Quantized Spatial Control in the Living Cell by J.C. Collins, PhD_Rev8-2011

8/6/2019 Quantized Spatial Control in the Living Cell by J.C. Collins, PhD_Rev8-2011

1/64


2/64

Dedicated to the lateProfessor William S. JohnsonThe University of Wisconsin

Stanford University,to

Professor Carl Djerassi

My Wife, Betty

Wayne State UniversityStanford University

and to


3/64

Dr. Collins received his degrees in Chemistry from Wayne University

The Author:

in Michigan and the University of Wisconsin. After employmentat General Motors Research, E. I. Dupont and Sterling Drug, heaccepted a position at I lli nois Wesley an Univ ersi ty as Chairman

of the Chemistry Department and Associat e Profes sor. I n 1967,he returned to Sterling Drug to direct drug research at SterlingWinthrop Research Institute until l987 when he retired to devotefull time to his driving interest in the role of water in the livingcell. He has a number of publications and patents to his creditand has had a synthetic organic reagent The Collins Rea gentnamed after him. However, natural molecular shape and cellularhydration have been his primary interests for many years. In thisshort treatise, he provides a pictorial view ofhow the dynamicproperties ofwater appear to regulate the motions and inter-actions of vital molecules in living cells.

Strange as it may seem, this work has beenplaced on the Internet for your enjoyment.Download it if you like and share it with whom-ever you like. My only desire, is that you enjoy it.Questions and comments can be addressed to the

F i r t s t e d i t i o n : T h e M a t r i x o f L i f e wasp u b l i s h e d i n 1 9 9 1 . I S B N 0 - 9 6 2 9 7 1 9 - 0 - 1L i b r a r y o f C o n g r e s s C a t a l o g C a r dN u m b e r 9 1 - 9 0 3 7 9

S e c o n d e d i t i o n : W a t e r : T h e V i t a l F o r c e o f L i f e w a s p u b l i s h e d i n 2 0 0 0 . I S B N 0 - 9 6 2 9 71 9 - 2 - 8L i b r a r y o f C o n g r e s s C a t a l o g C a r d

N u m b e r 0 0 - 9 0 3 2 5

I l l u s t r a t i o n s w e r e d e v e l o p e d o n

A p p l e M a c i n t o s h a n d D e l l c o m -p u t e r s u s i n g A d o b e I l l u s t r a t o r .D a t a f o r s t r u c u r a l a n a l y s e s a n dt h e p r e p a r a t i o n o f d r a w i n g s w e r eo b t a i n e d f r o m t h e p u b l i s h e d l i t e r -a t u r e . C u s t o m p h y s i c a l mode l -b u i l d i n g w a s p e r f o r m e d p r i m a r i l yw i t h F r a m e w o r k m o l e c u l a r m o d e lp a r t s ( P r e n t i c e H a l l , E n g l e w o o d

C l i s , N J 0 7 6 3 2 ) .

Q u a n t i z e d S p a t i a l C o n t r o l W i t h i n L i v i n g C e l l s

author at molepres2000@aol .com

R RR R

R

R


4/64

Water 9-16

Vital Molecules

Nucleotides and ATP

Ions 17-20

Elements, Atoms and Molecules 6-8

21-30

31-34

35-38

39-41

Oils, Fats and Membranes

Nucleotides and Nucleic Acids

DNA and the Genetic Code

The Living Cell

42-47

48-50

Hydrogen BondingWater and Proton QuantizationHydrocabons and Water

Linearity in WaterForms of IceNuclear (Proton) Magnetic Resonance

Forms of Water

Charge and Proton Transfer

Ionization

Sodium, Potassium and other Ions

Glucose and Cholesterol

Bond Energy and Motion

Proton-Powered Molecular MotorsPhotosynthesis

Regulator Molecules and Cell Function

Cellulose and Starch

Chemical-Bond EnergyHormones and Neurotransmitters

Proteins and EnzymesAminoacids and Polypeptides

Nucleic Acid Coupling

The Double Helix

Code Storage

Code Reading

Messenger and Transfer RNAs

Polypeptides to Proteins

Ribosomal Synthesis of Polypeptides

Chlorophyll and HemeFatty Acids and Phospholipids

Sodium/Potassium PumpsTransport

Resting and Excited States

Nerves

Muscles

References 51- 64

Oxidation and Reduction

Myelin Membrane

Proton Pulse Conduction

Cell Membranes

Introduction 5

CONTENTS 4within Living CellsQuantized Spatial Control


5/64

Background

For over fty years, I have had a passion for constructing three-dimensional models of molecules. As an

Associate Professor of Chemistry and Director of Research in Medicinal Chemistry, I began constructing

permanent molecular models of hundreds of pharmacologically-active substances, natural and synthetic,

in search of spatial correlations. Surprising as it seems, when aligned side by side, the molecules

fell into rather specic dimensional groups which diered in length by about 2.3 angstroms.

When the observation was rst made, it was considered simply a coincidence but, as more infor-

mation was gained and more molecules were analyzed, particularly proteins, it was realized that

the dimensions corresponded to l inear, hydrogen-bonded segments of water molecules. Certainly,

water molecules are too dynamic and linear segments too unstable to provide for structural order.

However, molecular orbital calculations by Hoyland and Kier in 1969 as well as crystallization studies andstudies of water by Narten and Levy in 1972 indicated that molecules on the surface form short-lived

linear, hydrogen-bonded elements and even longer elements adjacent to lipid surfaces. Thus, dimen-

sional correlations, published information and the mechanics of hydrogen bonding, supported the

Since submissions of articles to reputable journals were rejected as speculative, oral presentations

concept that transient linearization of water on surfaces provides for spatial order within living cells.

were given at Chemical Society Meetings in 1974, 1975, 1988 and 1993. Books were published

in 1991 and 2000 and web sites were established in 2006, 2008 and 2009 - all with the view that it is the

dynamic linearization of water which provides order. Although little evidence was available for order in bulk

liquid water when the concept was introduced in 1974, recent high-speed neutron and infrared studies

provide clear evidence for quantized linearization. Coupled with studies of hydrated collagen, poly-

saccharide and muscle bers back in the 70s, which illustrated that water is ordered adjacent to their

surfaces, it is clear that dynamic linearization in sur face water provides for spatial control within living cells.

5within Living Cells

Quantized Spatial Control


6/64

As you undoubtedly know, all matter is co mposed ofAtoms which combine in specic ways to form all known

For those with limited background in chemistry, here is chart of all the types of atoms which compose the material

world. Although it took many years to developAtomic-Molecular Theory, the basic principles are amazingly simple

andeasy to understand.

substances. Atoms ofElements in the middle of the chart, like iron, cobalt and nickel (Fe, Co and Ni) form stable

Atoms ofgases like uorine, Chlorine and Bromine (F, Cl and Br) react with Li, Na and K to form Salts. Carbon atoms

metals while lithium, sodium and potassium (Li, Na and K) are metals but they react with water to form Bases .

combine with each other and with hydrogen atoms to form hydrocarbon Molecules with Chemical Bonds between

the atoms. Molecules within living cells contain carbon chains bonded to hydrogen, oxygen and nitrogen in many

dierent ways. The challenge of the last century was to determine the structures of vital molecules - the challenge today is

to determine how the myriad of molecules and ions wh ich compose cells interact harmoniously to give us life.

H

Li Be B C N O F Ne

Na Mg Al Si P S Cl A

K ScCa V Mn Co Zn Ga KrBrSeAsTi Cr Fe Ni Cu Ge

Rb

321 4 5 6 7 8

YSr Nb Tc Rh Cd In XeITeSbZr Mo Ru Pd Ag Sn

Cs LaBa Ta Re Ir Hg Tl RnAtPoBiHf W Os Pt Au Pb

Fr AcRaPr Pm Eu Dy Ho LuYbTmCe Nd Sm Gd Tb Er

He

Periodic Table of Elements

Pa Np Am Cf Th U Pu Cm Bk

6The Elementswithin Living CellsQuantized Spatial Control


7/64

As expected, they are extremely stable and exist as single atoms as a gas. Since two electrons ll the

smallest orbital, thenext electron in the Lithium Atom(Li) goes into a larger, elliptical orbital which ca n

hydrogen gas Molecules (H ) are composed of two atoms with an electron pair rotating around both core protons.

Helium Atoms (He) have two protons and two neutral Neutrons in the nucleus and a pair of orbiting electrons.

more stable as coupled pairs. Thus,

trons in their inner orbital and six

in the outer, join together to form

Oxygen Molecules as a gas or with

two hydrogens to form Water, H O.

