BIOSCI 101 Lecture 2

Introduction and Course Context

  • Continuation of previous lecture; brief mention of Tour de France shirt (human physiology/locomotion lecture earlier the same day).
  • Lecturer’s focus differs slightly from the Campbell textbook: shifts toward medical/physiological angles and updates where textbook is outdated.

Organic Molecules in Space and Early Earth

  • Vast quantities of carbon-rich, “grease-like” material detected in space (≈ 10\,000\,000\,000 trillion-trillion t).
  • Mars probes have identified hydrocarbons similar to terrestrial organics.
  • 2014 comet-landing probe drilled core samples; on-board mass spectrometers detected:
    • methylamine
    • ethylamine
    • the amino-acid glycine
    → Demonstrates that protein building blocks are already “floating around” the universe.

The Miller–Urey Experiment (1952)

  • Goal: simulate primordial Earth atmosphere + ocean and test spontaneous synthesis of biomolecules.
  • Apparatus: sterilised glassware, boiling “sea” water, reducing atmosphere (ammonia, \text{H}_2, methane), continuous sparking for energy.
  • After 7\ \text{days} liquid turned deep red → analysis showed several amino acids + metabolic intermediates.
  • Modern re-analysis of stored samples (better detection) shows almost the full set of naturally occurring amino acids.

Natural Energy Sources for Prebiotic Chemistry

  • Beyond lightning: constant solar wind drags electrons from Earth’s core up through crust → continuous electric current.
    • Voltage potential above ground ≈ 100\ \text{V} within a few meters.
    • Reactions may have been catalysed on clays/muds at ocean margins where this current exits.
    • Explains electrically driven synthesis without rare lightning strikes.

Metabolism as the Core of Life – Harold J. Morowitz’s Ten-Compound Hypothesis

  • Comparative biochemistry shows only 10 “central metabolites” feed into virtually every biosynthetic route across all life.
  • All ten arise from:
    • Glycolysis (red line on classic pathway posters).
    • Citric Acid Cycle (blue circle).
  • Implication: these two ancient pathways pre-date DNA/RNA; early chemistry may have occurred slowly on mineral surfaces before enzymes evolved.
  • Examples of downstream products:
    • Amino acids – mostly from citric cycle & glycolytic pyruvate.
    • Nucleotides – from top of glycolysis & pentose-phosphate pathway.
    • Lipids – from acetate emerging at the citric-cycle top.
    • Porphyrins (chlorophyll, haem, cytochromes) from mitochondria-linked reactions.

Polymers and Macromolecules – General Principles

  • Life requires large macromolecules: proteins, polysaccharides, lipids, nucleic acids.
  • Polymerisation mechanism: dehydration synthesis (water removal).
  • Depolymerisation mechanism: hydrolysis (water addition).
  • Cellular composition (approx.): 80\% polymers vs. 20\% monomers/ small molecules.

Simple Reaction Cartoon

  • Short polymer-OH + Monomer-H → (enzyme) → longer polymer + \text{H}_2\text{O} (dehydration).
  • Reverse with \text{H}_2\text{O} + energy → hydrolysis.

Origin-of-Life Locales: Hydrothermal Vents vs. Tidal/Hot-Spring Cycling

  • Vents: plentiful energy, minerals, pH & thermal gradients, but permanently wet (continuous hydrolysis) + high salts.
  • Hot-spring/tidal pools (e.g.
    Yellowstone): dry-wet cycling enables repeated dehydration–rehydration.
    • NASA experiment: heating/cooling + wet/dry cycles polymerised free nucleotides into RNA strands – essentially a primitive natural PCR.
  • Possible resolution: both environments viable; later research shows amino acids can stabilise fatty-acid membranes at vent temperatures.

Lipids

From Acetate to Acyl Chains

  • Fundamental building block: acetate (2C).
  • Sequential dehydration adds acetate units → long fatty-acid (acyl) chains.

Triacylglycerol (TAG)

  • Structure: three fatty acids ester-linked to glycerol backbone.
  • Ester linkage mnemonic: oxygen “Easter-egg” (*little egg perched on C=O-O- bond*).
  • Function: compact energy store – fatty-acyl C–H bonds highly reduced → about 6\times more energy (per g) than carbohydrates.

