Amino Acid Classification Systems

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• Here, we will learn about the amino acids through three key classification systems: structural, nutritional, and catabolic (ie, breakdown).

• Start a table.

• Denote that there are 20 amino acids coded for in our genome.

• Let's define the three key classification systems to organize them:
  • Structural (meaning their Chemical R Groups)
  • Nutritional (meaning their dietary obtainability)
  • Catabolic (meaning their breakdown product, being a sugar or ketone)

Let's start with their structural classification, which we explore in detail elsewhere.

• Show that amino acids have a general structure of a central carbon (the alpha carbon) with four different atoms or groups bound to it.

• Hydrogen
• Carboxylic acid (COOH) group
• Amino (NH2) group
• Variable, R, group

• Denote that via this organization we can divide the amino acids into four general structural categories:
  • Hydrophobic
  • Aromatic
  • Polar, Charged
  • Special Cases.

#Let's look at each of these categories in some detail.

#First, the hydrophobic amino acids, which are so-named because they have nonpolar side chains. As a reminder, nonpolar means that the electrons in the bond are shared equally – these typically involve carbon-carbon or carbon-hydrogen bonds.

• Point out the following clinically-relevant nonpolar, branched chain amino acids: valine, isoleucine, and leucine.

• To solidify what we mean by this, draw a central carbon, an amino group, carboxylic acid, (leave out the hydrogen in this stick-figure format) and show a prototypical branched chain.

• Now, indicate the aromatic amino acids, show that their R group incorporates an aromatic ring.
• Next, include the polar group, so-named because they are hydrophilic – meaning electrons are unequally share along the polar bond.

• Now, the charged group.

• Specify that ACIDIC amino acids have a negative charge at physiologic pH.
  • Indicate that they are aspartate (thus called aspartic acid) and glutamate (thus called glutamic acid).

• Specify that the BASIC amino acids have a positive charge at physiologic pH.
  • Indicate that they are Lysine and Arginine (and sometimes Histidine – thus, you'll see it listed as charged or uncharged in differing resources).
• Finally, the special cases:
  • Glycine (which essentially has NO side chain – just a hydrogen, thus it is achiral)
  • Proline (which forms has a particularly unfavorable chain: an imino ring – the side chain is connected to the protein backbone).

Now, that we have a structural basis for our understanding of amino acids, let's learn about their nutritional classification.

• Denote that the 20 amino acids divide into:
  • 9 Essential amino acids.
  • 11 Nonessential amino acids.

• Denote that the "essential" refers to the fact that these amino acids must be obtained from the diet, whereas, the nonessential amino acids are synthesized endogenously.

• Note that histidine is only essential during the first 5 years of life, so some texts will state that there are 8 essential and 12 nonessential amino acids – we'll learn more about this when we address the conditionality of the nutritional obtainability of amino acids.

• Denote that essential amino acids produce a survival advantage because the metabolic pathways to create the essential amino acids are lengthy (these pathways are found in bacteria and plants).
  • Thus, animals obtain these amino acids in their diet to avoid wasting ATP on their elaborate synthesis – in essence, animals lost the ability to synthesize the difficult to create amino acids (the essential amino acids), as a means of energy efficiency.

So next let's divide the 20 amino acids based on their nutritional classification.

• Show that the 9 essential amino acids are:
  • Methionine
  • Threonine
  • Histidine
  • Valine
  • Phenylalanine
  • Isoleucine
  • Tryptophan
  • Lysine
  • Leucine.

• Place an asterix on histidine because although it is fully essential in the child diet, it is effectively recycled in the adult, so only small quantities are needed from the diet beyond childhood.

To remember this list, we use a fun acronym with their one letter abbreviations…

• My Tall (Handsome) Vegan Friend Is Watering Kale Leaves.
  • M Methionine, T threonine, H (histidine), V valine, F phenylalanine, I isoleucine, W tryptophan, K lysine, L leucine.

• Notice that all three of the branched chain amino acids are essential amino acids: Valine, Isoleucine, Leucine.

Now, consider that it is common to discuss the proteins based on their biological value.

• Write that the essential amino acid that is of lowest amount (the limiting amino acid) in a source of protein determines the protein's biological value.

• Write that we define complete proteins as those that comprise all the essential amino acids (typically meats and dairy: eggs, beef, fish) – thus, they have high biological protein value.
  • Whereas we designate incomplete proteins as those which are deficient in select amino acids (typically, plants).
  • Thus, vegetarian diets include combinations of plants to ensure satisfactory ingestion of the 9 essential amino acids. - For instance, wheat (gliadin) is deficient in lysine whereas beans are deficient in methionine, thus a person cannot survive on either wheat or beans as a protein source, alone.

• Let's now list out the rest of the amino acids (in alphabetical order); they are all nonessential:
  • Alanine
  • Arginine,
  • Asparagine
  • Aspartate
  • Cysteine
  • Glutamate
  • Glutamine,
  • Glycine
  • Proline
  • Serine and
  • Tyrosine.

Next, let's flesh-out a couple more situations that make amino acids conditionally essential.

• Newborns cannot adequately synthesize arginine, cysteine, or tyrosine – thus, clinicians supplement non-breast fed newborns with these amino acids.

• As well, immunosuppressed or pathologically stressed patients require exogenous arginine and glutamine supplements to make up for the body's inability to keep up with the functional requirements of these amino acids

Lastly, let's address the Catabolic Classification System of amino acids.

• Denote that we divide amino acids into those that are:
  • Glucogenic, meaning they form pyruvate or a TCA cycle intermediate
  • Ketogenic, meaning they form ketone bodies (specifically, acetyl-CoA or acetoacetate (aka acetoacetyl-coA)
  • Or form a combination of glucogenic and ketogenic breakdown products.

Let's highlight the various amino acids, accordingly.

• First, indicate that the two L's (Lysine and Leucine) are ketogenic.

• Next, we use the pneumonic These amino acids don't FITTT to remember that Phenylalanine, Isoleucine, Tryptophan, Threonine, and Tyrosine don't fit as either glucogenic or ketogenic alone – they are both glucogenic and ketogenic.

• Now, we know the rest are solely glucogenic:
  • All of the nonessential amino acids (except for tyrosine).
  • And the following essential amino acids: methionine, histidine, and valine

• We address amino acid catabolism (metabolism) elsewhere.