Tuesday 22 Feb 2005 Lecture 15 The biochemistry of functional groups and bonds Andrew Pearson

1. BC10M Introductory Biochemistry Tuesday 22 Feb 2005 Lecture 15 The biochemistry of functional groups and bonds Andrew Pearson

2. The biochemistry of functional groups and bonds What are functional groups? “The atom or group of atoms that defines the structure of a particular family of organic compounds and, at the same time, determines their properties is called the functional group.” (Morrison & Boyd, Organic Chemistry)

3. What are functional groups? “When we encounter a complicated molecule with a number of functional groups, we may expect the properties of the molecule to be roughly a composite of the properties of the various functional groups.” (Morrison & Boyd, Organic Chemistry)

4. Take a molecule like L-DOPA It has a number of functional groups which contribute to its properties.

5. ?

6. Carboxylic acid ?

7. Carboxylic acid Amino group ?

8. Carboxylic acid Amino group Methylene group ?

9. Carboxylic acid Amino group Methylene group Aryl group

10. Carboxylic acid Amino group Methylene group Aryl group Hydroxyl group

12. Properties of functional groups Carboxylic acids. Carboxylic acids, like all acids, “give up” their acidic protons. They become carboxylate anions. Such anions can be persuaded to accept protons if the pH is lower than the pKa value of the group.

13. Properties of functional groups Amines. Amines can accept protons. In fact it is fairly difficult to get the protons off: a very high pH (= low [H+]) is needed. If the pH of the surrounding medium is lower than the pKa of the amine group it will be protonated, and positively charged. This is in contrast to the behaviour of acids which are “reluctant” to accept protons unless [H+] is high.

14. Properties of functional groups Aldehydes. Aldehyde carbons have a planar rather than the usual tetrahedral structure. The oxygen nucleus is more “electronegative” than the carbon, hence takes more than its fair share of the double bond electrons. This thins the electron cloud above and below the carbon nucleus, exposing it the nucleophilic attack. Thus aldehydes are said to be quite reactive.

15. Properties of functional groups Alcohols. Alcohols react readily with acids to form esters by the elimination of water. Hydrolysis of esters requires little energy.

16. The same biochemistry is used by all living cells that have been studied. Electrons, protons and energy are the fundamental components of biochemistry and bioenergetics.

17. Essential cellular processes

18. Chemistry fundamentals: • Elements all have different nuclei. • Atomic nuclei are formed of : • protons (+ve charge) • neutrons (no charge) • electrons (-ve charge) are roughly equal in number to the no. of protons in the • nucleus. • Covalent bonds are the sharing of electrons • between consenting nuclei.

19. Chemistry fundamentals:

20. The s and p orbitals of electrons closest to the nuclei of carbon, hydrogen, oxygen & nitrogen, are those most frequently of importance in biochemical bonds, reactions and molecules.

21. The ability of carbon, oxygen & nitrogen to form “double” bonds gives rise to π- bonding molecular orbitals.

22. How strong are chemical bonds • relative to each other? • relative to other energies?

26. H-bonds Electrostatic Interactions Van der Waal’s

27. Chemistry fundamentals:

28. Far UV = 1200 kJ.mol-1 H-bonds Electrostatic Interactions Van der Waal’s UV = 480 to 343 kJ.mol-1 visible Near IR = 120 kJ.mol-1

29. Far UV = 1200 kJ.mol-1 UV = 480 to 343 kJ.mol-1 Near IR = 120 kJ.mol-1

30. “Amino acids” usually means “α-amino carboxylic acids” From Brock

31. From Brock

32. From Brock

33. It is the structure of the side group that distinguishes amino acids from each other. From Brock

34. The formation of a peptide bond between two amino acids From Brock

35. Enzymes achieve catalysis mainly by: • bringing reactants together in the optimum • orientation, to make new covalent bonds; • or breaking covalent bonds by: • causing the susceptible bond to weaken, by distorting its angle, or lengthening it; • causing the susceptible bond to weaken by attacking one of the bonding nuclei (nucleophilic attack); • causing the susceptible bond to weaken by withdrawing electrons from it.

37. Structures & functions of common carbohydrates

38. Basic units: called monosaccharides  are simple sugars such as glucose and fructose. The structures of monosaccharides can be drawn in different ways, to highlight different aspects: the Fischer projection is best for showing the stereoisomerism of the various substituents; but the Howarth projection is more useful to biochemists because it approximates the 3-D structures and helps explain stabilities.

40. Properties of monosaccharides. Containing many hydroxyl groups: sugars interact easily with water: they are hydrophilic & water-soluble. Containing many hydroxyl groups: sugars are highly oxidised and can be easily hydrolysed into fragments. Containing many hydroxyl groups: sugars are easily derivatised to give related molecules, including aminosugars, acetylated sugars, dimers, oligomers and polymers.

41. From Brock

42. cis double bonds between carbons 9 & 10 From Lehninger

43. Triacylglycerols a.k.a. triglycerides From Brock

44. From Brock

45. From Lehninger

46. From Brock