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Microbiology Exam 3 Flashcards

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
What are the net energy carriers in glycolysis?
2 ATP through substrate-level phosphorylation, 2NADH
26
Step 1 in glycolysis
``` Glucose + ATP → G-6-P + ADP -6 C to 6 C -hexokinase ATP- independent phosphotransferase can also bring in G6P -Energy carrier: -1ATP ```
27
Step 2 in glycolysis
glucose 6-phosphate is isomerized to fructose 6-phosphate by phosphoglucose isomerase
28
Step 3 in glycolysis
Fructose 6-phosphate is phosphorylated by reaction with ATP to form fructose 1,6 bisphosphate, by phosphofructokinase
29
Step 4 in glycolysis
Fruc-1,6-2P ↔ Dihydroxyacetone phosphate (DHAP) + Glyceraldehyde-3-phosphate (G3P) 6C to 3C+3C aldolase
30
Step 5 in glycolysis
Dihydroxyacetone phosphate (DHAP) ↔ Glyceraldehyde-3-phosphate (G3P) - 3C to 3C - triose phosphate insomerase (TIM)
31
Step 6 in glycolysis
G3P + NAD+ + Pi ↔ 1,3-bisphosphoglycerate + NADH + H+ 3C to 3C glyceraldehyde 3-phosphate dehydrogenase EC: 1 NADH
32
Step 7 in glycolysis
1,3-bisphosphoglycerate + ADP ↔ 3-phosphoglycerate (3PG) + ATP 3C to 3C Phophoglyserate kinase EC: + 1 ATP (substrate- level phosphorylation)
33
Step 8 in glycolysis
3-phosphoglycerate (3PG) ↔ 2-phosphoglycerate (2PG) 3C to 3C phosphorglycerate mutase Shift of phosphate functional group
34
Step 9 in glycolysis
2-phosphoglycerate (2PG) → phosphoenolpyruvate (PEP) + H2O 3C to 3 C Enolase
35
Step 10 in glycolysis
Phosphoenolpyruvate (PEP) + ADP → pyruvate + ATP 3C to 3C Pyruvate kinase EC: 1 ATP (substrate- level …
36
Where is NADH consumed
by PMF or fermentation
37
Where is NADPH consumed
anabolism/biosynthesis
38
What is the pyruvate dehydrogenase equation
pyruvate + CoA+ NAD+ goes to Acetyl-CoA+ CO2+ NADH+ 2H+
39
What is the movement of carbon atoms in the pyruvate dehydrogenase equation?
3C pyruvate goes to 2C acetyl+ 1C (CO2)
40
What are the energy carriers in pyruvate dehyrogenase?
Reducing power is 1 NADH/ pyruvate
41
TCA cycle is only found in organisms that have what?
Electron transport system/chain | Aerobic and anaerobic respiring organisms
42
What is the main point of TCA cycle
oxidize Acety-CoA (from pyruvate dehydrogenase) to 2CO2
43
What is the TCA equation?
Acetyl-CoA + 3 NAD+ + FAD + ADP + Pi → 2 CO2 + 3 NADH + 3 H+ + FADH2 + ATP
44
What is step 1 of TCA?
Oxaloacetate + acetyl-CoA + H2O → citrate + CoA 4C+ 2C → 6C Citrate synthase synthase rxn, no ATP
45
What is step 2 of TCA?
Citrate → cis-aconitate + H2O 6C → 6C Aconitase technically a dehydration rxn
46
What is step 3 of TCA?
Cis-aconitate + H2O → isocitrate 6C→6C Aconitase Steps 2 + 3: overall isomeration by aconitase
47
What is step 4 of TCA?
Isocitrate + NAD+ → α-ketoglutarate (α-KG) + CO2 + NADH + H+ 6C → 5C+ 1C Isocitrate dehydrogenase EC: 1 NADH formed
48
What is step 5 of TCA?
α-KG + NAD+ + CoA → succinyl-CoA + CO2 + NADH + H+ 5C → 4C+ 1C 2-oxogluterate dehydrogenase EC: 1 NADH formed
49
What is step 6 of TCA?
