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Chapter 2: The chemistry of life
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-1
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
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-2
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.)
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-3
Equilibrium (cont.)
•
Equilibrium constant
Keq 
•
concentrat ion of product(s)
concentrat ion of reactant(s )
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
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-4
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.)
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-5
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
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-6
Fig. 2.4a and b: Exergonic and endergonic
reactions
(a)
(b)
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
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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
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-8
Fig. 2.5a: Energy levels of molecules
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PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-9
Fig. 2.5b: Energy levels of molecules
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-10
Enzymes
•
Enzymes are biological catalysts that lower the
activation energy in reactants (substrates)
enzyme + substrate ↔ enzyme–substrate complex
enzyme–substrate complex → enzyme + product
(cont.)
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-11
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
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
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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
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-13
Fig. 2.10: Stages of an enzyme-catalysed
reaction
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
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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
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-15
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.)
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-16
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
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-17
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.)
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-18
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
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-19
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
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PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-20
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
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PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-21
Fig. 2.18: An electron transport chain
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PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-22
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.)
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-23
Oxidation–reduction reactions
(cont.)
(a)
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
E0′ is the standard redox potential relative to that of the H2 electrode at pH 7 (– 420 mV)
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-24
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
Copyright  2005 McGraw-Hill Australia Pty Ltd
PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint
2-25