Summary Notes: Atoms, Bonds, Water, and Biomolecules

Atoms and Subatomic Particles

Matter is composed of atoms; atoms contain subatomic particles: Protons (+1), Neutrons (0), Electrons (-1).
Protons and neutrons reside in the nucleus; electrons orbit around it.
Charges resemble magnets: opposite charges attract; like charges repel.

Elements, Atomic Number, and Isotopes

Elements are defined by the atomic number $Z$ (number of protons).
Neutral atoms have equal numbers of protons and electrons.
Example: Oxygen has $Z=8$ ; Hydrogen has $Z=1$ .
All atoms of an element share the same $Z$ , but neutrons can vary.

Atomic Mass and Isotopes

Atomic mass ≈ protons + neutrons; each proton/neutron ≈ 1 Dalton (Da).
Isotopes differ in the number of neutrons but have the same $Z e ext{?}$ ; thus different masses.
Hydrogen isotopes: $^11H$ , $^21H$ , $^3_1H$ (protium, deuterium, tritium).

Covalent Bonds

Atoms form molecules via covalent bonds: sharing of electrons.

Ions, Salts, and Ionic Bonding

Electron transfer creates ions: Cations (positive) and Anions (negative).
Ionic bonds occur between oppositely charged ions.
Salts example: $NaCl$ (sodium chloride).

Electronegativity and Bond Types

Electronegativity: an atom’s pull on shared electrons.
Polar covalent bonds: unequal sharing; results in partial charges (\delta^+ / \delta^-).
Water is a classic polar covalent molecule; O is more electronegative than H (O–H bonds).
Nonpolar covalent bonds: equal sharing; example: methane $CH_4$ .

Hydrogen Bonding

Polar molecules have partial charges; hydrogen bonds form between partially positive H and electronegative atoms (e.g., O).
In water, hydrogen bonds create cohesive interactions between molecules.

Properties of Water

1) Solvent: water dissolves many substances; hydrophilic vs hydrophobic.
2) Cohesion and adhesion: water sticks to itself and to surfaces (driven by partial charges).
3) High specific heat: energy goes into breaking hydrogen bonds before temperature rises.
4) Density anomaly: ice is less dense than liquid water, so ice floats.

The Fundamental Molecules of Life

Four main types: carbohydrates, proteins, nucleic acids, lipids.

Carbohydrates

General formula: $(CH2O)n$ ; monosaccharides (e.g., glucose $C6H{12}O_6$ ), fructose, galactose (isomers).
Disaccharides: glucose + fructose → sucrose; glucose + galactose → lactose.
Polysaccharides: starch and glycogen (energy storage); cellulose (structure; dietary fiber).
Plants store glucose as starch; animals store glycogen in muscle and liver.
Cellulose is indigestible and acts as dietary fiber.

Proteins

Proteins are polymers of amino acids (20 standard amino acids).
They catalyze reactions and provide structural components.
Genes encode proteins (DNA serves as recipes).

Nucleic Acids (DNA and RNA)

DNA: double-stranded; nucleotides A, G, C, T; base pairing is complementary: $A{-}T$ and $G{-}C$ .
RNA: single-stranded; no thymine, uses uracil (U) instead; acts as a go-between in protein synthesis.

Lipids

Lipids are hydrophobic; not polymers.
Major types: triglycerides, phospholipids, steroids.
Triglycerides: glycerol + 3 fatty acids; saturated (straight) vs unsaturated (kinked); saturated fats are solid at room temp, unsaturated are liquids.
Phospholipids: glycerol + two fatty acids + phosphate head; hydrophilic head and hydrophobic tails; key membrane component.
Steroids: four-ring structure; include hormones (e.g., testosterone, estrogen) and cholesterol (membrane component).

Digestion and Hydrolysis

Digestion uses hydrolysis to break down polymers into monomers: water is added to cleave bonds.
Enzymes hydrolyze proteins, carbohydrates, nucleic acids, and lipids.
Small molecules are absorbed through intestinal lining into the bloodstream and distributed to cells for building blocks and energy.
Process overview: ingestion → digestion (mouth, stomach, small intestine with pancreatic and liver enzymes) → absorption into blood → distribution → use; wastes eliminated.

Quick recall

Key bonds: covalent (sharing), ionic (electrostatic), hydrogen bonding (between polar molecules).
Water: solvent, cohesive/adhesive, high heat capacity, density anomaly (ice floats).
DNA base pairing: $A{-}T, G{-}C$ ; RNA uses U.
Lipids: triglycerides, phospholipids, steroids; membranes rely on phospholipids.
Carbohydrates: $(CH2O)n$ ; glucose $C6H{12}O_6$ ; starch/glycogen vs cellulose.