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
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Amino
Acid
Name

 A
b
r
e
v.

 A
b
r
e
v.

 

Structure
of R group (red)

Comments

Alanine

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.

QUES. List all amino acids with non-polar side chains.

Rank the following according to increasing non-polarity i.e. 1 = least non-polar, 4 = most non-polar.
leu; phe; val; ala

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.

QUES. List all amino acids by abbreviation which are considered
somewhat polar.

Rank the following amino acids by increasing polarity. i.e.
1 = more non-polar.
ser ; glu ; asp ; lys ; ala ; gln
Which amino acid is most insoluble in water: isoleucine or
alanine ?
 
Which amino acid is most soluble in water: lys or ser?  

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.