Chapter 02 Part B – Chemistry Comes Alive (Study Notes)

Part 2 – Biochemistry

General Classification of Biomolecules

• Biochemistry = study of chemical composition & reactions of living matter.
• Two fundamental categories:
  • Inorganic compounds – water, salts, many acids/bases; do NOT contain C.
  • Organic compounds – carbohydrates, lipids (fats), proteins, nucleic acids; contain C, usually large, covalently-bonded.
• Both inorganic & organic chemicals are equally essential to life.

2.6 Inorganic Compounds

Water – Most Abundant & Important Inorganic Molecule

• Accounts for ≈ 60–80 % of volume of living cells.
• Unique properties underpin life-supporting roles:
  • High heat capacity
  – Absorbs/releases large heat w/ little T° change → buffers sudden body T° shifts.
  • High heat of vaporization
  – Requires large heat input to evaporate → perspiration = efficient cooling.
  • Polar solvent properties
  – Dissolves/dissociates ionic substances; forms hydration shells around large charged solutes (e.g., proteins); principal transport medium.
  – Fig 2.12 shows dissociation of NaCl into Na^+ & Cl^- with hydration shells.
  • Reactivity
  – Reactant/product in hydrolysis & dehydration synthesis.
  • Cushioning
  – Physically protects organs (e.g., cerebrospinal fluid around CNS).

Salts

• Ionic compounds that dissociate in water → separate cations (+) & anions (–) except H^+ / OH^-.
• Dissolved ions = electrolytes (conduct current).
• Specialized physiological roles:
  • Na^+ & K^+ → nerve impulse & muscle contraction.
  • Ca^{2+} → blood clotting, muscle, bones.
  • Fe^{2+/3+} → hemoglobin.
• Ionic balance vital for homeostasis.
• Common physiological salts: NaCl, KCl, CaCO3, Ca3(PO4)2 (bone).

Acids & Bases

• Electrolytes that ionize & dissociate in water.
• Acids (proton donors) release H^+ (bare protons).
  • Key acids: HCl, H2CO3, HC2H3O_2 (HAc).
• Bases (proton acceptors) pick up H^+; dissociation releases OH^-.
  • Key bases: bicarbonate HCO3^-, ammonia NH3.

pH – Acid–Base Concentration

• pH = -\log[H^+] \;(\text{mol L}^{-1}); scale 0\rightarrow14 (logarithmic; 1 pH unit = 10× change in [H^+]).
  • Acidic: pH

Neutralization

• Mixing acid + base → displacement reaction → salt + water.

Buffers

• Resist large/abrupt pH swings by:
  • Releasing H^+ when pH rises,
  • Binding H^+ when pH falls.
• Convert strong acids/bases → weak equivalents.
• Major physiological system: carbonic acid–bicarbonate: CO2 + H2O \leftrightarrow H2CO3 \leftrightarrow H^+ + HCO_3^-.
• Clinical note: enzymes need narrow pH; arterial pH<6.85 rarely survivable.

2.7 Organic Compounds: Synthesis & Hydrolysis

• Carbon: electroneutral, forms 4 covalent bonds → versatility.
• Four major biomolecule classes: carbohydrates, lipids, proteins, nucleic acids.
• Many are polymers (chains of repeating monomers).
  • Dehydration synthesis → joins monomers, releases H2O. • Hydrolysis → breaks bonds, consumes H2O (Fig 2.14).

2.8 Carbohydrates

• Sugars & starches; elements C, H, O in 2 H : 1 O ratio.
• Classes:
  • Monosaccharides – 3-7 C simple sugars, formula (CH2O)n.
  – Pentoses: ribose, deoxyribose.
  – Hexose: glucose (“blood sugar”).
  • Disaccharides – two monosaccharides; too large for membrane transport.
  – Sucrose (glucose+fructose), maltose, lactose.
  – Made by dehydration: glucose + fructose \rightarrow sucrose + H_2O.
  • Polysaccharides – long polymers; insoluble.
  – Starch (plant storage), glycogen (animal storage, esp. liver & muscle).

2.9 Lipids

• Elements C, H, O (less O than carbs) ± P; water-insoluble.
• Four main types:

Triglycerides (Neutral Fats)

• 3 fatty acids + glycerol (via dehydration).
• Functions: energy storage, insulation, protection.
• Fatty-acid variants:
  • Saturated – all single C–C bonds; straight chains pack tightly → solid at RT (butter).
  • Unsaturated – ≥1 C=C; kinked → liquid at RT (olive oil).
  – Trans fats: artificially hydrogenated; unhealthy.
  – Omega-3: cardioprotective.

