Any of a class of 20 molecules that are combined to form proteins in living things. The sequence of amino acids in a protein and hence protein function are determined by the genetic code.


From the BioTech Dictionary at http://biotech.icmb.utexas.edu/. For further information see the BioTech homenode.

An amino acid is a carbon atom with a hydrogen atom, an organic acid {COOH}, an amino group {NH2}, and one other chemical group attached. The other chemical group is what gives each amino acid its specific properties.

Amino acids are linked together to form proteins.

The "building blocks" of muscles, nerves, and organ meat. Since the science of nutrition seems to still be in its infancy, different experts identify between 20 and 29 amino acids. Muscleheads, er I mean weightlifters, often consume amino acid supplements. My experience leads me to consider them as fun and effective as vitamins.
These are the 1 and 3 letter codes for the 20 amino acids commonly found in proteins.

A Ala Alanine
C Cys Cysteine
D Asp Aspartic acid
E Glu Glutamic acid
F Phe Phenylalanine
G Gly Glycine
H His Histidine
I Ile Isoleucine
K Lys Lysine
L Leu Leucine
M Met Methionine
N Asn Asparagine
P Pro Proline
Q Gln Glutamine
R Arg Arginine
S Ser Serine
T Thr Threonine
V Val Valine
W Trp Tryptophan
Y Tyr Tyrosine
The L is for Levo, meaning that the substance rotates the plane of polarized light to the left. If there is an isomer, the opposite (mirror image) would be the D (for Dextro) form.

When chemists whip up a batch of an amino acid, they may well end up with roughly half of each orientation, whereas all known forms of life on this planet can only (efficiently) make or use the L orientation.

It is one of the mysteries of science why this L preference occurred back in the goo stages of evolution.

Amino Acids - the building blocks of Protein

  • All have the same fundamental structure
    • Central Carbon Atom bonded to an amino group (-NH2) to a carboxyl group (-COOH) and to a hydrogen atom
    • In every amino acid there is also another atom or group of atoms designated by (-R)
    • A large variety is possible, but only twenty different kinds are used to build proteins.
    • The only difference in proteins is their (-R) group.
  • Example of condensation: Amino "head" of one amino acid can be linked to the carboxyl tail of another by removal of a molecule of water (Peptide bond).
    • forms dipeptide or polypeptide
    • sequence of amino acids in polypeptide chain determines the characters of the protein molecule.
    R            R
    |            |
H-N-C-C-OH   H-N-C-C-OH
  | | ||       | | ||
  H H O        H H O
H2O is extracted from the molecules in the middle and a single bond is formed. A peptide bond is a covalent bond formed by condensation.



    R     R
    |     |
H-N-C-C-N-C-C-OH
  | | ||| | ||
  H H O H H O
I wish there were a better way to do this, the Hydrogen is single-bonded to the nitrogen and the Oxygen shares a double bond with the Carbon.
There are 23 L-amino acids that form the basis for proteins in all the known life on this planet. (The L- refers to the organization of the subgroups around the chiral carbon, or alpha carbon. D-amino acids be structural mirror images of L-amino acids.) All amino acids have the same "backbone", or basic structure:
    COOH
    |
H2N-C-H
    |
    R

where "R" represents the defining subgroup.

There are three "types" of amino acids, as defined by the polarity of their subgroups.
R groups only shown, except Proline. In parentheses are three-letter and one-letter abbreviations
The nonpolar (uncharged, hydrophobic) amino acids are:


Alanine (Ala, A):  -CH3
                       CH3
                       |
Isoleucine (Ile, I):  -CH-CH2-CH3

                        CH3
                        |
Leucine (Leu, L):  -CH2-CH-CH3

Methionine (Met, M):  -CH2-CH2-S-CH3

                               C=C
                              /   \
Phenylalanine (Phe, F): -CH2-C     C
                              \\ //
                               C-C

Proline (Pro, P):       COOH
                        |
                     HN-C-H
                      / |
                   H2C   CH2
                     \  /
                      CH2

Tryptophan (Trp, W):  -CH2-C=CH
                           | \
                           |  NH
                           | /
                           C-C
                          // \\
                         C     C
                          \   /
                           C=C

                  CH3
                  |
Valine (Val, V): -CH-CH3

The polar but uncharged amino acids are:
                          NH2
                          |
Asparagine (Asn, N): -CH2-C=O

Cysteine (Cys, C): -CH2-SH

Glycine (Gly, G): -H  
Note: Glycine is not chiral, because there are two identical subgroups (hydrogen).

