Chemical and Cellular Basis of Life – Comprehensive Study Notes

Chemical & Cellular Basis of Life

• Living systems are explained by chemistry; the arrangement of atoms in molecules determines biological function.
• Biology embraces reductionism: understanding wholes by dissecting parts (e.g.
  molecules ➔ cells ➔ tissues ➔ organs ➔ organisms ➔ ecosystems).
• At every hierarchical level emergent properties appear that are not predictable from the level below.

Atoms, Elements & Molecules

• Atoms combine to form molecules whose shapes & interactions govern life‐processes.
• Life needs ~$25$ chemical elements; four major ones constitute the bulk: $C, H, O, N$.
• Typical elemental composition of protoplasm (by weight):
  • $O$ $66\%$, $C$ $10\%$, $H$ $10\%$, $N$ $2.5\%$, $Mg$ $1.5\%$, $P$ $0.9\%$, $K$ $0.3\%$, $Ca$ $0.3\%$, $S$ $0.2\%$, others trace.

Protoplasm

• Defined as the living substance inside the cell; displays all life activities.
• Historical milestones:
  • $1835$ Felix Dujardin – "Sarcode"; $1839$ Purkinje – "Protoplasm"; $1861$ Max Schultz – Protoplasm theory; $1868$ Huxley – "Physical basis of life"; $1946$ Von Mohl – role in cell division.
• Physical properties:
  • Colloidal system (particle diameter $10^{-6}-10^{-4}\,\text{mm}$).
  • Viscosity varies between sol (fluid) & gel (semi-solid); transitions = gelation/solation.
  • Exhibits Brownian motion, amoeboid movement, cyclosis (streaming), classified as rotation or circulation around vacuoles.
  • Color: intrinsically gray; appears translucent due to suspended particles.
• Chemical properties: mixture of the ~25 elements above performing all metabolic activities.

Water – The Molecule That Supports Life

• $H_2O$ is polar; unequal electron sharing makes $O$ partially $-$ & $H$ partially $+$.
• Hydrogen bonds (H-bonds): each molecule forms up to $4$; individually weak (≈$\tfrac1{20}$ of a covalent bond) but collectively confer extraordinary properties:
  • Cohesion (surface tension) ➔ water columns rise in plants; insects walk on water.
  • Adhesion ➔ capillary action (xylem, glass tubes, paper towels).
  • High specific heat $c=1\,\text{cal g}^{-1}\,^{\circ}!\text{C}^{-1}$ buffers climate & body temps.
  • High heat of vaporization (≈$540\,\text{cal g}^{-1}$) enables evaporative cooling (sweating, transpiration, climate moderation).
  • Density anomaly: ice < liquid ➔ lakes freeze top-down, seasonal turnover, environmental stability.
  • Universal solvent: forms aqueous solutions with ionic & polar solutes (hydrophilic) while excluding non-polar (hydrophobic) compounds.
• Boiling/freezing points at sea level: $100^{\circ}\text{C}$ / $0^{\circ}\text{C}$; boiling temp decreases with altitude.
• Homeostasis contributions: insulation, heat reservoir, coolant, solvent, ice shield.

Inorganic Compounds Beyond Water

• Acids: donate $H^+$; Bases: donate $OH^-$ or accept $H^+$.
• Water self-ionizes: $2H<em>2O \rightleftharpoons H</em>3O^+ + OH^-$.
• pH scale $0\,(\text{strong acid}) \rightarrow 14\,(\text{strong base});\; pH=-\log[H^+]$; each pH unit = $\times10$ change in $[H^+]$.
• Salts: ionic compounds from acid–base neutralization (e.g. $NaOH + HCl \to NaCl + H_2O$); their ions (e.g. $Na^+, K^+, Ca^{2+}$) underlie nerve & muscle function.
• Buffers maintain pH by reversible $H^+$ donation/acceptance.
  • Carbonic acid–bicarbonate ($H<em>2CO</em>3/HCO<em>3^-$), phosphate ($H</em>2PO<em>4^-/HPO</em>4^{2-}$), protein (–$COOH/–NH_2$) systems.

Organic Chemistry – Carbon & Macromolecules

Carbon

• $C$ has $4$ valence electrons ➔ forms up to $4$ covalent bonds, enabling large, diverse molecules.

Polymer Dynamics

• Dehydration synthesis (condensation): $\text{monomer}<em>1 + \text{monomer}</em>2 \to \text{polymer} + H_2O$.
• Hydrolysis: $\text{polymer} + H<em>2O \to \text{monomer}</em>1 + \text{monomer}_2$.

