Amino Acid Structures: Part II

Sections

Overview
Full-Length Text

AMINO ACID Structures: Part 2

Overview

Aromatic

Phenylalanine

The simplest of the aromatic amino acids: its side chain is a benzene ring attached at the beta carbon. To remember its one letter code, remember that phenylalanine begins with an F-sound even though it starts with a P.

Tyrosine

• Phenylalanine with an alcohol group attached at position 4 on the benzene ring. * Tyrosine and phenylalanine are closely related. In fact, tyrosine is synthesized in the body from phenylalanine.
  Clinical correlation: phenylalanine hydroxylase converts phenylalanine to tyrosine. Its deletion or inactivation results in phenylketonuria, a congenital metabolic disorder that can lead to toxic build-up of phenylalanine in the blood and brain.

Histidine

• An aromatic amino acid with a five-membered ring.
• Histidine's side chain can carry a charge because its ring structure makes the second nitrogen also able to accept a proton. To remember this, we add a hydrogen atom and a positive charge to the double-bonded nitrogen atom in histidine.

Tryptophan

• Has two rings.
• You can remember that the one-letter code of tryptophan is W by noticing that the side of the bulky indole ring has a bit of a W shape.

Charged

Aspartate (aka aspartic acid)

• Under physiological conditions, aspartate is negatively charged.
• Aspartate is one of the major components of the artificial sweetener aspartame, which is found in many diet sodas.

Glutamate (aka glutamic acid)

• Glutamate's structure is very similar to aspartate, it just has an extra CH2 before the carboxylic acid group.
• Glutamate's sodium salt, monosodium glutamate, or MSG is used in the food industry to enhance the flavor of savory foods.

Lysine

• Letter K was closest letter to L that was available.

Arginine

• Remember it's letter, remember that the word Arginine starts with an "R" sound.

Polar

The polar amino acids are: cysteine, serine, threonine, asparagine and glutamine.

Cysteine

• Contains a sulfur atom.
• The sulfhydryl group forms disulfide bridges, an important part of the protein structure.

Serine

• Serine is cysteine's cousin because they are identical except for one atom: it has an oxygen atom in place of the sulfur atom.
• Serine is one of the most commonly phosphorylated amino acids, which makes it very important in the activation and deactivation of proteins.

Threonine

• Threonine has a branch at the beta carbon.

Asparagine

Glutamine

• The carboxamide correlate of glutamate.

Full-Length Text

• Here we will continue learning the twenty major amino acids.
  • We have already learned the structures of glycine, proline, alanine, valine, leucine, isoleucine and methionine.
  • In this tutorial we will cover the other 13 amino acids: the aromatic, charged, and the polar amino acids.

Now we will draw the four amino acids with aromatic ring structures: phenylalanine, tyrosine, histidine and tryptophan. These four amino acids have three different kinds of ring structures with resonance, which are called aromatic rings.

Let's start with phenylalanine, the simplest of the aromatic amino acids: its side chain is a benzene ring attached at the beta carbon.

• Draw our general amino acid structure, then add a methyl group in the R group position.

• Add a benzene ring (a hexagonal ring with three double bonds) to the methyl group.
  • Notice that phenylalanine looks like we simply created a phenyl form to alanine.

• Write that phenylalanine is also denoted as Phe or F.
  • To remember the one letter code, remember that phenylalanine begins with an F sound even though it starts with a P.

Now let's draw tyrosine, which we can also write as Tyr or Y.

• Redraw phenylalanine, and add an alcohol group attached at position 4 on the benzene ring.
  • As you can see, tyrosine and phenylalanine are closely related. In fact, tyrosine is synthesized in the body from phenylalanine.
  • As a clinical correlation write that a deletion or inactivating mutation of the gene encoding the enzyme phenylalanine hydroxylase, which converts phenylalanine to tyrosine, results in phenylketonuria, a congenital metabolic disorder that can lead to toxic build-up of phenylalanine in the blood and brain.

Now let's draw histidine, an aromatic amino acid with a five membered ring.

• Indicate that histidine is also denoted as His, or H.

• Draw our general amino acid structure and add a methyl group.

• At the end of the methyl group, at the beta carbon position, add a pentagon shaped ring with nitrogen atoms at positions 3 and 5.

• Now add two double bonds to the ring, and a hydrogen atom to the nitrogen atom with only two bonds.
  • This is called an imidazole ring.

• Histidine's side chain can carry a charge, because its ring structure makes the second nitrogen also able to accept a proton.
  • To remember this, add a hydrogen atom and a positive charge to the double-bonded nitrogen atom in histidine.

The last amino acid in this group is tryptophan, which has a bit of a complicated structure, since it has two rings.

• Indicate that tryptophan is also written as Trp, or W.

• Draw our general amino acid structure, and add to it a methyl group.

• To the methyl group, add a pentagon shaped ring with a double bond between carbons 1 and 2, and an NH group at position 3.

• Then to the pentagon, add a benzene ring at carbons 4 and 5.
  • This double-ring structure is called an indole ring.
  • You can remember that the one-letter code of tryptophan is W by noticing that the side of the bulky indole ring has a bit of a W shape.

Review: now that we know a few more amino acids, let's spell a couple more words. Grab a blank sheet of paper and spell the words WHY and FLAP using amino acids.

