Foundations of life
Before any cell, any code: chemistry. Water gives life its strange forgivingness. Carbon gives it its scaffolding. The rest is arithmetic between them.
01.1Properties of Water
- Polarity — water is bent, with positive and negative ends
- Cohesion & adhesion — yields exceptionally high surface tension
- High specific heat — slow to warm, slow to cool
- Solid less dense than liquid — ice floats, lakes don't freeze through
- Universal solvent — dissolves polar and ionic substances
- Amphoteric — can act as acid or base; always carries some ions
01.2Basic Chemistry
The four primary elements of life are oxygen, carbon, hydrogen, and nitrogen. Bonds come in three flavors:
Two atoms share a pair of valence electrons. Strong, directional, the backbone of organic molecules.
An electron leaves one atom for another. The two ions — cation (+) and anion (−) — are held by attraction.
An electron drifts farther than it should from a hydrogen, exposing the proton. The partial-positive end attracts highly electronegative neighbors.
Important chemical groups
Carbon's four valence electrons license the entire vocabulary of biology. Isomers share atoms but not shape. The seven groups to memorize:
| Group | Formula | Group | Formula |
|---|---|---|---|
| Hydroxyl | −OH | Sulfhydryl | −SH |
| Carbonyl | >C=O | Phosphate | −OPO₃²⁻ |
| Carboxyl | −COOH | Methyl | −CH₃ |
| Amino | −NH₂ | — and the chains they make. | |
Dehydration synthesis builds bonds by removing H₂O. Hydrolysis breaks them by adding H₂O. Everything else is variation. — the central chemical motif
The four macromolecules
Life builds from four families. Each is a polymer of a particular monomer, each with its own architecture and its own job — though the jobs blur generously.
Shape: a chain of carbons, or a ring of carbons.
Function: energy storage and structure.
Shape: a head (glycerol) and tails (fatty acids). Steroids form four fused carbon rings. Saturated = no double bonds; unsaturated = at least one.
Function: energy storage, membranes, signaling.
Shape: central carbon bonded to H, carboxyl group, side chain, amino group; chains fold into 3D forms.
Function: enzymes, structure, transport.
Shape: nitrogen base + pentose + phosphate. DNA pairs deoxyribose strands with no uracil.
Function: the cell's instruction manual.
02.1Levels of Protein Structure
When the shape is wrong, the protein denatures — and stops working as intended.
02.2DNA vs. RNA
DNA
- Double stranded, antiparallel
- Sugar: deoxyribose
- Bases: A · T · G · C
- Pairing: A↔T, G↔C
- Form: double helix
- Job: stores genes
RNA
- Single stranded
- Sugar: ribose
- Bases: A · U · G · C
- Pairing: A↔U, G↔C
- Form: single helix
- Job: protein production
The cell, an inventory
An accountant's view of the cell — every organelle, what it does, and which domain of life it belongs to. Plus the membrane that holds the books.
03.1Organelle Reference
| Organelle | Found In | Function |
|---|---|---|
| Ribosomes | Both | Protein synthesis |
| Rough ER | Eukaryote | Protein synthesis & folding |
| Smooth ER | Eukaryote | Lipid synthesis & detoxification |
| Golgi Complex | Eukaryote | Modifies, sorts, transports proteins & lipids |
| Mitochondria | Eukaryote | Cellular respiration, ATP generation |
| Chloroplast | Plant cells | Photosynthesis, glucose from light |
| Lysosome | Mostly animal | Cell digestion & autophagy |
| Vacuole | Eukaryote | Storage / structure (esp. plants) |
The nucleus sits behind a double-membrane envelope, perforated with pores. Inside: chromatin (DNA woven with protein) and the nucleolus, where ribosomes are made. The centrosome assembles microtubules; vesicles are little sacs of membrane. From smallest to largest, the cytoskeleton goes: microfilaments → intermediate filaments → microtubules.
