The 24 Possible Algebraic Definitions of a 6-Dimensional Binary Vector

Space in the Set of the 64 Triplets of the Standard Genetic Code

Marco V. Jos
a,*
, Eberto R. Morgado
b
, Tzipe Govezensky
a
,

Gabriel Garduo
Soto
a


a
Theoretical Biology Group, Instituto de Investigaciones Biomdicas, Universidad
Nacional Autnoma de Mxico, Mxico D.F. 04510, Mxico.
b
Facultad de Matemtica, Fsica y Computacin, Universidad Central Marta
Abreu de Las Villas, Santa Clara, Cuba.



Abstract. Herein, we analyze the 24 different ways of constructing a 6-dimensional binary vector
space of the 64 triplets of the Standard Genetic Code. We also analyze the transformations that
lead to any model into each of the remaining models. In all the cases the definition of a given
ordering begins with a matching of the set { } N C, U, A, G = of the 4 nucleotide RNA bases with the
set { } 00, 01,10,11
(4)
of the 4 binary duplets. Since the set N has the structure of a Galois Field
of 4 elements, the 6-dimensional GF
2
hypercube becomes a in a 3-
dimensional vector space. We partition the set N into 3 classes: strong-weak, amino-keto and
pyrimidine-purine. For each of these classifications there are 2 classes of 3-dimensional cubes over
that preserve the correspondence of the algebraic complementarity. A new type of distance
( ) defined in the cube as a 3-dimensional vector space over the finite field GF is
introduced. The cube has been called the Hotel of Triplets, or Genetic Hotel, because of its
resemblance with a three-floor building. As the permutations that convert elements of a family into
elements of the other one are not isometries with respect to the distance D in the 3-dimensional
cube, the corresponding transformation may change the shape and the size of a condominium
of the Hotel. The prism RNY in the cube is geometrically highlighted and compared in the
Genetic Hotel for the different orderings.
NNN GF(4)
GF
D
N
(4)
NNN (4)
NNN
NNN


Keywords: strong-weak, amino-keto, and purine-pyrimidine base classification; algebraic and
geometrical structures of the genetic code; genetic hotels; Klein 4-group




1 Introduction

In earlier works [1-11], different ways in which a structure of a binary 6-dimensional
vector space in the set of the 64 triplets of the Standard Genetic Code have been
defined. In all the cases the definition begins with a matching of the set
{ } N C, U, A, G = of the four nucleotide RNA bases with the set { } 00, 01,10,11 of the
four binary duplets. Potentially this matching can be performed in 4! =24 different
ways. Herein, we analyze the 24 different ways of carrying out that construction,
1
together with the transformations that lead to any model into each of the remaining
ones.
The bitwise module two addition, or XOR operation, in the set of duplets, induces
in the set a structure of abelian group, the so called Klein 4 group.
Consequently, the addition in induces an addition in the set of
the 64 triplets, which, together with the obvious definition of the product of the
scalars 0 and 1 by all the triplets, conforms a structure of a 6-dimensional vector
spaces over the binary field
N
N N N N NNN =
{ }
2
0,1 = , isomorphic to ( , also called the 6-
dimensional hypercube. It also has a structure of a Boolean lattice or Boolean
algebra.
)
6
2

The so-called Hamming distance, provides to the hypercube ( )

6
2

a structure of
metric space, and it induces a distance in the
2
vector space . The
Hamming distance induces in an
NNN
( )
6
2
valued inner product, being the field
of real numbers, and hence it carries over the properties of orthogonality or
perpendicularity.

1.1 The binary partitions of the set N

It is well known that a set of 4 elements has exactly 3 different partitions as union
of 2 subsets, each of 2 elements. In the case of our set { } N C, U, A, G = the only 3
partitions are: { } { }
1
: N C, G U, A = , { } { }
2
: N C, A U, G = and,
{ } { }
3
: N C, U A, G =
{
. For every selected ordering we will use the
correspondence of a partition of with the partition of the set N
}
2
2
( ) 00, 01,10,11 =
2
2
( )
, as determined by algebraic complementarity. We understand
by algebraic complementarity, the one that exists between 2 duplets of zeros and
ones, when each is the bitwise Boolean negation of the other one. Then the
partition of by algebraic complementarity is { } { } 00,11 01,10 . The 3 partitions
are related with chemical properties of the nucleotides. The partition
1

