Amino Acid Structures Look for Similarities

not Differences
Your first major hurdle is to learn the structures of the amino
acids all 20 of them. This will tax anyones memory if it is not done
properly. Students who resort to flash cards or rote memory never
solidify the lesson. In reality flash cards only press the memory to see
structural differences which makes the chore of learning all 20 that much
more difficult. The best approach is to use logic and name recognition
and to look for similarities, not differences in structures. In this tutorial
you will see how the name tells you the structure. You will see how
structures build on one another and interrelate. Yes, some memory will
be needed before all the amino acids are mastered. But, follow these few
simple rules and what you learn will stay with you as you continue into
biochemistry. Learning amino acids now is preparing you later for
proteins structure, enzyme catalysis, and eventually metabolic pathways.

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).

H3N

COOH
C
R

H
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.

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

CH3

Phenylalanine

CH2

Tyrosine

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 alanines 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.

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
acid

Glutamic
Acid

Asparagine

Glutamine

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.

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

CH2

CH2

CH2

CH2

CH2

CH2

CH2

NH

NH

+
3

Epsilon amino

H2N=C

Histidine

CH2

HN

NH+
Imidazole

NH2

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 its the
guanidinium group and for histidine its the imidazole group. Remember these
group names and you will remember the structures of the basic amino acids.
Click to go on.

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

CH2OH

Threonine

H-C-OH
CH3

Cysteine

CH2SH

Methionine

CH2
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.

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).
Isoleucines 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 isoleucines branches are one methyl and one ethyl group (click 1).
Click to go on.
Leucine

Valine

C
C

C
C

Isoleucine

C C

C
C

Ethyl group

Tryptophan and Proline

The last 2 amino acid to consider are tryptophan (pronounced trip-toefane) 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 prolines 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

CH2

H2C

CH2
C

H2 C

Indole

N
H

N
H

H
COO

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.

Test Your Knowledge. Click to see the answer.

Q: What amino acid has the shortest carbon chain in its R group?
A: Glycine. It has no carbon in its R group.
Q: What structural feature is common to alanine, serine and cysteine?
A: All three have a single carbon in their R groups.
Q: Which amino acid has the longest straight chain of carbons in its R
group?
A: Lysine. It has 4. Leucine and isoleucine have 4 but their chains are branched
Q: What R group structural feature is common to phenylalanine, tyrosine,
tryptophan, and histidine?
A: All four have rings that are attached to the core via a CH2 group
Q: What structural feature is common to isoleucine and threonine
A: Both have an asymmetric carbon in their R group