Chapter 6

Question 1

True or false: Enzymes are powerful biological catalysts, responsible for the harmonious interplay of ALL cellular processes

Answer 1

True!

Question 2

Why do enzymes have a high degree of specificity?

Answer 2

Their specialized pockets called active sites (aka binding sites)

The shape, size, and chemical properties of the active site are complementary to the substrate, meaning that only specific molecules (substrates) can fit into this site.

Question 3

Describe the two concepts that explain the catalytic power of enzymes

Answer 3

1. They bind most tightly to the transition state of the catalyzed reaction and use binding energy to lower the activation barrier.
2. Evolution has organized or finely-tuned the design of active sites, such that multiple mechanisms of chemical catalysis can occur simultaneously.

Question 4

Explain how an enzyme uses binding energy to lower the activation barrier

Answer 4

Ultimately derived from the free energy released in forming many weak bonds between an enzyme and its substrate.

This binding energy contributes to specificity as well as to catalysis.

Weak interactions are optimized in the reaction transition state; enzyme active sites are complementary not to the substrates per se but to the transition states through which substrates pass as they are converted to products

Question 5

Describe Enzyme regulation: (reversible) covalent modifications

Answer 5

Phosphorylation and protein kinases/phosphatases.

Phosphorylation is the addition of a phosphate group (PO₄²⁻) to an enzyme, typically at serine, threonine, or tyrosine residues. It is catalyzed by kinases (enzymes that add phosphate groups).

Dephosphorylation is the removal of a phosphate group, typically catalyzed by phosphatases

Question 6

Describe Enzyme regulation: allosteric modulators

Answer 6

Enzyme regulation by allosteric modulators involves the binding of molecules (called allosteric effectors or modulators) to a site on the enzyme that is distinct from the active site, known as the allosteric site.

The binding of these molecules induces conformational changes in the enzyme that can either enhance (activate) or inhibit (deactivate) its activity

Question 7

Describe Enzyme regulation: proteolytic (de)activation

Answer 7

An enzyme is initially synthesized as an inactive precursor, known as a zymogen or proenzyme, and is activated by the irreversible removal of a portion of its polypeptide chain.

This process involves proteolysis, which refers to the cleavage of peptide bonds, typically at specific sites in the enzyme precursor.

This regulation allows the enzyme to be activated only when needed and in the appropriate cellular location, ensuring that its activity is tightly controlled

The activation of a zymogen is typically irreversible, meaning that once the cleavage has occurred, the enzyme remains active

Question 8

Describe Enzyme regulation: noncovalent interactions with other (regulatory) proteins

Answer 8

These interactions typically involve hydrogen bonds, ionic interactions, van der Waals forces, and hydrophobic interactions.

Regulatory proteins can act as activators or inhibitors of the target enzyme. They often bind to a site on the enzyme distinct from the active site, resulting in a conformational change in the enzyme that alters its activity.

could be allosteric, feedback regulation, etc.

Question 9

Describe Enzyme regulation: pH

Answer 9

Enzymes have an optimal pH at which they function most efficiently, and deviations from this optimal pH can lead to a decrease in enzymatic activity or complete inactivation

The optimal pH is determined by the enzyme’s structure and the environment in which it needs to perform its function

Acidic environments (low pH) can protonate amino acid residues, while basic environments (high pH) can deprotonate them.

These changes can disrupt the enzyme’s active site, reducing its ability to bind substrates or catalyze reactions effectively.

Question 10

What is a cofactor?

Answer 10

Cofactors assist in the formation of the enzyme-substrate complex participate directly in the chemical reaction.

Inorganic metal ions such as Zn²⁺, Fe²⁺, Mg²⁺, or Cu²⁺

Assist in stabilizing the enzyme’s structure or participate in the catalytic process by acting as electron carriers, cofactors in redox reactions, or coordinating with substrates

Question 11

What is a coenzyme?

Answer 11

Organic molecules that bind to the enzyme, often in a non-covalent manner, and are required for enzyme activity.

Cofactors often act as carriers of chemical groups or electrons

Question 12

Define prosthetic group

Answer 12

A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein is called a prosthetic group.

Question 13

Draw a free energy diagram of a catalyzed and uncatalyzed reaction. Be sure to include ground and transition state; activation energy; reaction intermediates; rate-limiting step; binding energy

Answer 13

Check Textbook for correct answer

Question 14

define DeltaG10

Answer 14

A biochemical standard free-energy change.

AKA the overall standard free-energy change in the direction S–>P

Question 15

What is DeltaG(with little tree)

Answer 15

Activation energy

Question 16

Define transition state

Answer 16

At the top of the energy hill is a point at which decay to the S or P state is equally probable (it is downhill either way).

The transition state is not a chemical species with any significant stability and should not be confused with a reaction intermediate (such as ES or EP). It is simply a fleeting molecular moment in which events such as bond breakage, bond formation, and charge development have proceeded to the precise point at which decay to either substrate or product is equally likely

Question 17

What does a higher activation energy correspond to?