When organic materials burn, carbon

form CO . Heat is generated when

within them combineswith oxygen to

hydrogen and carbon burn because

H O and CO have less Bond Energy.

accommodate eight electrons.

with a single, negatively-charged Electron

orbiting around it. Since electrons spinand generate magnetic elds, they are

positively-charged nucleus, called a Proton ,

Hydrogen Atoms (H) are composed of a

2

2

2

2 2

Oxygen Atoms (O), with two elec-

H

HHe 2

O22H

C2CO

O2

2 2

2H2

H

OLi

O2

7Atoms and Moleculeswithin Living CellsQuantized Spatial Control

Q i d S i l C l


8/64

Atoms and molecules can be pictured in many dierent ways but it must be remembered that

it is the electrons which form quantized waves around

the nucleus of an atom occupies very little space;

thenucle iand hold themtogether at parti cular an gles.

Even though single molecules are used to represent

substances, in the liquid state they are always in

contact with other molecules. In fact, the physical

properties of substances are not dened so much by the atoms they contain as the external shape

their molecules and the arrangement ofcharges on their surfaces.

central oxygen atom with positively-charged protons in electronic

orbitals on two corners and two negatively-charged, unoccupied,

orbitals on the other two corners. Thus, water molecules are like

magnets, they have high Polarity. In liquid state, water molecules

Bonds holding them together. Hydrogen bonds are only about 1/10th as strong as Covalent Bonds

preferred angles relative to each other. However, water molecules not only hydrogen bond with each

which hold atoms together in molecules but, as illustrated above, the water molecules are held at

other, they hydrogen-bond with oxygen and nitrogen atoms on the surfaces of other molecules and

are extremely dynamic; they are held together primarily by their

continually form extremely short-lived, proton-coupled linear elements to further delocalize charge.

For example, individual water molecules are composed of a

O2H2H

2O

2 2

O

O H

H

O

HH

8Hydrogen Bonds

high polarity but they continually form short linear units, like the Triplet shown above, with Hydrogen

within Living CellsQuantized Spatial Control

of

H

O

H

H

O H

H

O

HH

O

H H

O

H H

O

HH

Q ti d S ti l C t l


9/64

9Water and Proton Quantization

Cyclic Trimer TrimerDimer ++

+ +

+_

__

_ _

Quantized Linear-Wave Entanglement

_+

In fact, recent high-speed irradiation studies have

dramatically altered our view of the bonding and ordering

Entanglement which tie water molecules together. Although the coupling of protons within the same water

molecule is an accepted property, it appears that the high polarity of water molecules permits coupling

between neigboring molecules with the formation extended waves which last about 10 seconds.

In liquid water, these waves must form in all directions but, within living cells, studies on collagen, muscleand polysaccharides suggest that they follow the orientations of the fibers, membranes and surface charges.

ultra high-speed neutrons at 10 seconds and only 1.5

protons were detected per water molecule rather than 2.

This means that protons on adjacent water molecules exhibit the same Quantum Mechanical Properties

as electronson adjacent metal atoms: they exhibit both wave and particle properties and form waves of

properties of water molecules. First: infrared studies indicate

motions as anticipated by Newtonian Physics. Transitions between dimers and trimers, which continually

Third: of paramount importance, are studies of

Professor Chatzidimitriou-Driesmann and coworkers

in Germany who irradiated pure liquid water with

that water molecules move in quantized steps from one

hydrogen-bonded relationship to the next - they behave

take place in liquid water and last about 10 to 10 seconds, occur in specific steps, possibly involving the

cyclic trimer. Second: high speed neutron irradiation indicates that each water molecule in liquid water is

hydrogen-bonded to a maximum oftwo water molecules, as pictured above, not four as previously believed.

as anticipated by Quantum Mechanical Theory - in discrete energy-exchanging steps, rather than by smooth

-1 5

-12 -10

-1 8


d d b

Quantized Spatial Control


10/64

Water and Hydrocarbons

Of all the substances which exist, water is absolutely unique! Its molecules have two protons which couple

10

their spins and, in turn, couple with those on neighboring water molecules to produce waves of integral linear order.

Thus, it is not surpris ing that the physical proper ties of water are unique as well. For example, carbon

C

100

0

-100

-200

212 F

-77.4 F

-28.1 F

-257.8 F

BoilingP

oints(degreesCentigrade)

O2

H N3

H C4

HS2

H

O

H H

OH

H

O

HH

O

H

H

O

H H

H

H H

H

H

H

H

H

H

H H

H

H

H

H

H

H

H

H

H

C

C

C

C

C

O

H H

H

HH

H

CN

H H

H

S

H H

o

o

o

o

and hydrogen atoms, as shown on page 6,

have about the same anity for electrons.

attraction for each other; in the liquid state

Thus, Methane Molecules, CH , have minimal

A dramatic illustration of the eect of forces of attraction

they simply pack tightly together to ll the

space rather than being held in preferred

orientations like water molecules.

on physical properties can be seen in the boiling temperatures

of the substances shown on the right. Even Ammonia, NH ,

temperatures than water. If, now, we compare water withmethane which does not hydrogen bond, the temperature dier-

-ence is an amazing 470 degrees F . In fact, water molecules

have such strong attraction for each other that hydrocarbon

molecule s are forced out. As we shall later, this property of

separation between hydrocarbons and water is responsible for

much of the spontaneous assembly which occurs in living-cells.

4

3

and hydrogen sulde, H S, with two hydrogens, boil at lower


2

11H d bQuantized Spatial Control


11/64

HHH

Before we go further in our discussion of water, we should learn more about the bonding properties of

carbon and alternative ways of viewing structures. In contrast to most atoms, carbon atoms form rm bonds

with each other to form chains.

Each atom has four electrons in its

outer orbital which can overlap

with those of other carbons to

form a bond. In fact, two or three

of the orbitals can overlap with

those of neighboring atoms to

form multiple bonds. In Methane ,

a single carbon atom bonds with

four hydrogens to achieve stability. In propane, eight hydrogens are required to achieve "Saturation."

The carbons in Ethylene are joined by an "Unsaturated" double bond. As molecular structures become more

complex,graphic representations must be simplied in order to display their spatial features.

The easiest way is to remove hydrogensand reduce the size of the atoms. But,

remember, even though the hydrogens

are not shown, they are on the car-

bon and oxygen atoms. Molecules

like glucose and cholesterol are

much larger with their hydrogens.

H

H

H HC

CCC C C CC C

CC

H H

H

H

H

HH

H

H

HH

CCHH

CC C

H H

H H

Octane

Glucose Cholesterol

Methane EthyleneEthane Propane

11Hydrocarbonswithin Living CellsQuantized Spatial Control

12Li id W tQuantized Spatial Control


12/64

As discussed above, liquid water molecules are continually tied together by at least three forces and, if viewed

at any instant, are in a somewhat compressed state. The dynamics of molecular motion tend to counter

those forces and hold the molecules apart but, as water is cooled and molecular speeds decrease, the moleculesmove closer together and the density increases. At 4 C (39.2 F), water reaches maximum density and,

as it is cooled on down to 0 C, linear hydrogen-bonding

occurs with greater frequency. However, if the

surfaces in contact with water molecules do not have

atoms in hexagonal positions, simila r to those of water

molecules in the surface of ice, no freezing will occur. In fact,

water can be cooled to as much as 30 degrees below zero C

without crystallizing if hexagonal atom patterning is not present on contact surfaces. However, as pointed

on page 13, if oil is present on a surface, freezing and expansion to the ice lattice occurs immediately at 0 degrees C.

liquids with less hydrogen-bonding, likeresistance to surface penetration than

Spiders and bugs walk on water and, if metal needles or pins are placed carefully on the surface, they oat as well.

Bu t , not only the density of water increases as the temperature is lowered, surface tension increases as well.

All liquids exhibit surface tension but, as i l lustrated in the chart b elow, water(W ) has substantial ly more

alcohol (A) and gasoline (G). In fact, if

X-Raysare deected from the surface of

a pattern of circles is produced which

indicates orderly linear hydrogen bonding.

water and focused on photographic lm,

o

o

o

X-RayTube

Water Sample

PatternDiraction

X-RayBeam

W A G

surface

tension

12Liquid Waterwithin Living CellsQuantized Spatial Control

13S f W tQuantized Spatial Control


13/64

between molecules are not as rigid as the bonds

These two peaks are broad because hydrogen bonds

between atoms and they last for less than a billionth

of short, linear segments of water molecules on the surface

providing greater strength and a degree of order. Thus,

of liquid water appears to be due, in part, to polar inter-

actions and to the continous and random formation of

quantizedlinear elements of water molecules.

