Introduction to Chemistry in Microbiology

Study Strategies and Exam Preparation

• Review Process: The primary method for studying should involve going through the PowerPoint notes. If any difficulty arises with the PowerPoint material, the textbook should be used to fill in missing information.

• Self-Assessment: Use provided quizzes to identify potential types of questions. End-of-chapter test questions in the textbook are also recommended for self-testing.

• Problem Review: Review test questions as frequently as possible to reinforce complex topics.

The Role of Chemistry in Microbiology

• Prerequisite Knowledge: Chemistry is the foundational prerequisite for microbiology. This material is treated as a review, assuming students have some prior exposure to the topics.

• Biological Relevance: Biological organisms consist of organic molecules formed through chemical reactions. Life is sustained by the production of $ATP$ (Adenosine Triphosphate), which results from chemical reactions.

• Complexity: Organisms are essentially chemical-based structures. Understanding chemistry allows for a deeper comprehension of microbial processes and metabolism.

Fundamental Concepts of Atoms and Elements

• Definitions:

  • Chemistry: The study of interactions between atoms and molecules.

  • Atom: The smallest unit of matter that can participate in a chemical reaction. Atoms and elements are used essentially as synonymous terms.

• Periodic Table of Elements: Elements are organized on the periodic table and defined by their Atomic Number.

  • Atomic Number: This is the number of protons in an element. Changing the number of protons changes the element itself.

• Atomic Components:

  • Protons: Positively charged particles ($+1$).

  • Neutrons: Neutral particles ($0$).

  • Electrons: Negatively charged particles ($-1$).

• The Atomic Nucleus: Composed of protons and neutrons. The mass of the atom is concentrated here.

  • Atomic Mass: The sum of the number of protons and neutrons in the nucleus.

• Electrons and Orbitals: Electrons have negligible mass and are found in orbitals located within electron shells.

  • Generally, the number of protons equals the number of electrons, resulting in a neutral overall charge for the atom.

  • Electrons represent stored energy within the atom.

Chemical Reactivity and Valency

• Paired vs. Unpaired Electrons:

  • Paired electrons are generally unreactive.

  • Unpaired electrons are chemically reactive and are responsible for forming chemical bonds.

• Valence Electrons: These are the electrons located in the outermost energy shell.

  • The number of unpaired valence electrons determines how many chemical bonds an atom can form.

• Elemental Bonding Examples:

  • Hydrogen ($H$): Atomic number $1$, Atomic mass $1$. Contains $1$ proton, $1$ electron, and $0$ neutrons. It has $1$ unpaired valence electron and can form $1$ bond.

  • Carbon ($C$): Contains $4$ unpaired valence electrons. It can form $4$ bonds, serving as the versatile skeleton for organic molecules.

  • Nitrogen ($N$): Contains $3$ unpaired electrons but can more commonly make $3$ to $4$ bonds (sometimes up to $5$).

  • Oxygen ($O$): Contains $2$ unpaired electrons and forms $2$ bonds (e.g., $H_2O$).

  • Magnesium ($Mg$): Contains $2$ unpaired valence electrons. To reach stability, it loses these $2$ electrons rather than gaining $6$. It can form $2$ bonds.

Isotopes and Biological Tracers

• Isotopes: Forms of an element that differ in the number of neutrons, though the atomic number remains constant.

  • Oxygen Isotopes:

    • $O-16$: $8$ protons, $8$ neutrons.

    • $O-17$: $8$ protons, $9$ neutrons.

    • $O-18$: $8$ protons, $10$ neutrons.

• Radioisotopes: High-energy, unstable isotopes that release energy as they decay into a stable form.

• Biological Tracers:

  • Tritium ($H-3$): A radioactive isotope of hydrogen.

  • Carbon-14 ($C-14$): Used to measure plant growth rates by tracking its ratio in tissue after incubation. The energy released by these tracers is typically low enough that it does not harm the organism being studied.

