Appeal No. 2000-0137 Page 7
Application No.08/646,558
a single page from the cited text. The submitted page states that several amino
acids have aliphatic side chains:
The simplest one is glycine, which has just a hydrogen atom as its
side chain. . . . Alanine comes next, with a methyl group as its side
chain. Larger hydrocarbon side chains (three and four carbons
long) are found in valine, leucine, and isoleucine. These larger
aliphatic side chains are hydrophobic—that is, they have an
aversion to water. . . .
Proline also has an aliphatic side chain. . . . Proline, often found in
the bends of folded protein chains, is not averse to being exposed
to water.
Three amino acids with aromatic side chains are part of the
fundamental repertoire (Figure 2-11). [The legend to Figure 2-11
states that “[p]henylalanine, tyrosine, and tryptophan have aromatic
side chains.”]
Stryer, page 18 (emphases in original). Thus, as can be seen, Stryer does not
support the proposition for which it is cited by Appellants. Stryer states only that
Val, Leu, and Ile are hydrophobic, and either states or implies that Gly, Ala, and
Pro are not hydrophobic. The excerpt from Stryer provides no guidance on
whether or not the amino acids with aromatic side chains are hydrophobic, and
does not discuss any of the other eleven naturally occurring amino acids. In
particular, Stryer does not support Appellants’ statement that Phe, Trp, Tyr, Cys,
and Met are recognized in the art as being hydrophobic.
According to one art-accepted classification system, the hydrophobic
(non-polar) amino acids are Ala, Val, Leu, Ile, Pro, Met, Phe, and Trp. See
Lehninger, page 101. Lehninger classifies Tyr as “[p]olar but uncharged.” Note
also that under Lehninger’s classification, Gly and Cys are considered polar but
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