4.1. Introduction
of the concept of "physical
operator"
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Let's
consider hypothetical area of protein
synthesis in the structure
of the ribosome. Figure 35 shows the site of the synthesized protein
from the five amino acids (pentafragment),
associated with the ribosome (a) and matrix description of its conformation (b). As seen
in Figure 35, a, the hydrogen bond
of atoms NiH....Oi-4=C is the only area to which may affect the
side chain R
of just
attached to the protein of the i-th amino acid (marked
by dotted line). In this area the side chain of the protein can act as a physical
operator to recreate the encoded protein conformation. Description of this area can be made by the matrices of the six elements (Fig. 35, b). The most significant
in this
description is
the
variable x3, highlighted in red. |
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Fig.
35. To concept
introduction of "physical operator." a
- newly synthesized protein pentafragment associated with the ribosome, b - matrix description of the pentafragment
conformation. |
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Physical operators
can either promote the formation of hydrogen bonds (with the formation of
alpha-helical conformation of the protein), or prevent to it (then
not spiral acyclic conformation of the protein is formed). For this reason, we can distinguish two types of physical
operators: operators of connectivity and anti-connectivity. |
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OPERATORS OF CONNECTIVITY |
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Operators of
connectivity (Figure
36, a) are the protein amino acid side chains that promoting to
fixing the hydrogen bond NiH....Oi-4=C In the matrix (Fig.
36, b) х3 = 1, i.e. these operators recreate the
cyclic 4-link protein
fragments. For this reason they should be attributed
in a genetic code to blocks of triplets G and A. |
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Fig.
36. The physical operator of connectivity (a) and its matrix
description (b). |
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OPERATORS OF ANTI-CONNECTIVITY |
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Operators of anti-connectivity (Fig.
37, a) are protein amino acid side
chains that prevent the
formation of hydrogen bonds NiH....Oi-4=C In the matrix (Fig. 37, b) х3 = 0, i.e. these operators recreate the acyclic 4-link protein fragments. They must therefore be attributed in a genetic code
to the blocks of triplets C and и
U. |
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Fig. 37. The
physical operator of anti-connectivity (a) and its matrix description
(b). |
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To the
side chains of the protein carried out function of physical operators, they
should satisfy to a number of the requirements formulated below. These
requirements are compared with
the real properties of the side chains
of amino acids.
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REQUIREMENTS
TO SIDE CHAINS OF PROTEIN AS PHYSICAL OPERATORS |
COMPLIANCE OF SIDE CHAINS OF AMINO ACIDS TO THE FORMULATED
REQUIREMENTS |
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1.
By
its action of the operators should be directed back, to the start of the chain,
i.e. to be retro-operators. 2.
By
its size, operators should be
comparable to that area
on which
they operate. 3.
In
order the
structure could be correctly recreated, operators should have a uniform type
of a stereo-configuration, i.e. be chirally pure. |
1. The side chains of polar amino acids form hydrogen bonds, and are directed back to the start of the
chain, i.e. they can be considered as a retro-operators. 2. The length of the side chains is
comparable to the size of the
area to which they should operate. 3. All the side chains of
amino acids have a uniform stereo-configuration (refer
to the L-configuration), and are
chirally pure. |
Thus, the
side chains of amino acids can quite carry out function of physical operators. In
Section 4.2. the side chains of amino acids as physical operators are
considered in more detail .
