Amino Acids
Every amino acid = central α-carbon + amino group (–NH2) + carboxyl group (–COOH) + hydrogen + R group (side chain). Only the R group differs.
The 20 standard amino acids
| Name | 3-letter | 1-letter | Class | Charge (pH 7) | Key characteristics |
|---|---|---|---|---|---|
| Glycine | Gly | G | Nonpolar | Neutral | R = H. Smallest, achiral, very flexible; fits tight turns. |
| Alanine | Ala | A | Nonpolar | Neutral | R = CH₃. Small, hydrophobic, helix-friendly. |
| Valine * | Val | V | Nonpolar, branched | Neutral | Hydrophobic core. Glu→Val swap causes sickle-cell. |
| Leucine * | Leu | L | Nonpolar, branched | Neutral | Very common; buried in hydrophobic core; leucine zippers. |
| Isoleucine * | Ile | I | Nonpolar, branched | Neutral | Hydrophobic, two chiral centers. |
| Methionine * | Met | M | Nonpolar, sulfur | Neutral | Contains S (thioether). Start codon AUG; first residue of every protein. |
| Proline | Pro | P | Nonpolar, cyclic | Neutral | Side chain bonds back to N (imino acid). Rigid — helix breaker, found in turns. |
| Phenylalanine * | Phe | F | Nonpolar, aromatic | Neutral | Big hydrophobic benzene ring; stacking interactions. |
| Tryptophan * | Trp | W | Nonpolar, aromatic | Neutral | Largest residue, indole ring; absorbs at 280 nm (protein quantitation). |
| Serine | Ser | S | Polar uncharged | Neutral | –OH. Phosphorylation site; serine-protease active sites. |
| Threonine * | Thr | T | Polar uncharged | Neutral | –OH + methyl. Phosphorylation site; O-glycosylation. |
| Cysteine | Cys | C | Polar, sulfur | Neutral (pKa 8.3) | –SH thiol. Two Cys form a disulfide bond — only covalent bond in tertiary structure. |
| Tyrosine | Tyr | Y | Polar, aromatic | Neutral (pKa 10.1) | Aromatic + –OH; phosphorylation target; absorbs at 280 nm. |
| Asparagine | Asn | N | Polar uncharged | Neutral | Amide of Asp; N-linked glycosylation site. |
| Glutamine | Gln | Q | Polar uncharged | Neutral | Amide of Glu; nitrogen transport. |
| Aspartate | Asp | D | Acidic | Negative (pKa 3.9) | Carboxylate side chain; salt bridges, metal binding, catalysis. |
| Glutamate | Glu | E | Acidic | Negative (pKa 4.3) | One CH₂ longer than Asp; neurotransmitter. |
| Lysine * | Lys | K | Basic | Positive (pKa 10.5) | Long –NH₃⁺ chain; binds DNA backbone; acetylation site on histones. |
| Arginine | Arg | R | Basic | Positive (pKa 12.5) | Guanidinium — most basic, positive at nearly any pH; DNA binding. |
| Histidine * | His | H | Basic, aromatic | Partly + (pKa 6.0) | Only side chain that ionizes near physiological pH — buffering + acid/base catalysis; metal coordination. |
* = essential in humans (9 total: His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val — "PVT TIM HaLL").
Grouping to memorize: 9 nonpolar (G A V L I M P F W) · 6 polar uncharged (S T C Y N Q) · 2 acidic/negative (D E) · 3 basic/positive (K R H). Charged + polar face water on the outside; nonpolar bury in the core.
Peptide bond
The Genetic Code
- Triplet: 3 mRNA bases = 1 codon = 1 amino acid. 4³ = 64 codons.
- Degenerate/redundant: 61 sense codons for 20 amino acids; most redundancy at the 3rd base (wobble).
- Unambiguous: one codon never codes for two amino acids.
- Nearly universal across all organisms (mitochondria are the exception).
- Non-overlapping, read continuously from a fixed start — insertions/deletions cause frameshifts.
- AUG = start (Met; fMet in bacteria). UAA, UAG, UGA = stop (no tRNA; release factors bind).
Codon table (mRNA 5'→3')
| 1st ↓ / 2nd → | U | C | A | G | 3rd |
|---|---|---|---|---|---|
| U | Phe (F) | Ser (S) | Tyr (Y) | Cys (C) | U |
| Phe (F) | Ser (S) | Tyr (Y) | Cys (C) | C | |
| Leu (L) | Ser (S) | STOP | STOP | A | |
| Leu (L) | Ser (S) | STOP | Trp (W) | G | |
| C | Leu (L) | Pro (P) | His (H) | Arg (R) | U |
| Leu (L) | Pro (P) | His (H) | Arg (R) | C | |
| Leu (L) | Pro (P) | Gln (Q) | Arg (R) | A | |
| Leu (L) | Pro (P) | Gln (Q) | Arg (R) | G | |
| A | Ile (I) | Thr (T) | Asn (N) | Ser (S) | U |
| Ile (I) | Thr (T) | Asn (N) | Ser (S) | C | |
| Ile (I) | Thr (T) | Lys (K) | Arg (R) | A | |
| Met (M) START | Thr (T) | Lys (K) | Arg (R) | G | |
| G | Val (V) | Ala (A) | Asp (D) | Gly (G) | U |
| Val (V) | Ala (A) | Asp (D) | Gly (G) | C | |
| Val (V) | Ala (A) | Glu (E) | Gly (G) | A | |
| Val (V) | Ala (A) | Glu (E) | Gly (G) | G |
Mutation types
| Type | What changes | Effect on protein |
|---|---|---|
| Silent | Base change, same amino acid (usually 3rd position) | None |
| Missense — conservative | New amino acid with similar chemistry (e.g. Leu→Ile) | Often tolerated |
| Missense — non-conservative | New amino acid, different chemistry (e.g. Glu→Val) | Can destroy function (sickle-cell) |
| Nonsense | Codon → STOP | Truncated, usually non-functional |
| Frameshift | Insertion/deletion not a multiple of 3 | Everything downstream garbled — usually most severe |
Central Dogma
Direction rules: nucleic acids are always synthesized 5' → 3'; the template is read 3' → 5'. Proteins are synthesized N → C.
