Foundational Biology: Life's Machinery

0 · The MST Blueprintread first

The mid-semester test is invigilated, MCQ + short-answer, and it does two things: it makes you read diagrams (label a structure, name a stage, read a graph) and explain mechanisms (why this structure gives that function). So this sheet pairs our own schematics with dense structure→function notes.

Scope = mostly Topics 1–2 with some Topic-3 genetics. Side 1 = molecules→cell; Side 2 = information→energy→control.

1 · Chemistry of LifeL3 · bonds & water

Elements of life: C, H, O, N, P, S. Carbon forms 4 covalent bonds → stable backbone of organic molecules.

Electronegativity = a nucleus's pull on a shared bonding pair (more charge / fewer shells → higher; O>N). The difference predicts the bond: non-polar covalent → polar covalent → ionic.

Intermolecular forces (IMFs), weak→strong: LDF (temporary induced dipoles; stronger with bigger, less-branched molecules) → dipole–dipole → hydrogen bond (strongest; needs H bonded to F/O/N near a lone pair) → ion–dipole. IMFs are the hidden lever behind membrane fluidity, protein folding & DNA stability.

Water (from H-bonding): high heat capacity (thermal buffer), cohesion + adhesion (xylem rise), solvent for polar solutes (glucose in blood); amphiprotic (donates/accepts H⁺). pH = differences in H⁺ concentration.

1b · Is It Alive?L1–2

Living things: common elements · made of cells · carry genetic info · grow · respond · mutate · exist in populations & evolve. Viruses are the borderline case — they mutate & evolve but aren't cells, can't grow or extract their own energy (must hijack a host).

Prokaryote vs eukaryote (heavily tested): both share the genetic code, cytoplasm & a plasma membrane. Eukaryote = membrane-bound nucleus + organelles, DNA linear. Prokaryote = nucleoid (no membrane), no organelles, DNA circular; ribosomes also differ in size. Think open-plan studio (prokaryote) vs a house with separate rooms (eukaryote).

2 · The Master Reactionbuild vs break

Condensation = two monomers join, a water leaves, a bond forms (glycosidic / peptide / ester). Hydrolysis = water is added, the bond breaks. They are exact reverses — the single most reused idea in the course (it returns as anabolism vs catabolism in metabolism). A polymer is a chain of repeating monomer subunits (e.g. starch = many α-glucose). Snapping LEGO together pops out a drop of water (condensation); prying apart needs you to add one (hydrolysis).

3 · The Four BiomoleculesT1 · structure→function

1 · Carbohydrates

Monomer = monosaccharide (C₆H₁₂O₆). Glucose/galactose/fructose are structural isomers. α- vs β-glucose differ only in the C1 -OH (down = α, up = β) — and that one flip decides everything:

Functions: structure · signalling (glycoproteins) · energy (glucose) · storage (starch/glycogen). Glycosidic / ether bond links C1 of one sugar to C4 of the next (1,4); branches via 1,6. Cellulose microfibrils are held by H-bonds between -OH groups of adjacent chains + aggregate LDF — the same IMF idea, repeated.

2 · Lipids

Not true polymers — held by additive LDF, large non-polar fraction → hydrophobic. Triglyceride = glycerol + 3 fatty acids; phospholipid = glycerol + 2 tails + charged phosphate head (amphipathic → bilayer); steroid = fused rings (cholesterol). Saturation = the lever: saturated tails (C–C) pack tight → high LDF → solid (animal fat); unsaturated (C=C kink) pack loose → fluid oils. This directly sets membrane fluidity later. Phospholipids as surfactants: charged head ion-dipole/H-bonds water (hydrophilic), non-polar tail LDFs oils (hydrophobic) — being amphipathic lets them sit at a water–oil interface → the basis of the bilayer. Functions: energy store (energy-dense, lightweight), hormones (steroids e.g. estradiol), insulation (blubber), membranes, transport (lipoproteins).

