Building Blocks of Molecules

Introduction to Biochemistry and Matter

Biochemistry is the study of the chemistry of life, focusing on the molecules and reactions that occur in biological systems. Understanding these systems requires breaking them down into their component parts, studying these parts in isolation, and then reconstructing the system. The main components of life include proteins, nucleic acids, carbohydrates, and lipids, all of which are built from atoms and molecules.

• Matter: Physical material of the universe; anything that has mass and occupies space.

• Mass: The amount of matter present in a substance.

• Pure substance: A material with uniform chemical composition.

• Mixture: A material with variable composition that can be physically separated.

Atoms, Elements, Molecules, and Compounds

Atoms are the smallest particles of matter and are the fundamental building blocks of elements. Elements are pure substances composed of only one kind of atom. Molecules are the smallest units of a pure substance that retain its properties and are made up of atoms. Compounds are pure substances composed of multiple kinds of atoms chemically bonded together.

• Atom: Smallest particle of an element.

• Element: Homogeneous, pure substance with only one kind of atom.

• Molecule: Smallest unit of a pure substance, made up of atoms.

• Compound: Homogeneous, pure substance with multiple kinds of atoms.

Examples of Compounds

• Water: H2O (2 hydrogens, 1 oxygen)

• Table salt: NaCl (1 sodium, 1 chlorine)

• Glucose: C6H12O6 (6 carbon, 12 hydrogen, 6 oxygen)

Elements in Biological Systems

The structure of biological molecules determines their function. The most common elements found in cells and biological systems are carbon (C), nitrogen (N), oxygen (O), and hydrogen (H).

Subatomic Particles and Isotopes

Atomic Structure

Atoms are composed of subatomic particles: protons, neutrons, and electrons. The nucleus contains protons and neutrons, while electrons occupy the electron cloud surrounding the nucleus.

• Proton: Positively charged particle in the nucleus.

• Neutron: Neutral particle in the nucleus.

• Electron: Negatively charged particle outside the nucleus.

Definitions and Properties

• Neutral atom: Equal numbers of protons and electrons.

• Atomic number (Z): Number of protons in an element.

• Isotopes: Atoms with the same number of protons but different numbers of neutrons.

• Mass number (A): Number of protons plus neutrons.

• Atomic weight: Average mass of an element based on isotope abundance.

Hydrogen Isotopes

Calculating Atomic and Molecular Weights

• Atomic weight: Weighted average of the masses of an element's isotopes.

• Molecular weight: Sum of the atomic weights of all atoms in a molecule.

Example Calculations

• Water (H2O):

• Glucose (C6H12O6):

Electronic Structure and the Periodic Table

Periodic Table Organization

The periodic table is organized by atomic number and electron configuration. Elements with similar properties appear at regular intervals.

• Rows are called periods (shells).

• Columns are called groups or families (subshells).

Electronic Structure

• Electrons are arranged in energy shells (n=1, 2, 3, ...).

• Each shell contains subshells (s, p, d, f).

• Orbitals within subshells hold up to 2 electrons.

• Valence electrons are in the outermost shell and determine chemical properties.

Valence Electrons in Main Group Elements

Periodic Properties

Major Periodic Properties

• Metallic character: Ability to conduct heat/electricity, malleability, luster.

• Atomic size: Increases down a group, decreases across a period.

• Ionization energy: Energy required to remove an electron; increases across a period, decreases down a group.

• Electronegativity: Tendency to attract electrons; increases across a period, decreases down a group.

The Octet Rule and Bonding

Noble Gases and the Octet Rule

Noble gases have a full valence shell (8 electrons, s2p6) and are stable and unreactive. The octet rule states that atoms are most stable when they have 8 valence electrons. Atoms form bonds to achieve a stable octet.

• Ionic bonding: Atoms transfer electrons to form ions.

• Covalent bonding: Atoms share electrons to fill their octet.

Ions and Ionic Bonding

Ion Formation

• Simple ion: Element with unequal numbers of protons and electrons.

• Cation: Ion with more protons than electrons (positive charge).

• Anion: Ion with more electrons than protons (negative charge).

General Rules for Ion Formation

• Group 1: Forms 1+ ions

• Group 2: Forms 2+ ions

• Group 17: Forms 1- ions

• Group 16: Forms 2- ions

Polyatomic Ions

Polyatomic ions are covalently bonded groups of atoms with an overall charge. Common biological polyatomic ions include:

• NH4+ (ammonium)

• H3O+ (hydronium)

• OH- (hydroxide)

• HCO3- (bicarbonate)

• CO32- (carbonate)

• SO42- (sulfate)

• PO43- (phosphate)

• CN- (cyanide)

Ionic Compounds

Ionic compounds are formed by the electrostatic attraction between cations and anions. The formula represents the lowest possible ratio of ions to form a neutral compound.

• Na+ + Cl- → NaCl

• Mg2+ + F- → MgF2

• K+ + O2- → K2O

Summary

• Elements are made of atoms, which combine to form molecules and compounds.

• The most prevalent elements in biological systems are C, N, O, and H.

• Atoms are composed of protons, neutrons, and electrons; their properties are defined by atomic number.

• Isotopes have the same number of protons but different numbers of neutrons.

• The periodic table is organized by electron configuration and valence electrons, which determine chemical properties.

• Periodic trends include metallic character, atomic size, ionization energy, and electronegativity.

• The octet rule explains why atoms form bonds: to achieve a stable configuration of 8 valence electrons.

• Ions form when atoms gain or lose electrons, and ionic compounds are formed by the attraction between cations and anions.