Biochemistry
College of Allied Health Sciences
Bachelor of Science in Medical Laboratory Science
First Semester, A.Y. 2022-2023
[TRANS] WATER
HYDROGEN BONDING
 Hydrogen bonding
- Plays a crucial role in shaping the properties of water:
PROPERTIES OF WATER
 Bent Structure and Polarity:
o Water's "bent" molecular structure, with two
hydrogen atoms covalently bonded to one oxygen
atom, results in polarity. The electronegative oxygen
atom and the hydrogen atoms create a dipole,
making the molecule polar.
 Hydrogen Bond Formation:
o Water can both donate and accept hydrogen bonds.
Each water molecule can form up to four hydrogen
bonds with neighboring molecules. These strong
intermolecular attractions contribute to water's high
boiling point, melting point, heat of vaporization, and
surface tension.
 Structure of Ice:
o In the solid form (ice), hydrogen bonds create a
three-dimensional network with straight and
directional bonds. This structure causes ice to be
less dense than liquid water, allowing it to float.
 Cooperative Hydrogen Bonding:
o Hydrogen bonding in water is cooperative, meaning
that H-bonded water molecules become better
donors and acceptors, reinforcing the network of
hydrogen bonds.
 Liquid Water Structure:
o In liquid water, hydrogen bonds are disordered, and
molecules have an average of 4.4 close neighbors.
The structure lacks the regular lattice seen in ice, but
most hydrogen bonds persist even in the liquid state.
 Solvent Properties:
o Water's polarity makes it an excellent solvent for
ionic and polar substances. It forms hydration shells
around ions, allowing them to dissolve.
 High Dielectric Constant:
o Water's high dielectric constant diminishes the
attraction between oppositely charged ions in
solution, preventing them from forming neutral
molecules.
 Hydrogen Bonds with Polar Solutes:
o Water readily forms hydrogen bonds with polar
solutes like sugars, aiding their dissolution.
 Hydrophobic Interactions:
o Nonpolar solutes do not readily form hydrogen
bonds with water and tend to be sparingly soluble.
Water molecules reorganize around nonpolar
solutes, creating a clathrate structure. This is driven
by entropy, not direct interactions, and is known as
hydrophobic interactions.
 Amphiphilic Molecules:
o Amphiphilic molecules, containing both polar and
nonpolar groups, can form micelles in water. These
clusters allow the polar parts to hydrate while the
nonpolar parts interact with each other through
hydrophobic interactions.
In summary, hydrogen bonding in water leads to its
uniqueproperties, including polarity, strong
intermolecular attractions, and the ability to dissolve a
wide range of substances, making it essential for many
biological and chemical processes.
INFLUENCE OF SOLUTES ON WATER PROPERTIES
 Solutes (whether polar or nonpolar)
o Disrupt the structure of liquid water by affecting its
dynamic hydrogen bonding interactions.
o Solutes create local order by limiting the orientations
of neighboring water molecules, reducing the
dynamic interplay seen in pure water.
COLLIGATIVE PROPERTIES:
 The presence of solutes leads to colligative properties,
which depend solely on the number of solute particles per
unit volume and not on their chemical nature.
o These properties include
 Freezing Point Depression
 Boiling Point Elevation
 Vapor Pressure Lowering
 Osmotic Pressure Effects
 For instance, a 1 molal solution depresses the freezing
point by 1.86°C, raises the boiling point by 0.543°C, lowers
vapor pressure, and creates an osmotic pressure relative to
pure water of 22.4 atm.
OSMOTIC PRESSURE AND ITS SIGNIFICANCE
 Osmotic pressure
o A result of high solute concentrations in a solution,
which can be problematic for cells.
o Cells combat osmotic pressure by having rigid walls
or storing substances like amino acids and sugars in
polymeric form to reduce pressure.
WATER IONIZATION
 Water exhibits a slight tendency to form ions due to the
electronegative oxygen atom stripping an electron from a
hydrogen atom.
 This ionization results in the formation of hydronium ions
(H3O+) and hydroxyl ions (OH-).
KW - ION PRODUCT OF WATER
 The equilibrium constant for water ionization is Keq, which
is equal to [H3O+][OH-].
 The ion product of water (Kw)
o the product of these ion concentrations and is
approximately equal to 10^(-14) M^2 at 25°C.
 Kw
o shows the reciprocal relationship between [H3O+]
and [OH-] concentrations in aqueous solutions.
 In acidic solutions (higher [H3O+]), [OH-] is correspondingly
lower, and vice versa in basic solutions (higher [OH-]).
 In summary, the presence of solutes affects water's
structure and gives rise to colligative properties. Water
ionizes into hydronium and hydroxyl ions, with Kw
representing the equilibrium constant for this process
and demonstrating the relationship between [H3O+]
and [OH-] concentrations in solutions.
PH SCALE AND SØREN SØRENSEN
 Søren Sørensen
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o introduced the pH scale to simplify the
representation of hydrogen ion (H+) concentrations.
 The pH is the:
o negative logarithm (base 10) of the hydrogen ion
concentration ([H+]): pH = -log10[H+].
