Ch. 2 - Chemical Principles

The Structure of an Atom

Chemistry is fundamental to understanding microbiology, as it explains the interactions between atoms and molecules that compose all living things. Atoms are the smallest units of matter, and their interactions form the basis of molecular biology.

• Matter: Anything that has mass and occupies space.

• Atom: The smallest unit of matter, indivisible by chemical means.

• Atoms interact to form molecules.

Subatomic Particles

• Electrons: Negatively charged particles that orbit the nucleus.

• Protons: Positively charged particles found in the nucleus.

• Neutrons: Uncharged particles also located in the nucleus.

• The nucleus contains protons and neutrons; electrons move around the nucleus in shells.

Chemical Elements and the Periodic Table

Atoms with the same number of protons are classified as the same chemical element. The periodic table organizes all known elements by their atomic number and properties.

• Atomic number: Number of protons in the nucleus.

• There are 118 elements; 96 are naturally occurring, and about 26 are found in living things.

Electron Configuration

Electrons are arranged in shells around the nucleus, each corresponding to a different energy level. The arrangement of electrons is called the electron configuration.

• The innermost shell has the lowest energy level.

• Electron shells fill in the order: 2, 8, 18 electrons.

How Atoms Form Molecules: Chemical Bonds

Chemical Bonds

Atoms form molecules by combining to fill their outermost electron shells. The number of missing or extra electrons in the outermost shell is called the valence. Chemical bonds are attractive forces between atomic nuclei due to valence electrons.

• Ionic bonds: Formed by gaining or losing electrons.

• Covalent bonds: Formed by sharing electrons.

• Hydrogen bonds: Weak interactions involving hydrogen atoms covalently bonded to electronegative atoms (O or N).

Ionic Bonds

• Ions: Charged atoms that have gained or lost electrons.

• Cations: Atoms that lose electrons (positively charged).

• Anions: Atoms that gain electrons (negatively charged).

• Ionic bonds are attractions between ions of opposite charge.

Covalent Bonds

• Formed when two atoms share one or more pairs of electrons.

• Covalent bonds are stronger and more common in living organisms than ionic bonds.

Hydrogen Bonds

• Form when a hydrogen atom covalently bonded to O or N is attracted to another O or N atom in a different molecule.

• Hydrogen bonds are important in stabilizing the structures of proteins and nucleic acids.

Types of Chemical Reactions

Synthesis, Decomposition, and Exchange Reactions

• Synthesis (Combination) Reactions: Atoms or molecules combine to form larger, more complex molecules. Used in anabolic (building) processes. Example: Dehydration reaction (removal of water to join monomers).

• Decomposition Reactions: Breakdown of a molecule into smaller molecules or atoms. Involves catabolic (bond-breaking) reactions. Example: Hydrolysis (addition of water to break a large molecule).

• Exchange (Displacement) Reactions: Involve both synthesis and decomposition; bonds are both made and broken.

Redox Reactions

Reduction-oxidation (redox) reactions are essential in living systems. Atoms are reduced when they gain electrons and oxidized when they lose electrons.

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• Example: In cellular respiration, glucose is oxidized and oxygen is reduced.

Important Biological Molecules

Inorganic vs. Organic Compounds

• Inorganic compounds: Typically lack carbon; usually small and simple (e.g., water).

• Organic compounds: Contain carbon and usually hydrogen, oxygen, and/or nitrogen; structurally complex.

• The carbon skeleton forms the backbone of organic molecules.

Functional Groups

Functional groups are specific groups of atoms attached to carbon skeletons that determine the chemical properties of organic molecules.

• Common functional groups include hydroxyl, carboxyl, amino, and phosphate groups.

• The letter R is used to represent the rest of the molecule when describing functional groups.

Macromolecules

Small organic molecules can combine to form large macromolecules, which are usually polymers made of repeating monomers. Four major classes of macromolecules are carbohydrates, lipids, proteins, and nucleic acids.

• Dehydration synthesis: Joins monomers by removing water.

• Hydrolysis: Breaks polymers into monomers by adding water.

Carbohydrates

Carbohydrates serve as cell structures and energy sources. They include sugars and starches, and are composed of carbon, hydrogen, and oxygen (often with the formula CnH2nOn).

• Isomers: Molecules with the same chemical formula but different structures.

Monosaccharides

• Simple sugars with three to seven carbon atoms.

• Examples: Glucose (C6H12O6), Deoxyribose (C5H10O4).

Disaccharides

• Formed when two monosaccharides are joined by dehydration synthesis.

• Can be broken down by hydrolysis.

• Examples: Sucrose (glucose + fructose), lactose (galactose + glucose), maltose (glucose + glucose).

Polysaccharides

• Consist of tens or hundreds of monosaccharides joined through dehydration synthesis.

• Examples: Starch, glycogen, dextran, cellulose (all polymers of glucose with different bonding and functions).

Lipids

Lipids are primary components of cell membranes, consisting of carbon, hydrogen, and oxygen. They are nonpolar and insoluble in water, and are divided into simple (fats/triglycerides) and complex lipids.

Simple Lipids (Fats or Triglycerides)

• Contain glycerol and fatty acids, formed by dehydration synthesis.

• Can be saturated (no double bonds) or unsaturated (one or more double bonds).

• Cis and trans refer to the arrangement of hydrogen atoms around double bonds.

Complex Lipids

• Contain C, H, O, and additional elements such as P, N, or S.

• Phospholipids are complex lipids that make up cell membranes, consisting of glycerol, two fatty acids, and a phosphate group.

• Phospholipids have polar (hydrophilic) heads and nonpolar (hydrophobic) tails, crucial for membrane structure.

Steroids

• Structurally different from other lipids; contain four fused carbon rings.

• Sterols (steroids with an ―OH group) are part of membranes and help maintain membrane fluidity.

Proteins

Proteins are essential for cell structure and function. They are made of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur. Proteins serve as enzymes, transporters, structural components, and toxins.

Amino Acids

• Proteins are polymers of amino acids, each containing an alpha-carbon, a carboxyl group (-COOH), an amino group (-NH2), and a side group (R group).

Peptide Bonds and Protein Structure

• Amino acids are joined by peptide bonds (formed by dehydration synthesis).

• Protein structure has four levels: primary (sequence), secondary (helix/pleated sheet), tertiary (3D folding), and quaternary (multiple polypeptides).

• Proteins can be denatured by changes in temperature or pH, losing their function.

• Conjugated proteins contain amino acids plus other organic molecules (e.g., glycoproteins, nucleoproteins, lipoproteins).

Nucleic Acids

Nucleic acids store and transmit genetic information. They are polymers of nucleotides, each consisting of a five-carbon sugar, a phosphate group, and a nitrogenous base.

• Nucleoside: Pentose sugar + nitrogenous base (no phosphate).

DNA (Deoxyribonucleic Acid)

• Contains deoxyribose sugar.

• Double helix structure.

• Adenine pairs with Thymine; Cytosine pairs with Guanine.

• Sequence of bases encodes genetic instructions.

RNA (Ribonucleic Acid)

• Contains ribose sugar.

• Single-stranded.

• Adenine pairs with Uracil; Cytosine pairs with Guanine.

• Several types (mRNA, tRNA, rRNA) play roles in protein synthesis.

Adenosine Triphosphate (ATP)

• ATP is the energy currency of the cell, made of ribose, adenine, and three phosphate groups.

• Stores chemical energy released by reactions; releases energy by hydrolysis of phosphate bonds.