What Are Amino Acids?

Posted on 26 Jun 2011 19:22

Amino acids are the individual building blocks of proteins. Proteins are a fundamental ingredient of all forms of life on Earth. They fuel and direct biochemical actions and provide the structure of our bodies. Proteins can act as cell to cell signalers (hormones and cytokines), molecular transporters, enzymes, neurotransmitters and a host of other functions. In fact, all major structural and functional actions in the body are carried out by proteins, including the passing of genetic information though DNA and RNA. When most of us think of protein, however we think of muscle. Muscle is the largest reservoir of protein in our bodies and the second largest store of energy, next to adipose tissue (fat). The muscle tissue of other animals is the largest source of protein in our diets.

Muscle is made up of polymers of amino acid linked by peptide bonds. Amino acids, then, are the molecular constituents of proteins. Different amino acids form long chains in varying sequences and combinations to make a staggering variety of proteins. Amino means containing nitrogen and it is the nitrogen that differentiates amino acids from carbohydrate and lipids, all of which contain the same basic chemicals, carbon, hydrogen, and oxygen. Amino acids consist of an amino or amine group, which contains nitrogen, an acid group, a hydrogen atom, and a distinct side group of atoms attached to a central carbon atom. It is this side chain that gives each amino acid its distinctive qualities so that even though all amino acids share a similar structure their properties and roles in the body differ.

The Twenty Basic Amino Acids

There are around 300 amino acids which occur naturally, but among these there are but 20 common amino acids in the human body. In fact, the same 20 amino acids, with few exceptions, form most life on Earth and the same basic aminos that make up our bodies also form bacteria and even more primitive life. This has been true for billions of years. How can so few amino acids form such a staggering variety of different proteins, all with distinct characteristics and functions? In much the same way that we form so many different words, each with a distinct meaning, from only 26 letters. The amino acids are basically the alphabet for building proteins. The human body is estimated to contain about 30,000 different proteins, of which around 3000 have been studied. 1

The first of the 20 common amino acids discovered was asparagine, in 1806. It was named asparagine because it was found in asparagus. Other aminos derived their names similarly. Glutamine was identified in gluten, the protein from wheat and other grains. Tyrosine was found in cheese and so derived its name from the Greek word for cheese, tyros. Glycogine was named for its sweet taste, the Greek work glykos meaning sweet. The last of the aminos to be identified was threonine, in 1938. 2

The body cannot store amino acids, in large amounts, for later use, as it can carboydrates and fats. Therefore the amino acids must either be constantly replenished by the diet or manufactured by the body from simpler compounds (a process called "de novo synthesis"). The amino acid pool in the blood is dynamically controlled in a steady state of balance.

Essential and Nonessential Amino Acids

The body can synthesize more than half of these for itself from nitrogen, carbohydrates, and fats. Although these proteins are also delivered by the diet it is not always essential that they be and thus these amino acids are called nonessential amino acids (also called dispensable). Each of these amino acids have different metabolic roles in the body. When you take in protein, the amino acids can then be incorporated into other proteins, used in the formation of many other Nitrogen containing compounds, or oxidized for energy.

Nine amino acids either cannot be made by the body or cannot be made in sufficient quantities to meet the body's needs. These nine must be supplied by the diet and so are called essential amino acids (also called indispensable). Sometimes these classes of amino acids are alternatively referred to as dispensable and indispensable aminos.

Essential Amino Acids Nonessential Amino Acids
Histidine Alanine
Isoleucine* Arginine
Leucine* Asparagine
Lysine Aspartic Acid
Methionine Cysteine
Phenylalanine Glutamic Acid
Threonine Glutamine
Tryptophan Glycine
Valine* Proline
- Asparagine
- Serine

*branched chain amino acids

Conditionally Essential Amino Acids

In some circumstances certain amino acids that the body normally makes are made in insufficient quantities because of special circumstances such as disease, injury, or vigorous activity. Particularly, a nonessential amino acid may not be synthesized in sufficient quantities when the diet does not supply enough of it's precursors. These amino acids are called conditionally essential amino acids. Some amino acids that are considered to be conditionally essential, under the right circumstances, are glutamine, arginine, cysteine, histidine, proline, taurine, and tyrosine.

Classification of Amino Acids

Beside essentiality or nonessentiality in the diet, as shown above, amino acids can be classified according to structure, net charge, or polarity.

Most of the 20 amino acids seen in the human body are known as alpha amino acids or 2-amino acids. All 20, except for proline, have a free alpha-amino group and an alpha-carboxyl group. In these biologically important amino acids amino group (-NH2) is covalently bonded to the same tetrahedral "alpha" carbon that the carboxyl group (-COOH) is attached to. 3

alpha-amino.jpg

Amino Acid Structure: Side Chains

The "R" group in the image above refers to the side chain of the amino acid. Each different amino acid has its own R group. As stated previously, it is the side chains of the aminos that make up a particular protein it's functional characteristics in the body. These side chains also determine whether amino acid can be synthesized by the body or must be obtained through diet. They vary in size, shape, charge, hydrogen bonding capacity, chemical reactivity and hydrophobic character. Some of these properties are due to functional groups which are commonly found in amino acids such as alcohols, thiols, thioethers, carboxylic acids, carboxamides, and many others.