Phospholipids

• Glycerol + 2 fatty acids + phosphate group.
• Amphipathic: polar hydrophilic head / non-polar hydrophobic tails.
• Primary component of cell membranes (bilayer).

Steroids

• Four interlocking hydrocarbon rings.
• Cholesterol = parent molecule (produced by liver & dietary).
• Precursor for vitamin D, steroid hormones (cortisol, sex hormones), bile salts; stabilizes plasma membranes.

Eicosanoids

• Derived from arachidonic acid (20-C fatty acid) in membranes.
• Prostaglandins: roles in blood clotting, BP regulation, inflammation, labor.
• Actions inhibited by NSAIDs (aspirin, ibuprofen).

2.10 Proteins

• ≈ 20–30 % of cell mass; most functionally diverse.
• Elements C, H, O, N ± S, P.
• Monomers = 20 amino acids linked by peptide bonds (amide linkage).
  • Each aa has amino (–NH₂), carboxyl (–COOH), variable R-group → acid/base behavior (amphoteric).

Structural Organization

1. Primary – linear aa sequence.
2. Secondary – α-helix coils; β-pleated sheets (H-bonds).
3. Tertiary – 3-D folding via R-group interactions (disulfide, ionic, H-bond, hydrophobic).
4. Quaternary – aggregation of ≥2 polypeptides (e.g., hemoglobin).

Protein Categories

• Fibrous (structural) – strand-like, water-insoluble, stable (collagen, keratin, elastin).
• Globular (functional) – compact, water-soluble, sensitive (enzymes, antibodies, hormones, chaperones).

Denaturation

• Loss of 3-D shape (↓pH, ↑T°).
• Usually reversible if mild; irreversible if extreme (cooking egg).

Enzymes – Biological Catalysts

• Globular proteins; speed rxns by lowering activation energy without being consumed.
• Most are holoenzymes = apoenzyme (protein) + cofactor (metal ion) or coenzyme (vitamin-derived).
• Highly specific; names end in –ase (hydrolase, oxidase).
• Mechanism:
  1. Substrate binds active site → enzyme–substrate complex.
  2. Complex rearranges → product.
  3. Product released; enzyme free for new cycle (millions/min).

2.11 Nucleic Acids

• Largest biomolecules; elements C, H, O, N, P.
• Monomer = nucleotide = nitrogenous base + pentose sugar + phosphate.

DNA – Deoxyribonucleic Acid

• Double-stranded helix in nucleus.
• Sugar = deoxyribose.
• Bases: purines A, G; pyrimidines C, T.
• Complementary pairing: A–T, G–C via H-bonds.
• Stores genetic blueprint for protein synthesis.

RNA – Ribonucleic Acid

• Single-stranded, mostly cytoplasmic.
• Sugar = ribose; U replaces T.
• Types:
  • mRNA – carries genetic message.
  • tRNA – brings amino acids.
  • rRNA – forms ribosomes.

2.12 ATP – Biological Energy Currency

• Energy from glucose catabolism captured in ATP (adenosine triphosphate).
• Structure: adenine + ribose + three phosphate groups.
• Hydrolysis of terminal phosphate releases energy:
  ATP + H2O \rightarrow ADP + Pi + \text{energy}
  ADP + H2O \rightarrow AMP + Pi + \text{energy}
• Phosphorylation – transferred phosphate energizes target molecules → drives:
  • Chemical work (biosynthesis).
  • Transport work (pumping ions).
  • Mechanical work (muscle contraction).
• Provides immediate, usable energy for cellular processes.

Ethical & Clinical Connections

• Accurate pH vital for enzymatic activity; CPR outcomes worsen at arterial pH=7.0, survival rare below 6.85.
• NSAIDs modulate prostaglandin-mediated inflammation but carry gastric/renal side effects—illustrates biochemical basis of pharmacology.

Concept Integration & Real-World Relevance

• Carbon’s tetravalence underpins diversity of organic chemistry → structural & functional complexity in biology.
• Water’s properties explain phenomena from climate regulation to perspiration cooling.
• Understanding lipids informs cardiovascular health (trans fats vs. omega-3).
• Knowledge of protein denaturation applies to cooking, fever response, sterilization.
• ATP concept links metabolism, exercise physiology, and pharmacologic agents targeting cellular energetics (e.g., cyanide inhibits ATP production).