Atoms and Elements

Types of Atoms in Biology

Biological systems are primarily composed of four types of atoms: Hydrogen, Carbon, Nitrogen, and Oxygen. These elements account for approximately 96% of all matter in organisms.

• Structure affects function: The arrangement of subatomic particles determines atomic properties.

• Protons: Positively charged particles in the nucleus.

• Neutrons: Neutral particles in the nucleus.

• Electrons: Negatively charged particles orbiting the nucleus.

• Atoms are defined by their atomic number (number of protons).

• Mass number = number of protons + neutrons.

• Isotopes: Forms of an element with different numbers of neutrons.

• Dalton (Da): Unit for measuring atomic mass.

Example: Helium atom: Atomic number = 2 (protons), Mass number = 4 (protons + neutrons).

Atomic Structure and Chemical Bonds

Electron Shells and Orbitals

Electrons occupy specific regions called orbitals within electron shells. Each shell can hold a set number of electrons, and electrons fill shells from the lowest energy level upward.

• Valence electrons: Electrons in the outermost shell; determine chemical reactivity.

• Electronegativity: Tendency of an atom to attract electrons; oxygen is highly electronegative.

• Ionic bonds: Transfer of electrons between atoms, resulting in charged ions.

• Covalent bonds: Sharing of electrons between atoms; can be polar (unequal sharing) or nonpolar (equal sharing).

• Cation: Positively charged ion.

• Anion: Negatively charged ion.

Example: Water (H2O) has polar covalent bonds due to unequal sharing of electrons between hydrogen and oxygen.

Molecular Structure and Models

Representations of Molecules

Molecules can be represented in several ways to illustrate their structure and function.

• Molecular formula: Shows the numbers and types of atoms in a molecule.

• Structural formula: Shows how atoms are bonded together.

• Ball-and-stick model: Three-dimensional shape of molecules.

• Space-filling model: Depicts relative sizes of atoms.

Example: Methane (CH4) has a tetrahedral structure; water is planar.

Properties of Water

Water as a Solvent

Water is an excellent solvent due to its polarity and ability to form hydrogen bonds. This property is critical for biological processes.

• Hydrogen bonds: Weak interactions between the hydrogen atom of one water molecule and the oxygen atom of another.

• Hydrophilic substances: Ionic and polar molecules dissolve easily in water.

• Hydrophobic substances: Nonpolar molecules do not dissolve in water; they cluster together.

• Van der Waals interactions: Weak electrical attractions between hydrophobic molecules.

• Cohesion: Water molecules stick to each other.

• Adhesion: Water molecules stick to other polar substances.

• High surface tension: Water behaves like an elastic membrane.

Example: Water dissolves salts and sugars due to its polarity and hydrogen bonding.

Thermal Properties of Water

Water has unique thermal properties that are essential for life.

• High specific heat: Requires a large amount of energy to change temperature.

• High heat of vaporization: Requires high energy input to change from liquid to gas.

• Helps regulate temperature in organisms and environments.

Chemical Reactions and Energy

Types of Chemical Reactions

Chemical reactions involve the making and breaking of chemical bonds, often accompanied by energy changes.

• Dissociation reaction: Water molecules split into H+ and OH-.

• Acids: Donate protons (H+); increase hydronium concentration.

• Bases: Accept protons; decrease hydronium concentration.

• Buffers: Minimize changes in pH; important for homeostasis.

• Molarity: Number of moles of solute per liter of solution.

Equation:

Thermodynamics in Biology

Energy transformations are governed by the laws of thermodynamics.

• 1st Law: Energy is neither created nor destroyed, only transformed.

• 2nd Law: Entropy (disorder) increases in spontaneous reactions.

• Potential energy: Stored energy due to position or structure.

• Kinetic energy: Energy of motion.

• Gibbs Free Energy (G): Determines spontaneity of reactions.

Equations:

• : Spontaneous reaction

• : Nonspontaneous reaction (requires input)

• : Change in enthalpy (total energy)

• : Change in entropy (disorder)

Example: Cellular respiration:

Macromolecules and Polymers

Types of Biological Macromolecules

Cells contain four major classes of macromolecules: lipids, carbohydrates, proteins, and nucleic acids (DNA, RNA).

• Polymers: Large molecules made of repeating units called monomers.

• Monomer of proteins: Amino acids.

• Monomer of nucleic acids: Nucleotides.

• Monomer of carbohydrates: Monosaccharides.

Protein Structure and Function

Proteins are polymers of amino acids, and their structure determines their function.

• Primary structure: Sequence of amino acids.

• Secondary structure: Local folding (alpha-helix, beta-sheet) via hydrogen bonds in backbone.

• Tertiary structure: Overall 3D shape due to interactions between R-groups (side chains).

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

• Chaperone proteins: Assist in proper folding of other proteins.

• Enzymes: Proteins that catalyze chemical reactions; have specific active sites for substrates.

• R-groups: Determine chemical properties and function of amino acids.

Example: Insulin is a protein hormone that regulates blood sugar.

Formation of Polymers

Polymers are formed by condensation reactions (dehydration synthesis), which link monomers and release water.

• Peptide bond: Covalent bond between amino acids in proteins.

• Hydrolysis: Opposite of condensation; breaks polymers into monomers by adding water.

• Polymerization decreases entropy (increases order).

Equation:

Functional Groups in Organic Molecules

Common Functional Groups

Functional groups are specific groups of atoms within molecules that confer particular chemical properties.

• Amino group (-NH2): Found in amino acids.

• Carboxyl group (-COOH): Found in amino acids and fatty acids.

• Sulfhydryl group (-SH): Found in cysteine; forms disulfide bonds.

• Phosphate group (-PO4): Found in nucleic acids and ATP.

• Hydroxyl group (-OH): Found in alcohols and carbohydrates.

Example: The carboxyl and amino groups in amino acids form peptide bonds during protein synthesis.

Summary Table: Key Properties of Water

Summary Table: Protein Structure Levels

Additional info:

• Some context and terminology were expanded for clarity and completeness.

• Equations and tables were formatted for academic study purposes.