corresponds to the biological classification of nucleotide bases in strong { } S: C, G
(those which form 3 hydrogen bonds between them), and weak { } W: U,
2
A (those
which form 2 hydrogen bonds between them). In the case of , algebraic
complementarity is consistent with the chemical classification of nucleotides into:
amino nucleotides: { } M: C, A and keto nucleotides: { } K: U, G . Finaly, if
3
is
used, algebraic complementarity is assigned to nucleotide bases of the same
chemical kind: pyrimidines: { } Y: C, U , and purines: { } R : A, G . A selected list of
the different matchings that have been used according to this chemical
categorization of the bases is provided in Table I:

Table I

2






Orderings

00 01 10 11 References
U C A G Swanson [10]
A G U C Jimnez-Montao et al. [2]; Klump [6]
C U G A Karasev and Soronkin [5]
U C G A Stambuk [11]
C A U G He et al [1]; Jos et al. [3]
C U A G Snchez et al. [7,8]; Jos et al. [4]
G A U C Snchez et al. [7,8]
G U A C Snchez et al. [9]







1.2 The question about isometry

When we consider the 24 ways of selecting the matching of the set of nucleotides
with the set of duplets of zeros and ones two natural questions arise: Do these
different vector spaces lead to the same results? Are they not only pairwise
isomorphic but also isometric?
All the possible hypercubes are isomorphic and isometric with the hypercube
, and both, isomorphism and isometry, are transitive relations. Hence we can
assert that all of the obtained hypercubes are not only pairwise isomorphic, but
also pairwise isometric. The real questions are the following: Do the 24
permutations of a primary order
( )
6
2

( ) C, U, A, G induce isometric transformations of the

original hypercube, with respect to its Hamming distance? Do they induce
isomorphic affine transformation of that hypercube?
The question about isometry is related to the type of distance or metric we are
dealing with. In the 6-dimensional structure of the Z
2
-vector space the Hamming
distance is used. The Hamming distance between two triplets is induced by the
Hamming distance between their associated sextuples of zeros and ones.

1.3 The Hamming distance

The Hamming distance between 2 sextuples is defined as the number of bits that
have different values. Similarly, the Hamming distance between 2 triplets is
induced by the Hamming distance between their associated sextuples. The
hypercube can be envisaged as a graph, where the vertexes are the
sextuples and the edges are the binary subsets,
( )
6
2

{ }
1 2 3 6 1 2 3 4 5 6
, , , ) , , , , , (x x x , (y y y y y y )
1 5 6 1 2 3 4 5 6
H((x , x , x , x ), (y , y , y , y , y , y ))
1 2 3 4 6
(y , y , y , y )
4 5
, , x x x
2 3 4
, x , x
5
, y , y
, such that the Hamming distance,
, between 2 sextuples that differ in only
one bit is equal to 1. In this case, we say that both sextuples are adjacent. From
this, it follows that every sextuple has exactly 6 other sextuples that are adjacent to
it. The Hamming distance between the sextuples and
can be expressed, arithmetically, as the integer
1 2 3 4 5 6
(x , x , x , x , x , x )
3
1 1 2 2 3 3 4 4 5 5 6 6
x y x y x y x y x y x y + + + + +
)
6
2

, where the addition and

subtraction are the usual operations in the set of integers. The Hamming
distance also induces in ( an
Z

1 2 3 4 5 6
(y , y , y , y , y , y ) x
valued inner product, being the field of
real numbers, and together with it, the properties of orthogonality or
perpendicularity. This inner product of the sextuples and
is defined as the integer

1
, x
3 3
y
2 3 4 5 6
(x , x , x , x , x )
2 4 4 5 5
x x y x y
1 1
y
2 6 6
x y x y + + + + + ,
where the operations are the ordinary product and addition in the set of integers.
1
N
C 0
2
)
2
(
0 U 01 A 10 G 11
) (C, U, A
, ) +
, G
( )
2
2 2 2
=
2 2 2
=

2 Different families of hypercubes that are determined by the initial matching
between nucleotides and duplets

2.1 The hypercubes that are obtained by matchings that are consistent with
the correspondence of the partition of with the partition of by
algebraic complementarity

