Chapter 14: High-Yield Cheat Sheet

This is the MCAT biochemistry cheat sheet you wish you had the week before test day. Every amino acid side chain, enzyme class, metabolic pathway, and ATP yield from all 12 chapters, compressed into one page. The 20 amino acids with pKa’s, Michaelis-Menten kinetics, every inhibition type, glycolysis through oxidative phosphorylation, the urea cycle, hormonal regulation of fed and fasted states, DNA replication enzymes, and the codon table. All the tables you need to memorize, none of the prose you do not. If you can recall 80% of what is on this page, you will walk into Bio/Biochem already having answered half the passage questions in your head.

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1. Amino Acids (The 20-AA Master Table)

Every amino acid shares the same backbone: an α-carbon with an H, a protonated amino group (NH₃⁺), a deprotonated carboxyl group (COO⁻), and an R group. All standard AAs are chiral and exist as L-isomers in proteins, except glycine (R = H, achiral). Only proline has a secondary amine (a cyclic imino group) that kinks protein chains.

AA ($\frac{3}{1}$)	Side Chain Class	Essential?	R-group pKa
Glycine (Gly, G)	Nonpolar (H only, achiral)	No	-
Alanine (Ala, A)	Nonpolar	No	-
Valine (Val, V)	Nonpolar, branched	Yes	-
Leucine (Leu, L)	Nonpolar, branched	Yes	-
Isoleucine (Ile, I)	Nonpolar, branched	Yes	-
Methionine (Met, M)	Nonpolar, sulfur (no S-H)	Yes	-
Proline (Pro, P)	Nonpolar, cyclic imino	No	-
Phenylalanine (Phe, F)	Nonpolar, aromatic	Yes	-
Tryptophan (Trp, W)	Nonpolar, aromatic (indole)	Yes	-
Serine (Ser, S)	Polar, hydroxyl	No	-
Threonine (Thr, T)	Polar, hydroxyl	Yes	-
Cysteine (Cys, C)	Polar, thiol (forms S-S)	No	~8.3
Tyrosine (Tyr, Y)	Polar, aromatic phenol	No	~10.1
Asparagine (Asn, N)	Polar, amide	No	-
Glutamine (Gln, Q)	Polar, amide	No	-
Aspartate (Asp, D)	Acidic	No	~3.9
Glutamate (Glu, E)	Acidic	No	~4.1
Lysine (Lys, K)	Basic	Yes	~10.5
Arginine (Arg, R)	Basic (guanidinium)	Conditional	~12.5
Histidine (His, H)	Basic, aromatic imidazole	Yes	~6.0

α-COOH pKa ≈ 2 and α-NH₃⁺ pKa ≈ 9-10 for every AA. Only the R-group pKa varies.

Henderson-Hasselbalch tells you the protonation state at any pH:

Titration curve of an AA has two (or three, if ionizable R) plateaus at each pKa, separated by steep rises. The pI sits at the midpoint between the two pKa’s that bracket the zwitterion.

Histidine (pKa ~6) is the only AA that titrates near physiological pH 7.4. That is why His is in virtually every enzyme active site (acid/base catalysis), and why it is the buffer in hemoglobin (the Bohr effect).

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2. Protein Structure

Primary = linear sequence of AAs linked by peptide bonds (amide linkages formed by dehydration). The peptide bond has partial double-bond character from resonance, so it is planar and rigid. Reading direction is N-terminus → C-terminus.

Secondary = local folding stabilized by backbone H-bonds (not side chains).

• α-helix: right-handed spiral, ~3.6 residues per turn, C=O of residue n H-bonds to N-H of residue n+4. Side chains project outward. Broken by proline (kink) and long runs of glycine (too flexible).
• β-sheet: extended strands aligned side by side, H-bonds between adjacent backbones. Antiparallel sheets are more stable than parallel.
• Turns and loops: short reversals, often involve Gly and Pro.

Tertiary = overall 3D fold of one polypeptide chain. Driven by the hydrophobic effect (nonpolar side chains buried, polar on surface). Additional stabilizers: H-bonds, ionic bonds (salt bridges), disulfide bonds (covalent Cys-Cys), van der Waals.

Quaternary = assembly of multiple subunits (e.g., hemoglobin α₂β₂, DNA polymerase holoenzyme).

Denaturation = loss of higher-order structure while primary stays intact. Agents: heat, extreme pH, urea and guanidinium (disrupt H-bonds), SDS (disrupts hydrophobic interactions), β-mercaptoethanol (reduces S-S). Small denatured proteins can spontaneously refold (Anfinsen experiment with ribonuclease).

Common motifs and domains: helix-turn-helix, leucine zipper, zinc finger (all DNA-binding transcription factor motifs), Rossmann fold (nucleotide binding), Greek key, β-barrel.

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3. Nonenzymatic Protein Function

Motor proteins (use ATP for motion):

• Myosin walks along actin (muscle contraction, cytokinesis)
• Kinesin walks toward the plus end of microtubules (anterograde transport)
• Dynein walks toward the minus end (retrograde transport, axonemal beating)

Structural proteins:

• Collagen: triple helix of three α-chains in a Gly-X-Y repeat (X often Pro, Y often hydroxyproline). Vitamin C is required by prolyl hydroxylase to hydroxylate Pro; deficiency causes scurvy.
• Keratin: intermediate filament, hair/nails/skin.
• Elastin: cross-linked via desmosine; gives tissues recoil.
• Actin and tubulin: cytoskeleton.