Macromolecules
| Class | Monomer | Bond | Elements | Function / notes |
|---|---|---|---|---|
| Carbohydrates | Monosaccharide (glucose) | Glycosidic | C H O (1:2:1) | Energy + structure. Starch/glycogen = storage; cellulose/chitin/peptidoglycan = structure. |
| Lipids | Not true polymers — glycerol + fatty acids | Ester | C H O (little O) | Hydrophobic. Saturated = no C=C, solid; unsaturated = C=C kinks, liquid. Phospholipids are amphipathic → bilayer. Steroids = 4 fused rings. |
| Proteins | Amino acid | Peptide (amide) | C H O N (S) | Enzymes, structure, transport, signaling, defense. Most functionally diverse. |
| Nucleic acids | Nucleotide | Phosphodiester | C H O N P | Information storage/transfer. Nucleotide = phosphate + 5-carbon sugar + nitrogenous base. |
All polymers are built by dehydration synthesis (removes H₂O) and broken by hydrolysis (adds H₂O).
DNA vs RNA
| DNA | RNA | |
|---|---|---|
| Sugar | Deoxyribose (no 2'-OH) | Ribose (2'-OH → less stable) |
| Bases | A T G C | A U G C |
| Strands | Double helix, antiparallel | Usually single, folds on itself |
| Role | Long-term storage | mRNA message, tRNA adaptor, rRNA catalytic core |
Bonds & Non-Covalent Forces
| Interaction | Relative strength | What it is | Where it matters |
|---|---|---|---|
| Covalent (nonpolar) | Strongest (~80–100 kcal/mol) | Equal electron sharing (C–C, C–H) | Backbones of all macromolecules |
| Covalent (polar) | Strongest | Unequal sharing → partial charges (O–H, N–H) | Source of water's polarity |
| Disulfide bond | Strong covalent | Cys–S–S–Cys | Locks tertiary structure of secreted proteins |
| Ionic / salt bridge | Moderate (weak in water) | Full + attracts full – | Asp/Glu with Lys/Arg; strong when buried, shielded in water |
| Hydrogen bond | Weak (~1–5 kcal/mol), strong in bulk | H on N/O/F attracted to another N/O | DNA base pairing, α-helix, β-sheet, water properties |
| Van der Waals | Weakest | Transient dipoles, requires close contact | Tight-packed protein interiors, shape complementarity |
| Hydrophobic effect | Major driving force | Nonpolar groups cluster to free ordered water (entropy) | Protein folding, membrane bilayers |
Water: polar + H-bonding → cohesion/adhesion, high specific heat, high heat of vaporization, ice floats (less dense), universal solvent for polar/ionic solutes. Weak bonds are individually breakable but collectively decisive — that's what makes binding specific and reversible.
Base pairing
Levels of Protein Structure
| Level | What it is | Held together by | Examples |
|---|---|---|---|
| Primary | Linear amino acid sequence, N→C | Peptide bonds (covalent) | Encoded directly by the gene; determines all higher levels (Anfinsen) |
| Secondary | α-helix and β-pleated sheet (parallel/antiparallel), turns | H-bonds between backbone C=O and N–H | Keratin (α), silk fibroin (β). Pro breaks helices; Gly adds flexibility |
| Tertiary | Full 3-D fold of one polypeptide | R-group interactions: hydrophobic clustering, H-bonds, ionic/salt bridges, van der Waals, disulfides | Myoglobin; enzyme active site is formed here |
| Quaternary | Two or more folded subunits assembled | Same non-covalent forces, between chains | Hemoglobin (α₂β₂), collagen triple helix, DNA polymerase holoenzyme |
Denaturation (heat, extreme pH, urea, detergents, reducing agents) breaks weak bonds and unfolds the protein — primary structure survives, function does not. Often reversible if the sequence is intact. Structure determines function is the recurring exam point.
Enzymes, Reactions & ATP
Enzyme basics
- Biological catalyst — lowers activation energy (Ea), speeds the reaction, is not consumed and does not change ΔG or equilibrium.
- Active site binds substrate; induced fit — the site reshapes around the substrate.
- Specific for substrate and reaction. Named for what they act on: -ase.
- Sensitive to temperature and pH — beyond the optimum, denaturation kills activity.
