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Exam 2 Flashcards

1
Q

What percentage of total protein is ribosomal protein?

A

20%

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2
Q

Copy numbers of rRNA per type of cell

A

Archaea: 1 copy
Prokaryotes: 8 copies
Mammals: 100s of copies

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3
Q

What does increased gene dosage for rRNA increase?

A

ribosomal mRNA
NOT riboprotein
So riboproteins are involved in feedback inhibition of rmRNA

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4
Q

S15

A

Binds and causes pseudoknot which blocks the ternary complex

Ribosomal protein autogenous translational repression

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5
Q

What is rate limiting in ribosome synthesis?

A

Synthesis of rRNA

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6
Q

Core Promoter Structure

A

Consensus at -10
Near consensus at -35
Spacing optimal 17 bp (actually 16 bp)

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7
Q

UP Element

A

Upstream promoter
Third recognition element for RNAP
Enhancer?

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8
Q

Three RNAP recognition elements

A
  1. -10
  2. -35
  3. UP elements
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9
Q

Composition of P1

A

Fis sites - UP - -35 - -10

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10
Q

Fis

A

Small DNA binding protein
Positive transcription factor for rRNA promoters
Binds at 3 sites in P1 and recruits RNAP
10x effect
Correlates to growth like ribosome concentration
Redundancy

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11
Q

DksA

A

Impacts cell division, sigma S, amino acid biosynthesis, quorum sensing and virulence
Transcription factor that binds RNAP
Essential for regulation of rRNA promoters through ppGpp and iNTPs
Reduces lifetimes of rRNA promoter open complexes

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12
Q

DksA Mutant

A

Doesn’t shut down rRNA transcription in stationary, increasing in fresh medium, respond to aa starvation or show growth rate dependent regulation

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13
Q

How does DksA impact ppGpp?

A

Increases apparent Km of ppGpp for RNAP

Increases impact on open complex lifetime

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14
Q

How does DksA impact iNTP?

A

Increases concentration required for transcription

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15
Q

BoxA

A

RNAP interacts with host factors and undergoes allosteric change that allows it read through rho-dependent terminators within rRNA genes
Termination at rho independent sites are not affected

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16
Q

Stringent Response

A

During amino acid starvation
Shutoff of RNA synthesis
Produced in idling reaction between ribosomes and ppGpp synthase

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17
Q

Stringent Response is dependent on what?

A

Charged tRNAs, not AA pool

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18
Q

RelA

A

ppGpp synthase

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19
Q

Relaxed Response

A

RelA null allele
No ppGpp accumulation in response to AA starvation
In fact decrease in ppGpp levels

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20
Q

spoT

A

reversible ppGpp synthase and hydrolase (to GDP)

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21
Q

gpp

A

Guanosine pentaphosphate
ppGpp degradation
null allele = hyperproduction

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22
Q

ppGpp

A

Magic spot
GTP+ATP
Down regulates DNA replication, fatty acids, cell wall, lipids, ribosomal proteins, elongation factors, stable RNA
Up regulates stress proteins, amino acid biosynthesis, proteolysis, glycolysis, survival genes, oxidative and osmotic stress genes

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23
Q

ndk

A

Nucleoside diphosphate kinase

Creates precursor for ppGpp

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24
Q

How does ppGpp stop transcription of rRNA?

A

Binds at promoter P1

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25
Q

How could ppGpp negatively regulate?

A
  1. Open complex stability
  2. Promoter clearance
  3. Open complex formation
  4. Pausing during elongation
  5. Competition between ppGpp and NTP substrates
  6. Base pairing with cytosines
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26
Q

When do and which promoters require higher concentrations of NTPs?

A

Initiation

P1 promoters

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27
Q

What pieces of evidence support that NTP concentrations are not saturation for rRNA promoters in vivo?

A
  1. RNAP mutants requiring higher concentrations of iNTPs

2. Promoter mutants that no longer needed high concentrations of NTPs

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28
Q

What is one way you can control rRNA promoters in vivo?

A

Control the concentrations of GTP and ATP

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29
Q

How do Bacillus subtilis promoters differ from E. coli?

A
  1. Less dependence on UP elements and alpha CTD
  2. No Fis
  3. All promoters initiate with GTP
  4. ppGpp works indirectly by decreasing GTP
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30
Q

ppGpp deficiency genotype

A
  1. No growth w/o aa
  2. Filament formation
  3. Decreased survival
  4. Decreased virulence
  5. Decreased expression of sigma S genes
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31
Q

What is the largest group of metal resistance systems?