03.2Endosymbiotic Theory
A large prokaryote engulfed smaller ones, and the cell as we know it began.
- Mitochondria and chloroplasts have their own DNA.
- They reproduce independently of the cell.
- They have a double membrane — one from the host, one from the guest.
03.3Cell Membrane
Form the lipid bilayer itself.
Tunes the bilayer — keeps it neither too loose nor too rigid.
React to the outside environment; help with signaling without letting signals in.
Span the bilayer; ferry molecules that can't simply diffuse.
Carbohydrates extending out, helping the cell signal and identify itself.
Small non-polar: pass freely. Small uncharged polar: pass slowly. Large or ionic: require proteins.
03.4Active vs. Passive Transport
Passive
- No ATP needed
- Works with the gradient (high → low)
- Simple diffusion: through the bilayer
- Facilitated: channel & carrier proteins
- Example: aquaporin (channel)
Active
- ATP required
- Works against the gradient (low → high)
- Always uses carrier proteins
- Energy reshapes the protein to push
- Example: sodium-potassium pump
03.5Osmosis & Diffusion
Diffusion: the movement of substances from higher to lower concentration — entropy doing its quiet work. Osmosis: water moving across a selectively permeable membrane from low solute to high solute.
- Hypotonic — exterior has less solute than the cell
- Hypertonic — exterior has more solute than the cell
- Isotonic — concentrations are equal on both sides
Energy & enzymes
Cells run on a tiny industry of catalysts and currents. Enzymes lower the cost of doing business. Photosynthesis builds; respiration spends.
04.1Enzymatic Reactions
- The substrate binds the active site — either fitting exactly or via induced fit.
- The enzyme orients the substrates correctly, then encourages bonds to form or break.
- Mechanisms include forming temporary bonds or shifting local chemistry (e.g., acidity).
- The point of enzymes: a lower activation energy, so reactions run efficiently.
Environmental conditions
Regulation: a regulatory protein binds the active site (blocks substrate) or an allosteric site (changes shape — activates or disables). pH: shifting charges break efficiency; far-from-optimal pH denatures the protein. Temperature: a little heat speeds substrate interaction; too much, and the protein denatures.
04.2Photosynthesis
Light reactions
- PSII first: splits water into ½ O₂ + 2 H⁺; light excites electrons (P680 chlorophyll).
- The electron transport chain pumps 4 protons per H₂O across the membrane.
- PSI excites electrons again — yields 12 NADPH.
- ATP synthase makes 18 ATP (4 protons per ATP).
Calvin Cycle (per glucose, runs twice)
Consumes 18 ATP and 12 NADPH. Output per two cycles: 2 G3P, 12 NADP⁺, 18 ADP, 6 H₂O, 16 Pi. Three phases:
04.3Cellular Respiration
Glycolysis — the warmup
Oxidizes glucose into pyruvate, costing 2 ATP. Yields:
Krebs Cycle
Pyruvate is oxidized into Acetyl-CoA, joins oxaloacetate to form citrate, and is redoxed back to oxaloacetate. Per glucose:
Oxidative Phosphorylation
Electrons from NADH and FADH₂ build a proton gradient. Result: roughly 26 to 28 ATP and water enough to balance the books.
Without oxygen, the electron chain stalls. Fermentation recycles NADH into NAD⁺ — turning pyruvate into ethanol or lactate — and the cell limps along on the 2 ATP from glycolysis alone.
Quick definitions
- Reduction: gaining electrons. Oxidation: losing them.
- (−)ΔG = spontaneous · (+)ΔG = not
- Exergonic releases; endergonic uses.
- Catabolic (exergonic, breaks down) · Anabolic (endergonic, builds up)
- Hydrogen ions = protons.
Communication & cycles
Cells are not silent. They whisper to themselves, to neighbors, to distant parts of the body — and they keep careful, time-stamped records of when to divide and when to wait.
