BIOCHEM EXAM 2 SUFFERING

Michaelis-Menten Equation

V0 = (Vmax * [S]) / (Km + [S])

Vmax

The maximal velocity of an enzyme-catalyzed reaction when the enzyme is fully saturated with substrate ([S] is much greater than Km)

Km (Michaelis Constant)

The substrate concentration at which the reaction velocity is half of Vmax (V0 = 0.5 * Vmax). A lower Km indicates higher enzyme-substrate affinity

Km Formula

Km = (k-1 + k2) / k1

Mitochondrial ALDH (ALDH2)

Low Km (high affinity) isozyme for acetaldehyde that rapidly processes acetaldehyde under normal conditions

Cytoplasmic ALDH (ALDH1)

High Km (low affinity) isozyme for acetaldehyde

ALDH2*2 Mutation

A mutation causing a non-functional low-Km mitochondrial ALDH2 enzyme, leading to acetaldehyde buildup, facial flushing, nausea, and tachycardia upon alcohol consumption.

Disulfiram

An aldehyde dehydrogenase inhibitor used as aversion therapy for alcohol use disorder by mimicking the ALDH2*2 mutation

Allosteric Sigmoidal Kinetics

S-shaped V0 vs [S] saturation curve displayed by allosteric enzymes due to subunit cooperativity.

Allosteric T-state

The tense, low-affinity, less active conformational state of an allosteric enzyme.

Allosteric R-state

The relaxed, high-affinity, highly active conformational state of an allosteric enzyme.

Positive Allosteric Effectors

Activators that stabilize the R-state, shifting the kinetic curve to the left and decreasing K0.5

Negative Allosteric Effectors

Inhibitors that stabilize the T-state, shifting the kinetic curve to the right and increasing K0.5

Reversible Enzyme Regulation

Non-covalent binding of effectors or substrate analogs that can freely dissociate from the enzyme

Irreversible Enzyme Inhibition

Inhibitors that bind covalently or extremely tightly to active-site groups, permanently inactivating the enzyme

Covalent Modification

Reversible enzymatic addition or removal of chemical groups (such as phosphorylation via kinases) to alter enzyme activity

Zymogen Activation

Irreversible proteolytic cleavage of inactive pro-enzymes to produce active enzymes

Competitive Inhibitor

Binds to the active site, increases Km, leaves Vmax unchanged, and can be overcome by increasing [S]

Uncompetitive Inhibitor

Binds only to the ES complex, decreases both Km and Vmax, and maintains a constant Vmax / Km ratio

Noncompetitive Inhibitor

Binds to an allosteric site on free enzyme or ES complex equally, leaves Km unchanged, decreases Vmax, and cannot be overcome by increasing [S]

Irreversible / Suicide Inhibitor

Binds covalently to the active site to permanently inactivate the enzyme, requiring new enzyme synthesis for recovery

Lineweaver-Burk Plot Parameters

1/V0 = (Km / Vmax) * (1/[S]) + (1/Vmax); y-intercept is 1/Vmax, x-intercept is -1/Km, and slope is Km/Vmax

Lineweaver-Burk Competitive Plot

Lines intersect on the y-axis (same Vmax, increased Km)

Lineweaver-Burk Noncompetitive Plot

Lines intersect on the x-axis (same Km, decreased Vmax)

Lineweaver-Burk Uncompetitive Plot

Parallel lines (both Vmax and Km decrease proportionally).

Statins (Atorvastatin, Simvastatin)

Competitive inhibitors of HMG-CoA reductase used to lower cholesterol synthesis.

Methotrexate

Competitive inhibitor of dihydrofolate reductase (DHFR) that blocks folate metabolism needed for DNA synthesis in cancer cells

Aspirin

Irreversible inhibitor of COX-1 and COX-2 via covalent acetylation of a serine residue, blocking prostaglandin synthesis

Penicillin

Irreversible/suicide inhibitor of bacterial transpeptidase, blocking cell wall peptidoglycan crosslinking

ACE Inhibitors (Enalapril, Captopril)

Competitive inhibitors of Angiotensin-Converting Enzyme used to manage hypertension.

Catabolism

Degradative, oxidative breakdown of complex molecules into simpler end-products that is exergonic and yields ATP, NADH, FADH2, and NADPH.

Anabolism

Synthetic, reductive construction of complex biomolecules from simple precursors that is endergonic and requires ATP and NADPH

5 Principles of Metabolism

1) Pathways are irreversible (Delta G is much less than 0); 2) Every pathway has a committed step; 3) Catabolic and anabolic pathways are distinct; 4) Pathways are regulated at key enzymes; 5) Pathways in eukaryotes are compartmentalized

Monosaccharide Types

Simple sugars with formula (CH2O)n; classified as aldoses (Glucose, Galactose, Glyceraldehyde) or ketoses (Fructose, Dihydroxyacetone)

Disaccharides

Two monosaccharides joined by an O-glycosidic bond; Sucrose (Glucose + Fructose), Lactose (Glucose + Galactose), Maltose (Glucose + Glucose)

Glycogen Structure

Storage polysaccharide in animals made of glucose polymer with alpha(1-4) chains and alpha(1-6) branches every 8 to 12 residues