A

Efflux pumps

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32
Q

What are the two types of efflux pumps?

A
  1. ATPases

2. Chemiosmotic cation/proton antiporters

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33
Q

4 generalizations about metal resistance

A
  1. Highly specific
  2. No general mechanism for all heavy metal ions
  3. Resistance on plasmids in every group tested
  4. Resistance is usually efflux pumping or enzymatic conversion
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34
Q

Where genetically are efflux pumps found?

A

On both plasmids and chromosomes

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35
Q

Which metal resistance systems are highly conserved in bacteria and which aren’t?

A

Arsenic and mercury are conserved

Cadmium is not (evolved 3 times)

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36
Q

What are the 3 evolutionary paths of cadmium resistance?

A
  1. ATPases in G+ bacteria
  2. Antiporters in G- bacteria
  3. Metallothionein in cyanobacteria
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37
Q

Metal homeostasis

A

Metals are not free atoms in cell cytoplasm, they are bound to carriers

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38
Q

Thiol titration

A

Metals have natural affinity for sulfur.

R group of cysteine readily binds metals, blocks thiol use for normal function

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39
Q

Metal chaperones

A

Metals can be associated with chaperones and delivered to efflux pumps or enzymes

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40
Q

Metal Uptake

A

Poorly understood

Via import pumps that lack discriminatory activity?

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41
Q

Cd2+ ATPase motifsd

A 
G+
Cd2+ binding
Aspartyl kinase
Phosphatase
Membrane channel
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42
Q

P-type ATPases

A

All contain aspartyl kinase and phosphatase

Only transport ATPases that have a covalent phospho-protein intermediate

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43
Q

CadC

A

Binds to cad promoter/operator

Inducibly regulated by divalent cations

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44
Q

Family of metal binding proteins

A

ArsR, SmtB, CadC

  1. Respond to metals
  2. Repressors
  3. HTH with metal binding cys residues
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45
Q

Menkes Syndrome

A

Encode P-type ATPase
Lethal X-linked disease of copper starvation
Accumulates in upper intestinal mucosa but doesn’t move into blood
Copper requiring proteins are nonfunctional including superoxide dismutase

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46
Q

Wilson’s Disease

A

Copper overload

Impacts liver

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47
Q

Cadmium resistance Alcaligenes

A

Czc: efflux pump (chemiosmotic divalent cation/proton antiporter)
Mutations give Zn resistance
G-

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48
Q

Czc system components

A

Cadmium resistance

  1. CzcA: Basic inner membrane transport protein
  2. CzcC: outermembrane protein
  3. CzcB: membrane fusion proteins that bridges cell membrane

B C C B
A A

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49
Q

Enterococcus cop system

A

In response to both copper starvation and excess
CopA: uptake ATPase
CopB: efflux ATPase
CopY: repressor activated by intracellular Cu+
CopZ: anti-repressor

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50
Q

Levels of copper and Cop system response

A

Low: CopY is inactive
Medium: CopY is active
High: CopY is inactivated by CopZ

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51
Q

ars operons

A 
Found in G+ and G-
Reduce As(V) to As(III), which is more toxic
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52
Q

Components of ars operon

A 
ArsR: transcriptional repressor
ArsD: regulatory throttle protein (upper limit)
ArsA: membrane associated ATPase
ArsB: Arsenite transport protein
ArsC: Arsenate reductase
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53
Q

What two ars genes are missing from E. coli chromosomes and staphylococcal plasmids?

A

ArsA and ArsD

ArsD has little impact

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54
Q

What makes ArsA special?

A

Converts ArsB chemiosmotic complex into ATPase
Membrane transport that can switch between primary and secondary active transport is novel
Can transport antimonite
Homodimer - 4 ATP binding sites

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55
Q

How do staphylococcal and gram negative arsenate reductases differ?

A

Staphylococcal derives reducing power from thioredoxin

G- derive reducing power from glutaredoxin

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56
Q

What is one way that arsenate can diffuse out of cells?

A

Metal inactivation by volatilization
Methylation of As to volatile species
Methanobacterium

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57
Q

What is the most toxic metal in humans?

A

Mercury causes neurological and immunological dysfunction

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58
Q

What is the trend for mercury resistance across domains?

A

Bacteria: MIC=100uM
Archaea: MIC=300 nM
Eukarya: MIC=submicromolar

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59
Q

What is the mercury mechanism of toxicity?

