Chemistry of Life — Comprehensive Study Notes Summary & Study Notes

🔬 Overview & Matter vs Energy

Matter has mass and takes up space; it consists of elements and compounds. Energy moves matter (kinetic/potential) and can convert between forms (heat, light, sound).

🧪 Elements of Life & Atomic Structure

About 25 elements are biologically relevant; ~96% of living matter is O, C, H, N (remember CHNOPS including P, S, Ca, K and trace elements). An atom contains protons, neutrons, and electrons (protons = atomic number; mass number = protons + neutrons). Isotopes vary in neutron number; radioactive isotopes are tracers but can be harmful.

⚛️ Electrons & Valence

Electrons occupy discrete shells (energy levels). Valence electrons determine chemical behavior and bonding capacity.

🔗 Chemical Bonds

• Covalent bonds: sharing of electrons. Polar covalent (unequal sharing; e.g., $H_2O$) vs nonpolar covalent (equal sharing; e.g., $O_2$).
• Ionic bonds: attraction between oppositely charged ions (e.g., $Na^+$ and $Cl^-$); environment (like water) affects ionic bonds.
• Hydrogen bonds: weaker interactions between a hydrogen on a polar molecule and an electronegative atom on another.
• Van der Waals interactions: very weak, transient attractions at close range.

🧩 Structure & Reactivity

A molecule's shape determines function (e.g., drug-receptor mimicry). Chemical reactions convert reactants to products and can be reversible; equilibrium occurs when forward and reverse rates balance (no net concentration change). Examples: $6CO_2 + 6H_2O \rightarrow C_6H_{12}O_6 + 6O_2$.

💧 Water: Polarity & Hydrogen Bonding

Water is a polar molecule: unequal electron sharing between O and H creates partial charges. Each $H_2O$ can form up to four hydrogen bonds, underpinning water's special properties.

🌊 Four Emergent Properties of Water

• Cohesion & Adhesion: cohesion (water–water H‑bonding) yields high surface tension; adhesion (water–other surfaces) helps transport in plants (transpiration).
• High Specific Heat & Evaporative Cooling: water resists temperature change (stabilizes climates and organisms) and cools via high heat of vaporization (sweating, plant cooling).
• Expansion on Freezing: ice is less dense than liquid water, so it floats and insulates aquatic life beneath.
• Universal Solvent: polarity makes water an excellent solvent for polar molecules and ions; hydrophilic vs hydrophobic behavior follows "like dissolves like".

⚖️ Acids, Bases & pH

Water autoionizes: $H_2O \leftrightarrow H^+ + OH^-$. Also represented as $H_2O + H^+ \rightarrow H_3O^+$ for hydronium. Definition: acid increases $[H^+]$, base decreases $[H^+]$. Relationship: $[H^+][OH^-] = 10^{-14}$. pH: $pH = -\log[H^+]$ (e.g., if $[H^+] = 10^{-6}$, $pH = 6$).

🧪 Buffers & Environmental Impact

Buffers minimize pH changes (e.g., carbonic acid/bicarbonate system: $H_2CO_3 \leftrightarrow HCO_3^- + H^+$) and are vital for blood pH (~7.4). Ocean acidification: $CO_2 + H_2O \rightarrow H_2CO_3$ lowers ocean pH, threatening reefs.

🧩 Carbon & Molecular Diversity

Carbon is central to organic chemistry due to tetravalence (4 valence electrons), allowing up to four covalent bonds and diverse molecular architectures (chains, rings, branched).

🔁 Isomers & Biological Consequences

Isomers share molecular formulas but differ in arrangement: structural isomers, cis–trans isomers, and enantiomers (mirror images). Enantiomers can have drastically different biological effects (example: thalidomide's enantiomers).

🧪 Functional Groups (behavior determinants)

Common functional groups and typical formulas:

• Hydroxyl: $-OH$ (alcohols)
• Carbonyl: $>C=O$ (ketones/aldehydes)
• Carboxyl: $-COOH$ (acids)
• Amino: $-NH_2$ (amines)
• Sulfhydryl: $-SH$ (thiols)
• Phosphate: $-OPO_3^{2-}$ / $-OPO_3H_2$ (organic phosphates)
• Methyl: $-CH_3$ (methylated compounds)

Behavior of organic molecules is largely defined by these functional groups, not just the carbon skeleton.

🧬 Macromolecules: Monomers, Polymers & Reactions

Monomers link by dehydration synthesis (condensation) to form polymers; polymers are broken down by hydrolysis. Example notation: $\text{A + B} \rightarrow \text{AB} + H_2O$ (dehydration) and reverse for hydrolysis.

🧫 Proteins

• Monomer: amino acid (20 common types). Each has an amino ($-NH_2$), carboxyl ($-COOH$) and R side chain that determines properties (hydrophobic, hydrophilic, acidic, basic).
• Functions: enzymes, defense, storage, transport, hormones, receptors, movement, structure.
• Four levels of structure: primary (sequence), secondary (alpha helix, beta sheet via H‑bonds), tertiary (R‑group interactions: H‑bonds, ionic, disulfide bridges), quaternary (multi‑subunit assemblies).
• Folding principles: hydrophobic residues tend inward; hydrophilic outward; chaperonins assist folding. Denaturation (heat, pH) disrupts structure → loss of function.

🧬 Nucleic Acids

• Monomer: nucleotide = sugar + phosphate + nitrogenous base.
• DNA vs RNA: DNA is usually double‑stranded with sugar deoxyribose and bases $A,T,G,C$; RNA is single‑stranded with sugar ribose and $A,U,G,C$. Information flow: $DNA \rightarrow RNA \rightarrow protein$.

🍞 Carbohydrates

• Monomers: monosaccharides (e.g., glucose). General formula approximated as $(CH_2O)_n$.
• Functions: fuel (starch, glycogen) and structural (cellulose, chitin). alpha vs beta glucose orientation alters digestibility and structure.

🧴 Lipids

• Fats (triglycerides) = glycerol + 3 fatty acids (energy storage). Saturated (no C=C, solid at RT) vs unsaturated (C=C, kinks, liquid at RT).
• Phospholipids: hydrophilic head + hydrophobic tails assemble into bilayers—basis of cell membranes.
• Steroids (e.g., cholesterol) are lipid-based signaling/structural molecules.

These macromolecule concepts explain how cells build structure, store information and energy, and carry out catalysis and signaling.