Atoms and Elements

Atomic Structure and Properties

Atoms are the smallest chemical units of matter, composed of subatomic particles: protons (positive charge), neutrons (neutral), and electrons (negative charge). The atomic number is the number of protons in the nucleus and determines the element's identity. The atomic mass is the sum of protons and neutrons.

• Proton: Positive charge, located in the nucleus, 1 atomic mass unit.

• Neutron: No charge, located in the nucleus, 1 atomic mass unit.

• Electron: Negative charge, found in electron shells, negligible mass.

Example: Carbon has 6 protons, 6 neutrons, and 6 electrons; its atomic number is 6.

Ions and Isotopes

Ions are atoms with unequal numbers of protons and electrons, resulting in a net charge. Cations are positively charged (loss of electrons), while anions are negatively charged (gain of electrons). Isotopes are atoms of the same element with different numbers of neutrons; some are stable, others are radioactive and used in medicine (e.g., Carbon-14 in radiolabeling).

Chemical Bonds and Molecules

Molecules, Compounds, and Isomers

Molecules are formed when two or more atoms bond together. Compounds are molecules composed of more than one element. Isomers have the same molecular formula but different structures (e.g., glucose, fructose, and galactose: C6H12O6).

Organic vs. Inorganic Compounds

• Organic molecules: Contain both carbon and hydrogen (e.g., CH4, C6H12O6).

• Inorganic molecules: May contain carbon or hydrogen, but not both (e.g., CO2, H2O, NaCl).

• Functional groups: Specific groups of atoms within molecules that have characteristic properties and reactivity (e.g., hydroxyl, carboxyl, amino).

Solutions, Acids, Bases, and pH

Solutions and Concentration

A solution consists of a solute dissolved in a solvent. Concentration is the amount of solute per volume of solvent (e.g., mg/mL or % solution).

Acids, Bases, and Salts

Acids release hydrogen ions (H+) in solution, increasing acidity. Bases release hydroxide ions (OH−), increasing basicity. Salts are formed from the reaction of an acid and a base.

pH Scale and Buffers

The pH scale measures the concentration of H+ ions in a solution, ranging from 0 (most acidic) to 14 (most basic), with 7 being neutral. Buffers are compounds that stabilize pH by absorbing or releasing H+ ions, crucial for maintaining homeostasis in biological systems.

pH Indicators

pH indicators, such as phenol red, are used in microbiology to detect acidic, neutral, or basic by-products in growth media.

Chemical Bonds

Valence Electrons and Bonding

Valence electrons are the electrons in the outermost shell of an atom and are involved in chemical bonding. Atoms bond to achieve stable electron configurations.

Ionic Bonds and Electrolytes

Ionic bonds are formed by the electrostatic attraction between oppositely charged ions (e.g., Na+ and Cl− in NaCl). When ionic compounds dissolve in water, the resulting ions are called electrolytes, which are essential for nerve transmission and muscle contraction in biological systems.

Covalent Bonds

Covalent bonds involve the sharing of electron pairs between atoms. They can be single (one pair shared), double (two pairs), or triple (three pairs). Covalent bonds can be polar (unequal sharing, creating dipoles) or nonpolar (equal sharing).

Noncovalent Interactions

• Hydrogen bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like O or N) and another electronegative atom.

• Van der Waals interactions: Weak, transient attractions between molecules due to temporary dipoles.

Hydrophilic, Hydrophobic, and Amphipathic Substances

• Hydrophilic: "Water-loving" substances that dissolve easily in water (e.g., sugars).

• Hydrophobic: "Water-fearing" substances that do not dissolve in water (e.g., oils).

• Amphipathic: Molecules with both hydrophilic and hydrophobic regions (e.g., phospholipids), which can form micelles and bilayers in water.

Chemical Reactions

Types of Chemical Reactions

• Synthesis reactions: Build larger molecules from smaller ones (A + B → AB). Dehydration synthesis removes water to form a new bond.

• Decomposition reactions: Break down molecules into smaller units (AB → A + B). Hydrolysis adds water to break bonds.

• Exchange reactions: Swap components between molecules (AB + CD → AD + CB).

Activation Energy and Reaction Types

Activation energy is the minimum energy required to initiate a chemical reaction. Catalysts (including enzymes) lower activation energy, increasing reaction rates. Exergonic reactions release energy, while endergonic reactions require energy input. Some reactions are reversible and can reach equilibrium.

Biological Macromolecules

Carbohydrates

Carbohydrates have the general formula (CH2O)n and serve as energy sources, structural materials, and for cell recognition. They are classified as:

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

• Disaccharides: Two monosaccharides linked by a glycosidic bond (e.g., sucrose).

• Polysaccharides: Long chains of monosaccharides (e.g., glycogen, starch, cellulose, chitin, peptidoglycan).

Lipids

Lipids are hydrophobic molecules including fats, oils, waxes, and steroids. They function as energy stores, structural components of membranes, and signaling molecules.

• Saturated fats: No double bonds, solid at room temperature (e.g., butter).

• Unsaturated fats: One or more double bonds, liquid at room temperature (e.g., olive oil).

• Phospholipids: Amphipathic, major component of cell membranes.

• Steroids: Four fused rings (e.g., cholesterol).

Nucleic Acids

Nucleic acids (DNA and RNA) store and transmit genetic information. They are polymers of nucleotides, each consisting of a sugar, phosphate, and nitrogenous base. DNA contains deoxyribose and bases A, G, C, T; RNA contains ribose and bases A, G, C, U. Nucleotides are linked by phosphodiester bonds.

Proteins

Proteins are polymers of amino acids linked by peptide bonds. Each amino acid has an amine group, carboxyl group, and variable R group. Protein structure is organized into four levels:

• Primary: Linear sequence of amino acids.

• Secondary: Alpha-helices and beta-pleated sheets stabilized by hydrogen bonds.

• Tertiary: Overall 3D structure of a single polypeptide, stabilized by various interactions (ionic, hydrogen, van der Waals, disulfide bridges).

• Quaternary: Association of multiple polypeptide chains.

Proteins serve as enzymes, structural scaffolds, transporters, and in cell recognition and communication.