Chemical Formulas

• Molecular Formula: Represents the ratio of elements in a molecule (e.g., $H_2O$ indicates $2$ hydrogens for every $1$ oxygen).

• Structural Formula: Shows how the atoms are physically bonded together within the molecule.

Types of Chemical Bonds

• Ionic Bonds: Formed by the attraction between oppositely charged ions created when one atom loses and another gains an electron.

  • Cation: A positively charged ion ($lost$ an electron).

  • Anion: A negatively charged ion ($gained$ an electron).

  • Example: Sodium ($Na$) loses an electron to Chlorine ($Cl$). $Na^+$ and $Cl^-$ attract to form $NaCl$ (Salt).

  • Properties: Ionic bonds are relatively weak and easily broken by water (dissolved salts).

• Covalent Bonds: Formed when two atoms share one or more pairs of electrons. These are stronger and more stable than ionic bonds.

  • Single Covalent Bond: Sharing of $1$ pair of electrons.

  • Double Covalent Bond: Sharing of $2$ pairs of electrons.

  • Triple Covalent Bond: Sharing of $3$ pairs of electrons (strongest).

  • Nonpolar Covalent Bond: Electrons are shared equally. The molecule has no net charge and is typically hydrophobic (e.g., lipids, $CH_4$).

  • Polar Covalent Bond: Electrons are shared unequally due to differences in electronegativity. The molecule has slight electrical charges (deltas) and is hydrophilic (e.g., water, ammonia).

• Hydrogen Bonds: Weak attractions between polar molecules (specifically between a slight positive charge on hydrogen and a negative charge on another molecule).

  • Collective Strength: While weak individually, many hydrogen bonds together are extremely strong (e.g., holding skin tissues together).

  • Properties in Water: Each water molecule can form $4$ hydrogen bonds. This allows water to absorb and store significant heat energy, maintaining constant body and planetary temperatures.

Bioenergetics and Metabolism

• Chemical Reactions: Involve the making or breaking of chemical bonds, which in turn involves managing electron attractions.

• Energy Dynamics:

  • Endergonic Reactions: Require an input of energy (e.g., photosynthesis).

  • Exergonic Reactions: Release energy (e.g., $ATP \rightarrow ADP + P$).

• Metabolic Classification:

  • Substrates/Reactants: The starting materials (the arrow in a reaction always points to the Product).

  • Anabolism: Building complex molecules from simpler ones. These are endergonic reactions (require energy).

  • Catabolism: Breaking down complex molecules into simpler subunits. These are exergonic reactions (release energy).

• Coupling: Anabolic and catabolic reactions are coupled at the cellular level to conserve energy; the energy released by catabolism powers anabolism.

Inorganic vs. Organic Compounds

• Organic Compounds: Molecules that always contain Carbon ($C$), Hydrogen ($H$), and Oxygen ($O$).

  • Carbohydrates: $C, H, O$.

  • Proteins: $C, H, O, N$ (and sometimes $S$).

  • Lipids: $C, H, O$ (and sometimes $P$).

  • Nucleic Acids: $C, H, O, N, P$.

• Inorganic Compounds: Typically lack at least one of the three required organic elements ($C, H, or O$). Water ($H_2O$) is the most common inorganic solvent.

pH and Solutions

• Aqueous Solution: A homogeneous mixture where water is the solvent.

  • Salutes: Polar or ionic molecules (hydrophilic) dissolve in water.

  • Hydration Shell: Water surrounds ions (e.g., $Na^+$ is surrounded by the negative oxygen sides of water molecules), disrupting ionic bonds.

• Acid-Base Balance:

  • Acids: Dissociate into Hydrogen ions ($H^+$) and anions. More $H^+$ leads to a lower $pH$ ($0$ to $6.99$).

  • Bases: Dissociate into Hydroxyl ions ($OH^-$) and cations. More $OH^-$ leads to a higher $pH$ ($7.01$ to $14$).

  • Neutrality: At $pH$ of $7$, the concentration of $H^+$ equals the concentration of $OH^-$.