3 · Biomolecules • cont.nucleic acids & protein

3 · Nucleic acids

Nucleotide = base (A,T/U,C,G) + pentose (deoxyribose/ribose) + phosphate. Base pairing A–T (2 H-bonds), C–G (3 H-bonds) is the most stable fit — and is why DNA self-copies & self-repairs. Chargaff logic: %A≈%T & %C≈%G ⇒ double-stranded; presence of T ⇒ DNA not RNA. Strands are antiparallel (5′→3′ opposite) — a zipper whose teeth only fit their partner, run in opposite directions on each side.

3 RNAs • shape = job

mRNA = transcribed copy, carries codons. tRNA = key-shaped; CCA-3′ end holds the amino acid; the anticodon pairs with the mRNA codon — this is how a triplet becomes an amino acid. rRNA = folds into the two ribosomal subunits (site of synthesis).

4 · Proteins

Amino acid = α-C + H + -NH₂ + -COOH + variable R group. Peptide bond = condensation amide. R-groups drive folding (H-bond, ionic, ion-dipole, disulfide -S-S-, hydrophobic LDF).

Denaturation = loss of 2°/3° shape → loss of function (heat/pH/solvent). Heat is most powerful — kinetic vibration overcomes all R-group bonds; change 2° and 3° follows. Shape is function. R-groups are grouped charged / polar uncharged / special / non-polar hydrophobic. Protein functions: immune (antibodies), signalling (glycoproteins), transport (lipoproteins), contractile (myosin), enzymes (trypsin, pepsin), structural (keratin, collagen). From a linear sequence (1°) the fold emerges, and the fold is the function.

4 · The Cell & OrganellesL7–8 · the rooms

Each membrane-bound room runs one specialised job — division of labour. The endomembrane system is a connected set: nuclear envelope → ER → Golgi → vesicles/lysosomes → plasma membrane. Rough ER (ribosome-studded) makes protein; smooth ER does not. The ER is continuous with the nuclear envelope.

Organelle structure→function

Nucleus (from membrane invagination): DNA stored as chromatin = DNA wound on histones → nucleosomes → chromosomes. Packs metres of DNA tiny & lets it divide evenly. Mitochondria & chloroplasts have two membranes; the inner is folded (cristae / thylakoids) → high surface-area-to-volume → more membrane for ATP-making.

Endosymbiosis (tested): organelles were free-living bacteria engulfed by an early eukaryote. Evidence chain: double membrane · own circular DNA · own bacteria-like ribosomes · divide by binary fission. Secondary endosymbiosis (e.g. Euglena) adds a 3rd membrane (the eaten cell's) + a nucleomorph.

The secretory pathway

A flagship integrative answer: gene on → transcription → mRNA out a nuclear pore → translated on rough-ER ribosome → folded in ER → vesicle to cis Golgi → modified → leaves trans Golgi as a lysosome → fuses with the food vacuole → digestion. It links transcription + translation + endomembrane in one chain. Evolutionary origin of rough ER: some bacteria have ribosomes on the inner face of the cell membrane; invagination of that membrane is thought to give rough ER.

4b · Counting Membranesendosymbiosis MST

Membrane count = how many "swallowings" happened. 2 membranes = primary (chloroplast/mitochondrion). 3 = secondary (Euglena; the extra = the eaten cell's plasma membrane). 4 = cryptomonads (with 4 genomes: nuclear & nucleomorph linear/eukaryotic; plastid & mitochondrial circular/bacterial). Russian-doll logic — each shell = one more cell eaten. A nucleomorph is the vestigial remnant nucleus of the engulfed eukaryote.

5 · Membrane & TransportL7 · the border

Fluid mosaic: a phospholipid bilayer — hydrophilic heads out, hydrophobic tails in — with embedded proteins. An amphipathic molecule self-organises into a barrier that is fluid yet sealed to ions.