Answer 17

a slower reaction

Question 18

Define reaction intermediates

Answer 18

A reaction intermediate is
any species on the reaction pathway that has a finite chemical lifetime.

the ES and EP complexes occupy valleys in the catalyzed reaction coordinate diagram

Question 19

Define rate limiting step

Answer 19

the overall rate is determined
by the step (or steps) with the highest activation energy; this is called the rate-limiting step. In a simple case,
the rate-limiting step is the highest-energy point in the diagram for interconversion of S and P

Question 20

What is binding energy?

Answer 20

The energy derived from enzyme-substrate interaction is called binding energy, deltaGB. Its significance extends beyond a simple stabilization of the enzyme-substrate interaction. Binding energy is a major source of free energy used by enzymes to lower the activation energies of reactions

Question 21

Define Keq

Answer 21

The equilibrium constant.

Keq= [P]/[S]

Question 22

The the relationship between Keq
and deltaG10 can be described by the expression:

Answer 22

deltaG10= -RT ln Keq

Question 23

Describe how rate constant and rate equation are related for a first order reaction

Answer 23

The rate of any reaction is determined by the concentration of the reactant (or reactants) and by a rate constant, usually denoted by k.

For the unimolecular reaction S–>P, the rate (or velocity) of the reaction,
V—representing the amount of S that reacts per unit time—is expressed by a rate equation:
V = k[S]

In this reaction, the rate depends only on the concentration of S

Question 24

What is a first order reaction?

Answer 24

The rate depends only on the concentration of S

Question 25

What is a second order reaction?

Answer 25

If a reaction rate depends on the concentration of two different compounds, or if the reaction is between two molecules of the same compound, the reaction is second order and k is a second-order rate constant, with units of M-1s-1 .

Question 26

Give the rate equation of a second order reaction

Answer 26

V= k[S1][S2]

Question 27

What is the expression that relates the magnitude of a rate constant to the activation energy:

Answer 27

k =(KT/h)e^(-deltaG‡/RT)

Question 28

Give Boltzmann constant and Planck's constant

Answer 28

Boltzmann constant= K=1.38E−23 J/K Planck's constant= 6.626E −34 JS

Question 29

How does a catalyst circumvent unfavorable charge development during cleavage of an amide

Answer 29

May use acid-base catalysis to protonate or deprotonate functional groups in the transition state, reducing the overall energy of the transition state and lowering the activation energy of the reaction Protonation of the carbonyl oxygen (on the amide bond) stabilizes the developing negative charge on the oxygen, making it easier for the bond to break. Deprotonation of the nitrogen atom (from the amide bond) stabilizes the developing positive charge on the nitrogen, helping facilitate the bond cleavage. Histidine residues in enzymes (like serine proteases) are often involved in this type of acid-base catalysis because of their ability to accept or donate protons in response to changes in pH. also: - neucleophilic attack - electrostatic stabilization

Question 30

Describe how Amino acids work as acid-bases

Answer 30

The carboxyl group of an amino acid (-COOH) can act as an acid by donating a proton (H⁺) The amino group (-NH₂) of an amino acid can act as a base by accepting a proton (H⁺)

Question 31

Define Enzyme kinetics: pre-steady state

Answer 31

Refers to the initial phase of an enzyme-catalyzed reaction, immediately after the enzyme and substrate come together, but before the reaction has reached equilibrium or a steady rate of product formation. This phase is transient, with the formation of products and the consumption of substrates being fast and fluctuating.

Question 32

Define Enzyme kinetics: steady state

Answer 32

The concentrations of the enzyme-substrate complex (ES) remain constant over time. This occurs after the initial pre-steady state phase, once the system has stabilized, and is characterized by a balanced rate of enzyme-substrate complex formation and breakdown.

Question 33

Define Enzyme kinetics: initial rate/velocity

Answer 33

The rate at which product is formed (or substrate is consumed) in an enzyme-catalyzed reaction, measured during the early moments of the reaction, before significant changes in substrate concentration or product accumulation occur.

Question 34

Define Enzyme kinetics: maximum velocity (Vmax)

Answer 34

When the enzyme is fully saturated with substrate and operating at its maximum capacity. In this condition, all enzyme active sites are occupied by substrate molecules, and the enzyme cannot process substrate any faster

Question 35

Enzyme kinetics: Michaelis Menten equation

Answer 35

describes the rate of an enzyme-catalyzed reaction as a function of substrate concentration. It provides a mathematical model for how the reaction velocity (𝑉0) changes with varying substrate concentrations ([S]) V0= (Vmax[S]) / Km+[S]

Question 36

Enzyme kinetics: Km

Answer 36

Km is the substrate concentration at which the reaction rate is half of the maximum velocity (𝑉max). A lower 𝐾𝑚 indicates a higher affinity of the enzyme for the substrate, meaning the enzyme reaches half-maximal velocity at a lower substrate concentration.