Let us suppose, that our initial matching is , , , . It
means that we select the initial ordering as . Then, the Cayley Table of
the abelian group (N turns out to be:

Table II

+ C U A G
C C U A G
U U C G A
A A G C U
G G A U C


As we said above, Table II corresponds to the so called Klein 4-group, which is a
four abelian group in which every element, different of the neutral, has order 2. It
means that every element is its own inverse. All the Klein 4-groups are pairwise
isomporphic. Actually, the Klein 4-group is the smallest finite group that is not
cyclic, but it is the direct product of 2 binary cyclic groups. Then, the direct product
with the module 2 addition, is its canonical group theoretical
representation. The Klein 4-group has the property that every binary set that
contains the null element C, defines a binary subgroup. It means that the 2 classes
of any of the three binary partitions are the member classes of the factor group
over the binary subgroup that contains C. The Klein 4-group can be visualized as a
2-dimensional binary vector space, isomorphic to ( )
2
. It also has the
property that any permutation of its 3 non-null elements induces an automorphism,
that is, a bijective endomorphism. It is equivalent to the fact that any ordered pair of
non-null elements is a basis of the vector space, 2 of them being the only
orthonormal basis with respect to the Hamming inner product.
4

2.2 The role of translations as representative of mutations

The concept of translation in an additive group. In any additive group (G, ) + a
translation is a transformation of the form: being a fixed element
of . Obviously, the translation T , associated to the neutral element is the identity
function of . Every translation is a bijective function and the set , of all
the translations in , is closed under the composition. In fact, the ordered pair
, where denotes the composition of functions, is an abelian subgroup of
the symmetric group (S , of all the bijective transformations of the set G . The
correspondence is an injective homomorphism from
X
T :Y Y X, + X
G
(G
0
G
I G T(G)
G
X
(T ), )
(G), )
X
T (G, ) + in its symmetric
group , being the image of this homomorphism the group of
translations. Then, every abelian group is isomorphic to its group of translations.
(S(G), ) (T(G), )
The biological concept of mutation. In any chain of RNA nucleotides a mutation
is the substitution of any nucleotide bases by another one, from the set . A
mutation where a nucleotide is changed to another of the same chemical type, that
is, pyrimidine to pyrimidine, or purine to purine, is called a
N
transition. A mutation
where a nucleotide is changed to another of different chemical type, that is,
pyrimidine to purine, or purine to pyrimidine, is called a transversion. Moreover, we
have 2 different kinds of transversions: first, those that convert a nucleotide to
another of the same class, according to the partition
2
, the amino-keto
classification, and second, those that convert a nucleotide to another of the same
class, according to the partition
1
, the strongweak classification. Then, the latter
are transformations that convert nucleotides into their complementary.
The role of translations. The translations and T of the abelian group
may be taken as representatives of all the different kinds of mutations. The
translations , and
C U A
T , T , T ,
G
(N, ) +
1
,
N
I T =
C
,
U
T
G
,
associated to pyrimidines, represent transitions. The
first of them, the identity I , pointwise preserves the structure of the 3 partitions
2
and
3
of , while the second, T , preserves the members of the partition N
U
3
, of the pyrimidine-purine classification, and interchange the members of the
other 2 partitions
1
and
2
. The translations T and
A
A
T
G
T
,
associated to purines,
represent transversions. The first of them, , preserves the structure of the
partition
2
, of the aminoketo classification, and interchange the members of the
other 2, whereas the translation, , preserves the members of the partition
G
T
1
, of
the strong-weak classification, and interchange the members of the other 2
partitions
2
and
3
. The foregoing description is illustrated in the following
Diagram I:


Diagram I

5
C
U
T


U
A
T
T
G

A
T

A
U
T


G



The action of the three non-trivial translations are pointed out in Diagram I. Note
that one of them is a transition and the other 2 are transversions:
Horizontal: Transition T
U

(preserves the pyrimidine-purine classification)
Vertical: Transversion (preserves the amino-keto classification)
A
T
Diagonal : Transversion
G
T

(preserves the strong- week classification)

3 Embedding of the abelian group (N, ) + in the 2-dimensional vector
space

The abelian group can also be regarded as a bidimensional vector space
over the binary field
(N, ) +
{ }
2
=

