Molecular Interactions: Atoms, Bonds, and Biomolecules

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Ch. 2 Molecular Interactions

Atoms: The Smallest Unit of Matter

Atoms are the fundamental building blocks of all matter, including living organisms. Understanding their structure and properties is essential for grasping molecular interactions in physiology.

Atom: The smallest unit of an element that retains the properties of that element.
Element: A pure substance made of only one type of atom.
All matter consists of atoms, which combine to form molecules and compounds.

Atomic Structure:

Atoms are made of subatomic particles: protons (positive charge), neutrons (neutral), and electrons (negative charge).
Protons and neutrons are found in the nucleus; electrons orbit the nucleus in shells.

Particle	Charge	Location	Relative Mass
Proton	+1	Nucleus	1
Neutron	0	Nucleus	1
Electron	-1	Electron cloud	~0

Elements of Life

Living organisms are primarily composed of a small subset of elements, with carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur (CHONPS) being the most abundant.

Bulk elements: Required in large amounts (e.g., C, H, O, N).
Trace elements: Required in small amounts (e.g., Fe, Zn).

Atomic Properties

Atomic Number (Z): Number of protons in the nucleus.
Mass Number (A): Number of protons plus neutrons.
Isotopes: Atoms of the same element with different numbers of neutrons.

Electron Orbitals & Energy Shells

Electrons occupy energy shells around the nucleus. The arrangement of electrons determines chemical reactivity.

First shell holds up to 2 electrons; second shell up to 8, etc.
Valence electrons: Electrons in the outermost shell, important for bonding.

Octet Rule

Atoms are most stable when their valence shell is full (usually 8 electrons). Atoms will gain, lose, or share electrons to achieve a full valence shell.

Isotopes & Radioactivity

Isotopes: Same number of protons, different number of neutrons.
Radioactive isotopes: Unstable isotopes that decay, emitting energy and particles. Used in dating, imaging, and cancer treatment.

Chemical Bonds

Chemical bonds hold atoms together in molecules and compounds. The main types are covalent, ionic, and hydrogen bonds.

Covalent Bonds

Formed by sharing electrons between atoms.
Nonpolar covalent: Equal sharing of electrons (e.g., O2).
Polar covalent: Unequal sharing, leading to partial charges (e.g., H2O).
Electronegativity: The tendency of an atom to attract electrons in a bond.

Ionic Bonds

Formed by the transfer of electrons from one atom to another, creating ions (cations and anions).
Oppositely charged ions attract (e.g., NaCl).

Hydrogen Bonds

Weak attractions between a hydrogen atom (bonded to O, N, or F) and another electronegative atom.
Important for the structure of water, proteins, and nucleic acids.

Van der Waals Forces

Weak, transient attractions between nonpolar molecules.

Acids, Bases, and pH

Acid: Substance that increases [H+] in solution.
Base: Substance that decreases [H+] or increases [OH-].
pH scale: Measures hydrogen ion concentration; pH = -log[H+].

Buffers help maintain stable pH in biological systems (e.g., bicarbonate buffer in blood).

Carbon and Organic Molecules

Carbon forms the backbone of organic molecules due to its ability to form four covalent bonds.
Organic molecules contain carbon and hydrogen; may also include O, N, P, S.

Functional Groups

Groups of atoms that confer specific chemical properties to molecules (e.g., hydroxyl, carboxyl, amino, phosphate).

Biomolecules: Monomers and Polymers

Four major classes: carbohydrates, proteins, nucleic acids, lipids.
Monomers: Simple building blocks (e.g., monosaccharides, amino acids, nucleotides).
Polymers: Chains of monomers (e.g., polysaccharides, polypeptides, nucleic acids).
Polymers are formed by dehydration synthesis (removal of water) and broken down by hydrolysis (addition of water).

Carbohydrates

Composed of C, H, and O (general formula: CnH2nOn).
Monosaccharides (simple sugars), disaccharides, and polysaccharides (complex carbs).
Functions: energy storage (glycogen, starch), structural support (cellulose, chitin).

Proteins

Polymers of amino acids linked by peptide bonds.
Levels of structure: primary (sequence), secondary (alpha helix, beta sheet), tertiary (3D folding), quaternary (multiple polypeptides).
Denaturation: Loss of structure and function due to environmental changes.

Nucleic Acids

Polymers of nucleotides (DNA, RNA).
Nucleotide structure: phosphate group, pentose sugar (deoxyribose or ribose), nitrogenous base (A, T/U, G, C).
DNA stores genetic information; RNA involved in protein synthesis.
Base pairing: A-T (or A-U in RNA), G-C.

Lipids

Hydrophobic molecules including fats, oils, phospholipids, and steroids.
Functions: energy storage, membrane structure, signaling.

Summary Table: Types of Chemical Bonds

Bond Type	Strength	Example	Role in Biology
Covalent	Strong	H2O, CH4	Stable backbone of molecules
Ionic	Moderate	NaCl	Electrolyte balance, nerve impulses
Hydrogen	Weak	Between H2O molecules	Protein & DNA structure
Van der Waals	Very weak	Lipid interactions	Membrane fluidity

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