(Nursing Study Guide on BIOCHEMISTRY)

CHAPTER 2: WATER

I. Introduction
While current biochemistry focuses on the structure and function of molecules such
as proteins and DNA, it is vital to remember that the qualities of the medium in which
they are dissolved govern biomolecular structure and function. As a result, this chapter
provides an overview of water characteristics relevant to the structure and function of
biomolecules. Consider the creation of biological membranes as an example of the
relevance of water in biological systems. Because the acyl chains of
glycerophospholipids are insoluble in water, cell membranes eventually develop. As a
result, glycerophospholipids and other membrane lipids aggregate, forming structures
such as the cytoplasmic membrane and organelle membranes. In this chapter, we will
look at fundamental water features such as polar and nonpolar molecular solvation, water
ionization and pH, acid-base chemistry, and buffering systems. These themes are critical
for comprehending everything that follows in the text's subsequent chapters.
II. General Properties of Water Molecules
In a water molecule, the oxygen atom has an sp3 configuration of bonding
orbitals, with two H atoms and two unshared pairs of electrons arranged in a tetrahedral
pattern surrounding the oxygen. This configuration produces a net dipole in which the
end of the molecule carrying the unshared electrons is partially negative and the end
containing the two hydrogens is partially positive. Furthermore, because hydrogen and
oxygen share electrons unequally, each H-O- bond has a dipolar property. Water is
classified as a polar solvent because each water molecule contains a net dipole.
III. H-Bonding in Water
H-bonds hold neighboring molecules together in bulk water. Figure 1 shows the
atom arrangement in an H-bond. 2.3. In the image, the H-bond is the non-covalent
attraction (dashed line) between the partly positively charged H atom linked to the left
oxygen atom and one of the unshared electron pairs (not shown) of the oxygen atom on
the right. Each water molecule has two unshared electron pairs and two hydrogens that
can engage in H-bonding. As a result, each water molecule may form H-bonds with four
of its neighbors. Because sp3 molecular orbitals are orientated tetrahedrally, nearby water
molecules around a specific water molecule are also arranged tetrahedrally. Water
molecules in ice are arranged in a tight, perfectly tetrahedral crystalline lattice, with each
molecule H-bonded to four others. In liquid water, each water molecule is H-bonded to
an average of 3.4 others. Local groupings of molecules, often known as "flickering
clusters," survive for just nanoseconds. Despite the presence of an approximately
 tetrahedral arrangement of molecules, liquid water is denser than ice because the
somewhat uneven packing of molecules allows them to come together a little closer.
Water is extremely cohesive due to significant H-bonding. Despite water's modest
molecular weight (18 g/mol), the cohesion of molecules imparts a high melting and
boiling point. Water is a great thermal buffer for actively metabolizing cells and tissues
due to its high specific heat and heat of evaporation. It also explains why cold water
swiftly conducts heat away from a swimmer, potentially leading to hypothermia and
death.
IV. Behavior of Ionic and Polar Substances in Water
Ionic substances (electrolytes) and polar molecules are highly soluble in water
because water molecules are polar. Hydrophilic substances are those that dissolve easily
in water. Both the cationic (Na+) and anionic (Cl-) components of salts (e.g., NaCl) can
be solvated via interactions with the negative and positive ends of dipolar water
molecules. The salt dissolves because the interactions are energetically advantageous.
Ions that have been dissolved are said to be "solvated" or "hydrated." The ions are
shielded by the shells of surrounding water molecules, preventing them from forcefully
interacting and reconstructing the crystal. Water molecules also form hydrogen bonds
with polar functional groups in polar biomolecules like sugars and amino acids. The
many sorts of H-bonds that can develop are explained more below. It is worth noting that
many biomolecules include a mix of polar and nonpolar groups. As a result, the real
solubility of biomolecules varies greatly and is determined by the relative proportions of
polar and nonpolar areas.
V. Behavior of Nonpolar Substances
Nonpolar compounds are hydrophobic because they are relatively insoluble in
water. These compounds are generally hydrocarbons with methylene, methyl, and
aromatic ring functional groups. They often lack polar groups capable of interacting with
water molecules. Because water molecules cannot establish H-connections with a
nonpolar material, they become highly ordered in the compound’s proximity, producing
ice-like bonds with one another. Indeed, cage-like structures known as clathrates arise,
which may be thought of as stiff geodesic domes around the nonpolar molecule. All of
this structure reduces the chaos or entropy of the water, which is an energy-inefficient
process. To avoid this as much as possible, the suspended hydrophobic compounds
combine, reducing the surface area of the nonpolar molecules in contact with water.