0,1
12
= P
M
, where the only orthonormal basis, according to the
inner product, induced by the Hamming distance, are and . Then, the
only isometric linear transformations, or orthogonal transformation, are those with
matrices and . The matrix is obtained from the identity
matrix by the interchange of the first and the second rows. As it is well known,
these kind of matrices, called elementary permutation matrices, when multiplied to
the right by another matrix , perform on the same transformation, in these
cases permutations of the rows 1 and 2. If we identify the elements and
with the canonical unitary vectors e (
(U, A) (A, U)
2
1 0
I
0 1

=


0 1
1 0

1
12
P
, 0)
M
1
A 10 =
U 0 = , 1 = and
2
e (0,1) = in the Euclidean
coordinated plane the
2
=
2
vector space is embedded in the plane,
not as a subspace, but as a subset, of the plane. The 4 elements C, , and ,
correspond, respectively, to the vertexes , and (1 of a unit
square situated in the first quadrant of the plane. In the plane , the matrix
represents a reflexion, or axial symmetry, with respect to the line equation
N
), (1, 0)
A,
,1)
2
U G
12
P
y x
(0, 0), (0,1

= ,
the angle bisector of the first and the third quadrants. As it is well known, the
isometric transformation of any metric vector space are the compositions of its N
6
linear isometric transformation with all the translations. Then, in our present case,
the group of isometric transformation would have 2x4=8 elements. The 8
isometries are described in the following Table III:


Table III

Type of transformation Symbol Action over N Parity as permutation
of the set N
Linear and translation
2 C
I T =
(C, U, A, G) (C, U, A, G) Even
Translation
U
T

(C, U, A, G) (U, C, G, A) Even
Translation
A
T

(C, U, A, G) (A, G, C, U) Even
Translation T
G
(C, U, A, G) (G, A, U, C) Even
Linear
12
P

(C, U, A, G) (C, A, U, G) Odd
Composition
U 1
T P
2

(C, U, A, G) (U, G, C, A) Odd
Composition
A 1
T P
2

(C, U, A, G) (A, C, G, U) Odd
Composition
G 1
T P
2

(C, U, A, G) (G, U, A, C) ) Odd

Remark: Notice that the linear transformation is the same as the translation .
Hence, the linear transformation is the same as the composition . Then,
there are only 8 different hypercubes that are determined, respectively, by the
different orderings: CUAG, UCGA, AGCU, GAUC, CAUG, UGCA, ACGU, GUAC.
The first 4 are even permutations of the primary ordering CUAG, while the
remainders are odd permutations. It produces a partition of the set into 2 classes:
The class of those obtained by translations (even permutations), and the class
obtained by the linear transformation or the composition of with a
translation (odd permutations). It is straightforward to notice that every isometry of
the vector space , induces exactly an isometry of the 6-dimensional hypercube
. Then, the 8 selected permutations of the set
2
I
C
T
12
P
C 1
T P
12
P
2
12
P
N
( )
6
2
{ } N C, U = , A, G , induce
isometries of the metric space N N N of all the triplets, with respect to its
Hamming distance.

4 The hypercube as a 3-dimensional vector space over the Galois
Field of 4 elements.- The Genetic Hotel
2

GF(4)
NNN

Under the matching (C, U, A, G) (00, 01,10,11) if we identify every nucleotide with
the correspondig integer, in the decimal representation of the binary duplets, that
is, the numbers 0, 1, 2, and 3, the addition table of the group becomes
(Table IV):
(N, ) +

Table IV
7

+ 0 1 2 3
0 0 1 2 3
1 1 0 3 2
2 2 3 0 1
3 3 2 1 0


The set can be endowed with a structure of a field, by means of a suitable
definition of a product. In a forthcoming work [4], it has been made in such a way,
that the resulting table for multiplication is (Table V):
N

Table V


C U A G
C C C C C
U C U A G
A C A G U
G C G U A


And, under the numerical notation, Table V becomes (Table VI):

Table VI


0 1 2 3
0 0 0 0 0
1 0 1 2 3
2 0 2 3 1
3 0 3 1 2


The obtained field is an algebraic extension, of degree 2, of the binary field
{ }
2
0,1 = of 2 elements. It is up to isomorphisms, the so called Galois Field
of four elements. Since the set has the structure of the Galois Field , the
6-dimensional hypercube becomes a GF in a 3-dimensional vector
space.
GF(4)
4) N
NNN
GF(
2
(4)

