MCAT Bio/Biochem cheat sheet

Amino acids are zwitterionic near physiological pH: the carboxyl group is deprotonated (pKa ~2) and the amino group protonated (pKa ~9-10).

Peptide bonds form by condensation between the alpha-carboxyl of one amino acid and the alpha-amino of the next; the bond is planar and has partial double-bond character, restricting rotation.

At a pH equal to an amino acid's pI, the molecule carries zero net charge and does not migrate in an electric field.

Nucleotides consist of a nitrogenous base, a pentose sugar, and one or more phosphate groups; phosphodiester bonds link the 3'-OH of one sugar to the 5'-phosphate of the next.

DNA base pairing: A pairs with T via 2 hydrogen bonds; G pairs with C via 3 hydrogen bonds, so higher GC content raises melting temperature.

Fatty acids are amphipathic when ionized; saturated chains pack tightly (higher melting point) while cis-unsaturated kinks lower packing and melting point.

Enzyme kinetics follow Michaelis-Menten: v = Vmax[S]/(Km + [S]); Km equals the substrate concentration at half-maximal velocity and reflects substrate affinity (lower Km = higher affinity).

Competitive inhibitors raise apparent Km with unchanged Vmax; noncompetitive inhibitors lower Vmax with unchanged Km.

Prokaryotes lack membrane-bound organelles and a nucleus; their DNA is a circular chromosome located in the nucleoid region.

The fluid mosaic model describes membranes as a phospholipid bilayer with embedded proteins, cholesterol (in animals), and glycoproteins; small nonpolar molecules diffuse freely, while ions and polar molecules require channels or transporters.

Mitochondria and chloroplasts contain their own circular DNA and ribosomes, consistent with the endosymbiotic theory.

Na+/K+ ATPase pumps 3 Na+ out and 2 K+ in per ATP hydrolyzed, maintaining the resting membrane potential (inside negative).

Mitosis produces two genetically identical diploid daughter cells; meiosis produces four haploid gametes with genetic recombination via crossing over in prophase I.

Meiosis I separates homologous chromosomes (reductional division); meiosis II separates sister chromatids (equational division).

The cell cycle checkpoints are G1/S (size and DNA damage), G2/M (DNA replication completion), and the spindle checkpoint during metaphase.

Apoptosis is programmed cell death mediated by caspases; necrosis is uncontrolled lysis caused by injury.

Protein primary structure is the amino acid sequence; secondary structure includes alpha helices (intramolecular H-bonds) and beta sheets (intermolecular H-bonds between strands).

Tertiary structure is the 3D folding driven by hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges; quaternary structure involves multiple polypeptide subunits.

Denaturation disrupts secondary, tertiary, and quaternary structure but does not break peptide bonds (primary structure remains intact).

Enzymes lower activation energy by stabilizing the transition state; they do not change the equilibrium constant or the free energy change of a reaction.

Allosteric enzymes show a sigmoidal velocity curve and are regulated by effectors binding at sites distinct from the active site.

The Lineweaver-Burk plot (1/v vs 1/[S]) gives the y-intercept = 1/Vmax and x-intercept = -1/Km.

Cofactors are nonprotein helpers (metal ions, coenzymes); prosthetic groups are tightly bound cofactors such as heme.

Protein function often depends on specific binding: hemoglobin exhibits cooperative oxygen binding, shifting from a tense (T) to relaxed (R) state.

Glycolysis converts glucose to 2 pyruvate, netting 2 ATP and 2 NADH per glucose; it occurs in the cytosol and does not require oxygen.

Pyruvate dehydrogenase converts pyruvate to acetyl-CoA, producing 1 NADH and 1 CO2 per pyruvate; it links glycolysis to the citric acid cycle.

The citric acid cycle per acetyl-CoA yields 3 NADH, 1 FADH2, 1 GTP/ATP, and 2 CO2; it occurs in the mitochondrial matrix.

Oxidative phosphorylation: electrons flow from NADH (via Complex I) and FADH2 (via Complex II) to O2, pumping protons to build a gradient that drives ATP synthase.

Approximate ATP yield per glucose: ~30-32 ATP in eukaryotes (older textbooks cite 36-38); FADH2 yields ~1.5 ATP vs ~2.5 for NADH.

Fermentation regenerates NAD+ from NADH (lactate or ethanol) so glycolysis can continue without oxygen.

Gluconeogenesis synthesizes glucose from lactate, glycerol, and amino acids, mainly in the liver; it uses different enzymes at irreversible steps (e.g., pyruvate carboxylase, PEPCK).

Enzyme activity is regulated by covalent modification (phosphorylation) and allosteric feedback; ATP and citrate inhibit phosphofructokinase-1, while AMP activates it.