Chemistry of Life

Macromolecules, water, pH, and bonds — the chemical foundation of biology

BIO 111 — Chapter 2
Life is chemistry with an agenda. Every molecule in your body — from the DNA in your nucleus to the lipids in your cell membrane — follows the same rules of chemistry. Learn the rules, and biology starts to make sense.
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Carbohydrates
Monomer: monosaccharide · Polymer: polysaccharide

Carbohydrates are made of carbon, hydrogen, and oxygen in a roughly 1:2:1 ratio (CH₂O)ₙ. Their primary job is energy — they're the body's preferred quick fuel source. They also provide structural support (cellulose in plants, chitin in fungi/insects) and play roles in cell communication.

Monomer
Monosaccharides (glucose, fructose, galactose). Simple sugars with 3–7 carbons.
Polymers (examples)
Starch (energy storage in plants), glycogen (energy storage in animals), cellulose (plant cell walls), chitin (fungal walls, insect exoskeletons).
Bond type
Glycosidic bonds link monosaccharides. Formed by dehydration synthesis (water removed). Broken by hydrolysis (water added).
Lab connection 🔬
Lactose (milk sugar) is a disaccharide of glucose + galactose. Yogurt fermentation converts lactose to lactic acid — that's why yogurt is lower in lactose than milk.
Quick energy Glycosidic bonds Structural (cellulose) C, H, O only
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Lipids
Not a true polymer · Built from glycerol + fatty acids

Lipids are hydrophobic (water-fearing) molecules. They're not true polymers — they don't have a single repeating monomer unit. Instead they're diverse molecules that share the property of being insoluble in water. They store more energy per gram than carbohydrates, making them excellent long-term energy storage.

Types
Fats/oils (triglycerides), phospholipids (cell membranes), steroids (cholesterol, hormones), waxes.
Structure
Triglycerides: glycerol backbone + 3 fatty acid chains. Saturated = no double bonds (solid at room temp). Unsaturated = double bonds (liquid at room temp).
Functions
Energy storage (9 kcal/g vs 4 kcal/g for carbs), insulation, protection, hormone production, cell membrane structure.
Phospholipids
Have a hydrophilic head and hydrophobic tail — this is why they spontaneously form the bilayer of every cell membrane.
Hydrophobic Long-term energy Cell membranes Hormones
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Proteins
Monomer: amino acid · Polymer: polypeptide chain

Proteins are the most diverse and functionally important macromolecules. Built from 20 different amino acids, they can fold into an almost infinite variety of 3D shapes — and shape determines function. Enzymes, antibodies, structural proteins, transport proteins, and hormones are all proteins.

Monomer
Amino acids — 20 types. Each has a central carbon, amino group (–NH₂), carboxyl group (–COOH), hydrogen, and a unique R group (side chain) that determines its properties.
Bond type
Peptide bonds link amino acids (dehydration synthesis). A chain of amino acids = polypeptide. Folded polypeptide(s) = protein.
4 levels of structure
Primary (AA sequence), secondary (α-helix/β-sheet), tertiary (3D folding), quaternary (multiple chains). Shape = function.
Lab connection 🔬
Protein denaturation happens when pH or temperature disrupts bonds, unfolding the protein. Pasteurization works partly by denaturing pathogen proteins. Yogurt gel forms when acid denatures casein.
20 amino acids Peptide bonds Enzymes Most diverse
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Nucleic Acids
Monomer: nucleotide · Polymers: DNA and RNA

Nucleic acids store, transmit, and express genetic information. DNA is the permanent information archive; RNA carries instructions from DNA to ribosomes for protein synthesis. Every living cell uses nucleic acids — they are the molecular basis of heredity and the central dogma of biology: DNA → RNA → Protein.

Nucleotide structure
Each nucleotide = phosphate group + 5-carbon sugar (deoxyribose in DNA, ribose in RNA) + nitrogenous base (A, T, G, C in DNA; A, U, G, C in RNA).
DNA vs RNA
DNA: double-stranded, deoxyribose sugar, thymine (T). RNA: single-stranded, ribose sugar, uracil (U) instead of T. DNA stays in nucleus; RNA travels to ribosomes.
Base pairing
A pairs with T (DNA) or U (RNA). G pairs with C. Always. This complementary base pairing is how DNA replicates and how RNA copies the code.
Bond type
Phosphodiester bonds link nucleotides in the sugar-phosphate backbone. Hydrogen bonds hold the two DNA strands together (weak — allows unzipping).
DNA + RNA Genetic info Base pairing Central dogma

Click any macromolecule to expand · Know monomer, polymer, bond, and function for each

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Polarity & hydrogen bonding
Why water sticks to everything

Water is a polar molecule — oxygen pulls electrons toward itself more strongly than hydrogen, creating partial negative (δ−) and partial positive (δ+) charges. This makes water molecules attracted to each other (and to other polar/charged molecules), forming hydrogen bonds between the δ+ hydrogen of one water molecule and the δ− oxygen of another.