4.1 Embedding of the cube in the 3-dimensional NNN space
3
8

The interpretation of the duplets 00, 01, 10 and 11 as the binary representation of
the integers 0, 1, 2 and 3, allows us to insert the set as a subset of the
Euclidean 3-dimensional space,
3
N NNN =

3
= , being the field of real
numbers. The eight triplets CCC, GCC, CGC, GGC, CCG, GCG, CGG, GGG,
correspond to the vertexes of a cube or regular hexahedron, with 3 of its edges
lying over the coordinated axis. This cube has edges of length 3 and it is the union
of 27 unitary cubes, which are copies of the unitary cube whose vertexes are:
CCC, CCU, CUC, CUU, UCC, UCU, UUC, UUU, and that we denote as . The
set is a 3-dimensional

YYY
YYY
2
Z
YYY
vector subspace of , if we see it as a 6-
dimensional vector space. We will call it the elementary subcube of the cube
. We recall that the cube is a subgroup of the additive group
NNN
2
Z
NNN (NNN, ) +
of the vector space , but it is not a N NNN N subspace, since it is not closed
under multiplication of the scalars A or G of the field by vectors of . The
cube has been called the Hotel of Triplets, or Genetic Hotel, because of its
resemblance with a three-floor building [4].
N YYY
NNN

4.2 Definition of a distance in the cube NNN

In the 3-dimensional vector space NNN a new type of distance has been
defined, which is consistent with the graph-theoretical concept of a distance
between vertexes. For 2 triplets (X and of we define the
distance between them as the nonnegative integer
GF(4)
1 2 3
X X )
1 2 3
(YY Y ) NNN
1 1
X Y +
2 2 3 3
X Y X Y +
Z
)
,
where the operations are the ordinary addition and subtraction in the set of
integers. The latter definition of distance in is similar to the one used for the
definition of the Hamming distance in a hypercube . This distance gives us
the minimal number of edges or unitary segments between the 2 triplets. Obviously
the maximal distance in is equal to 9.
NNN
2
(
n
Z
NNN

Remark: Note that our distances defined in the set are a restriction of a
distance defined in the Euclidean 3-dimensional
NNN
space . Although it is not
the usual Euclidean distance, it is nonetheless a distance, according to the general
definition of this concept. The cube can be envisaged as a graph, where the
vertexes are the triplets and the edges are the binary subsets
3

NNN
{ }
1 2 3 1 2 3
(X X X ), (YY Y ) ,
such that the distance, D is equal to 1. In this case, we say that
both triplets are adjacent. It is easy to prove that, they are adjacent if, and only if,
they differ in only one component and these different components are consecutive
under the selected order (C . Our defined distance between two vertexes,
in a graph theoretical approach, coincides with the minimal length of a path
between both vertexes.
1 2 3 3
((X X X ), ))
, U, A, G
1 2
(YY Y
)

4.3 The situation with respect to the distance defined in the cube as
a 3-dimensional vector space over the finite field of 4 elements
D NNN
GF(4)
9

In our geometric model all the edges are contained in horizontal lines, parallel to
the vectorial lines or CN , or in vertical lines, that are parallel to the vectorial
line
NCC C
CCN
,

We recall the fact that the insertion of the vector N space
into the space , does not mean that it is a vector subspace, since the
operations are different, as the scalars fields are also different. Now, we observe
that the odd permutation:
3
N NNN =

3

C C, U A, A U, G G , that is, the matching

, which induces a linear transformation of the matrix of
the vector space , then a group homomorphism of the additive group
, is not homomorphic for the product
(C, (C,
N
(N,
U, A, G
2

) +
) A, U, G)
12
P
of the Galois Field GF . In fact, it
transforms the neutral element U of in the element A, which is not the neutral.
Hence, it does not induce a linear transformation of the cube , if it is seen as
an vector space. We see, for example, that it transforms the vector
into the vector UCC, which is not equal to the vector
. On the other hand, the odd permutation CUA , that is
isometric with respect to the Hamming distance, is not an isometry with respect to
the distance . In fact, it converts the unitary vectors UCC, CUC and CCU into the
vectors ACC, CAC, and CCA, that have length 2.
(4
CA
)
UG
N
NNN
G
N
UCC)
ACC)
A ( CC =
A ( CC =
D
A
G
As a remarkable result, we have that the 4 even permutations of the ordered set
, induce isometries with respect to the distance , but the odd
permutations do not.
(C, U, A, G) D