Carbohydrates $({CH<em>2O})</em>n$

• Functions: energy (primary cellular fuel), storage, structure.
• Monosaccharides: glucose, fructose, galactose, ribose, deoxyribose.
• Disaccharides: sucrose = glucose + fructose; lactose = glucose + galactose; maltose = glucose + glucose.
• Polysaccharides:
  • Starch – plant storage; digestible by humans.
  • Glycogen – animal storage (liver & muscle).
  • Cellulose – plant cell walls, dietary fiber; indigestible without symbiotic microbes.
  • Chitin – arthropod exoskeleton, surgical sutures.

Lipids

• Composed mostly of $C$ & $H$ with few $O$; ratio H:O>2:1.
• Insoluble in water; soluble in non-polar solvents.
• Functions: long-term energy, insulation, shock absorption, water-proofing, hormones, membranes.
• Triglycerides: glycerol + $3$ fatty acids.
  • Saturated (no $C=C$; solid, animal fats) vs unsaturated (≥1 $C=C$; liquid oils).
• Phospholipids: glycerol + $2$ fatty acids + phosphate head ➔ amphipathic; form bilayers.
• Steroids: 4 fused rings; cholesterol is base steroid; hormones (testosterone, estrogen). Synthetic anabolic steroids build muscle but risk health.
• Waxes coat leaves, honeycomb, etc.

Proteins

• Elements: $C,H,O,N,S$.
• Monomer = amino acid (20 types) with $\text{NH}_2$, $COOH$, $H$ & variable $R$ group.
• Levels of structure:
  1. Primary: amino‐acid sequence (peptide bonds).
  2. Secondary: $\alpha$-helix & $\beta$-sheet (H-bonds).
  3. Tertiary: overall 3-D folding (H-bonds, ionic, disulfide bridges).
  4. Quaternary: multiple polypeptide subunits (e.g.
     hemoglobin).
• Functions (mnemonic "STREMS"):
  • Storage – albumin
  • Transport – hemoglobin
  • Regulatory – hormones
  • Enzymatic – catalysts
  • Movement – actin, myosin
  • Structural – keratin, collagen
• Enzymes: globular proteins that lower activation energy; possess specific active sites.
  • Influenced by temperature, pH, ion strength.
  • Require cofactors (metal ions) or coenzymes (vitamins).
  • Competitive vs non-competitive inhibitors modulate activity.

Nucleic Acids

• Store & transmit genetic info; dictate protein synthesis.
• Monomer = nucleotide (pentose + phosphate + nitrogen base).
• DNA: deoxyribose, bases $A,T,C,G$; double helix $2\,\text{nm}$ wide, $10$ base pairs per $360^{\circ}$ turn; $\sim2\,\text m$ per human cell (enough to reach sun $400$×).
  • Base pairing (Chargaff’s rule): $A=T,\;G=C$ via H-bonds.
  • Located in nucleus, mitochondria, chloroplasts; controls transcription $\Rightarrow$ mRNA $\Rightarrow$ translation on ribosomes.
• RNA: ribose, bases $A,U,C,G$; single-stranded; types include mRNA, tRNA, rRNA.
• Discovery milestones: Rosalind Franklin (X-ray), Watson & Crick (model).

Cell Theory & History

• Hooke (1665): coined "cells" (cork).
• Leeuwenhoek (1670s): first living cells (bacteria, sperm).
• Schleiden (1838) & Schwann (1839): all plants/animals made of cells.
• Virchow (1858): cells arise from pre-existing cells.
• Modern tenets:
  1. All living things composed of cells.
  2. Cell = basic unit of structure & function.
  3. Cells come only from existing cells.

Cell Types & Sizes

Prokaryotes

• Bacteria & Archaea; $1–10\,\mu m$.
• No nucleus; circular DNA in nucleoid; lack membrane organelles.
• Structures: cell wall (peptidoglycan), plasma membrane, ribosomes $50S+30S$, capsule, pili (conjugation), flagella (flagellin), sometimes plasmids.

Eukaryotes

• Protists, fungi, plants, animals; $10–100\,\mu m$.
• Nucleus plus many organelles; linear chromosomes with histones.
• Cytoskeleton & compartmentalization enable complexity.

Size Constraint

• Surface area $=L\times W$ grows slower than volume $=L\times W\times H$; when SA/V ratio too low ➔ division occurs.

