Basics of Enzymes

Enzymes are complex protein biocatalysts that accelerate chemical reactions without being consumed by them. Due to the body’s constant metabolic needs, the absence of enzymes would make life unsustainable, as reactions would occur too slowly without these molecules. Enzymes have many functions, including macromolecule degradation and synthesis (catabolism and anabolism), signal transduction, energy generation (adenosine triphosphate [ATP]), ion pumps/active transport, defense and clearance reactions (oxidization, reduction, hydrolysis), cell regulation, movement (myosin ATPase, transport of intracellular substances), and immune responses.

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Overview

Definition

An enzyme is a protein that presents active sites which perform reactions by decreasing the activation energy of that reaction.

Enzyme characteristics

  • Complex protein and biocatalyst (catalyst of biological origin)
  • Remains unchanged after the reaction
  • Identified by the presence of the suffix “-ase” (e.g., lactate dehydrogenase)
  • Highly specific for particular substrates and products
    • Substrate (S): a substance upon which the enzyme acts
    • Enzyme-substrate (ES) complex: temporary molecule formed by the non-covalent binding of the enzyme and substrate via:
      • Ionic interactions: connections between charged molecules
      • Hydrophobic interactions
      • Van der Waals forces: weak intermolecular attractions between uncharged molecules
      • Hydrogen bonding
    • Product (P): molecule created by the enzymatic reaction
  • PH and temperature may alter its functions.
Enzyme kinetics

Relationship between substrates and enzymes, the reversible enzymatic reaction, and product formation and release

Image by Lecturio.

Active site

  • Area of an enzyme that binds to specific substrate molecules in order to facilitate a reaction
  • Consists of binding and catalytic sites
  • Binding sites: the area where the the substrate binds
  • Catalytic site: the area that reduces the activation energy (energy required for a reaction to proceed)
Enzyme

The location of the enzymatic active site and its relation with the substrate

Image by Lecturio.

Enzyme Specificity

  • Substrate specificity: Each enzyme can convert only 1 particular substrate. This is based on the “induced-fit” model, in which the binding site of the enzyme changes to match a particular substrate.
  • Stereospecificity: Substrates must be a specific isomer (e.g., lactate dehydrogenase can only convert L-lactate to pyruvate and not its mirror image, D-lactate).
  • Group specificity: Enzymes react with a specific chemical group (e.g., an amino group) located on the substrate.
  • Reaction specificity: Each enzyme can catalyze only a specific type of reaction (e.g., hydrolysis).

Classification

Enzyme naming

The first part of the name describes the substrate. The last part describes the enzyme function. The first part will describe the product if the following are true:

  • The product is biochemically important (e.g., pyruvate kinase).
  • The enzyme is in the ligase category outlined in the table below (e.g., glutamine synthetase).
  • An enzyme with the same function already exists and acts upon the substrate (e.g., pyruvate dehydrogenase and lactate dehydrogenase).

Enzyme classification

Main groupCatalytic reactionImportant subclasses (examples)
Oxidoreductases Transfer of reduction equivalents (1 mole of electrons); the electron donor is oxidized and increases its charge, the electron acceptor is reduced and decreases its chargeDehydrogenases (alcohol dehydrogenase), oxidases (xanthine oxidase), reductases (glutathione reductase)
Transferases Transfer of entire groups (e.g., amino groups)
  • Aminotransferases (aspartate aminotransferase [AST])
  • Phosphotransferases (glycogen phosphorylase)
Hydrolases Molecular fission with water addition = hydrolytic fission
  • Esterases (acetylcholinesterase)
  • Peptidases/proteases (α-amylase)
Lyases Break bonds between 2 carbons, or a carbon atom and oxygen, or carbon and sulfur
  • C-C lyases (aldolase)
  • C-O lyases (fumarase)
Isomerases Conversion of isomeric molecules into each other without changing the molecular formulaCis-trans isomerases (peptidyl-prolyl cis-trans isomerase, phosphoglucoisomerase)
Ligases Also called synthetases, energy-dependent linkage of compounds (e.g., dependent on ATP)
  • C-C ligases (pyruvate carboxylase)
  • C-N ligases (glutamine synthetase)

Isoenzymes, Coenzymes, and Prosthetic Groups

Enzymes can be modified in common ways to allow different organs to have the same activities or for substances outside of the substrate/enzyme/product sequence to influence enzymes.

