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Microbial Physiology > E2 > Flashcards

E2 Flashcards

1
Q

Site-specific inhibitors?

A

Carbon monoxide
cyanide
sodium azide
rotenone
antimycin A
amytal

  • any compound that stops electron transport will stop breathing
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2
Q

Phosphorylation inhibitor?

A

Oligomycin
- Electron transport can be stopped by inhibiting ATP synthesis (blocking the proton channel)

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3
Q

Uncouplers?

A

DNP and FCCP
- breaking the connection between ATP synthesis and electron transport

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4
Q

How is the ETC electron flow effected by oligomycin

A
  • not stopped
    -PMF can be uncoupled from ATP synthesis by diversion to alternative integral membrane proteins
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5
Q

What do hydrogen sulfide and hydrogen cyanide do

A

-binding and inhibiting complex IV and electron flow
-preventing O2 reduction and respiration

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6
Q

Aerobic respiration steps?

A

Glucose –> 2 pyruvate (with oxygen)–> 36 ATP
- a lot produced in oxidative phosphorylation

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7
Q

Fermentation steps?

A

Glucose –> 2 pyruvate (without oxygen)–> 2 ATP

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8
Q

Aerobic vs Anaerobic respiration?

A

Aerobic
- requires O2
- complete substrate oxidation
- water formed as the end product

Anaerobic
- never requires O2
- Incomplete substrate oxidation
- water is not formed

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9
Q

Anaerobic Respiration (Denitrification) steps

A

NO3 –(nitrate reductase–> NO2 –(nitrite reductase)–> NO –(NO reductase)–> N20 –(N2O reductase)–> N2

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10
Q

Subunits of Nitrate Reductase?

A

alpha, beta, 2 gamma sheets

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11
Q

Nitrate reductase function?

A

gamma transfers electrons to quinol to Fe-S
alpha subunit catalyzes reduction of NO3- to NO2-

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12
Q

How is denitrification regulated?

A
  • inhibited by O2 presence
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13
Q

What is the purpose of sulfate-reducing bacteria?

A

H2 or organic compounds usually serve as electron donors

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14
Q

Assimilatory NO3 reduction

A

If nitrogen is used for a new biomass

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15
Q

Dissimilatory NO3 reduction

A

if N2 gas is released

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16
Q

How to cells assimiliate N?

A
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17
Q

What is an ammoxosome?

A
  • found in plantomyces bacteria
  • structure that enabled PMF generation in the oceans
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18
Q

Nitrogen Fixation

A
  • energetically demanding
  • 16 ATP produced for every N2 reduced
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19
Q

Nitrogen fixation enzyme and function

A

Nitrogenase fixes N2 to ammonia
inactivated by O2

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20
Q

Ammonification

A

breaking down organic matter such as dead animals and plants and wastes like urea

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21
Q

Ammonification enzyme and funtion

A

Urease hydrolyzes urea to CO2 and ammonia

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22
Q

Nitrification performs what kind of respiration?

A

Aerobic respiration
- chemolithoautotrophic metabolism using NH3 for electrons for CO2 fixation

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23
Q

How is ammonia removal (nitrification) impacted by the environment?

A
  1. shocks (cold or hot spells)
  2. Toxicity (“slug” toxin from upstream)
  3. Solid loss (large rain event that can wash them out)
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24
Q

Denitrification

A

Progressive reduction of nitrate to N2 or N20
anaerobic respiration
dissimilatory

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25
Q

Strategies to prevent denitrification?

A
  1. Temporal separation
  2. High respiratory rate
  3. Spatial Separation
  4. Cellular Specialization
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26
Q

Aromatic Amino Acids

A

benzene ring derived from shikimate from condensation of PEP + Erythrose 4 phosphate

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27
Q

What is the key enzyme for aromatic AA synthesis?

A

EPSP synthase

28
Q

Glyphosate function

A
  • inhibits EPSP synthase
  • inhbiting the production of aromatic amino acids
29
Q

Nitrogen donor for most amino acids?

A

Glutamate

30
Q

Nitrogen donor for tryptophan, Histidine, Asparagine, and nucleotides?

A

GlutamINE

31
Q

Phosphoglycerate AA family

A
  • 3 phosphoglycerate converted to serine then glycine to cysteine
32
Q

Pyruvate AA family

A
  • pyruvate transaminated to form alanine
  • the enzyme is ALT (alanine amino transferase)
  • important for catabolism of non- essential amino acids
33
Q

Alpha-ketoglutarate AA family

A

Proline, Glutamate, Glutamine, Hisidine, Argenine

34
Q

Glutamate dehydrogenase

A

converts alpha ketoglutarate and NH4 to glutamate
- used to transaminate and form various AA
- reversible enzyme

35
Q

Transaminases

A

glutamate helps with the addition of amino group skeletons to synthesize most AA
- pyruvate: alanine, valine, leucine
- oxaloacetate to aspartate

36
Q

Aspartate is used for the synthesis of

A

threonine
methionine
lysine

37
Q

What is heme made of?

