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MICRB 265 > Topic 3 > Flashcards

Topic 3 Flashcards

1
Q

Metabolic requirements for all life:

A
  1. liquid water
  2. a source of E to do work
  3. a source of electrons for biochemical reactions
  4. nutrients (eg. sources of carbon, nitrogen, etc.)
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2
Q

What are enzymes?

A

Proteins made by cells that act as catalysts

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3
Q

RNA enzymes

A

ribozymes (very rare!)

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4
Q

In the absence of a catalyst, some reactions won’t occur at any appreciable rate. Why?

A

Activation E! Bonds need to be broken to initiate this reaction, in the absence of a catalyst, this takes a fair amount of E — won’t happen on its own at a meaningful rate!

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5
Q

T or F. Enzymes change the energetics (delta G) or the equilibrium of the reaction

A

F, they don’t change energetics or equilibrium! They simply work by lowering activation energy of a reaction

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6
Q

Enzyme activities can be controlled by

A

regulating the amounts of the enzymes or by controlling their activity

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7
Q

Competitive inhibitors

A

(of an enzyme) “fit” in the same active site as the substrates – inhibit substrate binding and thus the rxn!
Sulfa drugs work like this! (antibiotics that inhibit folate biosynthesis)

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8
Q

Allosteric activator vs. Allosteric inhibitor

A

Activator - positive effector; promotes binding of substrate and catalysis

Inhibitor - negative effector; prevents substrate form binding

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9
Q

A common strategy used to control metabolic pathways

A

feedback inhibition

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10
Q

Substrate-level phosphorylation

A

ATP generated as a product of a metabolic reaction – energy from an exergonic reaction (E-rich bond) used to power transfer of phosphate onto ADP to form ATP
EX: P from PEP

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11
Q

Oxidative phosphorylation

A

Energy from electron transfer reactions generate a proton motive force, that is used to generate ATP using ATP synthase
EX: respiration

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12
Q

Photophosphorylation

A

Energy captured from light is used to generate a proton motive force that is used to generate ATP using ATP synthase

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13
Q

Controlled E release of glucose

A

Glucose is broken down into a series of reactions in which high E substrates are gradually oxidized into lower and lower E molecules, ultimately into CO2. Electron acceptors like O2 act as an electron sink (ultimate e- acceptor in this rxn)

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14
Q

Very important metabolic pathway – conserved in all domains of life

A

Glycolysis

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15
Q

A quick way to produce some E from glucose also feeds into CAC

A

Glycolysis

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16
Q

Preferred pathway of chemoorganotrophs after glycolysis

A

CAC/ respiration (used to generate a great deal more ATP - oxidation of pyruvate)… but this requires available external electron acceptor

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17
Q

Some organisms can’t do ___________; only do ____________

A

respiration; fermentation (pyruvate doesn’t go anywhere)

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18
Q

CAC AKA

A

Kreb’s cycle or Tricarboxylic acid cycle (TCA)

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19
Q

CA C doesn’t solve the redox imbalance from glycolysis (made it worse!)…. how is NAD+ (and FAD) recycled and redox balance re-established?

A

Respiration - ETC!

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20
Q

Where does the ETC take place?

A

cytoplasmic membrane

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21
Q

Where are NADH electrons deposited to recycle back to NAD+?

A

NADH dehydrogenase transfers 2 e- to a flavoprotein (contain either FAD/FADH2 or FMN/FMNH2)

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22
Q

Quinones

A

NOT proteins; small molecules that move within the membrane; accept 2 electrons, transfer to next carrier in chain

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23
Q

Often serve to link Fe/S proteins to cytochromes

A

Quinones

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24
Q

Proteins that contain heme prosthetic groups (iron coordinated with organic molecule)

