BIO93 – Thermodynamics, Atoms, Bonds & Biomolecules

Thermodynamics & System Types

• Core Definition: Thermodynamics = physics of energy and matter flow within a system.

• System Classifications
  • Isolated: no exchange of heat, work, or matter (energy constant).
  • Closed: exchange energy (heat/work) but not matter (e.g., greenhouse).
  • Open: exchange both energy and matter; a permeable boundary allows matter passage.

• Laws of Thermodynamics
  • 1st Law (Energy Conservation): In an isolated system the total energy is constant.
  – Open-system form: $\Delta U = Q<em>{in} + W</em>{in} - Q<em>{out} - W</em>{out}$.
  • 2nd Law (Entropy): In an isolated system usable energy ↓, entropy (disorder) ↑; nature trends from order → disorder.
  – Practical consequence: life must remain open (constant energy/matter input) to maintain organization.

• Energy Flow Example (Elephant ears question)
  • Radiated heat ultimately originates from the Sun (answer a).
  • Radiated heat is lost from the biological system; ecosystems are not perfect recyclers of energy—matter cycles, energy flows one-way.

Biological Hierarchy & Emergent Properties

• Levels: Atoms → Molecules → Organelles → Cells → Tissues → Organs/Systems → Organisms → Populations → Communities → Ecosystems → Biosphere.

• Emergent property: the whole > sum of parts; new functions appear at higher levels (e.g., consciousness from neuronal networks).

• Complex Open System: Living organisms continually import energy/matter to counter entropy, enabling emergent order (walking, thinking vs. random gas cloud).

Chemical Elements & Atomic Structure

• Bulk Elements (~96 %): $O\,(65\%),\ C\,(18.5\%),\ H\,(9.5\%),\ N\,(3.3\%)$ .

• Minor Elements (~3.7 %): $Ca\,(1.5\%),\ P\,(1\%),\ K\,(0.4\%),\ S\,(0.3\%),\ Na\,(0.2\%),\ Cl\,(0.2\%),\ Mg\,(0.1\%)$.

• Trace (<0.01 %): Fe, Zn, Cu, I, etc.—critical for enzymes/hormones.

• Sub-Atomic Particles
  • Protons (+), neutrons (0) inside nucleus; electrons (–) in orbitals.
  • Atomic number = # protons.
  • Mass number = protons + neutrons (≈ atomic mass).

• Isotopes
  • Atoms w/ same Z but different neutrons (e.g., $^{12}C,\ ^{14}C$).
  • Radioisotopes decay, emitting particles/energy—used in C-14 dating, metabolic tracers, diagnostics.

• Bohr vs. Quantum Orbitals
  • Electrons occupy shells (n = 1,2,3…) with subshells s, p, etc.
  • Energy absorbed → electron jumps; falls back releasing photon.
  • Heisenberg Uncertainty Principle: cannot know exact position & momentum simultaneously → modern probability clouds.

• Valence Electrons & Reactivity
  • Full valence shell = inert (noble gases).
  • Incomplete shells drive bonding.

• Practice Q (atomic-mass problems) provided for mastery.

Chemical Bonds

• Covalent Bonds (nonmetal–nonmetal)
  • Share electron pairs.
  • Non-polar = equal share (\text{CH}4); polar = unequal (H$2$O).
  • Single, double ($O=O$), triple.

• Ionic Bonds (metal–nonmetal)
  • Electron transfer → ions: cation (+), anion (–); electrostatic attraction forms salts (NaCl).
  • Crystalline lattice in solids; dissociate in polar solvents.

• Hydrogen Bonds
  • H covalently bound to O/N & attracted to another O/N.
  • Weak individually, strong collectively (DNA strands, water cohesion).

• Van der Waals Interactions
  • Transient partial charges form “hot spots”; gecko adhesion.

• Bond Strength Hierarchy in Biology: Covalent > Ionic (in vacuum) ≈ H-bond (in water) > Van der Waals.

• Shape & Charge Principle: Molecular 3-D conformation + distribution of charge determine biological interaction (lock-and-key).

Properties of Water (H$_2$O)

• Cohesion & Adhesion
  • Hydrogen-bond network → surface tension (water strider, capillary rise).
  • Adhesion to polar surfaces explains capillary action.

• Temperature Moderation
  • High specific heat (1 cal g⁻¹ °C⁻¹) buffers temperature; evaporative cooling.

• Expansion Upon Freezing
  • Stable lattice in ice ↓ density; ice floats—aquatic life survives winter.

• Versatile Solvent
  • Polarity forms hydration shells around ions, dissolves polar molecules; large proteins dissolve if surface has polar/charged regions.

• Hydration Shell Example: MgCl$_2$ → $Mg^{2+}\,(aq) + 2Cl^-\,(aq)$ surrounded by water dipoles.

Acids, Bases & pH

• Water Auto-ionization: $2\,H<em>2O \rightleftharpoons H</em>3O^+ + OH^-$.
  • At $25\,^\circ\text{C}$, $[H^+][OH^-] = 10^{-14}$.

• pH Definition: $\text{pH} = -\log[H^+]$; neutral water $[H^+] = 10^{-7}\,\Rightarrow\,\text{pH}=7$.

• Acid = donor ↑$[H^+]$; Base = acceptor ↓$[H^+]$.

• Bicarbonate Buffer (Blood)
  • $CO<em>2 + H</em>2O \leftrightarrow H<em>2CO</em>3 \leftrightarrow H^+ + HCO<em>3^-$. • Carbonic anhydrase speeds first equilibrium. • Hyperventilation removes $CO</em>2$ → pH rises (alkalosis).