Transport proteins: hemoglobin (O₂/CO₂), myoglobin (muscle O₂ storage), albumin (plasma carrier).

Hemoglobin (α₂β₂, four heme groups each with Fe²⁺):

• Cooperative O₂ binding: T state (taut, low affinity) ↔ R state (relaxed, high affinity). First O₂ shifts the tetramer toward R and boosts affinity for the next three. Produces the sigmoidal dissociation curve.
• Right shift (unloads O₂ to tissues): ↑ CO₂, ↑ H⁺ (↓ pH), ↑ temperature, ↑ 2,3-BPG. This is the Bohr effect.
• Left shift (holds O₂): opposite conditions, plus fetal Hb (HbF, α₂γ₂) which binds 2,3-BPG poorly so it pulls O₂ from maternal blood.

Myoglobin = single subunit, hyperbolic binding curve (Michaelis-Menten-shaped), much higher O₂ affinity than hemoglobin at every $P_{O}$₂. Stores and releases O₂ in muscle.

Antibodies (immunoglobulins): Y-shaped with 2 heavy + 2 light chains joined by disulfide bonds. Fab region (variable) binds antigen; Fc region (constant) mediates effector function. Classes: IgG, IgM, IgA, IgE, IgD.

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4. Enzymes (Mechanism and Kinetics)

Enzymes lower activation energy. They do not change ΔG, Keq, or the position of equilibrium. They accelerate forward and reverse reactions equally.

Six enzyme classes (know the naming convention):

#	Class	What It Does	Examples
1	Oxidoreductase	Redox	Dehydrogenases, oxidases, reductases
2	Transferase	Move a functional group	Kinases (phosphate), transaminases
3	Hydrolase	Cleave using H₂O	Peptidases, phosphatases, lipases
4	Lyase	Cleave without water or redox	Aldolase, decarboxylases
5	Isomerase	Rearrange	Mutases, epimerases, racemases
6	Ligase	Join two molecules, uses ATP	DNA ligase, carboxylases

Cofactor = any non-protein helper. Coenzyme = an organic cofactor, often derived from a vitamin. Apoenzyme + cofactor = holoenzyme.

Vitamin	Coenzyme	Role
B₁ (thiamine)	TPP	Aldehyde transfer (PDH, α-KG DH)
B₂ (riboflavin)	FAD, FMN	2 e⁻ + 2 H⁺ carrier
B₃ (niacin)	NAD⁺, NADP⁺	Hydride (2 e⁻ + H⁺) carrier
B₅ (pantothenic acid)	Coenzyme A	Acyl group carrier
B₆ (pyridoxine)	PLP	Transamination, decarboxylation
B₇ (biotin)	Biotin	CO₂ carrier (carboxylases)
B₉ (folate)	THF	One-carbon transfers
B₁₂ (cobalamin)	Methylcobalamin	Methyl transfer, rearrangements
C (ascorbate)	-	Collagen hydroxylation

Inhibition summary (commit this to memory):

Type	Binds	Apparent Vmax	Apparent Km	Lineweaver-Burk
Competitive	Active site (competes with S)	Unchanged	↑	Shared y-intercept
Noncompetitive	Allosteric (both E and ES equally)	↓	Unchanged	Shared x-intercept
Uncompetitive	ES complex only	↓	↓ (by same factor)	Parallel lines
Mixed	E and ES unequally	↓	↑ or ↓	Intersect off-axes

Reversibility: competitive inhibition can be overcome by ↑ [S]. Noncompetitive, uncompetitive, and mixed cannot.

Allosteric regulation = effectors bind sites distinct from the active site and shift T/R equilibrium. Produces sigmoidal kinetic curves (cooperative, like hemoglobin). Positive effectors shift toward R (more active); negative effectors toward T.

Feedback inhibition = downstream product inhibits an upstream, usually committed, step. Example: CTP inhibits aspartate transcarbamoylase in pyrimidine synthesis.

Zymogens = inactive precursors, activated by proteolytic cleavage. Examples: pepsinogen → pepsin, trypsinogen → trypsin, chymotrypsinogen → chymotrypsin, prothrombin → thrombin, most coagulation factors.

Isozymes = different gene products that catalyze the same reaction but differ in kinetics or tissue distribution. Hexokinase (most tissues, low Km, inhibited by G6P) vs. glucokinase (liver and pancreatic β-cells, high Km, not feedback-inhibited). LDH, creatine kinase, and alkaline phosphatase isoforms are used as clinical markers.

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5. Carbohydrate Structure

Monosaccharides have 3 to 7 carbons. Aldoses have a C=O at C1 (glucose, galactose, ribose). Ketoses have C=O at C2 (fructose). Stereochemistry by Fischer projection: D (OH on the last chiral C on the right) vs. L (left). All human sugars are D.

