Fundamental Biochemistry Concepts for Microbiology

CHAPTER 2: Biochemistry Foundations in Microbiology

Difference Between Inorganic and Organic Compounds

Understanding the distinction between inorganic and organic compounds is essential in microbiology, as it underpins cellular structure and function.

• Inorganic Compounds: Typically lack carbon (except CO2), form mostly ionic bonds, and are small in size and fewer in number. Examples: Water (H2O), CO2, O2.

• Organic Compounds: Always contain carbon and hydrogen, form mostly covalent bonds, and are larger and more diverse. Examples: Proteins, carbohydrates, nucleic acids, ATP.

Inorganic Compounds: Water

Water is the most abundant inorganic compound in living cells and is vital for cellular processes.

• Composition: Inorganic

• Bonds Between Water Molecules: Polar covalent bonds within the molecule; hydrogen bonds between molecules.

• Characteristics Making Water a Medium for Living Cells:

  • Bonding: Hydrogen bonds between water molecules

  • Polarity: Solvent for polar substances, facilitates dissolving and transport

• Properties of Water:

  • High specific heat: Water absorbs heat

  • High heat of vaporization: Changes to vapor when temperature rises

  • Excellent solvent

  • Solid state: Lighter and tends to float

  • Ability to absorb and release heat

Importance of Acid-Base Balance in Living Systems

Acid-base balance is crucial for maintaining health in living systems, affecting enzyme activity and metabolic processes.

• Acidity increases with more hydrogen ions (H+); basicity increases with more hydroxide ions (OH-).

• Most organisms grow best between pH 6.5 and 8.5.

• Examples: Human blood, urine, milk.

Organic Compounds: Structure, Function, Functional Groups

Organic compounds are defined by the presence of carbon and functional groups that determine their chemical properties.

• Skeleton: Carbon chain or ring forms the backbone.

• Functional Groups: Responsible for most chemical properties. Examples: Hydroxyl (-OH), Amino (-NH2), Carboxyl (-COOH), Phosphate (-PO4).

• Organic compounds can exist as monomers or polymers.

Bonding, Hydrolysis, and Dehydration Synthesis Reactions

Cells build and break down macromolecules through hydrolysis and dehydration synthesis.

• Hydrolysis: Breaks polymers into monomers by adding water.

• Dehydration Synthesis: Forms polymers by removing water between monomers.

• Example Equation: $\text{Glucose} + \text{Fructose} \rightarrow \text{Sucrose} + \text{H}_2\text{O}$

Carbohydrates: Types and Functions

Carbohydrates are essential organic compounds, serving as energy sources and structural materials.

• Monosaccharides: Simple sugars with 3-7 carbon atoms. Examples: Glucose, Fructose, Ribose, Galactose.

• Disaccharides: Formed by bonding two monosaccharides. Examples: Sucrose (glucose + fructose), Lactose (glucose + galactose), Maltose (glucose + glucose).

• Polysaccharides: Consist of tens or hundreds of monosaccharides. Examples: Glycogen (animals), Starch (plants), Cellulose (plants), Chitin (fungi).

• Functions: Energy storage, structural support.

Type	Example	Function
Monosaccharide	Glucose	Primary energy source
Disaccharide	Sucrose	Transported sugar in plants
Polysaccharide	Cellulose	Structural support in plants

Lipids: Types, Subunits, Examples, Functions

Lipids are hydrophobic molecules essential for cell membranes, energy storage, and signaling.

• Simple Lipids (Fats): Triglycerides, composed of glycerol and fatty acids.

• Complex Lipids: Phospholipids and steroids. Phospholipids: Major component of cell membranes.

• Steroids: Four interconnected carbon rings. Example: Cholesterol.

• Functions: Energy storage, membrane structure, signaling.

Lipid Type	Subunit	Function
Triglyceride	Glycerol + Fatty acids	Energy storage
Phospholipid	Glycerol + Fatty acids + Phosphate	Membrane structure
Steroid	Four carbon rings	Signaling, membrane fluidity

Proteins: Building Blocks and Functions

Proteins are polymers of amino acids, performing diverse functions in cells.

• Subunits: Amino acids (20 types).

• Levels of Structure:

  • Primary: Sequence of amino acids.

  • Secondary: Alpha helices and beta sheets formed by hydrogen bonding.

  • Tertiary: 3D folding due to interactions among side chains.

  • Quaternary: Multiple polypeptide chains.

• Functions: Enzymes, transport, defense, signaling, structural support.

Protein Type	Function
Enzyme	Catalyzes chemical reactions
Transporter	Moves chemicals across membranes
Antibody	Defense against pathogens
Structural	Support cell shape

Nucleic Acids: DNA and RNA

Nucleic acids store and transmit genetic information. DNA and RNA are polymers of nucleotides.

• Subunits: Nucleotides (phosphate, sugar, nitrogenous base).

• DNA: Deoxyribose sugar, bases A, T, C, G. Double helix structure.

• RNA: Ribose sugar, bases A, U, C, G. Single-stranded.

• Base Pairing:

  • DNA: A-T, C-G

  • RNA: A-U, C-G

• Function: DNA stores genetic information; RNA translates genetic code into proteins.

Nucleic Acid	Sugar	Bases	Function
DNA	Deoxyribose	A, T, C, G	Genetic information storage
RNA	Ribose	A, U, C, G	Protein synthesis

ATP: The Energy Currency of the Cell

ATP (adenosine triphosphate) is the primary energy carrier in cells.

• Structure: Adenine, ribose, three phosphate groups.

• Function: Provides energy for cellular reactions.

• Equation: $\text{ATP} \rightarrow \text{ADP} + \text{P}_i$ (hydrolysis releases energy)

Summary Table: Macromolecules and Their Functions

Macromolecule	Subunit	Function
Carbohydrate	Monosaccharide	Energy, structure
Lipid	Fatty acid, glycerol	Energy, membrane
Protein	Amino acid	Enzyme, structure, transport
Nucleic Acid	Nucleotide	Genetic information

Additional info:

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

• Glycan: Polysaccharide component of bacterial cell walls (peptidoglycan).

• Clinical relevance: Understanding macromolecules is essential for interpreting microbial physiology and pathogenesis.