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Microbiology > Microbiology Exam 3 > Flashcards

Microbiology Exam 3 Flashcards

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1
Q

Terminal electron acceptors get what and then go where?

A

They get reduced and then exit the cell

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2
Q

Respiring organisms that use O2 are what?

A

aerobic, and O2 goes to H2O

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3
Q

Respiring organisms that use NO3- and SO4-2 are what?

A

anaerobic, NO3 -2 goes to NO2- and S compounds

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4
Q

Do respiring organisms use substrate-level phosphorylation or oxidative phosphorylation?

A

Both

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5
Q

Do respiring organisms have an ETC/ETS?

A

Yes they use NADH/FADH2

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6
Q

What are the recycled electron carriers in respiring organisms?

A

NAD+, FAD

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7
Q

Do fermenting organisms use substrate-level phosphorylation or oxidative phosphorylation?

A

Only substrate-level phosphorylation

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8
Q

What happens to NAD+ in fermenting organisms?

A

Needs to be regenerated

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9
Q

The main function of catabolic pathways is to what?

A

breakdown macromolecules and other compounds

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10
Q

What are the three sugar breakdown pathways?

A

Glycolysis, Entner-Doudoroff, Pentose phosphate

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11
Q

What happens in catabolism?

A

Oxidize macromolecules
Oxidize sugars
Produce energy, reducing power, and precursor metabolites

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12
Q

What happens when you oxidize macromolecules?

A

convert macromolecules into sugars or catabolic pathway intermediates

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13
Q

What are is the energy produced in catabolism?

A

ATP

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14
Q

What are the reducing powers in catabolism?

A

NADH, NADPH, FADH2

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15
Q

What is the lipid breakdown pathway?

A

lipases (hydrolysis) form glycerol and fatty acids and go to acetyl-CoA

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16
Q

What is the protein breakdown pathway?

A

Proteases hydrolysis amino acids

Amino acid decarboxylases and deaminases go to glycolysis

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17
Q

What is the carbohydrate breakdown pathway?

A

Amylases to form sugars

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18
Q

What is the Entner-Doudoroff equation?

A

C6H12O6+ NAD+ + NADP+ + ADP + Pi goes to 2 C3H4O3 + NADPH + 2 H+ + ATP

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19
Q

What is one microbe that undergoes Entner-Doudoroff?

A

VIbro cholera

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20
Q

What is unique about the Pentose phosphate pathway?

A

It is amphibolic.

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21
Q

What are some anabolic precursor metabolites for the pentose phosphate pathway?

A

Ribose-5-phosphate and erythrose-4-phosphate, nucleic acid and protein biosynthesis
Acetyl-CoA

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22
Q

Where does the pentose phosphate pathway lead?

A

glycolysis, watch for fermentation though

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23
Q

What is the product of the pentose phosphate pathway?

A

2 NADPH

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24
Q

What is the gycolysis equation?

A

C6H12O6 + 2 NAD+ + 2ADP + 2Pi goes to 2 C3H4O3 + 2NADH + 2H+ + 2ATP

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25
Q

What are the net energy carriers in glycolysis?

A

2 ATP through substrate-level phosphorylation, 2NADH

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26
Q

Step 1 in glycolysis

A 
Glucose + ATP → G-6-P + ADP
-6 C to 6 C
-hexokinase 
ATP- independent phosphotransferase can also bring in G6P
-Energy carrier: -1ATP
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27
Q

Step 2 in glycolysis

A

glucose 6-phosphate is isomerized to fructose 6-phosphate by phosphoglucose isomerase

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28
Q

Step 3 in glycolysis

A

Fructose 6-phosphate is phosphorylated by reaction with ATP to form fructose 1,6 bisphosphate, by phosphofructokinase

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29
Q

Step 4 in glycolysis

A

Fruc-1,6-2P ↔ Dihydroxyacetone phosphate (DHAP) + Glyceraldehyde-3-phosphate (G3P)
6C to 3C+3C
aldolase