- Cofactors = inorganic (Mg²⁺, Zn²⁺); coenzymes = organic (NAD⁺, FAD, coenzyme A — often from vitamins).
| Regulation | Binds where | Effect | Overcome by more substrate? |
|---|---|---|---|
| Competitive inhibitor | Active site | Blocks substrate binding | Yes |
| Noncompetitive / allosteric inhibitor | Allosteric site | Changes active-site shape | No |
| Allosteric activator | Allosteric site | Stabilizes the active form | — |
| Feedback inhibition | Allosteric site of the first enzyme | End product shuts down its own pathway | No |
Energy & ATP
| Term | Meaning |
|---|---|
| Exergonic (ΔG < 0) | Releases energy, spontaneous — catabolism (breakdown) |
| Endergonic (ΔG > 0) | Requires energy input — anabolism (building) |
| Coupled reaction | ATP hydrolysis drives an endergonic reaction |
| ATP structure | Adenine + ribose + 3 phosphates; energy sits in the repulsion of the negative phosphates |
| ATP → ADP + Pi | Exergonic, ≈ –7.3 kcal/mol; the cell's energy currency, constantly recycled |
| Redox | OIL RIG — Oxidation Is Loss of electrons, Reduction Is Gain. NAD⁺/FAD are electron carriers (reduced to NADH/FADH₂). |
Types of Organisms & Cell Composition
| Feature | Prokaryote (Bacteria, Archaea) | Eukaryote |
|---|---|---|
| Nucleus | None — nucleoid region | True membrane-bound nucleus |
| DNA | Single circular chromosome + plasmids | Multiple linear chromosomes with histones |
| Organelles | No membrane-bound organelles | Mitochondria, ER, Golgi, lysosomes, (chloroplasts) |
| Ribosomes | 70S (30S + 50S) | 80S (40S + 60S); 70S inside mitochondria |
| Cell wall | Peptidoglycan (bacteria) | Cellulose (plants), chitin (fungi), none in animals |
| Size | ~1–10 µm | ~10–100 µm |
| Transcription/translation | Coupled — same compartment, no introns | Separated by the nuclear envelope; mRNA processed first |
| Division | Binary fission | Mitosis / meiosis |
Organelles — structure & function
| Organelle | Function |
|---|---|
| Nucleus | Stores DNA; site of replication and transcription; bounded by a double envelope with pores |
| Nucleolus | Makes rRNA and assembles ribosomal subunits |
| Ribosome | Protein synthesis (translation); free in cytosol or bound to rough ER |
| Rough ER | Ribosome-studded; synthesizes and folds proteins for secretion or membranes |
| Smooth ER | Lipid and steroid synthesis, detoxification, Ca²⁺ storage |
| Golgi apparatus | Modifies, sorts, tags and ships proteins — the "post office" |
| Lysosome | Digestive enzymes (acidic interior); breaks down waste and worn organelles |
| Peroxisome | Breaks down fatty acids and detoxifies H₂O₂ using catalase |
| Mitochondrion | ATP production — Krebs in the matrix, ETC on the cristae; own circular DNA + 70S ribosomes |
| Chloroplast | Photosynthesis — light reactions in thylakoids, Calvin cycle in stroma; own DNA |
| Vacuole | Storage, waste, turgor pressure (large central vacuole in plants) |
| Plasma membrane | Selectively permeable phospholipid bilayer; transport and signaling (fluid mosaic model) |
| Cell wall | Rigid support — cellulose (plants), chitin (fungi), peptidoglycan (bacteria) |
| Cytoskeleton | Microfilaments (actin), intermediate filaments, microtubules — shape, transport, division |
| Centrosome / centrioles | Organizes microtubules and the mitotic spindle (animals) |
| Cilia & flagella | Movement; 9+2 microtubule arrangement |
Endosymbiotic theory: mitochondria and chloroplasts were once free-living bacteria — double membranes, circular DNA, 70S ribosomes, and they divide by binary fission.
Three domains: Bacteria, Archaea, Eukarya. Cell theory: all organisms are made of cells; the cell is the basic unit of life; cells come only from pre-existing cells. Viruses are acellular — not alive by these criteria. Elements by mass: C, H, O, N account for ~96% of living matter.
DNA Structure & Replication
- Double helix, antiparallel strands, sugar-phosphate backbone outside, bases inside.
- Backbone joined by phosphodiester bonds (5' phosphate to 3' OH); negatively charged → runs to the + electrode in a gel.
- Replication is semiconservative: each daughter duplex = 1 old + 1 new strand.
- DNA polymerase can only add to a free 3'-OH → synthesis is strictly 5'→3' and a primer is mandatory.
| Enzyme / protein | Job |
|---|---|
| Helicase | Unwinds the double helix at the origin, breaking H-bonds |
| Single-strand binding protein | Keeps separated strands from re-annealing |
| Topoisomerase / gyrase | Relieves supercoiling ahead of the fork |
| Primase | Lays down a short RNA primer to give pol a 3'-OH |
| DNA polymerase III | Main elongation enzyme, 5'→3'; proofreads with 3'→5' exonuclease |
| DNA polymerase I | Removes RNA primers, fills the gaps with DNA |
| DNA ligase | Seals nicks between Okazaki fragments (phosphodiester bond) |
| Telomerase | Extends chromosome ends in eukaryotes (end-replication problem) |
Transcription & Translation
Transcription
| Stage | What happens |
|---|---|
| Initiation | RNA polymerase binds the promoter. Bacteria: sigma factor recognizes –10 (TATAAT, Pribnow) and –35 boxes. Eukaryotes: transcription factors + TATA box recruit RNA pol II. |
| Elongation | Reads template (antisense) strand 3'→5', builds RNA 5'→3'. No primer needed. The coding/sense strand matches the mRNA (with U for T). |
| Termination | Bacteria: rho-dependent or hairpin (rho-independent). Eukaryotes: poly-A signal, then cleavage. |
| Processing (eukaryotes only) | 5' methyl-guanosine cap, 3' poly-A tail, splicing of introns by the spliceosome (snRNPs) leaving exons. Alternative splicing → multiple proteins from one gene. |
Eukaryotic polymerases: pol I → rRNA, pol II → mRNA, pol III → tRNA + 5S rRNA. Bacteria use a single RNA polymerase.
