22BM402 BIOSCIENCES IN MEDICAL ENGINEERING

UNIT 1 & LP 1 – BIOCHEMISTRY INTRODUCTION AND

WATER AS BIOLOGICAL SOLVENT

1. INTRODUCTION
Biochemistry is the study of life processes at the molecular level. Learn about the
various fields, their applications, and their significance.
Biochemistry has been defined as the scientific study of the chemistry and physiology
of living organisms. This branch of science deals with the chemical reactions and
interactions in living systems. From enzymes to hormones, biochemists study these
molecules and their actions.
Cellular biochemistry: This branch focuses on the chemical processes within cells. It
includes studying how cells produce energy, store and use nutrients, and how they
produce and maintain their structure.
Molecular biochemistry: This branch looks at the structure and function of
biomolecules, such as proteins, DNA, and carbohydrates. It includes understanding
how these molecules carry out biochemical reactions and how they interact.
Metabolic biochemistry: This branch focuses on the chemical reactions in the body to
maintain life. It includes studying energy production, nutrient metabolism, and
detoxification.
Biochemical genetics: This branch investigates the role of genes in biochemical
processes. It includes understanding how genes are involved in synthesizing proteins
and other biomolecules and how they function.
Application of chemistry to the study of biological process at the cellular and
molecular level.
1.1. The Chemistry of water
Water has a simple molecular structure. It is composed of one oxygen atom and two
hydrogen atoms. Each hydrogen atom is covalently bonded to the oxygen via a shared
pair of electrons. Oxygen also has two unshared pairs of electrons. Thus there are 4
pairs of electrons surrounding the oxygen atom, two pairs involved in covalent bonds
with hydrogen, and two unshared pairs on the opposite side of the oxygen atom.
Oxygen is an "electronegative" or electron "loving" atom compared with hydrogen.

An electrostatic attraction between the partial positive charge near the hydrogen atoms
and the partial negative charge near the oxygen results in the formation of a hydrogen
bond as shown in the illustration.

The ability of ions and other molecules to dissolve in water is due to polarity. For
example, in the illustration below sodium chloride is shown in its crystalline form and
dissolved in water. Water is a polar molecule, meaning it has an uneven distribution of
electrons, creating a partial negative charge on the oxygen atom and partial positive
charges on the hydrogen atoms. Sodium chloride (NaCl) is an ionic compound
composed of positively charged sodium ions (Na+) and negatively charged chloride
ions (Cl-). The polar nature of water allows it to interact with these ions effectively

Many other unique properties of water are due to the hydrogen bonds. For example, ice
floats because hydrogen bonds hold water molecules further apart in a solid than in a
liquid, where there is one less hydrogen bond per molecule. The unique physical
properties, including a high heat of vaporization, strong surface tension, high specific heat,
and nearly universal solvent properties of water are also due to hydrogen bonding. The
hydrophobic effect, or the exclusion of compounds containing carbon and hydrogen
(nonpolar compounds) is another unique property of water caused by the hydrogen bonds.
The hydrophobic effect is particularly important in the formation of cell membranes. The
best description is to say that water "squeezes" nonpolar molecules together.

1.1.1 Acids and Bases, Ionization of Water

Acid release H+ and Bases accept H+. We define the pH of a solution as the negative
logarithm of the hydrogen ion concentration.
• at pH 7.0, a solution is neutral
• at lower pH (1-6), a solution is acidic
• at higher pH (8-14), a solution is basic

1.1.2 Water as a biological solvent

Bonded by a covalent bond. Hydrogen carries a positive molecular charge,
while oxygen carries a negative molecular charge. Water molecules are attracted to
each other by a relatively low electrical attraction (‘hydrogen bond’)
H-bond: Negative hydrogen atoms attract positive oxygen atoms in other molecules.
• Basis of life on our planet.
• Exists in different physical states – solid, liquid and gas – and makes up 70% of
the surface of Earth.
• At low temperatures (below 0°C), it is a solid.
• When at “normal” temperatures (between 0°C and 100°C), it is a liquid.
• While at temperatures above 100°C, water is a gas (steam)
• 65 – 90% of the weight of all living organisms.  plays an important role in all
vital processes of living organisms
Bonded by a covalent bond. Hydrogen carries a positive molecular charge, while
oxygen carries a negative molecular charge. Water molecules are attracted to each
other by a relatively low electrical attraction (‘hydrogen bond’). Water has unique
properties because of its polarity and the hydrogen bonds between its molecules

