Chemistry of Life: Matter and Atoms

Definition and Properties of Matter

• Matter is anything that occupies space and has mass.

• Mass is the amount of matter in an object and remains constant regardless of location (Earth or space).

• Weight is the mass of an object affected by gravity.

Atomic Structure

• Atoms are the smallest stable units of matter and the building blocks of all materials.

• An atom consists of a nucleus (center, containing protons and neutrons) and an electron cloud (space where electrons orbit the nucleus).

• Proton (p+): Subatomic particle with a positive charge, located in the nucleus.

• Neutron (n0): Subatomic particle with no charge, located in the nucleus.

• Electron (e-): Subatomic particle with a negative charge, located in the electron cloud.

• Atomic number: Number of protons in an atom.

• Atomic mass: Sum of protons and neutrons in an atom.

• Isotopes: Atoms of the same element with different numbers of neutrons.

Elements and Ions

• Element: Pure substance distinguished from all other matter; cannot be created or broken down by ordinary chemical means.

• Principal elements: Most abundant in the body (oxygen, carbon, hydrogen, calcium, nitrogen, phosphorus, etc.).

• Trace elements: Present in very small amounts (zinc, copper, etc.).

• Ion: Atom that has gained or lost electrons, becoming electrically charged.

• Cation: Positively charged ion (lost electrons), e.g., Na+, K+, Mg2+, Ca2+.

• Anion: Negatively charged ion (gained electrons), e.g., Cl-.

Chemical Bonds and Molecules

Types of Chemical Bonds

• Ionic bonds: Formed by the transfer of electrons from one atom to another, resulting in oppositely charged ions (e.g., NaCl).

• Covalent bonds: Formed by sharing electrons between atoms to complete their outer shells.

• Nonpolar covalent bond: Electrons are shared equally (no charge on molecule).

• Polar covalent bond: Electrons are shared unequally, creating partial charges (e.g., water molecules).

• Hydrogen bonds: Weak attractions between the positive pole of one polar molecule and the negative pole of another (important in water and biological molecules).

Molecules and Compounds

• Molecule: Chemical substance made up of two or more atoms held together by covalent bonds (e.g., O2, CO2).

• Compound: Chemical substance made up of atoms of two or more different elements (e.g., H2O).

Chemical Reactions

Types of Chemical Reactions

• Chemical reaction: Process in which reactants are converted to products.

• Hydrolysis: Breaking a chemical bond by adding water; catabolic reaction.

• Catabolism: Breakdown of complex molecules into simpler ones, releasing energy.

• Synthesis (anabolism): Assembly of small molecules into larger ones; consumes energy.

• Dehydration synthesis: Joining of two molecules with the release of water.

• Exergonic reaction: Releases energy (common in the body).

• Endergonic reaction: Requires energy input to begin.

Metabolites and Nutrients

• Metabolites: Substances essential in chemical reactions; can be synthesized or broken down in the body.

• Nutrients: Essential metabolites obtained from the diet.

Water: Properties and Importance

Key Properties of Water

• Chemical reactant: Medium for chemical reactions in the body.

• Lubrication: Reduces friction between surfaces (e.g., joints, cavities).

• High heat capacity: Absorbs and retains heat, stabilizing body temperature.

• Solvent: Dissolves many organic and inorganic molecules.

• Water is a polar molecule.

Dissociation and Solubility

• Dissociation: Breaking chemical bonds in compounds to form ions in solution (e.g., NaCl in water).

• Hydrophilic molecules: Dissolve in water (e.g., NaCl).

• Hydrophobic molecules: Do not dissolve in water (e.g., fats, oils).

• Colloid: Solution containing large organic molecules in suspension (e.g., protein in plasma).

Regulation of Body Fluid pH

• Water molecules can dissociate into hydrogen ions (H+) and hydroxide ions (OH-).

• pH: Measures acidity or basicity of a solution; scale ranges from 0 to 14.

• Normal blood pH: Ranges from 7.35 to 7.45.

• Acid: Substance that increases H+ concentration in solution.

• Base: Substance that decreases H+ concentration (removes H+ or releases OH-).

• Acidosis: Blood pH below 7.35; can cause health issues.

• Alkalosis: Blood pH above 7.8; can cause sustained muscle contractions.

Organic Molecules: Monomers and Polymers

• Monomers: Small building block molecules.

• Polymers: Long chain molecules made from monomers joined by covalent bonds.

Carbohydrates

Structure and Function

• Organic molecules containing carbon, hydrogen, and oxygen in a 1:2:1 ratio.

• Major energy source: 4 kcal/g.

• Found in fruits, vegetables, whole grains.

Types of Carbohydrates

• Monosaccharides (simple sugars): 3-7 carbon atoms (e.g., glucose, fructose, galactose).

• Isomers: Molecules with the same type and number of atoms but different structures (e.g., glucose and fructose).

• Disaccharides: Formed by joining two monosaccharides via dehydration synthesis (e.g., sucrose = glucose + fructose).

• Polysaccharides: Complex carbohydrates formed by joining multiple monosaccharides (e.g., glycogen in animals, cellulose in plants).

Lipids

Structure and Function

• Contain carbon, hydrogen, and oxygen; lower oxygen content than carbohydrates.

• Hydrophobic (insoluble in water), but can be transported in blood by special mechanisms.

• Major energy storage molecules; 9 kcal/g.

• Essential for cell membranes and insulation.

Types of Lipids

• Fatty acids: Long hydrocarbon chains; can be saturated (no double bonds) or unsaturated (one or more double bonds).

• Glycerides: Lipids composed of glycerol attached to fatty acids.

  • Monoglyceride: Glycerol + one fatty acid.

  • Diglyceride: Glycerol + two fatty acids.

  • Triglyceride: Glycerol + three fatty acids; main form of stored fat.

• Steroids: Large lipid molecules with a carbon-ring framework (e.g., cholesterol, cortisol, estrogen, testosterone).

• Phospholipids and glycolipids: Derived from fatty acids; major components of cell membranes. Each has a hydrophobic tail and hydrophilic head.

Proteins

Structure and Function

• Chains of amino acids (20 types in the body) containing carbon, hydrogen, oxygen, and nitrogen.

• Functions: Build/repair tissues, make hormones and enzymes, energy source (4 kcal/g).

• Amino acids are linked by peptide bonds (covalent bond between carboxyl group of one amino acid and amino group of another).

• Dipeptides, tripeptides, polypeptides: Compounds formed by joining two, three, or many amino acids, respectively.

Enzymes

• Proteins that catalyze (speed up) chemical reactions.

• Each enzyme is specific to a particular reaction (substrate specificity).

High-Energy Compounds

• Adenosine triphosphate (ATP): Main high-energy compound in cells.

• ATP consists of adenosine (adenine + ribose) and three phosphate groups.

• High energy is stored in covalent bonds between phosphate groups.

• ATP hydrolysis: Reaction where ATP is broken down to ADP (adenosine diphosphate), a free phosphate, and energy.

  • Equation:

Nucleic Acids: DNA and RNA

• RNA: Ribonucleic acid; DNA: Deoxyribonucleic acid.

• Nucleic acids are long chains of nucleotides.

• Each nucleotide consists of:

  1. Nitrogenous base

  2. Five-carbon sugar (ribose in RNA, deoxyribose in DNA)

  3. Phosphate group

• Pyrimidines: Cytosine (in DNA and RNA), thymine (DNA only), uracil (RNA only).

• Purines: Adenine and guanine (in both DNA and RNA).