                              NH2
                              |
Glutamine (Gln, Q):  -CH2-CH2-C=O

Serine (Ser, S):  -CH2-OH

                      OH
                      |
Threonine (Thr, T):  -CH-CH3


                           C=C
                          /   \
Tyrosine (Tyr, Y):  -CH2-C     C-OH
                          \\ //
                           C-C
The charged amino acids are:

Aspartate (Asp, D):  -CH2-COO-

                                    NH2
                                    |
Arginine (Arg, R):  -CH2-CH2-CH2-NH-C=NH2+

Histidine (His, H): -CH2-C-NH
                        //  \
                       HC    CH
                        \  //
                         NH+

Glutamate (Glu, E):  -CH2-CH2-COO-

Lysine (Lys, K):  -CH2-CH2-CH2-CH2-NH3+

There are other amino acids, such as ornithine, histamine, and thyroxine, which are modified amino acids found only in certain proteins or that occur as precursors during biosynthesis.
Structures redrawn from Garrett and Grisham, Biochemistry, 2nd edition
Amino acids, the building blocks of proteins, are one of the most interesting biological molecules.

The Strecker Method
The Strecker synthesis is a way to make amino acids from aldehydes, and the aldehyde used determines the amino acid which results.

Simply add to the aldehyde ammonia, and remove the water. To the resultant imine (the nitrogen of the ammonia supplants the oxygen of the aldehyde), add hydrogen cyanide. This will create an amino nitrile. To this add aqueous acid, heat, and water, and voila, an amino acid.

Organic Chemistry: Structure and Function by Vollhardt and Schore is the book my instructer taught us from, and it seemed to do a fine job of teaching this chemistry and the rest of organic chemistry that one learns as an undergraduate. Amino acids are the building blocks of proteins. The following is one of several ways to synthesize amino acids. Its advantage over some other ways is the wide variety of amino acids which can be synthesized in this fashion.

The first step is to take potassium 1,2-benzene-dicarboxylic imide and add to it diethyl 2-bromo-propanedioate. The result is that the nitrogen of the prior reagent, which has a full negative charge, attacks the carbon which the bromine is attached to on the second reagent, kicking off said bromine.

At this point, one can replace the hydrogen on this carbon with a different side chain (this is where the variety I mentioned earlier is possible). Simply add sodium ethoxide and ethanol to deprotonate the carbon, and add your side chain attached to a halogen (chlorine, bromine, &c.).

Finally, heat it up in the presence of aqueous acid to clear out the protecting group (what the 1,2-benzene-dicarboxylic imide turned into).

The Gabriel Synthesis
The advantage of the Gabriel synthesis over some other ways is the wide variety of amino acids which can be synthesized in this fashion. The first step is to take potassium 1,2-benzene-dicarboxylic imide and add to it diethyl 2-bromo-propanedioate. The result is that the nitrogen of the prior reagent, which has a full negative charge, attacks the carbon which the bromine is attached to on the second reagent, kicking off said bromine.

At this point, one can replace the hydrogen on this carbon with a different side chain (this is where the variety I mentioned earlier is possible). Simply add sodium ethoxide and ethanol to deprotonate the carbon, and add your side chain attached to a halogen (chlorine, bromine, &c.).

Finally, heat it up in the presence of aqueous acid to clear out the protecting group (what the 1,2-benzene-dicarboxylic imide turned into).

An excellent explanation of thess and other amino acid syntheses can be found in Organic Chemistry: Structure and Function by Vollhardt and Schore.

Amino acid, as a term, means two things, with one use being a very small subset of the first. Chemically, as described above, an amino acid is a substance that has an amino group and a carboxyl group. Technically speaking, the term could probably be used in an even broader sense, I imagine that a molecule with a sulfuric acid group could also be called an "amino acid", but that would probably confuse people. But even the narrower definition of an amino group and a carboxyl group is much more broad than the usual usage of the term "amino acid", which refers to the 20 amino acids that are used to make up proteins. These 20 are distinguished by their "R-Group", an group of carbon chains or rings that attaches to the backbone of the amino acid.

