AP Biology Unit 1: Chemistry of Life Comprehensive Study Notes

CHNOPS

The six essential elements that primarily compose living organisms: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur.

Protons ($\text{p}^+$)

Positively charged subatomic particles located inside the atomic nucleus.

Neutrons ($\text{n}^0$)

Uncharged (neutral) subatomic particles located inside the atomic nucleus.

Electrons ($\text{e}^-$)

Negatively charged subatomic particles orbiting the atomic nucleus in electron shells or orbitals.

Isotopes

Atoms of the same element that contain an identical number of protons but a different number of neutrons in their nuclei (e.g., Carbon-14 vs. Carbon-12).

Ions

Atoms or molecules that have gained or lost electrons, resulting in a net electrical charge.

Cation

A positively charged ion formed when an atom loses one or more electrons (e.g., $\text{Li}^+$).

Anion

A negatively charged ion formed when an atom gains one or more electrons.

Ionic Bond

A chemical bond formed by the complete transfer of electrons from a metal atom to a nonmetal atom, creating full positive and negative charges on the resulting ions.

Non-polar Covalent Bond

A covalent bond resulting from the equal sharing of electrons between two atoms with similar electronegativities.

Polar Covalent Bond

A covalent bond resulting from the unequal sharing of electrons between atoms with differing electronegativities, generating partial charges ($\delta^-$ and $\delta^+$).

Hydrogen Bond

A strong intermolecular attraction occurring when a hydrogen atom covalently bonded to a highly electronegative atom (like oxygen or nitrogen) experiences attraction to another electronegative atom nearby.

Dipole-Dipole Interactions

Electrostatic attractions between the permanent dipoles of polar molecules.

London Dispersion Forces

Weak, temporary attractive intermolecular forces resulting from instantaneous dipole fluctuations in nonpolar molecules.

Cohesion

The attraction between like molecules, such as water molecules sticking to each other, creating high surface tension.

Adhesion

The attraction between water molecules and different polar or charged surfaces.

Capillary Action

The movement of liquid upward through narrow spaces against gravity, driven by combined cohesive and adhesive forces.

Transpiration

The transport process in plants where water enters roots, moves upward through xylem tubes via cohesion and adhesion, and evaporates through leaf stomata.

High Specific Heat Capacity

The property of water requiring substantial heat energy to raise its temperature because heat must first break hydrogen bonds before increasing molecular kinetic energy.

Evaporative Cooling

The dissipation of thermal energy from a surface as high-energy liquid water molecules evaporate into gas, helping regulate internal body temperature (e.g., sweating).

Ice Flotation Anomaly

Water expands upon freezing as stable hydrogen bonds form a rigid lattice, making solid ice less dense than liquid water so it floats and insulates underlying aquatic life.

Hydration Shells

Structures formed when water dissolves ionic compounds or polar molecules by surrounding positively and negatively charged ions with partial charges of water molecules.

Hydrophilic vs. Hydrophobic

Hydrophilic ('water-loving') substances are polar or ionic and dissolve in water; hydrophobic ('water-fearing') substances are nonpolar and do not dissolve in water.

Unsaturated vs. Saturated Solution

An unsaturated solution contains solute below its solubility threshold; a saturated solution contains the maximum possible concentration of dissolved solute.

Acid

A substance that increases hydrogen ion ($\text{H}^+$) concentration in aqueous solution, resulting in a $\text{pH} < 7$.

Base

A substance that reduces hydrogen ion concentration, often by releasing hydroxide ions ($\text{OH}^-$), resulting in a $\text{pH} > 7$.

pH Equations

$\text{pH} = -\log[\text{H}^+]$, $\text{pOH} = -\log[\text{OH}^-]$, and $\text{pH} + \text{pOH} = 14$.

Organic vs. Inorganic Compounds

Organic compounds contain carbon covalently bonded to hydrogen (C-H bonds, e.g., glucose, DNA); inorganic compounds usually lack C-H bonds (e.g., $\text{NaCl}$, $\text{CO}_2$).

Dehydration Synthesis

A condensation reaction that links monomers into polymers by removing a water molecule ($\text{H}_2\text{O}$) to form a new covalent bond.

Hydrolysis

A reaction that breaks down polymers into monomer subunits by adding a water molecule ($\text{H}_2\text{O}$) across a covalent bond.

Carbohydrates

Organic macromolecules with chemical ratio $\text{C}_n\text{H}_{2n}\text{O}_n$ ($1:2:1$ ratio) linked by glycosidic bonds, serving as quick energy and structural support.

Cellulose Digestibility

Humans cannot digest cellulose because human digestive enzymes lack the ability to hydrolyze $\beta\text{-glycosidic}$ linkages present in $\beta\text{-glucose}$ polymers.

Proteins

Macromolecules composed of amino acid monomers linked by peptide bonds, containing $\text{C, H, O, N}$, functioning in catalysis, movement, structure, and immunity.

Primary Protein Structure

The linear sequence of amino acids in a polypeptide chain determined by genetic code.

Secondary Protein Structure

Localized coiling ($\alpha\text{-helices}$) or folding ($\beta\text{-pleated sheets}$) along the polypeptide backbone, stabilized by hydrogen bonds.

Tertiary Protein Structure

The overall 3D shape of a single polypeptide chain, driven by R-group interactions (hydrophobic interactions, ionic bonds, hydrogen bonds, disulfide bridges).

Quaternary Protein Structure

The specific arrangement and interaction of multiple individual polypeptide subunits working together as a functional protein complex.

Protein Denaturation and Renaturation

Denaturation is the loss of 3D protein structure and function caused by heat or non-optimal pH; renaturation is the refolding back into its active native shape.

Lipids

Nonpolar, hydrophobic macromolecules made of $\text{C, H, O}$ (low oxygen ratio) linked by ester bonds, functioning in long-term energy storage and cell membrane structure.

Saturated vs. Unsaturated Fats

Saturated fats have only single $\text{C-C}$ bonds, pack tightly, and are solid at room temp; unsaturated fats have one or more double $\text{C=C}$ bonds with kinks and are liquid at room temp.

Nucleic Acids

Hydrophilic macromolecules containing $\text{C, H, O, N, P}$, composed of nucleotide monomers linked by phosphodiester bonds, responsible for storing and transmitting genetic info.

Nucleotide Subunits

The three components of a nucleotide: a phosphate group ($\text{PO}_4^{3-}$), a 5-carbon pentose sugar (deoxyribose or ribose), and a nitrogenous base.

Miller-Urey Experiment

A 1950s experiment simulating early Earth atmosphere ($\text{CH}_4$, $\text{NH}_3$, $\text{H}_2\text{O}$, $\text{H}_2$) with electric sparks, producing organic amino acids abiotically.

RNA World Hypothesis

The theory proposing that self-replicating $\text{RNA}$ molecules were evolutionary precursors to DNA and proteins because $\text{RNA}$ can both store genetic info and catalyze reactions as ribozymes.