A

Cytochromes

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25
Typically the last step before terminal acceptor
Cytochromes (ETC complexes have multiple of these)
26
Complex I vs Complex II
I - starts with NADH (lower E') - pumps 4 protons per 2 e- ... generates more E II - starts with FADH2 (higher E') - pumps fewer protons Quinone is reduced from either complex and then passes electrons to complex III
27
NADH to H2O in ETC (entering either complex I and II)
I - ten protons pumped per NADH | II - only 6
28
Very widely conserved enzyme -- ancient origins
ATP synthase
29
ATP synthase
related and functionally similar enzyme found in cytoplasmic membrane (prokaryotes) and in mitochondrial membrane (eukaryotes)
30
Fo and F1 parts of ATP synthase are connected by
stalk (y)
31
Fo vs F1
Fo = membrane; F1 = cytosol
32
In the ATP synthase, protons flow through ...
Fo, it spins like a turbine
33
T or F. F1 is held in place
T! it's connected to a membrane
34
What drive the conformational change of F1 in the ATP synthase?
Rotation of the stalk (axle)
35
What does the conformational change of F1 do ??
Powers addition of Pi to ADP to make ATP!
36
In the ATP synthase, how many protons are pumped to generate 1 ATP?
~3.3 H+
37
T or F. The ATP synthase is not reversible
F! IT IS! ATP hydrolysis can generate proton motive force (fermentative organisms)
38
Chemoorganotrophs prefer glucose if available, but if not ...
- Beta-oxidation: convert fatty acids to acetyl-CoA, which can then be fed into CAC - Amino acids can be converted to entry points to the /CAC (eg: pyruvate)
39
Catabolite repression
if a better E source (glucose) is around, enzymes to use other E sources are inhibited or not expressed
40
The glyoxylate cycle
- variation of CAC - used to grow on 2C molecules like acetate/acetyl-CoA - less reducing power (less ATP) but provides oxaloacetate building block for synthesis of AAs, glucose, etc.
41
This organism can assemble different ETCs
E. coli
42
Under anaerobic conditions, E. coli can ...
respire using nitrate (if available); if not available -- FERMENTATION
43
Chemotrophic metabolism without the use of an external electron acceptor
Fermentation (anaerobic)
44
Heterofermentive lactic acid fermenters
Bacteria that generate a mix of lactose + other fermentation products; useful to avoid lactate accumulation
45
Besides glucose, what else can microbes ferment?
fatty acids, amino acids, purines/pyrimidines, etc.
46
In addition to lactic acid and ethanol, what are other fermentation products that can be made?
"mixed acid fermentations" - acetate, lactate, succinate, formate)
47
Common theme for fermentation:
generate E-richen molecule (bond) that can be hydrolyzed to produce ATP, donate e- to (reduce) a metabolite and excrete to obtain redox balance!
48
"Lithotroph"
- rock-eater | - get their E from oxidizing inorganic molecules (minerals in many cases)
49
Most chemolithotrophs are
autotrophs
50
Rare phototrophs that get their carbon from organic molecules
photoheterotrophs
51
Eukaryotic phototrophs are usually
oxygenic (plants!)
52
Photosynthetic reaction center
- bacteriochlorophyll (P870) - absorbs light E (weak e- donor to very strong e- donor [P870*])
53
In purple bacteria (anoxygenic phototroph), how does the e- travel?
P870* donates e- tp quinone, enters ETC and generates PMF ; ATP synthase makes ATP ; e- cycle back to P870 (cytochrome does this) to return to its original state (cyclic photophosphorylation)
54
Light-sensitive pigments that absorb light and transfer E to ETC
(in phototrophs) - bacteriochlorophylls = anoxygenic - chlorophylls = oxygenic
55
Phototrophs basics
- photosynthetic rxn centers | - antenna pigments (embedded or associated with membrane); similar to heme groups used by cytochromes; Mg instead of Fe!
56
Antenna pigments
"light-harvesting complexes" of bacteriochlorophylls that capture light E to transfer to rxn center
57
Where electrons get excited and transferred to ETC
Photosynthetic rxn centers
58
T or F. Not all anoxygenic bacteria have cyclic electron flow
T! Not all like purple bacteria; some transfer electrons to an external acceptor
59
"Q-type" reaction center
Purple bacteria; transfer electrons to a quinone
