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08a: Protein Synthesis 2 Flashcards

1
Q

List the basic things required for bacterial protein synthesis.

A
  1. mRNA
  2. Ribosome
  3. Protein initiation, elongation, termination factors
  4. Activated tRNAs
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2
Q

Where exactly does ribosomal assembly take place in bacteria?

A

On mRNA

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3
Q

The mRNA in protein synthesis is read in which direction?

A

5’ to 3’

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4
Q

The initiator tRNA in bacteria is identical to which AA tRNA?

A

None! It’s unique to initiation

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5
Q

IF2-GTP function in (euk/prok).

A

Prokaryotes;

Helps bind Met-tRNA

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6
Q

EF-Tu-GTP function in (euk/prok).

A

Prokaryotes;

Delivery of aminoacyl tRNA to ribosomes

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7
Q

EF-G-GTP function in (euk/prok).

A

Prokaryotes;

Translocation factor

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8
Q

RF-3-GTP function in (euk/prok).

A

Prokaryotes;

Release of complete polypeptide chain

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9
Q

eIF2-GTP function in (euk/prok).

A

Eukaryotes;

Helps bind Met-tRNA

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10
Q

(Prok/euk) equivalent to eIF2-GTP.

A

Prokaryotic equivalent is IF2-GTP

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11
Q

There is/are (X) number of tRNAs for each AA.

A

X = at least 1

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12
Q

AA are activated with (X) (before/during/after) attachment to (Y), the adaptor molecules.

A

X = ATP

Before;

Y = tRNA

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13
Q

AA activation is carried out by which enzyme(s)?

A

Aminoacyl tRNA synthetases

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14
Q

AA attachment to tRNA is carried out by which enzyme(s)?

A

Aminoacyl tRNA synthetases

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15
Q

T/F: there are separate aminoacyl tRNA synthetases for each AA.

A

True - at least one for each AA

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16
Q

(X) number of high energy bonds are cleaved in AA activation

A

X = 2

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17
Q

What’s the key step in controlling accuracy of protein synthesis?

A

AA activation

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18
Q

How does the (X) enzyme correctly match the AA and tRNA in AA activation?

A

X = synthetase

Recognizes R Group on AA and some part of tRNA NT sequence

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19
Q

Each aminoacyl tRNA synthetase has which sites?

A
  1. Activation site (for activation/attachment)

2. Hydrolytic site (check/correct errors)

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20
Q

Once AA-tRNA complex leaves the synthetase, where is the last checkpoint for errors before it is used protein synthesis?

A

No further means of correcting errors after check by synthetase

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21
Q

The most differences between prokaryotic and eukaryotic protein synthesis takes place during which stage(s)?

A

Initiation

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22
Q

First step in initiation of bacterial protein synthesis involves formation of (X)-way complex, composed of:

A

X = 3

  1. Shine-Delgarno sequence (mRNA)
  2. 30S ribosomal subunit
  3. tRNA complex (initiator tRNA bound to fmet and IF2-GTP)
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23
Q

Prok: The initiator tRNA complex includes which components?

A
  1. Initiator tRNA
  2. fmet
  3. IF2-GTP
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24
Q

Prok: Which component(s) bind(s) the free 30S subunit to initiate translation?

A

ONLY initiator tRNA can bind the free 30S subunit

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25
Q

In prokaryotes, once the large, (X)S subunit binds, what is displaced?

A

X = 50

The initiation factors (IF1, IF3, and IF2-GDP) are released

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26
Q

First codon in prokaryotic protein synthesis:

A

AUG

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27
Q

First AA in prok protein synthesis:

A

formyl-met (fmet)

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28
Q

The small ribosomal subunit in prok binds at which sequence in mRNA?

A

At AUG codon

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29
Q

The entire ribosome assembles in prokaryotes at which sequence in mRNA?

A

At AUG codon

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30
Q

The Shine-Delgarno sequence in (prok/euk) is (X)-rich and base pairs with (Y).