Plasma Membrane & Transport

• Fluid mosaic: phospholipid bilayer + proteins moving laterally (≈$5\,\text{nm}$ thick).
• Hydrophilic heads out, hydrophobic tails in; proteins include channels, carriers, receptors; glycoproteins for cell recognition.

Cytoplasm & Cytosol

• Cytosol = semi-fluid matrix hosting metabolic pathways; cytoplasm = cytosol + suspended organelles.

Nucleus & Associated Structures

• Nuclear envelope (double, with pores) continuous with RER.
• Chromatin (non-dividing), chromosomes (dividing).
• Nucleolus synthesizes rRNA & assembles ribosomes.

Ribosomes & Endomembrane System

• Free or bound (RER); two subunits $60S+40S$ (eukaryotes).
• Rough ER: studded with ribosomes; synthesizes membrane & export proteins.
• Smooth ER: lipid synthesis, Ca$^{2+}$ storage, detoxification.
• Golgi apparatus: cis➔trans processing, glycosylation, packaging into vesicles.
• Secretory vesicles fuse with plasma membrane for exocytosis.

Energy & Metabolic Organelles

• Mitochondria: double membrane, cristae, matrix, own DNA; site of $C<em>6H</em>{12}O<em>6 + 6O</em>2 \to 6CO<em>2 + 6H</em>2O + ATP$; maternally inherited.
• Chloroplasts (plants): photosynthesis $6CO<em>2+6H</em>2O+light \to C<em>6H</em>{12}O<em>6+6O</em>2$.
• Peroxisomes: oxidative enzymes; convert $H<em>2O</em>2 \to H<em>2O + O</em>2$; fatty-acid to sugar conversion.
• Lysosomes: hydrolytic enzymes (pH≈$5$); autophagy & apoptosis.
• Vacuoles: storage; central vacuole in plants (tonoplast); contractile vacuole expels excess water in protists.

Cytoskeleton & Motility

• Microfilaments (actin): support, muscle contraction.
• Microtubules (tubulin): tracks for organelle movement, spindle fibers; 9+2 arrangement in cilia/flagella.
• Intermediate filaments: tension-bearing (keratins).
• Centrosome: MTOC with centrioles (animals) organizing spindle.
• Cilia & Flagella: powered by dynein; cilia numerous & short; flagella few & long.

Comparative Tables (Highlights)

• Prokaryote vs Eukaryote: size, nucleus, organelles, ribosome size, DNA form, movement structures, reproduction (binary fission vs mitosis/meiosis).
• Animal vs Plant Cells: plant cells possess cell wall, chloroplasts, large central vacuole, plasmodesmata; animal cells have centrioles, lysosomes, cilia/flagella.

Diversity of Cell Shapes & Functions (Selected Examples)

• Squamous (skin) – protection; Columnar (intestine) – absorption; Cuboidal (kidney) – filtration; Stellate (neuron) – communication; Fusiform (smooth muscle) – contraction; Biconcave (RBC) – gas transport; Flagellated (sperm) – motility.

Key Equations & Values

• Specific heat of water: $c=1\,\text{cal g}^{-1\,^{\circ}!C^{-1}}$.
• Heat of vaporization: $\approx 540\,\text{cal g}^{-1}$.
• pH formula: $pH=-\log[H^+]$.
• Dehydration reaction: $\text{monomer}<em>n + \text{monomer}</em>m \to \text{polymer}<em>{n+m} + H</em>2O$.
• DNA pitch: $10$ bp/turn, $34\,\text{Å}$ per turn, width $20\,\text{Å}$.

Ethical, Practical & Real-World Connections

• Water management crucial for agriculture, climate policy (heat sinks, ice melt).
• Dietary choices: saturated vs unsaturated fats; fiber (cellulose) benefits digestion.
• Anabolic steroid abuse in sports raises health & fairness concerns.
• Antibiotics target prokaryotic ribosomes/cell walls without harming eukaryotic hosts.
• Mitochondrial DNA tracing informs ancestry & evolutionary biology.
• Buffer systems are foundations for medical interventions (e.g.
  antacids, IV fluids).

Summary

• Life’s complexity emerges from chemical interactions governed by atomic structure.
• Water’s unique chemistry underpins homeostasis and global habitability.
• Organic macromolecules (carbs, lipids, proteins, nucleic acids) arise via dehydration & serve specialized functions.
• Cell theory unites biology; diverse prokaryotic and eukaryotic structures perform integrated roles.
• Understanding these foundations equips us to explore physiology, medicine, biotechnology & environmental science.