Memory tricks for the chemistry behind the body

Every atom has a nucleus containing protons (positively charged) and neutrons (neutral), surrounded by electrons (negatively charged) in energy shells. Atomic number = number of protons — this defines the element. Carbon always has 6 protons. Atomic mass = protons + neutrons. Isotopes = same protons, different neutrons (same element, different mass). Ions = atoms that have gained or lost electrons — Na+ lost one electron, Cl- gained one. Valence electrons (outermost shell) determine how atoms bond. Atoms with incomplete outer shells are chemically reactive — they want to achieve a full outer shell (octet rule).

Covalent bonds: atoms SHARE electrons — strongest bond. Nonpolar covalent = equal sharing (O2, H2). Polar covalent = unequal sharing (water — oxygen hogs electrons). Ionic bonds: electrons TRANSFERRED — one atom becomes + ion, other becomes − ion → electrostatic attraction. NaCl → Na+ and Cl-. Dissolve in water (dissociate). Hydrogen bonds: weak attraction between slightly positive H and slightly negative atom (O, N, F). Hold water molecules together, stabilize DNA double helix, maintain protein shape. Individual H bonds are weak but collectively very strong.

Water makes up 60-75% of body weight and is involved in virtually every physiological process. Cohesion: water molecules attract each other (hydrogen bonds) → surface tension → allows blood to flow through capillaries. Adhesion: water sticks to other polar surfaces → helps water move up in plants, through capillaries. Universal solvent: polar molecule dissolves ionic and polar substances → transports nutrients, wastes, and gases in blood. High specific heat: water resists temperature change → body temperature stays stable despite metabolic heat generation. Also: high heat of vaporization → sweating cools effectively.

pH measures the concentration of hydrogen ions (H+). Lower pH = more H+ = more acidic. Scale is logarithmic — pH 6 has 10× more H+ than pH 7. Acids donate H+ (HCl, lactic acid, carbonic acid). Bases accept H+ (NaOH, bicarbonate HCO3-). Normal blood pH = 7.35–7.45. Acidosis: pH below 7.35 — proteins denature, enzymes stop working, death if severe. Alkalosis: pH above 7.45 — muscle tetany, cardiac arrhythmias. Buffer systems prevent drastic pH changes: bicarbonate buffer (fastest acting), protein buffer, phosphate buffer. Respiratory system (CO2) and renal system (HCO3-) provide long-term pH control.

Carbohydrates: monomer = monosaccharide (glucose). Polymer = polysaccharide (glycogen, starch). Primary energy source. 4 kcal/g. Nucleic acids: monomer = nucleotide. Polymers = DNA (genetic code) and RNA (protein synthesis). Lipids: not polymers — glycerol + fatty acids. Energy storage (9 kcal/g), membrane structure (phospholipids), hormones (steroids). Proteins: monomer = amino acid (20 types). Polymer = polypeptide. Most versatile — enzymes, structural (collagen), transport (hemoglobin), antibodies, hormones. Shape determines function.

Primary structure: the sequence of amino acids — determined by DNA. Secondary structure: local folding patterns held by hydrogen bonds — alpha helix (coiled) and beta pleated sheet (folded accordion). Tertiary structure: overall 3D shape of one polypeptide — held by multiple bond types (H bonds, disulfide bridges, hydrophobic interactions). THIS is the functional shape. Quaternary structure: two or more polypeptide chains assembled — example: hemoglobin (4 chains). Denaturation: heat, pH change, or chemicals disrupt hydrogen bonds → protein loses shape → loses function. Egg white coagulating when cooked = denaturation.

Enzymes are biological catalysts — they lower the activation energy required for a chemical reaction, dramatically speeding it up without being consumed. Active site: the specific region where substrate binds. Lock and key model: rigid active site fits one specific substrate. Induced fit model: active site changes shape slightly to accommodate substrate — more accurate. Enzyme specificity: each enzyme acts on one substrate (substrate specificity). Factors affecting enzyme activity: temperature (optimal ~37°C for body enzymes — too hot = denaturation), pH (each enzyme has optimal pH), cofactors (minerals like Zn2+, Mg2+), coenzymes (vitamins). Inhibitors: competitive (block active site) or noncompetitive (change enzyme shape).

ATP (adenosine triphosphate) is the universal energy currency of all cells. Structure: adenosine + 3 phosphate groups. The bond between the 2nd and 3rd phosphate is high-energy. Hydrolysis: ATP + H2O → ADP + Pi + ~7.3 kcal/mol energy released. This energy powers muscle contraction, active transport (Na+/K+ ATPase), biosynthesis, and cell signaling. ATP is regenerated by cellular respiration: glucose + O2 → CO2 + H2O + ~38 ATP. The cell cycles through its entire ATP supply every 1-2 minutes at rest — millions of ATP molecules per second during exercise. Creatine phosphate provides immediate ATP backup in muscle (first 10 seconds).

DNA: double-stranded helix, deoxyribose sugar, bases A-T and G-C, stays in nucleus, stores genetic information long-term. RNA: single-stranded, ribose sugar, bases A-U and G-C (uracil replaces thymine), found throughout cell. Three types of RNA: mRNA (messenger — carries code from nucleus to ribosome), tRNA (transfer — brings amino acids to ribosome), rRNA (ribosomal — forms ribosomes). Central dogma: DNA → transcription → mRNA → translation → protein. Mutations = permanent changes in DNA sequence → may alter protein function.