Succinyl-CoA + ADP (or GDP) + Pi → succinate + ATP (or GTP) + CoA 4C → 4C Succinyl- CoA synthetase EC: 1 ATP (or GTP) formed
50
What is step 7 of TCA?
Succinate + FAD → fumarate + FADH2 4C →4C succinate dehydrogenase EC: 1 FADH2 formed- immediately consumed/ recycled by ETC
51
What is step 8 of TCA?
Fumarate + H2O → malate 4C → 4C fumarase hydration reaction
52
What is step 9 of TCA?
Malate + NAD+ → oxaloacetate + NADH + H+ 4C → 4C Malate dehydrogenase EC: 1 NADH formed
53
Why have fermentation?
oxidize NADH back to NAD+
54
When do you have fermentation?
No inorganic terminal electron acceptor available | No electron transport chain
55
What is the organic terminal electron acceptor in fermentation?
pyruvate or derivatives like Acetyl-CoA
56
Describe the specifics of Clostridium perfringens
``` Gram (+) Bacillus Obligate anaerobe (No SOD, catalase) Obligate fermenter (No ETC) Endospores Found in the Soil and intestines ```
57
What is gangrene?
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
What is the Catabolism of Clostridium perfringens
Chemoheteroorganotroph | Eats everything
59
What is the major virulence factor for Clostridium perfringens?
alpha-toxins= phospholipase+hemolysis
60
What metabolic pathway does Clostridium perfringens run?
glycolysis, no pyruvate dehydrogenase, no TCA
61
What are the products made by Clostridium perfringens after glycolysis in the two pathways?
Pathway 1- Ethanol, Acetate, Butyrate, H2+CO2 Pathway 2- Propionate, CO2
62
Describe branch 1 that clostridium can take after glycolysis
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
Describe branch 2 that clostridium can take after glycolysis
``` Lactate dehydrogenase Pyruvate + NADH + H+ → Lactate + NAD+ 3C → 3C Oxidizes NADH to NAD+ Lactate →→→ propionate + CO2 Oxidizes NADH to NAD+ More bubbling ```
64
Describe the specifics of Streptococcus pyogenes
Gram + Diplococcus Obligate fermenter (No ETC) Found in the Environment and Orally
65
What diseases does Streptococcus pyogenes make?
Pharyngitis, Rheumatic fever, Mastitis, Necrosizing fasciitis
66
What is the catabolism of Streptococcus pyogenes?
Chemoheteroorganotroph | Eats proteins and carbohydrates
67
What metabolic pathway does Streptococcus run?
glycolysis (no pyruvate dehydrogenase
68
What is Homolactic fermentation?
Uses lactate dehydrogenase pyruvate+ NADH + H+ → Lactate + NAD+ (3C → 3C) oxidizes NADH to NAD+
69
What microbes have homolactic fermentation?
Streptococcus pyogenes, Clostridium perfringens
70
Describe the specifics of lactobacilli
``` Gram + Bacillus Aerotolerant anaerobe (obligate fermenter, No ETC) Lives int intestines, and raw milk Acidophiles ```
71
What is the catabolism of lactobacilli
Chemoheteroorganotroph Some lactate only homolactic fermenter (no CO2) Some heterolactic fermenters
72
What is heterolactic fermentation
Start with pentose phosphate pathway Lactate + *CO2 + ethanol 6C → 3C + 1C + 2C Oxidizes NADPH and NADH
73
What are the benefits of probiotics?
Competition to inhibit pathogens | Antimicrobial production
74
What are some commercial products that contain probiotics
Milk, Kimchi, sauerkraut, pickles, chocolate
75
What is respiration
Donor oxidized by ETC/ETS → e-s go to a terminal electron acceptor, H+ pumped → PMF enables ATP synthase to produce ATP
76
What is oxidative phosphorylation?
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
What is the proton motive force?
[H+] outside > [H+] inside
78
Where do eukaryotes and prokaryotes have a proton motive force?
Eukaryotes: mitochondria Prokaryotes: cellular membrane
79
How many protons does ATP synthase use to make 1 ATP?
