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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
In prokaryotes, once the large, (X)S subunit binds, what is displaced?
X = 50 The initiation factors (IF1, IF3, and IF2-GDP) are released
26
First codon in prokaryotic protein synthesis:
AUG
27
First AA in prok protein synthesis:
formyl-met (fmet)
28
The small ribosomal subunit in prok binds at which sequence in mRNA?
At AUG codon
29
The entire ribosome assembles in prokaryotes at which sequence in mRNA?
At AUG codon
30
The Shine-Delgarno sequence in (prok/euk) is (X)-rich and base pairs with (Y).
Prok; X = purine Y = 3' end of 16S rRNA in small (30S) subunit
31
Is the Shine-Delgarno upstream or downstream from start codon, (X).
X = AUG Shine-Delgarno is about 7-10 bases upstream
32
T/F: The Shine-Delgarno sequence is found in the ORF (open reading frame).
False - in 5' UTR (untranslated region)
33
Prok: The (X) group is attached to which part of the initiator tRNA by transformylase?
X = formyl Added to Met group that's attached to tRNA
34
What are the tRNA binding sites in the ribosome?
1. A (aminoacyl) 2. P (peptidyl) 3. E (exit)
35
Prok: In assembly of the initiation complex, the (X) sequence positions the 30S subunit in a specific way so that:
X = shine delgarno fmet-tRNA is in P site
36
First step of elongation in prok protein synthesis.
Codon-specific binding of aminoacyl-tRNA to A site of ribosome (mediated by EF-Tu-GTP)
37
The first step of elongation in prok protein synthesis (does/doesn't) require energy. If so, how is it transferred?
Does; mediated by EF-Tu-GTP
38
Second step of elongation in prok protein synthesis.
Formation of peptide bond and transfer of growing peptide chain to tRNA in A site
39
The second step of elongation in prok protein synthesis is catalyzed by:
Peptidyl transferase
40
Peptidyl transferase is a component of:
Ribozyme component of 23S rRNA
41
Third step of elongation in prok protein synthesis.
Ribosome translocation; moves peptidyl-tRNA from A site to P site and free tRNA to E site
42
The third step of elongation in prok protein synthesis (does/doesn't) require energy. If so, how is it transferred?
Does; mediated by EF-G-GTP
43
The second step of elongation in prok protein synthesis (does/doesn't) require energy. If so, how is it transferred?
Doesn't require GTP
44
Termination of protein synthesis in prokaryotes occurs when (X) appears in (Y) site.
``` X = stop codon (UAA, UAG, UGA) Y = A ```
45
Why do stop codons terminate protein synthesis?
There's no tRNA with the complementary sequence
46
What are the steps in prokaryotic termination of translation?
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
During protein synthesis termination, the (X) bond is cleaved to release (Y). Which enzyme catalyzes this?
``` X = ester Y = peptide chain from tRNA ``` Peptidyl transferase
48
What is a very commonly prescribed drug that acts as inhibitor of protein synthesis?
Tetracycline
49
MOI of Tetracycline.
Blocks binding of aminoacyl-tRNA to A-site of ribosome
50
Tetracycline works as (X) in (prokaryotes/eukaryotes/both).
X = inhibitor of protein synthesis Prokaryotes only
51
Name a very "last resort" drug that acts as inhibitor of protein synthesis.
Chloramphenicol
52
MOI of Chloramphenicol.
Resembles peptide bond; competitive inhibitor of peptidyl transferase
53
Chloramphenicol works as (X) in (prokaryotes/eukaryotes/both).
X = competitive inhibitor of protein synthesis Prokaryotes only
54
List the key differences in protein synthesis initiation between eukaryotes and prokaryotes.
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
Euk: the small ribosomal subunit binds mRNA at:
cap
56
Is the Kozak sequence upstream or downstream from start codon, (X).
X = AUG Neither - AUG is part of Kozak sequence
57
When does the initiation complex in (prokaryotes/eukaryotes) stop scanning mRNA?
Eukaryotes; when AUG is in P-site
58
What mechanisms do eukaryotes use to facilitate ribosome recycling?
mRNAs form loop structure
59
In (eukaryotic/prokaryotic) mRNA loop structure, which proteins interact?
Eukaryotic; cap binding proteins interact with Poly-A binding proteins
60
(HCV/HIV) is an RNA virus.
Both
61
(HCV/HIV) is a retrovirus. (HCV/HIV) is a flavivirus.
HIV; HCV
62
HCV mainly infects (X) cells.
X = liver
63
HIV mainly infects (X) cells.
X = human immune
64
HIV mechanism of infection:
Inserts genetic material into host DNA and uses host genetic material to replicate
65
HCV mechanism of infection:
(+) strand uses host ribosomes to synthesize viral proteins
66
T/F: One thing HCV and HIV have in common is the insertion of viral genetic material into host DNA.
False - HIV does this, but HCV does not
67
There are mote deaths from (HIV/HCV).
HCV
68
(Active/inactive) eIF2-GDP interacts with (X) to cycle back to (Y).
Inactive; X = Guanine nucleotide exchange factor (eIF2B) Y = eIF2-GTP
69
List some situations in which cell won't want to make proteins, for fear of (X).
X = wasting energy 1. Detecting dsRNA 2. Stress/nutrient deprived 3. Lack of heme (in reticulocytes)
70
How might a cell under stress halt protein production?
Stimulates production of kinase that phosphorylates eIF2-GDP (preventing its conversion to active eIF2-GTP)
71
Phosphorylation of eIF2-GDP results in (X) because:
X = inhibition of protein synthesis Phosphorylated eIF2-GDP binds eIF2B 100x more avidly and doesn't release it
72
How might long dsRNA affect a cell, in terms of protein synthesis? Via which mechanism?
Will inhibit protein synthesis; 1. Produces interferon 2. Interferon stimulates production of kinase that phosphorylates eI2F-GDP
73
What's the function of Dicer?
Cleaves long dsRNA into small pieces that have 2 NT 3' overhang
74
RISC stands for (X) and functions as a(n) (Y).
``` X = RNA-induced silencing complex Y = endonuclease ```
75
Following association with RISC, what happens to dsRNA?
Sense strand is kicked out; antisense strand remains associated with and activates RISC
76
What is the function of activated RISC?
Binds target mRNA and cleaves it via slicer
77
T/F: Slicer is activated by RISC.
False - it's an enzyme within RISC
78
What's the difference in RNA interference between lower and higher euk?
Lower: long dsRNA initiates process Higher: dsRNA introduced in small pieces (25 NT)
79
Introducing miRNAs into mammalian cells will result in its localization to (X) compartment and processing by (Y).
miRNAs are naturally-occuring in mammalian cells (synthesized by RNA Pol II) Processed by Drosha in nucleus
80
Following processing of miRNA by (X), what's the fate of the processed product, aka (Y)?
``` X = Drosha Y = pre-miRNA ``` Transported to cytoplasm and processed by Dicer
81
Imperfect pairing of RISC to target mRNA results in (X). Perfect pairing of RISC to target mRNA results in (Y).
``` X = translational repression Y = cleavage via Slicer ```
82
RISC inhibits (X) of mRNA by binding to which region?
X = translation 3' UTR (results in deadenylation, decapping, degradation)

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