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Genetics 431: Molecular Genetics > quiz #4 > Flashcards

quiz #4 Flashcards

(100 cards)

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1
Q

tRNA shape

A

cloverleaf but actually “L” shaped

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2
Q

what side of tRNA is conserved?

A

3’ ACC

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3
Q

how many ntds are in tRNA?

A

73-93

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4
Q

base ….. codon binds base to …… of anticodon

A

3 codon
1 anticodon

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5
Q

stop codons and names

A

UAG = amber (this one is not good)
UAA = ocher
UGA = opal

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6
Q

arrangement minimizes the ……..

A

effect of mutation

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7
Q

stop tRNAs

A

there are no stop tRNAs

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8
Q

how many tRNAs are there?

A

45 (1 or more for each amino acid)

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9
Q

wobble base-pairing

A

tRNA structure allows more flexibility in base pairing at the 3rd position, so 1 tRNA can recognize multiple codons
(1st position of anticodon?)

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10
Q

what does inosine allow?

A

1 tRNA, 3 codons

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11
Q

what is the genetic code read by?

A

amino acyl-tRNA synthases

(one fo each amino acid which can charge all the corresponding tRNAs)

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12
Q

how are tRNAs charged?

A

amino acid + ATP –> aminoacyl-AMP
aminoacyl-AMP + tRNA –> charged tRNA

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13
Q

what happens if 2’ OH attacks?

A

migrates to 3’ OH by transesterification, so amino acid bound to 3’ OH when charging is complete

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14
Q

how do aminoacyl tRNA synthetases recognize proper tRNAs?

A

based on overall SHAPE, not anticodon sequence

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15
Q

why is accurate tRNA charging important?

A

ribosomes don’t check whether the tRNAs have proper amino acids

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16
Q

what proofreads?

A

aminoacyl-tRNA synthase (acylation site- uses it to bind to the thing that is wrong but cleaves it through hydrolysis)

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17
Q

how are unnatural amino acids incorporated?

A

make specific aminoacyl-RNA synthase for it to attach to a tRNA

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18
Q

how many ORF are there usually?

A

One!! but
shifting by 1 or 2 ntds –> stop codons

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19
Q

how could a cell recover from a mutation that creates a premature stop codon in an essential gene?

A
  1. mutation- 2 or 3 wrongs can make it close enough to right (triplet expansion diseases- ORF is preserved, but protein becomes unfunctional and/or the long (CAG)n regions can form heterochromatin)
  2. suppressor tRNA- insert aa at stop codon (UAG suppressors suppress UAG
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20
Q

Examples of why is the genetic code is said to be ALMOST universal

A

mitochondria have “simplified” code that requires only 22 tRNAs (mammalian mitochondria encode only 13 proteins)

in some fungi (candida albicans): CUG –> Ser instead of Leu
In related species, CUG is a rare codon, so it might have been altered without a lot of damage

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21
Q

Selenocysteine

A

good stop codon
RNA-binding protein so only do it for that one specific site

added using special tRNA that binds UGA with the help of special RNA seq

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22
Q

euk vs bacterial genome size

A

euk: 3 billion bp
bacteria: 4.4 million bp

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23
Q

where does bacteria and euk translation start?

A

bacteria: Shine-Dalgarno
euk: begin assembly at 5’ CAP and then scan downstream for Kozak

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24
Q

translational coupling

A

Ribosome finishes polypeptide at “stop” then backs up one ntd and starts new round of elongation