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30
Q

Step 5 in glycolysis

A

Dihydroxyacetone phosphate (DHAP) ↔ Glyceraldehyde-3-phosphate (G3P)

  • 3C to 3C
  • triose phosphate insomerase (TIM)
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31
Q

Step 6 in glycolysis

A

G3P + NAD+ + Pi ↔ 1,3-bisphosphoglycerate + NADH + H+
3C to 3C
glyceraldehyde 3-phosphate dehydrogenase
EC: 1 NADH

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32
Q

Step 7 in glycolysis

A

1,3-bisphosphoglycerate + ADP ↔ 3-phosphoglycerate (3PG) + ATP
3C to 3C
Phophoglyserate kinase
EC: + 1 ATP (substrate- level phosphorylation)

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33
Q

Step 8 in glycolysis

A

3-phosphoglycerate (3PG) ↔ 2-phosphoglycerate (2PG)
3C to 3C
phosphorglycerate mutase
Shift of phosphate functional group

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34
Q

Step 9 in glycolysis

A

2-phosphoglycerate (2PG) → phosphoenolpyruvate (PEP) + H2O
3C to 3 C
Enolase

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35
Q

Step 10 in glycolysis

A

Phosphoenolpyruvate (PEP) + ADP → pyruvate + ATP
3C to 3C
Pyruvate kinase
EC: 1 ATP (substrate- level …

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36
Q

Where is NADH consumed

A

by PMF or fermentation

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37
Q

Where is NADPH consumed

A

anabolism/biosynthesis

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38
Q

What is the pyruvate dehydrogenase equation

A

pyruvate + CoA+ NAD+ goes to Acetyl-CoA+ CO2+ NADH+ 2H+

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39
Q

What is the movement of carbon atoms in the pyruvate dehydrogenase equation?

A

3C pyruvate goes to 2C acetyl+ 1C (CO2)

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40
Q

What are the energy carriers in pyruvate dehyrogenase?

A

Reducing power is 1 NADH/ pyruvate

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41
Q

TCA cycle is only found in organisms that have what?

A

Electron transport system/chain

Aerobic and anaerobic respiring organisms

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42
Q

What is the main point of TCA cycle

A

oxidize Acety-CoA (from pyruvate dehydrogenase) to 2CO2

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43
Q

What is the TCA equation?

A

Acetyl-CoA + 3 NAD+ + FAD + ADP + Pi → 2 CO2 + 3 NADH + 3 H+ + FADH2 + ATP

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44
Q

What is step 1 of TCA?

A

Oxaloacetate + acetyl-CoA + H2O → citrate + CoA
4C+ 2C → 6C
Citrate synthase
synthase rxn, no ATP

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45
Q

What is step 2 of TCA?

A

Citrate → cis-aconitate + H2O
6C → 6C
Aconitase
technically a dehydration rxn

46
Q

What is step 3 of TCA?

A

Cis-aconitate + H2O → isocitrate
6C→6C
Aconitase
Steps 2 + 3: overall isomeration by aconitase

47
Q

What is step 4 of TCA?

A

Isocitrate + NAD+ → α-ketoglutarate (α-KG) + CO2 + NADH + H+
6C → 5C+ 1C
Isocitrate dehydrogenase
EC: 1 NADH formed

48
Q

What is step 5 of TCA?

A

α-KG + NAD+ + CoA → succinyl-CoA + CO2 + NADH + H+
5C → 4C+ 1C
2-oxogluterate dehydrogenase
EC: 1 NADH formed

49
Q

What is step 6 of TCA?

A

Succinyl-CoA + ADP (or GDP) + Pi → succinate + ATP (or GTP) + CoA
4C → 4C
Succinyl- CoA synthetase
EC: 1 ATP (or GTP) formed

50
Q

What is step 7 of TCA?