Cyclic forms: the C=O of the open chain reacts intramolecularly with an OH to form a hemiacetal (aldose) or hemiketal (ketose). The new chiral center at C1 (or C2) is the anomeric carbon: α has the OH below the ring (axial for glucose), β has it above (equatorial). Mutarotation = interconversion of α and β through the open chain.

Disaccharides (glycosidic bonds between anomeric C of one sugar and OH of another):

Name	Bond	Components
Maltose	α-1,4	Glucose-glucose
Lactose	β-1,4	Galactose-glucose
Sucrose	α,β-1,2	Glucose-fructose
Cellobiose	β-1,4	Glucose-glucose

Reducing sugars have a free anomeric carbon (hemiacetal) that can open to an aldehyde and reduce Tollens’ or Benedict’s reagent. Glucose, galactose, fructose, maltose, lactose are reducing. Sucrose is not (both anomeric carbons are locked in the glycosidic bond).

Polysaccharides:

• Starch (plant energy storage): amylose (linear α-1,4) + amylopectin (α-1,4 with α-1,6 branches ~every 24-30 residues).
• Glycogen (animal energy storage): like amylopectin but branched every 8-12 residues, for faster mobilization.
• Cellulose (plant structural): β-1,4 glucose. Humans lack β-glucosidase so cannot digest it. Gut bacteria in ruminants can.
• Chitin: β-1,4-linked N-acetylglucosamine (fungal walls, arthropod exoskeletons).

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6. Biological Membranes

Fluid mosaic: phospholipid bilayer + embedded proteins + cholesterol + carbohydrate labels.

Cholesterol buffers fluidity: at high T it packs between tails and stiffens; at low T it spaces them and keeps the membrane fluid.

Lipid rafts: cholesterol- and sphingolipid-rich microdomains that act as signaling platforms and entry points for some viruses.

Membrane proteins:

• Integral (intrinsic): span the bilayer, have hydrophobic transmembrane domains (often α-helices).
• Peripheral (extrinsic): attached to one face by non-covalent interactions, removable with salt or pH changes.
• Lipid-anchored: attached via GPI anchors or prenyl groups.

Transport quick table:

Type	ATP?	Direction	Example
Simple diffusion	No	Down gradient	O₂, CO₂, steroids
Facilitated diffusion	No	Down gradient	Glucose via GLUT, ion channels
Osmosis	No	Water, down water potential	Aquaporins
Primary active	Yes (direct)	Against gradient	Na⁺/K⁺ ATPase (3 out, 2 in)
Secondary active	Indirect	Couples to ion gradient	SGLT (Na⁺/glucose)
Endocytosis / exocytosis	Yes (bulk)	In / out	Receptor-mediated, synaptic release

Membrane potential: resting ~-70 mV in neurons. Dominated by K⁺ leak. Nernst equation gives equilibrium potential for a single ion:

$$E_\text{ion} = \frac{RT}{zF}\ln\frac{[\text{ion}]_\text{out}}{[\text{ion}]_\text{in}} \approx \frac{61~\text{mV}}{z}\log\frac{[\text{out}]}{[\text{in}]}~\text{(at 37°C)}$$

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7. Lipid Structure

Fatty acids = long hydrocarbon chain + -COOH. Chain length and saturation set the melting point.

• Saturated: no C=C, straight, high mp (solid, e.g., butter, palmitate C16:0).
• Unsaturated: one or more C=C, cis creates kinks, lower mp (liquid, e.g., oleate C18:1).
• Trans (industrial hydrogenation): straight like saturated, solid, raise LDL.

Essential fatty acids: linoleic acid (ω-6) and α-linolenic acid (ω-3). “ω-n” numbers from the methyl end.

Triacylglycerol (TAG) = glycerol + 3 fatty acid esters. Primary energy storage (more than twice the energy density of carbs).

Phospholipids = glycerol + 2 FAs + phosphate + head group (choline, ethanolamine, serine, inositol). Amphipathic: membrane building blocks.

Sphingolipids = sphingosine backbone instead of glycerol. Ceramide (sphingosine + FA) + head group → sphingomyelin, cerebrosides, gangliosides. Enriched in nervous tissue, myelin.

Steroids = four fused rings (3 six-membered + 1 five-membered). Include cholesterol, bile salts, steroid hormones (cortisol, aldosterone, estrogen, testosterone, progesterone), vitamin D.

Terpenes = built from isoprene (C5) units. Vitamins A, E, K are terpene-derived.

Eicosanoids = 20-carbon signaling lipids from arachidonic acid: prostaglandins, thromboxanes, leukotrienes. COX inhibitors (aspirin, NSAIDs) block prostaglandin synthesis.

Lipoproteins (shuttle lipids in blood, ordered least to most dense):

Lipoprotein	Carries	Role
Chylomicrons	Dietary TAG	Gut → tissues
VLDL	Endogenous TAG	Liver → tissues
IDL	Intermediate	Transition species
LDL	Cholesterol	Liver → tissues (“bad”)
HDL	Cholesterol	Tissues → liver (“good”)

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8. Glycolysis (Cytosol)

Net per glucose: glucose + 2 NAD⁺ + 2 ADP + 2 Pᵢ → 2 pyruvate + 2 NADH + 2 ATP + 2 H₂O + 2 H⁺.