The alpha-amino acids are also chiral, meaning they can actually exists in two different configurations that are mirror-images of each other. These are called the L isomer and the D isomer. For some reason, all the protein in our bodies are made up of L isomers. There is no satisfactory explanation for why this arrangement came about. It could be that the use of L-Mmino-acids in the proteins was arbitrary but became fixed in evolution.

Amino Acids Can Join Together

Although the R group side chains of the amino acids are what gives them a unique identity, just as important is their ability to polymerize to form peptides and proteins. It is the amino and carboxyl group that makes this possible.

Amino acids link together to form peptides and proteins in a similar fashion to how monosaccharides link to from disaccharides and fatty acids link with glycerol to form triglycerides - through enzyme mediated condensation reactions.

An OH group is removed from the carboxyl acid end of one amino acid and an H atom from the amino group of another. This allows a peptide bond to be formed between the two ends, leaving behind a molecule of water formed from the OH group and H atom. Thus forms a dipeptide. Further bonds can be formed by the same reaction wherein an H atom is removed from the acid end of the second amino and an OH group from the first, forming a tripeptide. As further amino acids are joined the resulting protein structure is called a polypeptide. Most proteins are made up of polypeptides of a few dozen to several hundred amino acids.

Amino Acids Fold in on Themselves to Form Complex Structures

Polypeptides do not from in simple straight chains. As stated above, the side chains each have particular characteristics such as charge, chemical reactivity, and hydrophobic character. Some side chains are attracted to water. Some side chains repel it. Some side chains, due to their charge, may be attracted to other side chains of an opposite charge, so on and so forth. All this causes a polypeptide chain to fold in on itself into complicated arrangements. The water-loving charged hydrophilic side chains tend to be arranged toward the outside surface of the protein, near the water, and the hydrophopic groups within, away from the water. The final arrangement of a protein is based on that which allows it to be most stable in the body's fluids.

Amino Acid Classification

The polarity of the side chains is probably the most useful way by which to classify the 20 amino acids. These can be grouped into four basic categories: 1) nonpolar or hydrophobic amino acids, 2) neutral (uncharged) but polar amino acids, 3) acidic amino acids with a net negative charge at PH7.0, and 4) basic amino acids with a net positive charge at neutral PH.

Nonpolar (Hydrophobic) Amino Acids

These have side chains that are only hydrogen and carbon, called alkyl groups. This includes the simplest amino acid, glycine, whose side chain consits of only a single hydrogen atom. Alanine is the next simplest amino acid which contains a methyl group, which is an alkyl group with one carbon and four hydrogens.

Others leucine, isoleucine, and valine, the branched chain amino acids, and also methionine, phenylalanine, and tryptophan. These hydrophobic aminos tend to cluster close together inside the protein away from the water of the body. The ability of these aminos to pack closely together within little space is an important force in the formation of the protein shapes and properties. 3,4,5

Polar Neutral (Uncharged) Amino Acids

Polar uncharged amino acids, excepting glycine, have side chains that can form hydrogen bonds with water, usually making them more soluble than nonpolar aminos. Examples are asparagine, cysteine, and glutamine. 3, 6

Acidic Amino Acids (Net Negative Charge at PH 7.0)

These amino acids, aspartic acid (aspartate) and glutamic acid (glutamate), have side chains containing additional carboxyl groups. These dicarboxylic amino acids are sufficiently acidic to have a net negative charge at neutral PH. These have important roles in proteins such as metal binding, nucleophiles in enzyme reactions, and electrostatic binding interactions. 3,6

Key Points to Remember

  • The main function of amino acids is for the synthesis of structural and functional proteins
  • Unlike carbohydrates and fats, there is no way for amino-acids to be stored by the body in large amounts so the amino acids your body needs must be constantly synthesized or derived from the diet
  • Those amino acids that can be synthesized by the body from simpler compounds ("de novo" synthesis) are called non-essential amino acids.
  • Those amino acids that cannot be synthesized by the body (either at all or in large enough amounts) are called essential amino acids.
  • There are some amino acids that can become essential during certain periods of time, when the body has a greater need for them than is normally met by de novo synthesis.
References
1. Rolfes, Sharon Rady., Kathryn Pinna, and Eleanor Noss. Whitney. "Chp. 6: Protein - Amino Acids." Understanding Normal and Clinical Nutrition. Belmont, CA: Wadsworth/Cengage Learning, 2009. 181-203. Print.
2. Lehninger, Albert L., David L. Nelson, and Michael M. Cox. "Chp. 3: Amino Acids, Proteins, and Peptides." Lehninger Principles of Biochemistry. New York: W.H. Freeman, 2005. 75-96. Print.
3. Garrett, R., and Charles M. Grisham. "Chp. 4: Amino Acids." Biochemistry. Belmont, CA: Brooks/Cole, Cengage Learning, 2010. 76-100. Print.
4. Tymoczko, John L., Jeremy M. Berg, and Lubert Stryer. "Chp. 3 Amino Acids." Biochemistry: a Short Course. New York: Freeman, 2010. 32-40. Print.
5. Alkyl Groups." Clackamas Community College Distance Learning. Web. 09 July 2011. <http://dl.clackamas.edu/ch106-01/alkyl1.htm>.
6. Groff, James L., and Sareen Annora Stepnick. Gropper. "Chp. 7: Protein." Advanced Nutrition and Human Metabolism. Belmont, CA: Wadsworth/Thomson Learning, 2000. 163-213. Print.


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