Section 1: From Atoms to Macromolecules

Atoms and Atomic Structure

Atoms are the basic units of matter, consisting of subatomic particles that determine their chemical properties and interactions.

• Subatomic Particles: Atoms are made up of protons (positively charged), neutrons (neutral), and electrons (negatively charged). Protons and neutrons are located in the nucleus, while electrons orbit the nucleus.

• Atomic Number: The atomic number is the number of protons in an atom and defines the element.

• Atoms vs. Ions: An ion is an atom or molecule with a net electric charge due to the loss or gain of electrons.

• Organic Molecules: Organic molecules are primarily composed of carbon atoms bonded with hydrogen, oxygen, nitrogen, and other elements.

• pH and Buffers: The pH of a solution measures its hydrogen ion concentration. A buffer is a substance that stabilizes pH by absorbing or releasing H+ ions.

• Acids and Bases: Acids donate H+ ions, while bases accept H+ ions or donate OH- ions. The term "alkaline" refers to basic solutions with a pH above 7.

Example: Sodium chloride (NaCl) is formed when sodium (Na) donates an electron to chlorine (Cl), resulting in the formation of Na+ and Cl- ions.

Section 2: Chemical Bonds

Types of Chemical Bonds

Chemical bonds are forces that hold atoms together in molecules. The type of bond affects the properties and functions of molecules.

• Valence Shell: The outermost electron shell of an atom; electrons here are involved in chemical bonding.

• Ionic Bonds: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other.

• Covalent Bonds: Formed when atoms share pairs of electrons. Covalent bonds can be polar (unequal sharing) or nonpolar (equal sharing).

• Hydrogen Bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like oxygen or nitrogen) and another electronegative atom.

• Hydrophilic vs. Hydrophobic: Hydrophilic molecules interact well with water; hydrophobic molecules do not.

• Amphipathic Molecules: Molecules, such as phospholipids, that have both hydrophilic and hydrophobic regions.

Example: Water (H2O) is a polar molecule due to unequal sharing of electrons between hydrogen and oxygen, resulting in hydrogen bonding between water molecules.

Section 3: Chemical Reactions

Types and Mechanisms of Chemical Reactions

Chemical reactions involve the making and breaking of chemical bonds, transforming reactants into products. They are essential for cellular processes.

• Reactants and Products: Reactants are substances that undergo change; products are the result of the reaction.

• Enzymes and Catalysts: Enzymes are biological catalysts that speed up chemical reactions without being consumed. Catalysts lower the activation energy required for reactions.

• Dehydration Synthesis: A reaction where two molecules join by removing a water molecule. Example: Formation of a peptide bond between amino acids.

• Hydrolysis: A reaction where a molecule is split into two by the addition of water.

• Metabolism: The sum of all chemical reactions in a cell, including anabolism (building molecules) and catabolism (breaking down molecules).

Example: The breakdown of starch into glucose by hydrolysis is a catabolic reaction.

Section 4: Biologically Important Molecules

Major Classes of Biomolecules

Cells are composed of four major classes of organic molecules: carbohydrates, lipids, proteins, and nucleic acids. Each plays a unique role in cellular structure and function.

• Carbohydrates: Serve as energy sources and structural components. The basic unit is the monosaccharide (e.g., glucose).

• Polysaccharides: Long chains of monosaccharides; examples include starch and cellulose.

• Lipids: Hydrophobic molecules used for energy storage, membrane structure, and signaling. Triglycerides consist of glycerol and three fatty acids.

• Proteins: Polymers of amino acids; perform structural, enzymatic, and regulatory functions. The basic unit is the amino acid.

• Protein Structure: Proteins have four levels of structure: primary (amino acid sequence), secondary (alpha helices and beta sheets), tertiary (3D folding), and quaternary (multiple polypeptides).

• Nucleic Acids: DNA and RNA store and transmit genetic information. Composed of nucleotides, which include a sugar, phosphate, and nitrogenous base.

• DNA vs. RNA: DNA contains deoxyribose and the bases A, T, C, G; RNA contains ribose and the bases A, U, C, G.

• ATP: Adenosine triphosphate is the energy currency of the cell.

Example: The hydrolysis of ATP releases energy for cellular processes:

Additional info: The questions in the file are foundational for introductory microbiology and biochemistry, covering atomic structure, chemical bonding, reaction mechanisms, and the major classes of biological macromolecules. These concepts are essential for understanding microbial physiology and genetics.