Polar covalent bond
O and H share electrons unequally. O is more electronegative — it hogs the electrons. Result: O end is slightly negative, H ends are slightly positive.
Hydrogen bonds
Not true bonds — just attractions between δ+ H and δ− O. Individually weak, but water molecules form thousands simultaneously. Collectively very strong.
Polar molecule H-bonds Electronegativity
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Cohesion & adhesion
Why water forms droplets and climbs up trees

Cohesion is water sticking to water. Adhesion is water sticking to other polar surfaces. Together these properties allow water to move against gravity up plant stems (transpiration), create surface tension strong enough for insects to walk on, and form the droplets that roll off leaves.

Cohesion
Water–water hydrogen bonds. Creates surface tension — the "skin" on water. Water striders walk on it. Tears form droplets.
Adhesion
Water–surface hydrogen bonds. Water wets glass, climbs paper towels, moves up xylem in plants (transpiration pull).
Cohesion Adhesion Surface tension Capillary action
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High specific heat & heat of vaporization
Why oceans stabilize climate and sweating cools you

Water resists temperature change better than almost any other substance — it takes a lot of energy to heat it up or cool it down. This is because breaking hydrogen bonds requires energy. This high specific heat stabilizes Earth's climate, keeps ocean temperatures stable, and allows organisms to maintain homeostasis.

Specific heat
Water absorbs a lot of heat before its temperature rises. Oceans stabilize coastal climates. Your body uses this to resist temperature swings.
Heat of vaporization
Evaporation requires breaking hydrogen bonds — this takes energy (heat). When you sweat, evaporating water pulls heat from your skin, cooling you.
Specific heat Temperature buffer Evaporative cooling
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Ice floats — and that's extraordinary
Why solid water is less dense than liquid water

Almost every substance is denser as a solid than as a liquid. Water is a major exception. When water freezes, hydrogen bonds lock into a crystalline lattice that holds molecules further apart than in liquid water. Ice is less dense than liquid water — so it floats. This has enormous biological consequences.

Why it happens
In liquid water, H-bonds are constantly breaking and reforming. In ice, they lock into a hexagonal lattice with more space between molecules — lower density.
Why life depends on it
Ice floats on top of lakes in winter, insulating the liquid water below. If ice sank, lakes would freeze solid from the bottom up — killing all aquatic life.
Ice less dense than water Crystalline lattice Insulates aquatic life
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Universal solvent
Why "like dissolves like" — and why water is life's solvent

Water dissolves more substances than any other liquid — earning the title "universal solvent." Ionic compounds and polar molecules dissolve in water; nonpolar molecules (lipids) do not. This selective solvency is fundamental to how cells work — nutrients, waste products, and signals all travel dissolved in water.

Hydrophilic
Water-loving. Polar and ionic molecules dissolve readily. Examples: glucose, salts, amino acids, proteins.
Hydrophobic
Water-fearing. Nonpolar molecules repelled by water. Examples: lipids, oils, waxes. These cluster together away from water.
Universal solvent Hydrophilic vs hydrophobic Ionic & polar dissolve

All 5 water properties are exam-ready topics

Interactive pH scale — drag to explore
012345 67891011 121314
7.0
Neutral
Pure water
🔋Battery acidpH 1
🍋Lemon juicepH 2
🥛YogurtpH 3.5–4.5
CoffeepH 4.5–5
🫧UrinepH 6–7
💧Pure waterpH 7
🩸BloodpH 7.35–7.45
🥛MilkpH 6.4–6.8
🫧Sea waterpH 8
🧼SoappH 9–10
🧹BleachpH 11–13
⚗️Drain cleanerpH 14
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Acids (pH < 7)
Donate H⁺ ions — increase hydrogen ion concentration

An acid is a substance that releases hydrogen ions (H⁺) — also called protons — into solution. The more H⁺, the more acidic (lower pH). Strong acids (like HCl) dissociate completely. Weak acids (like acetic acid in vinegar) dissociate partially. pH is a logarithmic scale — pH 4 is 10× more acidic than pH 5, and 100× more acidic than pH 6.

Biology examples
Stomach acid (pH 1.5–3.5) denatures proteins and kills pathogens. Lactic acid from fermentation drops yogurt pH to 4.0–4.5. Lysosomes maintain pH ~4.8 to activate digestive enzymes.
Lab connection 🔬
In yogurt production, lactic acid bacteria produce lactic acid that drops the pH from ~6.7 (milk) to ~4.5 (yogurt). This pH drop denatures casein protein, forming the gel — and inhibits spoilage organisms.
Donates H⁺pH < 7Logarithmic scale
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Bases (pH > 7)
Accept H⁺ ions — decrease hydrogen ion concentration

A base (or alkali) accepts hydrogen ions from solution, reducing H⁺ concentration and raising pH. Bases feel slippery (soap), taste bitter, and can be just as dangerous as strong acids. Blood is slightly basic (pH 7.4). Most cellular processes work optimally at near-neutral to slightly basic pH.