Tuning fluidity (structure→function)

Cholesterol: polar -OH head H-bonds the phospholipid heads; non-polar rings LDF the tails. At higher temp → more LDF → tighter packing → lower fluidity (a buffer). At low temp a cell raises its unsaturated phospholipids — kinks keep spacing, stop solidifying (taught via Tetrahymena). Cholesterol acts as a fluidity buffer / shock-absorber.

Crosses easily: small, non-polar, uncharged (O₂, CO₂). Cannot: large or charged. Water is small but polar → slow osmosis, fast via aquaporins.

Passive vs active

Primary active: ATP pumps an ion low→high, building a gradient. Secondary active: a co-transported ion flowing down its gradient drags another substance up (e.g. sucrose/H⁺ symporter). Carriers: uniporter · symporter (same way) · antiporter (opposite). Bulk: endocytosis (incl. phagocytosis) / exocytosis.

5b · Why It Selectsthe payoff

The cell trades free passage for control: passive crossing is free but uncontrolled; spending ATP on pumps buys the power to set concentrations, hold an ion gradient, and store energy it can later spend (secondary transport). Pump uphill into a tank (primary), then let the downhill flow turn a wheel (secondary). A plant sucrose/H⁺ symporter is the textbook secondary case: the H⁺ gradient (built by a primary pump) flows back in and drags sucrose up with it. The cell stores energy in the gradient itself, then spends it to move other cargo.

6 · The CytoskeletonL9 · thickness = job

MST inference: a drug that wrecks an amoeba's shape & movement has hit microfilament (actin) assembly.

7 · ClassificationL1 · sorting life

Prokarya = two domains, Bacteria + Archaea. Four eukaryotic kingdoms sort by wall, nutrition & cellularity:

MST trap: a cell with no chloroplast cannot be an autotroph. Autotroph = makes its own food (e.g. via a chloroplast); heterotroph = gets energy from other organisms. A phylogenetic key is read as a branching key to find nearest relatives / oldest lineage (tested with Australian elapid snakes). Note the course flags uni/multicellular as a simplification.

8 · Origin of LifeL1–2 · the story

Life began with the first liquid water (movement + UV protection); earliest fossils = cyanobacteria in stromatolites (~3.5 bya). Great Oxygenation: cyanobacterial photosynthesis (6CO₂+6H₂O→C₆H₁₂O₆+6O₂) flipped the air to O₂ → ozone (O₂→O*+O*; O*+O₂→O₃) → land became habitable → aerobic, multicellular eukaryotes. Why the ocean first? No ozone meant UV was lethal on land; water attenuates UV and shields early life.

8b · Water, Againit ties together

Every "why does water do that?" answer is one weak bond — the hydrogen bond — repeated billions of times: high heat capacity (marine-iguana thermoregulation), cohesion + adhesion (xylem rise), solvent action (glucose in blood). Individually weak, collectively a strong web — like holding hands in a crowd.

9 · DNA ReplicationL9 · semi-conservative

Semi-conservative: each new DNA keeps one old strand + one new. The intact old strand lets the cell proofread → fewer mutations.

The antiparallel problem: DNA pol III only builds 5′→3′ (reads template 3′→5′). So at the fork one strand is the continuous leading strand; the other is built in pieces (Okazaki fragments) as the lagging strand, primed by RNA primers.

Other players: helicase (unwinds), gyrase, primase, DNA pol I, ligase. Prokaryote = circular DNA, single origin; eukaryote = linear, multiple origins.

MST link — DNA repair (base-excision, nucleotide-excision, mismatch) works because DNA is double-stranded: the complementary strand is the template for the fix.

9b · DNA Packagingwhy it coils

DNA → wound on histones → nucleosomes → coiled into chromosomes. Metaphase chromosomes are tightly coiled (visible); interphase loosely coiled (not visible). Extreme coiling packs long DNA into a tiny, divisible package — like string wound on yo-yos, then coiled again and again. The advantage is twofold: it fits metres of DNA into a microscopic nucleus, and it lets the genome divide evenly at mitosis.

