Introduction
The foundation of biochemistry lies in the understanding of atomic and molecular structures. Atoms are the basic units of matter, and their arrangement and interactions define the properties and functions of molecules in biological systems.
Atomic Structure
The Atom
An atom consists of a nucleus surrounded by a cloud of electrons. The nucleus contains protons and neutrons, while electrons orbit in various energy levels.
- Protons (p⁺): Positively charged particles found in the nucleus.
- Neutrons (n°): Neutral particles also located in the nucleus.
- Electrons (e⁻): Negatively charged particles that orbit the nucleus.
Atomic Number and Mass Number
- Atomic Number (Z): The number of protons in an atom's nucleus. It defines the element.
- Mass Number (A): The total number of protons and neutrons in the nucleus.
Isotopes
Isotopes are atoms of the same element with the same number of protons but different numbers of neutrons. They have identical chemical properties but may differ in physical properties.
Electron Configuration
Electrons are arranged in energy levels or shells around the nucleus. The distribution of electrons determines how atoms interact with one another.
Energy Levels and Orbitals
- Shells: Denoted by principal quantum numbers (n = 1, 2, 3, ...).
- Subshells: Each shell contains subshells (s, p, d, f) with specific orbitals.
- s-orbital: 1 orbital, can hold 2 electrons
- p-orbital: 3 orbitals, can hold 6 electrons
- d-orbital: 5 orbitals, can hold 10 electrons
- f-orbital: 7 orbitals, can hold 14 electrons
Electron Configuration Notation
Electron configurations are written using the notation:
\[ \text{n}^{\#}\text{subshell}^{\#\text{ of electrons}} \]
For example, the electron configuration of carbon is \(1s^2 \, 2s^2 \, 2p^2\).
Aufbau Principle, Pauli Exclusion Principle, and Hund's Rule
- Aufbau Principle: Electrons fill the lowest energy orbitals first.
- Pauli Exclusion Principle: No two electrons in the same atom can have the same set of four quantum numbers (an orbital can hold a maximum of two electrons with opposite spins).
- Hund's Rule: Electrons will fill degenerate orbitals (orbitals of the same energy) singly before pairing up.
Periodic Table and Atomic Trends
The periodic table is a systematic arrangement of elements based on atomic number, and it reveals recurring chemical properties.
Periodic Table Structure
- Groups: Vertical columns (elements have similar chemical properties).
- Periods: Horizontal rows (elements have the same number of electron shells).
Periodic Trends
Atomic Radius
- Definition: The distance from the nucleus to the outermost electron shell.
- Trend:
- Decreases across a period (left to right) due to increased nuclear charge pulling electrons closer.
- Increases down a group due to the addition of electron shells.
Ionization Energy
- Definition: The energy required to remove an electron from an atom in its gaseous state.
- Trend:
- Increases across a period (left to right) as electrons are held more tightly by the nucleus.
- Decreases down a group as the outer electrons are farther from the nucleus and more shielded.
Electronegativity
- Definition: A measure of an atom's ability to attract and hold electrons in a chemical bond.
- Trend:
- Increases across a period due to higher nuclear charge.
- Decreases down a group as the atomic radius increases and electron shielding reduces the effective nuclear charge.
Electron Affinity
- Definition: The energy change that occurs when an electron is added to a neutral atom in the gaseous state.
- Trend:
- Becomes more negative (increases) across a period as atoms become more eager to gain electrons to complete their valence shells.
- Becomes less negative (decreases) down a group due to increased electron shielding and atomic size.
Molecular Structure
Atoms bond together to form molecules, and the type of bond influences the molecule's properties and function.
Types of Chemical Bonds
Ionic Bonds
- Definition: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other.
- Characteristics:
- Typically occur between metals and nonmetals.
- High melting and boiling points.
- Conduct electricity when dissolved in water or melted.
Covalent Bonds
- Definition: Formed when two atoms share one or more pairs of electrons.
- Characteristics:
- Usually occur between nonmetals.
- Low melting and boiling points compared to ionic compounds.
- Do not conduct electricity in most cases.
Polar Covalent Bonds
- Definition: A type of covalent bond where electrons are shared unequally between atoms, leading to a partial charge distribution.
- Characteristics:
- Occurs when atoms have different electronegativities.
- Molecules have a dipole moment (one end is slightly negative, and the other is slightly positive).
- Examples include water \( \text{(H}_2\text{O)} \) and hydrogen chloride \( (\text{HCl}) \).
Nonpolar Covalent Bonds
- Definition: A covalent bond in which electrons are shared equally between two atoms.
- Characteristics:
- Occurs when atoms have similar electronegativities.
- No significant charge separation across the molecule.
- Examples include diatomic molecules like oxygen \( \text{(O}2) \) and nitrogen \( \text{(N}2) \).
Metallic Bonds
- Definition: A bond formed by the attraction between positively charged metal ions and the delocalized electrons that surround them.