The 10 steps (and why each matters):

1. Glucose + ATP → Glucose-6-P (hexokinase; glucokinase in liver). Uses 1 ATP. Irreversible.
2. G6P → Fructose-6-P (phosphoglucose isomerase).
3. F6P + ATP → Fructose-1,6-bisphosphate (PFK-1, rate-limiting). Uses 1 ATP. Irreversible.
4. F1,6BP → DHAP + G3P (aldolase).
5. DHAP ↔ G3P (triose phosphate isomerase).
6. G3P + NAD⁺ + Pᵢ → 1,3-BPG + NADH (G3P dehydrogenase). 2 NADH per glucose.
7. 1,3-BPG + ADP → 3-PG + ATP (phosphoglycerate kinase). Substrate-level phosphorylation.
8. 3-PG → 2-PG (phosphoglycerate mutase).
9. 2-PG → PEP + H₂O (enolase).
10. PEP + ADP → Pyruvate + ATP (pyruvate kinase). Substrate-level phosphorylation. Irreversible.

Two ATPs invested (steps 1, 3) and four ATPs produced (two each at steps 7 and 10) → net +2 ATP. Two NADH.

Three irreversible, regulated steps:

• Hexokinase: inhibited by G6P (product inhibition). Liver isoform glucokinase has high Km and Vmax, is not product-inhibited, and lets the liver soak up glucose only when it is plentiful.
• PFK-1 (rate-limiting): activated by AMP and F-2,6-BP; inhibited by ATP and citrate. F-2,6-BP is made by PFK-2, which is active in the fed state (insulin) and inactive in fasting (glucagon). This is the main fed/fasted switch.
• Pyruvate kinase: activated by F-1,6-BP (feed-forward); inhibited by ATP and alanine; inactivated by glucagon via PKA phosphorylation in liver.

Fates of pyruvate:

• Aerobic: → acetyl-CoA via PDH → TCA.
• Anaerobic (no O₂ or limited ETC, e.g., exercising muscle, RBCs): → lactate via lactate dehydrogenase (regenerates NAD⁺).
• Yeast fermentation: → ethanol + CO₂ (two steps).
• Gluconeogenesis: → oxaloacetate via pyruvate carboxylase (biotin-dependent).
• Transamination: → alanine.

Why fermentation matters: glycolysis needs NAD⁺. In low-O₂ conditions, the ETC cannot reoxidize NADH fast enough, so lactate/ethanol fermentation regenerates NAD⁺ to keep glycolysis running.

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9. The Citric Acid Cycle (Krebs / TCA)

Location: mitochondrial matrix. Input per turn: 1 acetyl-CoA. Per glucose: 2 turns.

The PDH bridge (pyruvate dehydrogenase complex): pyruvate + CoA + NAD⁺ → acetyl-CoA + NADH + CO₂. Matrix. Irreversible. Uses five cofactors: TPP, lipoate, CoA, FAD, NAD. Inhibited by acetyl-CoA, NADH, ATP. Activated by insulin (via PDH phosphatase).

The 8 steps (per acetyl-CoA):

1. Acetyl-CoA + OAA → citrate (citrate synthase).
2. Citrate → isocitrate (aconitase).
3. Isocitrate → α-KG + CO₂ + NADH (isocitrate DH, rate-limiting).
4. α-KG + CoA + NAD⁺ → succinyl-CoA + CO₂ + NADH (α-KG DH; same TPP/lipoate/FAD/NAD machinery as PDH).
5. Succinyl-CoA + GDP + Pᵢ → succinate + GTP (succinyl-CoA synthetase; substrate-level phosphorylation).
6. Succinate + FAD → fumarate + FADH₂ (succinate DH = Complex II of ETC, the only membrane-embedded TCA enzyme).
7. Fumarate + H₂O → malate (fumarase).
8. Malate + NAD⁺ → OAA + NADH (malate DH).

Per acetyl-CoA yield: 3 NADH, 1 FADH₂, 1 GTP, 2 CO₂ released.
Per glucose (×2 turns): 6 NADH, 2 FADH₂, 2 GTP, 4 CO₂.

Regulation: NADH, ATP, acetyl-CoA, and succinyl-CoA inhibit key enzymes. ADP and NAD⁺ activate. Ca²⁺ activates PDH and isocitrate DH in contracting muscle.

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10. Electron Transport Chain and Oxidative Phosphorylation

Location: inner mitochondrial membrane (cristae). Purpose: use NADH/FADH₂ electrons to pump protons out of the matrix; use that proton-motive force to synthesize ATP.

The complexes:

Complex	Name	Electrons from	Pumps H⁺?
I	NADH dehydrogenase	NADH → Q	Yes (4 H⁺)
II	Succinate DH	FADH₂ → Q	No (lower energy entry)
III	Cytochrome bc₁	QH₂ → cyt c	Yes (4 H⁺)
IV	Cytochrome c oxidase	cyt c → O₂ → H₂O	Yes (2 H⁺)
V	ATP synthase	Uses proton flow	-

Mobile carriers: coenzyme Q (ubiquinone) (between I/II and III) and cytochrome c (between III and IV).