05.1Types of Signaling
| Type | Description | Example | Signal |
|---|---|---|---|
| Autocrine | Self signaling | Cancer cell growth | Growth factors |
| Paracrine | Adjacent cell signaling | Synaptic signaling | Neurotransmitters |
| Endocrine | Distant signaling via blood | Blood sugar regulation | Insulin / glucagon |
| Juxtacrine | Direct contact | T-cell activation | Membrane-bound ligands |
- Secondary messengers amplify the effect of a single ligand.
- Apoptosis is programmed cell death — clean exit when conditions fail.
- Cancer usually begins when checkpoints mutate and growth doesn't stop.
- Phosphorylation cascade: one kinase activates another, amplifying the signal.
- Tumor suppressor genes halt the cell cycle, repair DNA, or trigger apoptosis.
05.2Feedback Mechanisms
Negative feedback
- System self-regulates back to a setpoint
- Body temperature
- Blood sugar
- Homeostasis writ large
Positive feedback
- System amplifies its own signal
- Blood clotting
- Fruit ripening
- Climate change runaway
05.3The Cell Cycle
Interphase
Mitosis
Cyclins, CDKs & Checkpoints
- Checkpoints ask: is the cell ready to advance?
- CDKs (cyclin-dependent kinases) wave the cell through if cyclin levels permit.
- As cyclin levels rise, CDKs activate and the cell moves on. Different cyclins gate different phases.
- Fail a checkpoint: the cell repairs, exits the cycle, or dies.
Inheritance, the math
Mendel's bookkeeping. Two parents, four boxes, and a quiet probability that describes whole generations. The Punnett calculator below does the arithmetic for you — the understanding is still yours.
06.1Mitosis vs. Meiosis
Mitosis
- Growth, healing, asexual reproduction
- Two identical diploid cells
- Occurs in somatic cells
- One round of division
- Starts with regular chromosome pairs
Meiosis
- Sex cell production, genetic variation
- Four different haploid cells
- Occurs in germ cells
- Two rounds of division
- Starts with tetrads (homologous pairs)
06.2Genetic Variation Mechanisms
Three quiet forces shuffle the deck of every gamete:
During prophase I, tetrads form. Non-sister chromatids of homologous pairs swap segments — alleles trade places, and gametes inherit something neither parent quite had.
At the metaphase plate, tetrads line up; their orientation is random. Each daughter cell inherits a random mix of maternal and paternal chromosomes.
Any sperm can fertilize any egg. The final shuffle adds yet another layer of randomness to the resulting genome.
06.3Punnett Squares
The classic monohybrid cross — Aa × Aa — yields the textbook 1:2:1 ratio. Use the live calculator (in the dock) for any cross you like.
06.4Gene Linkage & Probability
Gene linkage shows up when offspring deviate significantly from the random ratios — the closer two genes sit on a chromosome, the less often crossing-over breaks them up. Linkage is suspected when recombination frequency = (recombinants ÷ total) × 100 < 50%. Mapping rule of thumb: each 1% RF = 1 map unit.
Product rule for independent events: 25%(AA) × 25%(BB) = 6.25%(AABB). Sum rule for mutually exclusive events: 25%(AA) + 25%(aa) = 50% (AA or aa).
Molecular biology
The cell as a tiny print shop: it copies, it edits, it translates. Errors are mutations. Tools that exploit the print shop are biotechnology.
07.1Mutations
Point mutations
- Substitution
- Insertion
- Deletion
Effects can be silent (no change), missense (different amino acid), nonsense (stop codon), or frameshift (every codon downstream changes).
Chromosome mutations
- Deletion
- Duplication
- Inversion
- Translocation
07.2Biotechnology
Cas9 enzyme cuts at a guide-RNA-defined sequence. Genes can be removed, replaced, or rewritten.
Engineered viruses deliver targeted genetic payloads into cells.
DNA fragments migrate through a gel under electric current — smaller pieces travel further.
Polymerase Chain Reaction: heat to separate strands, add polymerase, copies double each cycle.
Bacteria absorb plasmids and use the foreign DNA as their own.
