Chemistry Comes Alive

Matter and Elements

The human body is composed of matter, which is anything that has mass and occupies space. Understanding the chemical basis of matter is essential for studying anatomy and physiology.

• States of Matter: Solid, liquid, and gas forms are present in the human body.

• Atoms: The smallest particles that retain the properties of an element.

• Elements: Pure substances composed of only one type of atom. There are 92 naturally occurring elements, with hydrogen being the smallest and uranium the largest.

• Major Elements in the Body: Oxygen, carbon, hydrogen, and nitrogen are the most abundant, comprising 98% of body weight. Other important elements include calcium, phosphorus, sulfur, potassium, sodium, chlorine, magnesium, and iron.

Atomic Structure

Atoms are composed of three subatomic particles: protons, neutrons, and electrons.

• Protons: Positively charged, mass of 1 amu, located in the nucleus.

• Neutrons: Uncharged, mass of 1 amu, located in the nucleus.

• Electrons: Negatively charged, mass is 1/800th of a proton or neutron, located in orbitals around the nucleus.

• Atomic Number: Number of protons in an atom; unique to each element.

• Atomic Mass: Sum of protons and neutrons in the nucleus.

• Number of Neutrons:

• Number of Electrons: In a neutral atom, equals the number of protons.

Electron Shells and the Periodic Table

• Electrons occupy shells around the nucleus, each with a specific energy level.

• Shell capacities: 1st shell (2 electrons), 2nd shell (8 electrons), subsequent shells (8 electrons; higher shells may hold more).

• The periodic table organizes elements by atomic number (rows) and valence electrons (columns).

Isotopes and Radioisotopes

• Isotopes: Atoms of the same element with different numbers of neutrons, thus different atomic masses.

• Example: Carbon-12, Carbon-13, and Carbon-14 all have 6 protons but different numbers of neutrons.

• Radioisotopes: Unstable isotopes that emit radiation as they decay to a stable form.

• Half-life: Time required for 50% of a radioisotope to decay to a stable form.

Chemical Properties and the Octet Rule

• Valence electrons (outermost shell) determine chemical reactivity.

• Octet Rule: Atoms tend to gain, lose, or share electrons to achieve a full valence shell (usually 8 electrons).

• Inert Elements: Atoms with full valence shells are stable and non-reactive (e.g., noble gases).

Ions and Ionic Compounds

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

• Cation: Positively charged ion (loss of electrons).

• Anion: Negatively charged ion (gain of electrons).

• Elements on the left of the periodic table tend to form cations; those on the right form anions.

• Ionic Bonds: Electrostatic attraction between cations and anions, forming ionic compounds (salts).

• Example: Sodium chloride (NaCl) forms when sodium donates an electron to chlorine.

Covalent Bonding and Molecules

• Covalent Bonds: Atoms share electrons to achieve stability.

• Molecular Compounds: Molecules composed of two or more different elements.

• Molecular Formula: Indicates the number and type of atoms in a molecule.

• Structural Formula: Shows the arrangement of atoms and bonds; distinguishes isomers.

• Types of Covalent Bonds:

  • Single bond: One pair of electrons shared.

  • Double bond: Two pairs shared.

  • Triple bond: Three pairs shared.

• Carbon: Forms four covalent bonds; can create straight, branched, or ring structures (carbon skeletons).

Polarity of Covalent Bonds

• Electronegativity: The attraction an atom has for electrons in a bond.

• Nonpolar Covalent Bond: Electrons shared equally (e.g., O2).

• Polar Covalent Bond: Electrons shared unequally due to differences in electronegativity (e.g., H2O).

• Amphipathic Molecules: Contain both polar and nonpolar regions (e.g., phospholipids).

Intermolecular Attractions

• Hydrogen Bonds: Weak attractions between a partially positive hydrogen and a partially negative atom (important in water and biological molecules).

• Van der Waals Forces: Weak attractions due to temporary unequal electron distribution in nonpolar molecules.

• Hydrophobic Interactions: Nonpolar molecules aggregate in water to minimize contact with the polar solvent.

Water: Structure and Properties

Water is essential for life and has unique properties due to its molecular structure.

• Polar Molecule: Oxygen is more electronegative than hydrogen, creating partial charges and allowing hydrogen bonding.

• Phases: Exists as gas (vapor), liquid (water), and solid (ice).

• Cohesion: Attraction between water molecules (surface tension).

• Adhesion: Attraction between water and other substances.

• High Specific Heat: Water resists temperature changes due to hydrogen bonding.

  • Specific heat: Energy required to raise 1g of water by 1°C.

• High Heat of Vaporization: Energy required to convert 1g of water from liquid to gas.

• Universal Solvent: Dissolves many substances, especially polar and ionic compounds.

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

• Hydrophilic: Substances that dissolve in water (polar or charged).

• Hydrophobic: Substances that do not dissolve in water (nonpolar).

• Amphipathic: Molecules with both hydrophilic and hydrophobic regions (e.g., phospholipids in cell membranes).

