Chapter 7 - Enzyme mechanisms

Biochemistry chapter 7

Ribozymes are enzymes composed of

RNA

Most enzymes are

Proteins

Lock and key model

A biological concept explaining that a specific substrate fits into a specific enzyme's active site, similar to a key fitting into a lock.

induced-fit model

<span>A theory that suggests enzymes undergo a conformational change to better fit the substrate upon binding, enhancing the enzyme's activity and specificity.</span>

conformational selection

A model of enzyme interactions where the enzyme exists in multiple conformations and the substrate selectively binds to one preferred conformation.

Enzymes usually bind substrates with high specificity

due to their unique active site shapes and the presence of specific amino acid residues that interact with the substrate.

Substrate binding to the active site is often associated with structural changes in the enzyme

Induced fit modelsuggests that the enzyme changes shape to better bind the substrate.

Enzyme activity is highly regulated in cells

this is because it is necessary to maximizes energy balance between catabolic and anabolic pathways

The two primary modes of enzyme regulation are _______ and ________

Bioavailibility, activity

Bioavailbility

the amount of enzyme present in the cell as a result of regulated gene expression and protein turnover.

Enzymes alter the rate of reactions without

changing the ratio of substrates and products at equilibrium. They simply decrease the time it takes to reach equilibrium.

Catalase

an enzyme that decomposes hydrogen peroxide (H2O2)

Transition state theory

Transition state theory explains the process of bond formation and breaking during a chemical reaction. It focuses on the high-energy, unstable states (transition states) that exist momentarily as reactants transform into products. This theory helps in understanding the activation energy needed to initiate a reaction and the pathway taken by molecules as they progress from reactants to products.

What is this called? What does it do?

Reaction coordinate diagram. It measures the change in free energy between the ground states of products and reactants.

Activation energy

The energy required to reach the transition state (Delta G)

How does catalase work?

It provides a highly reactive Fe3+ porphyrin ring with a protected environment, which promotes product formation as a function of the reduced transition state energy barrier.

Cofactors

• Small molecules that aid in the catalytic reaction within the active site.

• Include inorganic ions such as Fe2+, Cu2+ and Mg2+

Holoenzyme

An enzyme with a bound cofactor

Apoenzyme

Enzyme without cofactor

Coenzymes

• Enzyme cofactors that require organic components (Non protein)

Prosthetic groups

coenzymes that are permanentyl associated with enzymes

Common cofactors used in catalysis are

typically trace elemnts found in the body

What is a heme

A prosthetic group found in enzymes and proteins that has a central Iron inside a porphyrin ring that is critical in forming reactions.

NAD+/NADH

Typically found in a redox reaction where NAD+ is the oxidized form and NADH is the reduced form.

NAD+/NADH Redox reaction

The NAD+/NADH redox reaction is a metabolic process where NAD+ acts as an electron carrier, converting to NADH by accepting electrons during cellular respiration. This conversion is crucial for ATP production, as NADH donates electrons to the electron transport chain.

Lipoamide

a redox-active cofactor derived from lipoic acid, playing a crucial role in enzyme-catalyzed reactions. It facilitates the transfer of acyl groups and electrons, thus participating in various metabolic pathways, including the pyruvate dehydrogenase complex and the alpha-ketoglutarate dehydrogenase complex. Lipoamide acts as a bridge in the transfer of acetyl and other acyl groups, contributing to ATP production and cellular respiration.

Most enzymes end in

“-ase”

Oxidoreductase

Participates in oxidation-reduction reactions and trasnfers either H or O atoms.

Transferase

Type of reaction: transfers functional groups

Hydrolase

Formation of two products by hydrolyzing (breaking chemical bonds using water) a substrate

Lyase

Cleavage of C-C, C-O, C-N and other bonds by means other than hydrolysis or oxidationI

Isomerase

Intramolecular rearrangements, transfer of groups within molecules

Ligase

Formation of C-C, C-O, C-S, C-N bonds using ATP cleavage

Enzymes increase the rate of reaction inside cells in three major ways

1. They stabilize the transition state, thus lowering the activation barrier

2. They provide an alternative path for product formation

3. They orient the substrates appropriately for the reaction to occur hence reducing entropy

What is happenning here?

The enzyme active site produces an optimal environment that promotes product formation by deterring random collisions and coordinating the reactants to from a stable product and aligns the reactive groups correctly.