A

Prok;
X = purine
Y = 3’ end of 16S rRNA in small (30S) subunit

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31
Q

Is the Shine-Delgarno upstream or downstream from start codon, (X).

A

X = AUG

Shine-Delgarno is about 7-10 bases upstream

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32
Q

T/F: The Shine-Delgarno sequence is found in the ORF (open reading frame).

A

False - in 5’ UTR (untranslated region)

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33
Q

Prok: The (X) group is attached to which part of the initiator tRNA by transformylase?

A

X = formyl

Added to Met group that’s attached to tRNA

34
Q

What are the tRNA binding sites in the ribosome?

A
  1. A (aminoacyl)
  2. P (peptidyl)
  3. E (exit)
35
Q

Prok: In assembly of the initiation complex, the (X) sequence positions the 30S subunit in a specific way so that:

A

X = shine delgarno

fmet-tRNA is in P site

36
Q

First step of elongation in prok protein synthesis.

A

Codon-specific binding of aminoacyl-tRNA to A site of ribosome (mediated by EF-Tu-GTP)

37
Q

The first step of elongation in prok protein synthesis (does/doesn’t) require energy. If so, how is it transferred?

A

Does; mediated by EF-Tu-GTP

38
Q

Second step of elongation in prok protein synthesis.

A

Formation of peptide bond and transfer of growing peptide chain to tRNA in A site

39
Q

The second step of elongation in prok protein synthesis is catalyzed by:

A

Peptidyl transferase

40
Q

Peptidyl transferase is a component of:

A

Ribozyme component of 23S rRNA

41
Q

Third step of elongation in prok protein synthesis.

A

Ribosome translocation; moves peptidyl-tRNA from A site to P site and free tRNA to E site

42
Q

The third step of elongation in prok protein synthesis (does/doesn’t) require energy. If so, how is it transferred?

A

Does; mediated by EF-G-GTP

43
Q

The second step of elongation in prok protein synthesis (does/doesn’t) require energy. If so, how is it transferred?

A

Doesn’t require GTP

44
Q

Termination of protein synthesis in prokaryotes occurs when (X) appears in (Y) site.

A 
X = stop codon (UAA, UAG, UGA)
Y = A
45
Q

Why do stop codons terminate protein synthesis?

A

There’s no tRNA with the complementary sequence

46
Q

What are the steps in prokaryotic termination of translation?

A
  1. Stop codon appears in A site
  2. RF3-GTP binds ribosome
  3. GTP hydrolysis
  4. Ester bond cleavage (peptidyl transferase)
  5. Release of protein, tRNA, mRNA, ribosome
47
Q

During protein synthesis termination, the (X) bond is cleaved to release (Y). Which enzyme catalyzes this?

A 
X = ester
Y = peptide chain from tRNA

Peptidyl transferase

48
Q

What is a very commonly prescribed drug that acts as inhibitor of protein synthesis?

A

Tetracycline

49
Q

MOI of Tetracycline.

A

Blocks binding of aminoacyl-tRNA to A-site of ribosome

50
Q

Tetracycline works as (X) in (prokaryotes/eukaryotes/both).

A

X = inhibitor of protein synthesis

Prokaryotes only

51
Q

Name a very “last resort” drug that acts as inhibitor of protein synthesis.

A

Chloramphenicol

52
Q

MOI of Chloramphenicol.

A

Resembles peptide bond; competitive inhibitor of peptidyl transferase

53
Q

Chloramphenicol works as (X) in (prokaryotes/eukaryotes/both).

A

X = competitive inhibitor of protein synthesis

Prokaryotes only

54
Q

List the key differences in protein synthesis initiation between eukaryotes and prokaryotes.

A
  1. mRNA cap plays important role
  2. Initiator tRNA (met-tRNA) not formulated
  3. eIF2-GTP
  4. Complex (ribosome subunit, met-tRNA, initiation factors) scan mRNA to find AUG
55
Q

Euk: the small ribosomal subunit binds mRNA at:

56
Q

Is the Kozak sequence upstream or downstream from start codon, (X).