Isoenzymes

  • Catalyze the same kinds of reactions, but differ slightly in their structure (different amino acid sequence) and in the organs on which they act (glycogen phosphorylase in the muscles vs. α-glucosidase in the heart)

Coenzymes

  • Small auxiliary molecules often needed to start the enzymatic reaction
    • These molecules have the capacity to attach/detach to the enzyme.
    • Serve a variety of functions (electron transfer, transfer of organic materials)
    • Vitamins often serve as precursors to many organic cofactors.
Coenzyme's role

The interaction between enzymes, coenzymes, and substrate attachment

Image by Lecturio.
Common coenzymes
The following presents a list of common coenzymes and the reaction types with which they are involved.
CoenzymeAssociated vitaminReaction typeEnzyme examples
Thiamine pyrophosphate B1Oxidative decarboxylation
  • Transketolase
  • Pyruvate dehydrogenase
  • α-ketoglutarate dehydrogenase
FAD/FADH2 B2Electron transferSuccinate dehydrogenase
NAD+/NADP+ B3Electron transferMany dehydrogenases
Lipoamide B4Oxidative decarboxylationPyruvate dehydrogenase
Coenzyme A (CoA) B5Acyl group transferα-ketoglutarate dehydrogenase
Pyridoxal phosphate B6TransaminationAlanine transaminase (ALT)
Biotin B7Carboxyl group transferPyruvate carboxylase
Tetrahydrofolate (THF) B9Transfer of C1 groups
  • Thymidylate synthase
  • Purine synthesis
5-deoxyadenosyl cobalamin B12Intramolecular rearrangements
  • Methylmalonyl-CoA mutase
  • Homocysteine methyltransferase

Prosthetic groups

  • Specific non-polypeptide units firmly bound to the enzyme and required for the biological function of some enzymes
  • These molecules are permanently attached to the enzyme.
The interaction between enzymes, prosthetic groups, and substrate attachment.

The interaction between enzymes, prosthetic groups, and substrate attachment

Image by Lecturio.

Clinical Relevance

The following conditions are caused by an enzymatic deficiency:

  • Glucose-6-phosphate dehydrogenase deficiency: inherited in an X-linked recessive manner. Can cause episodic intravascular hemolytic anemia when triggered by infections, certain medication, stress, or foods such as fava beans, with all the symptoms and signs of hemolytic anemia such as jaundice, pallor, dyspnea, fatigue, and tachycardia. It can also produce neonatal jaundice in newborns.
  • Galactosemia: most common and severe form of galactosemia. Produced due to a deficiency of galactose-1 phosphate uridyltransferase. Presents days after birth with clinical manifestations such as lethargy, failure to thrive, jaundice, and other features of liver injury
  • Chronic granulomatous disease: chronic disorder characterized by granuloma formation. Phagocytic cells are unable to produce bactericidal superoxide due to a defect in the nicotinamide adenine dinucleotide phosphate oxidase in the cells.
  • Lysosomal storage diseases: a group of genetic metabolic disorders caused by lysosomal defects that result in an accumulation of undigested metabolites and cellular death
    • Gaucher’s disease: inherited disorder that leads to the accumulation of undegraded glycolipid substrates in cells due to a deficiency of acid β-glucosidase
    • Krabbe’s disease: Also known as globoid cell leukodystrophy, this condition is produced due to a deficient activity of the galactocerebrosidase, which produces an accumulation of galactosylceramide.
    • Tay-Sachs disease: Produced due to a deficiency of hexosaminidase A, this autosomal recessive lipid storage disorder may cause blindness, hypotonia, progressive cognitive decline, and seizures.

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