Unit 1

• You cannot divorce Biology from Chemistry; the former is a special extrapolation of the latter
• Our body is a collection of chemicals
• The proteins that form our hair, nails, and muscle fibres are chemicals; the minerals that are the basis of our bones and teeth are chemicals; even the food and drink we consume every day are chemicals
• Any and every object that we see around us is an example of Chemistry in action: all are formed from a collection of millions of tiny atoms

  
• Biology and Chemistry explore the same thing – the world around us – but simply at different scales
• Chemistry explores life at the level of atoms and molecules: it is really all about understanding how atoms interact to form larger, more complicated substances, how these substances react with each other to form new substances, and how these substances behave
• Biology then looks at how these substances behave when they are combined on a larger scale – the scale of cells, tissues, organisms, populations, or ecosystems
• This reading pack is designed to reinforce and develop understanding of fundamental Chemistry concepts introduced in pre-university (e.g., 'A'-level or equivalent) study
• Concepts covered


  • Depiction
  • Functional groups
  • Nomenclature
  • Bonding
  • Electronics
  • Stereochemistry of organic molecules

  
• The emphasis here is very much on the application of fundamental chemistry concepts to the use of drugs
• This knowledge also serves as a base for the second part of the pack which focuses on the four fundamental macromolecular building blocks: proteins, nucleic acids, lipids and polysaccharides
• While their exact structures can differ, the basic chemistry of those building blocks is essentially similar in all biological systems
• Vitamins are also essential to life, however what constitutes a true vitamin, is dependent on species
• The aim is to introduce the fundamental structure and functions of the above-mentioned macromolecules, in order to provide a molecular understanding of how biological cells and systems work
• At the end of the pack, we introduce you to molecular recognition
• Every biological event involves molecular interactions. Molecules must interact to initiate an action, and then separate
• Whether it is an enzyme binding to its substrate, a drug interacting with its receptor site localised in a macromolecule, a hormone binding to its receptor on a membrane, all require to be bound in a precise orientation for a short time
• Such 'recognition' events are made possible through intermolecular interactions
• Molecular formula


  Provides information on the atoms present in a molecule but there is no information concerning connectivity or structure

  
• Structural formula


  Displays all atoms present and the arrangement of atoms within a molecule and their connectivity

  
• Skeletal formula


  Focuses on the carbon framework and omits hydrogen atoms attached to carbon, though those attached to other atoms are still included, therefore helping us to focus on the 2D shape of the molecule and its functional groups

  
• Molecular models


  3D representations that are useful when considering chemical reactivity and how molecules might interact with each other or with a protein

  
• Organic molecules are usually represented using skeletal formulae to simplify the structures and emphasise the features that are important to understanding the properties of the molecules
• Functional group


  An atom or a group of atoms within a molecule that serves as a site of chemical reactivity
• Functional groups contribute to the polarity of a drug molecule, confer hydrogen bond donor (NH, OH) and acceptor properties, and some are acidic or basic and may be charged, especially at physiological pH

  
• All of these interactions are important in defining how a drug molecule behaves in the body and interacts with its receptor
• Important functional groups and common ring systems in organic chemistry


  • Alcohol
  • Ether
  • Aldehyde
  • Ketone
  • Carboxylic acid
  • Ester
  • Amide
  • Amine
  • Nitrile
  • Halide
  • Alkene
  • Alkyne
  • Benzene
  • Pyridine
  • Furan
  • Thiophene

  
• Naming an organic compound


  1. Determine the parent chain

  2. Identify the highest priority functional group

  3. Determine the position of substituents
• The majority of drugs contain weakly acidic or weakly basic functional groups
• The ionisation state of a drug that contains acidic and/or basic functional groups will depend on the pH of the medium in which it is dissolved
• This in turn will influence the solubility of the drug, the way in which it is formulated as a medicine, its absorption and distribution within the body and its pharmacological activity
• Many of the pharmaceutical excipients that are used in formulating drugs as medicines also contain acidic or basic functional groups
• Chiral centre


  sp3 atom bearing four different substituents
• Enantiomers


  Isomers that are mirror images of each other and cannot be superimposed
• Diastereoisomers


  Stereoisomers that are not enantiomers
• Racemic mixture (racemate)


  An equal mixture of both enantiomers of a compound, has no measurable optical rotation
• Designation of (R) and (S) Enantiomers Cahn-Ingold and Prelog


  1. Assign priority to each atom attached to the chiral centre (according to atomic number)

  2. View the molecule with the lowest priority (4th) group (often H) directed away from the observer

  3. Observe the order of priority: join the 1, 2, 3 groups together, if the direction is clockwise, the isomer is rectus (R), if anticlockwise sinister (S)

  4. If two or more atoms attached to a chiral centre are the same, look to second and third atoms until it is possible to distinguish between groups

  5. For multiple bonds, treat as single bonds to duplicate or triplicate atoms of the same type

  
• Cis-trans diastereoisomers


  Found in molecules with double bonds and saturated rings
• Chiral Diasteroisomers


  Chiral isomers which are not enantiomers, i.e. not mirror images of each other. These differ in physical, chemical & biological properties. Found only in molecules with multiple chiral centres, e.g., sugars. Absolute stereochemistry (R or S designation) is the same at some centres but must differ in at least one.

  
• Chiral Diastereoisomers


  Chiral isomers which are not enantiomers, i.e. not mirror images of each other. These differ in physical, chemical & biological properties. Found only in molecules with multiple chiral centres, e.g., sugars. Absolute stereochemistry (R or S designation) is the same at some centres but must differ in at least one.