Enzyme Catalysis, Inhibition & Carbohydrate Chemistry – Core Vocabulary

Flashcards summarizing essential vocabulary from the lecture on enzyme mechanisms (covalent, metal ion, serine proteases), enzyme inhibition, and carbohydrate structure/chemistry.

Covalent Catalysis

Enzyme mechanism in which a transient covalent bond forms between an amino-acid side chain and the substrate, creating an alternative reaction pathway of lower energy.

Schiff Base (Imine)

A carbon–nitrogen double bond formed when a nucleophilic amine attacks a carbonyl; stabilizes reaction intermediates and is freely reversible.

Enolate

High-energy oxyanion intermediate produced by deprotonation α to a carbonyl; expensive to form without catalysis.

Catalytic Triad

Asp-His-Ser arrangement that aligns and activates a serine O-H for nucleophilic attack via relay proton transfers.

Serine Protease

Class of enzymes (e.g., chymotrypsin, trypsin, elastase) that hydrolyze peptide bonds using a catalytic serine.

Oxyanion Hole

Pocket of backbone NH groups that hydrogen-bond to and stabilize the tetrahedral oxyanion transition state.

Tetrahedral Transition State

Four-coordinate carbon intermediate formed after nucleophilic attack on a planar carbonyl during catalysis.

Selectivity (Specificity) Pocket

Binding cavity in serine proteases that accommodates particular side chains and positions one unique peptide bond for cleavage.

Sissile Bond

The specific peptide (or glycosidic) bond that an enzyme is going to cleave.

Chymotrypsin

Serine protease that cleaves on the C-terminal side of bulky hydrophobic residues (Phe, Trp, Tyr).

Trypsin

Serine protease whose binding pocket contains Asp; cleaves C-terminal to Lys or Arg.

Elastase

Serine protease with a narrow pocket that prefers small hydrophobes; cleaves C-terminal to Ala (and similar).

Metal Ion Catalysis

Rate acceleration achieved when a bound metal stabilizes charges, or generates a nucleophilic hydroxide from coordinated water.

Carbonic Anhydrase

Zn²⁺ enzyme that converts CO₂ + H₂O ⇌ HCO₃⁻ + H⁺ via a metal-activated hydroxide and a proton shuttle of water molecules.

Proton Wire (Proton Shuttle)

Chain of hydrogen-bonded waters and a histidine that relays protons from the active site to bulk solvent.

Competitive Inhibition

Reversible inhibition in which inhibitor and substrate compete for the same active site; increases apparent Km, Vmax unchanged.

Uncompetitive Inhibition

Inhibitor binds only to ES complex; lowers both apparent Km and Vmax proportionally; Lineweaver-Burk lines are parallel.

Non-competitive Inhibition

Special case of mixed inhibition (Ki = Ki′) where inhibitor binds E and ES equally; Vmax decreases, Km unchanged.

Mixed Inhibition

Inhibitor binds both free enzyme and ES with different affinities, altering both Km and Vmax unequally.

Inhibition Constant (Ki)

Equilibrium constant describing binding strength of an inhibitor to the enzyme (smaller Ki = tighter binding).

Alpha (α) Factor

Term (1 + [I]/Ki) that scales apparent kinetic parameters in the presence of reversible inhibitors.

Vmax

Maximum initial velocity when enzyme sites are saturated with substrate.

Km (Michaelis Constant)

Substrate concentration at which velocity is half-maximal; reflects ES affinity when k₂ ≪ k₋₁.

Transition-State Analog

Stable molecule mimicking the high-energy transition state; usually a potent competitive inhibitor.

Bisubstrate Analog

Single inhibitor that simultaneously resembles two different substrates of a multi-substrate enzyme, occupying both binding sites.

Irreversible Inhibition

Covalent or very tight modification that permanently inactivates an enzyme, lowering total active enzyme concentration.

Penicillin

β-lactam antibiotic that irreversibly acylates the active-site serine of bacterial transpeptidase, blocking cell-wall cross-linking.

