BIOSCI 106 Lecture 1

Course Logistics & Pep Talk

Initial reassurance: course has a $93\%$ overall pass rate; laboratories have a $98\%$ pass rate with an average mark of $91\%$ – “very passable, don’t panic.”
First two modules are chemistry-heavy; class contains students with widely different science backgrounds (some strong in chemistry, others in biology/physics).
• Catch-up tools provided; staff encourage you to “always tell us” if you struggle – help is available.
Class representative needed for both morning and afternoon streams (announcement by Julie).

Support & Extra Resources

“Diagnostic Quiz” (≈25 Qs) covers very basic chemistry/biology to locate knowledge gaps; no marks attached; immediate feedback with explanations.
Additional reading & even a (discouraged) research paper link for the curious.
Module pages:
• Slides (pre-lecture + updated post-lecture)
• Comprehensive worksheet for entire section (includes functional groups, protein structure, etc.)
• Extra background materials appear in an “Additional Stuff” folder after first week.
• Discussion notes + worksheet answers released ≈2–2.5 wks before test.
Weekly online quizzes: unlimited attempts, only best 10 count toward grade. Some quiz items require worksheet prep.
Tutorial session still to be scheduled.
Lecture recordings: morning session posted when complete; if morning overruns, afternoon version (faster, “gets act together”) is uploaded by 9 p.m.

Big Picture Questions & Learning Objectives

Lecture theme: “Aliens like us – a 14 billion-year history of biochemistry.”
Guiding questions:
• Are we alone?
• What evidence would we seek on Mars?
• Would aliens look/biochemically behave like us?
Formal objectives
1. Argue that biochemistry is governed by universal physical laws.
2. Outline a plausible origin for chemical elements and, later, biological molecules.
3. Explain why biology must be efficient and how modular evolution achieves that.

Key Chemical Vocabulary (must know)

Element: pure substance of one atom type.
Molecule: ≥2 atoms bonded.
Monomer → Polymer (Residues): Small repeating unit incorporated into biopolymers; once linked, each unit is called a residue.
Functional group: specific atom cluster conferring predictable chemical behavior (e.g., hydroxyl $–OH$ , carboxyl $–COOH$ , amine $–NH2$ , phosphate $–PO4^{3-}$ ).

Origin of the Elements (14 Ga ➜ Present)

$\sim14\,\text{Ga}$ : Big Bang → only $H_2$ & $He$ .
Gas clouds condense → 1st-generation stars.
Stellar fusion under high heat/pressure forges heavier nuclei ( $C, N, O, P, S,$ metals…).
Supernova explosions scatter elements across space.
Dust & gas reconsolidate → 2nd-generation stars (our Sun) and planets; Earth forms in habitable zone.

Periodic Table of Life (textbook graphic)

Tier-1 “bulk” atoms: $H, C, N, O$ (+ $P, S$ ).
• Abundance correlates with ability to form strong, versatile covalent bonds.
• $H$ and $O$ dominant due to prevalence of water ( $H_2O$ ~90 % of human body mass).
Tier-2/3/4 trace atoms (e.g., $Na, K, Ca, Mg, Fe, Cu, Zn, Cr$ ) enable catalysis, electron transfer, signalling; some are toxic in large doses (e.g., chromium).

Central Role & Geometry of Carbon

Valence = 4 → can create single, double, or triple bonds; scaffold for complex, diverse structures.
Typical geometries
• Tetrahedral: $109.5^{\circ}$
• Trigonal planar: $120^{\circ}$
• Linear: $180^{\circ}$
Example drug molecule displayed (anticancer candidate) illustrates mixture of C–C single/double/triple bonds with hetero-atom decorations (N, O, S) for functional diversity.

Requirements for the Emergence of Life on Early Earth (≈4 Ga)

Liquid water – universal solvent, medium for reactions.
Simple reducing gases: $CH4, NH3, H_2, CO,$ etc.
Energy source – lightning, UV, geothermal/volcanic heat ( $\text{→}$ electrical discharge).
Reducing atmosphere (very little $O_2$ ) – prevents oxidative destruction, facilitates bond formation.