Hydrophobic interactions are the clustering of nonpolar molecules such as membrane
lipids to prevent the entropically unfavorable process of ordering nearby water molecules.
It is vital to emphasize that hydrophobic interaction are not chemical bonds in and of
themselves.
Another significant family of compounds worth mentioning is amphiphiles. These
compounds have large amounts of both hydrophilic and hydrophobic functional groups.
Detergents such as sodium dodecyl sulfate (SDS), which has a very water-soluble sulfate
 group and a very insoluble 12-carbon alkyl group, are typical examples. When SDS is
introduced to water, this schizophrenic combination causes the hydrocarbon chains to
cluster together away from water contact. In this situation, the clusters generated are
micelles, which are spherical structures. SDS molecules line up at an air-water interface,
with their hydrocarbon tails facing up into the air and their sulfate groups in contact with
water. SDS is an effective detergent. Its hydrocarbon tail will adhere to nonpolar surfaces
like greasy dirt and disintegrate it within the micelle's interior. The dirt and detergent may
be washed away once the dirt-filled micelles are suspended in water by agitation.
VI. Noncovalent Interactions in Biomolecules
Interactions between biomolecules are mediated by weak, reversible bonds
(noncovalent bonds or noncovalent interactions). Noncovalent bonds are "individually
weak but collectively powerful," and they work together to sustain the complex structures
of biomolecules like proteins. Biomolecules, on the other hand, demonstrate flexibility
since they are individually weak, which is useful in activities such as enzyme catalysis.
Non-covalent interactions can allow for the reversible binding of tiny biomolecules to
enzymes and nucleic acids. Noncovalent interactions are typically less than one-tenth the
strength of covalent bonds such as the -C-H bond. The overall characteristics of each
form of noncovalent contact, as well as the energy necessary to break them.
a) Charge-charge interactions
 Charge-charge interactions occur between functional groups or ions that
are negatively charged. Ion pairing interactions and salt bridges are other
names for these connections. The strength of these bonds is proportional to
the square of the distance between the charges. The strength of contacts is
also affected by the medium in which they occur, with polar fluids such as
water reducing interactions through ion solvation. Repulsive pressures
between similar charges can also play a function in biological processes.
b) H-bonds
 H-bonds formed between water molecules are just one of several kinds
present in biomolecules. An H-bond is described in general as a dipolar
attraction between a hydrogen atom connected to one electronegative atom
and another electronegative atom. To create a molecular dipole, the H
atom must be covalently attached to an electronegative atom such as O or
N. The hydrogen donor is the atom with the covalently attached hydrogen
atom, while the hydrogen acceptor is the other atom. In an H-bond, the
distance between two electronegative atoms is 0.3 nm (3). The strength of
an H-bond is strongly reliant on the alignment of molecular orbitals of
interacting molecules, and it is greatest when they are properly aligned. As
a result, H-bonds are becoming more common. Specificity in molecular
interactions, such as A-T and G-C base pairing in DNA, is critical.
c) van der Waals forces
  These forces are attractors between oppositely oriented dipoles that are
created transiently in the electron clouds of closely interacting molecules.
When the interacting molecules are barely touching, the intensity of these
forces is greatest. In reality, as molecules are pushed closer together, these
pressures become destabilizing and drive them away. It is worth noting
that the van der Waals contact radius is defined as the distance at which
molecular attraction is greatest. Van der Waals forces are the least strong
of the noncovalent interactions. Van der Waals bonds, on the other hand,
are frequently significant in the packing of amino acids inside a folded
protein and the interactions between neighboring bases stacked within the
DNA double helix. They can also facilitate particular interactions because
they become collectively powerful when the interacting molecules have
precisely complementary forms and can come near to one other.
d) Water is a nucleophile
 Water is frequently used as a reactant in biological processes. Unshared
electron pairs in water molecules can act as nucleophiles, attacking an
electrophilic center in another molecule. The hydrolysis of peptide bonds
is an excellent example of water acting as a nucleophile. Even though this
is a favorable reaction, peptide bonds are fairly stable since the activation
energy for this reaction is quite large. As a result, unless catalyzed by an
enzyme, the process is exceedingly sluggish at physiological temperatures
and pH.
VII. Ionization of water
As a prerequisite to discussing pH, we must first examine water ionization, as it is
through this process that solution pH is eventually determined. A water molecule has a
modest propensity to dissociate, in which a proton is lost to another water molecule. This
reaction produces a hydronium ion (H3O+) and a hydroxyl ion (OH-).