A

protoporporphoryn IX ring and iron

38
Q

Leghemoglobin

A

A conjugated protein that combines apoprotein with heme prosthetic group to form a functional protein
- heme prosthetic group synthesized by rhizobium

39
Q

How is heme related to central metabolism?

A

synthesized by succinyl CoA

40
Q

What does ALA synthase do?

A

combines succinyl CoA and glycine to make ALA
- first enzyme in the process of making heme

41
Q

Ferrochelatase function

A

Adding central iron to protoporphyrin IX to form heme

42
Q

What enzyme links carb and lipid metabolism?

A

glycerol-3-phosphate dehydrogenase

43
Q

Phases of lipid biosynthesis

A
  1. initiation
    - formation of butyryl-ACP
    - catalyzed by malonyl- COA:ACP transacylase
  2. elongation
  3. termination
44
Q

what enzyme is used in neutral lipid biosynthesis

A

DGAT
- catalyzes the formation of triglycerides from diacylglycerol and acyl CoA

45
Q

Nucleotide biosynthesis pathways

A
  1. Salvage pathway
    Activated ribose+ base
  2. devnovo pathway
    activated ribose+ amino acids+ ATP+ CO2
46
Q

Mechanism of action of sulfa drugs

A
  • inhibits bacterial folate synthesis
    -folate needed for nucleic acid production so without it no DNA copied
47
Q

Cons of sulfa drugs

A
  • bacteriostatic instead of bactericidal
  • allergic reactions comon
  • not effective against all infections
  • resistance happens fast in microbes by plasmid or spontaneous mutation
48
Q

Peptidoglycan structure

A

sugar component made of alternating residues of beta-1,4 linked NAG and NAM
-NAM has short amino acid chain attached

49
Q

What is the NAG/ NAM monomer?

A

Fructose 6-phosphate used to make activated monomers (UDP-NAG and UDP -NAM)
- UDP is a nucleoside diphosphate ester if pyrophosphoric acid with the nucleoside uridine

50
Q

How is the NAG and NAM monomer made

A
  • glutamine donates amino group to fructose 6-phosphate forming glucosamine-6-phosphate
  • acetyl group is then transferred from acetyl CoA to amino group of glucosamine-6-phosphate making N- acetyl-glucosamine-6-phosphate
  • NAG-6-phosphate isomerized to NAG-1- phosphate
  • monophosphate site bunds to UTP
  • UTP-NAG converted to UTP-NAM
    -NADPH reduced to form NAM
  • peptides are attached to NAM only
51
Q

MurG function?

A
  • enzyme that makes lipid II by adding NGM to the NAM-peptide
52
Q

What is the function of transglycosylase?

A
  • catalyzes the polymerization step of the cell-wall biosynthesis
53
Q

What part of the cell wall does penicillin target?

A

transpeptidase

54
Q

What does transpeptidase do?

A

crosslinking peptides, solidifying cell wall

55
Q

What is the central dogma?

A

DNA –(translation)–> RNA –(transcription)–> Protein

56
Q

How do we overcome beta-lactam resistance?

A

beta- lactam antibiotics are given with beta lactamase inhibitors

57
Q

Explain how drug resistance is formed via conjugation

A
  • conjugated pili give plasmid from one bacteria to the next
58
Q

Explain how drug resistance is formed via transformation

A
  • put holes in the cell wall
  • introduce plasmid so it can be absorbed
  • close holes and select bacteria with new plasmid
59
Q

Topoisomerase

A

uncoils DNA to prepare for replication fork

59
Q

Topoisomerase

A

uncoils DNA to prepare for replication fork

60
Q

Helicase

A

separating strands by breaking H bonds

61
Q

DNA polymerase

A

catalyzes the correct base pairing and assembly of the complementary strand
- requires primer

62
Q

Primase

A

adding short complementary bp to form a primer

63
Q

What does a DNTP do?

A

gives energy to the new strand by forming a phosphodiester bond

64
Q

DNA Pol IV

A
  • an error-prone DNA repair system increasing the genetic diversity to make more mutants
65
Q

What is a sigma factor?

A

direct gene expression in response to environmental conditions

Microbial Physiology (2 decks)

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