5 Criteria for the selection of the ordering in the set of the four nucleotides

5.1 The two different classes of 3-dimensional cubes over the Galois Field
, that preserve the correspondence of the strong-weak classification
with the algebraic complementarity.
GF(4)

S far we have obtained two different families of 3-dimensional cubes:
1
: The 4 cubes obtained from the ordering CUAG, UCGA, AGCU and GAUC.
2
: The 4 cubes obtained from the ordering CAUG, UGCA, ACGU, and GUAC.

From the above results, we conclude that there are only 8 different ways of
defining a structure of a 6-dimensional hypercube, or 6-dimensional vector space
over the binary field , in such a way that biological complementarity of
nucleotides is consistent with the algebraic complementarity of the associated
duplets of zeros and ones. They also lead to the only 8 ways up to isomorphisms,
of defining a structure of vector space, being the set of DNA nucleotides,
endowed with the structure of the Galois Field of 4 elements. We can also
assert that the 4 permutations of the primary ordering CUAG, induced by additive
translations, that is, the orderings CUAG, UCGA, AGUC and GAUC, induce
isometries of the original 3-dimensional cube , which are also bijective affine
transformations. The other 4 permutations, induced by compositions of the
translations with the odd permutation CUA , neither induce isometric
2
N N
(4)
CA
GF
NNN
G UG
10
transformations with respect to the distance , nor affine transformations with
respect to vector space structure. Notwithstanding, the 8 permutations induce
isometric transformation of the binary 6-dimensional vector space , with
respect to its Hamming distance, and they are also affine transformations with
respect to the vector space structure. As the permutations that convert
elements of a family into elements of the other one are not isometries with respect
to the distance in the 3-dimensional
D
N
NNN
2

D N cube, the corresponding transformation
may change the shape and the size of a condominium of the Hotel. Thus, for
example, the set RNY that is a prism in the cube , with edges of length 3, 1,
1, is transformed, under the permutation (C,
NNN
, G) U, A (C, A, U, G) , into a bigger
prism of lengths 3, 2, 2 (see Figs. 1 and 2).
G 10,
} { M: C, A K =
M
NNN
1 0
1 1

A
N
21
A
) ( )
N
12
P
1 1
0 1



C, U, A,
D
G C, U,
2 1
A

Figures 1 and 2

5.2 Orderings where the amino-keto classification is consistent with
algebraic complementarity

Next, we will select the order of nucleotides in such a way that algebraically
complementary duplets correspond to nucleotides of the same class: the amino or
the keto class. First, we select the ordering CUGA, that is, the matching : C 00,
and A U 0 1 , that is consistent with the partition
{ }
2
: N : U, G
N
(amino-keto). If we examine the bijection that
transforms the initial ordering CUAG into the ordering CUGA, we see that it is, in
the vector space , the linear transformation with matrix
2

M
D
=
21

.
This
matrix is obtained from the identity matrix by the addition of the first row to the
second one, having the only non-null element that is off the main diagonal in the
place (2,1). As it is well known, in these kind of matrices the so-called addition
elementary matrices, when they are multiplied to the right by another matrix ,
perform on the same transformation.

Then, it fixes the vectors C and U, and
interchanges the vectors A and G. In the present case the linear transformation
represented by is not isometric with respect to the Hamming distance, since it
interchanges the vectors of module 1 and module 2, respectively. For the same
reason, we can say that it is not an isometry with respect to the distance ,
because it interchanges A of module 2 with G of module 3. It is easy to prove that
this transformation is not linear with respect to the structure of the vector space
of the set .
1, 1
As a conclusion, we see that the permutation ( G, A
=
is neither
isometric with respect to the original Hamming distance, induced by the ordering
CUAG, nor isometric with respect to the distance in the associated vector
space. The linear isometry, originally represented by the matrix , which
interchanges U and A, is now represented by the matrix , which
11
interchanges

U and G, and fixes C and A. Now, applying the new ordering CUGA
all the isometries of the vector space we obtain the following Table VII:
2
N
I T =
) A
U
T
) A
A
T
) A
G
T
) A
12
A
) A
U
T A
) A
A
T A
) A
G
T A
) A