Question 37

Enzyme kinetics: Lineweaver-Burk equation

Answer 37

This is a double reciprocal plot where 1/𝑉0 is plotted against 1/[𝑆]. The result is a straight line, which makes it easier to determine 𝑉max and Km from experimental data

Question 38

Enzyme kinetics: kcat aka turnover number

Answer 38

It represents the maximum number of substrate molecules that a single enzyme molecule can convert to product per unit of time, when the enzyme is fully saturated with substrate. Kcat= Vmax/[E total]

Question 39

Inhibition in enzyme kinetics: give the types of reversible inhibition

Answer 39

Competitive Uncompetitive Noncompetitive (mixed)

Question 40

Inhibition in enzyme kinetics: competitive

Answer 40

- Inhibitor binds in the enzyme active site – competes with normal substrate binding (forms EI complex) - Prevents substrate from binding and reacting - Usually looks like substrate (or transition state of reaction!)

Question 41

Describe competitive inhibitions effect on kinetics

Answer 41

Vmax remains constant Km increases - Dependent on alpha Apparent Km: aKm

Question 42

Inhibition in enzyme kinetics: uncompetitive

Answer 42

Inhibitor binds to enzyme-substrate complex at site distinct from active site Distorts the active site making it inactive via conformational change

Question 43

Describe uncompetitive inhibition effect on kinetics

Answer 43

Vmax & Km decrease Both dependent on a’ Apparent Km: Km/a’ Apparent Vmax: Vmax/a’

Question 44

Inhibition in enzyme kinetics: mixed

Answer 44

Inhibitor binds to either E or ES Rarely seen …

Question 45

Describe Mixed/Noncompetitive Inhibition effect on kinetics

Answer 45

Vmax decreases Km may increase or decrease Apparent Km: aKm/a’ Apparent Vmax: Vmax/a’

Question 46

Inhibition in enzyme kinetics: irreversible

Answer 46

Irreversible inhibition occurs when an inhibitor binds covalently to the enzyme, leading to permanent loss of enzyme activity.

Question 47

Inhibition in enzyme kinetics: mechanism-based inactivators

Answer 47

A subclass of irreversible enzyme inhibitors (AKA Suicide inhibitors) that selectively and covalently bind to the enzyme, leading to its inactivation. They are designed to mimic the enzyme’s normal substrate, but upon binding to the enzyme, they undergo a chemical transformation that results in the covalent modification of the enzyme, thereby irreversibly inactivating it.

Question 48

Inhibition in enzyme kinetics: transition-state analogs

Answer 48

A class of enzyme inhibitors that mimic the transition state of the enzyme-catalyzed reaction. These analogs are designed to resemble the high-energy, unstable intermediate state that the substrate transitions through during the reaction. Transition-state analogs can be potent inhibitors because they are often bound much more tightly by the enzyme than the substrate itself, effectively blocking enzyme activity

Question 49

What is chymotrypsin's function/relevant info?

Answer 49

A type of digestive enzyme, a serine protease. uses an active serine residue to perform hydrolysis on the C-terminus of aromatic amino acids of other proteins. Shows specificity for aromatic residues due to its hydrophobic pocket. Synthesis occurs in the pancreas, but is inactive and not activated until secretion into the ER lumin, where it is activated by trypsin.

Question 50

Draw the chymotrypsin mechanism

Answer 50

Check on sheet

Question 51

Name the seven types of enzymes and what they do

Answer 51

Classified according to reaction type:  1. Lyases: Addition of groups to double bonds or formation of double bonds by removal of groups 2. Isomerases: Transfer of groups within molecules to produce isomeric forms 3. Ligases: Formation of bonds by condensation reactions coupled to ATP cleavage 4. Hydrolases: Hydrolysis reactions: Transfer of functional groups to H2O 5. Oxidoreductases: Transfer of electrons 6. Transferases: Group transfer reactions 7. Translocases: Facilitate the movement of molecules, such as proteins or other substances, across cellular membranes

Question 52

Give the scheme for a simple enzyme catalyzed rxn which converts a single substrate into a single product.

Answer 52

E+S <--> ES <--> EP <--> E+P

Question 53

Do enzymes affect the rxn equilibria?

Answer 53

No. They just lower the activation energy, thereby speeding up the reaction - Accelerate interconversion of S and P. The free energy used to lower activation energy comes from binding energy

Question 54

Define the Ping-Pong enzyme mechanism, and draw the scheme.

Answer 54

CHECK SCHEME ON CHYMOTRYPSIN PAPER The Ping-Pong mechanism typically involves two substrates and two products, and the enzyme interacts with both substrates in sequence. The enzyme undergoes a covalent modification after it binds the first substrate, and this modification is crucial for the catalysis of the second substrate. the first product is released before the second substrate can bind to the enzyme. There will be a covalent intermediate formed.