10 2 3 4 5 6 7 8 9 10

A Narten and Levy (1972)

4.5A2.9A1A

6.8A

25 C

The distance of the rings from the center in the X- Ray diraction pattern shown on page 12 is a reection of

o

oo

o

o

o

o

o

the separation between the atoms in the water molecules. An intensity plot published by Drs. Narten and Levy

in 1972 illustrated that, at the instant of impact, most molecules were about 2.9 Angstroms apart. The broad

peak at 4.5 A corresponds to three, linearly hydrogen-bonded water molecules and the one at 6.8 A to four molecules.

of a second. As pointed out above, short units like this

form in bulk water but much more frequently on surfaces

where impacts absorb momentum and permit stronger,

more-linear bonding. In fact, linear hydrogen bonding is

most likely propagated across surfaces by the impact of

water molecules on the ends of chains to drive molecules

from the other end, like billiard balls on a table.

the exceptionally high resistance to surface penetration

If instant pictures could be taken, we would see a multitude

13Surface Waterwithin Living CellsQuantized Spatial Control

14

Order and Disorder in Surface WaterQuantized Spatial Control


14/64

However, if oil or gasoline are poured o n water, surface tension

the oil suspends as spheres, but it quickly aggregates to form a single layer. The driving force for this move-

freedom: they spontaneously move from conditions of order to disorder . If oil and water are mixed vigorously,

ment, as well as water's tendency to form balls on a wax surface, is that water attempts to minimize ordering

mentioned before, this is the

contact with hydrocarbons. As

reason for much of the spon-

taneous assembly in living cells.

increases even more. Waves on the sea are calmed and the sur-

perpendicular to the surface in layers and refract dierent wave-

face takes on an iridescent appearance as oil molecules align

lengths of light. Oil molecules spin around their axes and move

laterally, but they are restricted in rotating end over end. They, like

the mole cules of water, are ordered more at the interface with water

than they are with air. As mentioned before, pure water can be

supercooled well below 32 F (0 C) without crystallizing. But, if water is in

contact with oil or wax, it cannot be supercooled - it crystal lizes at 0 C.

The reason is that oil molecules, in contact with water, pack tightly

together in hexagonal arrangements with a distance of about 2.5

surface of ice - they provide the two-dimensional seed forice formation.

angstroms between them, about the same as water molecules in the

OIL OR WAX SURFACE

DROPLETS OF WATEROIL

WATER

o o

o

o

But, molecules of water in the liquid phase, even at 0 C, have high energy - they continually attempt to optimize

14Order and Disorder in Surface Waterwithin Living CellsQ p

15Forms of IceQuantized Spatial Control


15/64

Although interfaces between water and hydrocarbons provide for self-assembly and order within living

o

o

o

If this occurs, the water lattice which most

The reason is that water molecules hyro-

likely forms is cubic rather than hexagonal.

water as linear segments. If pure water is

cooled rapidly to -60 C, the linear elementswhich form initially, branch out at 120 angles

gen-bond together most rapidly in liquid

to form hexagonal sheets and then at 120 degrees away from the surface to yield

cubic ice. Thus, cubic ice is composed entirely of linear elements in chair forms , as shown

on the right, while the hexagonal form, which forms as ice warms to 0 C, contains

boat forms perpendicular to the surface. Snowakes, as they form in the cold upperatmosphere, crystallize in the cubic form but revert to hexagonal as they fall to earth.

micro- droplets of water which, even above freezing temper atures, crystall ize to form slush ice. Crude

cells, it causes major problems in the petroleum industry. When crude oil is pumped from wells, it contains

oil becomes so thick, even above 0 C, that it is almost impossible to pump. If living cells were composed totally

of hydrocarbons, much of the water within them would be ice. Of course, cellular water does not turn to ice

because oxygen and nitrogen atoms on the surfaces of molecules hydrogen-bond with water molecules at

explain orderly function, there is little evidence for the existance of persistant water structure. However, it is

distinctly possible that water molecules in conned spaces may exist in transient, t hree-dimensional forms.

angles which disrupt linear hydrogen bonding. Although it has been proposed that living cells contain ice to

CUBIC HEXAGONAL

CHAIR BOAT

15Forms of Icewithin Living Cellsp

16Nuclear (Proton) Magnetic ResonanceQuantized Spatial Control


16/64

16

order/disorder properties of water within and around living cells. Nuclear Magnetic Resonance (NMR) is based

on the fact that the nuclei of certain atoms, particularly protons, spin and, as we

have pointed out before, generate magnetic elds. If placed in a high magnetic eld

and irradiated with a par ticular radio-frequency, the spin can be reversed. When

the spin on the nucleus (the proton in the case of hydrogen) returns to its normal

direction, it releases a specic quantized radio frequency. The difference

the proton -the sharpness of the peaks depends on the rotational freedom of

the water molecules within the cells and tissues.

Water molecules with high rotational freedom give sharp peaks, restricted

ones give broad peaks. By recording the order/disorder properties in living

As our understanding of the structural properties of water increase,

our understanding of how cells per form their normal, health-producing functions should increase as we ll.

tissues, computers can be used to scan entire bodies to determine the com-

is not simply a solvent for molecules in living tissues; it was the

environment in which the molecules rst formed and, undoubtedly,

its linearizing properties were intimately-involved in the selection of

themolecular structures which were to compose living cells. As

might be expected, it is involved in virtually all interactions.

position of water in tissues. It is important to realize that water

between the irradiated and emitted frequency depends on the environment of

Amazing as it seems, one of the most important advances in medicine in the past century is based on the

N S

O2

H

hv

NMR

NMR-Imagingof the brain

Nuclear (Proton) Magnetic Resonancewithin Living Cells

17Ionsi hi Li i C llQuantized Spatial Control


17/64

But the environment in which the molecules of life rst formed and the one in which they function today is

not pure water - it contains many soluble components, particularly, sodium chloride. But the structural character

and properties of sodium and chlorine atoms in water are entirely dierent from those o f hydrocarbons

discussed above.

Sodium atoms (Na) have 11 positive charges on the nucleus and 11 electrons which orbit around the nucleus.

The inner orbitals are lled with 2 and 8 electrons, leaving the 11th electron in a new, outer orbital.

Chlorine, on the other hand, has a total of 17 electrons, with 7 in the outer orbit. When sodium and

chlorine atoms touch, the outer electron of sodium transfers to chlorine to

ll its outer orbital, leaving sodium with a positive charge and chlorine with

Cations, negatively-charged, Anions. Since the orbitals of both ions are

lled, they are extremely stable. In fact, blood contains about 3% sodium chloride,

the same as the sea water from which it came. In crystalline salt, the ions occupy

alternate positions in a rectangular lattice. Although the ions are pictured with lines

between them, the only thing holding them together is their opposite charges.

a negative charge. These charged atoms are called, Ions: positively-charged are

Na ClNa

Cl

17Ionswithin Living Cells

18Proton Transferwithin Living CellsQuantized Spatial Control


18/64

18

Sodium chloride dissolves so readily in water that you might think it is soluble in a number of

solvents. It is not - water is the only solvent in which salt is readily soluble. Once again, the extremely high

positive and negative charges on

surround ions with their oppositely-

the water molecules permit them to

By accepting some of the charge,

charged surfaces pointed toward them.

water permits the ions to separate.

However, water molecules stabilize the ions in several other ways as well. First: additional water molecules hydrogen

bond around the sodium ion to distribute the charge to more water molecules. Second: at short distances, the

A

positively-charged proton (A) on a water molecule next to a sodium ion jumps to a neighboring water molecule (B)

ion and a positively-charged water

molecule next to the chloride ion.

At short distances, Proton Transfer

stabilizes charges on ions but

proton entanglement does as well.

followed by a jump of a proton on that

water molecule to the next and on to

This leaves a negatively-charged

water molecule next to the sodium

a molecule next to a chlorine atom. B C

PROTON-TRANSFER S TABILIZATION

SALT SO LUTION

Proton Transferwithin Living Cells

19Ionizationwithin Living CellsQuantized Spatial Control


19/64

-15

In fact, protons pass extremely rapidly as linear waves of positive pulse through linear elements of

water molecules between ions, either in free water or on surfaces. However, pure water contains very few

ions. Only about 2 water

molecules per billion separate

to produce hydroxide and

hydronium ions.

If the levels of these ions are the same, the water is Neutral. If there are more hydroxide ions than hydro-

to water, it produces hydronium and chloride ions and the water becomes acidic. Ifsodium hydroxide

(NaOH) is added, the hydroxide ion makes it basic. If hydroxide and hydronium ions are added together

they combine to form neutral water molecules. But, as indicated above, the sodium and chloride ions do not

combine; they are extremely stable in water as their charges are dispersed to water molecules around them.

However, the discovery of proton

coupling in liquid water meansthat the charges on ions in cellular

water are continually being neutral-

ized by Quantized Waves of Protons

which last about 10 seconds, a thousand times faster than hydrogen bonding. Even if the water molecules are

not hydrogen bonded together, entanglement transfers protonic charge and water is linearized. Just as

electron quantization defines the space around atoms, proton quantization defines space around vital molecules.

nium the water is Basic - if more hydronium ions, it is Acidic. If an acid, like hydrochloric acid, HCl, is added

IONIZATION OF WATER

Ionization

Hydroxide Hydronium

Quantized Linear-Wave Entanglement

within Living Cells

Sodium and Potassium Ions 20within Living CellsQuantized Spatial Control


20/64

But, before we look at molecules and the eect of water on their structures, we must look more closely at ions.

