Atoms, Molecules, and Life

Introduction to Chemistry in Biology

Chemistry is fundamental to understanding biological organization because the interactions between atoms form the basis of all living matter. The lowest levels of biological organization involve atoms and molecules.

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

• Element: A substance that cannot be broken down into other substances by chemical reactions. Elements are composed of atoms.

Subatomic Particles

Atoms are made up of subatomic particles: protons, neutrons, and electrons.

• Protons are positively charged particles found at the core, or nucleus, of the atom.

• Neutrons are uncharged particles found at the nucleus of the atom.

• Electrons are light, negatively charged particles that orbit around the nucleus in electron shells.

Atomic Number, Atomic Mass, and Isotopes

The atomic number is the number of protons in an atom of a particular element. The atomic mass (weight) is the number of protons plus the number of neutrons.

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

Electron Shells and Energy Levels

Electron shells are three-dimensional spaces around the nucleus where electrons are likely to be found. Electrons are arranged in shells based on their energy level.

• Each shell occupies a specific distance from the nucleus; further shells have higher energy levels.

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

• An atom with a full outer shell is inert; one with vacancies is reactive.

Chemical Bonds and Molecules

Types of Chemical Bonds

Chemical bonds are attractions that hold atoms together to form molecules.

• Chemical bond: An attraction that holds two atoms together.

• Molecule: Two or more atoms held together by chemical bonds.

• 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).

Formation of Ions and Ionic Bonds

If an atom has an almost empty or almost full outer electron shell, it is likely to form an ion.

• Ion: A charged atom or molecule.

• Anion: Negatively charged atom or molecule.

• Cation: Positively charged atom or molecule.

• Ionic bond: Formed by the attraction between oppositely charged ions after electron transfer. Ionic compounds are called salts and usually form crystals.

Covalent Bonds

Covalent bonds are formed when two atoms share electrons.

• Single covalent bond: Sharing one pair of electrons.

• Double covalent bond: Sharing two pairs of electrons.

• Triple covalent bond: Sharing three pairs of electrons.

Nonpolar vs. Polar Covalent Bonds

• Nonpolar covalent bond: Electrons are shared equally.

• Polar covalent bond: Electrons are shared unequally, resulting in partial charges at different ends of the molecule.

Hydrogen Bonds

Hydrogen bonds form between polar molecules due to charge attraction.

• Hydrogen bond: Attraction between a hydrogen atom covalently bonded to one atom and another electronegative atom.

• Hydrogen bonds are about 20 times easier to break than covalent bonds.

• They help stabilize the three-dimensional shape of large molecules.

Properties of Water

Water Molecules and Hydrogen Bonding

Water's cohesive behavior is due to hydrogen bonding between water molecules and other molecules, resulting in cohesion and surface tension.

• Cohesion: Attraction of a molecule to the same kind of molecule.

• Surface tension: Force that increases the ability of a liquid's surface to stretch without breaking.

• Water has greater surface tension than most liquids due to hydrogen bonds at the surface.

Water as a Solvent

• Polar molecule: Water is a polar molecule, making it a versatile solvent.

• Hydrophilic: Substances that dissolve easily in water.

• Hydrophobic: Substances that do not dissolve in water; hydrophobic molecules clump together due to hydrophobic interaction.

Temperature Moderation by Water

Water helps moderate temperature changes due to its high specific heat and high heat of vaporization.

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

• Calorie (cal): Unit of energy; 1 cal raises 1 g of water by 1°C.

• Heat of vaporization: Quantity of heat a liquid must absorb for 1 g to be converted to gas.

• Water expands when it freezes.

Solutions, Acids, and Bases

Solute Concentration and Molarity

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

• Molarity: Number of moles of a substance per liter of solution.

• Mole: Specific quantity (6.022 × 1023 items).

• Molecular weight: Mass of one mole of any type of molecule.

Acids, Bases, and pH

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

• In pure water:

• Acid: Increases concentration of H+ ions.

• Base: Reduces concentration of H+ ions.

The pH Scale

• pH scale: Measures acidity of solutions, ranges from 0 to 14.

• For neutral solution:

• For acidic solution:

• For basic solution:

• In any aqueous solution:

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

• Most biological solutions are between pH 6 and pH 8.

Buffers

Buffers are substances that prevent large, sudden changes in pH by donating or accepting H+ ions.

• Buffers are combinations of H+ donors and acceptors.

• Example: Bicarbonate buffer system.

Additional info: The notes have been expanded with academic context, definitions, and examples to ensure completeness and clarity for General Biology students.