Saturated vs. Unsaturated

  • Saturated: every C carries H; straight chains; tight packing → solid at low T (e.g. butter, beef tallow).
  • Unsaturated (cis double bonds): kinks prevent close packing → liquids (e.g. sunflower oil); greater membrane fluidity, remain mobile when cold.
  • Physiological example: hibernating squirrels given poly-unsaturated diets can allow body temperature to drop lower than those fed saturated fat.

Phospholipids & Amphipathicity

  • Replace one fatty acid of TAG with phosphate + polar headgroup (e.g. choline).
  • Generates hydrophilic (head) and hydrophobic (tails) regions → self-assemble into:
    • Micelles (single-layer spheres).
    • Liposomes/vesicles (bilayer bubbles).
    • Bilayer sheets (cell membranes).
  • Self-assembly + growth-to-division of vesicles provides a plausible primitive replication mechanism (no DNA required).

Carbohydrates

Classification

  • Monosaccharides: single sugars (glucose, fructose, ribose).
  • Disaccharides: two sugars (maltose = glucose + glucose; sucrose = glucose + fructose; lactose).
  • Oligosaccharides: 3–10 units (dextrans, etc.).
  • Polysaccharides: large (>10) chains or branches.

Storage Polysaccharides

  • Starch (plants) and glycogen (animals) = \alpha(1\rightarrow4)‐linked glucose; occasional \alpha(1\rightarrow6) branches.
    • Glycogen has far more 1\rightarrow6 branches → denser packing (needed in motile animals; main stores = liver & muscle).
  • Stored as granules visible with iodine staining.

Structural Polysaccharides

  • Cellulose: \beta(1\rightarrow4) glucose; linear, rigid, forms wood/plant cell walls; indigestible to most animals (exceptions: termites + gut microbiota).
  • Chitin: \beta(1\rightarrow4) polymer of N-acetyl-glucosamine; exoskeletons of arthropods, fungal cell walls; additional N-acetyl side group enables cross-linking, adds toughness.

Nucleic Acids

  • Functions: information storage (DNA), information transfer & catalysis (RNA). ATP/GTP are nucleotides used for energy & signalling.
  • Ribose precursor synthesised via the pentose-phosphate pathway.

Structural Hierarchy

  1. Polynucleotide (DNA/RNA strand).
  2. Nucleotide = nucleoside + phosphate.
  3. Nucleoside = pentose sugar (ribose/deoxyribose) + nitrogenous base.

Bonds & Orientation

  • Nucleotides join via phosphodiester bonds (dehydration).
  • Strand polarity defined by sugar carbons: 5'\rightarrow3' direction – important in replication/transcription.
  • Deoxyribose lacks an \text{O} at C-2 → DNA chemically more stable than RNA.

Bases

  • Pyrimidines: cytosine (C), thymine (T, DNA only), uracil (U, RNA only).
  • Purines: adenine (A), guanine (G).
  • ATP = adenine + ribose + tri-phosphate; GTP analogous with guanine.

Proteins

  • Built from (≈) 23 proteinogenic amino acids (20 canonical + post-translationally modified forms like hydroxy-proline).
  • Peptide bond forms by dehydration between carboxyl (C-terminus) and amino (N-terminus) groups; cleaved by hydrolysis.
  • Amino-acid side chains:
    • Hydrophobic (non-polar) – tend to fold into protein interiors.
    • Polar/charged (acidic, basic) – often solvent-exposed, participate in catalysis or interactions.
  • Side-chain chemistry dictates 3-D structure and therefore function.

Summary & Key Take-Home Points

  • All major biological polymers (proteins, nucleic acids, polysaccharides, many lipids) form via dehydration synthesis and are broken via hydrolysis.
  • Space and pre-biotic Earth environments already supplied organic building blocks; energy could come from lightning or continuous geo-electrical currents.
  • Central metabolism (glycolysis + TCA) may pre-date genetic information, supplying the ten universal metabolites posited by Morowitz.
  • Lipid self-assembly offers a plausible first step toward compartmentalised proto-cells; vesicle growth/division obey simple physical laws – a primitive replication.
  • Physical properties of saturated vs. unsaturated fats influence membrane fluidity, energy density, and even animal survival strategies.
  • Polymer chemistry governs both life’s structure (cell walls, exoskeletons, membranes) and its information & energy systems (DNA/RNA, ATP).

Lab Exercise Mentioned

  • Course guide includes a term-matching activity: decide which descriptors (e.g., “ester linkage,” “(\beta(1\rightarrow4)) bond,” “charged side chain”) belong to proteins, sugars, or amino acids – useful self-test before exams.