http://www.ck12.org Chapter 26. Biochemistry
and other information for each of these amino acids are presented in theTable26.3.
TABLE26.3:
Amino Acid 3-Letter 1-Letter Side Chain Polarity Side Chain Charge
(pH 7.4)
Alanine Ala A nonpolar neutral
Arginine Arg R polar positive
Asparagine Asn N polar neutral
Aspartic acid Asp D polar negative
Cysteine Cys C nonpolar neutral
Glutamic acid Glu E polar negative
Glutamine Gln Q polar neutral
Glycine Gly G nonpolar neutral
Histidine His H polar positive (10%) neu-
tral (90%)
Isoleucine Ile I nonpolar neutral
Leucine Leu L nonpolar neutral
Lysine Lys K polar positive
Methionine Met M nonpolar neutral
Phenylalanine Phe F nonpolar neutral
Proline Pro P nonpolar neutral
Serine Ser S polar neutral
Threonine Thr T polar neutral
Tryptophan Trp W nonpolar neutral
Tyrosine Tyr Y polar neutral
Valine Val V nonpolar neutralProtein Structure
The structural features of complete proteins can be broken down into four levels, referred to as primary, secondary,
tertiary, and quaternary structures. These levels are illustrated in theFigure26.5.
Theprimary structureof a protein is simply the sequence of amino acids from which it is constructed. By
convention, this sequence is written starting with the N-terminal amino acid, which has a free –NH 2 group, and
ending with the C-terminal amino acid, which has a free carboxylic acid. Because protein sequences can be very
long, the abbreviations listed in theTable26.3 are commonly used. For example, the sequence lysine-histidine-
threonine-valine can be written as either Lys-His-Thr-Val or KHTV.
Thesecondary structureof a protein refers to local coiling or folding. This aspect of the structure applies only
to a section of the protein, not the entire structure. The two basic forms of secondary structure are thealpha helix
and thebeta sheet. Because they have to do with the ways that multiple amides pack together, one or both of these
substructures show up in most long protein strands. The appearance of alpha helices and beta sheets can be predicted
fairly well (by computers) from the primary sequence of amino acids.
Tertiary structurerefers to the overall three-dimensional shape of an entire protein chain. Because of the ways
that proteins can fold in on themselves, tertiary structure often involves interactions between amino acids that are
very far apart in the primary sequence. Ultimately, this is also dependent on the primary sequence of the protein, but
because of these long-range interactions, predicting tertiary structures from sequences of amino acids is still very
difficult.