There are theoretically an infinite amount of amino acids, since molecules could be made arbitrarily larger and still have those definitive functional groups on them. But even if we confine ourselves to amino acids the sizes of the ones that make up proteins, there are many different varieties of amino acids that could be used. There are many different organic molecules, and many different substitutions that can be made for them. For example, Phenylalanine has a Benzene Ring as its R-Group, but there is no intrinsic reason it couldn't include a Pyridine Ring instead. Or, for that matter, two linked Pyridine Rings. This is only one possible change, but by including other changes within it, for example adding methyl or hydroxy groups to various position on the different ring substitutes, the different combinations quickly become factorial. It is not that hard of a concept to understand, since it is very analogous to lego blocks: even with only a small amount of pieces that connect in seemingly small amount of ways, you can quickly reach millions of possible combinations.

So out of the millions of possible amino acids that could be used, why does life on earth only (normally) use 20? If, as Steven Jay Gould said in Wonderful Life, we could "rewind the tape" and let evolution proceed with a few different random occurrences, would we be living in a world where there was 32 amino acids, and three of them had Phosphorous atoms? Very possibly so. Which isn't to say that the current crop of amino acids is either inefficient or totally random, just that it is only one of many possible combinations that could be used. The basic reason that amino acids have different R-Groups is that the shape and electric charge on each one is different, which means that the amino acid, when incorporated into a protein, binds differently to different molecules, based on its shape and electric charge. The electric charge has to do with the varying electron affinities of Oxygen, Sulfur and Nitrogen atoms. In other words, even though amino acids could incorporate Bromine and Phosphorous, they don't need to. The twenty amino acids that we have work just fine for a great many functions.

To use an analogy, if were to rewind to the beginning of human written language, and reevolve the alphabet, we would probably still end up with some letters the same, such as the I and the O. Just like any set of amino acids would probably use alanine and glycine. However, we could very well have a Q that pointed the other way, with a dot in the middle, just like we could have a Tyrosine with an attached methoxy group. The main thing would be to have a set of symbols that were differentiable and combinable enough to make more complicated patterns.

This is of course, speculation, and a question that might not be answered until we find out if there is other carbon based life out in the galaxy. To return to a more prosaic level, the only thing that has to be remembered that "amino acid" has a technical meaning in chemistry, and a technical meaning in biology, and that people usually use it to refer to its more limited, biological meaning.

Amino Acid mnenumonic devices for the jaded biochemist (as arranged in Leninger's Biochemistry)

 

Amino Acids

 

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine

Green alien professors vampirize lonely innocent med-students.

Great, another pointless variety of lazy intellectualism: memorization.

God Ass Punched the Villianous Lecher, Inducing Mormonism

Gleefully, Al Pulverized the Victorious Lord, that Irreverant Minx.

 

Serine, Threonine, Cysteine, Asparagine, Glutamine

Shit, This Class Ain't Great

Surrender, Thou Cursed Asymmetrical Gimp!

Shriveled Tina Cornered the Angry Gremlin.

Sordid Tales of Canaries Attacking Gerbils.

Seething Terribly, Coco Ate Glue

 

Phenylalanine, Tyrosine, Tryptophan

Pointless, tiresome tasks

Please take two.

Peckish? Try Toad!

Perky Teens Triumph.

 

Lysine, Histidine, Arginine

Lick Herbert's Almonds

Like Hell, Asshat.

Lyse His Ass!

Lurk Hidden (in) Alleys

Life Heralds Annoyance

 

Aspartate, Glutamate

Agonizing Games

Artistic Guilt

Aack! Guck!

Ambiguous Girlfriend

Annoying Girlfriend

Ahoy, Giblets!

 

Mix, match, and alter:

God Ass-Punched the Villianous Lecher, Inducing Mormonism.

"Surrender, Thou Cursed Asymmetrical Gimp!," Proposed The Tyrant.

"Like Hell, Asshat!," Answered Greg.

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