DAT Biology Comprehensive Bullet-Point Notes

Matter, Atoms & Chemical Bonds

• Matter is built from atoms which link together via chemical bonds.
  • Atoms contain sub-atomic particles: protons (+), neutrons (0) in nucleus; electrons (–) in surrounding orbitals.
  • Molecules = groups of ≥2 atoms held by chemical bonds.
• Electronegativity = ability of an atom to attract shared electrons.
  • Higher electronegativity → electrons pulled closer to that atom (forms dipoles in polar bonds).
• Main bond types
  • Ionic bonds
  • Complete transfer of electrons between atoms with very different electronegativities → ions.
  • Covalent bonds (shared e⁻)
  • Non-polar: equal sharing (similar electronegativities).
  • Polar: unequal sharing → partial charges (dipole).
  • Hydrogen bonds (inter- / intra- molecular)
  • Requirements: H covalently bound to F/O/N, plus attraction to another F/O/N.
  • Van der Waals interactions – weak, transient attractions due to momentary e⁻ distribution; cumulative effect can be strong.

Water – Special Properties

• Highly polar; forms extensive H-bond network.
• Excellent solvent ("like dissolves like"): hydration shells form around ions/polar solutes.
• High heat capacity → thermal stability of organisms & climates.
• Density anomaly: ice < liquid water (rigid H-bond lattice keeps molecules further apart) → ice floats.
• Cohesion (water–water) → surface tension (water strider locomotion).
• Adhesion (water–other) + cohesion → capillary action (xylem transport, wet fingertip turning pages).

Essential Nutrients

• Minerals (inorganic ions) – Ca²⁺, K⁺ etc.
  • Roles: bone matrix, electrochemical gradients, hemoglobin cofactors.
• Vitamins
  • Fat-soluble (A, D, E, K) – stored in adipose; risk of toxicity if over-consumed.
  • A: vision, epithelium maintenance
  • D: \uparrow Ca²⁺ absorption (synthesized in skin under UV)
  • E: antioxidant vs. free radicals
  • K: blood clotting
  • Water-soluble (B-complex, C) – excess excreted.
  • B’s: coenzymes/precursors
  • C: collagen synthesis; deficiency → scurvy

Macromolecules Overview

• All contain carbon; formed via dehydration synthesis (monomer → polymer + H2O). Broken by hydrolysis (polymer + H2O → monomers).

Carbohydrates

• Functions: quick energy, energy storage, structural support.
• Monomer: monosaccharide (glucose, fructose, galactose).
• Polymer: polysaccharide.
• Linkage: glycosidic bond
  • \alpha vs \beta orientation (humans cannot cleave \beta linkages).
• Disaccharides: sucrose (Glc+Fru), lactose (Glc+Gal), maltose (Glc+Glc).
• Storage polysaccharides
  • Starch (plants, \alpha, branched)
  • Glycogen (animals, \alpha, highly branched)
• Structural polysaccharides
  • Cellulose (plants, \beta, linear)
  • Chitin (fungi walls, arthropod exoskeleton; \beta + N-acetyl groups)

Lipids

• Non-polar, hydrophobic; not true polymers.
• Roles: energy dense storage, insulation, hormones, membranes.
• Types
  • Triglycerides = glycerol + 3 fatty acids
  • Saturated (no C=C) – stack tightly → atherosclerotic plaques
  • Unsaturated (≥1 C=C) – kinks → fluid, healthier
  • Phospholipids = glycerol + 2 FA + phosphate (amphipathic) → bilayers
  • Steroids = 4 fused hydrocarbon rings (cholesterol, steroid hormones, vitamin D, bile acids)
  • Porphyrins = 4 pyrrole rings + metal (chlorophyll-Mg, hemoglobin-Fe)
• Membrane fluidity modulation
  • Cold: add cholesterol & unsaturated FA → prevent rigidity
  • Hot: add cholesterol & saturated FA → prevent excess fluidity (cholesterol buffers both extremes)

Proteins

• Monomer: amino acid (20 standard).
• Polymer: polypeptide; peptide bonds ((-CO-NH-)).
• Structural hierarchy
  1. Primary – aa sequence
  2. Secondary – \alpha-helix, \beta-sheet via backbone H-bonds
  3. Tertiary – 3-D folding via R-group interactions (H-bond, ionic, hydrophobic, Van der Waals, disulfide \bigl(Cys-S-S-Cys\bigr))
  4. Quaternary – multiple subunits (e.g. hemoglobin, antibodies)
• Denaturation (heat, pH, salts, UV, chemicals) disrupts 3-D shape → loss of function (primary intact).

