Organic molecules are the building blocks of life, forming the basis of microbial biochemistry. These compounds, made primarily of carbon, hydrogen, oxygen, and nitrogen, create diverse structures with unique properties that enable cellular functions.

From simple sugars to complex proteins, organic molecules in microbes play crucial roles in energy storage, genetic information, and cellular structure. Understanding their composition and interactions is key to grasping how microorganisms function and adapt to their environment.

Organic Molecules in Microbial Biochemistry

Elements of organic molecules

• Carbon (C)
  • Forms the backbone of organic molecules due to its ability to form stable covalent bonds with other elements
  • Can form single, double, or triple bonds with other carbon atoms, allowing for a wide variety of molecular structures
• Hydrogen (H)
  • Commonly bound to carbon in organic molecules, contributing to their overall structure and properties
  • Participates in hydrogen bonding, which is important for the structure and function of many biomolecules (water, proteins, nucleic acids)
• Oxygen (O)
  • Present in many functional groups, such as hydroxyl (-OH) and carboxyl (-COOH), which influence the properties of organic molecules
  • Involved in hydrogen bonding and contributes to the polarity of molecules (sugars, amino acids)
• Nitrogen (N)
  • Found in amino acids, which are the building blocks of proteins, and in nucleic acids (DNA, RNA)
  • Contributes to the basic properties of some functional groups, such as amines (-$NH_2$)
• Phosphorus (P) and Sulfur (S)
  • Present in certain organic molecules, such as ATP (energy currency) and cysteine (amino acid involved in disulfide bonds)
  • Phosphorus is a key component of nucleic acids and phospholipids, while sulfur participates in protein structure and function
• Structural features
  • Carbon-carbon single, double, and triple bonds create a variety of molecular geometries and influence chemical reactivity
  • Cyclic structures, such as benzene rings (aromatic compounds) and glucose rings (monosaccharides), contribute to the unique properties of many organic molecules

Molecular properties and interactions

• Covalent bonds form the basis of organic molecule structure, allowing for diverse molecular geometries
• Molecular geometry influences the overall shape and reactivity of organic molecules
• Chirality in organic molecules can lead to different biological activities and functions
• Polarity of molecules affects their solubility and interactions with other molecules
• Hydrophobicity plays a crucial role in the formation of cellular structures like membranes
• Resonance in certain molecules contributes to their stability and reactivity

Isomerism in microbial systems

• Isomers are compounds with the same molecular formula but different structural arrangements
• Structural isomers
  • Differ in the arrangement of atoms and bonds, resulting in distinct chemical and physical properties
  • Glucose and fructose are structural isomers, both having the formula $C_6H_{12}O_6$ but different arrangements of atoms
• Stereoisomers
  • Have the same connectivity but differ in the spatial arrangement of atoms, leading to different biological activities
  • Enantiomers are mirror images of each other, such as L- and D-amino acids, which have distinct roles in biological systems
  • Diastereomers are not mirror images, such as cis and trans isomers of unsaturated fatty acids, which affect membrane fluidity
• Significance in microbial systems
  • Isomers can have different biological activities and functions, as enzymes and receptors often recognize specific isomers
  • Bacterial cell walls contain D-amino acids, while proteins in living organisms are composed of L-amino acids

Functional groups and molecular properties

• Hydroxyl (-OH)
  • Increases polarity and hydrogen bonding, making molecules more soluble in water
  • Present in alcohols (ethanol), carbohydrates (glucose), and some amino acids (serine, threonine)
• Carboxyl (-COOH)
  • Acidic group that can form ionic bonds and participate in hydrogen bonding, contributing to the pH-dependent properties of molecules
  • Found in carboxylic acids (acetic acid), amino acids (glutamic acid), and fatty acids (palmitic acid)
• Amino (-$NH_2$)
  • Basic group that can form ionic bonds and participate in hydrogen bonding, influencing the pH-dependent behavior of molecules
  • Present in amino acids (lysine) and nucleotide bases (adenine, guanine)
• Phosphate (-$PO_4$)
  • Negatively charged group that contributes to the formation of phosphodiester bonds, which are essential for the backbone of nucleic acids
  • Found in nucleic acids (DNA, RNA), phospholipids (phosphatidylcholine), and ATP (energy currency)
• Sulfhydryl (-SH)
  • Participates in disulfide bond formation, which is important for the stability and structure of proteins
  • Present in the amino acid cysteine, which plays a crucial role in maintaining protein tertiary structure

Functional groups in microbial polymers

• Dehydration synthesis is the formation of a covalent bond between monomers with the release of a water molecule
• Hydrolysis is the breaking of a covalent bond between monomers by the addition of a water molecule
• Polysaccharides
  • Formed by the linkage of monosaccharides through glycosidic bonds, which are created by dehydration synthesis
  • Peptidoglycan in bacterial cell walls is a polysaccharide composed of alternating N-acetylglucosamine and N-acetylmuramic acid residues
• Proteins
  • Formed by the linkage of amino acids through peptide bonds, which are created by dehydration synthesis between the carboxyl group of one amino acid and the amino group of another
  • Functional groups of amino acids contribute to the folding and stability of proteins through interactions such as hydrogen bonding, ionic interactions, and disulfide bonds
• Nucleic acids (DNA and RNA)
  • Formed by the linkage of nucleotides through phosphodiester bonds, which are created by dehydration synthesis between the 5' phosphate group of one nucleotide and the 3' hydroxyl group of another
  • Phosphate groups and nitrogenous bases (adenine, guanine, cytosine, thymine, uracil) play crucial roles in the structure and function of nucleic acids, including base pairing and genetic information storage
• Lipids
  • Some lipids, such as triglycerides, are formed by the esterification of fatty acids and glycerol, which involves the formation of ester bonds through dehydration synthesis
  • Phospholipids contain phosphate groups that contribute to the formation of cell membranes by creating a hydrophilic head and hydrophobic tails, which spontaneously form bilayers in aqueous environments