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Cell Biology > Lecture 8 Slides > Flashcards

Lecture 8 Slides Flashcards

0
Q

What does 45S precursor rRNA break into after chemical modification and cleavage?

A

18S rRNA, 5.8S rRNA, 28S rRNA

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1
Q

What precursor rRNA is used to make two ribosomal subunits? How many nucleotides does it have?

A

455 precursor rRNA

13,000 nucleotides

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2
Q

What translates rRNA

A

RNA polymerase III

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3
Q

Which piece is incorporated into small ribosomal unit

A

18S rRNA

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4
Q

Which pieces are incorporated into large ribosomal unit

A

5.8S, 28S and 5S, which is not made from 45S

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5
Q

How is 45S rRNA precursor modified? What are resulting modifications?

A

Post transcriptional modification of bases by snoRNPs

Pseudouridine and 2’-O-methylated nucleotide

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6
Q

How are ribosomal RNA genes arranged

A

Tandemly repeated and packed with transcripts /nucleolus

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7
Q

What does nucleolus contain

A

Tandem repeats of rRNA genes from several chromosomal loci

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8
Q

When does nucleolus reform

A

In each cll cycle

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9
Q

What is at edge of nucleolus, on nuclear envelope

A

Peripheral heterochromatin

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10
Q

Pathway for assembly of ribosomal proteins

A

rRNA gene transcribed to 45S precursor
SnoRNAs come in and modify and process rRNA
Ribosomal proteins made in cytoplasm come into nucleolus
5S rRNA joins in from cytoplasm
RNAs and proteins involved in rRNA processing are constantly recycled
Immature large subunit assembled
Telomerase proteins enters nucleus from cytoplasm and form telomerase with telomerase RNA
Small subunit is built
Large or 60S subunit exits nucleus
Small or 49S subunit exits nucleus
Form ribososome for translation

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11
Q

How many amino acids does genetic code specify

A

20

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12
Q

In what directions are codons presented

A

5’-3’

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13
Q

What does redundancy mean

A

64 codons specify 20 amino acids

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14
Q

What do stop codons specify in some mitochondria

A

Amino acids

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15
Q

What do stop codons specify in some protozoan nuclear genes

A

Amino acids

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16
Q

What unusual amino acid is specified by stop codon in some cells

A

Selenocysteine

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17
Q

What sets correct reading frame

What does it specify in eukaryotes? Prokaryotes?

A

AUG start codon
Methionine in eukaryotes
Formyl methionine in prokaryotes

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18
Q

What do tRNAs do

A

Translate codons to amino acids

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19
Q

What synthesizes tRNAs

A

RNA polymerase III

Extensively modified before exported to cytoplasm

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20
Q

What does adaptation of nucleotide sequence to amino acid sequence require

A
  1. Aminoacyl tRNA synthetase couples amino acids to appropriate tRNA, resulting in an aminoacy-tRNA or “charged” tRNA
  2. TRNA anticodon pairs with mRNA codon
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21
Q

What does charged tRNA look like

A

Cross with attached amino acid at 3’ end
Anticodon at bottom loop
D loop on left
T loop on right

