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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 atoms, molecules, and their interactions is essential for studying life processes.

Atoms: Structure and Properties

Definition and Composition 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

Particle	Charge	Location
Proton	+1	Core of atom (nucleus)
Neutron	0 (uncharged)	Core of atom (nucleus)
Electron	-1	Orbiting nucleus in electron shells

• Element: A substance that cannot be broken down into other substances by chemical reactions. All atoms of the same type form an element.

• Atoms of a particular element may have different numbers of neutrons, resulting in isotopes.

Atomic Number and Atomic Weight

• Atomic number: Number of protons in the nucleus of an atom.

• Atomic weight: Sum of protons and neutrons in the nucleus.

• Isotopes: Atoms of the same element with different numbers of neutrons and thus different atomic weights.

Electron Shells and Chemical Behavior

Electron Shells

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

• Each shell occupies 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; the smallest unit retaining the properties 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, ocean water).

Formation of Ions and Ionic Bonds

• 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 form crystals, but break easily in water.

Covalent Bonds: Sharing Electrons

• Covalent bond: 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: Equal sharing of electron pairs.

• Polar covalent bond: Unequal sharing of electron pairs, resulting in partial charges.

Hydrogen Bonds

• Hydrogen bond: Weak bond formed by charge attraction between a hydrogen atom covalently bonded to one atom and attracted to another atom.

• Hydrogen bonds are about 20 times weaker than covalent bonds but are crucial for stabilizing biological molecules.

• Can form between molecules or within large molecules, helping stabilize three-dimensional shapes.

Water and Life

Properties of Water

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

• Water molecules exhibit cohesion and surface tension due to hydrogen bonding.

Cohesion and Surface Tension

• Cohesion: Attraction of water molecules to each other.

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

Polarity and Solubility

• Water is a polar molecule, making it a versatile solvent for polar and ionic substances (hydrophilic).

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

• Hydrophobic: Substances without an affinity for water; do not dissolve easily and tend to clump together due to hydrophobic interaction.

Water and Temperature Regulation

• Water helps moderate temperature changes due to:

  • High specific heat

  • 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): Energy needed to raise 1 gram of water by 1°C.

• Vaporization (evaporation): Transformation of liquid to gas.

• Heat of vaporization: Energy required for 1 gram of liquid to become gas; leads to cooling during evaporation.

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

Biological Solutions: Concentration and Acidity

Solute Concentration and Molarity

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

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

Term	Definition
Mole	Specific quantity (6.022 × 1023 items)
Molecular weight	Sum of atomic masses of all atoms in a molecule

Acids, Bases, and pH

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

$H_2O \rightleftharpoons H^+ + OH^-$

• The molar concentration of $H^+$ and $OH^-$ in pure water is $10^{-7}$ M.

• If $[H^+] > [OH^-]$, the solution is acidic.

• If $[OH^-] > [H^+]$, the solution is basic.

• Acid: Substance that increases $[H^+]$ in solution.

• Base: Substance that reduces $[H^+]$ in solution.

The pH Scale

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

• For a neutral solution: $pH = 7$, $[H^+] = [OH^-]$

• For an acidic solution: $pH < 7$, $[H^+] > [OH^-]$

• For a basic solution: $pH > 7$, $[OH^-] > [H^+]$

• In any aqueous solution: $[H^+][OH^-] = 10^{-14}$

• The pH scale is logarithmic; a change of one pH unit represents a tenfold change in $[H^+]$.

• Most biological solutions have pH between 6 and 8.

Buffers: Maintaining Constant pH

• Buffer: Substance that prevents sudden changes in pH by accepting or donating $H^+$ ions.

• Buffers are combinations of $H^+$ donors and acceptors.

• Example: Bicarbonate buffer system in blood.

Summary Table: Key Terms and Definitions

Term	Definition
Atom	Smallest unit of an element retaining its properties
Element	Substance that cannot be broken down by chemical reactions
Isotope	Atoms of the same element with different numbers of neutrons
Molecule	Two or more atoms held together by chemical bonds
Compound	Substance composed of two or more elements in a fixed ratio
Ionic bond	Bond formed by attraction between oppositely charged ions
Covalent bond	Bond formed by sharing electrons between atoms
Hydrogen bond	Weak bond formed by charge attraction between polar molecules
Hydrophilic	Affinity for water; easily dissolved
Hydrophobic	No affinity for water; not easily dissolved
Specific heat	Energy required to raise temperature of 1g of substance by 1°C
pH	Measure of acidity; $pH = -\log[H^+]$
Buffer	Substance that stabilizes pH by accepting/donating $H^+$

Additional info: These notes expand on the original content by providing definitions, examples, and equations for key concepts in atomic structure, chemical bonding, water properties, and solution chemistry, suitable for General Biology college students.