This document provides information about the 20 standard amino acids. It discusses their basic structures, including the central α-carbon and α-amino and α-carboxyl groups. It also classifies the amino acids based on the polarity of their side chains into hydrophobic/non-polar, polar, and charged groups. Additionally, it shows the structures of representative amino acids from each group.

1. Amino Acids
Anas Bahnassi

2. What Are Amino Acids?
• Amino acids are building blocks for proteins
– They have a central α‐carbon and α‐amino and
α‐carboxyl groups
– 20 different amino acids
– Same core structure,
but different side group (R)
– The α‐C is chiral (except glycine);
proteins contain only L‐isoforms.
• Amino acids are ampholytes:
– pKa of α‐COOH is ~2
– pKa of α‐NH2 is ~ 9
• At physiological pH most amino acids behave
as zwitterion.

3. Amino Acids Classification
• Amino acids can be classified according to
POLARITY to:
– Hydrophobic / non‐polar R group: Glycine,
alanine, valine, leucine, isoleucine, methionine,
proline, phenylalanine, tryptophan
– Polar R group (net charge 0 at pH 7.4): Serine,
threonine, cysteine, tyrosine, asparagine,
glutamine, histidine
– Polar R group (Charged ion at pH 7.4): aspartate,
glutamate, lysine, arginine

4. Non Polar R‐ Group
O O
C O-
+H3N CH C O-
CH3
+H2N
Proline alanine
O O
O
+H3N CH C O- +H3N CH C O-
+H3N CH C O-
CH2 CH CH3
CH CH3
CH CH3 CH2
CH3
CH3 CH3
valine leucine isoleucine

5. Non Polar R‐ Group
O O
+H3N CH C O-
+H3N CH C O-
CH2
CH2
CH2
O
S
HN +H3N CH C O-
CH3
CH2 Methionine
Tryptophan
Phenylalanine

6. O
Polar R‐ Group +H3N CH C O-
O
O
+H3N CH C O-
CH2
+H3N CH C O- CH OH
CH2
CH2 C O CH3 threonine
serine glutamine O
NH2
OH
+H3N CH C O-
CH2
O
+H3N CH C O-
O
+H3N CH C O- CH2
CH2 SH O tyrosine
OH
C O +H3N CH C O-
cysteine
NH2
H
asparagine Glycine

7. O O
Charged R‐ Groups
+H3N CH C O- +H3N CH C O-
CH2 CH2
O
CH2 CH2
+H3N CH C O-
lysine CH2
CH2 CH2
arginine
C O CH2 NH
O- O NH3+ C NH2+
aspartatic acid
+H3N CH C O- NH2
CH2
CH2
C O
glutamic acid
O-

8. Amino Acids Classification
• Amino acids can be classified according to R‐
Group to:
– Aliphatic: gly (G), ala (A) , val (V), leu (L), ile (I)
– Aromatic: Trp (W), Phe (F), Tyr (Y), His (H),
– Sulphur : Met (M), Cys (C)
– Hydroxyl: Ser (S), Thr (T), Tyr (Y)
– Cyclic: pro (P)
– Carboxyl: asp (D), glu (E)
– Amine: lys (K), arg (R)
– Amide: asn (N), gln (Q)

9. Aliphatic Side‐Chain Amino Acids
O O
+H3N CH C O- +H3N CH C O-
H CH3
glycine alanine
O O
O
+H3N CH C O- +H3N CH C O-
+H3N CH C O-
CH2 CH CH3
CH CH3
CH CH3 CH2
CH3
CH3 CH3
valine leucine isoleucine

10. Hydroxy‐Containing Amino Acids
O O
+H3N CH C O- +H3N CH C O-
CH2 CH OH
OH CH3
serine threonine
Sulfur‐Containing Amino Acids
O
O
+H3N CH C O-
+H3N CH C O-
CH2
CH2
CH2
SH
S
cysteine methionine
CH3

11. Acidic Amino Acids
O
O
+H3N CH C O- +H3N CH C O-
CH2 CH2
C O
CH2
O-
aspartatic acid C O glutamic acid
O-
Amides of Acidic Amino Acids
O O
+H3N CH C O- +H3N CH C O-
CH2 CH2
C O CH2
C O
NH2
asparagine NH2
glutamine

12. Basic Amino Acids
O O
+H3N CH C O- +H3N CH C O-
CH2 CH2
CH2 CH2
CH2 CH2
CH2 NH
NH3+ C NH2+
NH2
lysine arginine

13. Benzene‐Containing Amino Acids
O O
+H3N CH C O- +H3N CH C O-
CH2 CH2
OH
phenylalanine tyrosine

14. Heterocyclic Amino Acids
O O
O
+H3N CH C O- +H3N CH C O-
C O-
CH2 CH2
+H2N
N
NH
HN
Proline histidine tryptophan

15. Learn Amino Acids Structures
• The best approach is to use logic and name
recognition and to look for similarities, not
differences in structures.
• The Name should tell you the structure.
• Structures are built on one another and
interrelate.
• Learning amino acids prepares you for
understanding proteins structure.

16. BASICS
Lets start with the basics. All amino acids have a common structural unit that
is built around the alpha carbon (click 1). Lets call this the “core” structure. The figure
shows the core with one of the bonds on the ‐carbon unassigned. A group in this
location is represented by the letter R (click 1).
COOH

+H
3N C H
R R
R groups are the only variable groups in the structure. Consider R the only unknown and
focus on this group to learn the structures. Hence, Rule (1) is amino acids are composed
of a core group and an R group. Rule (2) is the R group gives an amino acid its structural
identity and, later as we will see, its unique biochemical properties. Thus, if you insist on
using flash cards, draw them as shown above (click 1) with the box representing the core.
Click to go on.