• Practice Q (Substance A neutralizes low-pH substance: correct answer D—base decreased proton concentration).

Carbon: The Backbone of Life

• Valence = 4 → forms up to 4 covalent bonds → tetravalent geometry $109.5^{\circ}$ (sp³) or planar with double bonds (sp²).

• Diversity
  • Chains vary length, branching, rings, double bonds, heteroatom substitution.
  • Hydrocarbons store energy (fats, fossil fuels).

• Stanley Miller Experiment demonstrated abiotic synthesis of organic molecules (supported idea life’s building blocks can form naturally).

Isomers & Stereochemistry

• Structural (Constitutional) Isomers: different connectivity (butane vs. isobutane).

• Geometric (cis/trans) Isomers: differ around double bond (cis-2-butene vs. trans-2-butene; cis fatty acid bend vs. trans straight—influences membrane fluidity).

• Enantiomers: mirror images (L- & D-alanine).
  • Biological systems usually use one enantiomer (e.g., S-ibuprofen active).

Functional Groups (Key Reactive Moieties)

• Hydroxyl (–OH): polar, hydrogen bonds, alcohols.

• Carbonyl (C=O): aldehydes (end) & ketones (internal); sugars classification (aldose/ketose).

• Carboxyl (–COOH): acidic, donates $H^+$, forms carboxylate (–COO⁻).

• Amino (–NH₂): basic, accepts $H^+$ (→ –NH₃⁺).

• Sulfhydryl (–SH): forms disulfide bridges (protein tertiary stabilization) — ANSWER to strong covalent-bond quiz.

• Phosphate (–OPO₃²⁻): acidic, high-energy bonds (ATP), adds negative charge.

• Methyl (–CH₃): non-polar, gene expression & hormone activity modulation.

• Quiz Connections
  • Ketones/Aldehydes = Carbonyl group.
  • Amino-acid backbone contains both Amino and Carboxyl groups.

Macromolecules: Formation & Breakdown

• Monomer ↔ Polymer
  • Dehydration (condensation): monomer + monomer → polymer + $H<em>2O$. • Hydrolysis: polymer + $H</em>2O$ → monomers (reverse).
  • General polymer = long chain of repeating subunits (carbs, proteins, nucleic acids).
  • Lipids are large but not true polymers.

Carbohydrates

• Functions: energy (fuel), structural (cell walls, exoskeleton), cellular recognition.

• Monosaccharides: $\text{(CH}<em>2\text{O)}</em>n$; classify by carbonyl type & carbon count.
  • Trioses (C₃), pentoses (C₅), hexoses (C₆).
  • Glucose, fructose, galactose are structural isomers (C₆H₁₂O₆).
  • Ring ↔ linear equilibrium; α vs. β anomer defined by orientation of C1 –OH.

• Disaccharides: two monosaccharides linked via glycosidic bond (dehydration).
  • Maltose = glucose-α1→4-glucose.
  • Lactose = galactose-β1→4-glucose.
  • Sucrose = glucose-α1→2-fructose.

• Polysaccharides
  • Storage:
  – Starch (plants): amylose (unbranched α1→4) & amylopectin (branched α1→6).
  – Glycogen (animals): highly branched; stored in liver & muscle.
  • Structural:
  – Cellulose (plants): β1→4 glucose; straight chains → microfibrils; indigestible by humans.
  – Chitin (arthropods/fungi): β1→4 N-acetyl-glucosamine; tough exoskeleton.

• Molecular Formula Question: Linking 3 glucoses via two dehydration reactions removes $2H<em>2O$ → $C</em>{18}H<em>{32}O</em>{16}$ (choice D).

Integrative Significance & Exam Connections

• Physics → Chemistry → Biochemistry → Biology: mastery of atomic/energetic principles underpins understanding of life.

• Shape-Charge Interplay recurs in enzyme catalysis, receptor-ligand binding, DNA base pairing.

• Elemental Composition connects to nutrition (need Fe, Mg, Zn), ecology (biogeochemical cycles), medicine (radioisotope imaging).

• Water Chemistry & pH vital for cellular homeostasis, ocean acidification, agriculture (soil pH).

• Organic Molecule Synthesis (Miller–Urey) informs origin-of-life research and synthetic biology.

Example/Hypothetical Scenarios Mentioned

• Cooling elephants vs. heat source (sun).

• Farmer Jim dissolving $MgCl_2$: ionic lattice breaks via hydration shells; Mg (chlorophyll center) & Cl (osmotic balance) aid crops.

• Hair “perms” break/reform disulfide (–S–S–) bonds in keratin.

Key Equations & Numbers (LaTeX Format)

• Energy balance (open system): $\Delta U = \sum Q<em>{in} + \sum H</em>{in} - \sum Q<em>{out} - \sum H</em>{out} - W_{system}$.

• pH: $\text{pH} = -\log[H^+]$, $[H^+][OH^-] = 10^{-14}$ at $25\,^\circ\text{C}$.

• Atomic relationships: $\text{Mass\,No.} = p + n$.

• Dehydration polymerization: $\text{C}<em>6\text{H}</em>{12}\text{O}<em>6 \times 3 - 2\,H</em>2O = \text{C}<em>{18}\text{H}</em>{32}\text{O}_{16}$.

Ethical & Practical Implications

• Radioisotope use demands safety and ethical oversight (medical exposure, nuclear waste).

• Trans fats (trans-isomers) linked to cardiovascular disease → public health policy on food labeling.

• Buffering capacity of blood highlights importance of respiratory/renal health.