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Microbiology > Chapter 3: Microbial metabolism > Flashcards

Chapter 3: Microbial metabolism Flashcards

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Biology 101 flashcards
1
Q

Metabolism

A

All biochemical reactions needed for life
-includes catabolism and anabolism
-relies on e donors and e acceptors

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2
Q

Exergonic

A

Reactions with negative delta G release free energy

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3
Q

Endergonic

A

Reactions with positive delta G require energy

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4
Q

Catabolic pathways

A

Cellular processes that generate free energy
-Free energy produced is conserved by synthesizing molecules like ATP

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5
Q

ATP produced from 1 mole of glucose in aerobic respiration

A

38

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6
Q

Anabolic pathways

A

Endergonic pathways in which cellular synthesis requires energy
-Energy comes from ATP hydrolysis

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7
Q

Reducing power

A

Ability to donate e

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8
Q

Biosynthesis requirements

A

-Free energy (ATP)
-Reducing power (electron carriers)

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9
Q

Phototrophs

A

-Obtain energy from sunlight
-Do not require chemicals as energy source
-Oxygenic and anoxygenic

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10
Q

Chemotrophs

A

Get energy from chemical receptors

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11
Q

Aerobic requirements

A

O2 as electron acceptor

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12
Q

Anaerobic requirements

A

use anything other than O2 as electron acceptor

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13
Q

Chemoorganotrophs

A

Obtain energy and reducing power from organics

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14
Q

Chemolithotrophs

A

Obtain energy and reducing power from inorganics

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15
Q

Heterotrophs

A

Obtain carbon from organics

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16
Q

Autotrophs

A

Obtain carbon from CO2
-Also called primary producers as they synthesise organic matter from inorganic matter

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17
Q

Electron carriers

A

Typically electron movement proceeds through consecutive reactions
-Soluble e carriers such as NAD needed to carry electrons

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18
Q

NAD+

A

nicotinamide adenine dinucleotide
redox couple = -0.32V
-Reduction requires 2 e and 1 H+
-It is a coenzyme

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19
Q

Free energy needed to synthesize ATP

A

Cells need compounds where delta G < -31.8kJ/mol
-eg Coenzyme A derivatives have energy rich thioester bonds while other compounds have rich phosphate bonds

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20
Q

3 mechanisms of ATP generation

A

-Substrate level phosphorylation
-Oxidative phosphorylation
-Photophosphorylation

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21
Q

Substrate-level phosphorylation

A

Energy rich substrate bond hydrolysed directly to drive ATP formation
-E.g. hyydrolysis of phosphoenolpyruvate

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22
Q

Oxidative phosphorylation

A

Movement of e generates proton motive force used to synthesize ATP

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23
Q

Difference between Eu and Pro oxidative phosphorylation

A

-Eu push e out of mitochondrial membrane
-Pro push e out of plasma membrane into periplasm

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24
Q

Photophosphorylation

A

Light used to form proton motive force

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25
Q

Activation energy

A

Minimum energy required for chemical reaction to begin

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26
Q

Catalyst mechanism

A

Lowers activation energy in order to increase the reaction rate as the activation energy is minimum energy required for chemical reaction to begin

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27
Q

Prosthetic groups

A

Tightly bound to enzymes, usually covalently and permanently
-e.g. heme in cytochromes

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28
Q

Coenzymes

A

Loosely, transiently bound
most are derivatives of vitamins

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29
Q

Enzyme catalysis

A

-Binding and proper positioning of substrate needed for catalysis
-Enzyme-substrate complex aligns reactive groups and strains specific bonds, reducing activation energy
-To catalyse endergonic reactions, coupling must take place to have overall negative delta G
-All enzymes are theoretically reversible but highly exergonic or endergonic usually goes in one direction

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30
Q

Glycolysis and citric acid cycle

A

Learn

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31
Q

Biosynthesis and Citric acid cycle

A

Alpha-ketoglutarate and oxaloacetate: precursors of several aa, OAA also converted if needed to phosphoenolpyruvate which is a glucose precursor

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32
Q

Succinyl CoA BS

A

Required for synthesis of cytochromes, chlorophyll and related molecules

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33
Q

Acetate BS

A

Fatty acid biosynthesis

34
Q

Other chemoorganotrophy pathways

A

Glycolysis and CAC can oxidise several C4-C6 compounds (glucose, citrate, etc)
-Unrelated catabolic pathways can be linked for oxidation (e.g. Isomerisation)
-Some C2 (acetate) compounds catabolised through glyoxylate cycle (includes CAC enzymes + isocitrate lyase and malate synthase)
-C3 compounds are carboxylated by pyruvate carboxylase or phosphoenolpyruvate carboxylase (glyoxylate cycle unneccessary)

35
Q

Glyoxylate cycle

A
36
Q

Principles of fermentation

A

-Involves substrate level phosphorylation and redox balance via pyruvate reduction + excretion as waste

37
Q

Fermentation Goals

A

-Conserve energy
-Redox balance
It needs to produce compounds with high energy bonds for ATP synthesis and oxidise NADH to NAD+ by donating e to e acceptor from organic donor

