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2) Biochemistry II > Protein Synthesis > Flashcards

Protein Synthesis Flashcards

1
Q

How often are proteins synthesized?

A
  • Only when they are required
  • Highly energy demanding (90% of cell’s energy)
  • Requirement = production
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2
Q

What is a common method of regulation of protein synthesis?

A

Degradation

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3
Q

In Eukaryotes, protein synthesis requires how many biomolecules?

A

> 300

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4
Q

In Eukaryotes, protein synthesis requires 70 ____________

A

ribosomal proteins (r-proteins)

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5
Q

In Eukaryotes, protein synthesis requires 20 ____________, and 20 ____________

A

amino acid activation enzymes

factors (enzymes) for initiation, elongation, and termination of translation

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6
Q

In Eukaryotes, protein synthesis requires 100 ____________

A

additional enzymes for final processing of protein synthesis

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7
Q

In Eukaryotes, protein synthesis requires 40 ____________

A

kinds of tRNAs and rRNAs

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8
Q

What are tRNAs also called? What is their function?

A
  • Adapters

- Brings amino acids to mRNA

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9
Q

What is the structure of tRNAs?

A
  • One end is charged with an amino acid

- An anticodon (triplet) complements the codons present in mRNA

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10
Q

How many codon combinations are there?

A
  • 3-letter code from 4 nucleotides

- 64 combinations

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11
Q

Do cells use overlapping or non-overlapping code? What does this mean?

A
  • Non-overlapping code

- There is a sequence of nucleotides in an mRNA, and they are read in successive triplets

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12
Q

Of the three nucleotides in the codon, which base is less important in binding to tRNA?

A

The third base

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13
Q

Which codon establishes the reading frame? What happens to the nucleotides before?

A
  • First codon

- The nucleotides before the start codon are ignored by tRNA

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14
Q

What happens if the reading frame is thrown off by a base or two?

A

All subsequent codons are out of order

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15
Q

____ out of 64 codons code for specific amino acids. What do the others code for?

A
  • 61

- Non-sense codons (stop codons)

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16
Q

What are the three stop codons?

A
  • UAA
  • UGA
  • UAG
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17
Q

What makes a termination codon terminate?

A

Since there are no tRNAs that can recognize these codons to bring in amino acids

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18
Q

What is selenocysteine coded by? What is it?

A
  • 21st amino acid

- Coded by UGA (typically a stop codon)

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19
Q

What is the initiation code? What is it also called? Why?

A
  • AUG

- Met codon since it synthesizes methionine

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20
Q

Can multiple codons code for a single amino acid? Which amino acids only have one codon each?

A
  • Yes

- Methionine and tryptophan

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21
Q

Who founded the RNA tie club?

A

Watson

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22
Q

What is the adaptor hypothesis?

A

Because nucleotides and amino acids are different, there must be an adaptor enzyme (tRNA)

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23
Q

What did George Gamow discover?

A

Triplet codon

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24
Q

What did Har Gobind Khorana discover?

A
  • Methods to synthesize short nucleotides

- Proved that three nucleotides form a triplet codon, and that it is a non-overlapping code

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25
Q

Where is the codon? Where is the anticodon?

A
  • Codon: mRNA

- Anticodon: tRNA

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26
Q

How does the mitochondrial genetic code differ?

A

o UGA encodes for Tryptophan instead of a STOP

o AGA/AGG encode for STOP instead of Arginine

27
Q

How is the amino acid activated?

A

tRNA is aminoacylated

28
Q

What is initiation of protein synthesis?

A
  • mRNA and the aminoacylated tRNA bind to the small ribosomal subunit
  • The large subunit then binds as well
29
Q

What is elongation of protein synthesis?

A
  • Successive cycles of aminoacyl-tRNA binding and peptide formation occur until the ribosome reaches a stop codon
30
Q

What is termination of protein synthesis?

A
  • Translation stops when a stop codon is encountered

- The mRNA and the protein dissociate and the ribosomal subunit are recycled

31
Q

What is the general structure of a tRNA?

A

Cloverleaf

32
Q

What does the anticodon arm contain?

A

Anticodon

33
Q

What is the Wobble position? Is it important or no?

