Lecture 9 - Enzymes are essential for life Flashcards
Enzymes
Enzymes are biological catalysts – i.e. they increase the rate of a chemical reaction. (take reactants to products faster than they would on their own)
Most enzymes are proteins. (Catalytic RNAs, ‘ribozymes’ including ribosomes, are important exceptions.)
Enzymes, like all catalysts, do not change the free energy level of products and reactants.
A living cell enhances specific chemical reactions to create organisation until it is overtaken by death, chemical equilibrium and entropy.
Gibbs free energy
Life is not at equilibrium. For any chemical or biological process, the relative abundance of substrates and products is predicted by the Gibbs free energy…
ΔG < 0 Energy released; products dominate. Spontaneous reaction
ΔG > 0 Energy required; substrates dominate. Tends to be spontaneous in the opposite direction
ΔG = 0 At equilibrium; substrates and products at equal concentration.
Remember that thermodynamics and kinetics are independent I.e. energy is independent of rate
Synthesis pathways have a series of enzyme catalysed steps, keeps individual steps from equilibrium, can couple reactions (join a spontaneous and non-spontaneous reaction to give an overall delta G < 0
Activation energy
Energy required to each a transition state
Enzymes and catalysis explained
Enzymes catalyse reactions by lowering the activation energy
Cannot make a non-spontaneous reaction spontaneous
Does not shift equilibrium position i.e. same amount made but occurs faster
Enzymes do not change delta G they instead change the rate.
Enzymes speeds up reaction, doesn’t alter thermodynamics - changes size of the hump, not the relative start and end points
Energy needed to maintain cellular integrity
The overall Gibbs free energy (ΔG) has components of enthalpy (ΔH) and entropy (ΔS):
ΔG = ΔH - TΔS (T = absolute temperature) To favour the forward reaction (ΔG < 0) either enthalpy must
decrease (ΔH < 0) or entropy must increase (ΔS > 0).
Cellular integrity means a decrease in entropy in the cell, so energy from elsewhere is required. Enzymes control where and when energy is released to maintain the cell.
When temperature increases disorder also tends to increase
Why are some reactions slower?
Reactions pass through high- energy transition states. Activation energy (ΔG °‡) to reach the transition state determines rate. - height of the activation energy (height from reactants to transition state) dictates the kinetics from which the reactants will move to products. Higher the activation energy, less frequently they get over the bump and the slower the reaction is) Activation energy of back reaction = ΔG ° + ΔG °‡ At equilibrium, free energy change (ΔG °) sets ratio [Products]/[Reactants].
Transition state
The highest energy level required for a reaction to take place, it is the least stable state so if it is reached, the reaction will go to completion
High energy state containing partially formed and partially broken bonds
Cycle of enzyme catalysed reactions
1- Substrates enter active site; enzyme changes shape so its active site embraces the substrate (induced fit)
2- Substrates held in active site by weak interactions such as hydrogen bonds and ionic bonds
3- Active site (and R groups of its amino acids) can lower activation energy and speed up a reaction by acting as a template for substrate orientation, stressing the substrates and stabilising the transition state, providing a favourable microenvironment, participating directly in the catalytic reaction by providing ionisable amino acid side chains that facilitate the chemical reaction
4- Substrates are converted into products
5- Products are released
6- Active site is available for new substrate
Enzymes and catalysis
Enzymes catalyse thermodynamically favourable reactions by lowering the activation energy.
Rate enhancement differs from ΔG
Aldolase – very positive ΔG°, but big rate enhancement
Adenylate kinase – ΔG° near zero, big rate enhancement
Cleavage of DNA phosphodiester backbone: negative ΔG° – nonetheless stable for thousands of years uncatalyzed – catalyzed by ribonuclease A in less than a millisecond
Classes of enzymes
Oxidoreductases - redox I.e. transfer of electrons
Transferases - Transfer of a functional group
Hydrolases - Hydrolysis reactions (using H2O)
Lyases - Non-hydrolytic breaking or making of bonds that doesn’t use H2O)
Isomerases - Transfer of atoms/groups within a molecule to yield an isomeric form
Ligases - Join two molecules together (i.e. form a new bond; usually coupled to ATP cleavage)
ATP hydrolyses examples that are very different
Muscle myosin uses energy from hydrolysis of ATP (general energy store) to drive muscle contraction
ATP synthase couples electrochemical gradient across the membrane to synthesise ATP.
Enzyme-substrate binding
Occurs at a specific site on the enzyme: the active site.
The active site:
o has amino acid side chains projecting into it.
o binds the substrate via several weak interactions. o determines the specificity of the reaction.
Substrate binds via
Weak interactions, types of enzyme-substrate bonds include : Ionic bonds Hydrogen bonds Van der Waals interactions Covalent bonds (rare, much stronger)
Weak interactions allow for specificity and reversibility
Active site
The active site: o has amino acid side chains projecting into it. o binds the substrate via several weak interactions. o determines the specificity of the reaction.
Highly specific for one reaction, particularly to the shape of transition state
Are specific i.e. there is molecular complementarity between enzyme and substrate
Types of enzyme-substrate bonds
Ionic bonds (a.k.a. salt bridges): o Make use of charged side chains (Asp, Glu, Arg, Lys).
Hydrogen bonds:
o Side chain or backbone O and N atoms can often act as hydrogen bond donors and acceptors.
Van der Waals interactions:
o Between any protein and substrate atoms in close proximity; weakest of the interactions, but abundant.
Covalent bonds:
o Relatively rare; much stronger than the other bonds.