38
Q

Alcoholic fermentation

A

Yeast ferments glucose to 2 ethanol and CO2
-ATP from glycolysis
-NAD+ regenerated by donating e to pyruvate

39
Q

quinone

A

nonprotein electron carriers

39
Q

Lactic acid fermentation

A

Ferment glucose to lactic acid
-Different enzymes reduce pyruvate to lactic acid
-NB in fermenting food andhuman health

39
Q

Reoxidation

A

-occurs during e transport
-occurs in cytoplasmic membrane
-Forms electrochemical gradient that conserves energy through ATP synthesis

40
Q

Respiration

A

E transferred from reduced e donors to external e acceptors like O2

41
Q

Need for respiration

A

NADH and FADH2 produced in glycolysis and CAC must be reoxidised for redox balance

42
Q

NADH dehydrogenases

A

Active site binds NADH, accepts two e and two protons that are transferred to flavoproteins, regenerating NAD+

43
Q

quinones description

A

-small hydrophobic nonprotein redox molecules
-can move within membrane
-Accept two electrons and two protons but transfer electrons only
-typically link iron-sulfur proteins and cytochromes
-Ubiquinone and menaquinone most common

43
Q

Flavoproteins

A

-Contains derivative of riboflavin as prosthetic group (eg, FMN) that accepts 2 electrons and two protons but only donate electrons

44
Q

E transport

A

e movements are exergonic, providing free energy to pump protons to outer surface of membrane
-Generates proton motive force
-H+ cannot diffuse across membrane
-Seperation of H+ and OH- creates pH difference and electrochemical potential across membrane

44
Q

Cytochromes

A

Proteins that contain heme prosthetic groups
-oxidised/reduced by 1 e via the iron atom (Fe2+ or Fe3+)
-Several classes, differ widely in reduction potentials, designated by ltters based on heme
-sometimes form complexes (cytochrome bc)

44
Q

Nonheme iron proteins

A

-Contain iron and sulfur clusters
-eg. ferredoxin: low reduction potential, important in H2 production
-Reduction potentials vary
-only carry e

45
Q

Complex IV

A

includes cytochromes a and a3
-terminal oxidase, reduces O2 to H2O
-Needs 4e and 4 H+ from cytoplasm
-pumps 1 H+ per e

46
Q

Complex III

A

Includes cytochrome bc complex
-transfers e from QH2 ubiquinol (reduced quinone) to cytochrome C
-pumps 2H+ from QH2 outside of cytoplasmic membrane
-Q cycle (electron bifurcation) sends e to cytochrome C and subunit bl; 4H+ transferred across membrane
-Cytochrome C shuttles e to complex IV

46
Q

Complex I

A

Includes; NADH, quinone oxioreductase and NADH dehydrogenase
-Begins e transport
-Composed of many proteins that function as a unit
-NADH oxidised to NAD+, quinone reduced
-diffuses to Complex III, 4 H+ released

47
Q

Complex II

A

Inculdes succinated dehydrogenase complex
-Alternative entry point
-2e from FADH2 and 2H+ from cytoplasm transferred to ubiquinone to make ubiquinol
-Less energy conserved due to lack of H+ translocation

48
Q

NADH accounting

A

For every 2 e from NADH to O2, 10H+ transferred outside membrane ( 4 at complex I, 4 at complex III, 2 at complex IV), 2 consumed in cytoplasm (H2O)

49
Q

FADH2 accounting

A

For every 2 from FADH2 to O2, 6 H+ transferred outside the membrane ( 4 at complex III, 2 at complex IV), 2 consued in cytoplasm (H2O)

50
Q

ATP Synthetase

A

-Uses energy from proton motive force to form ATP
-pmf generates torque and the mechancial energy catalyses ADP and phsophate
-Oxidative phosphorylation from respiratory electrons
-Photophosphorylation from light energy

51
Q

ATPase structure

A

-F1: Multiprotein complex extending into cytoplasm that catalyses ATP synthesis
-F0: membrane-integrated proton-translocating multiprotein complex
-Found in nearly all organisms and is highly conserved
-Reversible reaction

52
Q

ATPase production

A

-For every full rotation of F0 ring, 3 ATP formed by F1
-In E.coli., 3.3 H+ per ATP
-Number of c subunits varies between organisms and so # of H+ also varies

53
Q

Oxidative phosphorylation production

A

OP conserves much more energy because substrate is completely oxidised
-Eg. 38 ATP in aerobic respiration vs 2 ATP in lactic acid fermentation

54
Q

ATP hydrolyses in ATPases

A

ATPases are reversible
-ATP hydrolysis can reverse ATPase activity and transport protons out of cytoplasm, generating heat instead of dissipating pmf
-ATPases in strict fermenters generate pmf for motility and transport by hydrolysing ATP from substrate-level phosphorylation

