Biochemical Processes

Most chemical changes in a cell result from chains and cycles of biochemical
reactions, with each step controlled by a separate, specific enzyme. Metabolism is the
totality of the chemical reactions which occur within a cell, and can be divided into two
types:
 Anabolic reactions involve the synthesis of complex molecules from simpler ones
and usually require energy to form new bonds (endergonic)
 Catabolic reactions involve the breakdown of complex molecules into simpler ones
and usually release energy from breaking bonds (exergonic)

Energy Transformations
 Energy in living cells is stored and released in the chemical form of ATP (adenosine
triphosphate)
 ATP is made up of an RNA nucleotide (base = adenine) bonded to two additional
phosphate groups (three in total)
 These additional phosphates are connected by high energy bonds that release a large
amount of free energy when hydrolyzed
 The energy released from the hydrolysis of ATP (into ADP + P i) can be used by
the cell to fuel biochemical processes

ATP Hydrolysis

 ATP can be synthesized by the transmembrane enzyme ATP synthase (via both
photosynthesis and cell respiration)
 Photosynthesis uses light energy to synthesize ATP, which is then hydrolyzed in
order to synthesize organic molecules (anabolic reaction)
 Cell respiration breaks down organic molecules to release energy which is used to
synthesize ATP for use in cell processes (catabolic reaction)

Functions of ATP
 ATP provides an immediate source of energy when hydrolyzed and functions as
the energy currency of the cell. Biochemical processes that utilize ATP include:

 Growth and repair: Increase cell size and replace damaged tissue requires ATP
 Movement: The contraction of muscle fibres in order to generate movement in
organisms requires ATP
 Nerve transmissions: The generation and transmission of a nerve impulse (action
potential) requires ATP
 Active transport: Moving molecules against their concentration gradient, or by
cytosis, requires ATP
 Biosynthesis of macromolecules: Building complex organic molecules from
simpler subunits (anabolism) requires ATP
 Emission of light: Some cells may be capable of luminescence, and this process
requires ATP

Dialysis
Dialysis is a separation process whereby smaller molecules are segregated from
larger molecules (macromolecules) in a solution by virtue of their different rates of
diffusion through a specific membrane (or by nondiffusion, which is the criterion of the
colloidal state and forms the basis of separation of colloidal materials from crystalloids).

In 1861, chemist Thomas Graham (how developed Graham's Law) used the
process of dialysis, a process used to separate colloidal particles from dissolved ions or
molecules. Dialysis is possible because of the unequal rates of diffusion through
a semipermeable membrane. A semipermeable membrane is a membrane that lets some
molecules to pass through it while not letting others. Examples of semipermeable
membranes include parchment and cellophane.

The Rate of Dialysis

Dialysis is not a quick process; the rate of dialysis depends on the speed of the
unequal diffusion rates between the crystalloids and the colloids and the differences in
particle size. The rate of dialysis can be changed through heating, or if the crystalloids are
charged, then applying an electric field, called electrodialysis. Electrodialysis is the type
of dialysis in which electrodes are placed on the sides of the membrane. In this way,
positive ions can pass through one side of this membrane while the negatively charged ions
can pass through the other side of the membrane. This causes acceleration in the process
of dialysis.

Hemodialysis
 Hemodialysis is a method in which kidney failure is treated with the process of
dialysis. In hemodialysis, blood is removed, purified through dialysis, and returned to the
bloodstream. In kidney failure, there is a retention of salts and water, urea, and metabolic
acids. The patient is then connected to a dialysis machine, which is also called a
hemodialyzer. The blood flows through small channels made of semipermeable
membranes. The dissolved substances like urea and salts pass through a sterile solution.
Compounds like sugar and amino acids are added to the sterile solution. The dialysis
solution is on the other side of the membranes, and the molecules flow through the
membranes. The molecules diffuse from a higher concentration to low concentration area.
The concentrations of molecules needed to be removed from the blood are zero in the
dialysis fluid.

The process of hemodialysis helps many patients who have kidney failure because
a person who suffers from kidney failure are at great risk, because someone who has
complete kidney failure will need a kidney transplant within two weeks, or else he/she will
face death. Between the time that the person finds a suitable kidney to be transplanted, the
hemodialyzer comes into great help in facing the fight against death.

Osmosis
Osmosis is a type of diffusion that, in biology, is usually related to cells. Diffusion
is when molecules or atoms move from an area of high concentration to an area of low
concentration. Osmosis is when a substance crosses a semipermeable membrane in order
to balance the concentrations of another substance. In biology, this is usually when a
solvent such as water flows into or out of a cell depending on the concentration of a solute
such as salt. Osmosis happens spontaneously and without any energy on the part of the
cell.

