Building Blocks of Life

Atoms

Atoms are the fundamental units of matter, forming the basis of all substances in biology. Each atom consists of a nucleus containing protons and neutrons, surrounded by electrons.

• Protons: Positively charged particles in the nucleus.

• Neutrons: Neutral particles in the nucleus.

• Electrons: Negatively charged particles orbiting the nucleus.

Elements

An element is a pure substance consisting of only one type of atom, defined by its number of protons (atomic number). Examples include hydrogen (H), carbon (C), oxygen (O), and nitrogen (N).

Isotopes

Isotopes are atoms of the same element with different numbers of neutrons, resulting in different mass numbers. Some isotopes are stable, while others are radioactive.

• Example: Carbon-12 and Carbon-14 are isotopes of carbon.

Atomic Number, Mass, and Weight

• Atomic Number (Z): Number of protons in the nucleus.

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

• Atomic Weight: Average mass of all isotopes of an element, weighted by abundance.

Atomic Structure

Atoms have a central nucleus (protons and neutrons) and electrons arranged in orbitals around the nucleus.

Orbitals and Electron Shells

• Orbitals: Regions of space where electrons are likely to be found.

• Electron Shells: Energy levels containing one or more orbitals. Electrons fill lower energy shells first.

• Valence Shell: The outermost electron shell, important for chemical bonding.

Chemical Bonding

Covalent Bonds

Covalent bonds form when two atoms share one or more pairs of electrons. These are strong bonds that hold molecules together.

• Polar Covalent Bonds: Electrons are shared unequally, resulting in partial charges (e.g., H2O).

• Non-Polar Covalent Bonds: Electrons are shared equally (e.g., O2, N2).

Ionic Bonds

Ionic bonds form when electrons are transferred from one atom to another, creating oppositely charged ions that attract each other (e.g., NaCl).

Hydrogen Bonds

Hydrogen bonds are weak attractions between a hydrogen atom (covalently bonded to an electronegative atom) and another electronegative atom. Important in water and biological molecules.

Van der Waals Interactions

Weak, transient attractions between molecules due to temporary dipoles. Significant in large molecules like proteins.

Basic Molecular Geometry

The shape of molecules is determined by the arrangement of atoms and electron pairs, influencing function and interactions.

Molecular and Structural Formulas

• Molecular Formula: Shows the types and numbers of atoms (e.g., H2O).

• Structural Formula: Shows the arrangement of atoms and bonds (e.g., H–O–H).

Properties of Water

Solvent vs Solute

• Solvent: The substance that dissolves another (e.g., water).

• Solute: The substance being dissolved (e.g., salt).

Hydrophilic vs Hydrophobic

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

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

Cohesion and Adhesion

• Cohesion: Attraction between water molecules, leading to surface tension.

• Adhesion: Attraction between water molecules and other substances.

Density

Water is less dense as a solid (ice) than as a liquid, allowing ice to float. This is due to the hydrogen-bonded lattice structure in ice.

Specific Heat

Water has a high specific heat, meaning it can absorb or release large amounts of heat with little temperature change. This stabilizes temperatures in organisms and environments.

Heat of Vaporization

Water requires significant energy to change from liquid to gas, aiding in cooling mechanisms like sweating.

pH: Acids vs Bases

• pH: A measure of hydrogen ion concentration;

• Acids: Substances that increase [H+] in solution (pH < 7).

• Bases: Substances that decrease [H+] in solution (pH > 7).

Buffers

Buffers are substances that minimize changes in pH by accepting or donating H+ ions. They are crucial for maintaining homeostasis in biological systems.

Energy in Biological Systems

Potential vs Kinetic Energy

• Potential Energy: Stored energy due to position or structure (e.g., chemical bonds).

• Kinetic Energy: Energy of motion (e.g., movement of molecules).

Laws of Thermodynamics

• First Law: Energy cannot be created or destroyed, only transformed.

• Second Law: Every energy transfer increases the entropy (disorder) of the universe.

Spontaneous Reactions

A spontaneous reaction occurs without input of energy, typically when products have lower potential energy and higher entropy than reactants.

Carbon-Based Life

Functional Groups

Functional groups are specific groups of atoms within molecules that confer characteristic chemical properties. Common examples include hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), phosphate (-PO4), and sulfhydryl (-SH).

Monomers vs Polymers

• Monomer: A small molecule that can join with others to form a polymer (e.g., amino acids, nucleotides).

• Polymer: A large molecule made of repeating monomer units (e.g., proteins, nucleic acids).

Condensation Reaction

A condensation reaction (dehydration synthesis) joins two monomers by removing a water molecule, forming a covalent bond.

Hydrolysis

Hydrolysis is the process of breaking a covalent bond in a polymer by adding a water molecule, resulting in smaller subunits.