Enzymes are catalyst and

speed up reactions and are constantly moving

Active site conformation changes can:

1. Assist substrate binding

2. Bring catalytic groups into position

3. Assist in bond making and bond breaking

4. Facilitate conversion of substrate to product

Enzymes differ from ordinary chemical catalysts in

reaction rate, reaction conditions, reaction specificity, and regulation

The unique physical and chemical properties of the_____limit an enzymes activity to specific substrates and reactions

active sites

Some enzymes require

metal ions or organic cofactors

Enzymes catalyze________reactions, causing them to proceed at extraordinarily rapid rates

thermodynamically favored

what word is used to describe rates

kinetic

The catalyzed and uncatalyzed rate:

catalyzed: 3.0x10⁴sec^-1

uncatayzed: 3.0x10^-10sec^-1

How to calculate the ratio for catalytic power?

3.0x10⁴/3.0x10^-10=1.0x10¹⁴

Any chemical reaction in which the oxidation numbers of the atoms are changed

oxidation-reduction(redox) reaction

What is the classification of an oxidation-reduction reaction?

oxidoreductases

What is the classification of a transfer of functional groups?

transferases

What is the classification of a hydrolysis reactions?

hydrolases

What is the classification of a group elimination to form double bonds?

lyases

What is the classification of isomerization?

isomerases

What is the classification of a bond formation coupled with ATP hydrolysis?

Ligases

The_______from one molecule (the donor) to another (the acceptor)

transfer of functional groups

A chemical compound by a reaction with water. Breaks down a variety of polymers, including proteins, carbs, fats, and nucleic acids

Hydrolysis

Catalyze the breaking of various chemical bonds by means other than hydrolysis and oxidation, often forming new double bonds

Lyases

Structural rearrangement of isomers (same molecular weight, but diff. structural formulas)

Isomerization

Reaction joining of two large molecules by forming a new chemical bond

Ligases

the selectivity of enzymes for their substrates

Enzyme specificity

Exquisite stereospecificity is observed

for some enzymes

what are cofactors?

are non-protein groups that are needed in active sites to carry out functions that amino acid side chains cannot

Functional groups of proteins facilitate

-acid-base reactions

- transient(short-lived)covalent bonds

-Charge-charge interactions

Cofactors have

metal ions and coenzymes

Coenzymes have

Cosubstrates and prosthetic groups

Transiently associates with enzymes so that it functions as a substrate

cosubstrates

permanently(often covalently) attached to enzymes

Prosthetic groups

________are catalytically active enzymes with its cofactor complex

Holoenzymes

______enzyme without the cofactor

Apoenzyme

_______must be regenerated for completion of a "catalytic cycle"

Coenzymes

What are the five principles of regulated enzyme activity?

1. Allosteric control

2. Multiple forms of enzymes

3. Reversible covalent modification

4. Proteolytic activation

5. Controlling the amount of enzyme present

Are inactive precursors of enzymes

zymogens

Proteolytic cleavage produces the active enzyme

chymotrypsinogen---->chymotrypsin

are non-protein components essential to enzyme activity

Enzyme cofactors and coenzymes

An enzyme provides a lower-energy pathway from substrate to product but

does not affect the overall free energy change for the reaction

The active sites of enzymes bind the transition state of the reaction more tightly than they____

bind to the substrate

The transition state sits at the _____ of the energy profile in the energy diagram

apex

the reaction rate is proportional to the

concentration of reactant molecules that reached the transition-state energy

The higher the delta G^+-,

the slower the reaction

Decreasing delta G^+-,

increase the reaction rate (speeds up the reaction)

The catalytic role of an enzyme is to reduce the energy barrier between

substrate s and transition state X^+-

Rate acceleration by an enzyme means that the energy barrier between

ES and EX^+- must be smaller than the barrier between S & X^+-

The enzyme must stabilize the EX^+- transition state

more than it stabilizes ES

Binding cannot be too tight because the goal is to make

the energy barrier between ES EX^+- small

RAising the starting energy of ES to a more positive delta G,

will increase the catalyzed rate

The ES complex is a more highly ordered

for low-entropy state for the substrate

Amino-acid side chains that can donate or accept protons can participate in chemical reactions as acid and base catalysts

Acid/base catalysis

Groups can catalyze reactions through the transient formation of covalent bonds with the substrate

Nucleophilic attack

The unique electronic properties of a metal ion facilitate the reaction

Metal ion catalysis

Enzymes accelerate reaction by bringing reacting group together and orienting them for reaction

Proximity and Orientation

Significantly lowers the activation energy for a reaction

Transition state stabilization

A binding pocket determines the

substrate specificity of the various serine proteases

the catalytically active__________ residues of serine proteases were identified by chemical labeling and structural analysis

Ser, His, and Asp

what is step 1 of the mechanism of serine protease?

General base catalysis, nucleophilic attack to form tetrahedral intermediate

what is step 2 of the mechanism of serine protease?

General Acid Catalysis aids breakdown of
Tetrahedral Oxyanion Intermediate, leaving the
Acyl Enzyme Intermediate on Ser 195

what is step 3 of the mechanism of serine protease?

Amine product is released and replaced by water

what is step 4 of the mechanism of serine protease?

General Base Catalysis, Nucleophilic
Attack to form Tetrahedral, Oxyanion Intermediate

what is step 5 of the mechanism of serine protease?

General acid catalysis aids breakdown of tetrahedral intermediate to the carboxyl product and the active enzyme

Raising the energy of ES is accomplished by

A) loss of entropy

B) destabilization of ES complex by

-desolvation

-strain/distortion

Entropy loss is caused by the

formation of the ES complex. This complex is highly ordered, low-entropy state for a substrate

Desolvation is the result of

water loss which raises the energy of the ES complex

Destabilization is

provoking repulsion based on charges

Proximity and Orientation

Asp ¹⁰² functions only to orient His⁵⁷

Acid/base catalysis

His⁵⁷ acts as general acid and base

Nucleophilic attack

Ser¹⁹⁵ formas a transient covalent bond with peptide to be cleaved

trigonal to tetrahedral

transition state-stabilization

tetrahedral oxyanion intermediate is stabilized by the backbone N-H of Gly¹⁹³ and Ser¹⁹⁵ the Oxyanion Hole

Segments of RNA that display enzyme activity

riboenzymes