Chapter 3: Enzymes

enzymes

proteins that act as biological catalysts as they speed up the rate of reaction by reducing the activation energy

substrate

the substance that an enzyme operates on

active site

area on an enzyme consisting of a binding site and a catalytic site where the enzyme and substrate interact

catalytic site

area on an enzyme’s active site at which the reaction is catalyzed

binding site

area on an enzyme’s active site at which the substrate interacts with the enzyme through intermolecular interactions such that it gets positions properly relative to the catalytic site

enzyme-substrate complex

complex formed when the substrate interacts with the active site of an enzyme

orthosteric regulation

enzyme regulation in which the regulatory element interacts with the enzyme at its active site

allosteric regulation

enzyme regulation in which the regulatory element interacts with the enzyme at a location other than the active site

ligand

substance that an enzyme interacts with → could be a substrate or a regulatory molecule

lock and key theory

theory of enzyme-substrate interactions that posits that the active site of an enzyme and the substrate fit together like puzzle pieces, with no change in tertiary or quaternary structure

induced fit model

model/theory of enzyme-substrate interactions that posits that the enzyme and substrate affect each other by inducing changes in their respective tertiary and quaternary structures

oxidoreductases

class of enzymes that catalyze oxidation/reduction reactions

transferases

class of enzymes that transfer a functional group between molecules

hydrolases

class of enzymes that catalyze hydrolysis

lyases

class of enzymes that cleave bonds through non-hydrolysis mechanisms

isomerases

class of enzymes that catalyze isomerization (transforming a molecule into a different isomer)

ligases

class of enzymes that join molecules together with covalent bonds

phosphatases

enzymes that remove phosphate groups from a substrate

kinases

enzymes that add phosphate groups to a substrate (phosphorylation)

feedback regulation

the regulation of a process by downstream products

negative feedback

feedback regulation in which the downstream product of a pathway inhibits the pathway itself

positive feedback

feedback regulation in which the downstream product of a pathway activates/promotes the pathway itself

feed-forward regulation

feedback regulation in which a product produced earlier in the pathway activates another enzyme downstream of the same pathway

cooperativity

when an enzyme has multiple active sites and binding at one active site impacts binding at another (so binding the first substrate is the hardest)

Hill coefficient

value demonstrating the degree of cooperativity in an enzyme

\*\* > 1 means positive cooperative binding with higher values indicating greater cooperativity

\*\* = 1 means non-cooperative binding

\*\* < 1 means negative cooperativity in which binding the first ligand reduces the enzyme’s affinity for subsequent ligants

saturated

trait of an enzyme if all of the molecules of it are occupied/interacting with substrates

v = vmax \[S\] / Km + \[S\]

Michaelis-Menton equation of enzyme kinetics

vmax

aspect of the Michaelis-Menton equation that reflects the maximum rate/velocity or a reaction

Km

aspect of the Michaelis-Menton equation that reflects the concentration of substrate corresponding to half of the maximum rate of a reaction

\*\*reflects the affinity that an enzyme has for its substrate

reversible inhibitors

substances that reduce the effective activity of enzymes through noncovalent interactions (ie. hydrogen bonding, dipole-dipole interactions, and ionic interactions)

irreversible inhibitors

substances that reduce the effective activity of enzymes through covalently binding to enzymes

competitive inhibitors

inhibitors that interact with the active site of an enzyme, do not affect vmax, and increasing Km

noncompetitive inhibitors

inhibitors that interact with the enzyme allosterically and prevent it from working, do not affect Km, and decrease vmax

uncompetitive inhibitors

inhibitors that interact with the enzyme-substrate complex allosterically to prevent the enzyme from releasing the substrate, reduce vmax, and reduce Km

mixed inhibitors

inhibitors that allosterically bind to free enzymes or the enzyme-substrate complex, reduce vmax, and can increase Km (if it binds to a free enzyme) and decrease Km (if it binds to an enzyme-substrate complex)

serine, threonine, tyrosine

common targets of phosphorylation

glycosylation

the modification of enzymes or proteins by carbohydrate moieties

zymogens

inactive forms of enzymes that must be cleaved to become active

\*\*also called proenzymes

cofactors

chemical compounds required by an enzyme in order for it to carry out its biological function

\*\*can be organic or inorganic

coenzymes

organic cofactors that often contribute to the function of enzymes by carrying certain functional groups from one place to another in a reaction

\*\*many are vitamins or derivatives of vitamins

prosthetic groups

coenzymes that are tightly (or even covalently) bonded to their enzyme

holoenzyme

enzyme together with the coenzyme(s) and/or metal ions it needs to carry out its catalytic activity

apoenzyme

enzyme without the coenzymes/cofactors it needs to function correctly