O₂ is the final electron acceptor at Complex IV: ½ O₂ + 2 e⁻ + 2 H⁺ → H₂O.

ATP synthase (Complex V): F₀ rotor in the membrane (proton channel) + F₁ head in the matrix (catalytic). Proton flow down the gradient drives rotation and ATP synthesis. About 4 H⁺ per ATP made (3 through the rotor + 1 for Pᵢ transport).

P/O ratios (ATP synthesized per electron pair):

• NADH → ~2.5 ATP
• FADH₂ → ~1.5 ATP

Inhibitors:

• Complex I: rotenone
• Complex III: antimycin A
• Complex IV: cyanide (CN⁻), carbon monoxide (CO), sodium azide
• ATP synthase: oligomycin

Uncouplers (dissipate gradient as heat without making ATP): 2,4-dinitrophenol (DNP) (classic lab chemical, also a dangerous diet drug), thermogenin/UCP1 (physiological, abundant in brown adipose for cold-induced heat).

Total aerobic ATP per glucose:

• Glycolysis: +2 ATP + 2 NADH (cytosolic)
• PDH (×2): +2 NADH
• TCA (×2): +2 GTP + 6 NADH + 2 FADH₂
• Total: 4 direct + 10 NADH × 2.5 + 2 FADH₂ × 1.5 = 4 + 25 + 3 = 32 ATP (malate-aspartate shuttle)
• With glycerol-3-phosphate shuttle (muscle, brain), cytosolic NADH enters as FADH₂ → lose 1 ATP per cytosolic NADH → 30 ATP.

Older textbooks say 36-38 (they used P/O of 3 and 2). Current MCAT convention: 30-32 ATP per glucose.

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11. Fatty Acid and Amino Acid Metabolism

β-oxidation (in mitochondrial matrix; long-chain FAs enter via the carnitine shuttle, CPT-I rate-limiting and inhibited by malonyl-CoA (which signals fed state and FA synthesis)).

Each β-oxidation cycle shortens the FA by 2 carbons (releasing one acetyl-CoA) and produces 1 NADH + 1 FADH₂.

Palmitate (C16) math:

• 7 cycles → 8 acetyl-CoA + 7 NADH + 7 FADH₂
• Activation cost: 2 ATP equivalents (ATP → AMP + 2 Pᵢ)
• 8 acetyl-CoA × 10 ATP = 80
• 7 NADH × 2.5 = 17.5
• 7 FADH₂ × 1.5 = 10.5
• Total: 80 + 17.5 + 10.5 - 2 = 106 ATP

Ketogenesis (liver mitochondria, fasting/starvation/low-carb/diabetic ketoacidosis): excess acetyl-CoA → acetoacetate + β-hydroxybutyrate + acetone. Used by brain, heart, skeletal muscle when glucose is low. Liver cannot reuse them (no thiophorase/β-ketoacyl-CoA transferase).

Urea cycle (liver): NH₃ + CO₂ + aspartate → urea + fumarate. Costs 3 ATP (4 high-energy phosphate bonds) per urea.

1. CPS I (matrix, rate-limiting, activated by N-acetylglutamate): NH₃ + CO₂ + 2 ATP → carbamoyl phosphate.
2. Ornithine + carbamoyl-P → citrulline (exits to cytosol).
3. Citrulline + aspartate + ATP → argininosuccinate.
4. Argininosuccinate → arginine + fumarate.
5. Arginine + H₂O → ornithine + urea (urea to kidney, ornithine back to matrix).

Transamination (most AAs): α-amino acid + α-KG ↔ α-keto acid + glutamate (via PLP-dependent aminotransferases, e.g., ALT, AST; liver markers).

Deamination: glutamate dehydrogenase cleaves glutamate → α-KG + NH₃ (feeds urea cycle).

Glucogenic vs ketogenic:

• Glucogenic (feed into gluconeogenesis, most AAs): e.g., Ala → pyruvate; Asp → OAA; Glu → α-KG.
• Purely ketogenic (only Leu and Lys): cannot make glucose.
• Both (Ile, Phe, Trp, Tyr, Thr).

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12. Bioenergetics and Regulation

ATP hydrolysis: ATP + H₂O → ADP + Pᵢ has ΔG°′ ≈ -30.5 kJ/mol (-7.3 kcal/mol). Actual cellular ΔG ≈ -50 kJ/mol (due to concentrations). The phosphoanhydride bonds between phosphates carry the energy.

Other high-energy phosphates (ΔG°′ of hydrolysis more negative than ATP):

• PEP (≈ -62 kJ/mol, the highest)
• 1,3-bisphosphoglycerate
• Creatine phosphate (muscle ATP buffer)

ADP + AMP as signals: low ATP → high AMP activates AMPK (master catabolic kinase); high ATP suppresses it.

Coupled reactions: an unfavorable reaction (e.g., AA activation for translation) is driven by coupling to ATP hydrolysis.

