Fundamental Chemistry and Biomolecules for Microbiology

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Atomic Structure and Elements

Subatomic Particles

Atoms are composed of three main subatomic particles: protons, neutrons, and electrons. Understanding their properties is essential for studying chemical reactions and molecular biology.

Protons: Positively charged particles found in the atomic nucleus. The number of protons defines the atomic number and the identity of the element.
Neutrons: Neutral particles found in the atomic nucleus. They contribute to the mass number but do not affect the charge.
Electrons: Negatively charged particles found in orbitals surrounding the nucleus. The number of electrons in a neutral atom equals the number of protons.

Isotopes are atoms of the same element with different numbers of neutrons, resulting in different mass numbers.

Atomic Number, Mass Number, and Ions

Atomic Number (Z): Number of protons in the nucleus.
Mass Number (A): Sum of protons and neutrons in the nucleus.
Ions: Atoms that have gained or lost electrons. Cations are positively charged (more protons than electrons), and anions are negatively charged (more electrons than protons).

Element Table Example

The following table summarizes atomic structure for selected elements:

Element	Atomic Number	# of Protons	# of Neutrons	Mass Number	# of Electrons
Carbon 12C	6	6	6	12	6
Oxygen 16O	8	8	8	16	8
Oxygen 18O	8	8	10	18	8
Hydrogen 1H	1	1	0	1	1
Nitrogen 14N	7	7	7	14	7
Sulfur 32S	16	16	16	32	16
Phosphorus 31P	15	15	16	31	15

Chemical Bonds and Interactions

Types of Chemical Bonds

Chemical bonds are forces that hold atoms together in molecules. The main types include:

Ionic Bonds: Formed when electrons are transferred from one atom to another, resulting in attraction between oppositely charged ions. Represented by solid lines.
Covalent Bonds: Formed when atoms share electrons. Can be:
- Polar Covalent Bonds: Electrons are shared unequally, resulting in partial charges (e.g., water).
- Nonpolar Covalent Bonds: Electrons are shared equally (e.g., O2).
Hydrogen Bonds: Weak attractions between a hydrogen atom (attached to an electronegative atom) and another electronegative atom. Important in stabilizing the 3-D structure of large molecules like proteins and nucleic acids.

Bond Properties and Examples

Single Covalent Bond: Two electrons shared.
Double Covalent Bond: Four electrons shared.
Triple Covalent Bond: Six electrons shared.

Solutions, Acids, and Bases

Definitions

Solution: A homogeneous mixture of two or more substances.
Solute: The substance dissolved in a solution.
Solvent: The substance that dissolves the solute (e.g., water).

Properties of Water and pH

Hydration Shell: The structure formed when water molecules surround ions.
Hydrophilic: Substances that dissolve in water.
Hydrophobic: Substances that do not dissolve in water.
pH Scale: Measures the concentration of hydrogen ions () in a solution. Ranges from 0 (acidic) to 14 (basic), with 7 being neutral.

Relationship between and :

Acidic:
Neutral:
Basic:

Acids, Bases, and Buffers

Acids: Substances that increase the hydrogen ion concentration of a solution.
Bases: Substances that decrease hydrogen ion concentration, often by accepting or releasing .
Buffers: Compounds that resist changes in pH and help maintain homeostasis.
Salts: Ionic compounds formed when acids react with bases.

Organic and Inorganic Molecules

Classification

Organic Molecules: Contain carbon and hydrogen, often found in living organisms (e.g., fats, proteins, DNA).
Inorganic Molecules: Do not contain both carbon and hydrogen (e.g., water, carbon dioxide, salts, oxygen gas).

Functional Groups in Organic Molecules

Common Functional Groups

Carboxyl Group (-COOH): Acts as an acid.
Amino Group (-NH2): Found in amino acids; acts as a base.
Carbonyl Group (C=O): Found in ketones and aldehydes.
Hydroxyl Group (-OH): Found in alcohols.
Phosphate Group (-PO4): Involved in energy transfer (e.g., ATP).
Sulphydryl Group (-SH): Found in some amino acids; stabilizes protein structure.

Functions and Examples

Carboxyl and amino groups are found in all amino acids.
Phosphate groups are found in nucleic acids and ATP.
Sulphydryl groups stabilize protein structure via disulfide bonds.
Hydroxyl groups are found in carbohydrates and alcohols.

Carbohydrates

Types and Definitions

Monosaccharide: Simple sugar (e.g., glucose).
Disaccharide: Two monosaccharides joined by a glycosidic bond (e.g., sucrose).
Polysaccharide: Many monosaccharides linked together (e.g., starch, glycogen, cellulose).

Glycosidic Bond: The covalent bond formed between monosaccharides during dehydration synthesis.

Functions of Carbohydrates

Cellulose: Structural component in plant cell walls.
Starch: Energy storage in plants.
Glycogen: Energy storage in animals.
Chitin: Structural component in fungal cell walls and arthropod exoskeletons.
Peptidoglycan: Structural component in bacterial cell walls.
Lipopolysaccharide: Component of the outer membrane of Gram-negative bacteria.
Glycocalyx: Protective outer layer in some bacteria and animal cells.

Lipids

Characteristics and Types

All lipids are hydrophobic (insoluble in water).
Triglycerides: Composed of glycerol and three fatty acids.
Fatty Acids: Long hydrocarbon chains; can be saturated (no double bonds) or unsaturated (one or more double bonds).
Phospholipids: Contain a phosphate group; major component of cell membranes.

Functions

Energy storage: Triglycerides store energy.
Membrane structure: Phospholipids form bilayers in cell membranes.
Insulation and protection: Lipids provide insulation and protect organs.

Proteins

Structure and Function

Monomers: Amino acids.
Peptide Bond: Covalent bond formed between amino acids during dehydration synthesis.
Levels of Protein Structure:
- Primary: Sequence of amino acids (peptide bonds).
- Secondary: Local folding (alpha helices, beta sheets) stabilized by hydrogen bonds.
- Tertiary: 3-D folding stabilized by interactions among R groups (hydrogen, ionic, disulfide bonds).
- Quaternary: Association of multiple polypeptide chains.
Denaturation: Loss of protein structure (usually tertiary or secondary) due to heat, pH, or chemicals.

Protein Functions

Enzymes: Catalyze biochemical reactions.
Antibodies: Immune defense.
Structural proteins: Provide support (e.g., collagen).

Nucleic Acids

Structure and Components

Monomers: Nucleotides.
Nucleotide Components: Phosphate group, pentose sugar (ribose or deoxyribose), nitrogenous base.
Purines: Adenine (A), Guanine (G).
Pyrimidines: Cytosine (C), Thymine (T, DNA only), Uracil (U, RNA only).

DNA vs. RNA

DNA: Double-stranded, deoxyribose sugar, bases A, T, C, G.
RNA: Single-stranded, ribose sugar, bases A, U, C, G.
Base Pairing in DNA: A-T, C-G (hydrogen bonds stabilize the double helix).

ATP (Adenosine Triphosphate)

Structure: Adenine base, ribose sugar, three phosphate groups.
Function: Main energy currency of the cell; hydrolysis of ATP releases energy for cellular processes.

Additional info: These foundational chemistry and biomolecule concepts are essential for understanding microbial structure, function, and metabolism in microbiology.