Amino Acid Structures – Look for Similarities not Differences

1. 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.

2. COOH  +H3N H C R 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). 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.

3. CH2 CH2 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 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.

4. Aspartic acid Glutamic Acid Asparagine Glutamine C=O C=O CH2 CH2 CH2 CH2 NH2 NH2 CH2 COO– COO– CH2 COO– COO– 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. Aspartate Glutamate 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.

5. 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 Histidine Arginine CH2 CH2 CH2 CH2 CH2 CH2 CH2 HN NH+ CH2 NH Imidazole +H2N=C NH3+ NH2 Guanidinium Epsilon amino 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.

6. CH2 H-C-OH CH2 CH3 S CH3 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). Cysteine Serine Threonine Methionine CH2OH 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.

7. C C C C C C– C C C C C 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 Ethyl group

8. H2C CH2 H N CH2 C H2C N COO– H H 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 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. Indole

9. 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