`

Amino Acids

#2
0
 `
Introduction
- The central DOGMA of molecular :
• Is the flow of genetic information within a biological system
• DNA → mRNA → protein
• Each amino acid is specified with some codons (3 nucleotides):
❖ A single amino acid may have more than one codon that specify it
❖ While usually each codon code for one amino acid only
- Proteins:
• Are polymers of AA residues joins together by dehydration reaction forms peptide bond
• All proteins are commonly composed of 20 standard AAs

Amino Acids
- Basic structure of amino acid:
1. Alpha central Carbon atom:
• In the center of AA
2. Primary Amino group (α -NH2):
• pKa = 9.4
• Act as weak base
3. Carboxyl group (α -COOH):
• pKa = 2.2
• Act as weak acid
- STEREOCHEMISTRY:
• Chiral center:
❖ Is an atom within a molecule that has four different substituents attached to it.
❖ Asymmetric carbon → 4 different substituents
❖ This is responsible for optical activity of a molecule:
➢ All the amino acids are optically active, except glucine
➢ When light passes through such a compound, it rotates the plane of polarization
• Enantiomers:
❖ Enantiomers are a pair of molecules that exist as mirror images of each other but
cannot be superimposed.
❖ They have the same chemical formula but differ in their spatial arrangement
• Stereoisomers:
❖ Are isomers that differ in spatial arrangement of atoms, rather than order of atomic connectivity
❖ By convention, stereoisomers are defined relative to glyceraldehyde
❖ L-Glyceraldehyde ➔ left
❖ D-Glyceraldehyde ➔ right
❖ If amino group is towards right, it is D form
❖ If the amino group is towards left, it is L form
❖ All AAs derived from proteins have the L stereochemical configuration around the Cα
❖ Less than 1% being found in the D-configuration → Post translational enzyme catalyzed modification
❖ D-amino acids are found in some antibiotics and in bacterial cell walls

1
 `
- Based on the polarity & charge of R group, amino acids are classified as:
A. Non-polar (hydrophobic):
• They tend to reside in core of soluble protein chain & on tails
region of phospholipid in membrane proteins
• Include 9 AAs:

1. Glycine:
❖ Contains the simplest side chain (-H)

2. Proline:
❖ Has the side chain of cyclic pyrrolidine
❖ Contains secondary amine group (NH) instead of primary amine group
(NH2) → called (Imino acid)

3. Leucine & Isoleucine:

❖ Contain hydrocarbon-alkyl side chain (-CH)

4. Phenylalanine (phenyl) & Tryptophan (indole):

❖ Has aromatic side chains

5. Alanine, Valine & Methione (thioester)

2
`
B. Polar uncharged (Hydrophilic):
• Tend to reside on outer surface of a soluble protein & in the core of
membrane protein
• Uncharged polar AA can form H bonds
• Include 6 AA:
1. Serine & Threonine:
❖ Contain hydroxyl (–OH) group as a side chain
❖ Both of them can make hydrogen bond
❖ Lose a proton at an alkaline pH
❖ Attachment for structures /phosphate group
❖ Serine → Attachment for oligosaccharide chains in
glycoproteins

2. Asparagine & Glutamine:

❖ Contain carbonyl & amide group as a side chain
❖ They are very similar to aspartate and glutamate
❖ Asparagine → Attachment for oligosaccharide chains in
glycoproteins

3. Cysteine:
❖ Contains ➔ thiol (–SH) as a side chain.
❖ Form disulfide bridges with another cysteine by condensation reaction
(dehydration reaction)
❖ Disulfide bridges if important for protein folding structure & function
❖ pKa = 8.35

4. Tyrosine:
❖ Lose a proton at an alkaline pH
❖ pKa = 10.07

C. Polar charged AAs:

• Include 2 acidic AAs:

Aspartic acid Glutamic acid

- Fully ionized form called aspartate - Fully ionized form called glutamate

3
 `
• Include 3 Basic AAs:
Lysine Arginine Histidine
- R-group ➔ - R-group ➔ guanidino - R-group ➔ imidazolium
butylammonium - +ve charge at - Free form is weakly basic and largely uncharged at physiologic pH
- (+ve charge at physiological pH - Is the only amino acid with a side chain that can ionize within the
physiological pH physiologic pH range because its Pka is very close to the
physiological PH ➔ can act as a buffer especially in Hemoglobin

- Amino Acid Abbreviations:

Amino Acid Three-letter One-letter
1. Glycine Gly G
2. Alanine Ala A
3. Valine Val V
4. Leucine Leu L
5. Isoleucine Ile I
6. Methionine Met M
7. Proline Pro P
8. Serine Ser S
9. Theronine Thr T
10. Cysteine Cys C
11. Histidine His H

Amino Acid Three-letter One-letter

12. Asparagine Asn N
13. Aspartate Asp D
14. Glutamine Gln Q
15. Glutamate Glu E
16. Tryptophan Trp W
17. Tyrosine Tyr Y
18. Lysine Lys K
19. Arginine Arg R
20. Phenylalanine Phe F
21. Aspartate or Aspargine Asx B
22. Glutamate or Glutamine Glx Z
23. Undetermined AA X

