Enzymes

Flashcards covering general properties, mechanisms, kinetics, and regulation of enzymes based on the provided lecture notes.

Enzymes

Proteins with striking characteristics: biological catalysts, highly specific, extremely fast, and their activity can be regulated.

Activase (recombinant human tissue plasminogen activator)

Used as a 'clot buster'.

Bovine adenosine deaminase (ADA)

Used to treat patients with severe combined immunodeficiency disease (SCID) caused by ADA deficiency.

Biological catalysts

Accelerate chemical reactions.

Catalyst

A molecule that accelerates a chemical reaction and is regenerated at the end of the reaction.

ES complex (Michaelis complex)

The intermediate formed when an enzyme (E) binds to its substrate (S), E + S ES.

Fischer's Lock and Key model

Proposes that enzyme and substrate fit together perfectly like a lock and key.

Enzyme Active site

A 3D cleft formed by catalytic amino acids, typically a small, often nonpolar pocket where substrates bind via weak noncovalent interactions.

Induced fit model

Proposed by Daniel Koshland, it suggests that an enzyme changes its conformation upon binding a ligand (substrate), like a hand slipping into a glove, making the active site flexible.

Cofactor

A non-protein chemical component required for the enzyme's activity; can be metal ions or organic molecules (coenzymes).

Apoenzyme

The protein component of an enzyme that is inactive without its cofactor.

Holoenzyme

The complete, catalytically active enzyme, including both the apoenzyme and its cofactor.

Coenzymes

Small organic molecules, mostly derived from vitamins, that act as cofactors.

Isozymes

Enzymes that have different primary structures (different gene products) but catalyze the same chemical reaction on the same substrate(s), showing distinct expression in different tissues.

Myocardial infarction (heart attack) diagnosis

Diagnosed by an increase in LDH isozyme B4 and MB creatine kinase levels in the blood within 12-24 hours after heart muscle damage.

Activation energy (Ea)

The minimum energy required for two molecules to react. Enzymes lower this barrier.

Transition state

An unstable, high-energy intermediate formed during a chemical reaction, which enzymes stabilize to lower the activation energy.

Transition state stabilization

The mechanism by which enzymes create a new reaction pathway with lower activation energy by specifically binding more tightly to the transition state structure than to the substrate itself.

Covalent catalysis

A catalytic strategy where a covalent bond is transiently formed between the enzyme and the substrate.

General acid-base catalysis

A catalytic strategy where amino acid side chains donate or accept protons to facilitate a reaction.

Catalytic triad (chymotrypsin)

Composed of serine, histidine, and aspartate residues, which work together to create a potent nucleophilic serine residue at the active site.

Oxyanion hole

A space in the enzyme active site designed to bind and stabilize a negatively charged group, particularly the tetrahedral intermediate during catalysis, through hydrogen bonds.

Exergonic reaction

A reaction with a negative, favorable, free energy change, often coupled to endergonic reactions to drive them forward.

Endergonic reaction

An unfavorable reaction with a positive free energy change that requires an input of free energy to proceed.

Enzyme kinetics

The study of the rates of enzyme-catalyzed reactions, crucial for understanding metabolic regulation, designing drugs, and diagnosing diseases.

k1

The rate constant for the binding of enzyme to substrate (E + S ES).

k-1

The rate constant for the dissociation of the ES complex back into enzyme and substrate (ES E + S).

kcat

The rate constant of the enzyme reaction, representing how fast the ES complex is converted to product (ES E + P).

Km (Michaelis constant)

Experimentally, the substrate concentration at which the reaction velocity is half of Vmax; inversely proportional to the affinity of the enzyme for the substrate.

Vmax

The maximum velocity with which an enzyme can catalyze a reaction when all enzyme active sites are saturated with substrate.

Michaelis-Menten equation

A mathematical model describing the relationship between reaction velocity, substrate concentration, Km, and Vmax for simple enzyme kinetics.

Lineweaver-Burk plot (double reciprocal plot)

A linear plot of 1/v versus 1/[S] derived from the Michaelis-Menten equation, used to determine Vmax and Km.

kcat (turnover number)

The number of substrate molecules converted to product per enzyme molecule per second, representing the catalytic efficiency when the enzyme is saturated.

Catalytic efficiency (kcat/Km)

A ratio that estimates the enzyme's substrate preference and its overall catalytic performance, particularly at low substrate concentrations.

Effect of temperature on enzyme activity

Enzyme activity increases with temperature due to more frequent collisions, but high temperatures can cause denaturation and irreversible loss of activity.

Effect of pH on enzyme activity

Enzyme activity is optimal within a narrow pH range; extreme pH values can lead to irreversible denaturation, while moderate pH changes can alter ionization states of functional groups, reversibly affecting activity.

Enzyme inhibition

The process by which molecules bind to an enzyme and decrease its activity, forming the basis for many clinical drug therapies.

Irreversible inhibitors

Molecules that covalently bind to the enzyme, leading to permanent inhibition of its activity (e.g., penicillin, aspirin).

Reversible inhibitors

Molecules that bind non-covalently and reversibly to an enzyme, temporarily reducing its activity.

Competitive inhibitors

Reversible inhibitors that bind to the same active site as the substrate, competing with substrate binding.

Noncompetitive inhibitors

Reversible inhibitors that bind to a site separate from the active site, not competing with substrate binding, and decrease Vmax without changing Km.

Competitive inhibition kinetics

Characterized by an increased apparent Km and an unchanged Vmax on Lineweaver-Burk plots, meaning high substrate concentrations can overcome the inhibition.

Noncompetitive inhibition kinetics

Characterized by an unchanged Km and a decreased Vmax on Lineweaver-Burk plots, meaning high substrate concentrations cannot overcome the inhibition.

Remdesivir

A competitive inhibitor that blocks the RNA polymerase of Covid-19, having a similar structure to the natural substrate.

Transition state analogs

Stable molecules that resemble the geometric and/or electronic features of the highly unstable transition state, acting as potent enzyme inhibitors due to tighter binding.

Enzyme regulation

Mechanisms that control enzyme activity, including transcription regulation, mRNA degradation/translation, protein degradation, allosteric binding, phosphorylation/dephosphorylation, and sequestration.

Regulation by phosphorylation

A quick and reversible enzyme regulation mechanism involving the addition or removal of phosphate groups by protein kinases and phosphatases, often targeting serine, threonine, or tyrosine residues.

Feedback regulation

A common metabolic control mechanism where the end product of a pathway inhibits an enzyme earlier in the pathway, preventing overproduction.

Allosteric enzyme

An enzyme whose activity is regulated by the binding of an effector molecule at a site other than the active site (allosteric site), often exhibiting cooperative substrate binding.

Allosteric site

A regulatory site on an allosteric enzyme, distinct from the active site, where effector molecules bind to modulate enzyme activity.

Oligomeric enzymes

Enzymes composed of multiple protein subunits, a characteristic feature of allosteric enzymes.

Sigmoidal kinetics

The characteristic S-shaped curve observed when plotting reaction velocity against substrate concentration for allosteric enzymes, indicative of cooperative substrate binding.

T-state (allosteric enzyme)

The inactive conformational state of an allosteric enzyme that binds substrate weakly or has lower catalytic activity.

R-state (allosteric enzyme)

The active conformational state of an allosteric enzyme that binds substrate better and/or has higher catalytic activity.

Allosteric activator

A molecule that binds to an allosteric site and stabilizes the R-state (active conformation) of an enzyme, increasing its activity.

Allosteric inhibitor

A molecule that binds to an allosteric site and stabilizes the T-state (inactive conformation) of an enzyme, decreasing its activity.