1.1.3 Water is a polar solvent

When sodium chloride (NaCl) dissolves in water, it produces positive sodium ions and
negative chlorine ions. The positively-charged side of the water molecules are
attracted to the negatively- charged chloride ions and the negatively-charged side of
the water molecules are attracted to the positively- charged sodium ions

Water has the ability to ionize molecules, which are necessary for life. In biological
systems, ions play vital roles in cellular communication, enzymatic reactions, and
maintenance of pH balance. The presence of charged ions allows water to act as a
solvent for a wide range of molecules, facilitating the transport of nutrients, waste
removal, and the formation of complex structures like proteins and nucleic acids.
Additionally, the ionization of water contributes to its ability to buffer changes in pH,
providing a stable environment for biological reactions. This means that water has the
ability to disassociate the molecules necessary for life into positive and negative ions.
Water has high specific heat. Water has the highest specific heat on Earth due to the
hydrogen bonds between its molecules. This helps living organisms to have a constant
temperature which is essential for the vital processes occurring within their bodies.
This property enables water to absorb and store a significant amount of heat without
undergoing large temperature changes. In biological systems, this means that
organisms, especially those with a high water content, can resist rapid temperature
fluctuations in their environment. The stable internal temperature is crucial for
biochemical reactions and cellular functions to occur optimally. Organisms can
regulate their body temperature by absorbing or releasing heat through water,
preventing drastic shifts that could disrupt metabolic processes. This thermal buffering
effect provided by water's high specific heat is particularly essential for maintaining
the homeostasis necessary for life processes to function smoothly across a range of
environmental conditions.
1.1.4 Other Properties of water
• Water has low viscosity: Viscosity refers to a fluid's resistance to flow. Water's
low viscosity is due to its molecular structure and relatively weak
intermolecular forces compared to substances with higher viscosity, such as
honey or motor oil. This characteristic allows water molecules to move more
freely past one another, resulting in its fluidity. Water's low viscosity plays a
crucial role in various natural processes and human activities, such as its ability
to easily flow through pipes, facilitate transportation of nutrients in biological
systems, and contribute to its effectiveness as a solvent.
• High surface tension: Water has relatively high surface tension compared to
many other liquids. Surface tension arises due to the cohesive forces between
water molecules at the surface, which results in a "skin-like" effect on the
surface of the water, allowing it to resist external forces.
• Water density increases under 4◦C: Water molecules are arranged in a specific
structure when it freezes (0°C) and forms ice. This structure has empty spaces,
leading to a lower density compared to liquid water. As the temperature
increases from 0°C to 4°C, the water molecules start moving and vibrating
more, causing the ice-like structure to break down. This brings the molecules
closer together, resulting in increased density. However, beyond 4°C, the
typical behavior of liquids kicks in. As the temperature continues to rise, the
water molecules move even faster and further apart, leading to a decrease in
density.
• The freezing point of water decreases if it has substances dissolved in it: In pure
water, water molecules are free to arrange themselves in a crystal lattice
structure when the temperature reaches 0°C, causing it to freeze. When a
substance is dissolved in water (forming a solution), the dissolved particles
(solutes) interfere with the water molecules' ability to form this ordered
structure. This disrupts the freezing process, requiring a lower temperature for
the remaining water molecules to overcome the disruption and form ice
crystals.
 • Water can turn into vapour in temperatures lower than boiling point
(100◦C): ater can turn into vapour at temperatures lower than its boiling point
(100°C). This process is called evaporation. Here's the key difference between
evaporation and boiling: Evaporation: Occurs at any temperature, including
below the boiling point. It's a surface phenomenon where individual water
molecules at the surface gain enough energy to escape into the surrounding air
as vapor. The rate of evaporation is influenced by several factors like
temperature, humidity, and air movement. Boiling: Occurs only at the boiling
point of a liquid under specific pressure conditions. It's a bulk phenomenon
where bubbles of vapor form within the entire liquid due to the high
temperature and pressure overcoming the intermolecular forces holding the
molecules together.
• Water rise in capillary tubes: Surface tension: Water molecules have a strong
attraction to each other, creating a "skin" on the liquid surface. This invisible
film acts like a stretched membrane, resisting external forces and minimizing
the surface area. Adhesion: Water molecules also have an attraction to the
material of the capillary tube. When one end of the tube is placed in water, the
adhesive force pulls water molecules up the walls of the tube. Meniscus: The
combined effect of surface tension and adhesion creates a curved surface where
the water meets the tube wall, called a meniscus. In the case of water in a glass
tube, the meniscus is concave (curved upwards).