A

Succinate + FAD → fumarate + FADH2
4C →4C
succinate dehydrogenase
EC: 1 FADH2 formed- immediately consumed/ recycled by ETC

51
Q

What is step 8 of TCA?

A

Fumarate + H2O → malate
4C → 4C
fumarase
hydration reaction

52
Q

What is step 9 of TCA?

A

Malate + NAD+ → oxaloacetate + NADH + H+
4C → 4C
Malate dehydrogenase
EC: 1 NADH formed

53
Q

Why have fermentation?

A

oxidize NADH back to NAD+

54
Q

When do you have fermentation?

A

No inorganic terminal electron acceptor available

No electron transport chain

55
Q

What is the organic terminal electron acceptor in fermentation?

A

pyruvate or derivatives like Acetyl-CoA

56
Q

Describe the specifics of Clostridium perfringens

A 
Gram (+) 
Bacillus
Obligate anaerobe (No SOD, catalase) 
Obligate fermenter (No ETC)
Endospores 
Found in the Soil and intestines
57
Q

What is gangrene?

A

The loss of blood supply in the tissues, happens in the muscle, caused by clostridium spp. Tissues become infected, bloody discharge, swelling, severe pain, popping of skin

58
Q

What is the Catabolism of Clostridium perfringens

A

Chemoheteroorganotroph

Eats everything

59
Q

What is the major virulence factor for Clostridium perfringens?

A

alpha-toxins= phospholipase+hemolysis

60
Q

What metabolic pathway does Clostridium perfringens run?

A

glycolysis, no pyruvate dehydrogenase, no TCA

61
Q

What are the products made by Clostridium perfringens after glycolysis in the two pathways?

A

Pathway 1- Ethanol, Acetate, Butyrate, H2+CO2

Pathway 2- Propionate, CO2

62
Q

Describe branch 1 that clostridium can take after glycolysis

A

Pyruvate →→→ ethanol/acetate/butyrate + H2 + CO2
makes pyruvate synthase instead of pyruvate dehydrogenase, makes acetyl-CoA + CO2
Acetyl-CoA branches to make acetate, butyrate, ethanol Hydrogenase
H2 + CO2
More anaerobic
Gas bubbling

63
Q

Describe branch 2 that clostridium can take after glycolysis

A 
Lactate dehydrogenase
Pyruvate + NADH + H+ → Lactate + NAD+
3C → 3C
Oxidizes NADH to NAD+
Lactate →→→ propionate + CO2
Oxidizes NADH to NAD+
More bubbling
64
Q

Describe the specifics of Streptococcus pyogenes

A

Gram +
Diplococcus
Obligate fermenter (No ETC)
Found in the Environment and Orally

65
Q

What diseases does Streptococcus pyogenes make?

A

Pharyngitis, Rheumatic fever, Mastitis, Necrosizing fasciitis

66
Q

What is the catabolism of Streptococcus pyogenes?

A

Chemoheteroorganotroph

Eats proteins and carbohydrates

67
Q

What metabolic pathway does Streptococcus run?

A

glycolysis (no pyruvate dehydrogenase

68
Q

What is Homolactic fermentation?

A

Uses lactate dehydrogenase

pyruvate+ NADH + H+ → Lactate + NAD+ (3C → 3C)
oxidizes NADH to NAD+

69
Q

What microbes have homolactic fermentation?

A

Streptococcus pyogenes, Clostridium perfringens

70
Q

Describe the specifics of lactobacilli

A 
Gram + 
Bacillus
Aerotolerant anaerobe (obligate fermenter, No ETC) 
Lives int intestines, and raw milk
Acidophiles
71
Q

What is the catabolism of lactobacilli

A

Chemoheteroorganotroph
Some lactate only homolactic fermenter (no CO2)
Some heterolactic fermenters

72
Q

What is heterolactic fermentation

A

Start with pentose phosphate pathway
Lactate + *CO2 + ethanol
6C → 3C + 1C + 2C
Oxidizes NADPH and NADH

73
Q

What are the benefits of probiotics?

