Lecture 9: WHY ARE ENZYMES ESSENTIAL FOR LIFE? Flashcards
What are enzymes?
Biological catalysts which increase the rate of reaction by lowering the activation energy
What are most enzymes?
Proteins
What are exceptions to proteins being enzymes?
Catalytic RNA’s, ribozymes including ribosomes
What don’t enzymes change?
The free energy level (equilibrium) of products and reactants
What is the relative abundance of products and reactants predicted by?
The Gibbs free energy
What happens when Gibbs free energy is less than 0?
There is energy released and the products dominate
What happens when the Gibbs free energy is greater than 0?
Energy is required and the reactants dominate
What happens when the Gibbs free energy is equal to 0?
The reaction is at equilibrium (reactants and products are of equal concentrations)
What does overall Gibbs free energy have components of?
Enthalpy (H) and entropy (S)
What is T?
Absolute temperature
What must happen to favour the forward reaction?
Either enthalpy must decrease or entropy must increase
What does cellular integrity mean?
A decrease in entropy (disorder) in the cell so energy from elsewhere is required
What do enzymes control?
Where and when energy is released to maintain the cell
What do reactions pass through?
High energy transition states
What determines the rate of a reaction?
The activation energy required to reach the transition state
What is the activation of the back reaction?
The Gibbs free energy + the activation energy
What does free energy do at equilibrium?
Sets the ratio of products to reactants
What is the Gibbs free energy for cleavage of DNA phosphodiester backbone?
Negative
How long is the DNA phosphodiester backbone stable for uncatalyzed?
Thousands of years
What is the speed of ribonuclease A?
Less than a millisecond
What does aldolase have?
Very positive Gibbs free energy but a big rate enhancement
What does adenylate kinase have?
Gibbs free energy near zero but a big rate enhancement
What are isozymes?
Enzymes which differ in amino acid sequence but catalyse the same reaction
What are the classes of enzymes?
Oxireductases, transferases. hydrolyses, lyases, isomerases and ligases
What are oxireductases involved in?
Redox (transfer of electrons)
What are transferases involved in?
Transfer of a functional group
What are Hydrolyses involved in?
Hydrolysis reactions (using water)
What are lyases involved in?
Non-hydrolytic breaking or making of bonds (not using water)
What are isomerases involved in?
Transfer of atoms/groups within a molecule to yield an isomeric form
What are ligases involved in?
Joining two molecules together (forming a new bond) which is usually coupled to ATP cleavage
What does muscle myosin do?
Use energy from hydrolysis of ATP (general energy store) to drive muscle contraction
What does ATP synthase do?
Couple electrochemical gradient across the membrane to synthesise ATP
Where does enzyme substrate binding occur?
At a specific site on the enzyme called the active site
What does the active site have?
Amino acid side chains projecting into it
What does the active site do?
Bind the substrate via several weak interactions
What does the active site determine?
The specificity of the reaction
What are the types of enzyme substrate bonds?
Ionic bonds/salt bridges, hydrogen bonds, van der Waals interactions and covalent bonds
What do ionic bonds do?
Make use of charged side chains (Asp, Glu, Arg, Lys)
What happens in hydrogen bonds?
Side chain or backbone O or N atoms can often act as hydrogen bond donors and acceptors (prevalent and give specificity)
What are van der Waals interactions?
Between any protein and substrate atoms in close proximity (weakest interactions but abundant)
What are covalent bonds?
Relatively rare and much stronger than the other bonds
What are the models for enzyme substrate binding?
Lock and key and induced fit
What is the lock and key model?
The shape of the substrate and the conformation of the active site are complementary to one another
What is the induced fit model?
The enzyme undergoes a conformational change upon binding to substrate. The shapes of the active site becomes complementary to the shape of the substrate only after the substrate binds to the enzyme
Are enzymes dynamic or static?
Dynamic
What do many weak interactions ensure?
Specificity and reversibility
How does enzyme substrate binding show specificity?
Several bonds are required for substrate binding
When can weak bonds form?
Only if the relevant atoms are precisely positioned
What can weak bonds allow?
reversible binding
What is critical?
Molecular complementarity between enzyme and substrate
What is optimal binding?
Not too tight
How can activation energy be lowered?
By ground state destabilisation, transition state stabilisation and an alternate reaction pathway with a different (lower energy) transition state
How can ground state destabilisation and transition state stabilisation occur?
By having an active site that has shape/charge complementarity to the transition state, not the substrate
What are coenzymes?
Small organic molecules
What type of substrates are coenzymes?
Cosubstrates
What are cosubstrates carriers of?
Electrons, atoms or functional groups
What are cofactors often derived from?
Vitamins
