Week 4
Chemical Reactions and Enzymes
1. Explain the relationship between delta G, delta H and delta S and discuss how
delta G determines the direction of a chemical reaction
2. Be familiar with the first and second laws of thermodynamics
• Energy = the capacity to do work
 Kinetic Energy – the energy of motion
 Potential Energy – stored energy
• Most forms of energy can be converted to heat energy
 Heat energy is measured in kilocalories (1 kcal = 1000 calories)
Note: one calorie = amount of heat required to raise temp of water by 10C
• Energy transformations are described by the laws of thermodynamics
• First Law of Thermodynamics – Energy cannot be created or destroyed. Energy can
only be converted from one form to another
• The aim of a cell is to harness the potential energy of the chemical bonds of
compounds
• For any chemical bond, the amount of energy it takes to break that bond is exactly the
same amount of energy released when the bond is formed. This is called bond energy
• What determines bond energy for particular bond is the difference in the
electronegativity of the two atoms bonding together.
• Second Law of Thermodynamics – States that some energy is lost as disorder
increases. It is the law of entropy
 It concerns the transformation of potential energy into heat or random
molecular motion
• Entropy = degree of disorder or randomness in a substance.
• The second law states that the disorder in the universe (entropy) is continuously
changing
• One of the major laws of thermodynamics is:
• ∆G is the amount of free energy able to do work. It is determined by:
 Change in heat content (enthalpy) (∆H) determined by the making and breaking
of chemical bonds
 Change in entropy (∆S) determined by the molecular organisation of the system
 Tempearture (T)
• When products contain more free energy than reactants – ∆G is positive
• When reactants contain more free energy than products – ∆G is negative
• In our bodies an example of a reaction where ∆G is positive is in respiration, the
product, glucose, has stored energy for later breakdown to eventually form ATP
• Take the two reactions below
• For the first reaction ∆G is positive, therefore free energy is stored in the products and
can be used later
• For the second reaction ∆G is negative, meaning you’ve lost that energy as it has been
released into the environment
• When ∆G is positive, the reaction will be non-spontaneous and goes towards the
reactants
• When ∆G is negative, the reaction is spontaneous and favours the product
Note: A spontaneous process is a naturally occurring process that once started will
continue to happen without outside intervention. Non-spontaneous process is an
unnatural process that after it is started will NOT continue without outside intervention.
3. Explain how enzymes facilitate chemical reactions by lowering activation energy
• Most reactions require some energy to get started
• The activation energy = energy needed to destabilize existing chemical bonds and
initiate a chemical reaction
• Catalysts = substances that lower activation energy of a reaction e.g. enzymes
• Enzymes are molecules that catalyse reactions in living cells
 Most are proteins (not all though e.g. ribosome)
 They lower the activation energy required for a reaction
 They are not changed or consumed by the reaction
 They accelerate the rate of biological reactions
 They do not alter the equilibrium of the reaction
• Enzymes interact with substrates
 Substrate = molecule that will undergo a reaction
 Active site = region of the enzyme that binds to the substrate
• Enzyme-substrate interaction works like a lock and key. Each enzyme is specific for a
certain substrate. Binding of an enzyme to a substrate causes the enzyme to change
shape, producing a betterinduced fit between the molecules.
• Multi-enzyme complexes offer certain advantages:
i.
Product of one reaction an be directly delivered to the next enzyme
ii.
Possibility of unwanted side reactions is eliminated
iii.
All of the reactions can be controlled as a unit
4. Define Km, Vmax, turnover number, competitive and uncompetitive inhibitors,
equilibrium and rate constants.
• Factors that can change an enzymes 3D shape, change its function. They are:
i.
Temperature
ii.
pH
iii.
Inhibitors
Inhibitors
• Inhibitors = molecules that bind to enzyme and decrease enzymatic activity
• Competitive Inhibitor – binds to active site on enzyme and prevents substrates from
binding to them
• Non-competitive Inhibitors – bind to sites other than the enzymes active site,
changing the enzymes shape and making it unable to bind to substrate
• Allosteric site = area on enzyme where molecules besides substrate bind
 Allosteric inhibitors – bind to allosteric site and inactivate enzyme
 Allosteric activators – bind to allosteric site and activate enzyme
• The rate constant quantifies the speed of a chemical reaction
• If we have the reaction below, where E = enzyme, S = substrate, and P = product
K1 is rate constant for formation of ES
K-1 is rate constant for conversion of ES to E + S
K2 is rate constant for product formation
• If we use the same equation above, at high concentrations of S, the enzyme is said to
be saturated with respect to substrate.
• Vmax is the maximal velocity (speed of enzyme-substrate reaction) achieved by an
enzyme under special conditions where the substrate is fully saturated.
• Essentially Vmax = the maximum an enzyme can work
• So from above graph First order = [S] < [E] and Zero order = [S] > [E]
• Michaelis-Menten Equation shows what happens between initial enzyme-substrate
reaction and Vmax
 From this equation we get Km
• Km is the substrate concentration that gives half saturation of the enzyme
• Km is essentially a measure of [S] required for effective catalysis to occur
• Enzymes with a low Km have a high affinity (tight binding) for substrate and act at
maximal velocity at low substrate concentrations
• Enzymes with high Km have low affinity (weaker binding) for substrates because more
product being formed and reactions need to occur quickly (come and go, come and go).
It will act maximally at higher amounts of substrate
• The turnover number (kcat) is a direct measure of the catalytic production of product
under saturating substrate conditions
• Kcat is the maximum number of substrate molecules converted to product per enzyme
per unit of time
• Equilibrium is when forward reaction occurs at the same rate as backward reaction
5. Outline how enzyme molecules adopt a specific 3D shape that is stabilised by
weak interactions between amino acid side chains.
• Every protein has a 3D structure that reflects its function, determined by weka
multiple interactions:
• Hydrophobic interactions – major contributor to stabilise globular form of most
soluble proteins
• H-bonds and ionic bonds
• Covalent bonds – in polypeptide backbone and place constraints on structure
6. Be familiar with the concept of substrate specificity and discuss how weak
interactions between substrate and active site contribute to substrate binding and
enzyme catalysis.
• Interaction between enzyme and substrate is mediated by the same forces that
stabilise protein structure, i.e. H-bonds, hydrophobic and ionic bonds
• Formation of weak interactions in ES complex is accompanied by release of small
amount of free energy that provides a degree of stability to the interaction
• This (release) energy is called binding energy
 Binding energy is major source of free energy used by enzymes to lower the
activation energies of reactions
 Much of the catalytic power of enzymes is ultimately deried from the free energy
released in forming many weak bonds and interactions between enzyme and
substrate
 The binding energy contributes to specificity as well as catalysis