micro chapter 10

metabolism

catabolism leads to the production of

key precursors: PEP, F6P, Acetyl-CoA from respiration, NAM/NAG (for peptidoglycan synthesis)
reducing power: electron carriers (NADH, FADH2)
energy: ATP

catabolism provides the ___ for anabolism

ATP

NAD(P)H

building blocks

redox reactions

explain the movement of electrons from donor to acceptor

standard reduction potential

describes the ability to gain electrons

negative E

donate electrons freely

no energy needed

positive E

accepts electrons freely

spontanteous, large negative delta G

chemotrophs

source of energy is by breaking chemical bonds, capture energy as ATP

phototrophs

source of energy is from light, capture energy to ATP

organotroph

source of electrons are from organic compounds, captured electrons carried NAD(P)H

lithotrophs

source of electrons are from inorganic compounds, captured electrons carried NAD(P)H

autotrophs

source of carbon is inorganic (from CO2), fixes CO2 into own source of carbon

heterotrophs

carbon source is organic (glucose) and is consumed and made by another organism

photolithoautotroph

light energy source

co2 carbon source

inorganic electron source

photoorganoheterotroph

light energy source

organic carbon source

organic electron source

chemolithoautotroph

inorganic chemical energy source

co2 carbon source

inorganic electron source

important for nutrient cycling, biogeochemical cycels, and ecology

chemolithoheterotroph

inorganic chemical energy source

organic carbon source

inorganic electron source

chemoorganoheterotroph (most nonphotosynthetic organisms)

organic chemical energy source, often same as carbon source

organic carbon source

organic electron donor, often same as carbon source

glycolysis is actually 3 pathways

glycolysis (EMP pathway)

pentose phosphate pathway

ED pathways

glycolsis pathways are overall the conversion of

conversion of glucose to GAP by 3 different routes, eventually production of pyruvate

EMP pathway

glucose to 2 g3p (invests 2 ATP)

2 g3p oxidized to 2 pyruvate (payout 4 ATP, 2NADH)

(net 2 ATP)

substrate level phosphorylation

a direct metabolic process that produces ATP by transferring a phosphate group from a high-energy substrate molecule to ADP

done by kinases

EMP contributes to anabolic pathways

make amino acids, PLs, sugars (NAM, NAG)

pentose phosphate pathway

makes NADPH, no ATP generated

oxidation-decarboxylation of G6P to Ru5P

Isomeration of ribulose to X5P and R5P (which makes nucleotides)

sugar rearranged, these sugars can make NAM and NAG, or sugars can funnel back into EMP to make pyruvate

source of precursors for some amino acids

some organisms rely solely on PPP

ED pathway

glucose → gluconate (making NADPH, using 1 ATP) → pyruvate and GAP

gap → pyruvate (making 2 ATP)

makes NADPH, NADH, net 1 ATP

only seen in prokaryotes

some organisms rely only on ED

why is ED useful?

gives NADPH

use other sugars (aldonic acids),

allows for nutritional diversity, giving a competitive advantage

all these glycolysis pathways lead to the formation of..

pyruvate

reduced electron carriers

pyruvate oxidation

oxidatvely decarboxylation

pyr to acetyl coA, making NADH

TCA

acetyl coa input, generating 2 CO2, 3 NADH, 1 FADH2, 1 GTP/ATP

intermediates in TCA can make other amino acids

anaplerotic pathways

metabolic processes that replenish TCA intermediates when they get shuttled off, ensuring its continuous operation for energy production and biosynthesis

other carbs (breaking down lactose → galactose)

tagatose pathway, make gap

leloir pathway, uses UDP to exchange gal for glucose, proceeds to glycolysis to make gap

gap → lactic acid

aerobic respiration/ ETC in bacteria

less complexes, shorter ETC, less energy made

protons pumped across plasma membrane instead of mitochondrial membrane, causing surrounding environment to change pH

bacteria can change its ETC complexes based on environmental conditions

ecoli uses two different cytochomr oxidases

2 pathways electrons can go during enviroment changes

high o2: use bo branch/complex

low o2: use bd branch, does not pump H+

terminal electron acceptor in aerobic respiration is usually

oxygen, highest reduction potential (E)

terminal electron acceptors in anaerobic conditions

nitrate, sulfate, other organic electron acceptors

smaller reduction potenital, not as good as O2, does not produce as much energy

organisms that only differ by aerobic or anaerobic respiration are still

chemoorganoheterotrophs

aerobic v anaerobic respiration in ecoli (a facultative anaerobe)