A

Competition to inhibit pathogens

Antimicrobial production

74
Q

What are some commercial products that contain probiotics

A

Milk, Kimchi, sauerkraut, pickles, chocolate

75
Q

What is respiration

A

Donor oxidized by ETC/ETS → e-s go to a terminal electron acceptor, H+ pumped → PMF enables ATP synthase to produce ATP

76
Q

What is oxidative phosphorylation?

A

Use electron transport system/ chain
redox reaction in membrane electron carriers (proteins, and small molecules )
Oxidizes reduced electron carriers
Get NAD-/FAD+ back for more sugar breakdown

77
Q

What is the proton motive force?

A

[H+] outside > [H+] inside

78
Q

Where do eukaryotes and prokaryotes have a proton motive force?

A

Eukaryotes: mitochondria
Prokaryotes: cellular membrane

79
Q

How many protons does ATP synthase use to make 1 ATP?

A

3 H+

80
Q

Describe prokaryote respiration

A

Variable carriers – adapts to conditions
Dehydrogenase (enzyme) oxidizes electron donor (small molecule), reduces quinone (“Q”: small molecule)
Terminal oxidase (enzyme) oxidizes quinone, reduces inorganic terminal electron acceptor (O2, NO3-)
Energy released at each step pumps protons outside membrane

81
Q

What is the NADH dehydrogenase reaction

A

NADH + H+ + Q → NAD+ + QH2

82
Q

What is the Succinate dehydrogenase reaction

A

Succinate + Q → Fumarate + QH2
FAD → FADH2 (TCA) →FAD (electron transport)
Succinate+ Q+ FAD → Fumarate + QH2 +FAD

83
Q

What is the cyt bo oxidase reaction, cyt bd oxidase reaction

A

2QH2 + O2 (oxygen!) → 2Q + 2H2O

84
Q

What is the nitrate reductase reaction

A

QH2 + NO3- (NOT oxygen) → Q + NO2- + H2O

85
Q

What are the 3 dehydrogenases and how many protons do they pump

A

NADH dehydrogenase 1 (NDH-1)=4 protons
NADH dehydrogenase 2 (NDH-2)=0 protons
Succinate dehydrogenase = 0 protons

86
Q

What are the 3 terminal oxidases and how many protons do they pump?

A

Cytochrome bo quinol oxidase (cyt bo)=8protons
Cytochrome bd oxidase (cyt bd)= 4 protons
Nitrate reductase= 2 protons

87
Q

What is the theoretical maximum oxidative prokaryote yield?

A

37

88
Q

How many ATP’s can you produce with glycolysis?

A

6 ATP

89
Q

How many ATP’s can you produce with pyruvate dehydrogenase?

A

6 ATP

90
Q

How many ATP’s can you produce with TCA?

A

6NADH → 18 ATP

2 FADH2 → 3 ATP

91
Q

How many ATP’s can you produce with Oxidative phosphorylation?

A

33

92
Q

How many ATP’s can you produce with substrate level phosphorylation?

A

4 (2 from glycolysis and 2 from TCA)

93
Q

Why is the actual yield and theoretical yield so different?

A

Energy goes to
protons are used for other things outside the cell membrane
flagella movement (not the largest thing as non-flagellated microbes also loose the protons)
A major amount is lost due to Heat
Lost in electron transport and the protons hit oxygen and form superoxide radical and the microbe has to use super oxidedismutase to get rid of the radicals.

94
Q

What is Lithotrophy?

A

Use of inorganic compounds as a source of electrons for metabolism

95
Q

The opposite of Lithotrophy is what?

A

Organotrophy

96
Q

What is an example of lithotrophy?

A

Strain 121

97
Q

What is phototrophy?

A

Light as energy source

98
Q

Phototrophy usually occurs where and how?

A

In a photosystem

Excite an electron (photolysis), split from donor
transfer e-’s, pump H+= PMF
pigments, electron carriers and proteins= ETC/ETS!