07.3DNA Replication
DNA replicates in the 5' to 3' direction. One strand is built continuously (the leading strand); the other in fragments (the lagging strand, made of Okazaki fragments).
| Enzyme | Function |
|---|---|
| Topoisomerase | Relieves tension on the DNA |
| Helicase | Splits the double helix |
| Single-strand binding proteins | Hold the strands separate |
| DNA primase | Lays down the RNA primer |
| DNA polymerase III | Synthesizes most of the new DNA |
| DNA polymerase I | Replaces RNA primers with DNA |
| DNA ligase | Joins Okazaki fragments |
07.4Transcription & Translation
Transcription
RNA polymerase binds a promoter and reads the DNA template until a stop sequence. Pre-mRNA is then matured: spliceosomes remove introns and stitch exons; a poly-A tail caps the 3' end; a modified guanine cap the 5' end.
Translation
mRNA threads through the small ribosomal subunit; the large unit clamps over the top. tRNA arrives at the A site, matches its anticodon to the mRNA codon, and brings its amino acid. The chain hands off at the P site, then exits via the E site. Repeat until stop.
07.5Gene Regulation
In prokaryotes, operons coordinate gene expression by acting as switches over multiple genes. In eukaryotes, transcription factors bind regulatory regions to activate or repress transcription. Either way: the same DNA, very different cells.
Evolution, in motion
Populations are the unit of evolution, not individuals. The Hardy-Weinberg calculator below makes the math observable — and shows when a population isn't at equilibrium, which is most of the time.
08.1Causes of Natural Selection
For natural selection to operate, four conditions must hold:
- Variation — individuals in the species differ.
- Overproduction — more offspring are born than will survive.
- Heritability — traits can be passed on.
- Selective pressure — some traits prove more advantageous than others.
Natural selection is one mechanism of evolution — not its synonym.
08.2Mechanisms of Evolution
Five forces drive allele frequencies to change over time:
- Mutations — the raw material of variation.
- Gene flow — migration mixes populations.
- Sexual selection — mate choice shapes traits.
- Genetic drift — chance shifts allele frequencies.
- Natural selection — pressure favors certain traits.
Adaptive radiation: one species diversifies to fill many niches. Convergent evolution: unrelated species independently evolve similar traits — usually because they face similar environments.
Three Modes of Selection
Directional
A trait is wanted more (or less) — the curve drifts in one direction.
Stabilizing
The middle wins — extremes on either side are selected against.
Disruptive
Both extremes win — the middle is selected against.
08.3Population Genetics
- Mutations — permanent DNA changes that may produce new heritable traits.
- Genetic drift — allele frequencies shift by chance, not selection.
- Bottleneck effect — a sudden population crash leaves survivors' alleles dominant.
- Founder effect — a small breakaway group's allele frequencies define the new population.
- Gene flow — migration between populations changes their genetics.
08.4Hardy-Weinberg Equilibrium
A population is in Hardy-Weinberg equilibrium when none of the five evolutionary forces is acting. This requires:
- No mutations
- No gene flow
- Random mating
- Large population (no genetic drift)
- No natural selection
Where p² is homozygous dominant frequency, 2pq is heterozygous frequency, and q² is homozygous recessive frequency. Deviation from these proportions is evidence of evolution at work.
08.5Reproductive Isolation
Pre-zygotic
- Geographic — physical barrier
- Ecological — habitat difference
- Temporal — different mating times
- Behavioral — different courtship
- Mechanical — different body structures
- Gametic — fertilization fails
Post-zygotic
- Reduced hybrid viability — genes don't work
- Reduced hybrid fertility — no gametes
- Hybrid breakdown — second generation sterile or weak
08.6Human Effects on Biodiversity
The biggest human force on biodiversity is artificial selection: only the organisms with traits we like are allowed to breed and survive — variety quietly drains. Add habitat alteration and direct pressure on certain species, and you have the biological signature of the present.