Amino acid

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

Amino acids are linked together to form proteins.

Of the 20-odd amino acids, there are 8 (or 9, due to the expert factor) that the body cannot synthesize for itself. They are the "essential" amino acids:
• histidine
• isoleucine
• leucine
• lysine
• methionine
• phenylalanine
• threonine
• tryptophan
• valine
The rest of the amino acids can be synthesized by the body from the essential amino acids; they include:
• cysteine
• tyrosine
• alanine
• arginine
• asparagine & aspartic acid
• glutamine & glutamic acid
• glycine
• proline
• serine
Sometimes amino acids are referred to with an L- in front of the name, as in L-tryptophan. bonnet explains why, below.

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

    R     R
    |     |
H-N-C-C-N-C-C-OH
  | | ||| | ||
  H H O H H O

    COOH
    |
H2N-C-H
    |
    R

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

                          NH2
                          |
Asparagine (Asn, N): -CH2-C=O

Cysteine (Cys, C): -CH2-SH

Glycine (Gly, G): -H  

                              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

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+