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Chapter 5
Directions and Rates
of Biochemical
Processes
Key Questions
• What factors determine which way a
reaction will go?
• What factors determine the rate of a
chemical reaction?
• How do enzymes work?
• How can cells modify the activity of
enzymes?
Work and Energy
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Work: movement of an object against a
force
– Work can be stored as potential
energy: in a spring or battery
• Examples: lifting something
against gravity, winding a spring
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Energy: ability to do work; ability to
promote change
– 2 forms:
• Kinetic- associated with movement,
rock falling or muscle contracting
• Potential- due to structure or
location, can be gravitational,
electrical, chemical
• Chemical energy- energy in
molecular bonds
• Kinetic energy of molecules is heat
Thermodynamics
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Rules of chemical energy change
Used to predict the conversion of energy from one form to another
Determines the direction of the changes
First law: The total amount of energy in any process stays constant
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Law of conservation of energy
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Energy cannot be created or destroyed
– Energy may change form — from chemical to kinetic
• Ex. Doing a pushup; Muscles contract (work); Energy from
ATP becomes kinetic energy of movement and heat
Second law: entropy (chaos, disorder) continually increases in the
universe
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Transfer or transformation of energy from one form to another
increases entropy or degree of disorder of a system
Energy and Chemical Reaction
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Chemical reactions: one substance is changed into another, release &
store energy
– Reactants: molecules entering into the chemical reaction
– Products: changed molecules at the end of the reaction
– Free energy of activation: Energy is needed to initiate the reaction
between molecules
• Activation Energy:
– Initial input of energy to start reaction
– Allows molecules to get close enough to cause bond
rearrangement
– Can now achieve transition state where bonds are stretched
• Overcoming activation energy
– 2 common ways
• Large amounts of heat
• Using enzymes to lower activation
energy
Energy and Chemical Reaction
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Chemical reactions: one substance is changed into another, release &
store energy
– Exergonic reaction: Energy released from the reactants during the
reaction
• Energy released due to reactions breaking down complex
molecules into simpler molecules called catabolic reactions (分
解代謝).
– Endergonic reactions: Energy added to products during the
reaction. DO NOT occur spontaneously
• Anabolic reactions (合成代謝) are endergonic reactions that use
energy to build complex molecules from simpler molecules.
– Making bonds can store potential chemical energy
Direction of Reactions
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Chemical reactions usually go in the direction that releases heat
Heat is energy that is not available to do work
Energy input is required to reverse these reactions
H = G + TS
– H= enthalpy or total energy
– G= free energy or amount of energy for work
– S= entropy or unusable energy
– T= absolute temperature in Kelvin (K)
• Energy in a system that is available to do work
• Change in free energy determines direction
– Energy transformations involve an increase in entropy
– Entropy - a measure of the disorder that cannot be harnessed to do
work
Entropy
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Measure of disorder
Second law of thermodynamics, implies that disorder will increase
Going from ordered state to disordered releases energy to do work
Going from disorder to order requires energy
Concentration and Entropy
– Movement of molecules from concentrated to less concentrated
increases entropy, releases energy
ΔG = Δ H - T Δ S
• Equilibrium and Free Energy
• Exergonic
– ΔG<0 or negative free energy
change
– Spontaneous
• Occur without input of
additional energy
• Not necessarily fast
• Key factor is the free
energy change
• Endergonic
– ΔG>0 or positive free energy
change
– Requires addition of free
energy
– Not spontaneous
Sources of Free Energy
• Breaking of unstable bonds
and formation of stable
bonds
• ∆G of product lower than ∆G
of reactants
• High energy bonds —
unstable
• Hydrolysis of ATP
– ΔG = -7.3 kcal/mole
– Reaction favors
formation of products
– Energy liberated can
drive a variety of cellular
processes
Coupled Reactions
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Cells use ATP hydrolysis
– An endergonic reaction can be coupled to an exergonic reaction
– Endergonic reaction will be spontaneous if net free energy change
for both processes is negative
Glucose + phosphate → glucose-phosphate + H2O
ΔG = +3.3 Kcal/mole
endergonic
ATP + H2O → ADP + Pi
ΔG = -7.3 Kcal/mole
exergonic
Coupled reaction:
Glucose + ATP → glucose-phosphate + ADP
ΔG = -4.0 Kcal/mole
exergonic
Enzymes Act as Catalysts
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Catalyst- agent that speeds up the rate of a chemical reaction without
being consumed during the reaction
Enzymes can accelerate reactions as much as 1016 over uncatalyzed
rates!
– Ex.: Urease catalyzed rate: 3x104/sec
– Uncatalyzed rate: 3x10-10/sec
– Ratio is 1x1014 !
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Pepsin (protein digestion in stomach) works best at pH2; too much
food dilutes acid, inhibits digestion
Vinegar (acetic acid) denatures proteins in bacteria, killing them,
preserving food (pickles, herring)
Enzymes Features
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Catalyst- agent that speeds up the rate of a chemical reaction without
being consumed during the reaction
Enzymes- protein catalysts in living cells, speed up chemical reactions
– Do not affect free energy, cannot reverse a reaction
– Bind to reacting molecules (substrates) at the active site
– Binding is reversible (100,000 times per second)
– Binding is specific — only do 1 kind of reaction
Active site - location where reaction takes place
Substrate- reactants that bind to active site
Enzyme-substrate complex formed when enzyme and substrate bind
Each enzyme has optimum conditions: temperature, pH, salt
concentration
– High temperatures denature proteins
– pH influences 3-D structure of protein
– Salt can interfere with binding of substrates
Prosthetic groups - small molecules permanently attached to the
enzyme
Cofactor - usually inorganic ion that temporarily binds to enzyme
Coenzyme - organic molecule that participates in reaction but left
unchanged afterward
Enzymes Lower Activation
Energy of a Reaction
• Enzyme binds to substrate
with non-covalent bonds
• Holds substrate in position
for reaction
• Distorts substrate into a
transition state
• Enzyme is unchanged at the
end of a reaction
• Straining bonds in reactants
to make it easier to achieve
transition state
• Positioning reactants
together to facilitate
bonding
• Changing local environment
– Direct participation
through very temporary
bonding
Enzyme Mechanism
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Substrate binding
– Enzymes have a
high affinity or high
degree of specificity
for a substrate
– Used the example of
a lock and key for
substrate and
enzyme binding
Induced fit - interaction
also involves
conformational
changes
Regulation
• Factors that Affect Enzyme Activity
– Enzyme’s activity is sensitive to the
change in their 3-dimensional shape.
– Temperature and pH are two factors
that may make enzyme to lose its
shape or denature. (antifreeze
protein, hot spring protein)
• The 3-D shape of an enzyme can also be
affected by the binding of specific
chemicals called activators (facilitate
chemical reactions) and inhibitors (turnoff chemical reactions).
– Steric inhibitors bind to active site and
prevent substrate from binding; can be
overcome by increasing substrate
concentration
– Allosteric (non-competitive) inhibitors
bind at another site, change shape of
enzyme; some are reversible
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Enzyme activity within an organism is
often regulated by inhibitors under the
process called negative feedback
End-product inhibition