Energetics, Fermentation, Respiration

Metabolism

the sum of all chemical reactions that occur in a cell

catabolism

energy-releasing metabolic reactions

anabolism

energy-requiring metabolic reactions

Heterotrophs

aka chemoorganotrophs; obtain carbon from organic compounds

Autotrophs

obtain from carbon from CO₂; ex: chemolithotrophs & phototrophs

Chemolithotrophs

oxidize inorganic compounds (H₂, H₂S, NH₄⁺)

Phototrophs

convert light energy into ATP

Energy

measured in units of kilojoules (kJ) of heat energy; required or released in any chemical reaction

Free Energy (G)

energy released that is available to do work

ΔG^0’

change in free energy during a reaction under standard conditions

Exergonic

reactions with -ΔG^0’; release free energy; spontaneous

Endergonic

reactions with +ΔG^0’; require energy; nonspontaneous reactions

Only _____ reactions yield energy that can be conserved by the cell

exergonic

ΔG

free energy that occurs under actual conditions; considers equilibrium constant; uses Gibbs Free Energy to calculate

Redox Reactions

two half reactions: one substance is oxidized and one is reduced; energy from it is used in synthesis of energy-rich compounds

Electron donor

substance is oxidized; potential energy source; loses electrons/H⁺

Electron acceptor

the substance is reduced; gain electrons/H⁺

Reduction potential E₀^’

tendency to donate electrons; volts in comparison to H₂

Reduced substance of a redox couple with a _________ E₀^’ donates electrons to the oxidized substance of a redox couple with ___________ E₀’

more negative; more positive

More negative E₀’

donates electrons

More positive E₀’

acceptors electrons

Redox tower

represent a range of possible reduction potentials

Substances toward the top (reduced) of the redox tower prefer to ____ electrons

donate

Substances toward the bottom (oxidized) of the redox tower prefer to _______ electrons

accept

The farther the electrons “drop” on the redox tower, the ______ the amount of energy released

greater

What is the strongest significant natural electron acceptor?

oxygen

How much energy does it take to make 1 ATP under standard conditions?

30.5 kJ/mol

Redox carriers

facilitate redox reactions without being consumed; are recycled; inside the cell; hold electrons/H⁺; needed for enzymes to work; allows many different donors and acceptors to interact; ex: NAD⁺/NADH, NADP⁺/NADPH, FAD⁺/FADH₂

Where is chemical energy released in redox reactions primarily stored in?

phosphorylated compounds; mostly ATP, ADP in archaeal species, phosphoenolpyruvate, coenzyme A derivatives

ATP

prime energy currency; temporary storage of energy bc easily formed and broken (bonds)

Long Term Energy Storage

involves biosynthesis of insoluble polymers that can be oxidized to generate ATP; ex: glycogen, poly-beta-hydroxylbutyrate, polyhydroxyalkanoates, elemental sulfur

Activation Energy

minimum energy required for molecules to become reactive; usually need a catalyst

Catalyst

substance that facilitates a reaction without being consumed, lowers activation energy, does not affect energetics or equilibrium of a reaction, increases reaction rate

Enzymes

biological catalysts; typically, proteins (some RNAs); highly specific; has active site

Active site

region of enzyme that binds substrate

Prosthetic groups

small nonprotein, nonsubstrate molecules that participate in catalysis; sometimes have trace metals; tightly bound; usually bind covalently and permanently

Coenzymes

small nonprotein, nonsubstrate molecules that participate in catalysis; loosely bound; most are derivatives of vitamins

Enzyme catalysis

depends on substrate binding; position of substrate relative to catalytically active amino acids in active state; endergonic and exergonic reactions are coupled

Heterotrophs types

fermenters & respirers

Fermenter Types

lactic acid, alcoholic, mixed acid

Respirer types

sulfate reduction, oxygen reduction, nitrate reduction

Fermentation

anaerobic catabolism in which organic compounds donate and accept electrons; use organic molecules as electron acceptor (internal); does not use respiring chain; redox balance by production of fermentation products which are excreted; ATP synthesized by substrate-level phosphorylation

Respiration

aerobic or anaerobic catabolism in which an organic donor is oxidized with O₂ (aerobic) or another compound (anaerobic) as an electron acceptor; use exogenous molecules/elements; glycolysis or ED → citric acid cycle (TCA) and glyoxylate cycles → respiration chain; ATP yield of 38