A

Decreases RNA synthesis by blocking transcription

Depletes mRNAs

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60
Q

mer operon Genes

A 
MerR: Regulation (repression and activation)
MerP: periplasmic binding
MerT: Transport
MerA: Mercuric reductase
MerD: Regulation
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61
Q

merA

A

Mercuric reductase

Hg2+ > Hg0

62
Q

MerR

A

Unique positive acting activator protein that twists and bends the DNA region in the presence of Hg2+, allowing RNAP to bind
Bind at inverted repeats
Needed to help TBP and TFB

63
Q

MerB

A

Organomercurial lyase that breaks carbon-mercury bond in toxic substrates suck as phenylmercury acetate

64
Q

Narrow spectrum mer systems

A

Systems with MerA but not MerB

G-

65
Q

Broad spectrum mer systems

A

Systems with MerA and MerB

Confer resistance to organomercurials

66
Q

Baseball glove model

A

MerT and MerP
Bind Hg2+ by a pair of vicinal cysteins in merP, followed by passing Hg2+ from cysteine pair to cysteine pair in MerT and finally to MerA

67
Q

Chemical toxicity of uranium

A

Greatest risk
Interacts with phosphate groups of DNA
Kidneys

68
Q

How is uranium present in oxic environments?

A

Soluble salts of uranyl ion

When reduced from U(VI) to U(IV) it immobilizes

69
Q

Important uranium reducing Bacteria

A

Geobacter
Shewanella (MtrA/SO3300)
Terminal electron acceptor, cytochrome mediated

70
Q

Mutations in uranium reducing cytochromes negatively impacts

A

Fe(III) reduction rates with acetate as e- donor

71
Q

Nanowires

A

Geobacter
Interact with insoluble terminal electron acceptors through pili
Electrons flow from cell to electron acceptor
Implied by localization of precipitated UO2
Reduce Fe(III) or Mn(IV) for sure, uranium probably

72
Q

What can cause uranium oxidation?

A

Nitrate
Interaction with Fe(III), generating U(VI) and Fe(II) (coupled to oxidation of Fe(II) by nitrogen oxides created by nitrate reduction in bacteria)
Humic substances, siderophores and bicarbonate

73
Q

Argyria

A

Side effect of silver

Irreversible discoloration of the skin resulting from subepithelial silver deposits

74
Q

What metal can coat catheters?

75
Q

Silver resistance genes

A 
SilRS: sensor/responder
FilE: periplasmic Ag(I) binding protein
2 efflux pumps:
SilP: P-type ATPase
SilCBA: Chemiosmotic Ag(I)/H+ exchange system
76
Q

silE

A 
Binds Ag(I) between two His residues
Can bind 5 Ag
77
Q

Metallothioneins

A

Only in Synechoccus cyanobacteria
Related to small, thiolate-rich metal binding proteins of animals
SmtA protein contains 9 cysteine residues that bind divalent cations in N-terminal and C-terminal clusters

78
Q

Preference of cation binding in metallothioneins

A
  1. Zn2+
  2. Cd2+
  3. Cu2+
79
Q

SmtA

A

Uptake and efflux of Zn

Regulated without connection to SmtB

80
Q

5 Strategies of Metal Resistance

A
  1. Enzymatic Conversion
  2. Reduced sensitivity
  3. Permeability barrier
  4. Intra/extra-cellular binding
  5. Efflux
81
Q

ICP-MS

A

Inductively coupled plasma mass spec

Metal based approach to identify metalloproteins on a genome wide scale

82
Q

Terminator sequences functional component

83
Q

Intrinsic terminators

A

Rho-independent
GC rich palindrome
Poly-T and poly-U form an RNA stem loop

84
Q

Extrinsic terminators

A

Rho-dependent

85
Q

Rho

A

Homohexamer donut-shaped
Facilitates dissociation of RNAP-DNA-mRNA complex
N-terminal RNA binding domain
C-terminal ATPase domain
Translocates by ATP hydrolysis, unwinding RNA-DNA hybrid

86
Q

Rho-dependent terminator sites

A
  1. RUT (rho-utilization site)
  2. Termination sequence (pause RNAP)
    Over 200 bp
87
Q

Nonsense mediated polarity

A

Ability of nonsense mutations to reduce downstream gene expression
Only occurs in prokaryotic organisms
Coupled transcription and translation

88
Q

NMP located near what tend to be more polar?

A

The 5’ end of the gene (upstream)

89
Q

In what bacteria is rho essential?

A

E. coli, Rhodobacter and Caulobacter

90
Q

In what bacteria is rho nonessential?

