The hydroxyl group hydrogen bonded water

on/off biological switching

The study of the effect the hydroxyl group exercises on water molecules in their
proximity continues, with an ever increasing number of applications. Work on for
example antibody constructs, show that there are about 30 sugars on the Fab
fragments, sited at the Y junction of the antibody structure1. Sugar constructs are seen
in very many places in biological systems and even, in the nucleic acids the DNA and
RNA. Here, the sugar is integrated within the base sequence in the phosphate-sugar-
base assembly. Sugars are found in mucin, cytoplasmic proteins, membrane proteins,
collagen, blood cells, secreted proteins, mucopolysaccharides and many other sites in
the body.

The function of structural sugars in biological system remains unclear but my work on
the retardation of cement setting by sugars2 indicated that sugar properties are related
to the effect the hydroxyl group exercises on water in its immediate environment. It is
the dipolar effect of the electron rich oxygen and the electron depleted environment of
the hydrogen atom that provide the very powerful local effect on the surrounding
water molecules. The oxygen/hydrogen assembly which is covalently bonded and
form the hydroxyl group is in turn covalently bonded to the carbon atom of the sugar
residue.

The negative and the positive charge form a dipolar assembly that has a powerful
effect on the dipolar properties of the water molecules in the environment.
Glycobiologists point out that the 3 dimensional arrangement of water molecules
forming the hydrogen bonded construct surrounding a sugar molecule, form a precise
copy of the sugar molecule. The resultant hydrogen bonded construct, extends in all
directions from the hydroxyl group and forms a lattice of fixed water molecules that
surround the hydroxyl group, mimicking the sugar conformation.

In a fixed state the hydroxyl group/water molecular construct forms a barrier to

material transfer across this hydrogen bonded structure and impedes the transportation
of molecules in this volume. There is therefore a barrier to transportation of
cytoplasmic contents.

1 The relationship between cell wall structure and antibody specificity, Student Project, 1974,
http://www.scribd.com/doc/3033229/The-relationship-between-the-cell-wall-and-antibody-specificity

2 Cement Cellulose Composites, Branko R Babic,. Inorganically-Bonded Wood and Fibre Composite Materials, 1997, Vol 5,
49-63 .
Any molecules moving across this obstruction incurs an energy cost, ie, energy is
expended by biological systems in traversing this area of cytoplasm.

As an analogy, an example of a wall being built across a busy route can be envisaged.
Transportation of material is prevented at these sites but once the obstruction is
removed, the flow of materials can resume. In molecular terms, when the hydrogen
bonds are disengaged, the hydrogen bonded construct break down and a free passage
of materials can resume. The hydrogen bonded hydroxyl group and water
arrangement therefore acts as a barrier to cytoplasmic transfer.

If the sugar molecule is induced to interact with other charged sites, by for example
“inverting” the conformation of the sugar molecule so that the stereochemistry of the
protruding reactive groups changes in its position in space, the hydrogen bonding with
water is broken. The hydrogen bonded water arrangement loses its fixed structure and
the space becomes fluid again, to allow movement of biological materials across that
volume.

The stereochemistry of the hydroxyl group on the sugar molecules therefore exercises
a controlling effect on molecular movement in its environment. The hydroxyl groups
stereo chemical arrangement, is therefore speculated to control the flow of molecular
material in that region of the cytoplasmic environment.

This function of sugars can be considered as a biological on/off switch.

When hydrogen bonds are formed, the switch is said to be in the ON position, and no
biological mass traverses the space.
When the hydrogen bonding between the hydroxyl molecule and the water is
disrupted, the switch is said to be in the OFF position and biological material can
traverse the space again.

On/off switching of biological systems is experienced across biological processes. For

example, the 30 odd sugars that are found in immunoglobulin structures of antibodies
is proposed to control the interaction of the terminal amino acids interacting with
antigens. It becomes clear that if the sugar molecule is in the stereo chemical
arrangement allowing formation of hydrogen bonding than no interactions can occur
because the molecular movement in the reactive space is restricted. As the
stereochemical formation is re-arranged in the sugar the hydrogen bonds are broken
and molecular movement in the environment again becomes possible. The
immunoglobulin can then proceed to interact with the antigen to for example, breach
the protein layer.

The concept can be extended to examples where sugars are integrated with proteins
and for example in the Deoxyribonucleic Acid (DNA). The phosphate-sugar-base
sequence, possibly generating a switching mechanism by readjusting its 3
dimensional arrangement of the hydroxyl groups protruding into space from the
phosphate-sugar-base molecular assembly in DNA. The on/off switch can be applied
for example where the base sequence needs to be reproduced, copied, activated,
switched off etc depending on the DNA’s function and current requirement.

Note the difference between the deoxyribonucleotide and the additional hydroxyl
group in the ribonucleotide.

The ribonucleotide additional hydroxyl group on the sugar is proposed in this model
to reflect the increased activity of RNA and is said to provide additional hydrogen
bonding. The biochemistry of these processes is complex and involved but as a
fundamental step in the control of mass transfer in the region of the sugar molecules
the hydrogen bonding is put forward for discussion as a mechanism for controlling
fluid flow.

Not only does an excess infusion of polyhydroxy compounds reverse the osmotic
gradient in systems but the hydroxyl groups are proposed to provide a localised means
whereby transportation of biological and other materials are prevented by on/off
switches that form hydrogen bonded physical barriers. This mechanism is proposed as
a useful application in destroying damaged cells and controlling water flux in given
volumes. The concept was registered at the intellectual Property Office see:
GB9822509.7.