Atoms, Molecules, and Life: Foundations of Biological Chemistry

Study Guide - Smart Notes

Tailored notes based on your materials, expanded with key definitions, examples, and context.

Atoms, Molecules, and Life

Introduction to Chemistry in Biology

Understanding chemistry is essential in biology because the interactions between atoms form the basis of biological organization. Atoms and molecules are the fundamental units that compose all forms of matter, including living organisms.

Atoms: The Basic Unit of Matter

Structure of the Atom

Atom: The smallest unit of matter that retains the physical and chemical properties of an element.
Atoms are composed of three main subatomic particles:
- Protons: Positively charged particles located in the nucleus (core) of the atom.
- Neutrons: Uncharged (neutral) particles also found in the nucleus.
- Electrons: Negatively charged particles that orbit the nucleus in regions called electron shells.

Particle	Charge	Location
Proton	+1	Nucleus
Neutron	0 (uncharged)	Nucleus
Electron	-1	Electron shells (orbiting nucleus)

Elements and Isotopes

Element: A substance that cannot be broken down into other substances by chemical reactions. Each element is composed of atoms with the same number of protons.
Atomic number: The number of protons in an atom of a particular element.
Atomic weight: The sum of protons and neutrons in an atom.
Isotopes: Atoms of the same element that have different numbers of neutrons, and thus different atomic weights.

Electron Shells and Energy Levels

Electron shells: Three-dimensional regions around the nucleus where electrons are likely to be found, organized by energy level.
Each shell can hold a specific number of electrons; shells further from the nucleus have higher energy.
The valence shell is the outermost electron shell. Atoms with incomplete valence shells are reactive.

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

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 the transfer of electrons.
Ionic compounds are often crystalline solids (salts) and dissolve easily in water.

Covalent Bonds

Covalent bond: A bond formed when two atoms share electrons.
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 between atoms.
Polar covalent bond: Electrons are shared unequally, resulting in partial charges on the molecule.

Hydrogen Bonds and Weak Interactions

Hydrogen bond: A weak attraction between a hydrogen atom covalently bonded to one atom and attracted to another electronegative atom (often oxygen or nitrogen).
Hydrogen bonds are important in stabilizing the three-dimensional shapes of large molecules (e.g., proteins, DNA).
Weak bonds can be reversible and help in molecular interactions.

Water and Life

Properties of Water

Cells are 70–95% water; water covers about 70% of Earth's surface.
Water molecules are polar and form hydrogen bonds with each other, leading to unique properties.

Cohesion and Surface Tension

Cohesion: Attraction between molecules of the same kind (e.g., water molecules sticking together).
Surface tension: The force that increases the ability of a liquid's surface to resist breaking; water has high surface tension due to hydrogen bonding.

Water as a Solvent

Water is a polar molecule and an excellent solvent for ionic and polar substances (hydrophilic substances).
Hydrophilic: Having an affinity for water; dissolves easily in water.
Hydrophobic: Lacking an affinity for water; nonpolar substances that do not dissolve in water.

Temperature Moderation by Water

Water moderates temperature changes due to its high specific heat and heat of vaporization.
Specific heat: The amount of energy required to raise the temperature of 1 gram of a substance by 1°C.
Calorie (cal): The amount of energy needed to raise 1 gram of water by 1°C.
Heat of vaporization: The quantity of heat a liquid must absorb for 1 gram to be converted to gas.
Evaporation of water cools surfaces (e.g., sweating).
Water expands upon freezing, causing ice to float and insulate water below.

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 per liter of solution.
Mole: A specific quantity (6.022 × 1023 particles).
Molecular weight: The mass of one mole of a molecule, calculated by summing the atomic masses of all atoms in the molecule.

Acids, Bases, and pH

Acids and Bases

Water can dissociate into hydrogen ions (H+) and hydroxide ions (OH-).
In pure water:
Acid: A substance that increases the concentration of H+ in solution.
Base: A substance that reduces the concentration of H+ in solution (often by increasing OH-).

The pH Scale

pH scale: Measures the acidity of solutions, ranging from 0 (most acidic) to 14 (most basic).
Each pH unit represents a tenfold change in H+ concentration.
Neutral solution: pH = 7 ()
Acidic solution: pH < 7 ()
Basic solution: pH > 7 ()

Buffers

Buffers: Substances that minimize changes in pH by accepting or donating H+ ions as needed.
Buffers are combinations of H+ donors and acceptors (e.g., bicarbonate buffer in blood).

Example Table: Comparison of Bond Types

Bond Type	Strength	Mechanism	Example
Ionic	Strong (in crystals)	Electron transfer	NaCl (table salt)
Covalent	Very strong	Electron sharing	H2O, O2
Hydrogen	Weak (individually)	Attraction between polar molecules	Between water molecules

Additional info:

Isotopes can be stable or radioactive; radioactive isotopes are used in biological research and medicine.
Hydrogen bonds are critical for the structure of DNA and proteins.
Buffers are essential for maintaining homeostasis in biological systems.