Translation
| Component | Role |
|---|---|
| mRNA | Carries codons; read 5'→3' |
| tRNA | Adaptor: anticodon pairs with the codon (antiparallel), carries the amino acid at its 3' CCA end |
| Aminoacyl-tRNA synthetase | Charges each tRNA with its correct amino acid — one per amino acid; the real "reader" of the code |
| Ribosome | rRNA + protein. A site accepts incoming charged tRNA, P site holds the growing chain, E site exits the empty tRNA |
| Peptidyl transferase | rRNA ribozyme activity in the large subunit — forms the peptide bond |
| Release factor | Recognizes a stop codon, hydrolyzes the chain off the tRNA |
Bacteria start at a Shine-Dalgarno sequence with fMet-tRNA; eukaryotes scan from the 5' cap to the first AUG (Kozak). Many ribosomes on one mRNA = a polysome. Chain grows N-terminus → C-terminus.
Gene Regulation & the Lac Operon
| Lactose | Glucose | Repressor | cAMP–CAP | Transcription |
|---|---|---|---|---|
| Absent | Present | Bound to operator | Low cAMP, no CAP | Off |
| Absent | Absent | Bound to operator | High cAMP, CAP bound | Off (repressor wins) |
| Present | Present | Released (allolactose) | Low cAMP, no CAP | Low / leaky |
| Present | Absent | Released | High cAMP, CAP bound | Maximum |
Inducer: allolactose (lab substitute: IPTG) binds the repressor and inactivates it = negative control. CAP–cAMP = positive control; glucose lowers cAMP, so glucose is used first (catabolite repression). Inducible operon = normally off, turns on for catabolism (lac). Repressible operon = normally on, turns off when the product accumulates (trp).
Cellular Respiration & Fermentation
| Stage | Location | Input | Output per glucose |
|---|---|---|---|
| Glycolysis | Cytosol (all cells, no O₂ needed) | Glucose (6C), 2 ATP invested | 2 pyruvate (3C), net 2 ATP (substrate-level), 2 NADH |
| Pyruvate oxidation | Mitochondrial matrix | 2 pyruvate | 2 acetyl-CoA, 2 NADH, 2 CO₂ |
| Krebs / citric acid cycle | Mitochondrial matrix | 2 acetyl-CoA | 6 NADH, 2 FADH₂, 2 ATP (GTP), 4 CO₂ |
| Electron transport + chemiosmosis | Inner mitochondrial membrane (plasma membrane in prokaryotes) | NADH, FADH₂, O₂ (final electron acceptor) | ~26–28 ATP, H₂O |
Totals: ~30–32 ATP per glucose. NADH ≈ 2.5 ATP, FADH₂ ≈ 1.5 ATP. All CO₂ you exhale comes from pyruvate oxidation + Krebs; all O₂ you breathe ends up as water at complex IV.
Glycolysis — step by step
Cytosol · no oxygen required · universal to nearly all life · 10 enzyme steps, split into an investment phase (spend 2 ATP) and a payoff phase (make 4 ATP).
| # | Reaction | Enzyme | Energy change |
|---|---|---|---|
| ENERGY INVESTMENT PHASE (per glucose) | |||
| 1 | Glucose → glucose-6-phosphate | Hexokinase (glucokinase in liver) | –1 ATP; phosphate traps glucose inside the cell |
| 2 | G6P → fructose-6-phosphate | Phosphoglucose isomerase | — |
| 3 | F6P → fructose-1,6-bisphosphate | Phosphofructokinase-1 (PFK-1) | –1 ATP; rate-limiting / committed step. Inhibited by ATP & citrate, activated by AMP & F-2,6-BP |
| 4 | F-1,6-BP → DHAP + G3P (two 3C sugars) | Aldolase | — |
| 5 | DHAP ⇌ G3P | Triose phosphate isomerase | Now 2 × G3P — everything below happens twice |
| ENERGY PAYOFF PHASE (×2) | |||
| 6 | G3P → 1,3-bisphosphoglycerate | G3P dehydrogenase (GAPDH) | +1 NADH each (2 total) |
| 7 | 1,3-BPG → 3-phosphoglycerate | Phosphoglycerate kinase | +1 ATP each — substrate-level phosphorylation |
| 8 | 3-PG → 2-phosphoglycerate | Phosphoglycerate mutase | — |
| 9 | 2-PG → phosphoenolpyruvate (PEP) | Enolase | Releases H₂O, creates a high-energy bond |
| 10 | PEP → pyruvate | Pyruvate kinase | +1 ATP each — substrate-level |
Glycolysis balance sheet: 4 ATP made – 2 ATP spent = net 2 ATP, plus 2 NADH and 2 pyruvate per glucose. Runs with or without O₂ — this is the only ATP an anaerobic cell gets.
