Atoms, bonds, water, pH, and the four macromolecules — the chemistry of life explains how the body is built and fueled at the molecular level. Master these concepts and cellular physiology becomes far more intuitive.
Three subatomic particles — charge, location, and what determines element identity
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).
Protons
Positive charge, in nucleus. Atomic number = proton count. Defines the element.
Neutrons
No charge, in nucleus. Isotopes differ in neutron count.
Electrons
Negative charge, in shells. Valence electrons determine bonding behavior.
Three chemical bond types — strength, mechanism, and body importance
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.
Covalent
Shared electrons. Single, double, triple bonds. Strongest. DNA backbone.
Ionic
Electron transfer → ions. Electrolytes in body. Dissolve in water.
Hydrogen
Weak but abundant. Water cohesion, DNA base pairing, protein folding.
Van der Waals
Weakest — temporary dipoles. Important in enzyme-substrate fit.
Four unique properties of water that make life possible
Why water is essential for life — four key properties explained
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.
Cohesion
H2O sticks to H2O. Surface tension. Capillary action for blood.
Adhesion
H2O sticks to polar surfaces. Helps movement through vessels.
Solvent
Dissolves ionic and polar substances. Blood is 92% water.
High heat capacity
Resists temperature change. Sweating removes large amounts of heat.
pH Scale
0–6 Acid · 7 Neutral · 8–14 Base — Blood must stay 7.35–7.45
Four levels of protein structure — from amino acid sequence to functional protein
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.
Primary
Amino acid sequence. Set by DNA. Peptide bonds link amino acids.
Secondary
Alpha helix + beta sheet. Hydrogen bonds stabilize. Local patterns.
Tertiary
Overall 3D shape. Functional shape. Disulfide bridges, H bonds, hydrophobic core.
Enzymes lower activation energy · Lock and key OR induced fit
Biological catalysts — speed up reactions without being consumed
How enzymes work — and what can stop them
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).
Activation energy
Energy needed to start a reaction. Enzymes lower this — speed up reaction rate.
Induced fit
Active site molds around substrate — more accurate than rigid lock-and-key model.
Denaturation
Heat or pH extremes → enzyme loses shape → loses activity. Usually irreversible.
Inhibitors
Competitive: blocks active site. Noncompetitive: binds elsewhere, changes shape. Many drugs work this way.
ATP — Energy Currency
ATP → ADP + Pi + Energy — the universal energy transfer molecule
Adenosine Triphosphate — stores and releases energy via phosphate bonds
How ATP stores and releases energy — why it is called the energy currency
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).
ATP structure
Adenine + ribose + 3 phosphates. High-energy bond between P2 and P3.
Energy release
ATP → ADP + Pi + ~7.3 kcal. Powers all cellular work.
DNA stores genetic code · RNA carries and executes genetic instructions
DNA vs RNA — five key differences every A&P student must know
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.
DNA
Double helix, deoxyribose, A-T G-C. In nucleus. Genetic blueprint. Very stable.
Transfer. Brings amino acids to ribosome. Anticodon matches mRNA codon.
Central dogma
DNA → RNA (transcription) → Protein (translation). Information flows one direction.
🎓 Common Exam Questions
Q: What are the four macromolecules, their monomers, and key functions?
A: Carbohydrates: monomer = monosaccharide (glucose, fructose, galactose). Functions: immediate energy (glucose), energy storage (glycogen in animals, starch in plants), structural (cellulose in plants, chitin in fungi/insects). Key bonds: glycosidic bonds. Proteins: monomer = amino acid (20 types). Functions: structural (collagen, keratin), enzymatic, transport (hemoglobin), signaling (hormones), immune (antibodies), movement (actin, myosin). Key bonds: peptide bonds. Lipids: not polymers — glycerol + 3 fatty acids (triglycerides). Functions: long-term energy storage, membrane structure (phospholipids), hormones (steroids), insulation. Nucleic acids: monomer = nucleotide (sugar + phosphate + base). DNA stores genetic info; RNA expresses it. Key bonds: phosphodiester bonds.
Q: What are the properties of water and why are they important for life?
A: Polarity: O slightly negative, H slightly positive → hydrogen bonds between water molecules → high specific heat (resists temperature change — stabilizes body temp), high heat of vaporization (sweating cools effectively), cohesion (water molecules stick together — surface tension), adhesion (water sticks to other surfaces — capillary action in blood vessels), solvent properties (dissolves polar/ionic substances — 'universal solvent'). Density: solid (ice) less dense than liquid → ice floats → aquatic life survives winter. Ionization: water autoionizes → H+ and OH- → pH scale. Amphipathic molecules (phospholipids) arrange in water → cell membranes spontaneously form. Life is water-based because of these unique properties.
Q: Explain pH, buffers, and why pH matters in the body.
A: pH = -log[H+]. Scale 0-14: <7 acidic, 7 neutral, >7 basic/alkaline. Each unit = 10-fold change in [H+]. Body pH = 7.35-7.45 (slightly alkaline). Acidosis: pH <7.35 → alters protein shape → enzyme dysfunction → potentially fatal. Alkalosis: pH >7.45 → similar consequences. Buffers: resist pH changes by absorbing or releasing H+. Body's main buffer systems: Bicarbonate buffer (HCO3-/H2CO3) — most important in blood; pH 7.4 = buffering capacity. Phosphate buffer (HPO4/H2PO4) — important in urine and intracellular fluid. Protein buffer (histidine residues on Hgb and plasma proteins) — largest total buffering capacity. Respiratory compensation: fast (seconds — CO2 adjustment). Renal compensation: slow (hours-days — H+ and HCO3- adjustment).
Q: What is ATP and how is it used as energy currency?
A: ATP (adenosine triphosphate): adenosine + 3 phosphate groups. Energy stored in bonds between phosphates (especially β-γ bond). ATP → ADP + Pi: releases ~7.3 kcal/mol free energy → powers cellular work. Three types of work: mechanical (muscle contraction, cilia), transport (active transport pumps), chemical (biosynthetic reactions). ATP is regenerated by: Cellular respiration (aerobic): glucose + O2 → CO2 + H2O + ~36-38 ATP. Glycolysis (cytoplasm, no O2 needed): 2 ATP net. Krebs cycle (mitochondrial matrix): 2 ATP + electron carriers. Electron transport chain (inner mitochondrial membrane): ~34 ATP via oxidative phosphorylation. Fermentation (anaerobic): only 2 ATP from glycolysis → lactic acid (muscles) or ethanol (yeast). Phosphocreatine: immediate ATP regeneration in muscle (3-15 seconds of maximal effort).
Q: How do enzymes work and what factors affect enzyme activity?
A: Enzymes are biological catalysts — lower activation energy without being consumed. Active site: specific 3D region complementary to substrate (induced fit model — active site flexes to bind). Lock-and-key: older model (rigid complementarity). Factors affecting activity: Temperature: increases rate until denaturation occurs (optimal ~37°C for body enzymes). pH: optimal pH varies (pepsin pH 2, trypsin pH 8) — alters ionization of active site residues. Substrate concentration: rate increases until Vmax (all active sites saturated). Michaelis constant (Km): substrate concentration at half-Vmax — lower Km = higher affinity. Inhibition: Competitive — competes for active site, overcome by increasing substrate. Noncompetitive — binds allosteric site, changes active site shape, cannot be overcome by substrate. Irreversible — covalently binds (aspirin inhibits COX permanently). Cofactors/coenzymes: inorganic ions (Mg2+, Zn2+) or organic molecules (vitamins) required for activity.