Organic and Biological Chemistry

1. Organic and Biological Chemistry 4.8 Amides

2. Amides Amide functional group

3. Amides • Possible under high temp for extended time to prepare amide from a carboxylic acid and an amine or ammonia (condensation) RCOOH + NH3 RCOO– NH4+ RCOO– NH4+  +H2O

4. Amides • RCOOH + RNH2  RCOO– + RNH3+ • RCOO–RNH3+  +H2O • Amides are produced by the reactions of acid halides, acid anhydrides or esters with amines or ammonia

5. Lidocaine Prilocaine

6. Amides • Hydrolysis of amides will occur with extended refluxing under acid or alkaline conditions • Under acid conditions the amide will hydrolyse to form the carboxylic acid and protonated amine • RCONRH + H+ + H2O  RCOOH + NH3R+ • Under alkaline conditions the products are the carboxylate ion and an amine • RCONRH + OH– RCOO– + NH2R

7. Organic and Biological Chemistry 4.9 Proteins

8. amino acid Proteins: Amino acids • Amino acids have both an Amino and a carboxyl functional group • R group which varies giving 20 different natural amino acids • Simplest is Glycine where R= H General Form

9. Proline Histidine Methionine

10. + − Proteins : Amino acids • Amino acids can self ionise to form a ZWITTERION by transferring a proton from the carboxyl group to the amine group • The molecule does not have an overall charge

11. Proteins: Formation • Proteins are polyamides formed when amino acids (monomer) covalently bond with each other to form large molecules • The link between the amino acids is referred to as a peptide link or peptide bond (amide group) • The reaction is a condensation reaction which is catalysed by enzymes • Proteins are also referred to as polypeptides (long chain molecules with many peptide links) • Proteins don’t have a repeating unit as the R groups vary along the polypeptide

13. Proteins: Types of Bonding • Primary (covalent bonds) form the chains • Primary (ionic and covalent bonds) and secondary interactions between chains and secondary interactions within chains affect the shape of the protein

15. Proteins: Secondary interactions • Hydrogen bonding can occur between peptide links both within a protein chain and between protein chains • Hydrogen bonding can occur between polar R groups on protein chains • Hydrogen bonds will also form between the polypeptide and water molecules

17. Proteins • Hydrogen bonding (and other secondary interactions) within and between polypeptide chains results in each protein having a specific structure. • This structure is unique to the protein and is necessary for the protein to carry out its biological function.

18. Proteins • Within the structure of proteins are active sites which “fit” specific molecules. • If the structure of a protein is changed in any way by the disruption of the secondary interactions then the active sites will be changed and will no longer fit the specific molecules.

19. Proteins • If this occurs the protein is said to be denatured. • Consequently the protein loses its ability to perform its biological function. • Enzymes are proteins • Their ability to biologically catalyse reactions is affected if their spatial arrangement is disrupted

20. Proteins • Changes in pH • Alters ionic bonding between NH3+ and COO– groups • Acid: Converts ionic carboxylate ions to carboxylic acids RCOO – + H+  RCOOH • Alkali: Converts protonated amines to amine groups RNH3+ + OH–  RNH2 • This disrupts bonds between side groups destabilising the protein structure.

21. Proteins • Temperature • Proteins work effectively within a limited temperature range. • Raising a protein to 50oC or above disrupts secondary bonds destabilising the structure.