Because a hydronium ion may transfer its proton to another molecule, it is

classified as an acid (proton donor). Because a hydroxyl ion may take a proton from acid,
it is referred to as a base (proton acceptor). The ionization reaction is frequently denoted
as:

Water has a finite and determined ionization capacity, and the ionization process
has a distinctive equilibrium constant at any temperature.
 The electrical conductivity of clean water was used to determine Keq for water.
(Note that electrical conductivity is related to ion concentrations in water.) The Keq = 1.8
x 10-16 M. This Keq value, together with the water concentration ([H2O] = 55.5 M), may
be entered into the equilibrium equation to generate another equation that specifies the
quantities of [H+] and [OH-] in any water sample or biochemical buffer:

The constant KW is known as the water ion product. According to the derivation,
the product of the [H+] and [OH-,] concentrations in any water sample or buffer will
always equal 1 x 10-14 M2.
This conclusion immediately leads to the definition of a "neutral solution" and the
pH scale. A neutral solution is one in which [H+] equals [OH-]. [H+] = [OH-] = 1 x 10-7
M when these concentrations are comparable. Because this equilibrium reaction is
usually followed, the addition of proton-consuming base results in an excess of hydroxyl
ions and a basic solution. Similarly, adding an acid that consumes hydroxyl ions results in
a surplus of hydronium ions and an acidic solution.
VIII. The pH Scale
pH is merely a simpler means of defining the concentration of H+ ions in solution
(assuming logarithms are convenient!). The pH scale is as follows:

Concentrations in the range of 1 M to 10-14 M H+ are translated to values

between 0 and 14 using logarithms. A neutral solution's pH, for example, is:

Neutral solutions have a pH of 7.0 or above. Solutions with a pH of 7.0 are

considered "acidic," whereas solutions with a pH greater than 7.0 are called "basic."
IX. Acid dissociation constants of weak acids
a) Strong and weak acids and bases
 Most reactions are reversible, and equilibrium occurs when the rate of the
forward reaction equals the rate of the reverse reaction. The equilibrium
constant (Keq) for a general reaction is defined as the ratio of products to
reactants at equilibrium, as seen in the water ionization example above.
 Remember that all reactions have a specific Keq at a given temperature.
Many biomolecules are weak acids, such as amino acids. Weak acids, in
contrast to strong acids (HCl, H2SO4, etc.), only partially dissociate when
dissolved in water. The following equilibrium reactions exhibit the dissociation of
strong acids, strong bases, and the weak acid, acetic acid (CH3COOH).

The conjugate acid-conjugate base pair is the name given to the two
species in solution at the equilibrium of a weak acid.
b) Equilibrium constant (Keq) and the pKa
The equilibrium constant for weak acid (HA) dissociation is

The acid dissociation equilibrium constant, Ka, is also known as the acid
dissociation constant, and Ka = Keq. Keep in mind that "the greater the Ka, the
stronger the acid."
For weak acids, biochemists often use "pKa" values rather than Ka values,
as in the case of pH. pKa is defined in the same way that pH is.