A

Bacillus and Staphylococcus

91
Q

Bicyclomycin

A

Antibiotic that inactivates rho
Experimental tool
Increase basal level of tryptophanase operon
Relieved polarity

92
Q

tna operon

A

Tryptophan-induced relief from rho-mediation termination in leader region
Catalyze tryptophan from indole
Basal level is low

93
Q

NusG

A

Bacterial protein that modulates elongation and termination through interaction with RNAP and rho
Bridges Rho and RNAP
HELPS RHO

94
Q

NudA

A

Controls RNAP pausing and termination
Bacteria and Archaea
Anti-termination factor
Decreases rate of rho-dependent termination

95
Q

Archaea and extrinsic termination

A

In Methanogens upstream sequence influenced susceptibility to downstream termination site
Analogous to rho and RUT sites
Halobacterial bop gene shows strong transcriptional polarity
NMP in S solfataricus

96
Q

Sso mer operon NMP

A

merRHAI
Nonsense mutation at 12 codon of MerH
Mercury sensitive phenotype, same as MerA disruption mutant
Reintroduction of MerH elsewhere did not restore WT
MerH is important for downstream expression

97
Q

Transcription terminator in Sso

A 
At merHA junction
Two transcripts: HA and H
Thermometer
80°C: primary secondary structure is at MerHA junction
37°C: numerous secondary structures
98
Q

Transcription Termination in Archaea

A 
Polarity
NMP
Terminators
Rho is missing
NusA and NusG are present
RNAP is different
99
Q

Domains of RNAP

A

Alpha: interacts with promoters
Beta: RNA synthesis

100
Q

Sigma regions

A
  1. Binds promoter when bound to RNAP
  2. Binds -10 pribnow box
  3. Binds -35 element
101
Q

Sigma programming depends on

A
  1. Affinity
  2. Abundance
  3. Interference
102
Q

Sigma 32

A

rpoH
30°C > 42°C
Sigma 32 genes are turned on
Increased cellular concentration through enhanced synthesis and stabilization

103
Q

rpoH RNA thermometer

A

Small region downstream is responsible for high levels of expression (+)
Large region is required for thermal regulation, repression at low temps (-)

104
Q

Clp System

A

Degrades sigma S
ClpX: substrate binding
ClpP: proteolysis
RssB mediates recognition by binding both sigma S and ClpX

105
Q

RssB

A

Undergoes N-terminal aspartate phosphorylation to activate sigma S binding
Acetyl phosphate decreases in starvation

106
Q

Anti-sigma factors

A

Bind conserved regions

107
Q

Phage T4 AsiA

A

Alt protein ADP ribosylates alpha subunit of RNAP and decreases -35 affinity
AsiA binds sigma-70 blocks 4.2- -35 binding
Mod protein overcomes by providing RNAP alternate contact

108
Q

Sigma 28

A 
Flagellar assembly
Class 3 genes are delayed
FlgM binds FliA until basal body is complete
Basal body secretes FlgM
Free FliA transcribes Class 3 genes
109
Q

Archaeal transcription

A

TATA and TBP
TFB
RNAP
BRE

110
Q

Eukaryotic Pol I

A

Nucleolus
rRNA
alpha-amanatin resistant

111
Q

Eukaryotic Pol II

A

Nucleoplasm
hnRNA
Alpha amanatin sensitive

112
Q

Eukaryotic Pol III

A

Nucleoplasm
tRNA
Variable in response to alpha amanatin

113
Q

Eukaryotic Pol II Enzyme order

A
  1. TFIID, TBP and TAFs
  2. TFIIA (helps TFIID bind promoter)
  3. TFIIB assigns direction and recruits RNAP
  4. TFIIF and PolI
  5. TFIIE (clearance and further melting)
  6. TFIIH and TFIIJ (help create bubble)
114
Q

Archaeal Polymerase

A

Pol II like

12 subunits which are orthologs of Pol II

115
Q

Archaeal general transcription factors

A
  1. TBP, no TAFs
  2. TFIIB (TFB) directionality
  3. TFIIS fidelity
  4. TFIIE-alpha stimulation of promoters
116
Q

TBP evolution

A

Encoded in metazoan genomes for differentiation

117
Q

TIPS

A

TBP-interaction proteins
N terminal domain like TAF, stimulate transcription
ATP/GTP binding P loop, homology to helicase RuvB
Found in Archaea TAF like

118
Q

3 Ways to Repress Transcription

A
  1. Block RNAP
  2. Prevent activation
  3. Prevent elongation
119
Q

Lactose is composed of

A

Galactose + Glucose

120
Q

LacI

A

Formers tetramer

Represses in absence of lactose

121
Q

Lac genes

A

LacZ: B-galactosidase
LacY: permease
LacA: transacetylase

122
Q

B-galactosidase

A

Converts lactose to allolactose

123
Q

CAP binds

A

alpha-CTD of RNAP

Cooperative binding with DNA looping

124
Q

CAP impacts

A

Lactose and arabinose operons

125
Q

How can repressors stop RNAP binding?

