Atoms and Atomic Structure

Definition and Properties of Atoms

Atoms are the smallest units of matter that retain the properties of an element. They are composed of subatomic particles and are the building blocks of all matter.

• Subatomic particles:

  • Proton: Mass of 1, positive charge

  • Neutron: Mass of 1, no charge

  • Electron: Negligible mass, negative charge

• Atoms are electrically neutral when the number of protons equals the number of electrons.

• Atoms are organized in the periodic table by their properties.

• Six elements (C, H, O, N, P, S) are fundamental to all organisms.

Isotopes

Isotopes are atoms of the same element with the same number of protons but different numbers of neutrons.

• Most elements have several isotopes; some are more stable than others.

• Examples:

  • Hydrogen isotopes: 1H, 2H, 3H

  • Carbon isotopes: 12C, 13C, 14C

• Additional info: Some isotopes have special names (e.g., Deuterium for 2H, Tritium for 3H).

Electron Configuration and Chemical Behavior

The arrangement of electrons in shells determines how atoms interact and bond.

• Outermost shell (valence shell) determines chemical reactivity.

• Atoms are most stable when their outer shell is full.

• Reactive atoms have unpaired electrons in their outermost shell.

• The energy level of each shell increases with distance from the nucleus.

Chemical Bonds and Molecules

Types of Chemical Bonds

Chemical bonds are attractive forces that link atoms together to form molecules.

• Covalent Bonds: Shared electrons between atoms.

  • Polar covalent: Unequal sharing (atoms are different).

  • Nonpolar covalent: Equal sharing (atoms are identical).

• Ionic Bonds: Attraction between oppositely charged ions (cations and anions).

• Hydrogen Bonds: Weak bonds between polar molecules, important in water and DNA.

Definitions and Examples

• Element: Pure substance containing only one kind of atom.

• Molecule: Electrically neutral group of two or more atoms held together by chemical bonds (e.g., O2).

• Compound: Molecule made up of two or more elements in a fixed ratio (e.g., H2O, NaCl).

• Molecular weight: Sum of atomic weights of all atoms in a molecule.

Electronegativity

Electronegativity is the ability of an atom to attract electrons in a bond. The more electronegative an atom, the more strongly it pulls shared electrons toward itself.

Chemical Reactions

Nature of Chemical Reactions

Chemical reactions involve the making and breaking of chemical bonds, resulting in the transformation of substances.

• Reactants: Starting materials of a chemical reaction.

• Products: Final molecules of a chemical reaction.

• Law of Conservation of Matter: Chemical reactions cannot create or destroy matter.

Equation Example

Properties of Water

Importance of Water

Water is a polar molecule and is essential for life due to its unique chemical and physical properties.

• Water is a solvent for many biochemical reactions (aqueous solution).

• Water's covalent bonds are polar.

• Water forms hydrogen bonds with other polar molecules.

Hydrophilic and Hydrophobic Interactions

• Hydrophilic: Water-loving molecules that form hydrogen bonds with water.

• Hydrophobic: Water-hating molecules (e.g., hydrocarbons) that do not interact with water.

Special Properties of Water

• High specific heat: Amount of heat required to raise the temperature of 1 gram of water by 1 degree Celsius ().

• High heat of vaporization: Energy required to change water from liquid to gas.

• Cohesion: Water molecules stick together.

• Surface tension: Water molecules at the surface are hydrogen-bonded to those below.

• Ice floats: Solid water is less dense than liquid water due to hydrogen bonding.

Acids and Bases

• Acids: Release hydrogen ions (H+) in solution.

  • Strong acids ionize fully.

  • Weak acids do not.

• Bases: Accept hydrogen ions in solution.

  • Strong bases ionize fully.

  • Weak bases do not.

• Water is neutral (pH 7).

• Acidic solutions: pH < 7; Basic solutions: pH > 7.

• Most biological fluids: pH 6-8.

Homeostasis: Maintaining pH

• Organisms maintain constant internal conditions (homeostasis).

• Buffers help maintain constant pH by absorbing excess H+ or OH-.

Macromolecules

Carbon and Its Properties

Carbon atoms can form four covalent bonds, allowing for a variety of complex molecules essential for life.

• Carbon chains form the skeletons of most organic molecules.

• Carbon chains vary in length and shape.

Isomers

• Structural isomers: Same chemical formula, different bonding arrangement.

• Optical isomers: Mirror images of each other.

Functional Groups

Functional groups are specific groups of atoms within molecules that determine their chemical properties and reactions.

• Each functional group participates in chemical reactions in a characteristic way.

Monomers and Polymers

• Monomers: Small molecules that join to form polymers.

• Polymers: Large molecules made of repeating monomer units.

• Linked by condensation reactions (loss of water).

• Broken down by hydrolysis reactions (addition of water).

Carbohydrates

Types and Functions

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen. They serve as energy sources and structural components.

• Monosaccharides: Simple sugars (3-7 carbons).

  • General formula:

  • Examples: Glucose, ribose, fructose

• Disaccharides: Two monosaccharides linked by glycosidic bonds.

  • Examples: Maltose (glucose + glucose), Sucrose (glucose + fructose), Lactose (glucose + galactose)

• Oligosaccharides: 3-20 monosaccharide units, often involved in cell recognition.

• Polysaccharides: Many monosaccharide units joined by glycosidic linkages.

  • Examples: Starch (plants), Glycogen (animals), Cellulose (plant cell walls), Chitin (fungal cell walls, exoskeletons)

Carbohydrate Table

Nucleic Acids

Structure and Function

Nucleic acids store, transmit, and use genetic information. The two main types are DNA and RNA.

• Monomer: Nucleotide

• Polymer: Nucleic acid

• Composed of C, H, O, N, P

• Nucleotides are linked by phosphodiester linkages (phosphate group joins 3' carbon of one sugar to 5' carbon of another).

DNA Structure

• Double helix: Two strands held together by hydrogen bonds between nitrogenous bases.

• Bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T)

• Chargaff's Rules: A pairs with T, G pairs with C

RNA Structure

• Single strand

• Bases: A, G, C, U (Uracil replaces Thymine)

• Involved in protein synthesis

Nucleic Acid Table

Connection to Proteins

• The sequence of amino acids in a polypeptide is programmed by a gene (unit of inheritance).

• Genes are made of DNA; DNA is a nucleic acid composed of nucleotides.