Chemistry Comes Alive
Atoms, bonds, water, pH and the molecules of life
By the end of this unit you can…
- ✓Describe atomic structure, isotopes and the elements that make up the body
- ✓Compare ionic, covalent (polar/nonpolar) and hydrogen bonds
- ✓Classify chemical reactions and list factors that change their rate
- ✓Explain the properties of water, acids, bases, pH and buffers
- ✓Describe the building blocks and roles of carbohydrates, lipids, proteins, nucleic acids and ATP
- ✓Explain how enzymes work and why denaturation destroys function
Key terms
Practice →1Matter, energy & elements
Matter is anything that occupies space and has mass. Energy is the capacity to do work — it is either kinetic (doing work, energy in action) or potential (stored).
- Chemical energy
- Stored in the bonds of molecules (e.g. glucose, ATP). Released when bonds break.
- Electrical energy
- Movement of charged particles — ions crossing cell membranes create nerve impulses.
- Mechanical energy
- Directly moves matter — muscles shortening move your legs.
- Radiant (electromagnetic) energy
- Travels in waves — visible light (vision), UV light (vitamin D synthesis).
Energy conversions are never 100% efficient: some energy is always lost as heat. That “lost” heat is part of what keeps your body warm.
About 96% of body mass is just four elements: oxygen (≈65%), carbon (≈18.5%), hydrogen (≈9.5%) and nitrogen (≈3.2%). Calcium, phosphorus, potassium, sulfur, sodium, chlorine and magnesium make up most of the rest; trace elements (iron, iodine, zinc…) are needed in tiny amounts but are essential.
2Atoms & isotopes
| Particle | Location | Charge | Mass (amu) |
|---|---|---|---|
| Proton (p⁺) | Nucleus | +1 | 1 |
| Neutron (n⁰) | Nucleus | 0 | 1 |
| Electron (e⁻) | Orbitals around nucleus | −1 | ≈ 0 (1/2000) |
- Atomic number
- Number of protons — this defines the element. Atoms are electrically neutral, so it also equals the number of electrons.
- Mass number
- Protons + neutrons.
- Isotopes
- Atoms of the same element with different numbers of neutrons (so different mass numbers). Hydrogen-1, deuterium (²H) and tritium (³H).
- Atomic weight
- The average of the mass numbers of all an element's isotopes, weighted by abundance.
- Radioisotopes
- Unstable isotopes that decay, emitting radiation. Used in imaging (PET scans) and cancer therapy.
| Mixture | Particle size | Example in the body |
|---|---|---|
| Solution | Tiny; transparent; never settles | Saline, glucose dissolved in plasma |
| Colloid (emulsion) | Larger; scatter light; don't settle; can undergo sol–gel changes | Cytosol |
| Suspension | Large; settle out if left standing | Blood (cells settle when spun or left standing) |
3Chemical bonds
Bonds form because atoms tend to fill their outermost (valence) shell. The octet rule: atoms (other than H and He) are most stable with 8 valence electrons. Atoms with full valence shells — the noble gases — are chemically inert.
- Ionic bond
- One atom transfers electrons to another. The atom that loses electrons becomes a positive cation; the one that gains becomes a negative anion; opposite charges attract. Example: Na⁺Cl⁻ (table salt).
- Nonpolar covalent bond
- Electrons are shared equally (e.g. H₂, O₂, the C–H bonds of fats). CO₂ is a nonpolar molecule because its two polar C=O bonds are symmetrical and cancel out.
- Polar covalent bond
- Electrons are shared unequally because one atom is more electronegative (O, N). Creates partial charges (δ⁺ / δ⁻) — water is the classic polar molecule.
- Hydrogen bond
- A weak attraction between a partially positive H and an electronegative atom (O or N) on another molecule or another part of the same molecule. Too weak to bond atoms into molecules — but they hold DNA strands together and fold proteins.
4Chemical reactions
| Type | Pattern | Example |
|---|---|---|
| Synthesis (combination) | A + B → AB | Amino acids → protein (anabolic; builds tissue) |
| Decomposition | AB → A + B | Glycogen → glucose (catabolic) |
| Exchange (displacement) | AB + C → AC + B | ATP + glucose → ADP + glucose-phosphate |
Oxidation–reduction (redox) reactions transfer electrons: the substance that loses electrons is oxidized, the one that gains electrons is reduced. Breaking down glucose for energy is a redox reaction.
Reactions that release energy are exergonic (catabolic, oxidative); those that absorb energy are endergonic (anabolic). All reactions are theoretically reversible; in the body many proceed one way because products are removed.
Reaction rate increases with higher temperature, higher concentration of reactants, smaller particle size, and catalysts (enzymes).
5Water, salts, acids, bases & pH
Water makes up 60–80% of body mass. Its properties come from its polarity:
- High heat capacity — absorbs and releases a lot of heat before its temperature changes, stabilizing body temperature.
- High heat of vaporization — evaporating sweat carries away large amounts of heat.
- Polar solvent — the “universal solvent”; dissolves and transports nutrients, gases and wastes.
- Reactivity — a reactant in hydrolysis (water breaks bonds) and a product of dehydration synthesis.
- Cushioning — e.g. cerebrospinal fluid around the brain; amniotic fluid around a fetus.