9c · The Fork Playerswho does what

• Helicase — unwinds the double helix at the fork
• Primase — lays the RNA primer to start each piece
• DNA pol III — builds the new strand 5′→3′
• DNA pol I — swaps RNA primer for DNA
• Ligase — seals the Okazaki fragments together

Think of painting both sides of a road: one painter walks forward smoothly (leading), the other backs up in dabs (lagging).

9d · Prok vs Euk Replicationcontrast

Multiple origins let a big linear genome copy fast enough — many forks fire at once rather than one crawling round a loop.

10 · The Central DogmaL · DNA→RNA→protein

Information flows DNA → RNA → protein. Read a sequence in the MST: identify the template strand, the transcription direction, then the peptide from a codon table.

Transcription

RNA polymerase binds a promoter, opens a transcription bubble, reads the template strand 3′→5′, adds NTPs to build mRNA 5′→3′, stops at a termination signal, releases mRNA. Three phases: initiation / elongation / termination.

Translation

Ribosome subunits + mRNA assemble; initiator tRNA (Met) sits at the P site; a charged tRNA enters the A site; a peptide bond forms; the ribosome advances; spent tRNA exits the E site; a stop codon (UAA/UAG/UGA) ends it, releasing the polypeptide.

The genetic code

Triplet codons; redundancy (several codons → one amino acid, e.g. UUA & CUG = Leu); reading frame matters. Start = AUG = Met.

10b · DNA vs RNAquick contrast

Picture the players: mRNA = the recipe card, tRNA = the waiter carrying one ingredient, rRNA = the kitchen bench where it all comes together. Shape = job: a flat message, a key-shaped adaptor, a machine that reads.

10c · Reading a SequenceMST drill

1. Find the template — RNA pol reads it 3′→5′
2. Build mRNA 5′→3′ — complementary, with U for T
3. Split into codons from the start (AUG)
4. Read the codon table → the peptide, N→C

Mind the reading frame: shift by one base and every downstream codon changes. Because the code is redundant, a base change can be silent — but a frameshift rarely is.

10d · The Ribosome SitesA · P · E

• A site — arrival of the next charged tRNA
• P site — holds the growing peptide
• E site — spent tRNA exits

The ribosome ratchets one codon at a time until a stop codon is reached and the polypeptide is released.

11 · Cell Cycle & MitosisL9 · regulated division

Eukaryotic cell cycle: G0 (resting) / G1 (prep) / S (DNA synthesis) / G2 (prep) / M (mitosis). Gated at checkpoints by Cyclin–CDK complexes — the cell only divides after passing each.

Mitosis stages

Microtubules build the spindle & move chromosomes; microfilaments (actin) form the contractile ring. Cytokinesis: animals pinch via an actin ring; plants build a cell plate from fused Golgi vesicles. Prokaryotes don't do mitosis — they split by binary fission (B/C/D phases).

11b · Genetics • gene→traitT3 · L19–21

A gene = a DNA sequence expressed as an RNA/polypeptide; carried on chromosomes & inherited. Genotype (makeup) vs phenotype (observable). Allele = a variant; homozygous/heterozygous; dominant/recessive. Mutation = the primary source of variation (alters RNA/polypeptide).

Dominance, molecularly: complete (one product masks) · incomplete (blended — purple×white primula → all lilac; lilac×lilac → 1:2:1) · co-dominance (both fully shown).

12 · EnzymesL11–12 · catalysts

An enzyme = a biological catalyst (usually protein) that speeds a reaction by lowering the activation energy (Ea); it is not consumed. The substrate binds the active site (specific shape/chemistry) → enzyme–substrate complex → products (lock-and-key / induced fit). Specific shape → specific catalysis → reusable.

Key MST point: the enzyme lowers Ea, NOT ΔG. Same reactants & products, same energy difference — just a lower hill to climb (tunnel through the hill, don't move it).

Rate factors: temperature, pH (each enzyme has an optimum — pepsin ~pH 2–4, trypsin ~pH 8; read on an activity-vs-pH bell curve), substrate concentration, inhibitors. Beyond the optimum, denaturation drops activity. Apoenzyme (protein only) vs holoenzyme (+ cofactor/coenzyme) — both terms tested in MCQs. The enzyme doesn't move the destination, it digs a tunnel through the hill instead of climbing over it.