Nucleic Acids

• Monomer: nucleotide = N-base + pentose sugar + phosphate
  • Purines (A, G) – double ring; Pyrimidines (C, U, T) – single ring (mnemonic "CUT the PYE").
• DNA: deoxyribose; double helix, antiparallel 5'→3'; H-bonded base pairs (A=T 2 H-bonds, G≡C 3 H-bonds) → GC-rich DNA higher Tₘ.
• RNA: ribose (extra OH → more reactive); single-stranded; U replaces T; several forms (mRNA, rRNA, tRNA, ribozymes).
• Phosphodiester linkage forms sugar-phosphate backbone.
• Chargaff’s rule: A+G = C+T (purines = pyrimidines).

Cell Theory & Cell Types

• Seven postulates (all organisms made of cells, hereditary info passes via cells, metabolism occurs within, etc.).
• Common structures: plasma membrane, DNA, ribosomes, cytoplasm.
• Prokaryotes: no nucleus/organelles, smaller, 70S ribosomes.
• Eukaryotes: nucleus + membrane organelles, 80S ribosomes.

Biological Membranes

• Phospholipid bilayer (fluid mosaic)
  • Selectively permeable.
  • Permissive: small non-polar (O₂, CO₂, N₂, steroids); small uncharged polar (H₂O, glycerol) cross slowly; impermeable: large polar (glucose) & ions (Na⁺).
• Membrane proteins
  • Peripheral (surface; removable with salt/pH).
  • Integral→transmembrane (hydrophobic core; removed with detergent).
  • Functional classes: transport (channels, carriers), receptors, enzymes, glycoproteins (ID, immunity), adhesion/anchor.

Channels

• Aquaporins: rapid water flow.
• Ion channels: non-gated or gated (voltage, ligand, mechanical).

Cell Junctions in Animal Tissue

1. Tight junctions – sealing (BBB, gut epithelium)
2. Adherens – actin-anchored belts
3. Desmosomes – strong, keratin-anchored (skin, heart)
4. Hemidesmosomes – anchor to basement membrane
5. Gap junctions – connexon tunnels; electrical coupling (cardiac muscle)

Extracellular Structures

• Cell wall: plants (cellulose), fungi (chitin), bacteria (peptidoglycan – Gram⁺ thick, Gram⁻ thin + LPS endotoxin), archaea (polysaccharide).
• Glycocalyx: carbohydrate coat; protection, adhesion; pathogenic LPS fragments trigger immunity.
• ECM components: collagen (triple helix; most abundant), glycoproteins, proteoglycans, fibronectin, integrins; functions – support, anchoring, signaling.

Organelles

• Nucleus: double membrane, nuclear pores, lamina; houses DNA. Nucleolus forms rRNA → ribosomal subunits.
• Ribosomes (40S+60S euk, 30S+50S prok): free (cytosolic proteins) vs. bound (export/membrane).
• ER
  • Rough ER – translation, glycosylation.
  • Smooth ER – lipid & steroid synthesis, detox (liver), Ca²⁺ storage in sarcoplasmic reticulum (muscle).
• Golgi apparatus: cis → trans maturation; modifies, sorts, packages; forms lysosomes.
• Digestive organelles
  • Lysosomes (acid hydrolases, pH≈5): autophagy, apoptosis, pathogen destruction.
  • Peroxisomes: H2O2 metabolism via catalase; fatty acid \beta-oxidation.
  • Vacuoles: central (plants, turgor), food, transport, contractile (osmotic regulation in protists).
• Mitochondria: double membrane, cristae, matrix; own circular DNA; ATP production & FA oxidation; maternal inheritance.
• Chloroplasts: double membrane, stroma, thylakoids (grana, lumen); photosynthesis; own DNA; descended from cyanobacteria.
• Endosymbiotic theory evidence: size, binary fission, circular DNA, 70S ribosomes.

Cytoskeleton

1. Microfilaments (actin) – muscle contraction, cytokinetic furrow, pseudopods.
2. Intermediate filaments (e.g. keratin, lamins) – tensile strength, nuclear lamina.
3. Microtubules (tubulin dimers; 25 nm) – intracellular transport (kinesin, dynein), mitotic spindle, cilia/flagella (9×2 + 2 core, basal body 9×3), axonal tracks.

• Centrosome = 2 centrioles (animals) – MTOC for spindle. Plants use spindle pole bodies (no centrioles).
• Microvilli (actin core) increase absorptive surface (intestine).
• Cyclosis: cytoplasmic streaming driven by cytoskeleton.

