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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
Q

Can amino acids have more than one tRNA

A

Yes, with different anticodons

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25
Q

Bacteria wobble bases and possible anticodon bases

A

U. A,G, I
C. G, I
A. U,I
G. C,U

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26
Q

Wobble codon base for eukaryotes and possible anticodon bases

A

U. G,I
C. G,I
A. U
G. C

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27
Q

Prokaryotic ribosomes are composed of

A

50s and 30s combine to make 70s

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28
Q

50s molecular weight, parts and number of proteins

A

MW 1,600,000
5S rRNA and 23S rRNA
34 proteins

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29
Q

30S molecular weight, parts and protein no,

A

900,000 MW
16S rRNA
21 proteins

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30
Q

What makes up eukaryotic ribosome

A

60S and 40S combine to make 80S

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31
Q

60S molecular weight, parts and protein number

A

2,800,000 MW
5S and 28S
49 proteins

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32
Q

40s MW, parts, proteins

A

1,400,000 MW
18S
33 proteins

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33
Q

70s molecular weight

A

2,500,000 MW

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34
Q

80s molecular weight

A

4,200,000 MW

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35
Q

What are archaeal ribosomes composed of? What are their primary sequences closest to?

A

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

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36
Q

What binds mRNA

A

Ribosomes

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37
Q

How many sites in ribosome for tRNA binding

What are they

A

Three

E, P, A

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38
Q

What kind of enzyme is ribosome

A

Ribozyme

39
Q

What forms catalytic site for peptidyl transferase

A

RNA in large subunit

40
Q

Where does tRNA add amino acid

A

To the C-terminal end of the growing peptide chain

41
Q

Peptidyl transferase reaction

A

When activated tRNA adds to the C-terminal end of growing peptide

42
Q

How does GTPase molecular switch work

A

Protein conformation changes when bound to GTP vs GDP, thus affecting activity if interacting proteins

43
Q

What protein promotes exchange of GFP for GTP

A

Guanine nucleotide exchange factor (GEF)

44
Q

What helper protein promotes hydrolysis of GTP

A

GAP

45
Q

Is GTPase a protein kinase

A

No. No phosphate group is transferred

46
Q

What is first amino acid for eukaryotes

A

Methionine

47
Q

Where does initiator tRNA bind

A

P site of small subunit

48
Q

How does small subunit bind mRNA

A

It binds 5’ cap and begins to scan for first AUG

49
Q

Kozak sequence

A

AUG surrounded by sequence that indicates translation initiation point in eukaryotes

50
Q

What sequences on prokaryote mRNA bind small subunit at AUG codon

A

Shine-Dalgarno sequences

51
Q

Where does second charged tRNA bind

A

A site

52
Q

What happens when small subunit finds first AUG

A

It causes eIF2 to hydrolyze GTP and large subunit binds

53
Q

EF-Tu (EF1) role

A

Elongation factor. Checks accuracy of base pairing.

54
Q

What happens of base is incorrectly paired

A

TRNA dissociates

55
Q

EF-G (EF2)

A

Monitors translocation of ribosome along mRNA

56
Q

What does switch helix do

A

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
Q

EF-Tu eukaryote equivalent

A

EF1

58
Q

EF-G eukaryote equivalent

A

EF2

59
Q

Stop codons are

A

UAA
UAG
UGA

60
Q

Are there tRNAs for stop codons

A

No

61
Q

Release factors

A

Proteins that mimic tRNAs, bind in A site

62
Q

What does peptidyl transferase do at termination of translation

A

Catalyzes addition of water molecule to C-terminus. Peptide is released from ribosome.

63
Q

What is a polyribosome

A

Multiple ribosomes working on mRNA at once

64
Q

How does ribosome know if protein is destined for endoplasmic reticulum

A

A signal at N-terminal

65
Q

Benefits of circular structure of polyribosome

A

Facilitates structure of polyribosome

Stabilizes mRNA

66
Q

What determines whether ribosome is free or membrane bound

A

Information in nascent polypeptide

67
Q

What determines the energetically favored final 3d structure of a

A

protein sequence of amino acids

68
Q

Which proteins can reach folded state independently

A

Small proteins <100 aa

69
Q

What do larger proteins need to fold in cytosol

A

Chaperone proteins for folding in cytosol’s high protein concentration

70
Q

What does accumulation of misfiled proteins cause

A

Impaired cellular function

71
Q

What are some human diseases that involve miss folded proteins. (5)

A 
Alzheimer's 
Parkinson's
Cystic fibrosis
Jacob-Creutzfeldt disease
Inflammation
72
Q

Three ways folding of protein can go

A

On pathway folding
Off pathway folding
Irretrievable accidents

73
Q

What fixes protein if it has misfolded

A

Chaperone catalysis

74
Q

What happens if misfolded can’t be fixed

A

Digested by proteases

75
Q

Role of ribosome bound chaperone systems

A

Help proteins fold as they exit the ribosome

76
Q

How large is ribosomal tunnel

A

1-2 nm in diameter

77
Q

What ahopens through ribosomal tunnel

A

Unfolded polypeptide chains or alpha helices pass through. Peptides that are about 40 aa are contained within tunnel

78
Q

Role of trigger factor in bacteria

A

Its activity folds about 70% of proteins

79
Q

What folds bacterial protein besides tigger factor activity

A

Hsp60 and hsp70

80
Q

How does trigger factor work

A

It forms a cavity that protects and folds nascent protein chains of ~60 amino acids

81
Q

Role of chaperone systems

A

Facilitate protein folding

82
Q

Which cells do not have trigger factors

A

Archeal and eukaryotic

83
Q

Ribosome bound chaperones in archaeal and eukaryotic cells

A

NAC complex and RAC complex (hsp70 homolog). Play same role of folding nascent polypeptides.

84
Q

PFD

A

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
Q

NAC

A

Nascent polypeptide-associated complex

86
Q

RAC

A

Ribosome-associated complex, an hsp70 homolog

87
Q

How are nascent proteins recognized for the ER

A

Signal recognition particle (SRP)

88
Q

Role of Cytosolic chaperone system (hsp70 system)

A

Constitutive - carries out routine protein folding

Stress induced- accumulates rapidly when cells experience increased temperatures (heat shock) or other stresses

89
Q

What happens if protein is incompletely folded?

A

May be further folded by another round of hsp70, passed on the hsp60 or hsp90 chaperone

90
Q

When is folding accomplished

A

When hsp70 shields hydrophobic regions in the client protein

91
Q

Hsp60

A

Cytosolic chaperone system

Hsp60 family chaperones form a barrel structure; unfolded protein enters to be folded

92
Q

What does unfolded protein bind in hsp60. Folding process?

A

Hydrophilic residues exposed in GroEL surface
ATP and GroES bind
Expose hydrophilic residues in chamber, which drives protein folding

93
Q

How is hsp60 structured

A

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
Q

What makes up chaperonin family

A

Tcp1 in cytosol of eukaryotic cells
Hsp60 in mitochondria
GroEL and GroES in bacteria

Cell Biology (35 decks)

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