Lecture 8 Slides Flashcards Preview

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Flashcards in Lecture 8 Slides Deck (95):
1

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

18S rRNA, 5.8S rRNA, 28S rRNA

2

What translates rRNA

RNA polymerase III

3

Which piece is incorporated into small ribosomal unit

18S rRNA

4

Which pieces are incorporated into large ribosomal unit

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

5

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

Post transcriptional modification of bases by snoRNPs
Pseudouridine and 2'-O-methylated nucleotide

6

How are ribosomal RNA genes arranged

Tandemly repeated and packed with transcripts /nucleolus

7

What does nucleolus contain

Tandem repeats of rRNA genes from several chromosomal loci

8

When does nucleolus reform

In each cll cycle

9

What is at edge of nucleolus, on nuclear envelope

Peripheral heterochromatin

10

Pathway for assembly of ribosomal proteins

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

11

How many amino acids does genetic code specify

20

12

In what directions are codons presented

5'-3'

13

What does redundancy mean

64 codons specify 20 amino acids

14

What do stop codons specify in some mitochondria

Amino acids

15

What do stop codons specify in some protozoan nuclear genes

Amino acids

16

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

Selenocysteine

17

What sets correct reading frame
What does it specify in eukaryotes? Prokaryotes?

AUG start codon
Methionine in eukaryotes
Formyl methionine in prokaryotes

18

What do tRNAs do

Translate codons to amino acids

19

What synthesizes tRNAs

RNA polymerase III
Extensively modified before exported to cytoplasm

20

What does adaptation of nucleotide sequence to amino acid sequence require

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

21

What does charged tRNA look like

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

22

What does linkage of amino acid to tRNA require energy wise

ATP

23

Wobble baee pairing

Some tRNAs pair with more than one codon

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

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

95

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

455 precursor rRNA
13,000 nucleotides