Biochem

• Macromolecules are built up by condensation reactions
• Condensation reaction


  1. Amino acid + amino acid → Peptide (amide) bond

  2. Fatty acids + glycerol → Ester bond

  3. Sugar + sugar → Glycosidic (ether) bond
• In aqueous environment, equilibrium well over to left. Dehydrating agent needed to drive to right
• Dehydration = energy input
• Types of bonds


  • Peptide (amide) bond
  • Ester bond
  • Glycosidic (ether) bond
• Week 25-26 Overview: What you will be able to do after this week
• What you will be able to do after this week

  • Know and draw different structure diagrams of organic molecules
  • Identify major organic molecule functional groups
  • Know basic organic reaction types
  • Understand organic compound terminology
  • Understand basic IUPAC organic chemistry nomenclature
  • Identify, name and draw structural isomers of alkanes
  • Identify, name and draw configurational isomers of alkenes
  • Name and draw: Aromatic compounds, Compounds with heteroatoms, Alcohols, Carbonyl compounds
  • Understand and apply priorities when naming compounds with multiple functional groups
  • Identify biological examples of organic molecules
• Prior Knowledge required: Hybridisation of electron orbitals in CARBON
• Hybridisation of carbon


  • sp + p + p (sp + p^2) → sp^2 + p

  sp^3
• Condensed Formulae


  Where all atoms are shown but some (if not all) bonds are omitted
• Full Structural Formulae


  Show all hydrogen atoms and bonds explicitly
• Skeletal Structures


  Do not normally show hydrogen atoms (attached to carbon) and have a 'zig-zag' pattern to approximate structural shape
• Condensed Formulae, Full Structural Formulae and Skeletal Structures

  • Methane, CH4
  • Ethane, C2H6
  • Propane, C3H8
  • Pentane, C5H12
• Functional groups make biochemistry and organic chemistry diverse. This diversity is required for cells and organisms to operate correctly
• Functional Groups


  • Folic acid
• Organic Chemistry Oxidation Levels

  • 4 "CO2"
  • 3 "acid"
  • 2 "ketone"
  • 1 "alcohol"
  • 0 "alkane"
• A compound can have more than one name but a name must only describe one compound
• IUPAC Nomenclature: Alkanes


  Straight carbon chains are named based on the number of carbons. Open chain alkanes all follow a general formula of CnH2n+2
• Structural Isomers


  Compounds with the same chemical formula but different arrangements of atoms
• Naming Branched Alkanes


  Find the name of the longest carbon chain

  Identify and name the substituents attached to this chain

  Number the chain consecutively starting from the end nearest a branch point

  Designate each substituent by its branch number and name

  Write out the complete name
• Branched Alkanes


  • 2-methylbutane

  1. ethyl-2,6-dimethylheptane
• Cycloalkanes


  Alkanes with a ring structure, follow the formula CnH2n
• Cycloalkanes


  • Cyclobutane, Cyclopentane, Cyclohexane
• Conformers


  Different shapes that cyclohexane can exist in, such as chair and boat
• Substituted Cycloalkanes


  • 1-ethyl-2-methylcyclohexane

  1. ethyl-1,1-dimethylcyclopentane
• Alkenes


  Open chain compounds with a carbon-carbon double bond, follow the formula CnH2n
• Alkenes


  • Ethene, Propene, But-1-ene, cis-but-2-ene, trans-but-2-ene
• cis/trans Isomers


  Cis describes groups on the same side of the double bond, trans describes groups on opposite sides
• Vitamin A


  • (2E,4E,6E,8E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraen-1-ol
• Aromatic Compounds


  • Benzene, Ethylbenzene, Phenol, Phenylethene (Styrene), Methylbenzene (Toluene)
• Ortho/Meta/Para Substitution


  Describes the relative positions of substituents on a benzene ring
• Substituted Benzenes


  • 1,2-Dimethylbenzene (o-Methyltoluene)

  1,3-Dimethylbenzene (m-Methyltoluene)

  1,4-Dimethylbenzene (p-Methyltoluene)
• Alcohols


  Classified as 1°, 2°, 3° based on the carbon the -OH group is attached to
• Alcohols


  • Methanol, Ethanol, Propan-1-ol, Propan-2-ol, Pentane-1,2-diol
• Carbonyl Compounds


  Aldehydes have a carbonyl group at the end of a chain, Ketones have a carbonyl group in the middle of a chain
• There are no meth- or eth- ketones as by definition ketones all possess a carbonyl group flanked by a carbon either side
• Longer chain and cyclic ketones

  • Pentan-2-one, Cyclohexanone
• Pentane-1,2-diol


  2 CH3, 3 o alcohols (these are structural isomers, see next week)
• Alcohols


  Regularly defined as 1o, 2o, 3o in a similar manner to carbon centres
• Butanol


  C4H10O is the formula for butanol and its alcohol isomers