Pyruvate oxidation & the Krebs (citric acid / TCA) cycle
Link reaction: pyruvate enters the matrix, and pyruvate dehydrogenase complex strips a CO₂ and attaches coenzyme A → acetyl-CoA (2C) + NADH + CO₂. Happens twice per glucose. Irreversible — fat cannot be turned back into glucose from here.
| Step | Enzyme | Yield |
|---|---|---|
| Acetyl-CoA (2C) + oxaloacetate (4C) → citrate (6C) | Citrate synthase | — |
| Citrate → isocitrate | Aconitase | — |
| Isocitrate → α-ketoglutarate (5C) | Isocitrate dehydrogenase (rate-limiting) | NADH + CO₂ |
| α-ketoglutarate → succinyl-CoA (4C) | α-ketoglutarate dehydrogenase | NADH + CO₂ |
| Succinyl-CoA → succinate | Succinyl-CoA synthetase | GTP/ATP (substrate-level) |
| Succinate → fumarate | Succinate dehydrogenase (= Complex II, sits in the inner membrane) | FADH₂ |
| Fumarate → malate | Fumarase (+H₂O) | — |
| Malate → oxaloacetate | Malate dehydrogenase | NADH |
Per turn: 3 NADH · 1 FADH₂ · 1 ATP/GTP · 2 CO₂ — and the cycle turns twice per glucose, so 6 NADH, 2 FADH₂, 2 ATP, 4 CO₂. The cycle makes almost no ATP directly; its real product is reduced electron carriers. Regulated by ATP/NADH (inhibit) and ADP/NAD⁺ (activate). Requires O₂ indirectly — without it NADH piles up and the cycle stalls.
Electron transport chain & chemiosmosis
| Complex | Name | Electron flow | H⁺ pumped |
|---|---|---|---|
| I | NADH dehydrogenase | NADH → coenzyme Q | 4 |
| II | Succinate dehydrogenase | FADH₂ → coenzyme Q (enters after complex I) | 0 — this is why FADH₂ yields less ATP |
| III | Cytochrome bc₁ | Q → cytochrome c | 4 |
| IV | Cytochrome c oxidase | cyt c → O₂ + 4H⁺ → 2 H₂O | 2 |
| V | ATP synthase | Not a carrier — H⁺ flows back through it and it phosphorylates ADP (~4 H⁺ per ATP) | — |
Carriers are arranged in order of increasing electronegativity; oxygen is the final electron acceptor. Block O₂ and the entire chain backs up — NAD⁺ is never regenerated, Krebs stops, and only glycolysis/fermentation continues.
| Poison / uncoupler | Target | Result |
|---|---|---|
| Rotenone | Complex I | Electron flow stops → no gradient → no ATP |
| Antimycin A | Complex III | |
| Cyanide, carbon monoxide, azide | Complex IV | |
| Oligomycin | ATP synthase | Gradient builds but cannot be spent |
| DNP, thermogenin (brown fat) | Membrane — uncoupler | H⁺ leaks back; transport runs hot, ATP is not made — energy is released as heat |
ATP tally per glucose
| Stage | ATP (direct) | NADH | FADH₂ | ATP from carriers |
|---|---|---|---|---|
| Glycolysis | 2 (net, substrate-level) | 2 (cytosolic) | — | 3–5 (depends on shuttle) |
| Pyruvate oxidation (×2) | 0 | 2 | — | 5 |
| Krebs (×2 turns) | 2 (GTP, substrate-level) | 6 | 2 | 15 + 3 |
| Total | 4 substrate-level | 10 | 2 | ~26–28 oxidative |
Conversion: 1 NADH ≈ 2.5 ATP, 1 FADH₂ ≈ 1.5 ATP → ~30–32 ATP per glucose aerobically. Older textbooks say 36–38 (they assumed 3 and 2 and ignored transport costs). Cytosolic NADH must be shuttled into the mitochondrion: the glycerol-phosphate shuttle (yeast, muscle, brain) hands electrons to FADH₂ → 1.5 ATP each (total ≈ 30); the malate–aspartate shuttle (liver, heart) keeps them as NADH → 2.5 ATP each (total ≈ 32). Prokaryotes have no mitochondrion to import into, so they score highest (~38 theoretical).
Fermentation
Fermentation makes no ATP of its own. Its only job is to oxidize NADH back to NAD⁺ so glycolysis can keep turning — otherwise the cell runs out of NAD⁺ within seconds and even the 2 ATP stop.
| Type | Organism | Pathway | Products per glucose | Net ATP |
|---|---|---|---|---|
| Alcoholic | Yeast (Saccharomyces cerevisiae), Zymomonas | Pyruvate → acetaldehyde + CO₂ (pyruvate decarboxylase) → ethanol (alcohol dehydrogenase, oxidizes NADH) | 2 ethanol + 2 CO₂ | 2 |
| Lactic acid | Muscle cells, Lactobacillus | Pyruvate + NADH → lactate (lactate dehydrogenase) — one step, no CO₂ | 2 lactate | 2 |
Yeast: aerobic vs anaerobic side by side
| Aerobic (respiration, O₂ present) | Anaerobic (alcoholic fermentation, no O₂) | |
|---|---|---|
| Overall equation | C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O | C₆H₁₂O₆ → 2 C₂H₅OH + 2 CO₂ |
| Pathways used | Glycolysis + pyruvate oxidation + Krebs + ETC | Glycolysis only, then the 2-step ethanol branch |
| ATP per glucose | ~30–32 (yeast ≈ 30, glycerol-phosphate shuttle) | 2 |
| ATP source | Mostly oxidative phosphorylation (chemiosmosis) | Substrate-level only |
| Final electron acceptor | O₂ → water | Acetaldehyde (an organic molecule) → ethanol |
| Carbon products | CO₂ + H₂O — glucose fully oxidized | Ethanol + CO₂ — ethanol still holds most of the energy, which is why it burns |
| Efficiency | ~15–16× more ATP; ~34% of glucose energy captured | ~2% captured; yeast must burn glucose fast to compensate |
| Where CO₂ comes from | Pyruvate oxidation + Krebs | Pyruvate decarboxylase step only |
Yeast is a facultative anaerobe — it respires when O₂ is available and ferments when it is not. Pasteur effect: adding O₂ suppresses fermentation and glucose consumption drops (more ATP per glucose, so less sugar is needed). Crabtree effect: given high glucose, yeast ferments even with O₂ present. Applications: the CO₂ raises bread dough (ethanol bakes off), the ethanol makes beer and wine (fermentation self-limits around 14–15% alcohol, which is toxic to the yeast).