β-Lactam Ring

Strained four-membered cyclic amide essential for penicillin reactivity with transpeptidase (and β-lactamase).

Transpeptidase

Bacterial serine enzyme that cross-links peptidoglycan strands; target of β-lactam antibiotics.

β-Lactamase

Bacterial enzyme that hydrolyzes the β-lactam ring, conferring penicillin resistance.

Reducing Sugar

Monosaccharide or disaccharide with a free anomeric hydroxyl able to open to the linear aldehyde/ketone form.

Non-reducing Sugar

Sugar whose anomeric carbon is locked in a glycosidic bond; cannot mutarotate or reduce metal ions.

Anomeric Carbon

Carbonyl carbon that becomes chiral upon ring closure of a sugar; site of α/β configuration.

Mutarotation

Slow equilibrium inter-conversion between α and β anomers through the open-chain form.

Glycosidic Bond

C–O (or C–N) linkage between the anomeric carbon of a sugar and another group; forms by condensation.

Glycosidase

Enzyme that hydrolyzes glycosidic bonds; specificity defined by sugar type and α or β linkage.

Aldose

Sugar whose carbonyl is an aldehyde (e.g., glucose, galactose).

Ketose

Sugar whose carbonyl is a ketone (e.g., fructose).

Epimer

Two sugars differing in configuration at exactly one chiral center (e.g., glucose vs mannose at C-2).

Glucose

Primary fuel hexose; D-aldose with right-left-right-right OH pattern (C2-C5) in Fischer projection.

Mannose

C-2 epimer of glucose; D-aldose with left-left-right-right OH pattern (C2-C5).

Galactose

C-4 epimer of glucose; D-aldose with right-left-left-right OH pattern.

Fructose

D-ketose hexose whose C3-C6 stereochemistry matches glucose; forms furanose rings in solution.

Ribose

Five-carbon D-aldose (pentose) whose OH groups in Fischer projection all point right; backbone sugar of RNA.

Haworth Projection

Flat ring drawing of a cyclic sugar that shows axial/equatorial positions and α/β orientation.

Fischer Projection

Two-dimensional formula placing the most oxidized carbon on top; horizontal bonds project toward the viewer.

α-Anomer

Anomer in which the anomeric OH is trans (opposite side) to the terminal CH₂OH group in D-sugars.

β-Anomer

Anomer in which the anomeric OH is cis (same side) to the terminal CH₂OH group in D-sugars.

Pyranose

Six-membered (5C + 1O) cyclic sugar form (e.g., glucopyranose).

Furanose

Five-membered (4C + 1O) cyclic sugar form (e.g., ribofuranose).

Hexose

Monosaccharide containing six carbon atoms.

Pentose

Monosaccharide containing five carbon atoms.

D-Sugar

Sugar whose chiral center farthest from the carbonyl has the same configuration as D-glyceraldehyde (OH on right).

L-Sugar

Mirror image of the D-form; OH on the left at the reference carbon.

Maltose

Disaccharide of two glucoses linked α(1→4); reducing sugar.

Cellobiose

Disaccharide of two glucoses linked β(1→4); not digestible by human enzymes.

Alpha-1,4 Linkage

Glycosidic bond from the α-anomeric carbon of one sugar to the 4-OH of the next.

Beta-1,4 Linkage

Glycosidic bond from the β-anomeric carbon of one sugar to the 4-OH of another.

Stereochemistry

Spatial arrangement of atoms; crucial for enzyme recognition and sugar identity.

Active-Site Serine

Nucleophilic serine O⁻ generated by the Asp-His catalytic relay in serine proteases.

Oxyanion

Negatively charged oxygen species (e.g., ‑O⁻) formed in tetrahedral intermediates and stabilized in the oxyanion hole.

Metal-Activated Hydroxide

Strong nucleophile produced when water loses a proton upon coordination to a metal ion like Zn²⁺.

Protonated Histidine

His residue carrying an extra H⁺; can donate or accept protons during acid–base catalysis.