Chapter 10

Metabolism

total of all chemical reactions in the cell

Two divisions of metabolism

catabolism and anabolism

Catabolism

breakdown of sugars proteins and fats into precursor carbon skeletons ATP and reducing power

Anabolism

synthesis of complex organic molecules from precursor metabolites using energy and reducing power

Fueling reactions

catabolic reactions that provide ATP reducing power and precursor metabolites

Energy-conserving reactions

catabolic reactions that capture energy in ATP or reduced electron carriers

Reducing power

electrons carried mainly by NADH NADPH or FADH2 that can be used in metabolism

Precursor metabolites

intermediate carbon skeletons used to build amino acids nucleotides lipids DNA RNA proteins and membranes

Relationship between catabolism and anabolism

catabolism supplies ATP reducing power and precursors that anabolism uses to build the cell

Why microbial metabolism matters

microbes drive elemental cycling and convert waste into usable nutrients

Elements heavily cycled by microbes

C H O N P S

Nitrogen cycle significance

several steps are done only by microbes

Microbial nutritional diversity

microbes are represented in all five major nutritional types

Calorie cal

amount of energy needed to raise 1 gram of water by 1°C

Joule J

SI unit of energy

1 cal in joules

4.184 J

ΔG°′

standard free energy change under standard biological conditions

Exergonic reaction

releases free energy has negative ΔG°′ and proceeds spontaneously

Endergonic reaction

requires energy input has positive ΔG°′ and is not spontaneous by itself

Exergonic energy profile

substrates start at higher free energy and products end at lower free energy

Endergonic energy profile

substrates start at lower free energy and products end at higher free energy

Why exergonic and endergonic reactions are coupled

energy released by exergonic reactions drives endergonic reactions

ATP

major cellular energy currency

ATP hydrolysis reaction

ATP + H2O → ADP + Pi + H+

ΔG°′ of ATP hydrolysis

-7.3 kcal/mol or -30.5 kJ/mol

Why ATP is useful

ATP hydrolysis is exergonic and can be coupled to endergonic reactions

ATP high-energy bond idea

ATP is best understood as having high phosphate transfer potential rather than just “high-energy bonds”

ATP high-energy phosphoanhydride bonds

between alpha and beta phosphates and between beta and gamma phosphates

Phosphate transfer potential

tendency of a phosphorylated molecule to donate a phosphoryl group

What ATP donates

a phosphoryl group

High-energy phosphorylated compound

a phosphorylated compound whose hydrolysis releases about 30 kJ/mol or more

Not all phosphorylated compounds are high energy

some phosphates such as glucose 6-phosphate have much lower phosphate transfer potential than ATP

Substrate-level phosphorylation SLP

direct transfer of phosphate from a phosphorylated substrate to ADP to make ATP

SLP mechanism

high-energy phosphorylated substrate + ADP → product + ATP

GTP

nucleotide triphosphate used especially in protein-related energy reactions and associated with the TCA cycle

CTP

nucleotide triphosphate used especially in lipid synthesis

UTP

nucleotide triphosphate used to activate NAM and NAG during peptidoglycan synthesis

Why UTP matters in bacteria

it activates sugar precursors needed to build peptidoglycan

Oxidation

loss of electrons

Reduction

gain of electrons

OIL RIG

oxidation is loss reduction is gain

Redox pair

oxidized and reduced forms of the same substance

Oxidized form + e-

reduced form

Electron donor

substance that donates electrons and becomes oxidized

Electron acceptor

substance that accepts electrons and becomes reduced

Standard redox potential E0′

measure of a redox pair’s tendency to donate or accept electrons

Units of E0′

volts

More negative E0′

better electron donor

More positive E0′

better electron acceptor

Rule 1 of redox pairs

the reduced member of the more negative pair donates electrons to the oxidized member of the more positive pair

Rule 2 of redox pairs

the greater the difference in redox potential between donor and acceptor the greater the energy released

NAD+/NADH redox potential

-0.32 V

O2/H2O redox potential

+0.82 V

In the NADH and O2 pair electron donor

NADH

In the NADH and O2 pair electron acceptor

O2

Why NADH donates to O2

NADH has the more negative redox pair and O2 has the more positive redox pair

Substance oxidized in a redox reaction

electron donor reducing agent reductant

Substance reduced in a redox reaction

electron acceptor oxidizing agent oxidant

Formula for redox potential difference

ΔE0′ = E0′ of oxidizing agent − E0′ of reducing agent

Formula for free energy from a redox reaction

ΔG0′ = -nFΔE0′

n in ΔG0′ = -nFΔE0′

number of electrons transferred

Faraday constant in kcal

23 kcal/volt·equivalent

Faraday constant in kJ

96.5 kJ/volt·equivalent

ΔE0′ for NADH donating to O2

+1.14 V

ΔG0′ for NADH donating to O2

-52.44 kcal

Positive ΔE0′ usually means

negative ΔG0′ and a spontaneous forward reaction

Negative ΔG0′ means

spontaneous in the forward direction

Positive ΔG0′ means

spontaneous in the reverse direction not forward

ΔG = 0 and Ecell = 0

system is at equilibrium with no net reaction

Electron transport chain ETC

series of electron carriers that pass electrons stepwise to a terminal electron acceptor

Purpose of the ETC

conserve energy from electron transfer by generating proton motive force

Location of ETC in prokaryotes

cytoplasmic membrane

Location of ETC in eukaryotes

inner mitochondrial membrane or chloroplast membrane

First electron carrier in an ETC

the carrier with the most negative redox potential at the start of the chain

Direction of electron flow in ETC

from more negative redox carriers to more positive redox carriers

Why bacterial ETCs vary

their components can change with species strain environment and growth conditions

Major classes of electron carriers in ETCs

flavoproteins ubiquinone cytochromes and nonheme iron-sulfur proteins

Flavoproteins

carriers that transfer electrons and protons using flavin cofactors

Ubiquinone CoQ UQ

lipid-soluble mobile carrier that transfers electrons and protons within membranes

Cytochromes

heme-containing carriers that transfer electrons only

Nonheme iron-sulfur proteins FeS proteins

electron carriers containing iron-sulfur centers that transfer electrons only

NADH role in metabolism

major electron donor to the ETC during catabolism

NADPH role in metabolism

major electron donor for anabolic biosynthetic reactions

Proton motive force pmf

electrochemical gradient of protons across a membrane

How pmf is generated

ETC electron flow releases energy that is used to move protons across the membrane

Two components of pmf

membrane potential Δψ and proton concentration gradient ΔpH

ATP synthase

membrane enzyme complex that uses pmf to synthesize ATP

ATP synthase mechanism

H+ flows down its gradient through ATP synthase and the enzyme uses that energy to convert ADP + Pi into ATP

Oxidative phosphorylation

ATP synthesis powered by pmf generated by the ETC

Difference between oxidative phosphorylation and substrate-level phosphorylation

oxidative phosphorylation uses ETC + pmf + ATP synthase whereas SLP directly transfers phosphate from a substrate to ADP

Enzyme

biological catalyst that speeds up reactions without being consumed

Main thing enzymes do

lower activation energy Ea

Activation energy Ea

energy barrier that must be overcome for a reaction to proceed

Do enzymes change ΔG

no

Do enzymes change reaction equilibrium

no

Do enzymes make endergonic reactions exergonic

no

Active site

region of an enzyme where substrate binds and catalysis occurs

Enzyme-substrate complex

temporary complex formed when substrate binds the enzyme active site

Induced fit model

substrate binding changes enzyme conformation to improve catalysis

Lock-and-key model

older rigid model of enzyme-substrate binding