 The pH scale
o Ranges from 0 (high [H+]) to 14 (low [H+]), with a
reciprocal relationship between [H+] and [OH-].
 The pKw represents the relationship between pH, pOH, and
the ion product of water, Kw, and is equal to 14.
WATER IONIZATION AND KW
 Water ionizes to form hydrogen ions (H3O+) and hydroxyl
ions (OH-) due to the stripping of electrons by the oxygen
atom from hydrogen.
 Kw
o Represents the equilibrium constant for this
ionization process and is approximately 10^(-14)
M^2 at 25°C.
 The equation Kw = [H+][OH-]
o Relates the concentrations of hydrogen and hydroxyl
ions in water.
STRONG ELECTROLYTES
 Substances that almost completely dissociate into ions in
solution, increasing the electrical conductivity.
 Examples include salts like NaCl, strong acids like HCl, and
strong bases like NaOH.
 Dissociation of a strong acid like HCl in water leads to the
formation of hydronium ions (H3O+) and chloride ions (Cl-
).
WEAK ELECTROLYTES
 Only partially dissociate into ions in solution. Acetic acid
(CH3COOH) is an example.
 The acid dissociation constant (Ka) describes the extent of
ion formation in water.
 The Henderson–Hasselbalch equation (pH = pKa + log([A-
]/[HA])) relates pH, pKa, and the concentrations of a weak
acid (HA) and its conjugate base (A-).
TITRATION CURVES FOR WEAK ACIDS
 Titration
o Used to determine the amount of acid in a solution.
 Titration curve
o Shows the relationship between pH and the amount
of base (e.g., NaOH) added.
o At the midpoint of the curve, when half of the acid is
neutralized, pH = pKa.
o Weak acids with different pKa values have titration
curves with varying midpoints.
 Polyprotic acids like phosphoric acid (H3PO4) have multiple
dissociation steps, each with its characteristic pKa and
titration curve.
BUFFERING CAPACITY OF WEAK ACIDS
 Weak acids and their conjugate bases:
o Act as buffers, maintaining a relatively stable pH in a
certain range around their pKa values as acid or
base is added.
 In summary, Søren Sørensen introduced the pH scale
to simplify the representation of hydrogen ion
concentrations in a logarithmic scale. Water ionizes to
form H3O+ and OH-, with Kw representing the
equilibrium constant. Strong electrolytes dissociate
almost completely, while weak electrolytes only
partially dissociate, and their behavior can be
described using the Henderson–Hasselbalch equation.
Titration curves illustrate the progressive dissociation
of weak acids, with buffering capacity around their pKa
values.
BUFFER SYSTEMS:
 Buffers
o Solutions that resist changes in pH when acid or
base is added.
o Work by absorbing added H+ or OH- ions through
specific reactions, preventing significant pH
changes.
o
 Buffer system
o Typically consists of a weak acid and its conjugate
base.
 The pH of a buffer solution is close to the pKa of the weak
acid, and it maintains a relatively constant pH.
 The molarity of a buffer is the sum of the concentrations of
the weak acid and its conjugate base.
IMPORTANCE OF PH REGULATION
 Cellular processes and enzyme activities are highly
dependent on pH.
 Maintaining a constant pH is essential for the proper
functioning of metabolic pathways.
 Buffer systems play a vital role in protecting cells from
harmful pH changes.
INTRACELLULAR BUFFERING SYSTEMS
 Two major intracellular buffering systems are the
phosphate (HPO4^2-/H2PO4^-) system and the histidine
system.
o Phosphate buffer system is effective because pK2 is
near physiological pH (6.9 - 7.4).
o Histidine's imidazole group has a pKa of 6.04, which
can serve as a buffer.
 Protein-bound and dipeptide histidine can also contribute to
buffering in cells.
"GOOD" BUFFERS
 N. E. Good developed synthetic buffers with pKa values in
the physiological pH range (around 6-8).
 These buffers are useful for in vitro experiments and
provide options for maintaining pH near physiological
values.
PROPERTIES OF WATER
 Water is a powerful solvent capable of dissolving a wide
range of substances, making it important for biological
processes.
 Its poor solubility for nonpolar substances drives the
formation of membranes and cellular structures through
hydrophobic interactions.
 Water's high dielectric constant allows for ionization,
enriching the chemical diversity in living systems.
 Water's thermal properties, including high specific heat,
heat of fusion, and heat of vaporization, make it an effective
temperature buffer and regulator.
 Anomalous expansion of water as it cools near freezing
allows ice to form an insulating layer on bodies of water,
preserving liquid water below.
 Water's high surface tension and density impact capillary
action in plants and the shape of living organisms.
 Osmosis, the movement of water from dilute to
concentrated solutions across semipermeable boundaries,
affects the shape of cells and organisms.
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 In summary, buffer systems help regulate pH in living

organisms, ensuring proper cellular function. Water's
unique properties, such as its role as a solvent, thermal
characteristics, and surface tension, make it essential for
life and environmental fitness. Water's role in osmosis and
capillary action also influences the shape and behavior of
living organisms.

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