Biology examples
The small intestine (pH 7–8) — pancreatic bicarbonate neutralizes stomach acid. Blood (pH 7.4) — tightly buffered. Cytoplasm of most cells (pH ~7.2).
Everyday examples
Baking soda (pH 8.3), soap (pH 9–10), bleach (pH 11–13). Antacids work by neutralizing stomach acid with a base.
Accepts H⁺pH > 7Bitter taste
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Buffers
Resist changes in pH — critical for life

Buffers are weak acid/base pairs that resist pH changes by absorbing excess H⁺ or OH⁻. They are essential for life — your blood pH must stay between 7.35 and 7.45. Even a shift to 7.0 or 7.8 can be fatal. Cells use buffers to maintain the precise pH their enzymes need to function.

How buffers work
A buffer contains both a weak acid and its conjugate base. Add H⁺ → the base absorbs it. Add OH⁻ → the acid neutralizes it. pH stays stable.
Biology examples
Blood: carbonic acid/bicarbonate buffer system (H₂CO₃/HCO₃⁻). Cells: phosphate buffer. Many proteins also act as buffers via their amino acid side chains.
Resists pH changeWeak acid + conjugate baseBlood: 7.35–7.45

Drag the slider or click any example to explore the scale

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Covalent bonds
Strongest bond · Shared electrons

Covalent bonds form when two atoms share electrons. They are the strongest chemical bonds — requiring the most energy to break. All organic macromolecules (proteins, carbohydrates, lipids, nucleic acids) are held together primarily by covalent bonds. Can be nonpolar (equal sharing) or polar (unequal sharing).

Nonpolar covalent
Equal sharing of electrons between atoms of similar electronegativity. Examples: C–H bonds (in hydrocarbons), O₂, N₂. Hydrophobic.
Polar covalent
Unequal sharing — more electronegative atom hogs electrons. Example: O–H in water. Creates partial charges (δ+ and δ−). Hydrophilic.
Shared electronsStrongest bondPolar & nonpolarAll macromolecules
Ionic bonds
Electron transfer · Opposites attract

Ionic bonds form when one atom transfers electrons to another, creating oppositely charged ions (cations + and anions −) that attract each other. Strong in dry conditions but weaker in water (water molecules surround and separate ions). Table salt (NaCl) is the classic example — it dissolves easily in water.

Formation
Na loses 1 electron → Na⁺ (cation). Cl gains 1 electron → Cl⁻ (anion). Opposite charges attract → NaCl. In water, they dissociate into ions.
Biology examples
Sodium (Na⁺), potassium (K⁺), calcium (Ca²⁺), chloride (Cl⁻) — all key ions in nerve signals, muscle contraction, and osmosis. Ions are hydrophilic.
Electron transferCations & anionsDissolves in water
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Hydrogen bonds
Weak but everywhere · Hold DNA together

Hydrogen bonds are not true bonds — they're attractions between a δ+ hydrogen (attached to N or O) and a δ− atom (N or O) on another molecule. Individually weak (~1/20th the strength of a covalent bond), but when thousands form simultaneously they become collectively very important. They're responsible for water's unique properties and for DNA's double helix.

In water
Every water molecule can form up to 4 hydrogen bonds. This creates water's cohesion, high specific heat, and surface tension.
In DNA
A–T base pairs: 2 hydrogen bonds. G–C base pairs: 3 hydrogen bonds. This is why G–C rich DNA is more thermally stable. Also stabilizes protein secondary structures (α-helices, β-sheets).
Weak individuallyStrong collectivelyDNA base pairsWater properties
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Van der Waals forces
Weakest · But geckos use them to climb walls

Van der Waals forces are fleeting, weak attractions between all molecules caused by temporary fluctuations in electron distribution. When electrons briefly cluster on one side of an atom, they create a temporary dipole that induces an opposite dipole in neighboring atoms. Incredibly weak individually — but when many nonpolar molecules pack closely together, these forces add up.

Biology examples
Stabilize the interior of folded proteins where nonpolar side chains pack together. Important in lipid bilayer stability. Gecko toe pads use van der Waals forces to climb glass.
Bond strength ranking
Covalent > ionic > hydrogen bonds > van der Waals. Each plays an essential role — even the weakest matter when multiplied by millions.
Weakest forceTemporary dipolesProtein folding

Click any bond to expand · Know strength, mechanism, and biological role for each