- Characteristics:
- Metals have a "sea of electrons" that are free to move, leading to high electrical and thermal conductivity.
- Malleable and ductile due to the flexibility of the electron cloud.
- Lustrous appearance due to the interaction of light with the mobile electrons.
Intermolecular Forces
While ionic and covalent bonds are intramolecular forces (holding atoms within a molecule together), intermolecular forces are attractions between molecules that influence physical properties like boiling point, melting point, and solubility.
1. Van der Waals Forces
- Definition: Weak, temporary forces of attraction between molecules or atoms.
- Types:
- London Dispersion Forces: Present in all molecules, caused by temporary dipoles induced in atoms or molecules. Stronger in larger molecules with more electrons.
- Dipole-Dipole Interactions: Occur between polar molecules where the positive end of one molecule is attracted to the negative end of another.
2. Hydrogen Bonds
- Definition: A special type of strong dipole-dipole interaction that occurs when hydrogen is bonded to highly electronegative atoms like nitrogen, oxygen, or fluorine.
- Characteristics:
- Much stronger than typical dipole-dipole interactions.
- Crucial in biological structures like DNA (holding the two strands together) and proteins (stabilizing secondary and tertiary structures).
- Contributes to the high boiling point and unique properties of water.
3. Dipole-Dipole Interactions
- Definition: Forces of attraction between polar molecules, where the positive end of one molecule is attracted to the negative end of another.
- Characteristics:
- Occur in molecules with permanent dipoles (polar molecules).
- Stronger than London dispersion forces but weaker than hydrogen bonds.
- Influence the physical properties of polar compounds, such as higher boiling and melting points compared to nonpolar compounds of similar size.
Common Elements in Biochemistry
Overview
Biochemical processes are driven by a select group of elements that make up the majority of living organisms. These elements form the building blocks of macromolecules like proteins, nucleic acids, carbohydrates, and lipids.
Essential Elements
1. Carbon (C)
- Role:
- The backbone of all organic molecules.
- Forms stable covalent bonds with other elements, allowing for the creation of complex structures like chains, rings, and branches.
- Examples:
- Present in all macromolecules: proteins, nucleic acids, carbohydrates, and lipids.
- Functional groups like hydroxyl, carboxyl, and carbonyl are based on carbon structures.
2. Hydrogen (H)
- Role:
- Part of nearly every organic compound.
- Involved in energy transfer and storage (e.g., ATP).
- Plays a crucial role in maintaining the structure of molecules through hydrogen bonding.
- Examples:
- Constituent of water, the most abundant molecule in cells.
- Involved in reduction-oxidation reactions and pH regulation.
3. Oxygen (O)
- Role:
- Essential for cellular respiration as the final electron acceptor in the electron transport chain.
- Forms part of many functional groups, including hydroxyl, carbonyl, and carboxyl groups.
- Examples:
- Present in carbohydrates, lipids, proteins, and nucleic acids.
- Involved in metabolic reactions and energy production.
4. Nitrogen (N)
- Role:
- A key component of amino acids, the building blocks of proteins, and nucleotides, the building blocks of nucleic acids.
- Integral to the structure of enzymes, which catalyze biochemical reactions.
- Examples:
- Found in proteins, DNA, RNA, and other nitrogenous compounds like ATP.
- Crucial for the synthesis of neurotransmitters and hormones.
5. Phosphorus (P)
- Role:
- Vital for energy transfer through molecules like ATP and GTP.
- Part of the structural framework of nucleic acids (DNA and RNA) and phospholipids in cell membranes.
- Examples:
- Phospholipids form the bilayer of cell membranes, providing structural integrity and fluidity.
- Phosphate groups in nucleotides are essential for genetic information storage and transmission.
6. Sulfur (S)
- Role:
- Component of certain amino acids (cysteine and methionine) and vitamins (e.g., biotin and thiamine).
- Involved in the formation of disulfide bonds, which stabilize protein structures.
- Examples:
- Disulfide bridges in proteins contribute to tertiary and quaternary structure stability.
- Present in coenzymes and metabolic intermediates.
7. Calcium (Ca)
- Role:
- Essential for bone and teeth formation.
- Acts as a signaling molecule in many cellular processes, including muscle contraction, nerve impulse transmission, and blood clotting.
- Examples:
- Found in the extracellular matrix, providing structural support.
- Involved in enzyme activation and as a secondary messenger in signal transduction pathways.
Biological Macromolecules
The elements listed above combine to form the four major classes of biological macromolecules:
- Proteins: Composed of amino acids linked by peptide bonds; serve as enzymes, structural components, signaling molecules, and transporters.
- Nucleic Acids: Made of nucleotides; store and transmit genetic information (DNA and RNA).
- Carbohydrates: Consist of sugar molecules; provide energy, structural support, and play a role in cell recognition.
- Lipids: Include fats, oils, phospholipids, and steroids; crucial for energy storage, cell membrane structure, and signaling.