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Biological Molecules

Biological molecules include all of the compounds, material, and stuff found in living systems.  The biological molecules include water, salts, vitamins, minerals, lipids or fats, proteins, ribonucleic acid (RNA), and deoxyribonucleic acid (DNA).  Water is commonly known to exist in life and DNA frequents our mass media for the criminal system.  Most living systems are composed of approximately 70% water, 25% protein, and less than 0.1% DNA.

Protein is the foundation of life.  It forms the structure of and monitors, mediates, and catalyzes all chemical reactions within a living system.  Protein is the real “nuts and bolts” of life and a full understanding of protein will benefit all aspects of life, our ecosystem, our health and its management, and even our future technologies.  It is this motivating factor that inspires the PDP towards the detailed study of proteins.  This section will focus primarily on proteins and water.


Water forms the foundation of all living systems and that is the primary reason for life on this planet.  Water is a very simple molecule that happens to exhibit complex, and sometimes bewildering, characteristics.  For instance, the density of most solids is greater than that of the respective liquid, thus the solid will sink in its own liquid.  Ice, however, is less dense than water as exhibited by ice floating on water.

The structure of water is

(fig. B01)

where the HOH angle is 104.474°, as measured in the gas phase by infrared spectroscopy [Eisenberg, 1969 #259].  Under molecular orbital theory, the oxygen is sp3 hybridized which implies a tetrahedral orbital configuration.  The unperturbed angle of adjacent tetrahedral orbitals is 109.5°, however, water contains two lone pair of electrons which perturb the tetrahedral configuration and compress the HOH angle down to 104.474°.  The lone pair of electrons are centered above the oxygen, in and out of the 2D page, and the perturbation is based on the electrostatic repulsion of the lone pairs with the -OH bonds.

It is the structure of water that makes it so unique and perplexing.  For instance, the compressed HOH angle causes water to expand upon freezing and thus ice is less dense than water.  It is also the reason for water generally accepted as the “universal” solvent and excellent thermal stabilizer.  Both of these properties are because of the HOH angle, the two lone pairs of electrons, and the partial charges derived from the nonlinearity of the molecule.

Hydrogen bonds are a weak intermolecular bond between the partially positive hydrogen and the partially negative oxygen of a neighboring water molecule, or

(fig. B02)

Hydrogen bonds possess and energy of 4 to 12 kcal/mol and form throughout the liquid completing a complex lattice of highly dynamic semi-structured crystals, known as flickering clusters, imparting greater thermal stability within the liquid.

Water can also form hydrogen bonds with other molecules.  This is found in proteins, where bound water layers have been observed using X-ray crystallography, NMR, and dielectric spectroscopy.  It is believed that the bound water layers, both internally to and externally upon the surface of the protein, aid the protein in solvation, motion, catalysis, and charge transfer, distribution, and balancing.  The bound water of proteins will be an important factor in the study of the PDP.

Electrical Properties of Water

As shown in Fig. B02, the partial positive charges on the hydrogen and the partial negative charges on the oxygen form the basis of a permanent dipole moment.  The strength of the dipole is greatly enhanced by the presence of the two electron lone pairs in the sp3 hybridized oxygen for they compress the HOH angle and provide additional negative charge above the oxygen.

(fig. B03)

The strong charge separation creates a net and permanent dipole moment which possess its own electric field, E .  The strength of the dipole moment of steam is 1.84 ± 0.02 D (1.84 x10-18 e.s.u.) [Sanger, 1928 #258], [Smyth, 1955 #260].

Electrostatic theory states that water’s dipole moment will align in the presence of an applied electric field.  This is proven by pure water having an electric permittivity of approximately 80 at room temperature [Weast, 1982 #257].  The anomalous dispersion of water ranges from a permittivity of 88.3 at 0.5769 GHz and decreases down to a permittivity of 4.23 at 890 GHz with the resulting relaxation time on the order of 10 ps, or 16 GHz [Takashima, 1989 #224].  At 20° C, the dispersion curve for water is nearly constant from static to 1 GHz, exhibiting only a 0.3 % decrease of s at 1 GHz [Grant, 1978 #248].  Therefore, a  dielectric study under 1 GHz, of biological molecules in aqueous solution will require measuring a relatively small obscure biological dielectric signal through the rather large dielectric signal of bulk water.

Bound water, i.e. the water weakly bound externally to or embedded within a protein, would have a greater relaxation time than that of free water because of the stronger forces linking the water to the protein.  Bound water would be more ice-like than free water [Grant, 1978 #248].  Hence, a greater relaxation time would decrease the frequency of the observed dispersion.