in aerobic: uses cyt O, pumps H+

in anaerobic: uses nitrate reductase instead of cyt O, needs NO3 present, no protons pumping, but less energy produced bc less proton motive force

nitrate reduction in paraoccus denitrificans

full denitrification (NO₃^- → N₂

Com 1 → Coq → Nar (nitrate reductase) → Com 3 → cyt c → Nir (nitrite reductase) → Nor (nitric oxide reductase) → Nos (nitrous oxide reductase)

nitrate reduction chemical steps and enzymes

NO3 → NO2 → NO → N2O → N2

Nar → Nir → Nor → Nos

geobacter sulfurreducens

has a special conductive pilli to transfer e- to Fe 3+ → Fe2+

some species use ___ as a terminal electron acceptor, reducing it to be nontoxic

HAsO4 2-

anaerobic e- transfer pathways in shewanella oneidensis

gram -, rxns in periplasm

uses cym A: transfers e- to various e- acceptors

some e- acceptors are outside the cell: iron reductase and dmso (prevents toxic byproducts)

why do organisms like shewanella oneidensis have so many pathways?

enviroment is variable

hard to find particular resources, use what you can

full ___ makes more ATP than partial __ because

denitrification makes more ATP than partial denitrication (NO3→ NO2-)

because there is a bigger difference between reduction potenitals when reducing down to N2

fermentations occur in bacteria that cannot

have an ETC

“fermenters”

3 types of facultative anaerobes depending on metabolism

1) ferment when anoxic (fermenters)

2) use anaerobic resp when anoxic

3) use anaerboic resp first, then switch to ferm when all TEAs run out

the main purpose of fermentation is to produce ___

produce NAD+ to be reused in glycolysis

glycolysis continues to make ATP (even tho not much)

SOMETIMES PRODUCE ATP VIA SUBSTRATE LEVEL P USING SLP

big problem for fermenters (abt oxidation?)

how to re-oxidize NADH without ETC?

if no NAD+ made, no glycolysis, no starvation

solution for fermentation problem

dump electrons on pyruvate (electron sink) additional pathways can reduce pyruvate to make more NAD+

main fermentation pathways

acid or alcohol product

atp can be made from SLP

alcohol fermenters can produce

ethanol, isopropanol. butanol, 2,3-butanediol

prevents environment from becoming too acidic

acid fermenters can produce

lowers environmental pH

makes lactacte, acetate (makes ATP), butyrate (makes ATP), formate (makes H2 and CO2), propionate (involves TCA intermediates)

homoethanologenic

microbes that produce ethanol as primary fermentation product

Pathway: glucose → 2 pyruvate → 2 acetaldehyde + 2CO2 → 2 ethanol

acetaldehyde reducing to ethanol makes NAD+

homofermentative lactic acid fermenters

only makes lactate, uses EMP

heterofermentative lactic acid fermenters

makes lactate, ethanol, CO2

uses PPP, EMP

mixed acid fermentation

pyruvate dehydrogenase is repressed (no ETC bc theres no TEA like O2 or NO3-)
pyruvate formate lyase (PFL) is active, making formate and acetyl coa
gas is produced if microbe makes formate hydrogen lyase

acetyl coA made during the PFL reaction from pyruvate can make

acetaldehyde (which goes on to make ethanol, NAD+)

acetate (makes ATP)

formate made during the PFL reaction from pyruvate can make

aka formic acid, break down to prevent too much acid build up

makes non acidic gases: CO2 and H2

mixed acid fermentation products are made

based on enviromental conditions

ABE fermentation

acetone-butanol-ethanol fermentations in clostridia (a strict anaerobe)

makes these products when stressed out during sporulation (low nutrients, low space)

another problem fermenters must deal with

acidification: need to pump protons our to prevent internal acidifcation and make a proton motive force for transport

but have no etc

must run atp synthase backwards, pumps H+ out of cell

atp used to power ATPS can be from a fermentation reaction

horseshoe TCA cycle

makes NAD+, AcCoA, uses anaplueronic cycles
generates intermediates for anabolic processes

rank aerobic, anaerobic, and fermentation pathways based on amt of energy produced

most in aerobic, then anaerobic, then fermentation

fermenters grow slowly

fermentation vs anaerobic respiration

fermenterts reverse the ETC, e- acceptor is organic, pyruv is e sink