Membrane Transport Mechanisms

• Passive (no ATP, down gradient)
  • Simple diffusion, facilitated diffusion (channels/carriers), osmosis.
• Active (ATP or coupled gradient)
  • Primary active (Na⁺/K⁺ pump), secondary active (symport, antiport).
• Bulk transport
  • Endocytosis: phagocytosis (pseudopods), pinocytosis, receptor-mediated (clathrin coated pits).
  • Exocytosis: vesicle fusion → secretion.
• Tonicity effects
  • Hypotonic → animal lysis / plant turgid.
  • Isotonic → equilibrium / plant flaccid.
  • Hypertonic → crenation / plant plasmolysis.

Biothermodynamics & Metabolism

• Energy categories: kinetic vs. potential (chemical bonds).
• Reaction types
  • Exergonic: \Delta G < 0, spontaneous, energy releasing.
  • Endergonic: \Delta G > 0, non-spontaneous.
• Gibbs equation \Delta G = \Delta H - T\Delta S.
• Laws of Thermodynamics (1st, 2nd, 3rd).
• ATP – energy currency
  • Hydrolysis: ATP \rightarrow ADP + P_i (exergonic)
  • Synthesis via substrate-level or oxidative phosphorylation.
• Metabolism = catabolism + anabolism.

Enzymes

• Biological catalysts; lower activation energy; do not change \Delta G.
• Induced-fit model (active site molds on binding).
• Cofactors: metal ions (Mg²⁺, Fe²⁺) or coenzymes (organic)
  • Prosthetic groups (covalent, permanent); cosubstrates (reversible).
• Ribozymes = catalytic RNA; Zymogens = inactive precursors (pepsinogen).
• Factors affecting activity: pH, T, salinity → denaturation.
• Regulation levels: gene expression, vesicle storage, covalent mods, feedback inhibition (negative feedback maintains homeostasis).

Enzyme Kinetics

• V_{max}: max rate; increases with enzyme concentration.
• Km: [S] at \tfrac12 V{max}; inverse to affinity.
• Inhibition
  • Competitive: binds active site; Km ↑, V{max} unchanged; overcome by [S]↑.
  • Non-competitive (allosteric): binds elsewhere; V{max} ↓, Km unchanged.
• Cooperativity (hemoglobin): positive or negative binding effects.

Cellular Respiration (Aerobic)

Overall: C6H{12}O6 + 6O2 \rightarrow 6CO2 + 6H2O + \text{Energy} (exergonic, oxidative).

1. Glycolysis (cytosol, anaerobic)
   • Invest 2 ATP, produce 4 ATP (net 2 via substrate-level), 2 NADH, 2 pyruvate.
   • Key enzymes: hexokinase (trap glucose), PFK-1 (rate limiting; inhibited by high ATP).
2. Pyruvate decarboxylation (mitochondrial matrix)
   • 2 pyruvate → 2 acetyl-CoA + 2 NADH + 2 CO₂.
3. Citric Acid Cycle (matrix)
   • Per glucose: 6 NADH, 2 FADH₂, 2 ATP, 4 CO₂ (substrate-level phosphorylation).
4. Electron Transport Chain & Oxidative Phosphorylation (inner membrane)
   • NADH/FADH₂ donate e⁻ → complexes pump H⁺ into inter-membrane space.
   • O₂ final e⁻ acceptor → H₂O.
   • Proton-motive force drives ATP synthase: ~34 ATP.

• Total yield ≈ 36-38 ATP/glucose (varies by shuttle system).

Anaerobic Options

• Anaerobic respiration: ETC with non-O₂ acceptors (SO₄²⁻, NO₃⁻…).
• Fermentation (cytosol, no ATP produced beyond glycolysis)
  • Alcoholic (yeast): Pyruvate → acetaldehyde + CO₂; acetaldehyde + NADH → ethanol + NAD⁺.
  • Lactic acid (muscle, bacteria): Pyruvate + NADH → lactate + NAD⁺ (Cori cycle re-oxidizes lactate in liver).

Alternative Fuels

• Carbohydrates
  • Glycogenesis (glucose → glycogen) when insulin high.
  • Glycogenolysis & gluconeogenesis (glucagon high) when blood glucose low.
• Lipids
  • Lipolysis: triglyceride → glycerol (→ G3P) + FA.
  • \beta-oxidation (matrix) cuts 2-C acetyl-CoA units + NADH, FADH₂ → massive ATP; fats yield most ATP/gram.
  • Starvation: liver converts FA → ketone bodies for brain.
• Proteins (last resort)
  • Oxidative deamination removes NH₂ → keto acid (respiration intermediate); NH₃ → urea (excreted).
• Nucleic acids typically recycled, not catabolized for energy.

Photosynthesis

Overall: 6CO2 + 6H2O + \text{light} \rightarrow C6H{12}O6 + 6O2 (endergonic, reductive).