What do fermenters and respirers have in common?

first step with breakdown of glucose to pyruvate

Breakdown of glucose to pyruvate ways

Embden Myerhol Parnas Pathway (glycolysis); Entner Douderoff Pathway; Pentose Phosphate Pathway

Glycolysis/Embden-Meyerhof-Parnas pathway (EMP)

glucose → pyruvate (catabolism); ATP produced by substrate-level phosphorylation; anaerobic process; three stages: 6 carbon stage, oxidation stage, energy harvesting stage; make 2 pyruvates, 2 NADH, 2 ATP

Glycolysis/Embden-Meyerhof-Parnas pathway (EMP) input

glucose

Glycolysis/Embden-Meyerhof-Parnas pathway (EMP) output

2 pyruvate, 2 ATP, 2 NADH

Substrate Level Phosphorylation

uses energy rich intermediates in catabolic pathway are used to form ATP via kinases (enzymes); phosphate groups are configured into a high energy state; in cytoplasm; during fermentation

Entner-Doudoroff Pathway (ED)

glucose + NADP⁺ + NAD⁺ + ADP → 2 pyruvate + NADH + NADPH + ATP'; need NADP⁺ and NAD⁺ as cofactors; common in respiring organisms not fermenting bc make 20-30 ATP so losing 1 isn’t bad; partially oxidize glucose; less steps, reduces NADP⁺ faster

Entner-Doudoroff Pathway (ED) inputs

Glucose + NADP⁺ + NAD⁺ + ADP

Entner-Doudoroff Pathway (ED) outputs

2 pyruvate, NADPH, NADH, ATP

Pentose Phosphate Pathway (PP)

glucose → 1 pyruvate + 1 ATP + 3 NADH; amphibolic, anabolic pathway, heterolactic fermenters; ATP by substrate level phosphorylation

What do cells do with electrons removed by oxidation reactions?

need redox carriers in small amounts; need redox carriers to be quickly oxidized or glucose will stop; require terminal electron acceptor to oxidize redox carriers; reduced form becomes waste product

Lactic Acid Fermentation

pyruvate + NADH → lactic acid + NAD⁺; lactic acid is main fermentation product; found in lactic acid bacteria (Streptococcus, Bacillus); responsible for souring milk products (yogurt, cheese, buttermilk, sourcream); homofermentative or heterofermentative pathways

Lactic acid fermentation input

pyruvate, NADH

lactic acid fermentation outputs

lactic acid, NAD⁺

Homolactic Lactic Fermentation

glycolysis/EMP pathway; produce only lactic acid; yield 2 ATP/glucose; Streptococcus; more acidic waste products

Heterolactic Lactic Acid fermentation

pentose phosphate pathway; produce lactic acid, ethanol, CO₂; less acidic waste products + more NADH; yield 1 ATP/glucose; Leuconostoc

Alcoholic Fermentation

found in many fungi, yeasts, Zymomonas; ethanol is main product; human applicaitons like bread & alcoholic spirits; pyruvate → acetaldehyde + CO₂ w/ pyruvate decarboxylase then acetaldehyde + NADH → ethanol + NAD⁺ alcohol dehydrogenase

Alcoholic Fermentation inputs

pyruvate & NADH

Alcoholic outputs

CO₂, ethanol, NAD⁺

Mixed Acid fermentation

found in E. coli and Salmonella; EMP pathway; makes ehtanol, acetic acid, lactic acid, formic acid, succinic acid, H₂, CO₂; lower pH (4.4) than others; APT is about 2.5; CO₂:H₂ is 1:1 bc formate hydrogen lyase

Mixed acid fermentation outputs

ethanol, acetic acid, lactic acid, formic acid, succinic acid, H₂, CO₂

mixed acid fermentation inputs

pyruvate

Butanediol Fermentation

special type of mix acid; produces ethanol, acetic acid, formic acid, lactic acid, succinic acid, H₂, CO₂, lots of butanediol; CO₂:H₂ is 5:1; pH is not as acidic; in Klebsiella, Serretia

Butanediol Fermentation inputs

pyruvate

Butanediol Fermentation outputs

ethanol, acetic acid, lactic acid, formic acid, succinic acid, H₂, CO₂, butanediol

Role of Fermentation

part of carbon cycle under anaerobic conditions (ex: gut, soil, compost heaps, freshwater and marine habitats, subsurface environment, etc); make complex anaerobic food webs important in ruminants, insects (termintes), and humans