1.2. Weak Acid and bases

An acid is any hydrogen-containing substance that is capable of donating a
proton(hydrogen ion) to another substance. And a base is a molecule or ion able to
accept a hydrogen ion from an acid.
Arrhenius theory : “an acid generates H+ions in a solution whereas a base produces
an OH–ion in its solution”.
Bronsted-Lowry theory: an acid as a proton donor and a base as a proton acceptor
Lewis definition : acids as electron-pair acceptors and bases as electron-pair donors
Arrhenius theory : an acid generates H+ ions in a solution whereas a base produces
an OH–ion in its solution.
Bronsted-Lowry theory: an acid as a proton donor and a base as a proton acceptor
In an acid-base or neutralization reaction, an Arrhenius acid and base usually react to
form water and a salt. The Bronsted-Lowry acid is a substance which donates a proton
or H+ ion to the other compound and forms a conjugated base.

1.2.1 State differences between acids and bases

Acids and bases are two fundamental categories of substances in chemistry, and they
differ in several key ways:

Definition:
Acid: Acids are substances that can donate a proton (H+) or accept an electron pair in
a chemical reaction. In the Brønsted-Lowry definition, acids are proton donors.
Base: Bases are substances that can accept a proton (H+) or donate an electron pair in
a chemical reaction. In the Brønsted-Lowry definition, bases are proton acceptors.
pH:
Acids have a pH less than 7 on the pH scale. The lower the pH, the stronger the acid.
Bases have a pH greater than 7 on the pH scale. The higher the pH, the stronger the
base.
Taste and Feel: Acids often taste sour. For example, lemon juice is acidic. Bases often
taste bitter and feel slippery to the touch. For example, soap is a base.
Chemical Properties: Acids react with metals to produce hydrogen gas. Bases can react
with fats and oils (in a process called saponification) to form soap.
Examples:
Common examples of acids include hydrochloric acid (HCl), sulfuric acid (H 2SO4),
and acetic acid (found in vinegar).
Common examples of bases include sodium hydroxide (NaOH), potassium hydroxide
(KOH), and ammonia (NH3).
Neutralization: When an acid reacts with a base, they neutralize each other, forming
water and a salt. This reaction is called neutralization.
Indicator Dyes: Acids turn blue litmus paper red and Bases turn red litmus paper blue.
Strength: Acids and bases can be classified as strong or weak based on their ability to
ionize in solution. Strong acids and bases ionize completely, while weak ones only
partially ionize.
Chemical Formulas:
Acids often have the hydrogen ion (H+) in their chemical formulas, such as HCl for
hydrochloric acid.
Bases often have hydroxide ions (OH-) in their chemical formulas, such as NaOH for
sodium hydroxide.
It’s important to note that the Brønsted-Lowry definition of acids and bases is just one
of several definitions in chemistry. The Lewis definition, for example, focuses on
electron pair donors and acceptors and is more general, encompassing a wider range of
chemical reactions involving acids and bases

Weak acids and bases are only partially ionized in their solutions, whereas strong acids
and bases are completely ionized when dissolved in water.
When HCl is dissolved in H2O, it completely dissociates into H+(aq) and Cl−(aq) ions;
all the HCl molecules become ions:

Any acid that dissociates 100% into ions is called a strong acid. If it does not
dissociate 100%, it is a weak acid. HC2H3O2 is an example of a weak acid:

Weak bases : Ammonia NH3, Trimethyl ammonia N(CH3)3