Amino Acid Structures – Look for Similarities not Differences Your first major hurdle is to learn the structures of the aminoacids …all 20 of them. This will tax anyone’s memory if it is not doneproperly. Students who resort to flash cards or rote memory neversolidify the lesson. In reality flash cards only press the memory to seestructural differences which makes the chore of learning all 20 that muchmore difficult. The best approach is to use logic and name recognitionand to look for similarities, not differences in structures. In this tutorialyou will see how the name tells you the structure. You will see howstructures build on one another and interrelate. Yes, some memory willbe needed before all the amino acids are mastered. But, follow these fewsimple rules and what you learn will stay with you as you continue intobiochemistry. Learning amino acids now is preparing you later forproteins structure, enzyme catalysis, and eventually metabolic pathways.
BASICS Lets start with the basics. All amino acids have a common structuralunit 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 α-carbonunassigned. A group in this location is represented by the letter R (click 1). COOH α + H3N C H R RR groups are the only variable groups in the structure. Consider R the onlyunknown and focus on this group to learn the structures. Hence, Rule (1) isamino acids are composed of a core group and an R group. Rule (2) is the Rgroup gives an amino acid its structural identity and, later as we will see, its uniquebiochemical properties. Thus, if you insist on using flash cards, draw them asshown 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 Rgroups 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.
Acidic and Amide Amino Acids The acidic amino acids have (–) charges in their R group. There aretwo, aspartic acid and glutamic acid (click 1). Note their similarity. Glutamic acidhas one more –CH2 group (click 1). Note that both have a –COO– group whichgives the negative charge. Aspartic Glutamic Asparagine Glutamine acid Acid CH2 CH2 CH2 CH2 COO– CH2 C=O – COO CH2 COO– NH2 C=O – COO Aspartate Glutamate NH2The –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 glutamateyou give rise to asparagine and glutamine (click 1). Note name and structuresimilarities between the “open” and the corresponding “amide” amino acids. Clickto go on.
The (+) charged amino acids are represented by lysine, arginine andhistidine. Unfortunately, R structures for basic amino acids have little resemblanceto 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 Imidazole NH3 + + H2N=C NH2 Epsilon amino GuanidiniumIt will help you to remember that each (+) N is part of a group. For lysine thisgroup is called the epsilon amino group (click 1). In arginine it’s theguanidinium group and for histidine it’s the imidazole group. Remember thesegroup 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 inserine 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.
Valine, Leucine, Isoleucine These 3 branched-chain hydrophobic amino acids have only C and H intheir R groups. Valine is easy to remember because the carbon chain isarranged as the letter V (click 1). Leucine and isoleucine both have a 4 carbonR 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 youwould predict from the name (click 1). To distinguish the 3, focus only on thebranched 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
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 Rgroup? A: Lysine. It has 4. Leucine and isoleucine have 4 but their chains are branchedQ: 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 groupQ: What structural feature is common to isoleucine and threonine A: Both have an asymmetric carbon in their R group
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). Attachthis 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 ringlooks like “home plate” in baseball (click 1). Note proline does not have a corestructure. 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.