Lecture 6: Amino acids

1. All objects have mirror images (we can put anything in front of a mirror and see its reflection).

2. Sometimes the 3D structure of the mirror image is identical to the 3D structure of the object that we place in front of the mirror

3. We can place (superimpose) such objects (e.g. mugs) onto one another perfectly – they are superimposable

4. However, the 3D structure of the mirror images of some objects (like hands) are not identical

5. We cannot place (superimpose) them onto one another perfectly – they are non-superimposable

6. Molecules that are non-superimposable mirror images of one another are called stereoisomers

7. Stereoisomers have identical covalent structure but different 3D structures and molecular properties

8. If a molecule contains a carbon atom carrying 4 different substituents, the molecule will have 2 stereoisomers.

a. Such a carbon is called a chiral carbon, asymmetric carbon or chiral centreb. The molecule itself is referred to as a chiral molecule

9. All amino acids (except glycine) are chiral molecules and have two stereoisomers – we designate them D- and L-

10. All amino acids consist of an amino group (-NH2 or NH3+) linked to a carboxyl

group (COOH or COO-) via a carbon atom (called the alpha carbon). A side-chain (R-group) is carried on the alpha carbon and determines the individual properties of the amino acid (See slide 11).

11. We can represent stereoisomers using ‘Fisher projection’ (See slide 13). In Fischer projection, covalent bonds from a chiral carbon are represented as wedges

a. solid wedges represent groups that ‘stick out’ towards us from the pageb. dashed wedges represent groups that ‘stick back’ into the page

12. In order to determine whether an amino acid is the L- or D-isomer, we look at a Fischer projection of the molecule where the COOH group is at the top and the R-group at the bottom. If the amino group is pointing towards the left, the amino acid is L-, if not, it is D- (see slide 13).

13. Amino acids found in proteins are usually L-amino acids

14. There are 20 common amino acids. They can be represented by a 3 letter abbreviation as well as a 1 letter abbreviation. Make sure that you know these very well (see slide 15).

15. You have to be able to draw the structure of all 20 common amino acids (slides 20-25). When drawing them, remember:

a. Each carbon should have 4 substituentsb. Each nitrogen should have 3 substituents (except for –NH3

+ or -NH2+-)

c. ‘Fill up’ your structure with hydrogen atoms

16. The amino acids can be divided into 4 groups based on their chemical properties:

a. Group 1: non-polar, hydrophobic amino acidsb. Group 2: polar, uncharged amino acidsc. Group 3: acidic, negatively charged amino acidsd. Group 4: basic, positively charged amino acids

17. Make sure that you can identify functional groups found in the amino acids side chains (circled in red, slides 20-25)

18. The carbons in an amino acid can be uniquely identified by using the following nomenclature (see slide 19). Starting from the alpha carbon (the carbon connecting the amino and carboxyl group) and moving down the side-chain, they are designated alpha (), beta (), gamma(), delta(), epsilon() etc.

19. We refer to functional groups attached to specific carbons using the same system, e.g

a. Lysine has two amino groups: an alpha amino and epsilon amino groupb. Serine and threonine have beta hydroxyl groupsc. etc.

20. Non-polar side chains that do not contain a benzene (phenol) ring but are composed entirely of C and H are called ‘aliphatic’

21. Non-polar side chains that contain a benzene (phenol) ring are called ‘aromatic’

22. The hydroxyl groups on serine and threonine cannot lose a proton (H) under physiological conditions (i.e. conditions that we find in life)

23. The hydroxyl group of tyrosine can lose a proton under certain physiological conditions, it can therefore act as an acid (proton-donor).

24. Sulfhydryl (thiol) groups found in cysteine can react with one another to form a covalent bond (-S-S-) called a disulfide bond.

25. Histidine and arginine contain delocalised bond systems – the positive charge is therefore not always confined to a specific atom

26. Proline is the only circular amino acid. Since proline does not contain an -NH2 or –NH3

+ (amino) group, but an –NH- or –NH2+- (imino) group, it is sometimes

referred to as an imino acid.

27. Uncommon amino acids like hydroxyproline, hydroxylysine and thyroxine are only rarely found in proteins. They are derived from common amino acids

28. Hydroxyproline and hydroxylysine are found in collagen, an important structural protein in connective tissue.

29. Thyroxine is a hormone (derived from tyrosine) which is secreted by the thyroid and has a wide range of physiological effects.