Sea water and cells contain more than sodium and chloride, they contain calcium, magnesium, potassium

and many others at lower levels. Each

one has a unique capacity to associate

with water and other molecules. Calcium

and magnesium ions, with their two pos-

itive charges, tightly bind water and

other polar molecules.

Potassium ions, on other hand, have a single positive charge, like sodium, but their positive nuclear charges are

surrounded by eight more electrons than sodium. Even though more massive, they do not bind water molecules, theydisrupt hydrogen bonding and increase freedom; they are compatible with the linear quantization of water.

In fact, potassium ions coordinate with water mole cules at the same distances as water molecules bond to each other.

Thus, while sodium ions bind four to six water molecules and exchange them rapidly with surrounding

water, potassium ions, even though larger , move more rapidly through water

without binding. By drawing water molecules into spherical orientations around

them, sodium and calcium ion s, in the connes of living cells, disrupt linear

Resting the State of Muscle Cells, sodium and calcium ions are held in

binding sites; the linear orientation of surface water permits contractile

elements to relax and lengthen; potassium ions move freely to minimize

charge potential. However, in Excited States, sodium and calcium are released,

l inearity is disrupted and proteins contract; ions are extremely important.

2 2

K Na Ca0

5

10

RE

LATIVEION

MO

BILITIES

Calcium Ion Magnesium Ion Sodium Ion Potassium Ion Mobility

quantization: they draw water molecules into circular orientations. In the

within Living Cells

Glucose 21within Living CellsQuantized Spatial Control


21/64

Other than water, Glucose (also called dextrose) is the most abundant molecule on earth. As the major

product of photosynthesis, it is the primary energy-transport molecule between plants and animals. In fact,

glucose is the spatial analogue of

Hexagonal Water. As you can see,

glucose molecule are in the same

spatial positions as four of the

four of the oxygen atoms of the

oxygens in hexagonal water.

In fact, oxygens at positions 1 and 3 can hydrogen bond with linearized water above the glucose molecule and at 2 and

4 below. However, in the plane ofthe glucose molecule, its oxygens hydrogen bond at entirely dierent angles.

Thus, even though one might expect glucose molecules, with oxygens in the same hexagonal spatial positions

as those in the surface of ice, to seed ice - it does not! It depresses the freezing temperature of water because its

oxygens hydrogen-bond with neighboring water molecules in the plane at angles which disrupt normal linear

water-to-water hydrogen bonding. Planar protein molecules in the feet of penguins which withstand

Their angles also disrupt linearity

in surface water; they are called

Antifreeze Proteins. Angles

of hydrogen bonding with surface

water determine whether linearorder is reinforce or disrupted.

exremely cold temperatures without freezing also have oxygen atoms in hexagonal positions on their surfaces.

66

1

2

3

4

1

2

34

6

Views with and without polar hydrogens showing rotation of carbon 6

Front Views of glucose

Glucose

Glucose

6 612C H O 612H O

Hexagonal Water Hydrogen-BondingAngles

G ucosewithin Living Cells

Sugars 22within Living CellsQuantized Spatial Control


22/64

Since glucose molecules are planar and their oxygens hydrogen-bond into linearly-ordered water above and

and below the plane but disrupt water order in the plane, they exhibit the properties of a surfactant: they spon-

taneously migrate to water-ordering surfaces, like cell membranes, to displace ordered water and increase the freedom

cules to be moved into cells. The shapes of molecules and their hydrogen bonding

by plants. As shown on right, the oxygen on carbon-1 of glucose

it to move spontaneously to surfa ces, bind in sites occupied by triplets of water mole-

of water around them. Thus, the structu re of the glucose molecule permits

with water direct their motion within and on the sur faces of living cells.

But the beta-D form of glucose is not the only one which exists within the cell or the only sugar produced

11

2 4

readily ips from the beta to the alphaposition in w ater.The oxygens at 2 and 4 in D-mannose and D-galactose are xed.

However, there is another form

cyanide ion, two substances which were most likely present on earth

when the molecules of life rst formed, are dissolved in saline

water, the formaldehyde molecules join together spontaneously to

form a complex mixture of sugars with the formula (CH O) . Since

glucose is the most stable of the sugars which forms, it most

likely accumulated on earth at th e expense of all others.

of the beta-D form; it is beta-L-

Glucose. It does not occur in

nature but can be prepared synthetically. In fact, if formaldehyde and

CN

-

- -

--

-

-D-Glucose

-D-Glucose

-D-Glucose

-D-Galactose-D-Mannose

-D-Glucose

D-Glucose

Sugars

OtherMany

Formaldehyde2CH O

2 x

2 x

(CH O)

2 6(CH O)

-L-Glucose

g

of glucose: it is the mirror-image

within Living Cells


23/64

Cellulose 24within Living CellsQuantized Spatial Control


24/64

Of all the polymeric forms of sugars which exist, Cellulose is one of the most impor tant because it is a major

structural material in the plant kingdom. In contrast to starch, it is not produced simply by heating glucose

but is synthesized in plants by enzymes

alpha 1,4 attachments.The disaccharide,

which couple multiple glucose mole-

cules together bybeta rather than

Cellobiose , is produced initially, bu t

repeated additions produce linear

cellulose blades which hydrogen

bond together to form at cellulose

sheets which linearly order water on

both sides. The sheets are the primary

components of wood and leaves.

Cotton bers are almost pure cellulose.

Bacteria in termites and someants hydrolyze cellulose back to

glucose for food but most organisms

cannot break it down. Thus, it is extremely

stable and might well have been the

the rst carbon-containing, structural

material produced on earth. Flat Cellulose Sheets

Linear Cellulose Blades

11

4 Enzymes

4

-D-Glucose -D-Glucose D-Cellobiose

g

Bond Energy 25within Living CellsQuantized Spatial Control


25/64

in plants to produce Oxygen Gas and reactive Hydrogen Atoms. The hydrogen atoms are then held next

to carbon dioxide molecules by enzymes

which rapidly couples together to

to produce water and formaldehyde

produce D-glucose. It is amazing that

precisely the same reaction is used by

plants to produce glucose today, using

enzymes, which most likely was used to produce it at random when vital molecules rst formed, using cyanide.

Thus, sunlight energy is stored, r st in oxygen gas and hydrogen atoms, then i n the carbon-hydrogen bondsof formaldehyde; then in the carbon-hydrogen bonds of glucose and starch. But, starch has another

2

2 2

sunlight

Formaldehyde

Iodine

2CO

Oxygen Gas

Hydrogen Atoms

D-Glucose

The rst step in producing bond energy in glucose molecules is the electrolysis of water by the chlorophyll

property which may have been extremely important in the

early stage of biomolecule formation on earth. As illustrated

on page 23, starch tubules have hollow cores which are large

enough to hold small molecules. For example, iodine molecules

indicate that starch helices are extremely exible and dynamic

move into the cores to form a stable bright blue complex. But studies

and can expand to bind larger molecules. Since the cores have

ordered oxygens, like many reaction sites in enzymes, they might

well have served as early reaction sites by binding small molecules,

like aromatic bases and sugars, and, on dr ying, force themtogether to produce complex molecules like th e nucleotides.

Cholesterol and the Steroidal Hormones 26within Living CellsQuantized Spatial Control


26/64

Next to glucose, Cholesterol is one of the most important molecules in the b ody. Not only does it stabilize the

membranes of cells, particularly those of nerves and muscles, but it serves as the raw material for the biosynthesis

of a large number of steroidal hormones. In order to give you

an idea of the shape o f its molecule, the 45 hydroge n atoms

attached to the carbons are not shown but they store a great deal

of energy. One problem with cholesterol is that, in mimicking

linearly-ordered water, it is so insoluble in water that specic lipo-

proteins are required to carry it through blood vessels. If caloric

intake is too high , the excess cholesterol produced deposits in

blood vessels , hardens the arteries and restricts blood ow.

oxygen hydrogen-bonded to the oxygens of the fatty acids and to bridging water molecules. A discussion of cholesterol/

phospholipid membranes is included on page 46. Whether or not the cholesterol molecule evolved to mimic the

water unit shown is open todebate, but there is no doubt

that it is an extremely important

starting material for the form-

ation of a number of hormones

which mimic linear segments

of 6 and 7 water molecules.

As you can see, the molecule has a at lower surface and a rounded upper surface with an oxygen on one end.