A

X = AUG

Neither - AUG is part of Kozak sequence

57
Q

When does the initiation complex in (prokaryotes/eukaryotes) stop scanning mRNA?

A

Eukaryotes; when AUG is in P-site

58
Q

What mechanisms do eukaryotes use to facilitate ribosome recycling?

A

mRNAs form loop structure

59
Q

In (eukaryotic/prokaryotic) mRNA loop structure, which proteins interact?

A

Eukaryotic; cap binding proteins interact with Poly-A binding proteins

60
Q

(HCV/HIV) is an RNA virus.

61
Q

(HCV/HIV) is a retrovirus. (HCV/HIV) is a flavivirus.

62
Q

HCV mainly infects (X) cells.

63
Q

HIV mainly infects (X) cells.

A

X = human immune

64
Q

HIV mechanism of infection:

A

Inserts genetic material into host DNA and uses host genetic material to replicate

65
Q

HCV mechanism of infection:

A

(+) strand uses host ribosomes to synthesize viral proteins

66
Q

T/F: One thing HCV and HIV have in common is the insertion of viral genetic material into host DNA.

A

False - HIV does this, but HCV does not

67
Q

There are mote deaths from (HIV/HCV).

68
Q

(Active/inactive) eIF2-GDP interacts with (X) to cycle back to (Y).

A

Inactive;
X = Guanine nucleotide exchange factor (eIF2B)
Y = eIF2-GTP

69
Q

List some situations in which cell won’t want to make proteins, for fear of (X).

A

X = wasting energy

  1. Detecting dsRNA
  2. Stress/nutrient deprived
  3. Lack of heme (in reticulocytes)
70
Q

How might a cell under stress halt protein production?

A

Stimulates production of kinase that phosphorylates eIF2-GDP (preventing its conversion to active eIF2-GTP)

71
Q

Phosphorylation of eIF2-GDP results in (X) because:

A

X = inhibition of protein synthesis

Phosphorylated eIF2-GDP binds eIF2B 100x more avidly and doesn’t release it

72
Q

How might long dsRNA affect a cell, in terms of protein synthesis? Via which mechanism?

A

Will inhibit protein synthesis;

  1. Produces interferon
  2. Interferon stimulates production of kinase that phosphorylates eI2F-GDP
73
Q

What’s the function of Dicer?

A

Cleaves long dsRNA into small pieces that have 2 NT 3’ overhang

74
Q

RISC stands for (X) and functions as a(n) (Y).

A 
X = RNA-induced silencing complex
Y = endonuclease
75
Q

Following association with RISC, what happens to dsRNA?

A

Sense strand is kicked out; antisense strand remains associated with and activates RISC

76
Q

What is the function of activated RISC?

A

Binds target mRNA and cleaves it via slicer

77
Q

T/F: Slicer is activated by RISC.

A

False - it’s an enzyme within RISC

78
Q

What’s the difference in RNA interference between lower and higher euk?

A

Lower: long dsRNA initiates process
Higher: dsRNA introduced in small pieces (25 NT)

79
Q

Introducing miRNAs into mammalian cells will result in its localization to (X) compartment and processing by (Y).

A

miRNAs are naturally-occuring in mammalian cells (synthesized by RNA Pol II)

Processed by Drosha in nucleus

80
Q

Following processing of miRNA by (X), what’s the fate of the processed product, aka (Y)?

A 
X = Drosha
Y = pre-miRNA

Transported to cytoplasm and processed by Dicer

81
Q

Imperfect pairing of RISC to target mRNA results in (X). Perfect pairing of RISC to target mRNA results in (Y).

A 
X = translational repression
Y = cleavage via Slicer
82
Q

RISC inhibits (X) of mRNA by binding to which region?

A

X = translation

3’ UTR (results in deadenylation, decapping, degradation)

MFoM (20 decks)

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