Anaerobic respiration ≠ fermentation
| Aerobic respiration | Anaerobic respiration | Fermentation | |
|---|---|---|---|
| Final electron acceptor | O₂ | Inorganic, not O₂ (NO₃⁻, SO₄²⁻, Fe³⁺) | Organic (pyruvate, acetaldehyde) |
| Uses an ETC? | Yes | Yes | No |
| ATP yield | ~30–32 | Intermediate (fewer than aerobic) | 2 |
| Examples | Most eukaryotes | Denitrifying and sulfate-reducing bacteria | Yeast, muscle, Lactobacillus |
Other fuels entering the pathway
| Fuel | Broken into | Entry point |
|---|---|---|
| Fats (triglycerides) | Glycerol; fatty acids via β-oxidation | Glycerol → G3P (glycolysis); fatty acids → acetyl-CoA (Krebs). Most ATP per gram — ~9 kcal/g vs 4 for carbs |
| Proteins | Amino acids, deaminated (amino group → urea) | Pyruvate, acetyl-CoA, or Krebs intermediates depending on the residue |
| Other sugars | Fructose, galactose, glycogen | Converted into glycolysis intermediates |
Photosynthesis
6 CO₂ + 6 H₂O + light → C₆H₁₂O₆ + 6 O₂ — an endergonic, anabolic, redox process: CO₂ is reduced, water is oxidized. Respiration's balance sheet run backwards.
Chloroplast structure & pigments
| Part | What happens there |
|---|---|
| Thylakoid membrane (stacked into grana) | Light-dependent reactions — photosystems, ETC, ATP synthase all embedded here |
| Thylakoid lumen (inside the disc) | Where H⁺ accumulates; water is split facing this space |
| Stroma (fluid around the thylakoids) | Calvin cycle; also holds chloroplast DNA and 70S ribosomes |
| Double outer membrane | Envelope — evidence for endosymbiotic origin |
- Chlorophyll a — the only pigment in the reaction center; absorbs blue-violet (~430 nm) and red (~662 nm), reflects green.
- Chlorophyll b + carotenoids (carotenes, xanthophylls) = accessory pigments; widen the range absorbed and dissipate excess energy (photoprotection). Visible in fall once chlorophyll degrades.
- Absorption spectrum = light a pigment takes in. Action spectrum = light that actually drives photosynthesis. They match closely — Engelmann's bacteria clustered in red and blue light, proving chlorophyll drives the process.
- Antenna complex harvests photons and funnels the energy to the reaction-center chlorophyll, which passes an excited electron to the primary electron acceptor.
Light-dependent reactions (thylakoid membrane)
- PSII (P680) absorbs a photon; an excited electron leaves for the primary acceptor. P680⁺ is the strongest biological oxidizer known.
- Photolysis: the oxygen-evolving complex splits water to replace that electron → releases O₂ and dumps H⁺ into the lumen.
- Electron travels down the chain (PQ → cytochrome b₆f → PC); the b₆f complex pumps H⁺ into the lumen.
- PSI (P700) re-energizes the electron with a second photon → ferredoxin → NADP⁺ reductase makes NADPH in the stroma.
- Chemiosmosis: H⁺ flows from lumen back to stroma through ATP synthase = photophosphorylation → ATP.
| Noncyclic (linear) | Cyclic | |
|---|---|---|
| Photosystems used | PSII → PSI | PSI only (electron loops back to b₆f) |
| Products | ATP + NADPH + O₂ | ATP only — no NADPH, no O₂ |
| Why | Standard route | Tops up ATP when the Calvin cycle needs more ATP than NADPH (it needs 3:2) |
Same chemiosmotic principle as mitochondria — an ETC builds an H⁺ gradient, ATP synthase spends it. Differences: the gradient forms in the thylakoid lumen, the electron source is water (not NADH), and the final acceptor is NADP⁺ (not O₂). The O₂ you exhale-worth of atmosphere comes from split water, not from CO₂ — proven with ¹⁸O labeling.
