Biochem Exam 3

Michaelis–Menten model

Describes kinetics of single-substrate enzymes; ES complex forms then breaks down to product.

Bi-substrate reactions

Enzyme mechanisms that involve two substrates and two products; ~60% of known reactions.

Cleland notation

System used to symbolize substrates (A, B), products (P, Q), and enzyme forms in mechanism diagrams.

Pseudo–first-order conditions

One substrate is kept saturating so the reaction behaves as if it depends on one substrate.

Sequential reaction

Mechanism where all substrates bind before chemistry occurs and products are released.

Ordered sequential reaction

Substrates bind in a specific order; leading substrate must bind first.

Random sequential reaction

Substrates bind in any order but the EAB complex must form for chemistry.

Ping-pong reaction

One product leaves before all substrates bind; enzyme cycles between two forms (E and F).

Ping-pong hallmark

Parallel lines on a Lineweaver–Burk plot because Vmax/KM for first substrate is unaffected by second substrate.

Sequential hallmark

Intersecting lines on Lineweaver–Burk plot because Vmax and KM are affected by both substrates.

Vmax in LB plot

Equal to the inverse of the y-intercept (1/Vmax).

KM in LB plot

Equal to the negative reciprocal of the x-intercept (−1/KM).

Slope in LB plot

KM/Vmax.

Transition state

Highest-energy state; enzymes accelerate reactions by stabilizing the transition state.

Transition state analogue

Molecule resembling transition state; binds enzyme tightly and acts as a strong inhibitor.

Statins

Transition-state analogs that inhibit HMG-CoA reductase to lower cholesterol.

Protease inhibitors

Drugs that mimic transition state to inhibit HIV-1 protease.

Covalent catalysis

Enzyme forms temporary covalent bond with substrate to accelerate reaction.

Acid–base catalysis

Proton transfer from acids or bases stabilizes the transition state.

General acid catalysis

Reaction is accelerated by donation of proton in the transition state.

General base catalysis

Reaction is accelerated by abstraction of proton in the transition state.

Metal ion catalysis

Metal ions stabilize negative charges, orient substrates, or mediate redox changes.

Metalloenzyme

Enzyme with tightly bound metal ion such as Fe²⁺, Zn²⁺, Cu²⁺, Mn²⁺.

Metal-activated enzyme

Enzyme that loosely binds metal ions such as Na⁺, K⁺, Mg²⁺, Ca²⁺.

Carbonic anhydrase

Zn²⁺ enzyme that generates OH⁻ by making water more acidic.

Serine proteases

Protease family using Ser195, His57, Asp102 to catalyze peptide bond cleavage.

Catalytic triad (serine protease)

Asp polarizes His; His deprotonates Ser; Ser performs nucleophilic attack.

Oxyanion hole

Region stabilizing tetrahedral intermediate via hydrogen bonds.

Chymotrypsin cleavage site

Cleaves after aromatic residues: Phe, Tyr, Trp.

Trypsin cleavage site

Cleaves after basic residues: Lys, Arg.

Elastase cleavage site

Cleaves after small neutral residues: Ala, Gly.

Acyl-enzyme intermediate

Stable covalent intermediate formed during serine protease mechanism.

RNase A mechanism

Uses His12 as a base and His119 as an acid to hydrolyze RNA.

Enzyme regulation

Processes that alter enzyme availability or activity to control metabolism.

Regulation by synthesis

Changing rate of enzyme production (transcription/translation).

Regulation by degradation

Altering rate of enzyme breakdown to change enzyme levels.

Zymogen (proenzyme)

Inactive enzyme precursor activated by proteolysis.

Proteolysis regulation

Activation of enzyme by cleavage of peptide bonds.

Allosteric regulation

Binding of regulator at non-active site to change enzyme conformation/activity.

Allosteric effector

Molecule that binds “other site” to increase or decrease enzyme activity.

Positive effector

Shifts enzyme toward R-state, increasing activity.

Negative effector

Shifts enzyme toward T-state, decreasing activity.

Feedback inhibition

Downstream product inhibits earlier enzyme by allosteric binding.