In cell membranes, its hydrocarbon body extends into the central region next to fatty-acid chains with its terminal

Testosterone

Cholic AcidEstradiol

Progesterone

Hydrocortisone

Aldosterone

Neurotransmitters and Regulators 27within Living CellsQuantized Spatial Control


27/64

In addition to glucose and cholesterol, a number ofNeurotransmitter molecules of various shapes and sizes have

spatial dimensions s imilar to ordered units of water.

Since all of these molecules bind to sites on the

outer surfaces of cells to trigger responses inside,

water, in ordered forms of the type shown , may

occupy the binding sites as regulator molecules

enter or leave. Proposals for the hydration states

of ve receptor sites which have been identied

and several which have not been reported are

included in the web site www.molepres.com.The fact that correlations

also can be seen between

water and the aromatic

bases at the left may be fortuitous, but correlations in dimensions such as these

certainly assist water in its role of integrating interactions between molecules.

electrons rotating around the rings to give them additional stability. They are

produced enzymatically in the body from formaldehyde, ammonia and water but,

once again, they can be produced as complex mixtures by heating this mixture of

chemicals on various mineral surfaces. Thus, it appears that these molecules also may

have accumulated in the oceans and tidal pools as the starting m aterials for life.

These bases are at with nitrogen atoms in the ring and three extra pairs of

Acetyl Choline

Prostaglandin-PGE

Glycine

Histamine

++

-

+

Gama-aminoButyric Acid

Serotonin

+

+

+

Dopamine

--

-

-

-

2

Adrenaline

+-

Adenine

Uracil

Guanine

Cytosine

Uric AcidHypoxanthine

Aminoacids and Polypeptides 28within Living CellsQuantized Spatial Control


28/64

Aminoacids , like those shown here,

play such a dominant role in cellular

processes today that it is dicult

by subjecting aerosols of ammonia, form-

to imagine a world without them.

aldehyde and hydrogen cyanide to

sunlight and electrical discharge and,

have been produced at random that way.

l ike other simple vital molecules, may

Many of those shown can be produced

and joined together to produce polypeptides on huge molecular

Today, about 21 dierent ones are synthesized by specic enzymes

complexes called Ribosomes. If proper sequences ofpolypeptides are

produced, theyspontaneously wrap to give unique proteins. As linear

-+

-+

-+

-+

-+

+

-+

-+

+ -+

- -

+

-+

-+

-+

S

S

Hydrophilic

Lipophilic

Turn Groups

side chains often alternate from side to side

with hydrophilic (water-loving) groups on one

side and lipophilic (fat-loving) groups on the

other. Series of small peptides, like glycine and

serine, often cause the chains to turn.

polypeptide chains emerge from ribosomes, their

Alanine Serine Leucine Proline

CysteineLysine

Phenylalanine

TyrosineGlutamic Acid

Glycine

Histadine

TryptophaneMethionine

Amino

Acid-1 AminoAcid-2

Dipeptide-1,2

S

+

+

+

Proteins 29within Living CellsQuantized Spatial Control


29/64

The reason that Glycine and Serine

produce turns is that they are so small that

water molecules, which nomally are held

away by side chains, can bridge between

adjacent peptidesand produce -Turns. As

the chains turn, water molecules (W )

bridge cross to aid in the formation of-Sheets with similar side chains grouped

together as illustrated on page 28.

may form Helical Coils with hydrogen bonding

between every third peptide to permit those

groups to be close together. For example, the

InsulinMolecule is produced as a single

have wrapped spontaneously into their

linear chain. Once the A and B segments

preferred shapes, the central C-section,

which contains many mobile glycine

units, guides them into position so

lipid groups can be in the centerwith polar groups on the surface.

Lipophilic

Side SideHydrophilic

On the other hand, on turning, the chains

Helical Coil

WW

W

W

W

A C

B

AInsulin Molecule Assembly

Segment C is

removed once

assembly is complete.

-Turn

-Sheet

GlycineGlycine

SerineSerine

BS

Enzymes 30within Living CellsQuantized Spatial Control


30/64

On seeing the complexity of the polypeptide in the protein structure below, it seems incredible that it can wrap

into a single structure, based solely on the sequence of peptides in the chains. However, the assembly is not in air, it is

in an environment which is integrated by water molecules which continually linearize to guide the chai ns into

associations of lipid groups inside and polar outside.

If hydrogen-bonding and packing between the groups

are tight,the arrangements stay. If too many water

molecules are left between the chains, the chains are

forced apart to search of a rmer t.

Carboxypeptidase A is a hydrolytic enzyme which is

in the digestive tract of most animals. It removes aromatic

aminoacids, like tyrosine, from the ends of polypeptide chains.

The negatively-charged, acid end is drawn by linearizing water

into the reactionchannel by positively-charged groups in the

binding site. If the aminoacid lls the site and binds properly,

a water molecule held in a precise position by the two

(blue) nitrogen atoms in the site, reacts with the second

peptide to release the tyrosine. After the shortened chain

spontaneously in cell to form unique functional units.

to realize that proteins ten times this size assemble

Athough this enzyme seems complex, it is important

leaves, waterenters the site and displaces the tyrosine molecule.

-

-+

+

CARBOXYPEPTIDASE A

chain with aPolypeptide

Cut-awayshowing waterreacting with

the secondpeptide.

terminaltyrosine

ENZYME


31/64

32Powered Protein Motionwithin Living CellsQuantized Spatial Control


32/64

In fact, movement in proteins often involves the phosphory-

lation of neutral oxygen atoms to produce negatively-charged

Phosphate Esters. Positive-charges nearby move proteins to

neutralize the charges. Although movement is slight, it is

catalytic positions and, when performed on thousands of proteins

in unison, move muscles, arms and legs. Phosporylation triggers

contraction - hydrolysis with water permits relaxation.

An alternative mechanism for moving proteins is provided by

regulator molecules which bind in sites to hold proteins in specic

positions. An important regulator molecule, present in almost

every living cell, is Cyclic Adenosine Monophosphate(Cyclic

AM P) . It is produced from ATP by cyclizing the phosphate on the

ribose ring. Its major function is to bind in grooves in protein

enzyme, or to block

actions are mimicked

or blocked by drug

molecules.

its action. Many of its

activate a particularcomplexes, either to

enough to open pores in membranes, move enzymes into perfect

ATP

Cyclic AMP

ATP

WATER

RELAXATION

ACTIVATION

HYDROLYSIS

CONTRACTION

+REGULATOR (Cyclic AMP) BINDING

+

+

PHOSPHATE-POWERED MOTION

+

+

_

_

+

_

33Cyclic Adenosine Monophosphate

J h i l l i d 2 d i i k h l h f li



33/64

Just as the neurotransmitter molecules mentioned on page 27 tend to mimick the lengths of linear segments

of hydrogen-bonded water molecules, the c yclic AMP molecule is the same length as a linear segment of six

water molecules. Since poly-

peptide chains move more

slowly than the cyclic AMP

molecule, it is likely that

water molecules enter the

site and bridge the gap when

cyclic AMP is not there.

Of course, water moleculeshave too much energyto hold

the site in this state for very

for a number of receptor states, based on the linear hydration concepts, are included in www.molepres.com.

long, so the site would then either open further or close to permit most of the water to leave. Hydration states

natural regulator molecules, either to activate normal functions or inhibit them.

Many of these Receptor Sitesare in large proteins which pass through

cell membranes. Usually, these proteins are composed of a number of

helical coil segments which either bind regulator molecules on the outside

to control functions inside or have a central pore, like the potassium ion

channel shown on the left, to permit molecules and ions to enter and leave.

In fact most drug molecules bind to sites which normally are occupied by

+

+

_

_

+

_


34/64

35Nucleotides

N l i id i l id i l f di



35/64

NUCLEOTIDE COUPLING

Adenosine

THE A/U COMPLEX

Phosphate Phosphate

Guanosine

THE G/C COMPLEX

Phosphate

Uridine

PhosphateCytidine

Nucleic acids, in contrast to polypeptides, contain only four dierent

Nucleotide units. Since both nucleotides and nucleic acids are strong acids,

they exist as salts, usually of sodium or magnesium. Thus, they are highly

hydrated and avoid contact with fats and oils - they are very hydrophilic.

hydrogen-bonded dimers: Adenosine with Uridine (A/ U) and Guan-

osine with Cytidine (G/C ). Alternative,paired arrangements are con-

siderably less stable. This hydrogen-bonded dimer formation between

nucleotides is extremely important in the coupling of nucleic-acid chains.

by coupling nucleotides

together, using their

triphosphates, to form long segments with specic sequences

Nucleic acid chains have an acidic ribose-phosphate backbone,

again, with specic sequences of nucleotide bases in the chains.

Although single-strands of nucleic acid are not very stable in

cells today, at one time, before polypeptides and proteins existed, they and polysaccharides may have been the

of the A, U, G and C units . As each nucleotide is added, the

oxygen atom on the ribose ring of one nucleotide bonds withthe phosphate of another with the release of a diphosphate ion.