• Occurs in chloroplasts of plants/protists; cyanobacteria use thylakoid membranes.

Chloroplast Architecture

• Outer & inner envelopes; stroma (fluid) contains Calvin enzymes.
• Thylakoid membranes house chlorophyll in photosystems; stacks = grana; lumen = interior.

Light-Dependent Reactions (thylakoid membrane)

• Non-cyclic photophosphorylation: PS II → ETC → PS I → ETC.
  • Water photolysis at PS II replaces e⁻ & releases O_2.
  • H⁺ pumped into lumen; ATP synthase makes ATP to stroma.
  • PS I reduces NADP^+ + 2e^- + H^+ \rightarrow NADPH.
• Cyclic photophosphorylation (stromal lamellae): e⁻ from PS I cycled back to first ETC → more ATP, no NADPH/O₂.

Calvin Cycle (stroma, light-independent)

1. Carbon fixation: CO_2 + RuBP \xrightarrow{RuBisCo} 2\,3\text{-PGA}.
2. Reduction: PGA + ATP + NADPH → G3P.
3. Regeneration: majority of G3P + ATP → RuBP.

• 6 turns → 2 G3P → 1 glucose.

Photorespiration (C₂ pathway)

• RuBisCo fixes O2 instead of CO2 → phosphoglycolate (waste), consumes ATP, releases CO_2.
• Adaptations
  • C₄ (spatial separation): Mesophyll fixes CO_2 to malate (PEP carboxylase, no O₂ affinity), shuttles to bundle-sheath (Calvin cycle isolated from O₂).
  • CAM (temporal): Stomata open at night; CO2 fixed to malic acid (stored in vacuole) → daytime decarboxylation supplies CO2 while stomata closed.

Cell Division Fundamentals

• DNA packaged: chromatin → duplicated chromosome (2 sister chromatids joined by centromere & kinetochores).
• Ploidy: Haploid n (gametes); diploid 2n (somatic). Humans n=23, 2n=46.
• Cell cycle phases
  • Interphase: G₁ (growth), S (DNA & centrosome replication), G₂ (prep, organelles), possible G₀ (resting/senescent).
  • M phase: karyokinesis + cytokinesis.
• Size constraints: surface-to-volume & genome-to-volume ratios; skeletal muscle adapts via multinucleation (↑G:V) & elongated shape (↑S:V).

Mitosis (somatic)

1. Prophase – chromatin condenses, spindle forms, nucleolus disappears.
2. Prometaphase – nuclear envelope breaks; MTs attach to kinetochores.
3. Metaphase – chromosomes line at metaphase plate (karyotyping stage).
4. Anaphase – centromeres split; sister chromatids (now chromosomes) pulled apart.
5. Telophase – two nuclei reform; chromosomes decondense; spindle disassembles.

• Cytokinesis
  • Animal: actin-myosin contractile ring → cleavage furrow.
  • Plant: vesicle-derived cell plate → new wall.
• Outcome: 2 genetically identical 2n daughter cells.

Meiosis (germ cells) – Reductive division

• Meiosis I (homologs separate, 2n→n)
  • Prophase I: synapsis forms tetrads; crossing over at chiasmata (genetic diversity).
  • Metaphase I: homologous pairs align.
  • Anaphase I: homologs disjoin.
  • Telophase I + cytokinesis: 2 haploid cells; chromosomes still duplicated.
• Meiosis II (sister chromatids separate) resembles mitosis.
  • Results in 4 unique haploid gametes.
• Sources of genetic variation: crossing over, independent assortment, random gamete fusion.

Cell-Cycle Control & Cancer

• Checkpoints: G₁ (restriction), G₂ (DNA damage), M (spindle).
• Other regulations: density-dependent inhibition, anchorage dependence.
• p53 tumor-suppressor governs arrest/apoptosis; mutations → malignancy.

Chromosome & Chromatid Counting Cheat Sheet

• Mitosis (start x chromosomes)
  • Prophase–Metaphase: x chromosomes, 2x chromatids.
  • Anaphase–Telophase: 2x chromosomes (separated), 2x chromatids.
  • Post-cytokinesis: each daughter x chromosomes, x chromatids.
• Meiosis I (diploid parent x)
  • Up to Anaphase I: x chromosomes, 2x chromatids.
  • After division: \tfrac{x}{2} chromosomes (duplicated), x chromatids per cell.
• Meiosis II
  • Prophase II–Metaphase II: \tfrac{x}{2} chromosomes, x chromatids.
  • Post-Meiosis II gametes: \tfrac{x}{2} chromosomes, \tfrac{x}{2} chromatids.
  • For humans: gamete has 23 chromosomes, 23 chromatids.