In addition to the relaxation time, the static permittivity, s, of ice is nearly equal that of free water, therefore that of bound water would be within the range of 80 to 100.  The infinite-frequency permittivity, ¥, of ice is 3.2 and that of water is 4 to 4.5, in which the anticipated value for bound water would similarity lie within that range.   Therefore, it is reasonable to conclude that the dielectric constants of bound water lie within the regions of ice and water with a shifting of the relaxation time for bound water.

Amino Acids

Proteins are extremely large complex molecules.  For instance, a very small protein can have as many as a thousand atoms.  Thankfully, proteins are composed of subunits called amino acids.  There are only twenty different amino acids found in all living systems in which they all have the same basic structure, as follows

(fig. B04)

The Hydrogen bonded to the primary carbon is always Hydrogen.  This is important for the polarity and hydrophobicity of the overall protein and in how a protein will eventually fold in on itself.

The term amino acid obviously comes from the amino functional group on the left and the carboxylic acid group on the right.  It is noteworthy to state that the amino group is inherently a base and the carboxylic acid group is an acid, therefore, amino acids, and thus proteins, are both acids and bases.  Molecules that are both acids and bases are known as amphoteric and possess the quality of being buffers.  Buffers have the ability to stabilize the pH of a solution within a specific pH range. 

All twenty amino acids are the same except for the R group.  The simplest R group is a Hydrogen and equates to the amino acid Glycine.  The most complex amino acid would by Tryptophan where the R group is a complex Nitrogen-containing double ring structure known as an indole group. 

The distinguishing R group imparts on the amino acid its physical and chemical properties.  Some R groups are very polar and thus readily dissolve in water, others are nonpolar and thus hydrophobic.  The hydrophobicity of the R group is important for it will determine the shape and function of the protein.

Proteins are formed by simply bonding the amino group of one amino acid to the carboxylic acid group of another amino acid in a dehydration reaction where water is given off. 

(fig. B05)

Two amino acids bonded together are a dipeptide.  Polypeptides are proteins or peptides with many amino acids.  Most functional proteins require at least thirty amino acids in length.  Insulin has 51 amino acids.

Electrical Properties of Amino Acids and Peptides

The nitrogen in the amino functional group has a lower electronegativity then its -bonded hydrogens, therefore the nitrogen will exhibit a partial positive charge.  The carbonyl oxygen on the carboxylic carbon will be strongly electronegative because of the additional -bonding.  This will create a strong negative charge on the carbonyl oxygen.  The presence of the positive charge on the amino nitrogen and the negative charge on the carbonyl oxygen, separated by an atomic distance, is a permanent dipole moment.  Therefore, free amino acids in solution will exhibit an orientational dielectric response.  Depending on the R group of the amino acid, it can also have an additional additive or subtractive effect on the net permanent dipole moment.  Essentially, those amino acids with polar R groups will exhibit different dielectric responses as opposed to nonpolar R groups.


Proteins are a class of biomolecules that perform two primary functions in all living cells.  The first function is structural.  Proteins form the structural basis of an organism.  For instance, skin, bone, hair, and finger nails are pure forms of protein.  Collagen is a sheet-like protein in your skin that keeps it tight and young looking.  As we age the bonds in the collagen weaken and the face begins to age.

The second function of proteins is catalytic, or they aid in causing chemical reactions.  Proteins that act as catalysts are called enzymes.  Insulin is an enzyme that maintains the level of glucose in your blood stream.  When the level or efficiency of this enzyme is abnormal, then diabetes is expressed.

Although extremely large and complex, a protein’s structure can be broken down into four stages of complexity.  The first is the primary structure in which the exact amino acid length and linear sequence of amino acids determine the protein. 

The secondary structure is the initial folding of the protein upon itself.  The length and sequence of the primary structure along with the hydrophobicity of the R groups determine how the initially linear backbone of the protein will fold in on itself.  The -helix, the -sheet, and the random coil form the three secondary configurations of folding and twisting.  Essentially, hydrophilic R groups will face outward on the protein and hydrophobic R groups will form a tight inner core.  This is due to the water environment of the cell in which proteins reside.

Tertiary structure occurs when certain R groups physically bond with other R groups.  The primary bond would be a disulfide bride between the two sulfur containing amino acids, cysteine and methionine.  These chemical bonds formalize the folding of the protein into a more rigid and permanent structure.