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25
eukaryotic and prokaryotic ribosome subunits
euk: 40s + 60s = 80s prok: 30s + 50s= 70s
26
what are polysomes?
RNA + ribosomes
27
how much area does a ribosome cover on mRNA?
80 nucleotides
28
large vs small SU
large: has peptidyl transferase center- protein synthesis, connects small: has decoding center- mRNA and tRNA binding sites
29
how big is ribosome exit tunnel?
wide enough for alpha helix
30
in initiation, what is blocked if ribosome cannot assemble vs when tRNA cannot bind?
E site block: ribosome cant assemble A site block: tRNA blocked
31
what is the first tRNA in prokaryote? what start sequence does it carry?
fmet-tRNAfmet 3'UAC5'
32
eIF4 functions
1. binds cap proteins and recruits 43s complex 2. acts as helicase- threads mRNA through 43s complex until get to Kozak sequence 3. binds A tail to make a circle (protects against nucleases) 4. binds IRES (used by viruses to get polysystine RNA)
33
what is the kozak sequence in euk?
AUG in the correct neighborhoods
34
why does eIF4F associate with 5'cap and polyA tail?
1. mRNA circularization 2. more efficient translation 3. greater resistance to degradation
35
what can translate mRNAs that lack 5' cap?
some viruses and cellular mRNAs
36
IRES
* allow ribosomes to initiate translation without the need for 5' cap * still use eIF4 and continues translating messages normally
37
why might hosts and viruses need IRES?
viruses: with IRES, can still translate messages while messing up the host hosts:need RNA that doesnt have cap to fight fire with fire- will have its own IRES because caps have been compromised
38
what is accomodation in prokaryote elongation?
EF-Tu-GDP release allows tRNA in A site to rotate, positioning aa of P-site in close to aa in A site
39
Peptidyl transferase reaction
forms peptide bond in large SU
40
what proteins look like tRNAs?
* EF-G-GTP * RF 1 or 2 * Puromycin (antibiotic)
41
what euk complex assembles before associating with mRNA?
43s preinitiation complex
42
Puromycin
antibiotic that mimics a charged tRNA and cause premature peptide termination
43
Examples that ribosome is a ribozyme
50S subunit is enough to catalyze the peptidyl transferase reaction. only RNA components are essential for catalytic activity.
44
how does EF-G help ribosome move to the next codon after peptide bond formation
by mimicking a tRNA bound to EF-Tu
45
mRNAs which lack stop codons translate polyA tail →
poly Lys Protein with poly Lys tail are degraded Poly Lys also recruits Ski7 →degrades the mRNA that lacks stop codons
46
how does CI activate its own transcription?
binds to PM --> activates PM --> make more CI (positive feedback)
47
lambda immediately ...... after injection into cells via ...... site
circularizes cohesie (cos)
48
N gene product
antiterminator
49
what does Cro product do?
turns off CI repressor production from Pm
50
what does CI do?
blocks lytic infection
51
what genes does PI activate?
genes for integration into bacterial genome
52
what do large amounts of CI do?
1. shut off PL & PR 2. activate PM --> activates its own transcription
53
what do C2 and C3 activate?
Pe and Pi
54
how are lysogens immune to further infection by another lambda phage?
**prophage make CI**!!!! which inactivates PL & PR to make bacteria immune to further infection
55
cI857 repressor
**works at 32C**: inactivates PL and PR; blocks Cro **inactive** at 42C
56
why can lysogeny not be re-established once CI is gone?
CI needs PM, but PM needs CI to keep making CI
57
DNA damage
single strand DNA binds RecA → cleaves lexA → induce SOS genes (can also cleave CI)
58
In a Lytic infection, phage particles are more like to ……. Than ….. bacteria
survive than damaged bacteria
59
what happens when cro binds: PM, PL/PR
PM: blocks CI PL/PR: turn off CI, C2, and cro
60
what happens when CI binds PL/PR?
blocks them and shuts off Cro
61
CI and Cro binding affinities
CI: O1, 2, 3 Cro: 3,2,1
62
PE has a ......... consesus sequence and normally ...... active
poor -35 not very active
63
how does C2 binding activate PE?
by stabilizing polymerase binding
64
what is C2 degraded by?
hfl protease, which is inhibited by cAMP and C3
65
if glucose levels are low, is lysogeny or lytic high?
