Chapter 3: Microbial metabolism Flashcards
Metabolism
All biochemical reactions needed for life
-includes catabolism and anabolism
-relies on e donors and e acceptors
Exergonic
Reactions with negative delta G release free energy
Endergonic
Reactions with positive delta G require energy
Catabolic pathways
Cellular processes that generate free energy
-Free energy produced is conserved by synthesizing molecules like ATP
ATP produced from 1 mole of glucose in aerobic respiration
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Anabolic pathways
Endergonic pathways in which cellular synthesis requires energy
-Energy comes from ATP hydrolysis
Reducing power
Ability to donate e
Biosynthesis requirements
-Free energy (ATP)
-Reducing power (electron carriers)
Phototrophs
-Obtain energy from sunlight
-Do not require chemicals as energy source
-Oxygenic and anoxygenic
Chemotrophs
Get energy from chemical receptors
Aerobic requirements
O2 as electron acceptor
Anaerobic requirements
use anything other than O2 as electron acceptor
Chemoorganotrophs
Obtain energy and reducing power from organics
Chemolithotrophs
Obtain energy and reducing power from inorganics
Heterotrophs
Obtain carbon from organics
Autotrophs
Obtain carbon from CO2
-Also called primary producers as they synthesise organic matter from inorganic matter
Electron carriers
Typically electron movement proceeds through consecutive reactions
-Soluble e carriers such as NAD needed to carry electrons
NAD+
nicotinamide adenine dinucleotide
redox couple = -0.32V
-Reduction requires 2 e and 1 H+
-It is a coenzyme
Free energy needed to synthesize ATP
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
3 mechanisms of ATP generation
-Substrate level phosphorylation
-Oxidative phosphorylation
-Photophosphorylation
Substrate-level phosphorylation
Energy rich substrate bond hydrolysed directly to drive ATP formation
-E.g. hyydrolysis of phosphoenolpyruvate
Oxidative phosphorylation
Movement of e generates proton motive force used to synthesize ATP
Difference between Eu and Pro oxidative phosphorylation
-Eu push e out of mitochondrial membrane
-Pro push e out of plasma membrane into periplasm
Photophosphorylation
Light used to form proton motive force
Activation energy
Minimum energy required for chemical reaction to begin
Catalyst mechanism
Lowers activation energy in order to increase the reaction rate as the activation energy is minimum energy required for chemical reaction to begin
Prosthetic groups
Tightly bound to enzymes, usually covalently and permanently
-e.g. heme in cytochromes
Coenzymes
Loosely, transiently bound
most are derivatives of vitamins
Enzyme catalysis
-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
Glycolysis and citric acid cycle
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Biosynthesis and Citric acid cycle
Alpha-ketoglutarate and oxaloacetate: precursors of several aa, OAA also converted if needed to phosphoenolpyruvate which is a glucose precursor
Succinyl CoA BS
Required for synthesis of cytochromes, chlorophyll and related molecules
Acetate BS
Fatty acid biosynthesis
Other chemoorganotrophy pathways
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)
Glyoxylate cycle
Principles of fermentation
-Involves substrate level phosphorylation and redox balance via pyruvate reduction + excretion as waste
Fermentation Goals
-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
Alcoholic fermentation
Yeast ferments glucose to 2 ethanol and CO2
-ATP from glycolysis
-NAD+ regenerated by donating e to pyruvate
quinone
nonprotein electron carriers
Lactic acid fermentation
Ferment glucose to lactic acid
-Different enzymes reduce pyruvate to lactic acid
-NB in fermenting food andhuman health
Reoxidation
-occurs during e transport
-occurs in cytoplasmic membrane
-Forms electrochemical gradient that conserves energy through ATP synthesis
Respiration
E transferred from reduced e donors to external e acceptors like O2
Need for respiration
NADH and FADH2 produced in glycolysis and CAC must be reoxidised for redox balance
NADH dehydrogenases
Active site binds NADH, accepts two e and two protons that are transferred to flavoproteins, regenerating NAD+
quinones description
-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
Flavoproteins
-Contains derivative of riboflavin as prosthetic group (eg, FMN) that accepts 2 electrons and two protons but only donate electrons
E transport
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
Cytochromes
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)
Nonheme iron proteins
-Contain iron and sulfur clusters
-eg. ferredoxin: low reduction potential, important in H2 production
-Reduction potentials vary
-only carry e
Complex IV
includes cytochromes a and a3
-terminal oxidase, reduces O2 to H2O
-Needs 4e and 4 H+ from cytoplasm
-pumps 1 H+ per e
Complex III
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
Complex I
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
Complex II
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
NADH accounting
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)
FADH2 accounting
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)
ATP Synthetase
-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
ATPase structure
-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
ATPase production
-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
Oxidative phosphorylation production
OP conserves much more energy because substrate is completely oxidised
-Eg. 38 ATP in aerobic respiration vs 2 ATP in lactic acid fermentation
ATP hydrolyses in ATPases
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
aerobic respiration
Uses O2 as terminal electron acceptor
Anaerobic respiration
uses other e acceptor
difference between respiration and fermentation
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
Methods of growth of E.coli
Aerobic respiration
Fermentation
anaerobic respiration
Basic organisation of E.coli
-Complex I, Complex II, quinones, terminal reductase
-Can swap components
-Alternative quinones
-alternative dehydrogenases/terminal reductases
E.coli optimise respiration
-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
Nitrate respiration in E.coli
-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
Chemolithotrophy respiration
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
Phototrophy
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
Purple bacteria
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
difference between respiratory and photosynthetic e transport in purple bac
Cyclic photophosphorylation
e are returned
Generation of reducing power
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
Nitrogen significance
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
Calvin cycle requirements
Requires CO2, a CO2 acceptor, NADPH, ATP, ribulose bisphophate carboxylase (RubisCO), and
phosphoribulokinase
Calvin cycle usage in diffeerent species
Used by many autotrophs, including all oxygenic phototrophs
Found in purple bacteria, cyanobacteria, algae, green plants, most chemolithotrophic Bacteria, few Archaea
Calvin cycle reactants and products
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
Calvin cycle steps
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
Nitrogen fixation significance
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)
Nitrogenase enzyme complex
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
Nitrogenase oxygen significance
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