• Dissociation: Ionic compounds, acids, and bases may dissociate in water, forming ions (electrolytes).

Acids, Bases, pH, and Buffers

• Acid: Proton donor; dissociates in water to release H+.

• Base: Proton acceptor; accepts H+ in solution.

• pH Scale: Measures hydrogen ion concentration; ranges from 0 (acidic) to 14 (basic), with 7 being neutral.

• pH Calculation:

• Neutralization: Addition of acid or base to return solution to pH 7.

• Buffer: Substance or group of substances that resists changes in pH by accepting or donating H+.

Water Mixtures

• Suspension: Large particles (>100 nm) in water; do not remain mixed unless agitated (e.g., blood cells in plasma).

• Emulsion: Suspension of nonpolar liquid in water (e.g., breast milk).

• Colloid: Medium-sized particles (1–100 nm); remain mixed (e.g., cytosol, plasma proteins).

• Solution: Homogeneous mixture with particles <1 nm (e.g., salt water).

Expressions of Solute Concentration

• Mass/Volume: Grams of solute per volume of solution.

• Mass/Volume Percent: Grams of solute per 100 mL of solution.

• Molarity (M): Moles of solute per liter of solution.

• Molality (m): Moles of solute per kilogram of solvent.

• Osmole (osm): Number of osmotic active particles in a solution.

• Osmolarity: Number of osmoles per liter of solution.

• Osmolality: Number of osmoles per kilogram of water.

• Mole: particles (Avogadro's number).

Biological Macromolecules

Four classes of organic macromolecules are essential for life: lipids, carbohydrates, nucleic acids, and proteins.

General Characteristics

• Large organic molecules containing carbon, hydrogen, and usually oxygen; may also contain nitrogen, phosphorus, and sulfur.

• Carbon Skeleton: Backbone of organic molecules; may be straight, branched, or ring-shaped.

• Hydrocarbons: Molecules containing only carbon and hydrogen.

• Functional Groups: Specific groupings of atoms that impart characteristic chemical properties.

• Polymers: Chains of repeating subunits (monomers); formed by dehydration synthesis and broken by hydrolysis.

Lipids

• Diverse group; not true polymers; insoluble or partially insoluble in water.

• Functions: Energy storage, membrane structure, hormones.

• Classes of Lipids:

  • Triglycerides: Glycerol + 3 fatty acids; energy storage, insulation, cushioning.

  • Phospholipids: Glycerol + 2 fatty acids + phosphate group; amphipathic; main component of cell membranes.

  • Steroids: Four-ring structure; includes cholesterol, steroid hormones, bile salts.

  • Eicosanoids: Modified 20-carbon fatty acids; include prostaglandins, thromboxanes, leukotrienes, prostacyclins.

• Glycolipids: Lipids with attached carbohydrates; important for cell recognition.

• Fat-Soluble Vitamins: Vitamins A, E, and K.

Carbohydrates

• Monomers are monosaccharides (simple sugars); general formula (CH2O)n.

• Monosaccharides: Single sugar units (e.g., glucose, fructose, galactose).

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

• Polysaccharides: Many monosaccharides linked (e.g., glycogen in animals, cellulose in plants).

• Pentose Sugars: Ribose (RNA), deoxyribose (DNA).

Nucleic Acids

• Store and transfer genetic information.

• Monomer: Nucleotide (nitrogenous base + pentose sugar + phosphate group).

• DNA: Double-stranded; bases are adenine (A), cytosine (C), guanine (G), thymine (T); found in nucleus and mitochondria.

• RNA: Single-stranded; bases are adenine (A), cytosine (C), guanine (G), uracil (U); found in nucleus and cytoplasm.

• ATP: Adenosine triphosphate; energy currency of the cell.

• NAD+ and FAD: Nucleotides involved in cellular respiration and ATP production.

Proteins

• Polymers of amino acids (20 types); functions include enzymes, defense, transport, support, movement, regulation, and storage.

• Amino Acid Structure: Central carbon, amino group, carboxyl group, R group (side chain).

• Peptide Bonds: Covalent bonds linking amino acids (formed by dehydration synthesis).

• Protein Structure Levels:

  • Primary: Linear sequence of amino acids.

  • Secondary: Alpha helix or beta-pleated sheet (due to hydrogen bonding).

  • Tertiary: Three-dimensional folding (globular or fibrous).

  • Quaternary: Multiple polypeptide chains (e.g., hemoglobin).

• Protein Folding: Assisted by chaperone proteins; stabilized by hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges.

• Denaturation: Loss of protein structure (and function) due to changes in pH or temperature.

Table: Major, Lesser, and Trace Elements in the Human Body

Additional info: Table content inferred from standard anatomy & physiology textbooks.

Summary Table: Types of Chemical Bonds

Additional info: Table content inferred for clarity and completeness.

Key Equations

• Number of Neutrons:

• pH Calculation:

• Avogadro's Number: particles

Additional info: Some explanations and tables were expanded for academic completeness and clarity, based on standard Anatomy & Physiology textbooks.