A
  • First nucleotide from the 5’ end of the anticodon
  • Least important
  • Corresponds to the third position of the codon
34
Q

Where is the CCA sequence located? Is it 3’ to 5’ or 5’ to 3’

A
  • Amino acid arm of tRNA

- 5’ to 3’

35
Q

When is the CCA sequence added?

A

Once the tRNA is completely expressed - after transcription of tRNA

36
Q

What is the first step to the aminoacylation of tRNA?

A
  • a-carboxyl of the amino acid attacks a-phosphate of ATP, forming an aminoacyl adenylate
  • Remains bound to the active site
37
Q

What happens after an aminoacyl adenylate is formed?

A
  • Amino acyl group is transferred to tRNA

- Mechanism is different between the two classes

38
Q

What happens to Class I aminoacyl-tRNA synthetases?

A

o The amino acyl group is transferred initially to the 2’-hydroxyl group of the 3’-terminal A residue
o Then, to the 3’-hydroxyl group by a transesterification reaction

39
Q

What happens to Class II aminoacyl-tRNA synthetases?

A

The aminoacyl group is transferred directly to the 3’-hydroxyl group of the terminal adenylate

40
Q

Where is the activated amino acid charged? Which position is that?

A
  • “A” of the CCA sequence

- 3’ position

41
Q

What are the two types of tRNAs for met?

A

fMet and Met

42
Q

In the mitochondria, what is the first amino acid in a peptide coded by?

A

Initiation tRNA inserts N-formylmethionine (fMet) with AUG as first codon

43
Q

In Eukaryotes, do proteins being with Met or fMet?

A

Met

44
Q

What are the three spaces in the 40S subunit?

A

o A: amino acyl site
o P: peptide site
o E: exit site (site from which the tRNA exit)

45
Q

What is the 43S preinitiation complex formed of?

A
  • 40S
  • tRNA (methionine)
  • EIF1 to EIF5
46
Q

What does EIF4F do?

A

Brings tRNA to the preinitiation complex

47
Q

When does scanning stop, and initiation being?

A

When AUG comes to the P site

48
Q

At which site does elongation occur?

A

At the A site

49
Q

What is the function of EF-Tu-GTP?

A

Brings in aminoacyl-tRNA to the A site

50
Q

What is the function of Elongation Factor P (EF-P)?

A

Forms the bond between the carboxyl end of the first AA, and the amino end of the incoming AA

51
Q

Where does an empty tRNA move to?

A

To the E site

52
Q

What is translocation?

A

Lengthened amino acid shifts from the A site to the P site

53
Q

What does EF-G-GTP do?

A
  • Pushes dipeptidyl tRNA to the P site

- A site is empty to receive another AA-containing tRNA for the subsequent codon

54
Q

What happens when a termination codon arrives at the A site?

A
  • A release factor binds

- Peptidyl-tRNA is hydrolyzed and the synthesized AA chain is dissociated

55
Q

Provide examples of post-translational modifications of proteins.

A

o Enzymatic removal of the formyl group from the first residue, or removal of methionine and sometimes additional residues
o Acetylation of N-terminal residue
o Removal of signal sequences or other regions
o Forming disulfide links, creating a 3D structure
o Attaching carbohydrates (glycosylation): occurs on most proteins

56
Q

Are all proteins degraded?

A

Yes, it is inevitable

57
Q

How is the half-life of hemoglobin?

A

Long-lived since they do not have a nucleus

58
Q

How is the half-life of proteins for rapidly changing needs?

A

Short-lived

59
Q

What is the function of ubiquintin?

A

Ubiquintin is covalently linked to proteins slated for destruction via an ATP-dependent pathway involving three enzymes: E1, E2, E3

60
Q

What are the three enzymes for ubiquintin protein destruction?

A
  • E1: activating enzyme
  • E2: conjugating enzyme
  • E3: ligating enzyme
61
Q

How is ubiquintin activated?

A
  • E1 has a SH (thiol) group that interacts with the carboxyl group of ubiquintin
  • Requires energy (ATP)
62
Q

What happens after ubiquintin is activated?

A
  • Transferred to E2

- Transferred to the target protein at the LYSINE residue (catalyzed by E3)

63
Q

Ubiquintin is transferred to the target protein at which residue?

A

Lysine

2) Biochemistry II (23 decks)

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