Hormonal control (the fed/fasted master table):

State	Insulin	Glucagon	Dominant Direction
Fed	High	Low	Anabolism: glycogen, TAG, protein synthesis
Fasted	Low	High	Catabolism: glycogenolysis → gluconeogenesis → ketogenesis
Exercise	Low	High + ↑ epi	Glycogenolysis, lipolysis

Insulin activates (fed): GLUT4 insertion, glycogen synthase, PFK-2 (↑ F-2,6-BP → ↑ PFK-1), acetyl-CoA carboxylase (ACC, for FA synthesis), HMG-CoA reductase.
Insulin inactivates: glycogen phosphorylase, hormone-sensitive lipase.

Glucagon/epinephrine activate (fasted/stressed, via cAMP/PKA): glycogen phosphorylase, hormone-sensitive lipase (lipolysis), PEPCK (gluconeogenesis). Inactivate: glycogen synthase, PFK-2, pyruvate kinase.

Cori cycle (lactate shuttle): muscle glycolysis → lactate → blood → liver gluconeogenesis → glucose → blood → muscle. Offloads the ATP cost to the liver (net: liver spends 6 ATP to make glucose; muscle gains 2 ATP from glycolysis).

Alanine cycle: similar, but muscle sends alanine (NH₃ carrier) instead of lactate.

Pentose phosphate pathway (PPP / HMP shunt) (cytosol, two phases):

• Oxidative: G6P + 2 NADP⁺ → ribulose-5-P + 2 NADPH + CO₂. G6PDH is rate-limiting; deficiency causes hemolytic anemia (low glutathione-SH → RBCs cannot neutralize ROS).
• Non-oxidative: reversible sugar interconversions that yield ribose-5-P (for nucleotide synthesis) or feed back into glycolysis as F6P/G3P.
• Purpose: NADPH (for reductive biosynthesis, fatty acid/cholesterol synth, glutathione regeneration) and ribose-5-P (nucleic acids).

Rate-limiting enzymes by pathway (high-yield):

Pathway	Rate-limiting enzyme
Glycolysis	PFK-1
Gluconeogenesis	Fructose-1,6-bisphosphatase
TCA cycle	Isocitrate dehydrogenase
Glycogen synthesis	Glycogen synthase
Glycogen breakdown	Glycogen phosphorylase
FA synthesis	Acetyl-CoA carboxylase (ACC)
FA β-oxidation	CPT-I (carnitine shuttle)
Cholesterol synthesis	HMG-CoA reductase (statin target)
Ketogenesis	HMG-CoA synthase
Urea cycle	CPS I
Pentose phosphate	G6PDH

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13. Aerobic Respiration, Summarized

Compartments:

• Cytosol: glycolysis, pentose phosphate pathway, fatty acid synthesis, gluconeogenesis (most steps), urea cycle (second half).
• Mitochondrial matrix: PDH, TCA, β-oxidation, ketogenesis, urea cycle (first half).
• Inner mitochondrial membrane: ETC + ATP synthase.

Shuttle systems (cytosolic NADH cannot cross the inner membrane):

• Malate-aspartate shuttle (liver, heart, kidney): preserves NADH on the matrix side. ~2.5 ATP per cytosolic NADH.
• Glycerol-3-phosphate shuttle (muscle, brain): converts to FADH₂. ~1.5 ATP per.

ATP tally per glucose:

Step	Direct ATP (GTP)	NADH	FADH₂
Glycolysis	+2	2 (cytosolic)	-
PDH (×2 pyruvate)	0	2	-
TCA (×2 turns)	2	6	2
Total	4	10	2

ATP from electron carriers: (10 × 2.5) + (2 × 1.5) = 28. Grand total = 32 (malate-aspartate) or 30 (glycerol-3-phosphate).

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14. DNA and Biotechnology

DNA replication enzymes:

Enzyme	Job
Helicase	Unwinds the double helix
Topoisomerase / DNA gyrase	Relieves supercoiling ahead of fork
Single-strand binding proteins	Prevent reannealing
Primase	Lays an RNA primer
DNA polymerase III (prokaryote)	Main replicative polymerase, 5’→3’ synthesis, 3’→5’ proofreading
DNA polymerase I (prokaryote)	Removes RNA primer, fills gap
DNA polymerases δ, α, ε (eukaryote)	Replicative + primer
DNA ligase	Seals nicks (Okazaki fragments on lagging strand)
Telomerase	Extends 3’ telomere with RNA template (a reverse transcriptase)

Mutation types:

• Silent: codon change, same AA.
• Missense: codon change → different AA.
• Nonsense: new stop codon → truncated protein.
• Frameshift: insertion/deletion not a multiple of 3.
• Transition (purine ↔ purine or pyr ↔ pyr) vs transversion (purine ↔ pyrimidine, rarer and more damaging).

DNA repair:

• Mismatch repair (MMR): after replication, fixes misincorporated bases.
• Nucleotide excision repair (NER): removes bulky lesions (UV-induced thymine dimers).
• Base excision repair (BER): glycosylase removes small damaged base; AP endonuclease cuts; polymerase + ligase fill.
• Double-strand break repair: non-homologous end joining (NHEJ, error-prone) vs homologous recombination (HR, accurate, S/G₂).

PCR (polymerase chain reaction): 3 steps, 25-35 cycles, exponential amplification.

