AMINO ACIDS Proteins Amino Acid Molecular Structures  Elmhurst College Amino Acid Structures Reactions  Chemistry Department Amino Acid Review Peptide Bonds  Virtual ChemBook

Structures of Amino Acids R = any number carbons in a hydrocarbon chain *CHIME plug-in required to view these images. Amino Acid Name (graphic) Chime*  A b r e v.  A b r e v.   Structure of R group (red) Comments Alanine Chime ala  A Neutral Non-polar  Arginine arg  R   Basic Polar  Asparagine asn  N    Neutral Polar Aspartic Acid asp  D Acidic Polar  Cysteine cys  C Neutral Slightly Polar  Glutamic Acid glu  E Acidic Polar  Glutamine   gln  Q Neutral Polar  Glycine  gly  G Neutral Non-polar  Histidine  his  H  Basic Polar  Isoleucine  ile  I  Neutral Non-polar  Leucine  leu  L  Neutral Non-polar  Lysine  lys  K  Basic Polar  Methionine  met  M  Neutral Non-polar  Phenyl- alanine  phe  F  Neutral Non-polar  Proline  pro  P  Neutral Non-polar  Serine  ser  S  Neutral Polar  Threonine  thr  T  Neutral Polar  Trypto- phan  trp  W    Neutral Slightly polar  Tyrosine  tyr  Y  Neutral Polar  Valine  Val  V  Neutral Non-polar	Characteristics and Properties of Amino Acids Introduction: Each amino acid has at least one amine and one acid functional group as the name implies. The different properties result from variations in the structures of different R groups. The R group is often referred to as the amino acid side chain. Amino acids have special common names, however, a three letter abbreviation for the name is used most of the time. A second abbreviation , single letter, is used in long protein structures.Consult the table on the left for structure, names, and abbreviations of 20 amino acids. There are basically four different classes of amino acids determined by different side chains: (1) non-polar and neutral, (2) polar and neutral, (3) acidic and polar, (4) basic and polar. Principles of Polarity: The greater the electronegativity difference between atoms in a bond, the more polar the bond. Partial negative charges are found on the most electronegative atoms, the others are partially positive. Review the polarity of functional groups. Non-Polar Side Chains: Side chains which have pure hydrocarbon alkyl groups (alkane branches) or aromatic (benzene rings) are non-polar. Examples include valine, alanine, leucine, isoleucine, phenylalanine. The number of alkyl groups also influences the polarity. The more alkyl groups present, the more non-polar the amino acid will be. This effect makes valine more non-polar than alanine; leucine is more non-polar than valine. Polar Side Chains: Side chains which have various functional groups such as acids, amides, alcohols, and amines will impart a more polar character to the amino acid. The ranking of polarity will depend on the relative ranking of polarity for various functional groups as determined in functional groups. In addition, the number of carbon-hydrogens in the alkane or aromatic portion of the side chain should be considered along with the functional group. Example: Aspartic acid is more polar than serine because an acid functional group is more polar than an alcohol group. Example: Serine is more polar than threonine since threonine has one more methyl group than serine. The methyl group gives a little more non-polar character to threonine. Example: Serine is more polar than tyrosine, since tyrosine has the hydrocarbon benzene ring. Comments on the Electrostatic Potential graphics available in Chime: Review: Organic Functional Group Polarity and Electrostatic Potential The molecular electrostatic potential is the potential energy of a proton at a particular location near a molecule. Negative electrostatic potential corresponds to: partial negative charges (colored in shades of red). Positive electrostatic potential corresponds to: partial positive charges (colored in shades of blue). As you view the graphics, the idea is to develop the concept of polarity in a visual manner. The more areas of red and blue that you see, the more polar is the compound and the functional group in the compound. Look at the amide, and acid groups as being particularly polar in asp, glu, asn, and gln. The more areas of gray and lighter shades of red and blue, the more non-polar properties are being depicted. Look at the amino acids which have purely hydrocarbon branches such as leu, ile, val, phe.
	Acid - Base Properties of Amino Acids: Acidic Side Chains: If the side chain contains an acid functional group, the whole amino acid produces an acidic solution. Normally, an amino acid produces a nearly neutral solution since the acid group and the basic amine group on the root amino acid neutralize each other in the zwitterion. If the amino acid structure contains two acid groups and one amine group, there is a net acid producing effect. The two acidic amino acids are aspartic and glutamic. Basic Side Chains: If the side chain contains an amine functional group, the amino acid produces a basic solution because the extra amine group is not neutralized by the acid group. Amino acids which have basic side chains include: lysine, arginine, and histidine. Amino acids with an amide on the side chain do not produce basic solutions i.e. asparagine and glutamine. Neutral Side Chains: Since an amino acid has both an amine and acid group which have been neutralized in the zwitterion, the amino acid is neutral unless there is an extra acid or base on the side chain. If neither is present then then the whole amino acid is neutral. Amino acids with an amide on the side chain do not produce basic solutions i.e. asparagine and glutamine. You need to look at the functional groups carefully because an amide starts out looking like an amine, but has the carbon double bond oxygen which changes the property. Amides are not basic. Even though tryptophan has an amine group as part of a five member ring, the electron withdrawing effects of the two ring systems do not allow nitrogen to act as a base by attracting hydrogen ions.