7.1 Organic Molecules

Organic Molecules in Microbial Biochemistry

Organic molecules are the carbon-based compounds that make up every part of a microbial cell. Understanding their structure and behavior is essential for microbial biochemistry because the shape, charge, and bonding patterns of these molecules determine how microbes store energy, build cell walls, replicate DNA, and interact with their environment.

Elements of Organic Molecules

Carbon, hydrogen, oxygen, and nitrogen are the four most abundant elements in organic molecules, but phosphorus and sulfur also play critical roles.

• Carbon (C) forms the backbone of organic molecules. It can make four stable covalent bonds, including single, double, or triple bonds with other carbons. This bonding flexibility is why carbon-based molecules come in such a huge variety of shapes and sizes.
• Hydrogen (H) is commonly bonded to carbon throughout organic molecules, shaping their overall structure. Hydrogen also participates in hydrogen bonding, which is critical for the 3D structure of proteins, nucleic acids, and water itself.
• Oxygen (O) appears in many functional groups, including hydroxyl ($-OH$) and carboxyl ($-COOH$). It contributes to molecular polarity and hydrogen bonding, which is why oxygen-containing molecules like sugars and amino acids tend to be water-soluble.
• Nitrogen (N) is found in amino acids (the building blocks of proteins) and in the nitrogenous bases of DNA and RNA. Amine groups ($-NH_2$) give nitrogen-containing molecules basic properties.
• Phosphorus (P) is a key component of nucleic acids, phospholipids, and ATP (the cell's energy currency). Sulfur (S) appears in the amino acid cysteine, where it forms disulfide bonds that stabilize protein structure.

Carbon-carbon bonds also create cyclic structures like glucose rings (monosaccharides) and benzene rings (aromatic compounds), each with distinct chemical properties relevant to microbial metabolism.

Molecular Properties and Interactions

The behavior of organic molecules depends on several physical and chemical properties:

• Covalent bonds hold organic molecules together and allow for diverse molecular geometries. The angles and lengths of these bonds determine a molecule's 3D shape.
• Chirality means a molecule and its mirror image are not superimposable (like left and right hands). This matters because enzymes typically recognize only one chiral form of a substrate.
• Polarity arises when electrons are shared unequally in a bond. Polar molecules dissolve well in water, while nonpolar (hydrophobic) molecules do not. This difference is what drives membrane formation: hydrophobic lipid tails cluster away from water, forming bilayers.
• Resonance occurs when electrons are delocalized across multiple bonds in a molecule, increasing its stability. You'll see this in molecules like the carboxylate ion and aromatic rings.

Isomerism in Microbial Systems

Isomers are compounds that share the same molecular formula but differ in how their atoms are arranged. This seemingly small difference can have major biological consequences.

• Structural isomers differ in which atoms are bonded to which. Glucose and fructose both have the formula $C_6H_{12}O_6$, but their atoms are connected differently, giving them distinct properties and metabolic roles.
• Stereoisomers have the same connectivity but differ in spatial arrangement:
  • Enantiomers are mirror images of each other. The classic microbiology example: proteins in living organisms use L-amino acids, while bacterial cell walls incorporate D-amino acids. This distinction is one reason bacterial cell walls are resistant to many of our own enzymes.
  • Diastereomers are stereoisomers that are not mirror images. Cis and trans isomers of unsaturated fatty acids are a good example. Cis double bonds create kinks in fatty acid chains, increasing membrane fluidity, while trans configurations pack more tightly.

Isomerism matters in microbial systems because enzymes and receptors are highly specific. They often recognize only one isomer of a molecule and ignore the other.

Functional Groups and Molecular Properties

Functional groups are specific clusters of atoms that give organic molecules their chemical behavior. Each group has predictable properties:

• Hydroxyl ($-OH$) increases polarity and water solubility through hydrogen bonding. Found in alcohols (ethanol), carbohydrates (glucose), and amino acids like serine and threonine.
• Carboxyl ($-COOH$) is an acidic group that donates a proton ($H^+$) in solution, making the molecule negatively charged at physiological pH. Found in fatty acids (palmitic acid), amino acids (glutamic acid), and carboxylic acids (acetic acid).
• Amino ($-NH_2$) is a basic group that accepts a proton, becoming positively charged at physiological pH. Found in amino acids (lysine) and nucleotide bases (adenine, guanine).
• Phosphate ($-PO_4$) carries a negative charge and forms phosphodiester bonds, which make up the backbone of DNA and RNA. Also found in phospholipids and ATP.
• Sulfhydryl ($-SH$) can form disulfide bonds ($-S-S-$) between two cysteine residues, which stabilize the 3D structure of proteins.

Functional Groups in Microbial Polymers

Microbes build their macromolecules by linking small monomers into long polymers. Two reactions drive this process:

1. Dehydration synthesis joins two monomers by removing a water molecule ($H_2O$) and forming a covalent bond.
2. Hydrolysis breaks that bond by adding a water molecule back in.

These two reactions are essentially the reverse of each other, and they apply to all four major classes of biological macromolecules:

Polysaccharides form when monosaccharides are linked by glycosidic bonds via dehydration synthesis. A key microbial example is peptidoglycan, the structural polymer in bacterial cell walls, built from alternating units of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM).

Proteins form when amino acids are linked by peptide bonds. Each peptide bond forms between the carboxyl group of one amino acid and the amino group of the next, releasing water. Once the chain is assembled, the R-group functional groups of individual amino acids drive protein folding through hydrogen bonds, ionic interactions, and disulfide bonds.

Nucleic acids (DNA and RNA) form when nucleotides are linked by phosphodiester bonds between the 5' phosphate of one nucleotide and the 3' hydroxyl of the next. The nitrogenous bases (adenine, guanine, cytosine, thymine in DNA, uracil in RNA) encode genetic information through specific base pairing.

Lipids don't always follow the same polymerization pattern, but triglycerides form through ester bonds between fatty acids and glycerol via dehydration synthesis. Phospholipids have a hydrophilic phosphate head and two hydrophobic fatty acid tails. In water, this arrangement causes them to spontaneously assemble into bilayers, forming the structural basis of cell membranes.