1. Denature (~95 °C) - melt dsDNA
2. Anneal (~55 °C) - primers bind
3. Extend (~72 °C) - Taq polymerase synthesizes

After n cycles, you have ~2ⁿ copies.

Gel electrophoresis: DNA is negatively charged (phosphate backbone), migrates toward the + anode. Smaller fragments run farther. Agarose for DNA; SDS-PAGE for proteins (SDS coats proteins with uniform negative charge → separates by size alone; β-mercaptoethanol breaks disulfides).

Blotting (detect specific molecules after gel):

• Southern: DNA probe for DNA
• Northern: DNA probe for RNA
• Western: antibody probe for protein

Sanger sequencing: chain termination with fluorescent ddNTPs (lack 3’-OH → polymerase stops). Read peaks on a capillary gel for the sequence.

Next-gen sequencing (Illumina): massively parallel, millions of short reads, barcoded samples.

Restriction enzymes: bacterial endonucleases that cut at palindromic sites. EcoRI recognizes GAATTC and leaves 5’ “sticky ends.” Used to cut and paste DNA into vectors.

Cloning vectors: plasmids (small circular dsDNA, origin of replication + selection marker + multiple cloning site), phages, cosmids, BACs, YACs.

CRISPR-Cas9: guide RNA (gRNA) directs Cas9 to a genomic target; Cas9 makes a double-strand break; cell repairs via NHEJ (knockout) or HDR with template (precise edit).

DNA libraries: genomic (all DNA, introns included) vs cDNA (made from mRNA via reverse transcriptase; only expressed, spliced genes, no introns).

Gene therapy: delivery of a functional gene via viral vector (AAV, lentivirus, adenovirus) or lipid nanoparticle.

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15. RNA and the Genetic Code

Transcription (nucleus in eukaryotes): RNA polymerase II makes mRNA. (Pol I makes rRNA, Pol III makes tRNA and 5S rRNA.) Uses the DNA template (antisense) strand; the resulting mRNA matches the coding strand sequence (with U replacing T).

Promoters: TATA box (~-25), CAAT box, GC box. General transcription factors assemble at the promoter; enhancers/silencers act at a distance through DNA looping.

Post-transcriptional processing (eukaryotes only):

• 5’ cap: 7-methylguanosine, added co-transcriptionally; needed for ribosome recruitment and stability.
• 3’ poly(A) tail: ~200 adenines, added after cleavage at the poly(A) signal.
• Splicing: spliceosome (snRNPs + proteins) removes introns (GU-AG rule), joins exons. Alternative splicing produces multiple proteins from one gene.

RNA types:

• mRNA: codes for protein.
• tRNA: carries amino acid; anticodon pairs with codon.
• rRNA: ribosome structure + catalysis (peptidyl transferase is a ribozyme).
• snRNA: spliceosome.
• miRNA / siRNA: gene silencing (RISC complex).

Genetic code:

• Degenerate/redundant: multiple codons code for most AAs.
• Unambiguous: each codon codes for one AA.
• Nonoverlapping.
• Near-universal (mitochondria have minor exceptions).
• Start codon: AUG (Met; fMet in prokaryotes).
• Stop codons: UAA, UAG, UGA (do not code for any AA).
• Wobble: the 3rd codon position pairs flexibly with the tRNA anticodon, which is why a single tRNA can read multiple codons.

Translation (cytosol; co-translational on rough ER for secreted/membrane proteins):

• Initiation: small subunit + mRNA + initiator Met-tRNA find AUG; large subunit joins. Uses initiation factors + GTP.
• Elongation: charged tRNA enters A site; peptide bond forms (peptidyl transferase, a ribozyme); ribosome translocates (A → P → E); uses GTP.
• Termination: stop codon recognized by release factors; peptide released; ribosome dissociates.

Post-translational modifications:

• Phosphorylation (Ser/Thr/Tyr, reversible, major signaling switch)
• Glycosylation (N-linked on Asn, O-linked on Ser/Thr; in ER/Golgi)
• Acetylation (Lys; histones, transcription regulation)
• Methylation (Lys, Arg)
• Ubiquitination (tags proteins for 26S proteasome degradation)
• Disulfide bond formation (Cys-Cys, in ER)
• Proteolytic cleavage (activates zymogens)
• Lipidation (prenylation, palmitoylation; membrane anchoring)

Signal peptides: N-terminal sequences that target proteins to the rough ER. SRP (signal recognition particle) binds, pauses translation, and docks the ribosome on the ER.

