BMS124 Applied Biochemistry – Enzymes, Proteins & Oral Biology

Vocabulary flashcards covering key terms related to amino acids, protein structure, enzyme function, kinetics, regulation, clinical diagnostics, salivary enzymes, and the role of matrix metalloproteinases in periodontal disease.

Amino Acid

The basic building block of proteins, consisting of an α-carbon attached to an amino group, carboxyl group, hydrogen atom, and distinctive side chain (R-group).

Essential (Indispensable) Amino Acids

Amino acids the human body cannot synthesize in sufficient amounts and therefore must be obtained from the diet.

Non-essential (Dispensable) Amino Acids

Amino acids that can be synthesized by the human body and are not required in the diet.

Hydrophobic Amino Acid

An amino acid whose non-polar side chain is poorly soluble in water, driving proteins to fold so these residues are buried inside.

Hydrophilic Amino Acid

An amino acid with a polar or charged side chain that readily interacts with water, often found on protein surfaces.

Chirality of Amino Acids

Property whereby all standard amino acids (except glycine) exist as optical L- and D-isomers; proteins are built almost exclusively from the L-form.

Peptide Bond

The covalent amide linkage formed between the α-carboxyl group of one amino acid and the α-amino group of another, releasing water.

Primary Protein Structure

The linear sequence of amino acids in a polypeptide chain joined by peptide bonds.

Secondary Protein Structure

Regular local folding patterns such as α-helices and β-sheets stabilized mainly by hydrogen bonds between backbone atoms.

Tertiary Protein Structure

The overall three-dimensional folding of a single polypeptide chain, stabilized by hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges.

Quaternary Protein Structure

The arrangement and interaction of multiple polypeptide subunits in a multisubunit protein.

Protein Misfolding

Incorrect folding of a protein that can lead to loss of function and aggregation-related diseases.

Alzheimer’s Disease (Aβ Peptides)

Neurodegenerative disorder characterized by accumulation of insoluble, neurotoxic β-amyloid peptides in the brain.

Prion Protein (PrPc)

Normal cellular prion protein rich in α-helices, sensitive to proteolysis.

PrPsc (Scrapie Form)

Infectious prion isoform containing β-sheets, resistant to proteolytic degradation and prone to form insoluble aggregates.

Transmissible Spongiform Encephalopathies

Fatal neurodegenerative diseases (e.g., Creutzfeldt-Jakob and mad cow) caused by prion accumulation; no effective treatment exists.

Enzyme

A biological catalyst, usually a protein, that accelerates reaction rates without being consumed.

Active Site

The specific region of an enzyme where substrate binding and catalysis occur.

ES complex

substrate binds enzyme

Catalytic Efficiency

Measure of how well an enzyme converts substrate to product (kcat/Km).

Enzyme Specificity

The ability of an enzyme to select a particular substrate and reaction.

Holoenzyme - mostly Zn2+ or Fe2+

The catalytically active form consisting of an apoenzyme (protein part) plus its required cofactor.

Enzyme Kinetics

Study of the rate of enzyme-catalyzed reactions and how they change with variables such as substrate concentration.

Michaelis–Menten Equation

v = (Vmax [S]) / (Km + [S]); relates initial velocity to substrate concentration for many enzymes.

Km (Michaelis Constant)

Substrate concentration at which reaction velocity is half of Vmax; inversely related to substrate affinity.

Vmax

Maximum reaction velocity achieved at saturating substrate concentration for a given enzyme amount.

Lineweaver–Burk Plot

Double-reciprocal plot (1/v vs 1/[S]) used to derive Vmax and Km from Michaelis–Menten kinetics.

Transition State

High-energy, fleeting state substrates must reach during a reaction; enzymes stabilize it to lower activation energy.

Activation Energy (ΔG‡)

Energy barrier that must be overcome for reactants to become products; reduced by enzymes.

Allosteric Regulation

Modulation of enzyme activity via binding of effectors at sites other than the active site, causing conformational change.

Homotropic Effector

An allosteric modulator that is also the enzyme’s substrate (e.g., O₂ on hemoglobin).

Heterotropic Effector

An allosteric modulator different from the substrate (e.g., citrate inhibiting phosphofructokinase-1).

Covalent Modification

Reversible attachment/removal of chemical groups (e.g., phosphorylation) that alters enzyme activity.

Competitive Inhibitor

Molecule that binds the active site, raising Km but leaving Vmax unchanged.

Non-competitive Inhibitor

Molecule that binds a site other than the active site, lowering Vmax without affecting Km.

β-lactam Antibiotics

Drugs like penicillin that inhibit bacterial cell-wall-synthesizing enzymes, leading to cell death.

ACE Inhibitors

Drugs (captopril, enalapril, lisinopril) that block angiotensin-converting enzyme, causing vasodilation and decreased blood pressure.

Alanine Aminotransferase (ALT)

Liver enzyme measured in plasma; elevated levels indicate hepatocellular injury.

Creatine Kinase-MB (CK-2)

Heart-specific isoenzyme released after myocardial infarction; used in cardiac diagnosis.

Cardiac Troponin I (cTnI)

Regulatory protein unique to heart muscle; its plasma rise is a sensitive marker of myocardial infarction.

Glucose Oxidase

Enzyme incorporated into glucose meters to oxidize blood glucose, generating an electron signal detected by the device.

Polymerase Chain Reaction (PCR)

Technique that amplifies DNA sequences through cyclic denaturation, annealing, and extension.

Reverse-Transcription qPCR (RT-qPCR)

PCR method that first converts RNA to cDNA, then quantitatively amplifies it; used in SARS-CoV-2 diagnostics.

Salivary Amylase

Major salivary enzyme that hydrolyzes dietary starch and facilitates dental plaque formation.

Lysozyme (Saliva)

Antimicrobial salivary enzyme that breaks β(1→4) linkages in bacterial cell walls.

Matrix Metalloproteinases (MMPs)

Zinc-dependent enzymes that degrade extracellular matrix proteins; overactivity contributes to periodontal tissue destruction.

Tissue Inhibitors of Metalloproteinases (TIMPs)

Endogenous proteins that bind and inhibit MMPs, maintaining extracellular matrix balance.

Periodontal Disease (MMP Role)

Inflammatory oral disease where excessive MMP activity degrades collagen in periodontal tissues, causing attachment loss.