55
Q

aerobic respiration

A

Uses O2 as terminal electron acceptor

56
Q

Anaerobic respiration

A

uses other e acceptor

57
Q

difference between respiration and fermentation

A

Respiration requires an external e acceptor, generates ATP by oxidative phosphorylation
-Fermentation does not require an external e acceptor and generates ATP by susbstrate-level phosphorylation

58
Q

Methods of growth of E.coli

A

Aerobic respiration
Fermentation
anaerobic respiration

59
Q

Basic organisation of E.coli

A

-Complex I, Complex II, quinones, terminal reductase
-Can swap components
-Alternative quinones
-alternative dehydrogenases/terminal reductases

60
Q

E.coli optimise respiration

A

-with organic carbon source, grows fastest by aerobic respiration
-Grows faster with nitrate respiration than fermentation
-Can insert many different proteins in electron transport chain

61
Q

Nitrate respiration in E.coli

A

-If no O2 present and nitrate is, it will use nitrate reductase as terminal reductase
-NO3/NO2 couple is less electropositive
-provides less energy
-only 6H+ exchanged for every 2 electrons

62
Q

Chemolithotrophy respiration

A

Both chemoorganotrophs and chemolithotrophs depend on oxidative phosphorylation
-Can be aerobic or anaerobic
-Major difference is source of cellular carbon:
-Chemoorganotrophs are heterotrophs using organics as carbon source, chemolithotrophs typically use CO2 as carbon source and use reverse e transport to form reducing power

63
Q

Phototrophy

A

Uses light to generate proton motive force
-ATP synthetase makes ATP by photophosphorylation
-Oxygenic, forming O2 as waste product or anoxygenic
-Anoxygenic phototrophs evolved first, more metabolic diversity

64
Q

Purple bacteria

A

They are anoxygenic phototrophs that are common in anoxic aquatic environments
-Produce photosynthetic reaction centre that converts light into chemical energy
-Reaction centres contain photopigments
-Photopigments absorb light, transfer energy to photosynthetic reaction center, forms pmf that is used to make ATP

65
Q

difference between respiratory and photosynthetic e transport in purple bac

A

Cyclic photophosphorylation
e are returned

66
Q

Generation of reducing power

A

Reducing power (NADH) is NB to produce cellular material
-Can come from variety of e donors (H2S)
-Uses reverse e transport (Pushing e from quinone pool backward to reduce NAD+ to NADH
-must electron donors like H2S

67
Q

Nitrogen significance

A

 Cells require carbon and nitrogen to perform biosynthesis
 Atmospheric sources (CO2 and N2) must be chemically reduced for assimilation (CO2 fixation and
N2 fixation)
 Requires ATP and reducing power

68
Q

Calvin cycle requirements

A

Requires CO2, a CO2 acceptor, NADPH, ATP, ribulose bisphophate carboxylase (RubisCO), and
phosphoribulokinase

69
Q

Calvin cycle usage in diffeerent species

A

Used by many autotrophs, including all oxygenic phototrophs
 Found in purple bacteria, cyanobacteria, algae, green plants, most chemolithotrophic Bacteria, few Archaea

70
Q

Calvin cycle reactants and products

A

Easiest to consider cycle as six molecules of CO2 required to make one hexose (C6H12O6)
 6 ribulose bisphosphate and 6 CO2 required
 Results in 6 molecules of ribulose 5-phosphate (30 carbons) + one hexose (6 carbons) for biosynthesis
 Phosphoribulokinase phosphorylates each ribulose 5-phosphate to regenerate ribulose bisphosphate
 12 NADPH and 18 ATP required to synthesize one glucose

71
Q

Calvin cycle steps

A

First step catalyzed by RubisCO, forming two molecules of 3-phosphoglyceric acid (PGA) from ribulose
bisphophate and C O2
 PGA then phosphorylated and reduced to glyceraldehyde-3-phosphate
 Glucose formed by reversal of glycolysis

72
Q

Nitrogen fixation significance

A

 Nitrogen needed for proteins, nucleic acids, other organics
 Most microbes obtain this nitrogen from “fixed” nitrogen (ammonia, NH3, or nitrate, NO3−)
 Many prokaryotes can conduct nitrogen fixation: form ammonia (NH3) from gaseous dinitrogen (N2)

73
Q

Nitrogenase enzyme complex

A

Consists of dinitrogenase and dinitrogenase reductase
 Iron-molybdenum cofactor (FeMo-co) of dinitrogenase is where N2 reduction occurs
 Triple bond stability makes activation and reduction very energy demanding
-Electron donor-> dinitogenase reductase-> dinitogenase-> N2
 6 electrons needed; 8 actually consumed because H2 must be produced
 16 ATP required to lower protein’s reduction potential, enabling dinitrogenase reductase to
reduce dinitrogenas

74
Q

Nitrogenase oxygen significance

A

Inhibited by oxygen
 In obligate aerobes, nitrogenase is protected from
oxygen by combination of removal by respiration,
production of oxygen-retarding slime layers,
localization of nitrogenase in differentiated
heterocyst

75
Q
A

Microbiology (6 decks)

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