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16. Master Pathway and Formula Sheet

ATP yields (summary):

• Glycolysis: +2 ATP, +2 NADH, 2 pyruvate
• PDH (×2 pyruvate): +2 NADH
• TCA (×2 turns): +2 GTP, +6 NADH, +2 FADH₂
• Aerobic total per glucose: ~30-32 ATP
• β-oxidation of palmitate (C16): ~106 ATP
• Each β-oxidation cycle: 1 NADH + 1 FADH₂ + 1 acetyl-CoA
• Each NADH via ETC: ~2.5 ATP; each FADH₂: ~1.5 ATP

Rate-limiting enzymes (repeat, because they are always tested):
Glycolysis → PFK-1; gluconeogenesis → F-1,6-BPase; TCA → isocitrate DH; FA synthesis → ACC; FA oxidation → CPT-I; cholesterol synthesis → HMG-CoA reductase; urea cycle → CPS I; PPP → G6PDH.

pKa cheat sheet (for buffer and titration questions):

Group	pKa
α-COOH (any AA)	~2
α-NH₃⁺ (any AA)	~9-10
Asp, Glu side chain	~4
His imidazole	~6
Cys thiol	~8
Tyr phenol	~10
Lys ε-amine	~10.5
Arg guanidinium	~12.5
H₂PO₄⁻ / HPO₄²⁻ (biological phosphate)	~7.2
H₂CO₃ / HCO₃⁻ (bicarbonate)	~6.1

Vitamin → coenzyme (high-yield):

Vitamin	Coenzyme (function)
B₁	TPP (PDH, α-KG DH, transketolase)
B₂	FAD / FMN (redox)
B₃	NAD⁺ / NADP⁺ (redox; NADP used in biosynthesis)
B₅	CoA (acyl transfer)
B₆	PLP (transamination, decarboxylation)
B₇	Biotin (carboxylation)
B₉	THF (one-carbon units, thymidine synthesis)
B₁₂	Methylcobalamin (homocysteine → Met; methylmalonyl-CoA mutase)

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17. The 25 Facts Most Likely to Show Up on Test Day

1. Glycolysis yields 2 ATP + 2 NADH + 2 pyruvate per glucose.
2. PFK-1 is the rate-limiting step of glycolysis; activated by AMP and F-2,6-BP; inhibited by ATP and citrate.
3. PDH links glycolysis to TCA; requires 5 cofactors (TPP, lipoate, CoA, FAD, NAD); irreversible; activated by insulin, inhibited by acetyl-CoA/NADH/ATP.
4. TCA per acetyl-CoA: 3 NADH + 1 FADH₂ + 1 GTP + 2 CO₂.
5. Isocitrate DH is the rate-limiting step of the TCA cycle.
6. NADH → ~2.5 ATP; FADH₂ → ~1.5 ATP (modern P/O).
7. Total aerobic yield per glucose: ~30-32 ATP (30 with glycerol-3-P shuttle, 32 with malate-aspartate).
8. ETC inhibitors: rotenone (I), antimycin A (III), cyanide/CO (IV), oligomycin (ATP synthase). DNP is an uncoupler.
9. Start codon = AUG (Met); stop codons = UAA, UAG, UGA.
10. Genetic code is degenerate, unambiguous, near-universal, and uses wobble in the 3rd position.
11. Michaelis-Menten: Km = [S] at half Vmax. Low Km = high affinity.
12. Competitive inhibition raises apparent Km, Vmax unchanged. Noncompetitive lowers Vmax, Km unchanged. Uncompetitive lowers both.
13. Hemoglobin cooperative binding → sigmoidal; right-shifted by CO₂/H⁺/heat/2,3-BPG (Bohr effect). Fetal Hb is left-shifted.
14. Disulfide bonds form between Cys residues; stabilize tertiary/quaternary structure.
15. Essential AAs: PVT TIM HaLL (9 AAs); Arg is conditionally essential.
16. pI = pH at which the amino acid has zero net charge. Compute by averaging the two pKa’s flanking the zwitterion.
17. β-oxidation of palmitate (C16) yields ~106 ATP; each cycle releases acetyl-CoA + 1 NADH + 1 FADH₂.
18. Ketogenesis occurs in the liver during fasting or diabetic ketoacidosis. Brain adapts to β-hydroxybutyrate after ~3 days of fasting.
19. Urea cycle costs 3 ATP (4 high-energy bonds) per urea; CPS I is the rate-limiting, matrix-located enzyme.
20. Liver glycogen releases glucose to blood (liver has glucose-6-phosphatase); muscle glycogen is used locally (no G6Pase).
21. Cori cycle: lactate (muscle) → glucose (liver). Alanine cycle: alanine carries N and C to liver.
22. Pentose phosphate pathway produces NADPH + ribose-5-P. G6PDH deficiency → hemolytic anemia (low glutathione).
23. DNA polymerase synthesizes 5’ → 3’ only; leading strand is continuous, lagging uses Okazaki fragments sealed by ligase.
24. PCR cycles: denature (~95 °C) → anneal (~55 °C) → extend (~72 °C, Taq).
25. Cholesterol buffers membrane fluidity; HMG-CoA reductase is the rate-limiting step of cholesterol synthesis (statin target).

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18. Test-Day Mnemonics

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Next Steps

If something on this page feels unfamiliar, open the corresponding chapter and re-study the mechanism behind the fact. Biochemistry rewards two things equally: raw recall of charts (amino acids, enzyme classes, ATP yields) and a mechanistic picture of pathways that lets you reason about regulation when the MCAT gives you a novel enzyme or mutant. This cheat sheet gets you to 80% recall on test day; the full 12 chapters give you the reasoning you need for passage-based questions. Bookmark this page and return to it the night before every practice test and on the morning of the real exam.