low gluclose → high cAMP → high C2 → lysogeny more likely
66
what is Int transcribed by?
PL and PI
67
retroregulation
mRNA from PI has a normal terminator and is stable mRNA from PL has Nut site →Binds NusA and interferes with termination → longer transcript (has RNase III cleavage site) → mRNA is degraded
68
what acts as an inducer in the lac operon? how?
allolactose by binding to the repressor
69
affinity of lac repressor to operator vs lac inducer to repressor
repressor to operator: 10^10 inducer to repressor: 10^13
70
constitutive expression
inactivate lacI (repressor) or lacO (operator)
71
what did partial diploids show?
1. lacI is trans-acting factor (diffusible) 2. lacO is cis-acting factor (only affects genes that are physically linked to it)
72
lac repressor structure
helix-turn helix (HTH) protein binds to major groove bind as dimers to inverted repeats
73
lac O2 and O3 binding sites
inverted repeat that can bind both sides on a lacI dimer each lacI is a tetramer that can bind both O12 or O13
74
lacO1 repression of lacZ vs complete system repression
100 fold 1000 fold (difference between on and off)
75
how is cAMP made?
adenyl cyclase
76
effect on CRP when there is no cAMP
CRP has no effect
77
effect on CRP when cAMP is present
CRP activates lac operon, which compensates for poor lac promoter census sequence HIGH EXPRESSION!!! (increase by 50x)
78
what molecule bends DNA 90 degrees?
CRP
79
what does IPTG mimic?
allolactose
80
what does blue color indicate in lac operon biotech?
cleavage of X-gal (LacZ)
81
Lac oepron affinity problem
LacI binds to operator 10^4 tighter than random DNA, even with allolactose but there are 4x10^6 wrong sites massive over-expression of LacI would inhibit LacZ production, even with allolactose
82
Gal operon regulation
no galactose: repressor binds (allows pol binding but blocks open conformation) galactose: repressor conformation changes, allows some transcription but promoter is weak on its own no glucose: high CRP+cAMP, high levels of gal expression
83
Arac operon regulation
**without arabinose**: araC binds as dimer to araO2 and I1 site; araC dimer bends DNA, doesnt recruit RNAP, even if glucose is low --> very tight regulation **with arabinose**: araC binds as as dimer to araI1 and araI2, which allows activation **with arabinose + low glucose**= CRP-cAMP binds --> further activation due to RNAp recruitment
84
Trp operon regulation
transcriptional attenuation: premature termination of transcription by 3=4 loop
85
Trp operon when high levels of Trp
transcription initiation blocked by TrpR repressor
86
Trp operon when no Trp present
* ribosome stalls at Trp-Trp * 2=3 hairpin (doesnt affect RNAP, not followed by U rich, no termination) * no 3-4 terminator * TRANSCRIBE AND TRANSLATE STRUCTURAL GENES (downstream)
87
Trp operon when adequate/low Trp present
* ribosome does NOT stall at Trp-Trp * advances enough to block 2 * 3=4 hairpin followed by Urich * pol terminates after U rich region
88
SOS genes
* not on operon * repressed by LexA
89
What does RecA bind?
ssDNA
90
riboswitches
changing RNA conf can prevent transcription and translation once it changes cannot change again
91
ribosomes make up ....... of bacterial dry weight
45%
92
stringent response
unnocupied A site --> synthesis of ppGpp --> dont need to make rRNA and tRNA
93
lambda genes and bp
50 genes 50,000 bp
94
how many proteins are in a ribosome?
50
95
what blocks translation of r-protein mRNA
excess r-proteins (repressor bound)
96
rescue of ribosomes stalled on broken mRNA
5’ end of tmRNA folds like an Ala tRNA and binds to stalled ribosome After forming peptide bond, ribosome continues to read codons on tmRNA Amino acids from tmRNA are added to end of the peptide, but mark the peptide for degradation no ligating, no peptide bonds
97
how do bacteria secrete proteins?
using ATP-driven SecA,B, C because dont have ER
98
Mitochondrial protein have .......... used after translation
amino terminal signal sequences
99
secreted and membane proteins have .......... signal sequences and are translated on ..........
amino-terminal signal sequences ER-bound ribosomes
100
when are EJCs removed?
during first round of translation

Genetics 431: Molecular Genetics (8 decks)

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