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22
Q

What does linkage of amino acid to tRNA require energy wise

A

ATP

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23
Q

Wobble baee pairing

A

Some tRNAs pair with more than one codon

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24
Can amino acids have more than one tRNA
Yes, with different anticodons
25
Bacteria wobble bases and possible anticodon bases
U. A,G, I C. G, I A. U,I G. C,U
26
Wobble codon base for eukaryotes and possible anticodon bases
U. G,I C. G,I A. U G. C
27
Prokaryotic ribosomes are composed of
50s and 30s combine to make 70s
28
50s molecular weight, parts and number of proteins
MW 1,600,000 5S rRNA and 23S rRNA 34 proteins
29
30S molecular weight, parts and protein no,
900,000 MW 16S rRNA 21 proteins
30
What makes up eukaryotic ribosome
60S and 40S combine to make 80S
31
60S molecular weight, parts and protein number
2,800,000 MW 5S and 28S 49 proteins
32
40s MW, parts, proteins
1,400,000 MW 18S 33 proteins
33
70s molecular weight
2,500,000 MW
34
80s molecular weight
4,200,000 MW
35
What are archaeal ribosomes composed of? What are their primary sequences closest to?
30S and 50S subunits join to make a 70S particle | Primary sequences of both RNA and protein components are closer to eukaryotes than to those of prokaryotes
36
What binds mRNA
Ribosomes
37
How many sites in ribosome for tRNA binding | What are they
Three | E, P, A
38
What kind of enzyme is ribosome
Ribozyme
39
What forms catalytic site for peptidyl transferase
RNA in large subunit
40
Where does tRNA add amino acid
To the C-terminal end of the growing peptide chain
41
Peptidyl transferase reaction
When activated tRNA adds to the C-terminal end of growing peptide
42
How does GTPase molecular switch work
Protein conformation changes when bound to GTP vs GDP, thus affecting activity if interacting proteins
43
What protein promotes exchange of GFP for GTP
Guanine nucleotide exchange factor (GEF)
44
What helper protein promotes hydrolysis of GTP
GAP
45
Is GTPase a protein kinase
No. No phosphate group is transferred
46
What is first amino acid for eukaryotes
Methionine
47
Where does initiator tRNA bind
P site of small subunit
48
How does small subunit bind mRNA
It binds 5' cap and begins to scan for first AUG
49
Kozak sequence
AUG surrounded by sequence that indicates translation initiation point in eukaryotes
50
What sequences on prokaryote mRNA bind small subunit at AUG codon
Shine-Dalgarno sequences
51
Where does second charged tRNA bind
A site
52
What happens when small subunit finds first AUG
It causes eIF2 to hydrolyze GTP and large subunit binds
53
EF-Tu (EF1) role
Elongation factor. Checks accuracy of base pairing.
54
What happens of base is incorrectly paired
TRNA dissociates
55
EF-G (EF2)
Monitors translocation of ribosome along mRNA
56
What does switch helix do
EF-Tu undergoes conformational change after GTP hydrolysis. Switch helix in domain 1 allows domains 2 and 3 to rotate as a single unit to release tRNA
57
EF-Tu eukaryote equivalent
EF1
58
EF-G eukaryote equivalent
EF2
59
Stop codons are
UAA UAG UGA
60
Are there tRNAs for stop codons
No
61
Release factors
Proteins that mimic tRNAs, bind in A site
62
What does peptidyl transferase do at termination of translation
Catalyzes addition of water molecule to C-terminus. Peptide is released from ribosome.
63
What is a polyribosome
Multiple ribosomes working on mRNA at once
64
How does ribosome know if protein is destined for endoplasmic reticulum
A signal at N-terminal
65
Benefits of circular structure of polyribosome
Facilitates structure of polyribosome | Stabilizes mRNA
66
What determines whether ribosome is free or membrane bound
Information in nascent polypeptide
67
What determines the energetically favored final 3d structure of a
protein sequence of amino acids
68
Which proteins can reach folded state independently
Small proteins <100 aa
69
What do larger proteins need to fold in cytosol
Chaperone proteins for folding in cytosol's high protein concentration
70
What does accumulation of misfiled proteins cause
Impaired cellular function
71
What are some human diseases that involve miss folded proteins. (5)
``` Alzheimer's Parkinson's Cystic fibrosis Jacob-Creutzfeldt disease Inflammation ```
72
Three ways folding of protein can go
On pathway folding Off pathway folding Irretrievable accidents
73
What fixes protein if it has misfolded
Chaperone catalysis
74
What happens if misfolded can't be fixed
Digested by proteases
75
Role of ribosome bound chaperone systems
Help proteins fold as they exit the ribosome
76
How large is ribosomal tunnel
1-2 nm in diameter
77
What ahopens through ribosomal tunnel
Unfolded polypeptide chains or alpha helices pass through. Peptides that are about 40 aa are contained within tunnel
78
Role of trigger factor in bacteria
Its activity folds about 70% of proteins
79
What folds bacterial protein besides tigger factor activity
Hsp60 and hsp70
80
How does trigger factor work
It forms a cavity that protects and folds nascent protein chains of ~60 amino acids
81
Role of chaperone systems
Facilitate protein folding
82
Which cells do not have trigger factors
Archeal and eukaryotic
83
Ribosome bound chaperones in archaeal and eukaryotic cells
NAC complex and RAC complex (hsp70 homolog). Play same role of folding nascent polypeptides.
84
PFD
Prefoldins bind a subset of proteins including the cytoskeletal proteins actins, alpha-tubulin, beta-tubulin Brings client proteins to chaperonin complex (hsp60) for folding
85
NAC
Nascent polypeptide-associated complex
86
RAC
Ribosome-associated complex, an hsp70 homolog
87
How are nascent proteins recognized for the ER
Signal recognition particle (SRP)
88
Role of Cytosolic chaperone system (hsp70 system)
Constitutive - carries out routine protein folding | Stress induced- accumulates rapidly when cells experience increased temperatures (heat shock) or other stresses
89
What happens if protein is incompletely folded?
May be further folded by another round of hsp70, passed on the hsp60 or hsp90 chaperone
90
When is folding accomplished
When hsp70 shields hydrophobic regions in the client protein
91
Hsp60
Cytosolic chaperone system | Hsp60 family chaperones form a barrel structure; unfolded protein enters to be folded
92
What does unfolded protein bind in hsp60. Folding process?
Hydrophilic residues exposed in GroEL surface ATP and GroES bind Expose hydrophilic residues in chamber, which drives protein folding
93
How is hsp60 structured
Two identical stacked rings, each containing eight different proteins Complex is 800 KD Cycle is ATP regulated, but folding is accomplished by cycles of protein encapsulation
94
What makes up chaperonin family
Tcp1 in cytosol of eukaryotic cells Hsp60 in mitochondria GroEL and GroES in bacteria

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