The chains are formed

The unique feature of the four nucleoti des is that they form specic,

PP

PP

U

A

primary polymeric components of life on earth. It is likely that most of those early molecular forms no longer exist.

G

A

U

PP

G

FORMATIONNUCLEIC ACIDFORMATION

36Nucleic Acids



36/64

BASE-PAIR

HELICAL LOOP

HELICAL LOOP SEGMENT

COUPLED HELIX

C

A

U

P

G

A

U

U

W

U

P

GC

AU

UA

U U

P

P

As soon as nucleic acid chains form, they begin searching for

base-pair coupling partners. Often, the strands are several

thousand units long as highly hydrated ionic gels with sodium

charges. Once again, water molecules bridge between the strands

to direct their coupling. Ifthe base-pairs do not match, like the

U/U pair at the end of the chains on the ri ght, water bridging

between them prevents coupling.

regions but bond angles do not permit the formation of at planes -instead, they form linear

coils, like polypeptides, but

with hydrogen bonds be-

tween the base-pairs holding

the chains together.

If U/A or C/G coupling is

interrupted, the chains search for new pairing sequences. Often, nucleic acid

chains wrap back on themselves to form helical loop-turns, usually invol-

ving about seven nucleotides. At times, carbon atoms are attached to

nucleotides to break the coupling and force a loop. Just as with polypeptides,

nucleic acids spontaneously wrap to form functional units, once again, withwater directing the wrapping and bridging beween the coiled segments.

Thus, nucleic acids are composed both of coupled and uncoupled

and magnesium ions bound within them to neutralize the negative

MAJOR

STRUCTURAL

FORMS

NUCLEIC ACID

COUPLING

CHAIN

37Transfer RNA and Aminoacid Coding

Wh h d bl h li f DN A d b



37/64

When the double-helix structure for DN A was rst proposed by

Watson and Crickin 1953, most scientists felt that nucleic acids were

involved in coding protein production, but they did not know how.

DNA turned out to be one of the factors, but small nucleic acids,

called Transfer RNAs, also are involved. Virtually every living cell,

in both plants and animals, contain twenty or more t-RNAs, one for

each of the aminoacids. In fact, most t-RNAs are almost identical

except for a Triplet Nucleotide Codeon the loop end of the molecule.

Th e sequence of these three nucleotides determines which amino-

acid will be attached to the opposite Adenosine End .

identical except at the coding and attachment ends. For example, the

triplet code at the loop end of the t-RNA for Phenylalanine is AAA ,

fo r Serine is AGA, for

Leucine,GAG

. Enzymeswhich attach phenyl

alanines bind only

t-RNAs which have AAA

on the loop end. Since linear elements of water molecules

occupy the sites in the ribosomes where t-RNAs bind, the

shapes of the t-RNA molecules display those linear lines.

+

Aminoacid attachments are carried out on enzymes which are almost

AAA, t-RNA Codefor Phenylalanine

TripletCode

AminoacidAttachment

Phenylalanine

Phenylalanyl-t-RNA

A

A AA

A AA

Adenosine

Aminoacid+ATP

ATP

t-RNA /ENZYME

t-RNA - CODED

AMINOACID

COMPLEX

TRANSFER RNA

38Ribosomal Protein Synthesis

Ribosomes are huge particles composed of two subunits which hold



38/64

a long strand ofCoded Messenger RNA and Aminoacyl Transfer RNAs

in precise positions to produce specic sequences ofpolypeptides.

These protein-synthesis machines represent a large portion of the

mass of cells. The two subunits of the ribosome shown are composed

A Coded Messenger RNA (mRNA), produced in the nucleus of the

of three RNAs and fty-ve proteins. On heating in saline solution,

water, they spontaneouslyassemble to form the original complex.

cell, binds to the ribosome with its Initiation Code (AUG) attached to a

specic site. An Initiator Aminoacyl tRNA, with its complimentary code

(UAC), then binds and is followed by a second aA-tRNA which binds to the

next triplet

code site.

As shown

on the left,

the amino-

acid on the

rst aA-tRNA bonds to the aminoacid on the second, the pair

moves over to allow a third aA-tRNA to bind, transfer its

aminoacid and move again. The coded linear polypeptide

passes down through a tunnel in particle B and wraps to

form the nished protein. What an Incredible Machine!!

Ribosomes are huge particles composed of two subunits which hold

Messenger RNA

AA

CU

UU U

U

m-RNA

Aa-t-RNAs

m-RNA

AA

AG

PARTICLE BPARTICLE A

CODE-COUPLING AMINOACID TRANSFERON m-RNA

RIBOSOMAL SYNTHESIS OF POLYPEPTIDES

Polypeptide

the units separate into all fty-eight parts - on cooling, thanks to


39/64

40DNA Hydration

I th l 50' h i ti



40/64

In the early 50's, when many scientic groups were

attempting to determine the spatial structure of DNA,

it was Rosiline Franklinat King's College in London who,

by spraying a crystalline sample with water, obtained

an interpretable X-Ray diraction pattern. When

JamesWatson and Francis Cricksaw the pattern, they

realized that the 3.4 angstrom band must be the

distance between the base pairs in the helix. They

Molecular Genetic Theory was given birth.

Second: water molecules in the wide groove continually hydrogen bond in a dynamic fashion to fill the

space and bridge between polar atoms. Third: anionic phosphates hydrogen bond to water molecules to t ransfer

central N-region of the helix but water plays a critical role in stabilizing this important Beta-Form of DNA.

First: elements of water molecules hydrogen-bond to the A/T and G/C base pairs inthe narrow grooves.

their charge into the red zone. Fourth: water molecules aline in layers ofquantized entanglement in the

free water, Q zone, to delocalize the negative charge. Fifth: spherically hydrated, cationic sodium ions surround

the helix to neutralize the charge. These hydrated sodium ions are held out away from the helix by the

linearizing water molecules just as they are as water linearizes to formi ice. In spite of the dynamic character

of the water molecules around DNA, they display the same infrared peaks as the ordered linear elements in ice.

completed their model, published their paper and

coupling between the A/T and G/C nucleotides in the

The primary structure of the helix is provided by tight

T A

GC

AT

CG

AT

AT

Na

Na

Na

P

P

P

PP

P

P

P

P

Na

Na

NQ Q

Na

Na

41DNA Code-Reading and Storage

Since the water molecules which ll the grooves of DNA are extremely dynamic they



41/64

Since the water molecules which ll the grooves of DNA are extremely dynamic, they

permit the helix to bend and turn but they also g uide the coils of regulator pro teins

into the major grooves. The protein shown on the right binds to specic base-pairs in the

groove to stabilize the helix and prevent code-reading. Proteins which read the code, bind

series ofnucleotides or deoxynucleotidesin precise positions to produce daughter

strands of RNA and DNA with complimentary sequences to those in the parent DNA.

Of course, transcription of the code is only one function of DNA, the code also must be

for playing. As pointed out above, transcription occurs on

huge Polymerase Enzymeswhich unwrap the double helix at

particular codes which signal when to begin and end the readings.

If coding errors are introduced into the double helix, other enzymes correct them.

stored inthe nucleus of the cell in a form that can be retrieved readily for reading.

To do that, the double helix wraps around positively-charged, spherical proteins,calledHistones . Eight of these bind

to the surface of the helix and wrap

it around to form coils which pack in

such a way that the coils can be retrieved for code -reading

in the same way as the disks on a record player are retrieved

All living organisms on earth use the same basic mechanisms and, at times, precisely the same molecules,

to produce proteins. Truly, if we were to dene a time when "reproductive life" rst began, it was when a code onon a strand of DNA was transcribed into the rst specic polypeptide and protein. What an Incredible Process!!

HISTONE DNASTORAGE

in the same grooves, disrupt linear hydration, unwind the strands and couple together

42Lipids

Although a variety of hydrocarbons are considered to have been broughtFATTY ACIDS



42/64

g y y g

18 34

to earth by asteroids, lipid molecules which compose the membranes of living

cells undoubtedly formed much later. Early "Life-forms" most likely existed as

gelatinous masses oating in the oceans and tidal pools. Only when simple

water into oxygen and hydrogen, could Acetic Acid, the fundmental starting

photoelectric complexes began to absorb the energy of sunlight and electrolyze

material for Fatty Acids and other Lipid Compounds, become readily available.

Just as small molecular units had coupled together to form poly-

saccharidesand proteins, ATP energy powered the attachment of acetic

acid units togetherto produce fatty acids. Some, like Stearic

Acid, had all

Saturated , single bonds between the carbons; others, like Oleic Acid, had

Unsaturated double bonds. Acetic acid is coupled together to make a tremendous variety of fatty, lipid com-

to give Isoprenoids which absorblight and carry active hydrogen from

one region of the cell to another.