What are the three specific physical and chemical properties of enzyme active sites that contribute to their catalytic properties?

• The sequestered microenviornment of the active site

  • Excludes excess solvent

  • Provides optimal orientation of the substrate relative to the reactive chemical group

• binding interactions between the substrate and the enzyme that facilitate formation of the transition state

• The presence of catalytic functional groups

What is happenning here?

Substrate binding to the enzyme (E+S) leads to the formation of an enzyme-substrate complex (ES) followed by the conversion of the enzyme-bound substrate to an enzyme bound product (EP). Finally, the product is released from the enzyme (E+P).

Transition state analogs

A molecule that mimics the transition state of a chemical reaction but is actually stable causing no reaction to occur.

What are the three most common catalytic reaction mechanisms in the active enzyme site?

• Acid base catalysis

• Covalent catalysis

  • Metal-ion catalysis

Acid-base catalysis

The removal or addition of a proton. Can happen in specific acid-base catalysis or general acid-base catalysis.

Specific acid-base catalysis

Involves water to transfer protons

General acid base catalysis

Involves a functional group to transfer protons. (i.e water and zinc)

Covalent catalysis

Creates an unstable intermediate that promotes the catalytic reaction by forming a transient covalent bond between the substrate and the enzyme. This is done because the nucleophile group on the enzyme attacks the electrophilic group on the center of the substrate.

Metal ion catalysis

• Metals are used to promote proper orientation of bound substrates and can aid in redox reactions

The three general categories of enzyme mediated reactions are:

• Coenzyme-dependent redox reactions

• Metabolite transformation reactions

• Reversible covalent modification reactions

Coenzyme-dependent redox reactions

Redox reactions that involve coenzymes, allowing for the transfer of electrons and protons in biochemical reactions.

• Include dehydrogenases

• Involve NAD+/NADH, NADP+/NADPH, FAD/FADH2 and FMN/FMNH2

Metabolite Transformation reactions

The chemical transformation of metabolites to generate reactive intermediates

Three types of reactions are the most common in metabolic pathways:

• Isomerization

• Condensation

  • Hydrolysis/Dehydration

Isomerization

Reactions that do not change the molecular formula of the product compared to that of the substrate

Condensation

Combines two substrates to form a larger molecule with the loss of a smaller molecule

Hydrolysis or dehydration

involve the addition or removal of water. For many hydrolysis reactions, the substrate is cleaved when water is added.

Reversible covalent modifications

These are chemical modifications on proteins or other biomolecules that can be easily added or removed. Common modifications include phosphorylation, acetylation, methylation, and ubiquitination. These modifications play crucial roles in regulating protein function, including enzyme activity, protein stability, localization, and interactions with other molecules, allowing for dynamic control of biological processes

Chymotrypsin: A serine protease

• Aids in digestion to cleave the peptide backbone of dietary proteins

• Uses His, Asp, Ser to form a hydrogen bonded network required for catalysis

  • Ser is converted to a highly reactive nucleophile

Describe the two phases of the mechanism of chymotrypsin

1. In the first phase, and acyl-enzyme intermediate is formed which promotes cleavage of scissile peptide bond. The carboxyl terminal is then released.

   1. In the second phase, the enzyme is regenerated after a series of steps that results in de-acylation and release of the amino-terminal polypeptide fragment.

Chymotrypsin reaction mechanism

Enolase

An enzyme that contains two divalent metal ions which are required for a reaction used in gluconeogenesis.

Enzyme regulation is mediated by two primary mechanisms

• Bioavailability with regard to the amount of enzym in different tissues and cellular compartments

• control of catalytic efficiency through protein modification

Stimulatory enzyme activity

Enzyme activity that enhances or accelerates metabolic processes.

Inhibitory regulation of enzyme activity

Control mechanism that decreases enzyme activity and slows metabolic processes.

Allosteric regulation of catalytic activity

R state

Enzyme is active and is ready to be binded to ATP hence starting a reaction

T state

inactive enzyme- binding of CTP (feedback inhibition) stopping a reaction

Competitive inhibitor

When the inhibitory competes with a subtrate for the same space in the enzyme active site

Uncompetitive inhibition

The inhibitor binds only once the substrate is bound to the active site

Mixed inhibition

Mixed inhibition occurs when an inhibitor decreases the activity of an enzyme by binding to both the enzyme and the enzyme-substrate complex, resulting in reduced reaction rates.