Table VII


Type of transformation Symbol Action over N Parity as permutation
of the set N
Linear and translation

2 C
( ( ) C, U, G, C, U, G, A
Even
Translation
( ( ) C, U, G, U, C, A, G
Even
Translation
( ( ) C, U, G, A, G, U, C
Even
Translation
( ( ) C, U, G, G, A, C, U
Even
Linear
( ( ) C, U, G, C, G, U, A
Odd
Composition
12
( ( ) C, U, G, U, A, C, G
Odd
Composition
12
( ( ) C, U, G, A, U, G, C
Odd
Composition
12
( ( ) C, U, G, G, C, A, U
Odd

5.2.1 The 2 different classes of 3-dimensional cubes over the Galois Field
, that preserve the correspondence of the aminoketo classification
with algebraic complementarity
GF(4)

From Table VII we see that we have 2 other different families of 3-dimensional
cubes:
3
: The 4 cubes obtained from the orderings CUGA, UCAG, AGUC and GACU.
4
: The 4 cubes obtained from the orderings CGUA, UACG, AUGC, and GCAU.
Here we have again that, as the permutations that convert elements of a family into
elements of the other one are not isometries with respect to the distance D in the
3-dimensional cube, the corresponding transformation may change the shape
and the size of a figure. Thus, for example, the set RNY that is a prism in the cube
with edges of length 3, 1, 1, is converted in itself under the permutation
, and under the permutation
N
C, U
NNN
C, U, ( ) ( A, G , G, A ) ( ) C, U, G, A (C, G, A) U, , is
converted into the union of 2 cubes, one of sides with lengths 3 and the other with
sides of lengths 1 (see Figs. 3 and 4).

Figures 3 and 4

5.3 Orderings where the pyrimidine-purine classification is consistent with
algebraic complementarity

12
Now we will select the order of nucleotides in such a way that algebraically
complementary duplets correspond to nucleotides of the same class: the
pyrimidine ( or the purine classes ) Y ( ) R
,
. First, we select the ordering CAGU, that
is, the matching: C 00 , A 01 G 10, U 11, that is consistent with the
partition { } { }
3
: N Y: C, U R : A, G , =
U,
(pyrimidine-purine). If we examine the
bijection that transforms the initial ordering CUAG into the ordering CAGU, we see
that it is a linear transformation with matrix in the vector space
. The matrix
1 1
1 0


12
N
=
12
A P
2

N
12
12
P
( ) A, G
D

is

obtained from the identity matrix by permutation of its
columns: when it is multiplied to the left by another matrix M, it performs on the
same transformation. The matrix
M
12 12
A P

performs a cyclic permutation over the
vectors U, A and G. In the present case the linear transformation represented by
is not isometric with respect to the Hamming distance, since it converts A of
module 1 into G of module 2, and G, of module 2 into U of module 1. For the same
reason, we can say that it is not an isometry with respect to the distance ,
because it converts U of module 1 into A of module 2, A of module 2 into G of
module 3 and G, of module 3 into U of module 1. As a conclusion, we see that the
permutation is neither an isometry with respect to the
original Hamming distance, induced by the ordering CUAG, nor an isometry with
respect to the distance in the associated
12
A P
D
(C, A, G, U) C,
vector space. The linear isometry,
originally represented by the matrix , which interchanges U and A, is now
represented by the matrix
12
P
1 0

1 1
=
21
A
,
which interchanges

A and G, and fixes C
and U. Now, according to the new ordering CAGU all the isometries of the
vector space are shown in the following Table VIII:
2
N

Table VIII
Type of transformation Symbol Action over N Parity as permutation
of the set N
Linear and translation

2 C
I T =
( ) ( ) C, A, G, U C, A, G, U
Even
Translation

U
T
( ) ( ) C, A, G, U U, G, A, C
Even
Translation

A
T
( ) ( ) C, A, G, U A, C, U, G
Even
Translation

G
T
( ) ( ) C, A, G, U G, U, C, A
Even
Linear

1 2
A
( ) ( ) C, A, G, U C, G, A, U
Odd
Composition
U 1
T
2
A
( ) ( ) C, A, G, U U, A, G, C
Odd
Composition
A 1
T
2
A
( ) ( ) C, A, G, U A, U, C, G
Odd
Composition
G 1
T
2
A
( ) ( ) C, A, G, U G, C, U, A
Odd
13


5.3.1 The two different classes of 3-dimensional cubes over the Galois Field
, that preserve the correspondence of the pyrimidine-purine
classification with the algebraic complementarity
GF(4)

From Table VIII we see that we have 2 other different families of 3-dimensional
cubes:

5
: The 4 cubes obtained from the orderings CAGU, UGAC, ACUG and GUCA.

