Chemistry of Life — AP Biology Key Concepts

Water and Membranes

• Water is polar; drives interactions with membranes.
• Phospholipid membrane: hydrophilic heads face water; hydrophobic tails face interior.
• Result: a bilayer that forms the basic structure of cell membranes.

Matter, Atoms, and Big Questions

• Life asks: What is matter? Where does it come from? How do atoms interact to build life’s raw materials?
• Atoms and bonds underpin all biology; bonding patterns explain material properties.

Essential Elements in Life

• About $25$ elements are essential for life.
• Four most abundant in living matter: $C$, $H$, $O$, $N$.
• Four most common in the remaining $4\%$ of mass: $P$, $Ca$, $S$, $K$.

Energy & Atoms

• Energy interacts with electrons, holding them near the nucleus.
• Absorbing energy moves electrons to higher energy levels; returning to lower levels releases energy as EM radiation.
• Expression: $ext{Energy change} = E<em>{ ext{upper}} - E</em>{ ext{lower}}$.

Atoms and Bonding basics

• Valence electrons determine chemical behavior; atoms in the same group have similar properties.
• Atoms gain or lose electrons to complete their outer shell, driving chemical reactions and bond formation.

Types of Bonds in Biology

• Covalent bonds: share a pair of electrons; very strong.
  • Examples: $H<em>2$, $H</em>2O$ (within molecules).
• Nonpolar covalent bonds: electrons shared equally; e.g., hydrocarbons like $CH_4$.
• Polar covalent bonds: electrons shared unequally; e.g., water, due to higher electronegativity of O.
• Ionic and hydrogen bonds: weaker interactions between charged or polar regions.
• Intermolecular hydrogen bonds important for water properties and biomolecule interactions.
• Hydrogen bonds form attractions such as H–O–H between water molecules.

Covalent Bonding: Why strong and how it shapes molecules

• Strength comes from shared electron pairs, keeping atoms attached reliably.
• Covalent bonds form molecules like $H<em>2O$ and $CH</em>4$.

Bonding Polarities and Water

• Nonpolar: equal sharing (e.g., $CH_4$).
• Polar: unequal sharing (e.g., $H_2O$) due to electronegativity differences.
• Polarity leads to distinct molecular properties.

Hydrogen Bonding and Water Properties

• Polar water molecules attract each other via hydrogen bonds.
• Hydrogen bond: attraction between $ext{H}^+$ in one water molecule and $ext{O}^{-}$ in another.
• Hydrogen bonding explains water’s high cohesion, surface tension, and solvent properties.

Shape Determines Function

• Bonding patterns determine molecular shape.
• Structure and function are intimately related in biology.

Chemical Reactions: Bonds Break and Form

• All chemical reactions involve breaking and forming bonds.
• In reactions, mass, energy, and charge are conserved.
• Example: $2\,\mathrm{H<em>2} + \mathrm{O</em>2} \rightarrow 2\,\mathrm{H_2O}$.

What You Must Know about Carbon

• Carbon is central to organic chemistry and life.
• Major life elements: $CHNOPS$ (carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur).
• Carbon can form large, diverse molecules due to tetravalence.

Diversity of Carbon

• Carbon has 4 valence electrons (tetravalent) and can form up to 4 covalent bonds.
• Common bonding partners: $H, O, N$.
• Bonds can be single, double, or triple.
• Carbon forms large macromolecules: carbohydrates, proteins, lipids, nucleic acids.
• Molecules can be chains, rings, or branched.

Isomerism: Same Formula, Different Structures

• Structural isomers: different covalent arrangement.
• Cis-trans isomers: different spatial arrangement around a double bond.
• Enantiomers: mirror-image isomers with different biological activity.
• Example: Thalidomide enantiomers have different therapeutic effects.

Functional Groups: Core Chemistry of Biomolecules

• Functional groups largely determine molecule behavior.
• Common groups:
  • Hydroxyl group (-OH) — Alcohols; example: $\mathrm{CH<em>3CH</em>2OH}$.
  • Carbonyl group (>C=O) — Ketones (inside skeleton) and Aldehydes (at end); examples: Acetone $\mathrm{CH<em>3COCH</em>3}$; Propanal $\mathrm{CH<em>3CH</em>2CHO}$.
  • Carboxyl group (-COOH) — Carboxylic acids; example: Acetic acid $\mathrm{CH_3COOH}$.
  • Amino group (-NH2) — Amines; example: Glycine $\mathrm{NH<em>2CH</em>2COOH}$.
  • Sulfhydryl group (-SH) — Thiols; example: Ethanethiol $\mathrm{CH<em>3CH</em>2SH}$.
  • Phosphate group (-OPO3^{2-}) — Organic phosphates; example: Glycerol phosphate $\mathrm{HO-CH</em>2-CH(OH)-O-PO_3^{2-}}$.
  • Methyl group (-CH_3) — Methylated compounds; example: 5-methyl cytidine.