60
Anoxygenic bacteria that use "FeS type" reaction centers
electrons are transferred to an Fe/S cluster carrier (lower reduction potential (E'), stronger electron donor
61
Making electrons excited
more negative
62
Reverse electron transport
use proton motive force (costs a LOT of energy) to drive electrons in opposite direction in ETC (reduce NADP to NADPH); used by some chemo- and autotrophs
63
Two distinct photocenters of oxygenic phototrophs
- PSI (P700 - FeS type) | - PSII (P680 - Q-type)
64
Where are reaction centers of oxygenic phototrophs found?
Membranes (cyanobacteria - cytoplasmic membrane ; eukaryotes like algae - chloroplast thylakoid membranes)
65
Noncyclic electron flow in photosystems generates
PMF
66
Photosystems: how do they work?
- PSII excited by light transfers electrons to ETC (becomes highly electropositive) - PSII accepts e- from H2O to make H+ (not easy b/c H2O is VERY weak e- donor) - PSII now back to OG state, can be re-excited again - electrons from PSII passed to quinones, down ETC (PMF); ultimately, low energy electrons transferred to PSI - PSI excited by light reduce NADP+ to NADPH - NADPH for CO2 fixation - CO2 is ultimate electron acceptor
67
The Calvin Cycle
- phototrophic bacteria, most chemolithotrophic bacteria, algae, some archaea - CO2 converted to organic molecules - costs ATP and NAD(P)H - for every 36C that go in -- 6C is used for Calvin Cycle - RuBisCO enzyme is key carboxylation step
68
T or F. The Calvin Cycle is NOT the only way to fix CO2
T
69
N2
readily available in the atmosphere but metabolically useless because it has a triple bond which makes it very stable
70
Nirogenase
converts N2 to NH3 (much more useful)
71
Diazotrophs
Some bacteria and archaea can produce nitrogenase (cyanobacteria, rhizobia, some archaea methanotrophs)
72
Nitrogenase is comprised of
Two proteins -- dinitrogenase and dinitrogenase reductase (use Fe/Mo cofactors)
73
Path of e- in nitrogenases
Electrons come from Fe/S proteins such as flavodoxin --> dinitrogenase reductase dinitrogenase --> to N2
74
Nitrogen fixation is a very expensive process
2 ATP per electron; 16 ATP per 2NH3 produced
75
Gluconeogenesis
Production of glucose (for carbon/energy storage OR as a precursor for biosynthesis) Basically reversal of glycolysis (same steps in reverse)
76
Precursor for biosynthesis
Glucose-6-phosphate
77
How can glucose be "activated'?
- by the addition of nucleotide diphosphates such as ADP-glucose, UDP-glucose (using ATP, UTP)
78
Activated form of glucose is used to produce polysaccharides for:
- LPS (gram neg OM) - NAM/NAG (peptidoglycan) - storage molecules like glycogen/starch to use later for carbon/E source
79
What serves as the direct precursor for a lot of things that glucose gets incorporated into (storage molecules, etc.)
UDP-glucose (Activated form of glucose)
80
Key enzymes in using inorganic nitrogen sources such as NH3 to build nitrogen-containing molecules (AAs)
glutamate dehydrogenase and glutamine synthase = efficiently incorporate NH3 even at low levels
81
Glutamine/glutamate then act
as nitrogen donors to produce many other key nitrogen-containing molecules in the cell
82
How are fatty acids built?
2 carbons at a time by adding malonyl-CoA (3C) to growing chain - CO2 released as byproduct
83
ACP
acyl carrier protein | "holder" of substrates for fatty acid synthesis (involved in the chemistry)
84
Malonyl-ACP
made form malonyl-CoA (made form acetyl-CoA from CAC)
85
Basic building blocks for nucleotides
pentoses (5C sugar, ribose) and nucleobases
86
Pentose phosphate pathway
- parallel to glycolysis - generates ribose-5-phosphate from glucose-6-phosphate - this pathway also generates NADPH and a range of other important carbon skeletons
87
Nucleobase biosynthesis: purines and pyrimidines
purines (A/G) built using one pathway - very complicated; key intermediates= IMP pyrimidines (U/T,C) uses another pathway; key intermediates = orotate
88
Nucleobase biosynthesis: RNA vs DNA
Ribonucleotides (RNA) produced first Ribonucleotide reductase then converts ribonucleotides into deoxyribonucleotides for DNA synthesis

MICRB 265 (6 decks)

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