Lactase Deficiency

Lack of brush-border lactase enzyme causing lactose intolerance, leading to bacterial fermentation, cramps, flatulence, and diarrhea

Glycolysis Net Yield

Breakdown of 1 glucose into 2 pyruvate, yielding a net 2 ATP and 2 NADH

Hexokinase vs Glucokinase

Hexokinase (tissues) has low Km and product inhibition by G6P; Glucokinase (liver) has high Km, high Vmax, no G6P inhibition, and acts as a glucose sensor

Phosphofructokinase-1 (PFK-1)

The primary committed, rate-limiting enzyme of glycolysis; inhibited by high ATP and citrate, activated by AMP and Fructose-2,6-bisphosphate

Pyruvate Kinase

Converts PEP to pyruvate generating ATP; activated by F-1,6-BP (feed-forward) and inhibited by ATP, Acetyl-CoA, Alanine, and glucagon.

Lactic Acid Fermentation (Anaerobic)

Cytosolic conversion of pyruvate to lactate by Lactate Dehydrogenase (LDH) to regenerate NAD+ for glycolysis under hypoxic conditions.

Gluconeogenesis Bypasses

1) Pyruvate to OAA via Pyruvate Carboxylase and OAA to PEP via PEPCK; 2) F-1,6-BP to F-6-P via FBPase-1; 3) G6P to Glucose via Glucose-6-Phosphatase

Rate-Limiting Step of Gluconeogenesis

Conversion of Fructose-1,6-bisphosphate to Fructose-6-phosphate by Fructose-1,6-Bisphosphatase (FBPase-1)

Cori Cycle

Muscle converts glucose to lactate anaerobically; lactate travels via blood to liver, where gluconeogenesis converts it back to glucose at the cost of 6 ATP

Pyruvate Dehydrogenase (PDH) Complex

Mitochondrial enzyme converting pyruvate to Acetyl-CoA, CO2, and NADH; requires TPP (B1), FAD (B2), NAD+ (B3), CoA (B5), and Lipoic acid

Citric Acid Cycle Yield

Per Acetyl-CoA oxidized: 3 NADH, 1 FADH2, 1 GTP (ATP), and 2 CO2

Rate-Limiting Step of TCA Cycle

Conversion of isocitrate to alpha-ketoglutarate by Isocitrate Dehydrogenase; activated by ADP, inhibited by ATP and NADH.

Arsenic Poisoning

Inactivates lipoic acid, inhibiting PDH and alpha-ketoglutarate dehydrogenase, causing pyruvate accumulation and energy depletion.

Thiamine (Vitamin B1) Deficiency

Impairs TPP-dependent enzymes (PDH, alpha-KGDH), reducing mitochondrial energy production in CNS and cardiac tissue

Proton Pumping in ETC

Complexes I, III, and IV pump protons from matrix into intermembrane space to create an electrochemical proton motive force

ETC Complex Inhibitors

Complex I (Rotenone, Amytal), Complex III (Antimycin A), Complex IV (Cyanide, CO, Azide), Complex V (Oligomycin)

Uncouplers (DNP, Thermogenin / UCP-1)

Dissipate the inner mitochondrial proton gradient as heat, halting ATP synthesis while increasing oxygen consumption.

Glycogen Synthase

Rate-limiting enzyme of glycogenesis that adds UDP-glucose via alpha(1-4) glycosidic bonds.

Glycogen Phosphorylase

Rate-limiting enzyme of glycogenolysis that cleaves alpha(1-4) bonds using inorganic phosphate to yield Glucose-1-Phosphate

Liver vs Muscle Glycogenolysis

Liver expresses Glucose-6-Phosphatase to release free glucose into blood; muscle lacks this enzyme and uses G6P internally for ATP

Insulin (Well-Fed State)

Activates phosphatases to dephosphorylate target enzymes; stimulates glycogenesis, glycolysis, and lipid synthesis while inhibiting gluconeogenesis

Glucagon (Fasting State) :

Binds GPCR to raise cAMP and activate PKA to phosphorylate target enzymes; stimulates glycogenolysis, gluconeogenesis, and lipolysis.

Pentose Phosphate Pathway (PPP) Functions

1) Generates NADPH for reductive biosynthesis and glutathione reduction; 2) Produces Ribose-5-Phosphate for nucleotides.

G6PD Deficiency

X-linked recessive lack of Glucose-6-Phosphate Dehydrogenase, leading to decreased NADPH, Heinz body formation under oxidative stress, and acute hemolytic anemia

Saturated vs Unsaturated Fatty Acids

Saturated fatty acids have no double bonds, pack tightly, and have high melting points; unsaturated fatty acids contain cis double bonds that introduce kinks and lower melting points

Triacylglycerols (TAGs)

Glycerol backbone esterified to 3 fatty acids; primary nonpolar energy storage lipid in adipocytes.

Glycerophospholipids

Glycerol backbone with 2 fatty acids, a phosphate group, and a polar head group; main structural component of biological membranes

Sphingolipids

Sphingosine backbone with 1 fatty acid and a polar head group; enriched in neuronal plasma membranes and myelin sheaths

Essential Fatty Acids

Linoleic acid (omega-6) and alpha-linolenic acid (omega-3); required in the diet because humans lack delta-12 and delta-15 desaturase enzymes