Salts are ionic compounds with cations other than H⁺ and anions other than OH⁻. In water they dissociate into ions — electrolytes, which conduct electricity (essential for nerve and muscle function).
- Acid
- A proton (H⁺) donor. Strong acids dissociate completely (HCl); weak acids partially (carbonic acid).
- Base
- A proton acceptor (e.g. OH⁻, bicarbonate HCO₃⁻, ammonia).
- pH
- Measure of H⁺ concentration: pH = −log[H⁺]. 7 is neutral, below 7 acidic, above 7 basic (alkaline). Each unit is a 10-fold change.
- Buffer
- Resists sharp pH changes by releasing H⁺ when pH rises and binding H⁺ when pH falls. Most important: the carbonic acid–bicarbonate system (H₂CO₃ ⇌ H⁺ + HCO₃⁻).
6Carbohydrates & lipids
Organic molecules contain carbon bonded covalently. Most large biological molecules are polymers built from monomers by dehydration synthesis (a water molecule is removed) and broken down by hydrolysis (water is added).
| Carbohydrate | Examples | Notes |
|---|---|---|
| Monosaccharides (simple sugars) | Glucose, fructose, galactose (hexoses); ribose, deoxyribose (pentoses) | Glucose = blood sugar, the universal cellular fuel |
| Disaccharides (double sugars) | Sucrose = glucose + fructose; lactose = glucose + galactose; maltose = glucose + glucose | Must be digested to monosaccharides to be absorbed |
| Polysaccharides | Glycogen (animals), starch (plants), cellulose (fiber) | Glycogen is stored in liver and skeletal muscle |
Lipids are insoluble in water and contain C, H and O (with relatively little oxygen); phospholipids also contain phosphorus.
- Triglycerides (neutral fats)
- Glycerol + 3 fatty acids. The body's most concentrated energy store; also insulate and cushion. Saturated fatty acids have only single C–C bonds (solid at room temp, animal fats); unsaturated have one or more double bonds (liquid oils). Trans fats (hydrogenated oils) raise cardiovascular risk; omega-3 fatty acids appear protective.
- Phospholipids
- Glycerol + 2 fatty acids + a phosphorus-containing group. Amphipathic: hydrophilic (polar) head, hydrophobic (nonpolar) tails — the basis of cell membranes.
- Steroids
- Four interlocking rings. Cholesterol is the parent molecule: it stabilizes membranes and is the raw material for vitamin D, steroid hormones (cortisol, estrogen, testosterone) and bile salts.
- Eicosanoids
- Derived from arachidonic acid — prostaglandins play roles in inflammation, blood clotting and labor contractions.
7Proteins & enzymes
Proteins make up 20–30% of cell mass and do most of the work of the body. Their monomers are amino acids — 20 kinds, each with an amine group, a carboxyl (acid) group and a variable R group that gives it its identity. Amino acids are joined by peptide bonds (dehydration synthesis).
| Structure level | What it is |
|---|---|
| Primary | The sequence of amino acids (the “letters”) |
| Secondary | α-helix or β-pleated sheet, held by hydrogen bonds |
| Tertiary | The overall 3-D folding of one polypeptide (R-group interactions) |
| Quaternary | Two or more polypeptide chains together (e.g. hemoglobin = 4 chains) |
Fibrous (structural) proteins are strand-like, insoluble and very stable — collagen, keratin, elastin. Globular (functional) proteins are compact, water-soluble and chemically active — enzymes, antibodies, many hormones, hemoglobin.
Denaturation: heat or extreme pH breaks hydrogen bonds, the protein unfolds and loses its function — an enzyme's active site is destroyed.
- 1The substrate binds the enzyme's active site (a precise fit).
- 2The enzyme–substrate complex undergoes internal rearrangements that form the product.
- 3The product is released; the enzyme is unchanged and can be reused.
Enzymes are biological catalysts: they lower the activation energy needed for a reaction, they are highly specific, and most names end in -ase (lipase, protease). Many need a cofactor (a metal ion like Zn²⁺ or Mg²⁺) or a coenzyme (organic, usually derived from a vitamin).
8Nucleic acids & ATP
Nucleotides are the monomers of nucleic acids. Each has a nitrogenous base, a pentose sugar and a phosphate group.
| Feature | DNA | RNA |
|---|---|---|
| Sugar | Deoxyribose | Ribose |
| Bases | A, G, C, T (thymine) | A, G, C, U (uracil) |
| Strands | Double helix | Single strand |
| Location | Nucleus (and mitochondria) | Made in nucleus, works mostly in cytoplasm |
| Job | Stores genetic instructions; replicates before cell division | Carries out instructions for protein synthesis (mRNA, tRNA, rRNA) |
Complementary base pairing: A–T (A–U in RNA) and G–C. Purines (A, G) are double-ring bases; pyrimidines (C, T, U) are single-ring.
ATP (adenosine triphosphate) is the cell's energy currency: adenine + ribose + three phosphate groups. Hydrolysis of the terminal high-energy phosphate bond releases energy (ATP → ADP + Pᵢ), which powers muscle contraction, active transport and synthesis reactions. The phosphate is transferred to other molecules (phosphorylation), priming them to do work.