6
: The 4 cubes obtained from the orderings CGAU, UAGC, AUCG, and GCUA.
Here again, we have that, as the permutations that convert elements of a family
into elements of the other one are not isometries with respect to the distance in
the 3-dimensional cube, the corresponding transformation may change the
shape and the size of a figure. So, for example, the set RNY that is a prism in the
cube , with sides of length 3, 1, 1, is converted in a prism of sides of lengths
3, 2, 2, under the permutation
D
N
NNN
( ) ( ) C, U, A, G C, A, G, U
) U
, and under both
permutations and ( ) ( C, U, C, A, G, A, G ( ) ( ) U CUAG CGA , is transformed
into the union of 2 prisms, one of sides with lengths 3, 1, 3 and the other with
sides of lengths 1, 1, 3 (see Figs. 5 and 6).

Figures 5 and 6


6 Conclusions

In this work we have analyzed the 24 possible matchings of the set of the 4
nucleotides with the 4 binary set of duplets. The set was partitioned into 3
classes: strong-weak, amino-keto and pyrimidine-purine. For each category, there
are 2 classes, each with 4 cubes, over , that preserve the correspondence of
the algebraic complementarity. The cube has been christened as The Hotel
of Triplets, or Genetic Hotel, because of its resemblance with a three-floor building.
As the permutations that convert elements of a family into elements of the other
one are not isometries with respect to the distance in the 3-dimensional
cube, the corresponding transformation may change the shape and the size of
a condominium of the Hotel. The prism RNY adopts different shapes in the set
depending upon the selected ordering.
N
D
GF(4)
NNN
N
NNN
A priori there is any biological reason to prefer one ordering over others. Assuming
a primaeval genetic code, such as the RNY code, different evolutionary
mechanisms can lead to the same Standard Genetic Code [3]. Different orderings
could be better than others in terms of the properties (e.g. physicochemical,
evolutionary, and symmetrical) that are under study and that one finds convenient
to be highlighted.



14
Acknowledgments

M. V. Jos was financially supported by PAPIIT IN205307, UNAM, Mxico and by
the Macroprojecto: Tecnologas para la Universidad de la Informacin y la
Computacin (MTUIC). E. M. was supported by the MTUIC and by Universidad
Central Marta Abreu de las Villas, Santa Clara, Cuba.


References

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15


Figure 1. The prism RNY in the cube under the ordering CUAG NNN







































AGU
AGC
GGU
GGC
AAU
AAC
GAU
GAC
AUU
AUC
GUU
GUC
ACU
ACC
GCU
GCC
CUAG





16



Figure 2. The prism RNY in the cube under the ordering CAUG NNN
















GC













GC






AGU
AGC
AUU
AUC
GGU
GGC
AAU
AAC
GUU
GUC
ACU
ACC
GAU
GAC
U
C
CAUG








17




Figure 3. The prism RNY in the cube under the ordering CUGA NNN




































GAU
GAC
AAU
AAC
GGU
GGC
AGU
AGC
GUU
GUC
AUU
AUC
GCU
GCC
ACU
ACC
CUGA






18


Figure 4. The prism RNY in the cube under the ordering CGUA NNN






































GAU
GAC
GUU
GUC
AAU
AAC
GGU
GGC
AUU
AUC
GCU
GCC
AGU
AGC
ACU
ACC
CGUA






19


Figure 5. The prism RNY in the cube under the ordering CAGU NNN






































AUU
AUC
GUU
GUC
AGU
AGC
GGU
GGC
AAU
AAC
GAU
GAC
ACC
ACU
GCU
GCC
CAGU






20


Figure 6. The prism RNY in the cube under the ordering CGAU NNN




GUU
GUC
AUU
AUC
GAU
GAC
AAU
AAC
GGU
GGC
AGU
AGC
GCC
GCU
ACU
ACC
CGAU
21