Light-independent reactions — the Calvin cycle (stroma)
Called "dark reactions" but they run in daylight — they just do not use photons directly, they spend the ATP and NADPH the light reactions made.
| Phase | What happens | Cost per 3 CO₂ |
|---|---|---|
| 1. Carbon fixation | Rubisco attaches CO₂ to RuBP (5C); the 6C product immediately splits into two 3-phosphoglycerate (3-PGA, 3C) | — |
| 2. Reduction | 3-PGA → 1,3-BPG (uses ATP) → G3P (uses NADPH) | 6 ATP + 6 NADPH |
| 3. Regeneration of RuBP | 5 of the 6 G3P are rearranged back into 3 RuBP; 1 G3P exits | 3 ATP |
Per G3P: 3 CO₂, 9 ATP, 6 NADPH, 3 turns. Per glucose: 6 CO₂, 18 ATP, 12 NADPH, 6 turns — two G3P join to make one glucose. G3P also feeds into starch, cellulose, lipids and amino acids. Rubisco is the most abundant protein on Earth and is slow, which is why plants make so much of it.
Photorespiration and the C3 / C4 / CAM strategies
The problem: rubisco also accepts O₂ instead of CO₂. On hot, dry days stomata close to save water — CO₂ inside the leaf falls, O₂ builds up, and rubisco starts fixing O₂. That is photorespiration: it consumes ATP, releases CO₂ and makes no sugar, wasting up to ~25% of the plant's fixed carbon.
| C3 | C4 | CAM | |
|---|---|---|---|
| First stable product | 3-PGA (3C) | Oxaloacetate → malate (4C) | Oxaloacetate → malate (4C) |
| Initial fixing enzyme | Rubisco | PEP carboxylase — high affinity for CO₂, ignores O₂ | PEP carboxylase |
| Separation strategy | None — everything in mesophyll cells | Spatial: CO₂ fixed in mesophyll, pumped to bundle-sheath cells where rubisco works (Kranz anatomy) | Temporal: stomata open at night to fix CO₂ into malate (stored in vacuole); Calvin cycle runs by day with stomata shut |
| Photorespiration | High in heat/drought | Very low | Very low |
| Water efficiency | Lowest | Better | Best |
| Energy cost | Cheapest per CO₂ | Extra ATP to regenerate PEP | Extra ATP; slowest growth |
| Best conditions | Cool, moist, moderate light | Hot, sunny, moderately dry | Arid deserts |
| Examples | Wheat, rice, soybean, most trees (~85% of species) | Corn, sugarcane, sorghum, crabgrass | Cacti, succulents, pineapple, agave, jade plant |
Both C4 and CAM solve the same problem the same way — concentrate CO₂ around rubisco so it cannot grab O₂. They differ only in how they separate the two steps: C4 separates them in space (different cells), CAM in time (night vs day).
Photosynthesis vs respiration
| Photosynthesis | Cellular respiration | |
|---|---|---|
| Equation | 6 CO₂ + 6 H₂O → C₆H₁₂O₆ + 6 O₂ | C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O |
| Energy | Endergonic — stores light energy in bonds | Exergonic — releases it as ATP |
| Organelle | Chloroplast | Mitochondrion |
| Electron carrier | NADP⁺ / NADPH | NAD⁺ / NADH, FAD / FADH₂ |
| Carbon | CO₂ reduced to sugar | Sugar oxidized to CO₂ |
| Who does it | Plants, algae, cyanobacteria | Essentially all organisms — including plants, day and night |
Mendel's Laws & Pedigrees
- Law of segregation: the two alleles of a gene separate during meiosis; each gamete gets one.
- Law of independent assortment: genes on different chromosomes assort independently.
- Dominance: the dominant allele masks the recessive in a heterozygote.
- Genotype = alleles carried; phenotype = trait shown. Homozygous (AA/aa) vs heterozygous (Aa).
| Cross | Genotypic ratio | Phenotypic ratio |
|---|---|---|
| Monohybrid Aa × Aa | 1 AA : 2 Aa : 1 aa | 3 : 1 |
| Dihybrid AaBb × AaBb | — | 9 : 3 : 3 : 1 |
| Testcross Aa × aa | 1 Aa : 1 aa | 1 : 1 (reveals unknown genotype) |
| Incomplete dominance Aa | 1 : 2 : 1 | 1 : 2 : 1 (blended, e.g. pink snapdragons) |
| Codominance | 1 : 2 : 1 | Both alleles fully expressed (AB blood type) |
Punnett square — Aa × Aa
Inheritance patterns in pedigrees
| Pattern | Tell-tale signs |
|---|---|
| Autosomal recessive | Skips generations; affected child from two unaffected carriers; sexes equally affected; consanguinity raises risk |
| Autosomal dominant | Appears every generation; affected child always has an affected parent; sexes equally affected |
| X-linked recessive | Mostly males; passed from carrier mother to son; affected father → all daughters are carriers, no son affected |
| X-linked dominant | Affected father → all daughters affected, no sons; more females affected overall |
| Y-linked | Father → all sons only |
| Mitochondrial | Affected mother → all children; fathers never transmit |
Pedigree symbols: square = male, circle = female, filled = affected, half-filled/dot = carrier, horizontal line = mating, double line = consanguineous.
Linkage, Recombination & Maps
- Genes on the same chromosome are linked and violate independent assortment — parental combinations outnumber recombinants.
- Crossing over in prophase I of meiosis breaks linkage; the closer two genes are, the less often it happens.