A 
Binding a site that overlaps the binding site of RNAP
Lamba CI
LexA
p4
LacI
126
Q

How does LacI impede RNAP?

A

Allows binding to promoter

Allows short abortive transcripts, but inhibits promoter clearance

127
Q

CytR

A

Binds to -70, flanked by cyclic AMP receptor proteins at -40 and -90
Doesn’t overlap RNAP binding site

128
Q

Low sequence specificity high abundance proteins

A

Block transcription at promoter by covering relatively large DNA regions at a nucleation site
p6 from phage phi29
DnaA (oligomerizes)
H-NS

129
Q

Repressors that block transition for closed to open complex

A

Unable to open DNA strands at -10 region
Group I: bind sites that overlap with RNAP
Group II: bind sites that do not overlap with RNAP

130
Q

Repressor inhibiting promoter clearance

A
  1. RNAP is stalled at +6 to +12 when binding consensus element too tightly
    p4 interacts with alpha-CTD
  2. Promoter clearance is inhibited when repressor binds downstream from RNAP
    LacI
131
Q

Histidine operon

A

E. coli and S. typhimurium

132
Q

Histidine biosynthesis

A

ATP + PRPP > IGP > Histidinol phosphate > histidinol > histidine
40 molecules of ATP per histidine

133
Q

What are the three ways histidine biosynthesis is regulated?

A
  1. Allosteric control of enzymes
  2. Attenuation
  3. ppGpp
134
Q

HisG

A

ATP phosphoribosyl transferase (first step) is feedback inhibited by histidine
Homohexamer
Binding and inhibition are cooperative
AMP and ADP inhibit

135
Q

His attenuation needs

A
  1. presence of his residues in leader sequence
  2. mutually exclusive secondary structures
  3. RP pausing
136
Q

What secondary structure terminates his operon?

A

EF and poly U terminate (caused by a lack of stalling in leader peptide)

137
Q

His antiterminator

A

Anything that prevents EF

DE is physiological antiterminator (caused by stalling)

138
Q

Histidine excess

A

EF termination structure forms

139
Q

Histidine Limitation

A

No attenuator forms

DE antiterminator

140
Q

Histidine superattenuation

A

AB, CD and EF

Upstream stalling

141
Q

His Unlinked Mutations

A
  1. hisR: tRNAhis mutants in hisR promoter - less charged tRNA - stimulates starvation - antiterminator
  2. hisS: histidyl tRNA synthase
  3. hisT: pseudourine synthase, decrease function of tRNA
  4. hisW: gyrA decreased gyrase activity, decrease strength of hisR promoter
  5. hisU: ribozyme that results in decrease tRNAhis
142
Q

Tryptophan operon repression

A

Low: no repression, dimer repressor cannot bind
High: repression, dimer binds

143
Q

Tryptophan attenuation

A

Leader sequence has trp encoded
Starvation - stall - 2 and 3 form, no termination
Abundance - no stall - 1 and 2, 3 and 4 form, terminator hair pin

144
Q

pyrC

A

UMP > CTP in pyrimidine nucleotide biosynthesis
High CTP: pyrimidine excess, SD is obscured dur to mRNA binding
Low CTP: no mRNA binding, SD is available to ribosome

145
Q

TRAP

A

G+, Bacillus subtilis
Ring-shaped multimer of 11 subunits
binds RNA segments containing NAG repeats
Gene expression decreases, overlaps antiterminator sequence
Shine Delgarno is hidden in hairpin

146
Q

AT

A

Anti-TRAP protein
deficiency of charged tRNATrp
Gene expression increases

147
Q

Tryptophan synthase genes

A

TrpA and B

148
Q

T box mechanism

A

Uncharged tRNA pairs with leader RNA, favoring formation of RNA antiterminator structure

149
Q

rtpA

A

AT
Lacks tryptophan - insensitive synthesis
Leader has tRNATrp sensing

150
Q

rtp operon response to tRNA Trp

A

Charged: Transcription stops due to terminator loop
Mild charge: transcription proceeds, but RNAP inhibits rtpA translation
Severe charge deficiency: Ribosome stalls and doesn’t block translation

Microbial Physiology (2 decks)

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