Atoms, Molecules, and Life

Introduction to Chemistry in Biology

Chemistry is fundamental to biology because the interaction between atoms forms the basis of biological organization. Understanding atomic structure and chemical bonds is essential for comprehending biological processes.

Atoms: Structure and Subatomic Particles

Definition and Properties of Atoms

• Atom: The smallest unit of matter that retains the physical and chemical properties of an element.

• Atoms are composed of subatomic particles: protons, neutrons, and electrons.

Subatomic Particles

• Protons: Positively charged particles located in the nucleus of the atom.

• Neutrons: Uncharged particles also found in the nucleus.

• Electrons: Negatively charged particles that orbit the nucleus in electron shells.

Elements and Isotopes

• Element: A substance that cannot be broken down into other substances by chemical reactions; composed of atoms of the same type.

• Atomic number: The number of protons in an atom, which defines the element.

• Isotopes: Atoms of the same element with different numbers of neutrons, resulting in different atomic weights.

Electron Shells and Chemical Reactivity

Electron Shells

• Electron shells: Three-dimensional spaces around the nucleus where electrons are likely to be found, organized by energy level.

• Each shell holds electrons at a specific distance from the nucleus; higher shells have higher energy.

• The chemical behavior of an atom is determined by the number of electrons in its outermost shell.

• Atoms with incomplete outer shells are reactive; those with full shells are inert.

Chemical Bonds: Joining Atoms to Make Molecules

Types of Chemical Bonds

• Chemical bond: An attraction that holds atoms together.

• Molecule: Two or more atoms held together by chemical bonds, representing the smallest unit of a compound.

• Compound: Composed of two or more elements in a fixed ratio (e.g., NaCl).

• Mixture: Composed of two or more elements and/or compounds in a variable ratio (e.g., air, seawater).

Ions and Ionic Bonds

• Ion: A charged atom or molecule.

• Anion: Negatively charged ion.

• Cation: Positively charged ion.

• Ionic bond: Formed by the attraction between oppositely charged ions after electron transfer. Ionic compounds are called salts and usually form crystals; they are strong in crystals but break easily in water.

Covalent Bonds

• Covalent bond: A bond formed when two atoms share electrons.

• Single covalent bond: Shares a single pair of electrons.

• Double covalent bond: Shares two pairs of electrons.

• Triple covalent bond: Shares three pairs of electrons.

• Nonpolar covalent bond: Electrons are shared equally.

• Polar covalent bond: Electrons are shared unequally, resulting in partial charges on the molecule.

Hydrogen Bonds

• Hydrogen bond: A weak bond formed by the charge attraction when a hydrogen atom covalently bonded to one atom is attracted to another atom. Hydrogen bonds are about 20 times weaker than covalent bonds but are crucial in biological systems.

• Hydrogen bonds can stabilize the three-dimensional shape of large molecules and can form between or within molecules.

Water and Life

Properties of Water

• Cells are 70-95% water; water covers 70% of Earth's surface.

• Water molecules exhibit cohesion (attraction between molecules of the same kind) and surface tension (force that increases the ability of a surface to stretch without breaking).

• Water is a polar molecule due to polar covalent bonds, making it a versatile solvent.

• Hydrophilic substances dissolve easily in water; hydrophobic substances do not.

Water's Role in Temperature Regulation

• Water has a high specific heat and high heat of vaporization, helping to stabilize temperature.

• Specific heat: The amount of energy required to raise the temperature of 1 gram of a substance by 1°C.

• Heat of vaporization: The quantity of heat a liquid must absorb for 1 gram to be converted to the gaseous state.

• Water expands when it freezes, causing ice to float and insulate water below.

Solutions, Moles, and Molarity

Solute Concentration and Molarity

• Solute concentration: The amount of a substance present in a given volume of solution.

• Molarity: The number of moles of a substance present in a liter of solution.

Mole and Molecular Weight

• Mole: A specific quantity of a substance, equal to items.

• Molecular weight: The mass or weight of one mole of any type of molecule, calculated by adding the atomic masses of all atoms in the molecule.

Acids, Bases, and pH

Dissociation of Water

• Water molecules can dissociate, forming hydrogen ions (H+) and hydroxide ions (OH-).

Acidity, Basicity, and the pH Scale

• The molar concentration of M and M in pure water.

• Acid: A substance that increases the concentration of in a solution.

• Base: A substance that reduces the concentration of in a solution.

• pH scale: Measures the acidity of solutions, ranging from 0 (most acidic) to 14 (most basic).

• In any aqueous solution:

• The pH scale is logarithmic; a change of one pH unit represents a tenfold change in concentration.

• Most biological solutions have pH between 6 and 8.

Buffers

• Buffer: A substance that prevents large, sudden changes in pH by accepting or donating ions.

• Buffers are combinations of donors and acceptors.

• Example: Bicarbonate buffer system in blood.

Key Equations

• Relationship between and in water:

• Calculation of molecular weight:

Examples and Applications

• Table salt (NaCl) is an example of an ionic compound.

• Water (H2O) is a polar molecule, essential for life.

• Bicarbonate buffer helps maintain blood pH.