Lecture 10: Enzymes as Catalysts Flashcards
What are the six types of enzymes?
- Oxidoreductases
- Transferases
- Hydrolases
- Lyases
- Isomerases
- Ligases
Oxidoreductase
Enzyme that catalyzes oxidation-reduction reactions.
Transferase
Enzyme that catalyzes transfer of a chemical group.
Hydrolase
Enzyme that catalyzes lysis by water.
Lyase
Enzyme that catalyzes a cleavage reaction without the use of water.
Isomerase
Enzyme that catalyzes changes in molecular configurations.
Ligase
Enzyme that joins two compounds.
How efficient are enzymes compared to the uncatalyzed reaction?
10^3 to 10^14 times faster.
Substrate
The molecule whose transition state is stabilized by the enzyme. It is bound to the enzyme by multiple weak, but specific interactions.
Active Site
Usually a crevice that is a small part of the enzyme where the enzyme exerts its action.
Serine Proteases
Proteolytic enzyme family that includes the enzymes trypsin, chymotrypsin, and elastase.
What kind of mechanism does chymotrypsin use?
Hydrolysis.
What kind of molecule does chymotrypsin act upon?
Peptides.
What side of does chymotrypsin act on?
The C terminal side.
Chymotrypsin acts upon which three residues?
- Phenylalanine
- Tyrosine
- Tryptophan
What weak interactions hold a substrate on the enzyme?
- van der Waals
- Hydrogen bonds
- Electrostatics
What is the role of the specificity pocket on the enzyme chymotrypsin?
To recognize the bulky hydrophobic side-chain of a suitable peptide and position the substrate in the correct orientation for catalysis.
How specific is enzyme binding?
It can distinguish chiral centers in a substrate.
What is the nature of chymotrypsin’s specificity pocket?
Hydrophobic.
What is the nature of trypsin’s specificity pocket?
Negative, therefore binding positively charged peptides, such as arginine and lysine.
Describe elastase’s specificity pocket.
It is narrow, therefore binding only amino acids with small side chains, such as glycine.
What are the four essential features of an enzyme binding on substrate?
- The active site is usually located in a crevice that is a small part of the enzyme.
- The substrate is bound by multiple weak interactions.
- The binding is specific.
- The substrate is positioned to place bond in the correct orientation for manipulation by the atoms of the catalytic machinery of the enzyme.
True or false?
The atoms catalyzing the reaction in an enzyme are always the same as the ones that bind the substrate.
False.
The atoms catalyzing the reaction in an enzyme can sometimes be different than the ones that bind the substrate.
Hydrolytic enzymes catalyze reactions at what pH?
Neutral pH.
Acidcatalysis
A group with H+.***
Basecatalysis
A group with OH-.***
Catalytic Triad
The heart of the catalytic machinery of a serine protease. Also called a “charge relay.”
Comprising the side-chain functional groups of aspartic acid, histidine, and serine at the enzyme’s active site.
Transition State
The high-energy intermediate between substrate and product.
The four steps of enzyme-mediated catalysis for a serine protease are:
- Binding of substrate.
- Attack by serine.
- Transition state.
- Release of products.
Oxyanion
A negatively charged atom on a substrate.***
Oxyanion Hole
Residues in the pocket of an enzyme that stabilize the negative charge of an oxyanion.
What is the chief role of an enzyme?
Stabilization of the transition state, which lowers the activation energy.
What is bioenergetics?
The application of thermodynamics to biological processes.
Reactions are…
…reversible.
What is free energy?
Also written as ΔG, it is the energy that is availabile to do work.
Also known as Gibb’s free energy.
What are two factors that can drive a reaction (change ΔG)?
- Heat, or ΔH.
2. Entropy, or ΔS.
What is the equation for Gibb’s Free Energy?
ΔG = ΔH - TΔS
When ΔG is negative, the reaction is…
…spontaneous, or exergonic.
When ΔG is positive, the reaction is…
…nonsponstaneous, or endergonic.
ΔG°
Standard free energy.
ΔG
Gibb’s Free Energy
ΔS
Entropy
ΔH
Heat
Q
[sub 1] x [sub 2]
Keq
The equilibrium constant, AKA Q.
What is to be said about reactions with a very large -ΔG?
They are functionally irreversible due to having such a large product to substrate ratio.
One can calculate ΔG from ____, and vice versa.
Q
ΔG cannot be calculated from ΔG° unless…
…the reactant and substrate concentrations (Q) are known.
The amount of energy to reverse a reaction is equal in ____, but opposite in ____.
Magnitude, sign.
What is one way a reaction can be driven?
Reducing the [product].
What does one need to know in order to theoretically predict if a reaction will proceed to equilibrium?
ΔG, [products], and [reactants].
What does one need to predict the rate of a reaction?
ΔG‡, the free energy of activation.
True or false?
A catalyst changes the free energy of a substrate, it’s products, and equilibrium.
False.
It does not change any of these things.
What does a catalyst do?
Lowers the activation energy.
Catabolism
Fuel (or food) is degraded to smaller molecules with the release of energy, which is captured in the form of ATP.
Anabolism
Reactions/processes that require input of energy, which comes in the form of ATP.
____ is the central currency of the body.
ATP.
What is the quantitative amount of energy released each time ATP breaks one of it’s phosphate bonds?
-7.3 kcal/mol
ATP-using enzymes…
…make the impossible possible.
Enzyme Kinetics
Measuring the amount and efficiency of a given enzyme.
At low ____, _____ is proportional to enzyme velocity.
[s], [s]
At high [s], enzyme is said to be ____.
Saturated.
Any addition of more substrate cannot increase the reaction rate.
What is the point at which addition of more substrate does not increase the enzyme’s velocity?
Vmax.
____ levels of [s] are best for assays of substrate concentration.
Low.
Because the initial enzyme velocity is directly proportional to the amount of substrate.
____ levels of [s] are suitable for assays of enzyme concentration.
High.
Because the velocity is at it’s highest.
Km
Measures enzyme affinity for substrate.
Equal to [substrate] at 1/2 Vmax.
An enzyme with high affinity for its substrate would likely have a ____ Km.
Low.
If an enzyme has a ____ Km, one would expect a low affinity for its substrate.
High.
Km loosely corresponds to…
…. 1/affinity of enzyme for substrate.
What is the purpose of a Lineweaver-Burke plot?
To make easier and more precise measurements of Km and Vmax.
Where can one find the Vmax on a Lineweaver-Burke plot?
The y-intercept.
Where can one find the Km on a Lineweaver-Burke plot?
The x-intercept.