Laboratory Test of the Hypothesis: Miller–Urey (1953)

Apparatus: boiling flask (water steam) → gas chamber containing the reducing mix ${CH4, NH3, H2, H2O}$ → continuous electrical spark $\big(E \approx 60\,000\,\text{V}\big)$ → condenser → aqueous “primordial soup” trap.
Results: within a week produced a rich mixture of organic molecules, notably ALL 20 proteinogenic amino acids plus several non-natural ones.
Later variants (2007 re-analysis, phosphate-buffered systems) also yield nucleobases and simple sugars.
Demonstrates plausibility of prebiotic synthesis without enzymes.

Modularity & Biological Efficiency

Building macromolecules atom-by-atom would exceed the universe’s age; evolution solved this via prefabricated parts (monomers) — analogous to shipping-container architecture.
Four major macromolecule classes
1. Polypeptides (proteins) – polymers of amino-acid residues.
2. Polynucleotides (DNA/RNA) – polymers of nucleotide residues.
3. Polysaccharides (cellulose, glycogen) – polymers of monosaccharide residues.
4. Lipids – do not polymerise but self-assemble into membranes/compartments (critical for cellular life).
Polymer formation mechanism: condensation (dehydration) reaction → monomer₁ + monomer₂ $\rightarrow$ polymer + $H_2O$ .
• Same chemical logic across proteins (peptide bond), nucleic acids (phosphodiester bond), carbohydrates (glycosidic bond).

Key Bond & Functional Examples

Peptide bond: $\mathrm{\ –C(O)NH–}$ link between amino-acid $–COOH$ & $–NH_2$ .
Glycosidic bond in cellulose: $\beta\,(1\rightarrow4)$ linkage between glucose residues.
Phosphodiester bond in DNA: $\mathrm{–PO_4^{2-}}$ bridges $3'$ -OH to $5'$ -OH of adjacent sugars.

Functional-Group Recognition vs Memorisation Philosophy

Course will provide structural figures in assessments; emphasis on interpreting chemical behavior (polarity, hydrogen-bonding, hydrophobicity, acidity/basicity, aromaticity) rather than rote name recall.
• Eg. Recognise tyrosine side chain: aromatic ring = hydrophobic, $–OH$ can H-bond.

Water – Why It Matters (worksheet pp. 18–19)

High dielectric constant: dissolves ions, stabilises charges.
Cohesion & adhesion: support capillary action, blood flow.
High specific heat & heat of vaporisation: thermal buffering.
Participates directly in hydrolysis/condensation.

Searching for Extraterrestrial Life

Mars rovers seek evidence of past liquid water, organic molecules, and redox-active minerals rather than “little green heads.”
If life is elsewhere, expectation: carbon-based chemistry operating in aqueous environments, using proteins (or analogues) for catalysis, nucleic-acid-like polymers for information, lipid-like assemblies for compartmentalisation, and energy currencies analogous to ATP.

Class Poll & Humour Highlights

Majority believe aliens exist; mixed views on similarity to humans. Answers ranged from serious (shared carbon chemistry) to comedic (Mark Zuckerberg cameo, licking communication, fear of POPHL 111).

Take-Home Messages

The laws of chemistry/physics are universal, hence biochemistry should be similar everywhere (universality principle).
Stellar evolution supplies the elemental toolkit; prebiotic chemistry can spontaneously build life’s monomers under plausible early-Earth conditions.
Efficiency via modularity is essential; life constructs complexity by linking ready-made parts.
Studying functional groups, reaction mechanisms, and structure–function relationships is far more valuable than memorising molecule names.
You are literally “made of stardust” – every atom in your body was forged in ancient stars, a reminder of our cosmic connection.

“Fear nothing. You have a little piece of stardust in you – every single one of you.” – Lecture closing quote

Exam & Study Tips (implicit from lecture)

Do diagnostic quiz to pinpoint weak chemistry areas early.
Use worksheet problems both during and after lectures; some quiz items rely on them.
Focus revision on:
• Recognising bond types/angles, functional groups, condensation vs hydrolysis.
• Explaining why certain atoms dominate biomolecules.
• Applying the universality argument to hypothetical extraterrestrial scenarios.
Expect a few more mid-semester test questions from Lecture 1 this year – easy marks if concepts above are clear.