99
Q

Describe photosystem II

A 
Anaerobic/anoxygenic 
Facultative anaerobes
Electron donor:  bacteriochlorophyll
Cyclic phosphorylation: donor oxidized and reduced 
Energy carriers
  No e-’s to transfer 
  NO NADPH (reducing power) 
  ATP (photophosphorylation)
100
Q

Describe photosystem !

A 
Anaerobic/anoxygenic 
Obligate anaerobes
Electron donor:  H2S, Fe+2, organic donor (microbe-dependent) 
Lithotrophs! 
Noncyclic phosphorylation: donor permanently oxidized 
Energy carriers
   NADPH (reducing power) 
   ATP (photophosphorylation)
101
Q

Describe the oxygenic Z pathway

A 
Aerobic
Obligate aerobes
Parts of PS I and PS II 
Electron donor:  H2O →O2
Noncyclic phosphorylation 
Energy carriers
NADPH (reducing power) 
ATP (photophosphorylation)
102
Q

Where is NADH and NADPH consumed

A

NADH is consumed by PMF or
fermentation
NADPH is consumed by anabolism/ biosynthesis

103
Q

Describe carbon fixation and the different types of reactions

A

CO2 (inorganic)→→→ organics

Calvin cycle
reductive/reverse TCA cycle
Acetyl-CoA pathway
3-Hydroxypropionate cycle

104
Q

Describe the Calvin cycle

A 
typically obligate aerobes 
Substrates:  CO2, NADPH, ATP
Products: Glucose, NADP+, ADP + Pi
Chloroplasts (eukaryotes) 
Anabaena spiroides
Prochlorococcus marinus 
No archaea (yet)
105
Q

Describe the reductive/reverse TCA cycle

A

Some archaea, some obligate/ facultative anaerobes
Similar to (not exact) backwards TCA cycle
“original” carbon fixation cycle
Substrates: CO2, ATP, NADH (??)
Products: Acetyl-CoA, ADP + Pi, NAD+

106
Q

Describe the Acetyl-CoA pathway

A 
Some archaea, some obligate/ facultative anaerobes 
Substrates:  CO2, H2, ATP
Products: CH4, Acetyl-CoA, ADP + Pi 
Methanogenic archaea 
Some Clostridia, related species
107
Q

Describe the 3-Hydroxypropionate cycle

A

Some archaea, some facultative anaerobes
Substrates: CO2 (HCO3-), NADPH, ATP
Products: Glyoxylate (→ pyruvate), NADP+, ADP + Pi

108
Q

Describe nitrogen fixation

A 
N2 → NH4+ /NH3 (section 2) 
Nitrogenase
Many Clostridia (obligate anaerobes) 
Many Cyanobacteria (Anabaena spiroides) (“heterocysts”) 
Substrates:  N2, H+, ATP
Products: NH4+/NH3, ADP + Pi
109
Q

Describe the fatty acid biosynthesis (FAS II)

A 
Multi-enzyme complex 
Different than eukaryotes (“selective toxicity”) 
Target for isoniazid (TB) and triclosan 
Substrates:  Acetyl-CoA, NADPH, ATP
Products: Fatty acids, NADP+, ADP + Pi
110
Q

Describe the biosynthesis of Erythromycin

A

Polyketide synthase (PKS)
Substrates: Malonyl-CoA, NADPH
Products: Erythromycin precursor, NADP+

111
Q

Describe the biosynthesis of Vancomycin

A

Non-ribosomal peptide synthetase (NRPS)
Energy: ATP → AMP + PPi (irreversible)
Substrates: amino acids, ATP
Products: Vancomycin precursor, AMP + PPi

112
Q

Describe the biosynthesis of Penicillins

A

Energy: ATP → AMP + PPi (irreversible)
Substrates: amino acids, ATP
Products: Penicillins, AMP + PPi

Microbiology (4 decks)

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