Regulation

Allosteric regulation: a molecule binds a site other than the active site, changing shape/activity. Feedback inhibition: a pathway's end-product switches off an earlier enzyme. MST: block ATP at the allosteric site of PFK and glycolysis keeps running despite high ATP (lost negative feedback). Feedback inhibition is a thermostat — the product shuts off its own production once there is enough. Allosteric enzymes are precisely the ones regulated this way (common MCQ).

12b · Optima & Inhibitionread the graph

Each enzyme is tuned to where it works: pepsin peaks in stomach acid (~pH 2–4), trypsin in the basic intestine (~pH 8) — athletes who each peak only in their own climate. A bell curve's apex is the optimum; the slopes are reduced activity, then irreversible denaturation. Raising substrate concentration speeds the rate until enzymes saturate, then it plateaus. Inhibitors lower activity — competitive ones block the active site; allosteric/non-competitive ones bind elsewhere and reshape the enzyme.

13 · Metabolism & ATPL10,13 · the currency

ATP = the cell's energy currency; its job is to capture & transfer free energy. Hydrolysing a high-energy phosphate bond (ATP → ADP + Pi) releases energy.

ATP is a rechargeable battery, not a fuel tank — constantly cycled, never stockpiled. Energy coupling: endergonic anabolic building is driven by being coupled to the exergonic hydrolysis of ATP.

Catabolism vs anabolism

Catabolism = break big→small, releases energy (protein→aa, fat→FA+glycerol, ATP hydrolysis). Anabolism = build small→big, requires energy (nucleotides→nucleic acids). It's the same condensation/hydrolysis logic from biomolecules — build vs break. The cell pays for building by burning down.

Where ATP is made (context)

Glycolysis (cytosol; control at PFK) → TCA (matrix) → oxidative phosphorylation on the inner membrane: an electron transport chain builds a H⁺ gradient that drives ATP synthase (chemiosmosis). In prokaryotes the chain sits on the inner face of the plasma membrane. No O₂ → fermentation regenerates NAD⁺ (yeast→ethanol+CO₂; muscle→lactate). MST: a low-O₂, yeast-like Mars cell does ethanol fermentation. The proton gradient is the real driver — like water behind a dam turning a turbine; a thylakoid gradient set up artificially makes ATP even without light (acid-bath experiment).

14 · Cell SignallingL18 · sense & respond

Three stages: reception → transduction → response. A ligand binds a receptor; transduction often runs through second messengers (e.g. cAMP); then a cellular response.

Specificity: a cell responds only if it has the matching receptor. Why one hormone does different things in different tissues: the same second messenger (cAMP) hits different target proteins in different cells — same doorbell, different households. Signals are classed by source & distribution (autocrine, paracrine, endocrine/hormonal, direct contact). So specificity comes from which receptors & target proteins a cell carries — same messenger, different outcome.

15 · structure→function recapthe spine

1. IMFs explain everything — saturation→packing→fluidity; R-groups→fold→function; base pairing→DNA stability.
2. Condensation/hydrolysis = anabolism/catabolism — build-vs-break recurs.
3. Surface-area-to-volume — folded inner membranes (cristae/thylakoids) maximise reaction surface.
4. Endosymbiosis evidence — double membrane + circular DNA + own ribosomes + binary fission.
5. Specificity via shape — active sites, receptors, anticodon–codon, base pairing: right shape unlocks function.

16 · MST Diagram Disciplinebefore you submit

• Read the axes/labels first — a graph's units & a diagram's arrows carry the answer.
• Name the stage/structure exactly — "metaphase", "leading strand", "allosteric site".
• State the function the structure forces — never stop at naming.
• Watch direction — 5′→3′, down vs against gradient, Ea vs ΔG.
• For "why" questions, give the IMF / shape reason.