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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
Q

Typically the last step before terminal acceptor

A

Cytochromes (ETC complexes have multiple of these)

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26
Q

Complex I vs Complex II

A

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

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27
Q

NADH to H2O in ETC (entering either complex I and II)

A

I - ten protons pumped per NADH

II - only 6

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28
Q

Very widely conserved enzyme – ancient origins

A

ATP synthase

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29
Q

ATP synthase

A

related and functionally similar enzyme found in cytoplasmic membrane (prokaryotes) and in mitochondrial membrane (eukaryotes)

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30
Q

Fo and F1 parts of ATP synthase are connected by

A

stalk (y)

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31
Q

Fo vs F1

A

Fo = membrane; F1 = cytosol

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32
Q

In the ATP synthase, protons flow through …

A

Fo, it spins like a turbine

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33
Q

T or F. F1 is held in place

A

T! it’s connected to a membrane

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34
Q

What drive the conformational change of F1 in the ATP synthase?

A

Rotation of the stalk (axle)

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35
Q

What does the conformational change of F1 do ??

A

Powers addition of Pi to ADP to make ATP!

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36
Q

In the ATP synthase, how many protons are pumped to generate 1 ATP?

A

~3.3 H+

37
Q

T or F. The ATP synthase is not reversible

A

F! IT IS! ATP hydrolysis can generate proton motive force (fermentative organisms)

38
Q

Chemoorganotrophs prefer glucose if available, but if not …

A
  • 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
Q

Catabolite repression

A

if a better E source (glucose) is around, enzymes to use other E sources are inhibited or not expressed

40
Q

The glyoxylate cycle

A
  • 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
Q

This organism can assemble different ETCs

A

E. coli

42
Q

Under anaerobic conditions, E. coli can …

A

respire using nitrate (if available); if not available – FERMENTATION

43
Q

Chemotrophic metabolism without the use of an external electron acceptor

A

Fermentation (anaerobic)

44
Q

Heterofermentive lactic acid fermenters

A

Bacteria that generate a mix of lactose + other fermentation products; useful to avoid lactate accumulation

45
Q

Besides glucose, what else can microbes ferment?

A

fatty acids, amino acids, purines/pyrimidines, etc.

46
Q

In addition to lactic acid and ethanol, what are other fermentation products that can be made?

A

“mixed acid fermentations” - acetate, lactate, succinate, formate)

47
Q

Common theme for fermentation:

A

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
Q

“Lithotroph”

A
  • rock-eater

- get their E from oxidizing inorganic molecules (minerals in many cases)

49
Q

Most chemolithotrophs are

A

autotrophs

50
Q

Rare phototrophs that get their carbon from organic molecules

A

photoheterotrophs

51
Q

Eukaryotic phototrophs are usually

A

oxygenic (plants!)

52
Q

Photosynthetic reaction center

A
  • bacteriochlorophyll (P870) - absorbs light E (weak e- donor to very strong e- donor [P870*])
53
Q

In purple bacteria (anoxygenic phototroph), how does the e- travel?

A

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
Q

Light-sensitive pigments that absorb light and transfer E to ETC

A

(in phototrophs)

  • bacteriochlorophylls = anoxygenic
  • chlorophylls = oxygenic
55
Q

Phototrophs basics

A
  • photosynthetic rxn centers

- antenna pigments (embedded or associated with membrane); similar to heme groups used by cytochromes; Mg instead of Fe!

56
Q

Antenna pigments

A

“light-harvesting complexes” of bacteriochlorophylls that capture light E to transfer to rxn center

57
Q

Where electrons get excited and transferred to ETC

A

Photosynthetic rxn centers

58
Q

T or F. Not all anoxygenic bacteria have cyclic electron flow

A

T! Not all like purple bacteria; some transfer electrons to an external acceptor

59
Q

“Q-type” reaction center

A

Purple bacteria; transfer electrons to a quinone

60
Q

Anoxygenic bacteria that use “FeS type” reaction centers

A

electrons are transferred to an Fe/S cluster carrier (lower reduction potential (E’), stronger electron donor

61
Q

Making electrons excited

A

more negative

62
Q

Reverse electron transport

A

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
Q

Two distinct photocenters of oxygenic phototrophs

A
  • PSI (P700 - FeS type)

- PSII (P680 - Q-type)

64
Q

Where are reaction centers of oxygenic phototrophs found?

A

Membranes (cyanobacteria - cytoplasmic membrane ; eukaryotes like algae - chloroplast thylakoid membranes)

65
Q

Noncyclic electron flow in photosystems generates

A

PMF

66
Q

Photosystems: how do they work?

A
  • 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
Q

The Calvin Cycle

A
  • 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
Q

T or F. The Calvin Cycle is NOT the only way to fix CO2

A

T

69
Q

N2

A

readily available in the atmosphere but metabolically useless because it has a triple bond which makes it very stable

70
Q

Nirogenase

A

converts N2 to NH3 (much more useful)

71
Q

Diazotrophs

A

Some bacteria and archaea can produce nitrogenase (cyanobacteria, rhizobia, some archaea methanotrophs)

72
Q

Nitrogenase is comprised of

A

Two proteins – dinitrogenase and dinitrogenase reductase (use Fe/Mo cofactors)

73
Q

Path of e- in nitrogenases

A

Electrons come from Fe/S proteins such as flavodoxin –> dinitrogenase reductase dinitrogenase –> to N2

74
Q

Nitrogen fixation is a very expensive process

A

2 ATP per electron; 16 ATP per 2NH3 produced

75
Q

Gluconeogenesis

A

Production of glucose (for carbon/energy storage OR as a precursor for biosynthesis)
Basically reversal of glycolysis (same steps in reverse)

76
Q

Precursor for biosynthesis

A

Glucose-6-phosphate

77
Q

How can glucose be “activated’?

A
  • by the addition of nucleotide diphosphates such as ADP-glucose, UDP-glucose (using ATP, UTP)
78
Q

Activated form of glucose is used to produce polysaccharides for:

A
  • LPS (gram neg OM)
  • NAM/NAG (peptidoglycan)
  • storage molecules like glycogen/starch to use later for carbon/E source
79
Q

What serves as the direct precursor for a lot of things that glucose gets incorporated into (storage molecules, etc.)

A

UDP-glucose (Activated form of glucose)

80
Q

Key enzymes in using inorganic nitrogen sources such as NH3 to build nitrogen-containing molecules (AAs)

A

glutamate dehydrogenase and glutamine synthase = efficiently incorporate NH3 even at low levels

81
Q

Glutamine/glutamate then act

A

as nitrogen donors to produce many other key nitrogen-containing molecules in the cell

82
Q

How are fatty acids built?

A

2 carbons at a time by adding malonyl-CoA (3C) to growing chain - CO2 released as byproduct

83
Q

ACP

A

acyl carrier protein

“holder” of substrates for fatty acid synthesis (involved in the chemistry)

84
Q

Malonyl-ACP

A

made form malonyl-CoA (made form acetyl-CoA from CAC)

85
Q

Basic building blocks for nucleotides

A

pentoses (5C sugar, ribose) and nucleobases

86
Q

Pentose phosphate pathway

A
  • 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
Q

Nucleobase biosynthesis: purines and pyrimidines

A

purines (A/G) built using one pathway - very complicated; key intermediates= IMP

pyrimidines (U/T,C) uses another pathway; key intermediates = orotate

88
Q

Nucleobase biosynthesis: RNA vs DNA

A

Ribonucleotides (RNA) produced first

Ribonucleotide reductase then converts ribonucleotides into deoxyribonucleotides for DNA synthesis

MICRB 265 (6 decks)

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