Amino acid properties and nomenclature

Question 1

Describe the ionisation state of amino acids

Answer 1

1. In the physiological pH range, both the carboxylic acid and the amino groups of alpha-amino acids are completely ionised.
2. The amino acid can therefore act as either an acid or a base- amphoteric

Question 2

Describe link between the ionisation states of amino acids and the pH

Answer 2

1. Amino acids in solution at neutral pH exist predominantly as dipolar ions (also called zwitterions).
2. In the dipolar form, the amino group is protonated (-NH3+) and the carboxyl group is deprotonated (-COO-).
3. In acid solution (e.g., pH 1), the amino group is protonated (-NH3+) and the carboxyl group is not dissociated (-COOH).
4. As the pH is raised, the carboxylic acid is the first group to give up a proton, inasmuch as its pKa is near 2.
5. The dipolar form persists until the pH approaches 9, when the protonated amino group loses a proton.

Question 3

Describe the physical properties of amino acids

Answer 3

1. Amino acids are zwitterions so their physical properties are characteristic of ionic compounds
2. Higher melting points
3. More soluble in polar solvents than in non polar solvents- very soluble in water but largely insoluble in most organic solvents.

Question 4

Define chiral compounds

Answer 4

1. A compound that contains an asymmetric center (chiral atom or chiral center)
2. thus can occur in two nonsuperimposable mirror-image forms (enantiomers).

Question 5

Why are amino acids chiral

Answer 5

1. Amino acids are chiral (optically active) because of central carbon atom
2. Have L and D isomer- mirror images which you cannot superimpose- different characteristics

Question 6

Describe why L and D isomers have different properties

Answer 6

1. The D & L forms of compounds are different shapes and enzymes recognise substrates partly by their shape.
2. Wrong shape means no reaction and enzymes are nearly always geared up to recognise the D-form of sugars and the L-form of amino acids.

Question 7

Give an example of L and D isomers of amino acids

Answer 7

1. D- Thalidomide- given as sedative

2. L- Thalidomide- teratogenic- causes defects in development

Question 8

Which amino acid is not optically active

Answer 8

1. Glycine

2. R-group is H so has two H substituents so is superimposable on its mirror image

Question 9

What are the 3 commonly used systems of nomenclature where a stereoisomer of an optically active molecule can be classified

Answer 9

1. Operational Classification
   - Optical rotation
2. Fisher Convention
   - Configuration based on glyceraldehyde
3. Cahn-Ingold-Prelog System
   - Absolute nomenclature

Question 10

Describe the operation classification system of nomenclature

Answer 10

1. Classified as dextrorotatory (right) (+) or levorotatory (left) (-).
2. This depends on whether they rotate the plane of plane-polarised light clockwise or anti-clockwise
3. An equal mix of the two has no polarising effect on light.
4. Not yet possible to predict reliably the magnitude or the sign of a molecules specific rotation.

Question 11

Problem with the operation classification system of nomenclature

Answer 11

1. Provides no presently interpretable idication of absolute configuration of the chemical groups about a chiral centre.
2. A molecule with more than one asymmetric centre may have an optical rotation that is not obviously related to the rotary powers of the individual centres.

Question 12

Describe the Fischer Convention method of nomenclature

Answer 12

1. Configuration based on glyceraldehyde
2. D(+) L(-) Small upper-case letters
3. Only 50% chance he would assign them right- but he did
4. If the OH on the bottom chiral centre points to the right, it is referred to as D-
5. If the OH on the bottom chiral centre points to the left, it is referred to as L- .

Question 13

Problems with Fischer Convention method

Answer 13

1. Awkward and sometimes ambiguous for molecules with more than one asymmetric centre

Question 14

Describe the Cahn-Ingold-Prelog system of nomenclature

Answer 14

1. Absolute nomenclature system
2. Four groups surrounding chiral centre are ranked according a priority system
3. Lowest priority group faces back. S- left R-right
4. S- if 1,2,3 are to left, anti-clockwise
5. R- if 1,2,3 to right, clockwise
6. CORN

Question 15

What is the priority of groups in the CIP system

Answer 15

1. Atoms of higher atomic number bonded to the chiral centre are ranked above those of lower atomic number.
2. If atom bonded to chiral centre are the same, priority of group is established by second, third etc.
3. SH > OH > NH2 > COOH > CHO > CH2OH > C6 H5 > CH3 > H

Question 16

What is an advantage of the CIP system

Answer 16

1. Chiralities of compounds with multiple asymmetric centres can be unambiguously described