But remember, hydrogens in the

structures are not shown - the formula

for oleic acid is C H O - it occupies

considerably more space than shownabove.

acetic acid units couple together

pounds. In addition to fatty acids,

PLASTOQUINONE

VITAMIN K2

ISOPRENOIDS

FATTY ACIDS

VITAMIN A

ACETIC ACID

ISOPRENOL

GLUCOSE

O2H

2

OLEICACID

STEARICACID

2

43Chlorophyll and Heme

PORPHYRINS

Another class of compounds produced



43/64

PORPHYRINS

-e

-1+e

-1

HEME

CHLOROPHYLL a HEME

OXIDATION AND REDUCTION

+3 +2

QUINONES DIHYDRO-FORMS

Mg

from acetic acid is the Porphyrins .

Of course, Chlorophyll absorbs sunlight

the component of red-blood cells which

carries oxygen to all parts of the body,

but heme molecules also carry single

electrons. The central Iron Ion accepts

an electron from one m olecule, goes

energy to produce sugars and Heme is

from the +3-state to the +2-state, carries the electron to another

part of the cell and transfers it to anoth er molecule. Quinones, like

one shown on the left and on the previous page, accept two

hydrogen atoms from one molecule and transfer them to another.

been Oxidized - if they gain electrons or hydrogen atoms, they have

been Reduced. Both processes occur on enzymes which convert molecules

from one form to another in order to tie them together or take them apar t.

Both plants and animals use quinones and heme for chemical con-

versions, but most animals have lost the genetic codes required to

tions of the codes required to make many molecules. In fact, some of our DNA may be fragments of codes

make chlorophyll. As the genetic complexity of animals increased, it appears that they either lost all or por-

If molecules lose electrons or hydrogen atoms, we say they have

for molecules which are no longer needed - "survival of the most stable and most used on the molecular level."

Fe

Fe Fe

H

H

H

H

As more and more fatty acids were produced, ATP

44Phospholipidswithin Living CellsQuantized Spatial Control


44/64

4ATP

4H O

++

-

+

-

+

--

-

2

LECITHIN

PHOSPHOLIPID BIOSYNTHESIS

CHOLINEGLYCERINE

FATTY

ACIDS

+

-

-

PHOSPHOLIPID HEAD GROUPS

LECITHIN PHOSPHATIDIC ACID

PHOSPHATIDYL

SERINE

PHOSPHATIDYL

ETHANOL AMINE

PHOSPHATIDYL

INOSITOL

y p

attached them to all kinds of molecules including

glycerine, phosphate and polysaccharides . An

important class of compounds which resulted was

th e Phospholipids with two fatty-acid chains

and a variety of head groups as shown below.

Phospholipids are unique in that they spontaneously

assemble in water to form bilayer membranes with

the middle of the membrane and the head-groups

toward water on the surfaces as on page 45.

Actually, these bilayer membranes wrap around to form spherical cells

from the outside. The fatty acid chains withi n them also are unique in that, as

which,just like the ones which compose our bodies, isolate the inside from

shown above, they exist in several dierent quantized states. At low temperatures,

th e chains are relatively straight; they move laterally and rotate around

their axes and the h ead groups move, but there is limited motion in fatty

acid chains. However, at specic temperatures, both chains absorb energy, they

kink, bend and spin and the head-groups tilt down toward the membrane.

the fatty-acid tails pointingtoward each other in

ENERGY STATES

+E

-E

- +

45Cell Membranes

Phospholipid Membranes which



45/64

PHOSPHOLIPID CELL MEMBRANES

p p

enclose most cells are amazingly

dynamic and functional. The

central, lipid region prevents

hydrophilic molecules, like water

and ions, from entering or leaving.

As mentioned before, the fatty

acid chains of phospholipids

exist in both straight and kinked

states. Often, the lipid chains in

membranes are picutured as

being in chaotic random motion.

Dont believe it!! In spite of the fact that the chains have high energy and are dynamic, they exist in distinct

modes of motion and accept quantized units of thermal energy in going from one state to the other.

Since most fatty-acid chains in the lipid region are in the high- energy, alpha-state, membranes are extremelyversatile and, as illustrated above, can accommodate proteins with a tremendous variety of shapes and sizes. Some of

proteins stabilize the membrane and some bind regulator molecules on the outside to control reactions inside.

Some cone-shaped proteins cause the membrane to bulge in or out to form blister-like buds which, on

binding particular regulator molecules release components outside or inside. But, no matter where processes

occur within living cells, they are all regulated and integrated by the quantized, linearizing properties of water

molecules.

NUCLEUS

MITOCHONDRIA

RIBOSOMES

46Active and Insulating Membranes

LIPID-STATE TRANSITION AND PORE OPENING SURFACEN

In Nerve and Muscle Cells , where



46/64

LIPID STATE TRANSITION AND PORE OPENING

ATP-POWEREDCO

MPRESSION

LIPID CHAIN

ENERGYENERGY

LIPID CHAIN

ENERGY

WATERNa

ENERGYWATER

SURFACE

rapidly to surrounding regions, shifting them from Resting to Active states.

But some regions of nerve-cells are not "active"- they do not contain pores - their

function is to insulate the inside of the cell from the outside to insure that ionic

impulses inside do not escape to the outside. Just as in the active regions, phospho-

lipids in these Myelin regions are primarily in their, high-energy alpha-state. However,

they are complexed with Cholesterol molecules which hydrogen bond to the fatty-

acid esters and spin around their axes to maintain the lipid chains in the alpha state.

conduction and contraction, fatty-

acid chains in the Alpha State are

compressed laterally to the Beta

State as pressure waves pass.

Units of quantized energy move

from the lipid chains to the sur-

face. With lateral pressure reduced,

membranal proteins relax, poresopen and ions and molecules

ATP energy is released rapidly in

enter and leave. As rapidly as the chains straightened, they return to the alpha-state;

energy moves back into the membrane, pores close and the membrane returns to its

resting state. In this way, energy released at one point in the membrane is transmitted

ALPHA-STATE LECITHIN-

CHOLESTEROL

COMPLEX

47Myelin Membrane

Electron- and Neutron-Scattering

f bbi ll d



47/64

N

N

N N

N

N

N

NN

N

N

S

40.5

Angstroms

NSES

Ionic Zone

Ionic Zone

INSIDE THE CELL

OUTSIDE THE CELL

FAST-CURRENT PROTON CONDUCTION

curves for rabbit nerve cells reported

by Kirshner and Casper in 1972 provide

good evidence for the location of

lecithin/cholesterol complexes inMyelin membrane. Electron-scattering

neutron-scattering (NS) is highest

(ES) is highest in ionic regions while

where there is the most water. As you

can see, ions and water are excluded

from the l ipid region but are in

expected regions on the surfaces.

also where they would be expected.

Groups on the helical polypeptide are

provide stability, they also provide for extremely rapid conduction ofpositive pulses . By packing tightly together, lecithin head groups are in

proper positions to produce anions in surface water. Strong positive charges

generated in nerve endings aline the entanglement waves of water molecules

parallel to the surface so that protons can be conducted extremely

rapidly from the end to the nodes to the terminal end. In electrical

circuits, wires are metal - in nerve cells, linearized water is the wire.

Cholesterol/Lecithin Complexes in myelin regions of axons not only

48The Living Cell

As noted above, phospholipids and seawater, when mixed together,ION PUMPS AND TRANSPORT



48/64

3Na

A D

CB

Essential Molecule

2K

K

K

p p p g

form small cells. If the cells are analyzed, more potassium ion is found inside

than expected and more sodium outside - also, the cells have a slight

negative charge. A number of explanations have been advanced for this

but the most widely accepted is the fact that potassium ions do not bind

circular. Sodium ions are dehydrating; in the resting states of cells,

water moleules and shift water-to-water bonding from from linear to

other hand, have just the opposite eect - they move more slowly, bind

water molecules - they move rapidly through it, increasing the freedom of

water to penetrate and hydrate ordering surfaces. Sodium ions, on the

they are bound in sites to permit water to linearize and relax the proteins.

Thus, it appears that potassium ions move into these synthetic cells to increase the entropy of water. Since sea

water contains more sodium than potassium, the cells develope a negative charge. As "living" cells began to form,

energy to pump sodium ions out and potassium ions in. Most ATP-poweredpumps are composed of a number of

they took full advantage of this natural distribution ofions by assembling protein pores in membranes which used ATP

helical polypeptides which open to the inside of the cell to bind 3 sodium ions and ATP in a pore (A). When the

ATP molecule is in the proper position, it transfers a phosphate to an oxygen on the wall of the pore, releases energy,

opens the pore to the outside, discharges the sodium ions (B) and closes inside. Two potassium ions then bind to

the open site (C), catalyze the hydrolysis of phosphate on the wall, release energy, open the pore to the inside and

discharge potassium ions, ADP and phosphate into the cell (D) . The negative charge inside the cell now draws

sodium ions bound to essential molecules, like glucose, through other pores into the cell. An amazing process!!