17. Building an R Group
You saw the importance of the R group. Now, you will see how R groups build
and interrelate. Four that illustrate this point are “glycine, alanine, phenylalanine and
tyrosine. The R groups of each will be shown below (click 1).
Glycine Alanine Phenylalanine Tyrosine
H CH3 CH2 CH2
OH
With an H, glycine is the simplest amino acid, so named because of its sugary taste (click 1).
Alanine with a methyl group is the next simplest (click 1). The red color helps you see how
each R group structure differs from the preceding. Phenylalanine arises when a phenyl
group replaces an H on alanine’s methyl group (click 1). Tyrosine evolves by adding an –OH
group to the para position on the phenyl ring of phenylalanine (click 1). Click to go on.

18. Acidic and Amide Amino Acids
The acidic amino acids have (–) charges in their R group. There are two,
aspartic acid and glutamic acid (click 1). Note their similarity. Glutamic acid has one
more –CH2 group (click 1). Note that both have a –COO– group which gives the negative
charge.
Aspartic Glutamic Asparagine Glutamine
acid Acid
CH2 CH2 CH2 CH2
COO– CH2 COO–
C=O CH2
COO– NH2 C=O
COO–
Aspartate
Glutamate NH2
The –COO– can exchange a proton with the solvent and hence behave as an acid. The
suffix “ate” is used to designate an ionized acid (more properly called a salt). Hence, you
will see aspartic acid and glutamic acid referred to as “aspartate” and “glutamate” (click
1). By forming the amide derivatives of aspartate and glutamate you give rise to
asparagine and glutamine (click 1). Note name and structure similarities between the
“open” and the corresponding “amide” amino acids. Click to go on.

19. The (+) charged amino acids are represented by lysine, arginine and histidine.
Unfortunately, R structures for basic amino acids have little resemblance to one another.
But each is characterized by a (+) N in the R group.
Lysine Arginine Histidine
CH2 CH2 CH2
CH2 CH2
CH2 CH2
HN NH+
CH2 NH
+H Imidazole
NH3+ 2N=C
NH2
Epsilon amino Guanidinium
It will help you to remember that each (+) N is part of a group. For lysine this group is
called the epsilon amino group (click 1). In arginine it’s the guanidinium group and for
histidine it’s the imidazole group. Remember these group names and you will
remember the structures of the basic amino acids. Click to go on.

20. Serine,Threonine, Cysteine and Methionine
Start with serine. Serine has a simple –CH2OH for it R group (click 1).
Threonine is serine with a methyl group (click 1). And, if you replace the O in serine
with an S, you generate cysteine (click 1).
Serine Threonine Cysteine Methionine
CH2OH H‐C‐OH CH2SH CH2
CH3 CH2
S
CH3
Methionine appears to combine cysteine with threonine. The name tells you
methionine has a sulfur (thio) and a methyl group in the structure. Like threonine
methionine has a 2 carbon chain attached to the alpha carbon (click 1). This is
followed by sulfur and ends with a methyl on the sulfur. Click to go on.

21. Valine, Leucine, Isoleucine
These 3 branched‐chain hydrophobic amino acids have only C and H in their R
groups. Valine is easy to remember because the carbon chain is arranged as the letter
V (click 1). Leucine and isoleucine both have a 4 carbon R group. Leucine resembles
valine but with a ‐CH2 before the V (click 1). Isoleucine’s side chain resembles the letter
L, just the opposite of what you would predict from the name (click 1). To distinguish
the 3, focus only on the branched chains in the R structure. Valine and leucine have
only methyl groups, whereas isoleucine’s branches are one methyl and one ethyl group
(click 1). Click to go on.
Leucine Isoleucine
Valine
C C C– C
C C C C
Ethyl group
C C C

22. Tryptophan and Proline
The last 2 amino acid to consider are tryptophan (pronounced trip‐toe‐fane)
and proline. Tryptophan is unique in having an indole ring (click 1). Attach this ring to
the core via a CH2 group and you complete the structure of tryptophan (click 1). Proline
also has a ring, but this ring is saturated. In fact proline’s ring looks like “home plate” in
baseball (click 1). Note proline does not have a core structure. This is because the alpha
amino group is incorporated into the ring.
Tryptophan
Proline
H2C CH2
CH2 H
H2C C
N COO–
N H
H
Indole This completes all the amino acids.
Review this lesson as many times as necessary.
Use paper and pencil to draw out the structures.
Soon you will have mastered amino acid structures. Click
to go on to quiz.

23. Test Your Knowledge. Click to see the answer.
Q: What amino acid has the shortest carbon chain in its R group?
A.
Q: What structural feature is common to alanine, serine and cysteine?
A:
Q: Which amino acid has the longest straight chain of carbons in its R group?
A:
Q: What R group structural feature is common to phenylalanine, tyrosine,
tryptophan, and histidine?
A:
Q: What structural feature is common to isoleucine and threonine
A:

24. Pharmaceutical
Biotechnology
Anas Bahnassi PhD RPh
abahnassi@gmail.com
http://twitter.com/abahnassi
http://www.linkedin.com/in/abahnassi
http://www.udemy.com/Biotechnology
http://www.slideshare.net/abahnassi
attribution – non-commercial – share alike