Quaternary structure will only occur when multiple polypeptide chains bond to form an even larger functional protein.  Not all polypeptides require bonding to other peptides to be a functional protein.

The four stages of protein structure are shown below.

Myoglobin and Hemoglobin

Myoglobin and Hemoglobin are molecules that transport Oxygen from the lungs, upon inhalation, to the tissues through the blood stream.  When the oxygen is released from the molecule, it then accepts Carbon dioxide waste from the cells, delivers it back to the lungs in which it is released upon exhalation.  Myoglobin is usually found in lesser evolved animals, such as fish, and Hemoglobin is found in mammals and primates.  Both are responsible for making blood the color red.

The cells use the Oxygen in cellular respiration to metabolize glucose and derive energy or ATP through the oxidation of that glucose.  The six carbons in each glucose are oxidized to the point of producing Carbon dioxide, which is then considered waste by the cell and expelled.  Myoglobin and Hemoglobin ensure that each of the cells in the organism have an ample supply of oxygen and properly remove the Carbon dioxide waste.

Myoglobin is the more simple of the two molecules.  It primary structure consists of a single polypeptide chain of 153 amino acids in length, as shown 

The secondary structure contains eight sublengths of -helicies with a random coil between each -helix.

where the above diagram is actually two different concept drawings of the same single Myoglobin molecule.  Notice how the -helicies and tight turns are similar between both renderings.

Anemia is the lack of red blood cells and more specifically a lack of Myoglobin or Hemoglobin in the blood to carry enough Oxygen to the cells or remove the CO2 waste.  Increasing the intake of Iron (Fe) will often stimulate the production of Myoglobin or Hemoglobin and thus increase the concentration of red blood cells in the stream.  Iron is an integral and necessary part of the Myoglobin and Hemoglobin molecule.  It forms the center of the heme group which is embedded in the center of the polypeptide chain, as shown above.  The chemical structure of the heme is as follows

When Oxygen is bound to the Fe atom it causes the heme ring structure to pucker.  This puckering causes the peptide portion of Myoglobin to break any bonds with the CO2 waste the molecule is carrying back from the cells.  The CO2 is actually carried on the N-terminal end of the peptide, or at the end of the A -helix in the above Myoglobin diagram.  Therefore, Myoglobin and Hemoglobin not only act as a dual transport system, they do it efficiently because the molecules will never carry O2 and CO2 at the same time.

Hemoglobin performs the same job as Myoglobin.  It is structurally a bit different then Myoglobin in that Hemoglobin requires four polypeptide chains to bond in a full quaternary structure.  This four times more massive molecule is much more efficient at performing its duties then Myoglobin. 

The primary structure of Hemoglobin is slightly modified to account for the larger more complex molecule.  Two of the four Hemoglobin polypeptides are known as the -chains, the other two are the -chains.  The -chain is 141 amino acids in length and the -chain is 146 amino acids long.  The primary structure is shown below in which the identical regions are shown in red.

The secondary and quaternary structure can be seen in the following diagram

When we inhale, the blood in our lungs has a very high concentration of O2.  This high concentration of O2 in the blood forces bonding of O2 with the heme Fe atom.  The puckering of the heme group occurs.  Any CO2 still bound to the N-terminal end of the polypeptide will be released from the molecule and then exhaled.  Hemoglobin is more efficient then Myoglobin because after the first O2 molecule bonds to the heme Fe atom in Hemoglobin, it not only induces the release of CO2, but also sends a signal to the other three polypeptides.  This chain reaction will stimulate them to bind much more easily to other free O2 molecules.  Myoglobin acts independently and does not have this interpeptide communication as does Hemoglobin, for it can work in concert as a massive four polypeptide molecule.

When the O2-rich Hemoglobin arrives to an area with a very low concentration of O2 and a high concentration of CO2, the Hemoglobin is stimulated to release its O2 cargo and bond to CO2.  The same interpeptide stimulation occurs, but in the reverse.  Once the first O2 molecules is released, it stimulates the other three to release O2 that much easier and pickup CO2.

Electrical Properties of Proteins


Baum, S., Introduction to Organic and Biological Chemistry, 3rd Edition, MacMillan Publishing Company, Inc., New York, (1982).

Darnell, J., Lodish, H., Baltimore, D., Molecular Cell Biology, Scientific American Books, New York, (1986).

Trefil, J., Hazen, R.M., The Sciences, An Integrated Approach, 3rd Edition, John Wiley and Sons, Inc., New York, (2001).

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