3 H+
80
Describe prokaryote respiration
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
What is the NADH dehydrogenase reaction
NADH + H+ + Q → NAD+ + QH2
82
What is the Succinate dehydrogenase reaction
Succinate + Q → Fumarate + QH2 FAD → FADH2 (TCA) →FAD (electron transport) Succinate+ Q+ FAD → Fumarate + QH2 +FAD
83
What is the cyt bo oxidase reaction, cyt bd oxidase reaction
2QH2 + O2 (oxygen!) → 2Q + 2H2O
84
What is the nitrate reductase reaction
QH2 + NO3- (NOT oxygen) → Q + NO2- + H2O
85
What are the 3 dehydrogenases and how many protons do they pump
NADH dehydrogenase 1 (NDH-1)=4 protons NADH dehydrogenase 2 (NDH-2)=0 protons Succinate dehydrogenase = 0 protons
86
What are the 3 terminal oxidases and how many protons do they pump?
Cytochrome bo quinol oxidase (cyt bo)=8protons Cytochrome bd oxidase (cyt bd)= 4 protons Nitrate reductase= 2 protons
87
What is the theoretical maximum oxidative prokaryote yield?
37
88
How many ATP's can you produce with glycolysis?
6 ATP
89
How many ATP's can you produce with pyruvate dehydrogenase?
6 ATP
90
How many ATP's can you produce with TCA?
6NADH → 18 ATP | 2 FADH2 → 3 ATP
91
How many ATP's can you produce with Oxidative phosphorylation?
33
92
How many ATP's can you produce with substrate level phosphorylation?
4 (2 from glycolysis and 2 from TCA)
93
Why is the actual yield and theoretical yield so different?
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
What is Lithotrophy?
Use of inorganic compounds as a source of electrons for metabolism
95
The opposite of Lithotrophy is what?
Organotrophy
96
What is an example of lithotrophy?
Strain 121
97
What is phototrophy?
Light as energy source
98
Phototrophy usually occurs where and how?
In a photosystem Excite an electron (photolysis), split from donor transfer e-’s, pump H+= PMF pigments, electron carriers and proteins= ETC/ETS!
99
Describe photosystem II
``` 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
Describe photosystem !
``` 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
Describe the oxygenic Z pathway
``` Aerobic Obligate aerobes Parts of PS I and PS II Electron donor: H2O →O2 Noncyclic phosphorylation Energy carriers NADPH (reducing power) ATP (photophosphorylation) ```
102
Where is NADH and NADPH consumed
NADH is consumed by PMF or fermentation NADPH is consumed by anabolism/ biosynthesis
103
Describe carbon fixation and the different types of reactions
CO2 (inorganic)→→→ organics Calvin cycle reductive/reverse TCA cycle Acetyl-CoA pathway 3-Hydroxypropionate cycle
104
Describe the Calvin cycle
``` typically obligate aerobes Substrates: CO2, NADPH, ATP Products: Glucose, NADP+, ADP + Pi Chloroplasts (eukaryotes) Anabaena spiroides Prochlorococcus marinus No archaea (yet) ```
105
Describe the reductive/reverse TCA cycle
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
Describe the Acetyl-CoA pathway
``` Some archaea, some obligate/ facultative anaerobes Substrates: CO2, H2, ATP Products: CH4, Acetyl-CoA, ADP + Pi Methanogenic archaea Some Clostridia, related species ```
107
Describe the 3-Hydroxypropionate cycle
Some archaea, some facultative anaerobes Substrates: CO2 (HCO3-), NADPH, ATP Products: Glyoxylate (→ pyruvate), NADP+, ADP + Pi
108
Describe nitrogen fixation
``` 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
Describe the fatty acid biosynthesis (FAS II)
``` 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
Describe the biosynthesis of Erythromycin
Polyketide synthase (PKS) Substrates: Malonyl-CoA, NADPH Products: Erythromycin precursor, NADP+
111
Describe the biosynthesis of Vancomycin
Non-ribosomal peptide synthetase (NRPS) Energy: ATP → AMP + PPi (irreversible) Substrates: amino acids, ATP Products: Vancomycin precursor, AMP + PPi
112
Describe the biosynthesis of Penicillins
Energy: ATP → AMP + PPi (irreversible) Substrates: amino acids, ATP Products: Penicillins, AMP + PPi

Microbiology (4 decks)

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