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Amino AcidsAnas Bahnassi
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.
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
Non Polar R‐ Group
+H3N CH C
CH3
O-
O
+H3N CH C
CH
O-
O
CH3
CH3
+H3N CH C
CH2
O-
O
CH CH3
CH3
+H3N CH C
CH
O-
O
CH3
CH2
CH3
Proline alanine
valine leucine isoleucine
+H2N
C O-
O
Non Polar R‐ Group
Tryptophan
Phenylalanine
Methionine
+H3N CH C
CH2
O-
O
+H3N CH C
CH2
O-
O
HN
+H3N CH C
CH2
O-
O
CH2
S
CH3
Polar R‐ Group
Glycine
+H3N CH C
H
O-
O
+H3N CH C
CH2
O-
O
CH2
C
NH2
O
+H3N CH C
CH2
O-
O
C
NH2
O
asparagine
glutamine
+H3N CH C
CH2
O-
O
OHtyrosine
+H3N CH C
CH
O-
O
OH
CH3
+H3N CH C
CH2
O-
O
OH
serinethreonine
+H3N CH C
CH2
O-
O
SH
cysteine
Charged R‐ Groups+H3N CH C
CH2
O-
O
CH2
CH2
CH2
NH3+
+H3N CH C
CH2
O-
O
CH2
CH2
NH
C
NH2
NH2+
lysine
arginine
+H3N CH C
CH2
O-
O
C
O-
O
+H3N CH C
CH2
O-
O
CH2
C
O-
O
aspartatic acid
glutamic acid
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)
Aliphatic Side‐Chain Amino Acids
+H3N CH C
H
O-
O
+H3N CH C
CH3
O-
O
+H3N CH C
CH
O-
O
CH3
CH3
+H3N CH C
CH2
O-
O
CH CH3
CH3
+H3N CH C
CH
O-
O
CH3
CH2
CH3
glycine alanine
valine leucine isoleucine
Hydroxy‐Containing Amino Acids
Sulfur‐Containing Amino Acids
+H3N CH C
CH
O-
O
OH
CH3
+H3N CH C
CH2
O-
O
OH
serine threonine
+H3N CH C
CH2
O-
O
SH
+H3N CH C
CH2
O-
O
CH2
S
CH3cysteine methionine
Acidic Amino Acids
Amides of Acidic Amino Acids
+H3N CH C
CH2
O-
O
C
O-
O
+H3N CH C
CH2
O-
O
CH2
C
O-
Oaspartatic acid glutamic acid
+H3N CH C
CH2
O-
O
CH2
C
NH2
O
+H3N CH C
CH2
O-
O
C
NH2
O
asparagine glutamine
Basic Amino Acids
+H3N CH C
CH2
O-
O
CH2
CH2
CH2
NH3+
+H3N CH C
CH2
O-
O
CH2
CH2
NH
C
NH2
NH2+
lysine arginine
Benzene‐Containing Amino Acids
+H3N CH C
CH2
O-
O
+H3N CH C
CH2
O-
O
OH
phenylalanine tyrosine
Heterocyclic Amino Acids
+H2N
C O-
O
+H3N CH C
CH2
O-
O
N
NH
+H3N CH C
CH2
O-
O
HN
Proline histidine tryptophan
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.
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).
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.
R
BASICS
R
COOH
C+H3N
H
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).
CH3 CH2
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.
H CH2
OH
Glycine Alanine Phenylalanine Tyrosine
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.
CH2
Aspartic acid
COO–
CH2
CH2
GlutamicAcid
COO–
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.
CH2
COO–C=O
NH2
Asparagine
CH2
CH2
COO–C=O
NH2
Glutamine
Aspartate
Glutamate
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.
CH2
CH2
CH2
CH2
NH3+
Lysine
CH2
CH2
CH2
NH+H2N=C
NH2
CH2
HN NH+
Arginine Histidine
Guanidinium
Imidazole
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.
Epsilon amino
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).
CH2OH H‐C‐OH
CH3
CH2SH
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.
CH2
CH2
S
CH3
Serine Threonine Cysteine Methionine
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.
CCC
C–
C
C
C
C
CCC
Valine Leucine Isoleucine
Ethyl group
CH2
Tryptophan
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 and Proline
NH
Proline
N COO–
H
CH2
H2C
H2C
CH
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.
Q: What structural feature is common to alanine, serine and cysteine?
Test Your Knowledge. Click to see the answer.
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:
Q: What amino acid has the shortest carbon chain in its R group?
A.
Q: Which amino acid has the longest straight chain of carbons in its R group?
A:
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Anas Bahnassi PhD RPh
Pharmaceutical Biotechnology
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