Atoms, Ions, and Molecules

Matter, Atoms, Elements, and the Periodic Table

Matter is anything that has mass and occupies space. It exists in three forms in the human body:

• Solid (e.g., bone)

• Liquid (e.g., blood)

• Gas (e.g., oxygen)

An atom is the smallest particle of an element that retains its chemical properties. There are 92 naturally occurring elements, organized in the periodic table.

Components of an Atom

• Neutrons: Mass = 1 amu, no charge, located in the nucleus

• Protons: Mass = 1 amu, charge = +1, located in the nucleus

• Electrons: Mass ≈ 1/1800 amu, charge = -1, located in electron orbitals around the nucleus

Elements and the Periodic Table

• Chemical symbol: Unique to each element (e.g., C for carbon)

• Atomic number: Number of protons; determines the element

• Average atomic mass: Sum of protons and neutrons

• Determining subatomic particles:

  • Protons = atomic number

  • Neutrons = atomic mass − atomic number

  • Electrons = protons (in a neutral atom)

Example: Sodium (Na): Atomic number = 11, Atomic mass = 23, Neutrons = 23 − 11 = 12

Diagramming Atomic Structures

• Electrons occupy energy levels called shells around the nucleus

• First shell: up to 2 electrons; second shell: up to 8 electrons

• Shells fill from the inside out

Isotopes and Radioisotopes

• Isotopes: Atoms of the same element with different numbers of neutrons (e.g., Carbon-12, Carbon-13, Carbon-14)

• Radioisotopes: Unstable isotopes that emit radiation (alpha, beta, gamma) as they decay

• Physical half-life: Time for 50% of a radioisotope to decay

• Biological half-life: Time for half of a substance to be eliminated from the body

Chemical Stability and the Octet Rule

• Elements are organized by the number of valence electrons (outer shell electrons)

• Octet rule: Atoms tend to gain, lose, or share electrons to achieve 8 electrons in their valence shell (chemical stability)

• Noble gases (e.g., helium, neon) have full valence shells and are chemically inert

Ions and Ionic Compounds

• Ions: Atoms with a net charge due to loss or gain of electrons

  • Cations: Positive charge (loss of electrons)

  • Anions: Negative charge (gain of electrons)

  • Polyatomic ions: Ions with more than one atom (e.g., HCO3-, PO43-)

• Ionic bonds: Electrostatic attraction between cations and anions (e.g., NaCl, MgCl2)

Covalent Bonding, Molecules, and Molecular Compounds

• Covalent bond: Electrons are shared between atoms

• Molecular compounds: Molecules with different elements (e.g., CO2)

Chemical Formulas: Molecular and Structural

• Molecular formula: Shows number and type of atoms (e.g., H2CO3)

• Structural formula: Shows arrangement of atoms (e.g., O=C=O for CO2)

• Isomers: Same molecular formula, different structure (e.g., glucose, galactose, fructose)

Covalent Bond Types and Carbon Skeletons

• Atoms share electrons to achieve stability

• Common elements forming covalent bonds: H, O, N, C

• Number of bonds:

  • H: 1 bond

  • O: 2 bonds

  • N: 3 bonds

  • C: 4 bonds

• Single, double, and triple covalent bonds possible

• Carbon skeletons: Chains or rings of carbon atoms, forming the backbone of organic molecules

Nonpolar and Polar Covalent Bonds

• Electronegativity: Atom's attraction for electrons

• Nonpolar covalent bond: Equal sharing of electrons (e.g., O2, C—H)

• Polar covalent bond: Unequal sharing of electrons (e.g., O—H in water)

• Electronegativity order (common in biology): H < C < N < O

• Partial charges: More electronegative atom gets δ−, less gets δ+

• Exception: C—H bonds are considered nonpolar

Nonpolar, Polar, and Amphipathic Molecules

• Nonpolar molecules: Only nonpolar bonds or polar bonds that cancel (e.g., CO2)

• Polar molecules: Contain polar bonds (e.g., H2O)

• Amphipathic molecules: Have both polar and nonpolar regions (e.g., phospholipids)

Intermolecular Attractions

• Hydrogen bonds: Attraction between partially positive H and partially negative atom (important in water, DNA, proteins)

• Van der Waals forces: Weak attractions due to temporary unequal charge distribution

• Hydrophobic interactions: Nonpolar molecules cluster in polar environments

Molecular Structure and Properties of Water

• Water: Inorganic, polar molecule (H2O), forms up to four hydrogen bonds

• Phases: Gas (vapor), liquid (body fluids), solid (ice)

• Functions:

  • Transport

  • Lubrication

  • Cushioning

  • Excretion of wastes

• Cohesion: Water molecules stick together

• Surface tension: Inward pull at water's surface (important in lungs; surfactant prevents alveolar collapse)

• Adhesion: Water molecules stick to other substances

• High specific heat: Water resists temperature change

• High heat of vaporization: Energy needed to convert water from liquid to gas (basis for sweating)

• Universal solvent: Dissolves many substances; forms hydration shells around solutes

Water as a Solvent: Hydrophilic, Hydrophobic, and Amphipathic Substances

• Hydrophilic: Polar molecules and ions dissolve in water (e.g., glucose, NaCl)

• Hydrophobic: Nonpolar molecules do not dissolve (e.g., fats, cholesterol); require carrier proteins in blood

