The activity of certain macromolecules as catalysts within living systems is a central biological process. Macromolecules that act as catalysts are enzymes. Most, but not all, enzymes are proteins. A few ribonucleoprotein enzymes have been discovered in which the catalytic activity is in the RNA portion of the molecule rather than the protein part. Enzymes bind temporarily to one or more reactants and lower the activation energy of the reaction.
Enzyme concepts including mechanics, kinetics and regulation are centrally important for the new MCAT, in which biochemistry has such strong emphasis. To understand enzyme activity at the superior level you need to fully involve your general chemistry and organic chemistry. Beyond simple retention of information, try your best to embed your understanding of this material in all of its conceptual underpinnings from the rest of science.
Conceptual Vocabulary for Enzyme Activity
Enzymes are proteins that act as biological catalysts (biocatalysts).
Enzyme catalysis is the increase in the rate of a process made possible by the activity of an enzyme.
A binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity.
The active site is region of an enzyme where substrate molecules bind and undergo a chemical reaction.
A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's activity as a catalyst (a catalyst is a substance that increases the rate of a chemical reaction).
A conformational change is a change in the shape of a macromolecule, often induced by environmental factors.
Chemical specificity is the ability of a protein's binding site to bind specific ligands. T
Negative feedback (or balancing feedback) occurs when some function of the output of a system, process, or mechanism is fed back in a manner that tends to reduce the fluctuations in the output, whether caused by changes in the input or by other disturbances.
Isozymes are enzymes that differ in amino acid sequence but catalyze the same chemical reaction.
A protein complex is a group of two or more associated polypeptide chains.
A multienzyme complex contains several copies of one or several enzymes (polypeptide chains) packed into one assembly.
Stereospecificity is the property of a reaction mechanism that leads to different stereoisomeric reaction products from different stereoisomeric reactants, or which operates on only one (or a subset) of the stereoisomers.
A protease is an enzyme that catalyzes (increases the rate of) proteolysis, the breakdown of proteins into smaller polypeptides or single amino acids.
A protein domain is a region of the protein's polypeptide chain that is self-stabilizing and that folds independently from the rest.
A kinase is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates.
Ribozymes are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes.
An oxidoreductase is an enzyme that catalyzes the transfer of electrons from one molecule, the reductant, also called the electron donor, to another, the oxidant, also called the electron acceptor.
A transferase is any one of a class of enzymes that enact the transfer of specific functional groups (e.g. a methyl or glycosyl group) from one molecule (called the donor) to another (called the acceptor).
Hydrolase is a class of enzyme that commonly perform as biochemical catalysts that use water to break a chemical bond, which typically results in dividing a larger molecule into smaller molecules.
Isomerases are a general class of enzymes that facilitate intramolecular rearrangements in which bonds are broken and formed.
A ligase is an enzyme that can catalyze the joining (ligation) of two large molecules by forming a new chemical bond.
Flavoproteins are proteins that contain a nucleic acid derivative of riboflavin: the flavin adenine dinucleotide (FAD) or flavin mononucleotide (FMN).
An enzyme repressor is a substance that negatively regulates the amount of an enzyme by decreasing the rate of its biosynthesis.
A dehydrogenase is an enzyme belonging to the group of oxidoreductases that oxidizes a substrate by reducing an electron acceptor, usually NAD+/NADP+ or a flavin coenzyme such as FAD or FMN.
A phosphatase is an enzyme that uses water to cleave a phosphoric acid monoester into a phosphate ion and an alcohol.
Serine proteases are enzymes that cleave peptide bonds in proteins, in which serine serves as the nucleophilic amino acid at the active site.
A lyase is an enzyme that catalyzes the breaking (an "elimination" reaction) of various chemical bonds by means other than hydrolysis (a "substitution" reaction) and oxidation, often forming a new double bond or a new ring structure.
Enzyme promiscuity is the ability of an enzyme to catalyse a fortuitous side reaction in addition to its main reaction.
A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.
Substrate presentation is a biological process that activates a protein. The protein is sequestered away from its substrate and then activated by release and exposure of the protein to its substrate.
Flavin mononucleotide is a biomolecule produced from riboflavin (vitamin B2) by the enzyme riboflavin kinase and functions as the prosthetic group of various oxidoreductases, including NADH dehydrogenase.
A cofactor that is present in all living systems, thiamine pyrophosphate is a vitamin B1 derivative.
Carboxy-lyases, also known as decarboxylases, are carbon–carbon lyases that add or remove a carboxyl group from organic compounds.
An oxidase is an enzyme that catalyzes an oxidation-reduction reaction, especially one involving dioxygen (O2) as the electron acceptor.
Folate, also known as vitamin B9, is required for the body to make DNA and RNA and metabolise amino acids necessary for cell division.
S-Adenosyl methionine is a common cosubstrate involved in methyl group transfers, transsulfuration, and aminopropylation.
An antimicrobial enzyme that forms part of the innate immune system, lysozyme is a glycoside hydrolase that catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan.
The EC number is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze.
Glycosidases catalyze the hydrolysis of glycosidic bonds in complex sugars.
Dehydratases are a group of lyase enzymes that form double and triple bonds in a substrate through the removal of water.
Myristoylation is a common lipidation modification that allows for weak protein–protein and protein–lipid interactions and plays an essential role in membrane targeting, protein–protein interactions and functions widely in a variety of signal transduction pathways.
Conformational proofreading is a general mechanism of molecular recognition systems in which introducing a structural mismatch between a molecular recognizer and its target, or an energetic barrier, enhances the recognition specificity and quality.