Recombination frequency (RF) = (recombinant offspring / total offspring) × 100. 1% RF = 1 map unit = 1 centimorgan (cM). RF maxes out at 50% — that means unlinked (or far apart on the same chromosome).
| Concept | Meaning |
|---|---|
| Testcross | Heterozygote × homozygous recessive — offspring phenotypes read out gamete frequencies directly |
| Parental classes | The two most numerous phenotypes; match the original chromosome arrangement |
| Double crossover class | The two rarest classes; compare them to the parentals — the gene that flipped is the middle gene |
| Three-point cross | Maps order and distance for three genes in one experiment |
| Interference | One crossover suppresses another nearby. Coefficient of coincidence = observed / expected doubles; interference = 1 – c.o.c. |
Recombinant DNA & Cloning
| Tool | What it does |
|---|---|
| Restriction endonuclease | Cuts DNA at a specific palindromic site. EcoRI = G↓AATTC → sticky ends; SmaI → blunt ends. Bacterial defense against phage; host DNA protected by methylation. |
| DNA ligase | Seals the insert into the vector (phosphodiester bonds) |
| Plasmid vector | Needs an origin of replication, a selectable marker (antibiotic resistance), and a multiple cloning site |
| Other vectors | Phage λ (bigger inserts), cosmid, BAC, YAC — capacity rises in that order |
| Transformation | Getting the plasmid into competent bacteria (heat shock, electroporation) |
| Blue/white screening | Insert disrupts lacZ → white colonies carry the insert; blue colonies (X-gal + IPTG) are empty vector |
| Reverse transcriptase | Makes DNA from an RNA template — the enzyme behind cDNA (from retroviruses) |
Cloning workflow
- Cut insert DNA and vector with the same restriction enzyme → compatible ends.
- Ligate insert into vector = recombinant plasmid.
- Transform into bacteria.
- Select on antibiotic plates (only transformed cells grow).
- Screen for the right clone — colony hybridization with a labeled probe, or antibody for an expression library.
- Grow up and purify the amplified DNA or expressed protein.
Genomic vs cDNA library
| Genomic library | cDNA library | |
|---|---|---|
| Starting material | Total chromosomal DNA, restriction-digested | mRNA + reverse transcriptase |
| Priming | — | Oligo-dT primer anneals to the poly-A tail, so only mature mRNA is copied |
| Contents | Every sequence: exons, introns, promoters, junk | Only sequences expressed in that tissue, introns already spliced out |
| Same for every tissue? | Yes | No — it is a snapshot of that tissue/time |
| Best for | Regulatory regions, gene structure | Expressing a eukaryotic protein in bacteria (which cannot splice); a full-length clone gives the entire coding sequence |
An expression library puts cDNA behind a bacterial promoter so protein is made — screen it with an antibody instead of a nucleic-acid probe.
Lab Methods
| Method | How it works | Detects / gives you |
|---|---|---|
| Gel electrophoresis | DNA is negative → migrates toward the positive electrode through agarose. Small fragments travel fastest/farthest. | Fragment sizes vs a ladder. Stained with ethidium bromide (UV) or SYBR |
| PCR | Cycles: denature 94–95 °C → anneal primers 50–65 °C → extend 72 °C with heat-stable Taq polymerase. Product doubles each cycle (2ⁿ). | Millions of copies of a target region from tiny samples |
| RT-PCR / qPCR | Reverse-transcribe RNA first / track fluorescence in real time | Gene expression levels |
| Sanger sequencing | Chain termination with ddNTPs (no 3'-OH → extension stops); fragments separated by size, fluorescent readout | The base sequence |
| Southern blot | DNA on a gel → membrane → labeled DNA probe hybridizes | Presence of a specific DNA sequence |
| Northern blot | Same, but RNA is separated | RNA — is the gene transcribed? |
| Western blot | Proteins separated (SDS-PAGE), probed with an antibody | Protein presence and size |
| Restriction mapping / RFLP | Compare fragment patterns after digestion | Sequence differences between individuals |
| Microarray / RNA-seq | Hybridization to a chip / sequencing of all transcripts | Expression of thousands of genes at once |
| CRISPR-Cas9 | Guide RNA targets Cas9 to a matching sequence; it cuts, and repair edits the gene | Targeted genome editing |
Memory hook for blots: Southern = DNA, Northern = RNA, Western = protein ("SNoW DRoP").
Classic Experiments
| Experiment | Setup | Conclusion |
|---|---|---|
| Griffith (1928) | Heat-killed S strain + live R strain killed mice | A "transforming principle" moves between bacteria |
| Avery, MacLeod & McCarty (1944) | Destroyed protein, RNA or DNA in turn; only DNase stopped transformation | The transforming principle is DNA |
| Hershey & Chase (1952) | Phage labeled with 35S (protein) or 32P (DNA); blender + centrifuge | 32P entered the cells → DNA is the genetic material |
| Chargaff | Measured base composition across species | %A = %T, %G = %C — set up base pairing |
| Franklin & Wilkins | X-ray diffraction (Photo 51) | Helical, uniform width, 3.4 Å per base |
| Watson & Crick (1953) | Model building from the above | Antiparallel double helix; suggested a copying mechanism |
| Meselson & Stahl (1958) | 15N → 14N shift, CsCl density gradient. Gen 1 = all hybrid; Gen 2 = half hybrid, half light | Replication is semiconservative (rules out conservative and dispersive) |
| Beadle & Tatum | Neurospora mutants needing single supplements | One gene → one enzyme (updated: one gene → one polypeptide) |
| Garrod | Alkaptonuria in families | Inborn errors of metabolism — genes control biochemical steps |
| Nirenberg & Matthaei | Poly-U RNA in a cell-free system → polyphenylalanine | Cracked the first codon: UUU = Phe |
Recall Practice — name the thing
Function or description is given; pick the name from the list. Options are drawn from the same topic, so guessing by elimination is hard.
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