Chapter 6 (without enzyme kinetics) Flashcards
What about the makeup of enzymes allows them to carry out very specific reactions?
The 3D structure is designed to fit certain substrates, so only those resulting reactions can take place
Without enzymes, the hydrolysis of a peptide bond would take ____ years
20
What are the four properties of enzymes that make them the best biocatalysts?
High reaction rates, great specificity, can react in mild conditions, and they can be regulated well
If there are many paths available to a reaction, enzymes will choose the ____ favorable one
Most
Oxidoreductases catalyze _____ reactions
Oxidation-reduction
Transferases catalyze ____
The transfer of functional groups
Hydrolases catalyze ______ reactions
Hydrolysis
Lyases catalyze ______
The elimination of a group to form a double bone
Isomerases catalyze _____
Isomerization
Ligases catalyze ____
Bond formation coupled with ATP hydrolysis
ATP has to be USED in the reaction, not just present (ATP –> ADP + P)
The three types of bonds utilized in substrate-enzyme binding are:
H-bonding, salt bridges, hydrophobic interactions
The substrate refers to the _____
reactant
What is the generic purpose of a cofactor?
To assist enzymes in their reactions
Compare and contrast cofactors and coenzymes
Cofactors are the overall name of the group and can either be metal ions (Mg2+, Cu2+, Zn2+) or coenzymes
Coenzymes are more complex molecules with different functional groups and can either be bound or unbound to the enzyme
When a cofactor is covalently bound to the enzyme it’s called a ______
Prosthetic group
If a cofactor participates in a reaction it must be ______ for that reaction to proceed
Regenerated
The rate of a reaction is determined by its _____
Activation energy
A reaction whose products are lower in energy than their reactants is ______, while a reaction whose products are higher in energy than their reactants is ____
Exergonic
Endergonic
Where is the transition state located?
The very highest point of the activation energy
ΔGB refers to the ______ energy, which is created by the weak interactions between the enzyme and susbtrate
Binding
General acid base catalysis stabilizes intermediates by ____
The transfer of protons to and from the substrate. This is done by a molecule other than water (usually an AA)
Covalent bond catalysis occurs when ____
A transient covalent bond forms between the substrate and enzyme, which requires the presence of a sidechain
Usually the nucleophilic group is on the enzyme and the electrophilic group is on the substrate
How does entropy reduction help catalyze a reaction?
It decreases the angle from which the substrate can enter the enzyme so it has a higher chance of binding at the proper angle for the reaction to take place. The enzymes also have to be relatively large for this to work
(Less ability to move around lowers the overall entropy)
Tunneling has not been verified, but it suspected to help catalyze reactions when _____
Electrons jump back and forth when the enzyme and substrate are far apart from each other
What role do metal ions play in metal ion catalysis?
The enzyme holds onto the metal ion to maximize the reaction between it and the substrate
Metal ions can optimize substrate orientation through ionic interactions, mediate redox reactions, stabilize negative charges the develop during the reaction, and polarize some groups
Inhibitors often mimic the ______ of the enzyme’s designated substrate and are irreversible because _____
Transition state
They bind so well to the enzyme that they are impossible to remove
Why is the enzyme’s active site in the formation of the transition state and not that of the substrate alone?
If the enzyme was in the formation of the substrate, the two would bind too well with each other to overcome the transition state and the reaction would never be completed (products would never form). So, the enzyme is in the shape of the transition state so that it is easier to overcome the activation energy
What is the role of the catalytic triad (Ser, His, Asp) in chymotrypsin?
Serine is deprotonated by histidine, which creates a very strong alkoxide ion. Histidine’s pKa is also altered by the proximity of aspartate, which helps to orient His and make it a better proton acceptor