4
 `
Amino Acid with ionizable groups & Titration
- pH > pKa :
• Loss H+
• Converted from protonated to Deprotonated
• RH → R-
• When the pH is high The deprotonated base form ( – COO−) is the
predominant rather than protonated ( - COOH)
• High pH ➔ High -ve charge for the protein
- pH < pKa :
• Gain H+
• Converted from Deprotonated to protonated
• R- → RH
• When the pH is low The protonated base
form ( – COOH) is the predominant rather pK1 (-COOH) pK2 (-NH3+) pKR
than deprotonated ( - COO-) Glycine - 2.34 - 9.6
Alanine - 2.34 - 9.69 -

- At physiological pH ~(7.4): Proline - 1.99 - 10.96 -

Valine - 2.32 - 9.62 -
• The –NH2 and -COOH of AA readily ionize
Leucine - 2.36 - 9.6 -
• The amino groups ➔ is protonated (NH3+)
Isoleucine - 2.36 - 9.68 -
• The carboxylic acid groups ➔ is
Methionine - 2.28 - 9.21 -
deprotonated (COO-)
Phenylalanine - 1.83 - 9.13 -
• So, at physiological pH amino acids known
Tyrosine - 2.2 - 9.11 - 10.07
as Zwitterions Molecules (Dipolar):
Tryptophan - 2.38 - 9.39 -
❖ Bear charged groups of opposite
Serine - 2.21 - 9.15 -
polarity, both positive & negative
Threonine - 2.11 - 9.62 -
charges
Cysteine - 1.96 - 10.28 - 8.18
Asparagine - 2.02 - 8.8 -
- pH < 1.5 ➔ All ionizable groups all protonated
Glutamine - 2.17 - 9.13 -
(there's no pKa value less than 1.5 )
Lysine - 2.18 - 8.95 - 10.53
- pH > 13 ➔ All ionizable groups all deprotonated Histidine - 1.82 - 9.17 - 6
(there's no pKa value more than 13) Arginie - 2.17 - 9.04 - 12.48
Aspartate - 1.88 - 9.6 - 3.65
- Any Amino acid will have at least 2 pKa values:
Glutamate - 2.19 - 9.67 - 4.25
• pKa 1 ➔ for carboxylic acid (α COOH)
• pKa 2 ➔ for amino group (α NH3+ )

- pH increase until it reach the value of the pKa 1:

• Cause ionization of the carboxylic acid ➔ COO-
• Amino group do not change (α NH3+ )
- pH still increase until it reach the value of pKa 2:
• Cause deionization of the amino group ➔ NH2

5
 `
- Amino acids with three pk values ;if the R group is ionizable then:
• pKa 1 ➔ carboxylic acid group (α COOH)
• pKa R ➔ side chain
• pKa 2 ➔ amino group (α NH3+ )

- Isoelectric point (PI) :

• Is the pH at which an amino acid carries no net charge (zwitterion)
• If the pH above this point, amino acid becomes a negative ion
• If the pH below the amino acid becomes a positive ion.
• PI = 0.5 (pKi + pKj)
• If the amino acid have 3 pKa, we use the 2 values that are closet together
• Separation of plasma proteins by charge typically is done at a pH above the pI of the major proteins.
❖ Therefore, the charge on the proteins is negative
❖ In an electric field, the proteins will move toward the positive electrode at a rate determined by
their net negative charge.
❖ Variations in the mobility pattern are suggestive of certain diseases
Neutral R-Groups at pH=0: +ve R-Group at pH=0
- When they lose H+ they become negatively - When they lose H+ they become neutral
charged
- Include: - Include:
❖ Aspartic Acid ❖ Arginine
❖ Glutamic acid ❖ Histidine
❖ Cysteine ❖ Lysine
❖ Tyrosine

- Titration of Glycine :
• 2 ionizable groups
• 2 pKa values
• 2 Titration curves
• 2 equivalence points
• 2 buffer regions:
❖ pH = 1.34 to 3.34
❖ pH = 8.6 to 10.6
• PI = 0.5 (2.34 + 9.6) = 5.97
• Start with +ve Charge
• Then 0 charge
• Then -1 charge

6
`
- Titration of aspartic acid (& Glutamic acid ):
• 3 ionizable groups
• 3 pKa values
• 3 Titration curves
• 3 equivalence points
• 3 buffer regions:
❖ pH = 1.1 to 3.1
❖ pH = 2.9 to 4.9
❖ pH = 8.8 to 10.9
• PI = 0.5 (3.9 + 2.1) =2
• Start with +1 Charge
• Then 0 charge
• Then -1 charge
• Then -2 charge
- Titration of arginine (histidine & Lysine):
• 3 ionizable groups
• 3 pKa values
• 3 Titration curves
• 3 equivalence points
• 3 buffer regions:
❖ pH = 1.1 to 3.1
❖ pH = 8 to 10
❖ pH = 11.5 to 13.5
• PI = 0.5 (9 + 12.5) = 10.75
• Start with +2 Charge
• Then +1 charge
• Then 0 charge
• Then -1 charge
- Some drugs are weak acid or weak bases:
• Only the uncharged form of the drug can pass through membrane
• Weak acid:
❖ In the stomach pH=1.5 → uncharged → absorbed
❖ In small intestine pH = 6.5 → charged → not absorbed
• Weak base:
❖ In the stomach pH=1.5 → charged → not absorbed
❖ I n small intestine pH = 6.5 → uncharged → absorbed
- Question: In the peptide below, what is the net charge at pH 10
• Answer: -2
- Question: Name the following polypeptide :
• Alanine – Tyrosine – Aspartate – Glycine
• Ala – Tyr – Asp – Gly
• A–Y–D-G