ADP PATP

3Na2K

Na

Na

ION PUMPS AND TRANSPORT

PumpsSodium Out

PumpsPotassium In

Potassium

Pore Pore

Transport

49Nerve Cell Pulse Transmission

ATP not only powers the Na/K pumps, it powers Ca/K, H/K and Ca/Na pumps



49/64

feed-back mechanisms. For example, enzymes which produce ATP often

bind ATP at other sites on the enzyme to turn o its own production.

However, much of the control within cells is by molecules which bind to

proteins on the outside to release regulator molecules inside. Cyclic-AMP,

which was discussed on p. 32 and 33, is one of the most important of these

to proteins onthe outside to control processes inside. In fact, life for nerve cells is controlled by neurotransmitterInternal regulators. Hormones like insulin and the neurotransmittersall bind

molecules. They use Na/K-pumps to move sodium out and potassium in but ion and transport poresremain closed

stabilize the membrane and laments - the nerve cell is in its Resting State.

cto permit surface charge to reach high levels. With sodium outside and

potassium inside, proteins inside relax. Linear entanglement waves

Then neurotransmitters, NT, released from another cell, bind to

ion channels on the ends of the nerve cells. As sodium ions rush in,

surface water aligns by entanglement in myelin arms and protons

ash through at high speed to the nodes. Once again, sodium

entry is triggered there and the pulse continues on to the nerve

ending to release its own neurotransmitter - all at incredible speed.

to charge cells and move nutrients in and out. Some pores permit ions

like potassium and chloride to pass freely in and out but levels of water and

ions are carefully controlled. Sometimes, this control is by internal

CELL REGULATION

Regulator

3Na

Ion Pumps

Regulators

Ion Pores

Transporters

ATP

2K

ADP P

Molecules

Cl

K

ATP

cyclic-AMP

NERVE PULSE TRANSMISSION

Resting State

Myelin

Excited State

Node

2K

3Na

3Na

Na

NT

Na

K

2K

K

Na

50Muscle Contraction

RELAXED MUSCLE Resting NTExcitedWhen neurotransmitters



50/64

Na

Na

Na

NT

K

Na

Na

Na

swivel and apply force, millions of times, actin laments are driven into the myosin - muscles contract an d

the feet swivel to apply force to the beads on the actin laments. As millions of front and back feet bind,

widen, bones shiftat their joints and arms and legs move. ATP has performed another of its vital functons.

Then the pumps take over, sodium is pumped out, potassium moves in, calcium returns to its sites, nerves and

muscles relax and the cells, once again, are in their resting state with ATP in the feet ready for the next walk.

Literally billions of molecules are involved, all operating in concert - All Coordinated by Cellular Water!!

K

KCa

Ca+2

Ca

RELAXEDMUSCLE

CONSTRICTEDMUSCLE

MUSCLERECEPTOR

RestingState State

NTExcited

Ca

bind to the receptors on

muscle cells, once again,

pores open and sodium

ions rush in. Calcium

binding sites by sodium ,

ions, released from their

activate legs on large

Myosin lments to

attach their feet to thebeads on thin Actin

laments. As soon as

they attach, ATP in the

feet react with water,

energy is released and

51Re f e r en c e sINTRODUCTION

Alth h tt t h b d

References are included, not only to support

information presented b t to gi e credit to



51/64

L. B. K ier, Molecular Orbital Theory in Drug Research

(Academic Press, 1971).E. J. Lloyd and P.R. Andrews, J. Med. Chem.29 : 453

(1986). A Common Structural Model for Central

Nervous System Drugs and Their Receptors.

Structure and Pharmacological Activity

Modern Concepts in the Relationship between

K. J. Br unings, , and P. Lindgren, , (eds.)

(MacMillian, 1971).

Molecular Interpretations of Adenylate Cyclase

(Second International Conference on Cyclic

Chemical Society, 1974).

A Unified Approach to the Analysis of Biomolecular Systems (Northeastern Section, American

AMP, Vancouver, B.C., 1974).

Although numerous attempts have been made information presented but to give credit to

individuals who provided critical information.to publish the Li near Hydration Concepts in

reputable journals, they have been rejected

by reviewers as too speculative. Below are

the major oral and written presentations.

Molecular Interpretations for Receptor

Responses in Plasma Membranes (170th

National Meeting of the American Chemical

Society Meeting, Chicago, Ill., 1975).

Membrane Receptor Models (196th National

Meeting of the American Chemical Societ y,

Los Angeles, CA, 1988).The Matrix of Life (Molecular Presentations,

Water: The Vital Force of Life (Molecular

1991).

Presentations, 2000).

Transient Linear Hydration Hypothesis

(67th Annual Meeting of th e Americ anChemical Society, Toronto, Canada, 1993).

A. Szent-Gyorgi, The Living State (Academic

Press,1972). Also, Bioenergetics (Academic

Press, 1957).

E. Schrodinger, What is Life?, Cambridge

University Press (1944) . See also, What

is Life?with Mind and Matter. Cambridge

University Press (1967).

C. F. Hazelwood, ed. Ann. N.Y. Acad. Sci.204

(l973). Physicochemical state of ions andwater in l iving tissues and model systems.

C. A. Chatzidimitriou-Driesmann , Physica B., 385(1):

1 (2006). Attosecond Quantum Entanglement in

Neutron Compton Scattering from Water in the

KeV Range.

Atomic and Molecular Structure Liquid Water

l d l h h

52Re f e r en c e swithin Living CellsQuantized Spatial Control


52/64

the Structure of Molecules and Crystals

The nature of the chemical bond. Application

of results obtained from quantum mech-

anics and from a theory of paramagnetic

susceptibility to the structure of molecules.

L. Pauling, The Nature of the Chemical Bond and

A. Rich and N. Davidson, eds., Structural

Chemistry and Molecular Biology (Freeman,

1968). A Tribute to Linus Pauling

L. Stryler, Biochemistry (Freeman, 1995). An

molecular biology and biochemistry.

excellent presentation of structural

(Cornell University Press, l961).

L. Pauling, J. Am. Chem. Soc., 53: 1367 (1931).

A. L. Patterson,Z. Krist. 90 : 5171 (1935)

A Direct Method for the determination of the

components of interatomic distances in crystals.

M. Hanack, Conformation Theory(Academic

Press, 1965).

P. M. Wiggins, J. Theor. Biol.32: 131 (1971).

Water structure as a determinant of ion

distribution in living tissue.

H. S. Frank, Science169: 635 (1970).

The structure of ordinar y water.

J. Del Bene and J. A. Pople, J. Chem. Phy.52 :

4858 (1970) . Molecular orbital calculations

J. R. Hoyland and L. B. Kier, Theor. Chim. Acta.

15 : 1-11 (1969). Molecular orbital calculations.

G. J. Saord, P. S. Leung, A. W. Naumann and

P. C. Schaer, J. Chem. Phys.50: 4444 (1969).

A. K. Covington and P. Jones, eds. Hydrogen-

Bonded Solvent Systems (Taylor and Francis,1968).

D. Eisenberg and W. Kauzmann, Structure

and Properties of Water (Oxford University

Press, 1969).

J. D. Bernal and R. H. Fowler, J. Chem. Phy. 1: 515(1933) . A theory of water and ionic solution,

with particular reference to hydrogen and

hydroxyl ions.

Yu. G. Syrnikof, (USSR), Tepl. Dvizhenie. Mol.

the structure of water and solutions.

Mezhmol. Vzaimodeistvie Zhidk. Rastvorakh

445 (1969). Topological methods for describing

D. E. Ingher,Sci. Amer. 278: 48 (1998). The

Architecture of Life

A. Berk, L. Zipursky, P. Matsudaira, D. Baltimore,

and H.F. Lodish, eds. Molecular Cell Biology

(W. H. Freeman, 1999).

S N Vinogradov and R H Linnell Hydrogen

LIQUI D WATER

E S h di M h P f h C b id Phil

Re f e r en c e s 53

QUANTUM MECHANICS OF LIQUID WATER


..


53/64

S. N. Vinogradov and R.H. Linnell, Hydrogen

Bonding (Van Nostrand Reinhold, 1971).

F. Franks, (ed.) Water - A Compre hensive

Treatise (Plenum, 1972).

A. T. Hagler and H . A. Scheraga, Ann. N.Y.

Acad. Sci.204: 51 (1973). A Review of

Water Model Hypotheses.

M. C. R. Symons, Na

Date post:	07-Apr-2018
Category:	Documents
Upload:	dr-joe-collins
View:	215 times
Download:	0 times

Quantized Spatial Control in the Living Cell by J.C. Collins, PhD_Rev8-2011

Documents