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THE PURINE-PYRIMIDINE CLASSIFICATION SCHEME
REVEALS NEW PATTERNS IN THE GENETIC CODE
Swetlana Nikolajewa and Thomas Wilhelm Institute
of Molecular Biotechnology Jena, Germany,
http//www.imb-jena.de/tsb
We present a new classification scheme of
the genetic code, based on a binary
representation of purines (A, G 1) and
pyrimidines (U, C 0). On the basis of this
logical organization we detect codon regularities
(strong, mixed and weak codons) and patterns of
amino acid properties and show symmetry
characteristics of the genetic code. We present
the codon - reverse codon pattern and use it to
remove the only ambiguity which had remained in
our recently proposed new classification scheme
of the genetic code. The purine-pyrimidine scheme
has now found its final form. We show that
the codon - reverse codon pattern is correlated
to aspects of the tRNA anticodon distribution in
all organisms. It is well known that there is no
tRNA with an anticodon for any of the STOP
codons we found that there is also no tRNA
containing reverse STOP anticodons.
The classification scheme of the genetic
code is based on a binary representation
of purines  (G,A)        -   1, pyrimidines
(C,U)  -   0. The eight rows (23 8) and four
columns are sufficient to place the 20 amino
acids, as well as the termination codons.
The four combinations of the first column (CC,
GC, CG, and GG) always imply 6 hydrogen bonds
in complementary base-paring with the
corresponding anticodon of the tRNA. Accordingly,
they are called strong codons.
The first two bases guarantee 5 H-bonds mixed
codons.
Weak codons have just 4 H-bonds .
Each row contains exactly 4 different amino acids
(including the stop codon).Exceptions in the
standard code are the second row with two
leucines and the fourth row with the AU start
codon.
The common table of the standard genetic code
Interestingly, in 5 different mitochondrial codes
(including yeast) AU(A/G) always encodes for Met
and UG(A/G) encodes Trp. Thus, 32 positions code
for 32 entries and each row contains exactly
four different amino acids. In this spirit the
mitochondrial code is the most regular one.
The codon-anticodon symmetry the red horizontal
line marks the symmetry axis. For instance, codon
CCC (Pro, first column, first row) has the
anticodon GGG (Gly, first column, last row).
The point symmetry corresponds to Halitskys
family nonfamily symmetry operation (E-M
bifurcation, Halitsky 2003). For instance, the
family codon GUA (Val) is mapped into the
nonfamily codon UGC (Cys). Thus, this point
symmetry is behind the family nonfamily
symmetry in our scheme (shaded vs. unshaded
regions).
In 8 different mitochondrial codes UG(A/G)
encodes Trp.
The arrows represent codon - reverse codons
pairs.
Codon - Reverse Codon Pattern
The arrows in the above table indicate codon -
reverse codons pairs the reverse codon of a
codon XYZ is defined as ZYX, where X, Y, Z can be
any base. For instance, the reverse codon of GGA
(Gly) is AGG (Arg). There exist 15 different
amino acids in the rows 000, 101, 010 and 111
where the codon is reverse to itself, e.g. Lys
(AAA), Tyr (UAU).

• The table can be divided into four blocks (codon
  - reverse codon groups) of the same size, for
  instance the upper left block with Pro (P), Ser
  (S), Ala (A) and Thr (T). Each block shows the
  same arrow pattern. All strongly evolutionary
  conserved groups of amino acids (Thompson et al.,
  1994) are subsets of exactly one codon - reverse
  codon group, e.g. the MILV amino acids belong to
  the upper right block in the table. The other
  conserved strong groups belonging to one block
  are STA, NEQK, NHQK, NDEQ, QHRK, MILF, HY. The
  only exception is FYW.
• 2. We studied all known tRNA genes of 104
  different organisms (Sprinzl et al., 1999). It is
  known that the STOP codons do not have any tRNA.
  We found that there are also no tRNA genes
  containing anticodons reverse to the STOP
  anticodons (ACT, ATC and ATT in Table 2). The
  only exception is H. sapiens, possessing one
  tRNAAsn gene with the anticodon ATT, but humans
  also have three different possible suppressor
  tRNA genes (Lowe and Eddy, 1997).

Table 2. The amino acid codon- reverse codon
pairs and the number of tRNA genes for the
corresponding anticodons.
3. There are some anticodons, where the reverse
anticodon has no tRNA, e.g. all 104 studied
organisms have at least one tRNA for Tyr with
anticodon GTA (some organisms, for instance
H.sapiens, have different tRNAs with the same
anticodon, altogether there are 189 different
tRNAs with the anticodon GTA in the 104 species),
but no organism has a tRNA for His with anticodon
ATG. Table 2 lists different codon - reverse
codon pairs. In the whole superkingdom bacteria
the number of tRNA genes for the reverse part of
table 2 is always zero, the few exceptions are
only in eukaryotes and archaea. Another unique
property of all bacteria is that there is no tRNA
with anticodons for the self reverse codons UUU
(Phe), UCU (Ser), UGU (Cys) and UAU (Tyr).
Generally, table 2 shows that anticodons with an
A at the third position are strongly preferred,
whereas A anticodons are significantly
suppressed.
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