Chapter 1.2: Chemical Foundations

• Bulk elements include hydrogen, carbon, nitrogen, oxygen, sodium, phosphorous, sulfur, chlorine, potassium, and calcium.
• Trace elements include magnesium, vanadium, chromium, manganese, iron, cobalt, nickel, copper, zinc, selenium, molybdenum, iodine, and tungsten.
• Carbon atoms have a characteristic tetrahedral arrangement of their four single bonds.
• There is free rotation around each single bond.
• There is limited rotation about the axis of a double bond.
• Diagram

  A) Methyl group

  
• Ethyl group

  
• Phenyl group

  
• Aldehyde group

  
• Ether group

  
• Ester group

  
• Acetyl group

  
• Anhydride group

  
• Guanidinium group

  
• Imidazole group

  
• Sulfhydryl or thiol group

  
• Disulfide group

  
• Ketone group

  
• Carboxyl group

  
• Hydroxyl group

  
• Enol group

  
• Amino group

  
• Amido group

  
• Imine group

  
• Thioester group

  
• Phosphoryl group

  
• Mixed anhydride group

  
• Phosphoanhydride functional group

  
• An important functional group in biomolecules is thioesters.
• Many biomolecules are polyfunctional
• Central metabolites are common amino acids, nucleotides, sugars and their phosphorylated derivates, and mono, di and tricarboxylic acids.
• Secondary metabolites are specific to the organism.
• The metabolome is the entire collection of small molecules in a given cell under a specific set of conditions.
• Metabolomics is the systematic characterization of the metabolome under very specific conditions.
• Macromolecules are the major constituents of cells.
• Macromolecules are polymers with molecular weights of above 5000 that are assembled with relatively simple precursors.
• Marcomolecules include proteins, nucleic acids, and polysaccharides.
• Oligomers are shorter polymers, typically 8 to 12.
• Informational macromolecules are the name for proteins, nucleic acids, and some oligosaccharides, given their information rich subunit sequences.
• Proteins are long polymers of amino acids.