Transcript Amino Acids tutorial

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 anyone’s 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).

+H N
3
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
H
Alanine
CH3
Phenylalanine
Tyrosine
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.
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
Aspartate
Glutamate
C=O
COO–
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
NH3
Epsilon amino
+
+H N=C
2
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 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.
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).
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
Valine
C
C
C
C
Isoleucine
C
C– C
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 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
CH2
H2C
CH2
C
H2C
N
H
Indole
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