"The lower the pKa, the stronger the acid," when comparing pKas.
c) Henderson-Hasselbalch equation
In buffer solutions, the Henderson-Hasselbalch equation provides the
quantitative connection between pH and pKa. It may be used to plot a titration
curve. In class, the HH equation will be deduced from the equation giving the
equilibrium constant for ionization of a weak acid, Ka = [H+ ][A- ]/[HA]. The
HH eq in its ultimate form is
 According to the equation, the pH of a solution is determined by the pKa
and the ratio of conjugate base to conjugate acid components present. The
equation may be used to compute the pH of a weak acid solution when the ratio of
[A-]/[HA] is known, or to calculate the ratio of [A-]/[HA] when the pH is known.
d) Measurement of pKa by titration
Titration is used to determine pKa values. A weak acid in solution is
transformed to its conjugate base in a titration experiment by the addition of a
strong base. Remember that a strong base (e.g., NaOH) will convert a weak acid
to its conjugate base stoichiometrically (1 part to 1 part). As a result, the number
of moles of a weak acid in solution equals the number of moles of a strong base
required to convert all conjugate acid molecules to the conjugate base form. An
example acetic acid titration equation is presented below.

Two equilibrium processes are taking place concurrently throughout the

titration.

In other words, as an OH- ion is introduced to the solution, it joins forces

with an existing H+ ion. A molecule of the conjugate acid form of acetic acid
dissociates a proton to restore equilibrium when the H+ ion is withdrawn. The
base changes all of the CH3COOH presents to CH3COO- as a result of the
titration.
Similar to how a strong acid (like HCl) stoichiometrically changes a weak
base into its conjugate acid,

The pKa turns out to be the center of the plot of a titration curve, as will be
mathematically demonstrated using the Henderson-Hasselbalch equation, see
below.
For a given amount of base supplied, observe that the pH varies quickly at
the extremes of the titration curve and moderately in the center. At the middle of
the curve, or after the addition of 0.5 equivalents of the strong base, the pH shift is
the smallest. The middle portion of the curve, where the pH changes the least in
response to the addition of a strong basic or strong acid, is the best buffering zone
for the weak acid. [CH3COOH] equals [CH3COO-] at the halfway point.
 With weak acids that contain more than one dissociable proton, such as
phosphoric acid, the titration behavior and its quantitative treatment using the HH
equation are comparable. The sole distinction is that the titration curve of a
"polyprotic" chemical has a plateau for each of its dissociable protons rather than
having a single plateau. One conjugate acid/base pair predominates in solution
across each plateau, with the pKa of the acid group that is giving up the proton
serving as the plateau's midpoint.
X. Buffers
As seen above for the acetic acid titration curve, a buffer is "a solution that tends
to resist a change in pH on the addition of a tiny quantity of strong acid or base." Near the
midway of the curve, the pH of a solution undergoing titration varies very little. The
solution's maximum buffering capacity is reached at halfway when pH = pKa and
[CH3COOH] = [CH3COO-]. The ideal buffering area typically spans a pH unit on each
side of the pKa. Due to the largest concentrations of both buffering species, HA and A-,
this pH range has the strongest buffering capacity. Based on their pKa values and the pH
range that has to be buffered, buffers are chosen.
Phosphate serves as a cell's primary buffer. The second dissociation process in
this instance, with pK2 = 7.2 (Fig. 2.19) offers to buffer.

The CO2-carbonic acid-bicarbonate system functions as a buffer in the blood.

Carbonic acid and bicarbonate are the main buffering forms in this situation. Despite the
reaction's pKa
 At just 6.4, H2CO3 easily breaks down into CO2 and H2O, shifting the carbonic
acid bicarbonate balance to the left (to a higher pKa) and bringing it closer to the pH of
the blood. It's interesting to note that hemoglobin also functions as a blood buffer, and
Chap shall explain how this happens. 4.

Logarithms and Antilogarithms

Definition of a Logarithm:
The exponent needed to represent a number as a power of ten is given by the number's
logarithm.
Relationship between Logarithmic and Exponential Equations:

You determine the exponent x when you take a number's logarithm. You may return a
number to its exponential form, or the number represented in scientific notation, by taking its
antilogarithm.
Application to pH
By analogy to the above, pH = - log10 [H+] expresses the same relationship as 10-pH =
[H+].