Anaerobic food webs

ruminants (can’t digest grass → cattle, deer, goats) so designed as a large fermentation vat to encourage degradation of the glass by bacteria and protozoa; rely on microbial anaerobic food webs in theri stomachs to degrade the grass into fermentation products which are then absorbed for growth + eat bacteria

Cud

regurgetated adn continue to chew before passing through again

rumen process

sugars → CO₂ + H₂ + butyrate + lactate + propionate + acetate; protozoa usually just give H₂ and CO₂ so monesin is given to kill htem to favor growth of Succinomonas sp for more propionate so more carbon is absorbed by the cow

Aerobic Respiration

oxidation using O₂ as the terminal electron acceptor

Anaerobic respiration

oxidation using other compounds as terminal electron acceptors like nitrate (NO₃^-), ferric iron (Fe³⁺), sulfate (SO₄^2-), carbon dioxide (CO₂), and certain organic compounds (ex: fumarate); less energy conserved compared to aerobic bc less difference in redox potential; requires electron transport, generates proton motive force, uses ATPase

Citric Acid Cycle/Tricarboxylic acid cycle

pyruvate is completely oxidized to CO₂; glucose (2 pyruvate) → 6 CO₂ + 4 NADH + 1 FADH + 1 GTP; amphibolic pathway; most enzymes are reversible

Amphibolic pathway

catabolism & anabolism

TCA input

2 pyruvates

TCA outputs

6 CO₂, 4 NADH, 1 FADH, 1 GTP

How are NADH and FADH oxidized after being reduced in TCA?

electron transport chain that consumes electrons and produces ATP

Biosynthesis from TCA

α-Ketoglutarate and oxaloacetate (OAA): precursors of several amino acids; succinyl-CoA: required for synthesis of cytochromes, chlorophyll, and other tetrapyrrole compounds; Acetyl-CoA: for fatty acid biosynthesis

Electron Carriers in Respiration

membrane/cytoplasmic-associated or membrane bound; many oxidation-reduction enzymes (NADH dehydrogenase, flavorproteins, iron-sulfur proteins, cytochromes); quinones; ordered in increasingly more psoitive reduction potential; alternate from those that accept H to those that accept electrons only at certain points in the chain

NADH dehydrogenase

accepts & donates two electrons and two protons; membrane associated redox protein; active sites bind NADH and transfer electrons & protons to flavoproteins to generate NAD⁺

Flavoproteins

accept and donate 2 electrons and protons; membrane bound FMN redox protein; contains flavin prosthetic group

Iron Sulfur Protein

accepts and donates electrons only; membrane bound redox protein; nonheme iron; contain clusters of iron and sulfur (ex: ferredoxin)

Quinones

accept 2 electrons and protons; membrane bound; small hydrophobic nonprotein organic redox molecules that can move within the membrane; typically link iron-sulfur proteins and cytochromes; ex: ubiquinone & menaquinone

Ubiquinone

coenzyme Q

Cytochromes

accept 1 electron via iron in atom heme (Fe²⁺ or Fe³⁺); redox proteins that contain heme prosthetic groups; sometimes form complexes (ex: cytochrome bc₁)

Electron Transport System

oriented in cytoplasmic membrane so electrons are separated from protons; 1- protons are released on outside from NADH & dissociation of water; gets pH gradient and electrochemical potential across membrane for proton motor force as inside is negative + alkaline (OH^-) & outside acidic + positive (H⁺); final carrier in the chain donates the electrons and protons to the terminal electron acceptor (ex: O₂, nitrate, sulfate, fumarate)

ATP synthase

aka ATPase; complex that converts proton motive force into ATP; reversible catalysis of ADP + P_i to ATP; consumes 3-4 H⁺ per ATP & 2e^- for 3 ATP; fdissipates/creates proton motive force; F₁ w/ multiprotein extramembrane complex entending into cytoplasm & F_o w/ membrane-integrated proton-translocating multiprotein complex; all microbes have it as source of energy, mostly conserved, oxidative phosphorylation

ATPases in strict fermenters

generate proton motive force for flagellar rotation and transport of nutrients and waste products

Oxidative phosphorylation

uses a respiratory chain (ETC) that generates proton motive force; uses enzyme complex ATPase; occurs in cytoplasmic membrane; occurs during respiration