• Amphipathic: Molecules with both polar and nonpolar regions (e.g., phospholipids form bilayers in cell membranes)

Water: A Neutral Solvent

• Water can dissociate:

• Hydronium ion:

• Equal numbers of H+ and OH- ions; water is neutral

Acids and Bases

• Acid: Proton donor; increases H+ in solution (e.g., HCl)

• Base: Proton acceptor; decreases H+ in solution (e.g., NH3, HCO3-)

• Strong acids/bases dissociate/absorb H+ more completely than weak ones

pH, Neutralization, and Buffers

• pH: Measure of H+ concentration; scale 0–14

  • pH 7 = neutral

  • pH < 7 = acidic

  • pH > 7 = basic (alkaline)

  • Each pH unit = 10-fold change in H+ concentration

• Neutralization: Adding acid to base (or vice versa) to return to pH 7

• Buffers: Prevent drastic pH changes by accepting or donating H+ (e.g., carbonic acid–bicarbonate buffer in blood)

Water Mixtures

• Mixtures: Two or more substances physically combined, not chemically bonded

• Types:

  • Suspension: Large particles, settle out (e.g., blood cells in plasma)

  • Colloid: Medium particles, do not settle, scatter light (e.g., cytosol)

  • Solution: Small particles, do not settle, do not scatter light (e.g., salt water)

  • Emulsion: Special colloid; nonpolar liquid in water (e.g., oil and vinegar, breast milk)

Expressions of Solution Concentration

• Concentration: Amount of solute per amount of solution

• Common expressions:

  • Mass/volume (e.g., g/L)

  • Mass/volume percent (e.g., g/100 mL)

  • Molarity (mol/L):

  • Molality (mol/kg solvent):

  • Osmolarity (osmoles/L)

  • Osmolality (osmoles/kg water)

• Mole: particles; mass in grams equals atomic/molecular mass

• Molecular mass: Sum of atomic masses of all atoms in a molecule

Biological Macromolecules: General Characteristics

• Large organic molecules (contain C, H, O; sometimes N, P, S)

• Carbon skeletons: Chains/rings of carbon atoms

• Functional groups: Specific groups of atoms that confer chemical properties (e.g., carboxyl, amine)

• Polymers: Chains of repeating subunits (monomers)

  • Carbohydrates: sugar monomers

  • Nucleic acids: nucleotide monomers

  • Proteins: amino acid monomers

• Dehydration synthesis: Joins monomers, releases water

• Hydrolysis: Breaks polymers, uses water

Lipids

• Nonpolar, water-insoluble molecules; energy storage, membrane structure, hormones

• Classes:

  • Triglycerides: Glycerol + 3 fatty acids; energy storage

  • Phospholipids: Glycerol + 2 fatty acids + phosphate; amphipathic, form cell membranes

  • Steroids: Four-ring structure (e.g., cholesterol, hormones)

  • Eicosanoids: 20-carbon signaling molecules (inflammation, nervous system)

• Other lipids: Glycolipids, fat-soluble vitamins (A, D, E, K)

Carbohydrates

• Composed of C, H, O; general formula (CH2O)n

• Monosaccharides: Simple sugars (e.g., glucose, fructose, galactose)

• Disaccharides: Two monosaccharides (e.g., sucrose, lactose, maltose)

• Polysaccharides: Many monosaccharides (e.g., glycogen, starch, cellulose)

• Glycogen: Storage form of glucose in liver and muscle

• Glycogenesis: Formation of glycogen; Glycogenolysis: Breakdown of glycogen; Gluconeogenesis: Formation of glucose from non-carbohydrate sources

Nucleic Acids

• Store and transfer genetic information

• Types:

  • DNA: Double-stranded, deoxyribose sugar, bases A, T, C, G

  • RNA: Single-stranded, ribose sugar, bases A, U, C, G

• Nucleotide: Sugar + phosphate + nitrogenous base

• ATP: Adenosine triphosphate; energy currency of the cell

Proteins

• Functions: Enzymes, structure, movement, transport, protection

• Structure:

  • Monomers: Amino acids (20 types)

  • Peptide bonds link amino acids

  • Oligopeptide: 3–20 amino acids; Polypeptide: >20; Protein: one or more polypeptides

  • Glycoproteins: Proteins with carbohydrate attached

• Amino acids classified by R group: nonpolar, polar, charged, special functions

Amino Acid Sequence and Protein Conformation

• Conformation: 3D shape, essential for function

• Levels of structure:

  • Primary: Sequence of amino acids

  • Secondary: Alpha helix, beta sheet (hydrogen bonds)

  • Tertiary: 3D folding of a single polypeptide

  • Quaternary: Multiple polypeptides (e.g., hemoglobin)

• Intramolecular interactions: hydrophobic exclusion, hydrogen bonds, ionic bonds, disulfide bonds

• Denaturation: Loss of structure and function due to heat or pH changes; often irreversible

Table: Types of Water Mixtures

Table: Classes of Biological Macromolecules

Additional info:

• Knowledge check questions at the end of the chapter are designed to reinforce understanding of atomic structure, chemical bonding, water properties, macromolecules, and their relevance to physiology.

• Understanding these chemical principles is foundational for topics such as cell structure, metabolism, and physiological regulation in later chapters.