ATCase role

Catalyzes first step in pyrimidine synthesis.

ATCase regulation

ATP activates (R-state), CTP inhibits (T-state).

Cooperativity

Sigmoidal kinetics where binding of one substrate increases affinity of others.

Hill coefficient

n>1 indicates positive cooperativity; n=1 indicates no cooperativity.

PFK committed step

Phosphorylates F6P to F1,6-BP in glycolysis.

PFK regulation

AMP activates PFK during low-energy conditions.

Covalent modification regulation

Reversible modification (often phosphorylation) changes enzyme activity.

Kinase

Enzyme that adds phosphate group to Ser, Thr, Tyr.

Phosphatase

Enzyme that removes phosphate group.

Glycogen phosphorylase

Regulated by both allostery and covalent modification.

Glycogen phosphorylase T-state

Inactive; stabilized by ATP and glucose-6-phosphate.

Glycogen phosphorylase R-state

Active; stabilized by AMP.

Monosaccharide

Basic carbohydrate unit with formula (CH₂O)n.

Aldose

Monosaccharide with aldehyde group.

Ketose

Monosaccharide with ketone group.

Triose

Three-carbon sugar.

Pentose

Five-carbon sugar.

Hexose

Six-carbon sugar.

Fischer projection

2D representation for showing chiral center configurations.

D-sugar

OH on right of chiral carbon furthest from carbonyl.

L-sugar

OH on left of chiral carbon furthest from carbonyl.

Epimer

Sugars differing at one chiral center (e.g., glucose/mannose).

Enantiomers

Mirror-image stereoisomers (D-glucose vs L-glucose).

Anomer

Isomers differing at anomeric carbon (α vs β).

Anomeric carbon

Carbonyl carbon that becomes chiral during ring closure.

Hemiacetal

Formed when aldehyde reacts with alcohol during cyclization.

Hemiketal

Formed when ketone reacts with alcohol during cyclization.

Pyranose

6-membered sugar ring.

Furanose

5-membered sugar ring.

β-D-glucose

Ring form where anomeric OH is up.

α-D-glucose

Ring form where anomeric OH is down.

Reducing sugar

Has free anomeric carbon that can open to aldehyde.

Lactose

Disaccharide of galactose + glucose via β(1→4) linkage.

Sucrose

Disaccharide of glucose + fructose via α(1→2)β linkage; non-reducing.

Cellulose

β(1→4) glucose polymer; structural component in plants.

Chitin

β(1→4) polymer of N-acetylglucosamine; exoskeletons and fungi.

Starch

Mixture of amylose and amylopectin; plant storage polysaccharide.

Amylose

α(1→4) glucose polymer; unbranched.

Amylopectin

α(1→4) with α(1→6) branches.

Glycogen

Highly branched animal storage polysaccharide.

Sugar acid

Oxidized sugar (e.g., glucuronic acid).

Sugar alcohol

Reduced sugar (e.g., sorbitol).

Amino sugar

Sugar containing NH₂ instead of OH (e.g., glucosamine).

Fatty acid

Long-chain carboxylic acid; building block of lipids.

Saturated fatty acid

No double bonds; higher melting point.

Unsaturated fatty acid

Contains double bonds; lower melting point.

Polyunsaturated fatty acid

Two or more double bonds.

Omega-3 fatty acid

Double bond three carbons from methyl end.

Triacylglycerol

Three fatty acids esterified to glycerol; energy storage.

Glycerophospholipid

Membrane lipid with glycerol backbone, two FAs, phosphate head group.

Sphingolipid

Lipid with sphingosine backbone; important in membranes.

Ceramide

Sphingosine + fatty acid via amide bond.

Sphingomyelin

Sphingolipid with phosphocholine head group; found in myelin sheath.

Cerebroside

Ceramide with one sugar head group.

Ganglioside

Ceramide with 3+ sugars including sialic acid.

Steroid

Lipid with four fused rings; cholesterol is major example.

Cholesterol

Precursor for steroid hormones; modulates membrane fluidity.