

Do bacteria or eukaryotes have a ribosome binding site?

A

Bacterial (shine-dalgarno sequence)

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13
Q

What are the ribosome positioning mechanisms for eukaryotes?

A

Cap-dependent and cap-independent

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14
Q

What are the bacterial ribosome subunits?

A

30S + 50S = 70S

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15
Q

What are the eukaryotic ribosomal subunits?

A

40S + 60S = 80S

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16
Q

What are the 3 sites on the ribosome and describe?

A

A = tRNA binding site and accepts charged tRNA
P = contains previous tRNA attached to the growing polypeptide
E = exit for uncharged tRNA

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17
Q

Elongation of AA in bacteria is catalyzed by formation of peptide bonds by ___ rRNA

A

23S

18
Q

Where is the shine-dalgarno sequence located in bacteria?

A

5-10 nucleotides upstream of FMet (AUG)

19
Q

What IF binds to mRNA to position the ribosome in the correct place in bacteria?

A

IF-1 and IF-3

20
Q

What helps bind tRNA FMet to the P site in bacteria?

A

IF-2:GTP

21
Q

When does the 50S ribosome bind to 30S in bacteria?

A

With the removal of IF-1 and IF-2 and hydrolysis of GTP to GDP

22
Q

Bacteria initiation steps:

A
  1. IF-1 and IF-3 bind to 30S subunit
  2. IF-2:GTP recognizes tRNA with F-Met and helps it bind to P site
  3. Triggers release of IF-3
  4. IF-1, IF-2, and GDP are ejected
  5. 50S subunit comes in = 70S subunit formed
23
Q

Bacteria elongation steps

A
  1. EF-G with GTP enters ribosome and catalyzes ribosome translocation
  2. EF-Tu + GTP brings in charged tRNA to A site
  3. Hydrolysis of GTP kicks EF-Tu + GTP +Pi out of ribosome
  4. EF-Tu is recycled, so GDP is displaced by EF-Ts to form EF-Tu/EF-Ts complex → EF-Ts is replaced with GTP → EF-Tu + GTP to bring in another charged tRNA
    A to P to E site
  5. Peptide bond forms formed between AA (at carboxyl group) on P site and AA in A site
  6. Translocation of growing peptide chain onto A site
24
Q

Termination in bacteria:

A
  1. Uncharged tRNA causes RF-1 (UAA and UAG) or RF-2 (UAA or UGA) to come in
  2. Ribosome release factor (RRF) and EF-G:GTP cause 70S dissociation
25
Q

Define polysomes

A

Complex of several ribosomes attached to mRNA
- In bacteria

26
Q

2 reasons why transcription and translation occur simultaneously in bacteria

A
  • Increases rate of protein synthesis
  • protect mRNA from nucleases
27
Q

Why are there pausing sites in transcription in bacteria?

A

RNAP moves faster than ribosomes, so by having RNAP pause it allows the ribosomes to catch up

28
Q

Is there a ribosome binding site in eukaryotes?

A

No

29
Q

rRNA and ribosomal proteins are assembled in the

A

Nucleus

30
Q

Where are the ribosomal subunits assembled in eukaryotes?

A

in the cytosol

31
Q

What does translation need in eukaryotes?

A

5’-cap, 3’ poly A tail, and initiation factors

32
Q

What scans mRNA until it reaches AUG?

A

43S preinitiation complex

33
Q

What is the 43S preinitiation complex made of?

A

40S ribosome, eIF2-GTP, and tRNA Met

34
Q

When does the large ribosomal subunit bind in eukaryotes?

A

Once 40S subunit reaches the start codon

35
Q

Steps for initiation in eukaryotes:

A
  1. Formation of 43S preinitiation complex
  2. It then binds to 5’ cap
  3. PABP binds to poly A tail
  4. Initiation complex scans until it reaches AUG
  5. 60S joins to form 80S ribosome
36
Q

Steps for elongation in eukaryotes:

A
  1. EF-1A + GTP brings in charged tRNA to A site
  2. Hydrolysis of GTP kicks EF-1A + GTP out of ribosome
  3. EF-1A is recycled, so GDP is displaced by EF-1Balpha to form EF-1A/EF-1Balpha complex → EF-1B is replaced with GTP → EF-1A + GTP to bring in another charged tRNA
37
Q

Steps for termination in eukaryotes:

A
  1. Uncharged tRNA causes RF-1 (UAA and UAG) or RF-2 (UAA or UGA) to come in
  2. RF-3 aids in the activities of RF-1 and RF-2
  3. Ribosome release factor (RRF) and EF-2:GTP cause 80S dissociation
38
Q

What are the post-translational modifications?

A
  • Removal of Fmet or Met
  • processing
  • modification
  • chelation (metals)
39
Q

Why is enzyme degradation important?

A

Limits the activity and is a regulatory control

40
Q

Most proteins in bacteria degrade by

A

AAA+ ATPases

41
Q

Most eukaryotes degrade by

A

ATP-dependent
Lysosomal protein turnover

42
Q

Why would proteins be degraded?

A

If they’re defective or damaged they AA are recycled to prevent mishaps

601 - Exam 2 (11 decks)

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