Now let's learn the charged amino acids. Aspartate and glutamate are negatively charged, and lysine and arginine are positively charged.

Let's start with aspartate, also known as aspartic acid.

• Indicate that aspartate's codes are Asp and D.

• As usual, draw our general amino acid structure.

• Add a beta and gamma carbon, and to the gamma-carbon attach a carboxylate group.

• Under physiological conditions, aspartate is negatively charged.
  • Aspartate is one of the major components of the artificial sweetener aspartame, which is found in many diet sodas.

Next, let's draw glutamate, also known as glutamic acid.

• Write that glutamate's abbreviated codes are Glu and E.

• Glutamate's structure is very similar to aspartate, it just has an extra CH2 before the carboxylic acid group.

• Glutamate's sodium salt, monosodium glutamate, or MSG is used in the food industry to enhance the flavor of savory foods.

• Draw our general amino acid structure. Add a beta, gamma and delta carbon, and to the delta-carbon attach a carboxylate group.
  • Remind yourself that glutamate is one CH2 group bigger than aspartate, and its one-letter code is one letter further down the alphabet.
  • Like aspartate, it is also negatively charged under physiological conditions.

The other two amino acids in this group, lysine and arginine, are positively charged. Remember from elsewhere that histidine is also a member of this group, as it too can be positively charged under physiological conditions.

Lets' draw lysine and arginine now.

• Indicate that lysine is also denoted as Lys and K.

• Draw our general amino acid structure.

• Add a beta, gamma, delta and epsilon carbon, and add an NH3 group to C-epsilon.
  • Don't forget to give nitrogen its positive charge!

• The letter K was chosen to symbolize lysine because all the other letters had been taken by other amino acids beginning with those letters, and K was the closest letter to L of the remaining letters of the alphabet.

• Write that arginine is also denoted as Arg or R.

• To draw arginine, start with the general amino acid structure, as we have been doing.

• Add three more carbon atoms: the beta, gamma and delta carbons.

• To the delta carbon, add a nitrogen atom with a hydrogen atom and another carbon attached.

• To this carbon attach a single bonded NH2 group and a double-bonded NH2 group.
  • Add the positive charge to the nitrogen that is double bonded to the carbon.
  • As you might have surmised, this side-chain structure has resonance.

• Remember that the word arginine starts with an "R" sound…like a pirate

Review: let's spell some more words with our new letters! Grab a blank piece of paper and spell the words REMIND, HAWK, and WAFER.

Our final grouping of amino acids is the polar amino acids. These are: cysteine, serine, threonine, asparagine and glutamine. Keep in mind that several of the other amino acids that we have discussed previously are also polar.

Let's start with cysteine.

• Cysteine is our second amino acid that contains a sulfur atom (the first was methionine).

• We also write cysteine as Cys or C.

• Draw our general amino acid structure, and add a methyl group.

Do you remember what amino acid has this structure? It's alanine!

• Now add a sulfhydryl (SH) group to alanine.
  • The sulfhydryl group of cysteine is very important because it forms disulfide bridges, an important part of protein structure.

Next we'll draw serine.

• Indicate that we denote serine as Ser or S.
  • Serine is cysteine's cousin, because they are identical except for one atom: it has an oxygen atom in place of the sulfur atom.

• Redraw cysteine with an OH group in place of the SH group.

• Serine is one of the most commonly phosphorylated amino acids, making it very important in the activation and deactivation of proteins.

Now let's draw threonine, which is closely related to serine.

• We can also denote threonine as Thr or T.

• Redraw serine, and add a methyl group at the beta carbon (in addition to the alcohol group).

• Notice that threonine has a branch at the beta carbon.

Which other amino acids also have beta-branching? Valine and isoleucine, of course!

The last two amino acids, asparagine and glutamine, are the cousins of aspartate and glutamate respectively. Recall that aspartate and glutamate have negatively charged carboxylate groups in their side chains. On the other hand, asparagine and glutamine have carboxamide groups as their side chains.

Let's draw them now, starting with asparagine.

• Indicate that asparagine can also be written as Asn or N.

• Draw our general amino acid structure, and add a beta and gamma carbon.

• To the gamma carbon, add two functional groups:
  • A double-bonded oxygen (carbonyl group), and
  • An NH2 (amino group).
  • This is what is called a carboxamide, or amino carbonyl group.

• We can remember the one-letter code by noticing that all the preceding letters of asparagine have been taken by other amino acids beginning with those letters.

Now let's draw glutamine, the carboxamide correlate of glutamate. This also means that it has one more CH2 group than asparagine does.

• Glutamine's code forms are Gln and Q.

• Draw our general amino acid structure, and add beta, gamma and delta carbons.

• To the delta carbon, as we just did with asparagine add a double bonded oxygen, and
  an NH2.

• We can remember the one-letter code of glutamine by noticing that Q is one of the closest letters to N in the alphabet, to show the close relationship between glutamine and asparagine.

• It's helpful to know that the amine forms have the letter "n" as the 3rd letter in their code; for instance, asparagine is Asn, versus aspartate, which is Asp.
  • Glutamine and glutamate have a similar relationship in their code.

Review: now that we know all of the amino acids, practice them by spelling the following words: QATAR, SWEDEN, CHILE, and EGYPT.