Functional Groups

• Hydroxyl ($OH$): Found in alcohols, carbohydrates, and lipids. Highly hydrophilic.

• Methyl ($CH_3$): Nonpolar and hydrophobic. Important in DNA regulation.

• Amino ($NH_2$): Hydrophilic and vital for proteins.

• Carboxyl ($COOH$): Acts as an acid. Found in proteins.

• Phosphate ($PO_4$): High-energy group found in $ATP$, DNA, RNA, and phospholipids.

• Sulfhydryl ($SH$): Assists in protein structural stability.

Macromolecules: Polymers and Monomers

• Polymers: Large molecules made of covalently bonded repeating subunits called monomers.

  • Carbohydrate polymers: Polysaccharides (monomer: monosaccharide).

  • Protein polymers: Polypeptides (monomer: amino acid).

  • Nucleic acid polymers: DNA/RNA (monomer: nucleotide).

  • Exceptions: Lipids are NOT polymers.

• Reaction Types:

  • Condensation (Dehydration Synthesis): Joins monomers together by removing water ($H_2O$).

  • Hydrolysis: Breaks polymers into monomers by adding water ($H_2O$).

Carbohydrates and Lipids

• Carbohydrates: Provide structure and energy storage.

  • Structural: Cellulose (plants), Chitin (fungi/insects).

  • Energy: Starch (plants), Glycogen (animals).

  • Monosaccharide: Glucose ($6$ carbons).

  • Disaccharide: Sucrose (table sugar).

• Lipids:

  • Triglycerides: Glycerol + $3$ fatty acids. Used for energy storage.

    • Saturated: All single bonds, straight chain, solid at room temperature (typically animal-derived).

    • Unsaturated: At least one double bond (cis/trans), bent chain, liquid at room temperature (oils, typically plant-derived).

  • Phospholipids: Amphipathic molecules (hydrophilic head, hydrophobic tails) that form the plasma membrane core.

  • Sterols: Four-carbon rings fused together. Includes Cholesterol (animal membranes), Ergosterol (fungal membranes), and hormones (Estrogen, Testosterone).

Proteins

• Functions: Enzymes (catalysts), transport proteins, motility (flagella/cilia), toxins, and antibodies.

• Amino Acid Structure: Central carbon with an amino group, a carboxyl group, and a side chain ($R$ group). There are $20$ different amino acids distinguished by their side groups.

• Levels of Protein Structure:

  1. Primary: The specific sequence of amino acids held by covalent peptide bonds. This is the most critical level.

  2. Secondary: Folding into alpha-helices or beta-pleated sheets held by hydrogen bonds.

  3. Tertiary: The overall three-dimensional shape of one polypeptide, held by hydrogen, ionic, covalent (disulfide), and hydrophobic interactions.

  4. Quaternary: Two or more polypeptides interacting together to form a protein (e.g., hemoglobin), held by the same interactions as tertiary structure.

Nucleic Acids and ATP

• Components of Nucleotides: Five-carbon sugar, phosphate group, and nitrogenous base.

• DNA (Deoxyribonucleic Acid):

  • Sugar: Deoxyribose.

  • Structure: Double-stranded helix.

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

  • Function: Stores genetic information in the nucleus.

• RNA (Ribonucleic Acid):

  • Sugar: Ribose.

  • Structure: Single-stranded.

  • Bases: Adenine ($A$), Uracil ($U$), Cytosine ($C$), Guanine ($G$).

  • Function: Found in nucleus and cytoplasm; aids in converting DNA into proteins.

• ATP (Adenosine Triphosphate): A modified nucleotide (adenine) with three high-energy phosphate groups. Breaking the bond with the third phosphate releases significant energy for cellular work.

Questions & Discussion

• Question (Tim): What is the best strategy for studying?

  • Response: Prioritize PowerPoint notes, use the textbook for clarification on difficult spots, and utilize quizzes and end-of-chapter test questions for self-testing.

• Instructor Note: Exam one material is now complete. The lecture recording will be made available to students.