2-1Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Chapter 2: The chemistry of life

2-2Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Energy and entropy• Chemical and energy transformations in cells

– metabolism

• Sequence of chemical reactions– metabolic pathways

• Energy is the capacity to do work– potential energy is stored energy– kinetic energy is expressed as movement

• Energy transformations are governed by the laws of thermodynamics

2-3Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Equilibrium

A ↔ B + C

• A reaction is at equilibrium when there is no net change in the concentration of reactant or products

• Reactions must be out of equilibrium to do work

(cont.)

2-4Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Equilibrium (cont.)• Equilibrium constant

• If the reactants and products contain the same chemical energy per molecule, Keq = 1.0

– in this case, there must be a high concentration of reactants or low concentration of products in order to do work

• If reactants and products contain different amounts of chemical energy, then Keq ≠ 1.0

– reaction will be out of equilibrium when concentration of reactants and products are equal

)reactant(s ofion concentrat

product(s) ofion concentrateq K

2-5Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Free energy• Free energy (G) represents the maximum amount

of useful work obtainable from a reaction• Change in free energy (ΔG) is the useable energy

(chemical potential) of a reaction– depends on

change in heat content (ΔH) determined by the making and breaking of chemical bonds

change in entropy (ΔS) determined by the molecular organisation of the system

temperature (T) in degrees Celsius above absolute zero

ΔG = ΔH – TΔS

(cont.)

2-6Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Free energy (cont.)

• Change in free energy is related to the concentration of reactants and products

– R is universal gas constant

ΔG = – RTlogeKeq

• When ΔG < 1.0, energy is released in exergonic reaction

– spontaneous reactions

• When ΔG > 1.0, energy is needed for endergonic reaction

2-7Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Fig. 2.4a and b: Exergonic and endergonic reactions

(a)

(b)

2-8Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Rates of chemical reactions• Rate of reaction towards equilibrium (kinetic

energy of reaction) is independent of Keq or ΔG– depends on kinetic energy of reacting molecules

• Activation energy is minimal level of energy necessary to break existing bonds at the moment that molecules collide

• Rate of reaction can be increased by– heat

raises kinetic energy of molecules– catalysis

reduces activation energy of reactants

2-9Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Fig. 2.5a: Energy levels of molecules

2-10Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Fig. 2.5b: Energy levels of molecules

2-11Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Enzymes

• Enzymes are biological catalysts that lower the activation energy in reactants (substrates)

enzyme + substrate ↔ enzyme–substrate complex

enzyme–substrate complex → enzyme + product

(cont.)

2-12Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Enzymes (cont.)

• Enzymes are specific in their substrates• Active site is specialised region formed from

folding of polypeptide chains• Site lined by R-groups of amino acids

– substrate-binding amino acids– arrangement determines specificity of binding enzyme to

substrate

• Catalytic amino acids

2-13Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Enzyme action

• Substrate fits active site on enzyme molecule• Active site changes shape when substrate

attaches to it – induced fit

• Once fitted to active site, substrate is under strain and ready for reaction

– transition state– transition state activation

2-14Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Fig. 2.10: Stages of an enzyme-catalysed reaction

2-15Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Enzyme activity• Rate of enzyme activity affected by factors that

change shape of active site so substrate does not bind

– pH– temperature– may alter active site irreversibly (denature)

• Rate of enzyme activity affected by concentration of

– substrate– cofactors– coenzymes

2-16Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Metabolism

• Metabolic reactions result from enzyme activity• Enzyme activity is regulated to prevent over- or

under-production• Short-term control of enzyme activity by modifying

structure of enzyme– covalent modification

phosphorylation (addition of phosphate residues) increases or decreases activity

– allosteric inhibition or activation binding of organic molecule to sites on enzyme surface

(cont.)

2-17Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Metabolism (cont.)

• Concentration of enzyme can be increased by synthesis of more enzyme protein

• Concentration of enzyme can be decreased by specific breakdown of enzyme protein

– removed to lysosome– marked for breakdown with polypeptide marker

2-18Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

ATP

• Energy from reactions in which reduced bonds in fuel molecules are oxidised is conserved in ATP (adenosine triphosphate)

• Components of ATP– ribose sugar– adenine– triphosphate group

two high-energy covalent bonds link these three phosphate groups

(cont.)

2-19Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

ATP (cont.)

• Biologically useful attributes of ATP– equilibrium constant of the ATP hydrolysis reaction is

high reaction is out of equilibrium at low concentrations of ATP,

ADP and P

– ATP formed in single steps in the pathways of glycolysis and cellular respiration

– ATP is a common intermediate between degradative and synthetic metabolic pathways

2-20Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Classes of enzymes

• Transferases and ligases are involved in biosynthesis of cellular constituents

• Hydrolases break down complex molecules• Lyases and isomerases are involved in pathways

that transform compounds into substrates for oxidoreductases

• Oxidoreductases trap potential energy by coupling reactions with ATP formation

2-21Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Electron transport pathways

• Membrane-bound enzymes and cofactors that operate in a sequence

• Electrons transferred from donor to acceptor– molecule that loses electron is oxidised– molecule that gains electron is reduced

• Transfer reactions are oxidation–reduction reactions

2-22Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Fig. 2.18: An electron transport chain

2-23Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Oxidation–reduction reactions

• In oxidation–reduction reactions, the tendency to donate or accept electrons can be measured as the oxidation–reduction (redox) potential

– E0′

• Redox reaction is thermodynamically favourable if electrons are transferred from a carrier with more negative potential with one to less negative (more positive) potential

(cont.)

2-24Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Oxidation–reduction reactions (cont.)

Oxidation–reduction system E0′ (mV) (a)

2H+ + 2e- ↔ H2– 420

NAD+ + 2H+ ↔ NADH + H+ – 320

FMN + 2H+ ↔ FMNH2 + 2e- – 120

Coenzyme Qox + 2e- ↔ Coenzyme Qred– 170

Cytochrome b (Fe3+) + e- ↔ Cytochrome b (Fe2+) + 120

Cytochrome c (Fe3+) + e- ↔ Cytochrome c (Fe2+) + 220

Cytochrome a (Fe3+) + e- ↔ Cytochrome a (Fe2+) + 290

½O2 + 2H+ ↔ H2O + 815

(a) E0′ is the standard redox potential relative to that of the H2 electrode at pH 7 (– 420 mV)

2-25Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint

Energy in fuel molecules• Carbohydrates, lipids and proteins provide cells

with energy– fuel molecules

• Energy can only be extracted from certain bonds of fuel molecules

– C—C– C—H– C—N

• Lipids have more energy per C atom than do carbohydrates or proteins because they have more energy-rich C—H bonds