5. Enzymes Flashcards
1
Q
What are catalysts (6)?
A
- Speed up the rate of chemical reactions
- Not consumed in the process
- Most are proteins but can be RNA
- Sometimes require organic coenzymes/metal ions
- apoprotein/apoenzyme: protein component of an enzyme that requires a cofactor for activity
- holoenzyme = protein and coenzyme
2
Q
What are the 6 classifications of enzymes?
A
- Oxidoreductases: transfer electrons as H or H-
- Transferases: group transfer
- Hydrolases: bond breakage through the addition of water
- Lyases: formation/addition of double bonds
- Isomerases: group transfer yielding isomers
- Ligases: formation of carbon bonds coupled to ATP cleavage
3
Q
Why are enzymes necessary? (5)
A
- Most biological molecules are stable at ph=7 and temp of 37 in water
- Enzymes are specific, usually no side-reactions
- Regulated
- Easily denatured
- Functions via changes in conformation - constantly in motion
4
Q
How does enzyme specificity work? (2)
A
- Specific reacting molecules called substrates (S) bind to the enzyme (E) active site and are converted into a product (P).
- The active site fits the substrate like a hand in a glove
5
Q
Explain the phosphofructokinase example of enzyme specificity (2)
A
- Phosphofructokinase transfers a phosphate group from ATP to fructose-6 phosphate forming Fructose 1,6 bisphosphate and ADP
- The reaction is controlled by the binding of ADP in the allosteric binding site.
6
Q
Explain the trypsin, chymotrypsin and elastase example of enzyme specificity (1)
A
Trypsin, chymotrypsin and elastase recognize different amino acid classes based on the size and the shape of their binding site
7
Q
Explain the aconitase example of enzyme specificity (2)
A
- Aconitase can distinguish between the two ends of citrate
even though there is no chiral carbon - Aconitase is able to do this because the enzyme is a 3-dimensional molecule with 3 different sites of interaction
8
Q
Give the example of less specific enzymes (2)
A
- Hexokinase phosphorylates glucose, fructose and mannose
- Enzymes provide a binding site that is complimentary to the steric and electronic features of the substrate: ‘hand in glove’
9
Q
How do enzymes work to speed up reactions? (2)
A
- Enzymes provide a special environment in which bond
formation/breakage is easier - Enzyme catalysts work by lowering the activation energy
- E binds the transition state of substrate tightly and formation of bonds release binding energy which reduced G
10
Q
Explain the reaction co-ordinate diagram (4)
A
- A way to keep track of G changes
- Shows the changes in free energy when using enzymes to go from substrate to product
- G must be added to stretch and break bonds
- Transition state: highest point on the curve equal probability of bonds forming and breaking
- Change in gibbs: The difference in free energy between the reactants and the transition state. It’s the energy barrier that must be overcome for the reaction to proceed.
11
Q
How is Keq affected by a catalyst? (3)
A
- It is NOT affected.
- If the enzyme increases the forward rate, the backward rate will also be increased
- Since Keq depends on the difference in G between P and S, it’s path independent
12
Q
Explain this graph
A
- Black = without enzyme
- Red = with enzyme
- Small increase: Represents the initial phase of the reaction where enzyme and substrate are coming together by flexing. Factors like diffusion and the time it takes for the enzyme-substrate complex to form can contribute to a slower initial rate.
- Bigger increase: Represents the period where the enzyme is actively catalyzing the reaction. Once a sufficient number of enzyme-substrate complexes are formed, the rate of product formation will increase more dramatically.
13
Q
A
- Specificity: Just as a magnet only attracts specific materials like iron, enzymes are highly specific and only interact with certain molecules called substrates. This specificity arises from the shape and chemical properties of the enzyme’s active site, a specialized region on the enzyme that binds to the substrate. The active site is complementary in shape and charge to the substrate, ensuring a precise fit, much like a lock and key mechanism.
- Attraction and Binding: Similar to the magnetic force drawing the iron rod towards the magnet, the enzyme’s active site attracts and binds to the substrate. This interaction involves various weak forces like hydrogen bonds, electrostatic interactions, and van der Waals forces, creating a temporary enzyme-substrate complex.
14
Q
What is binding energy also used for
A
- Entropy reduction - enzymes hold the substrates close together in the proper orientation for reaction
- Desolvation - substrate molecules are surrounded by water hydration shell that usually must be removed for reactions to occur
- Strain reduction
- Induced fit - change conformation of the enzyme to obtain the proper orientation of the active site AA
15
Q
Explain the chymotrypsin example of enzymes in amino acid side chain chemical transformations
A
- Acids donate H+ and accept electron pairs while bases donate H+ and donate electron pairs
- The side chain of His, Asp, Ser in chymotrypsin active site form a catalytic triad.
- The first step, S binds to E
- Electron flow from general base catalytic triad into S and creates the 1st transition state
- The oxyanion is stabilized by H-bonding to groups in the protein. Covalent bond formed between E and S
- Electrons flow from the S to the general acid catalytic triad
- The c-terminal peptide and n-terminus is released by hydrolysis
