ATOMS, MOLECULES AND LIFE

Introduction

An understanding of chemistry is essential in biology because the interaction between atoms forms the basis of biological organization. The smallest unit of all forms of matter is the atom.

Atoms: Structure and Properties

Subatomic Particles

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

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

• Protons: Positively charged particles found at the core, or nucleus, of the atom.

• Neutrons: Uncharged particles also found in the nucleus.

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

Elements and Isotopes

• Element: A substance that cannot be broken down into other substances by chemical reactions.

• Elements are composed of atoms.

• Atomic number: The number of protons in an atom of a particular element.

• Atomic weight: The sum of protons and neutrons in an atom.

• Atoms of the same element may have different numbers of neutrons, resulting in isotopes.

• Isotopes: Atoms of the same element with different atomic weights.

Electron Shells

• Electron shells: Three-dimensional spaces around the nucleus where electrons are likely to be found, arranged by 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 the outermost shell (valence shell).

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

Chemical Bonds: Joining Atoms to Make Molecules

Types of Chemical Bonds

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

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

• Compound: A substance 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 shell, it is likely to form an ion.

• Ion: A charged atom or molecule.

• Anion: Negatively charged ion.

• Cation: Positively charged ion.

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

Covalent Bonds

• Covalent bond: Formed when two atoms share electrons to fill their outer shells.

• Single covalent bond: Shares one 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 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 are important for stabilizing 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's cohesive behavior is due to hydrogen bonding, leading to cohesion and surface tension.

• Cohesion: Attraction of a molecule to others of the same kind (holds water together).

• Surface tension: The force that increases the ability of a surface of a liquid to stretch without breaking; water has high surface tension due to hydrogen bonds.

• Water is a polar molecule and an excellent solvent for ionic and polar substances (hydrophilic), but not for nonpolar substances (hydrophobic).

Hydrophilic and Hydrophobic Substances

• Hydrophilic: Substances with an affinity for water; easily dissolve in water.

• Hydrophobic: Substances that do not have an affinity for water; do not dissolve in water.

• Hydrophobic molecules cluster together in water due to hydrophobic interactions.

Water's Role in Temperature Regulation

• Water moderates temperature changes due to its high specific heat and high heat of vaporization.

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

• Calorie (cal): The amount of energy needed to raise the temperature of 1 gram of water by 1°C.

• Vaporization (evaporation): The transformation of matter from liquid to gas.

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

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

Solutions, Concentration, and Molarity

Solute Concentration

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

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

• Formula:

• Mole: A specific quantity (6.022 × 1023 items).

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

Acids, Bases, and pH

Acids and Bases

• Water can dissociate to form hydrogen ions (H+) and hydroxide ions (OH-).

• In pure water:

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

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

The pH Scale

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

• Formula:

• For a neutral solution:

• For an acidic solution:

• For a basic solution:

• In any aqueous solution:

• Each pH unit represents a tenfold change in H+ concentration.

Buffers

• Buffers: Substances that prevent large, sudden changes in pH.

• Buffers are combinations of H+ donors and acceptors.

• They function by accepting H+ ions when in excess and donating H+ ions when depleted.

• Example: Bicarbonate buffer in blood.