Reverse Osmosis
 Reverse osmosis is the process by which excess pressure is placed on one end of a
semipermeable barrier in order to drive a solution from an area of high solute concentration
to that of a low solute concentration. Opposite from general osmosis, the solvent does not
go down a concentration gradient. In this case, the cell membrane serves as a filter.
However, the key difference between osmosis
and filtration is that in reverse osmosis,
separation is done by diffusive mechanisms
rather than size exclusion or staining. Reverse
osmosis has been used industrially for water
treatment. Salt water collected from the ocean
is transformed to pure water by setting an
external pressure equal to the air pressure at sea
level. Water purification is only one industrial
use of reverse osmosis. Metals and chemicals
are also recycled through this process.

Types of Solutions
In biology, there are three different types of solutions that cells can be in: isotonic,
hypotonic, and hypertonic. Different types of solutions have different impacts on cells due
to osmosis.
Isotonic
An isotonic solution has the same concentration of solutes both inside and outside
the cell. For example, a cell with the same concentration of salt inside it as in the
surrounding water/fluid would be said to be in an isotonic solution. Under these conditions,
there is no net movement of solvent; in this case, the amount of water entering and exiting
the cell’s membrane is equal.
Hypotonic
In a hypotonic solution, there is a higher concentration of solutes inside the cell
than outside the cell. When this occurs, more solvent will enter the cell than leave it to
balance out the concentration of solute.
Hypertonic
A hypertonic solution is the opposite of a hypotonic solution; there is more solute
outside the cell than inside it. In this type of solution, more solvent will exit the cell than
enter it in order to lower the concentration of solute outside the cell.
How Osmosis Affects Cells
Osmosis affects plant and animal cells differently because plant and animal cells
can tolerate different concentrations of water. In a hypotonic solution, an animal cell will
fill with too much water and lyse or burst open. This is a process called lysis. However,
plant cells need more water than animal cells, and will not burst in a hypotonic solution
due to their thick cell walls; hypotonic solutions are ideal for plant cells. The optimal
condition for an animal cell is to be in an isotonic solution, with an equal amount of water
and solutes both inside and outside. When a plant cell is in an isotonic solution, its cells
are no longer turgid and full of water, and the leaves of the plant will droop. In a hypertonic
solution, water will rush out
of both animal and plant cells,
and the cells will shrivel (in
plants, this is called
plasmolyzation). Cell
shrinkage is also called
crenation. This is why slugs
and snails shrivel and die
when salt is sprinkled onto
them; water leaves their cells
in order to balance the higher
concentration of salt outside
the cells.
Examples of Osmosis
Osmosis is how plants are able to absorb water from soil. The roots of the plant
have a higher solute concentration than the surrounding soil, so water flows into the roots.
In plants, guard cells are also affected by osmosis. These are cells on the underside of
leaves that open and close to allow gas exchange. When the plant’s cells are full of water,
the guard cells swell and open the stomata, small holes that allow the plant to take in carbon
dioxide and release oxygen.
Osmosis can have adverse effects on animals such as fish. If freshwater or saltwater
fish are put into water that has a different salt concentration than they are used to, they will
die from having too much water enter or leave their cells. Osmosis can affect humans as
well; in a person infected with cholera, bacteria overpopulate the intestines, leaving the
intestines unable to absorb water. The bacteria actually reverse the flow of absorption
because osmosis causes water to flow out of the intestinal cells instead of in. This causes
severe dehydration and sometimes death. A milder effect of osmosis is the way fingers
become pruney when placed in water for an extended period of time. They look that way
as a result of being bloated from increased water flowing into the cells.

Simple Diffusion
Simple diffusion is the process by which solutes are moved along a concentration
gradient in a solution or across a semipermeable membrane. Simple diffusion is carried out
by the actions of hydrogen bonds forming between water molecules and solutes. Water
molecules move in to surround individual solute molecules, which maximizes hydrogen
bonding. Hydrogen bonds are extremely temporary, however, and the solution is constantly
stirred as a result. This helps distribute
the solute evenly throughout the solution.
If the molecules are small enough, this
simple diffusion can happen across cell
membranes, between the individual
phospholipids that make up the
membrane. Water can move along its
concentration gradient through a cell
membrane in this manner, a form of
simple diffusion known as osmosis.
Uncharged Solute
For uncharged solute such as oxygen, carbon dioxide, ethanol, glucose and etc..
they can move down their concentration gradient across the cell membrane very easily.
 During equilibrium there will be no net movement of solutes across the membrane.
To measure the flux of a certain substrate:
- Fick's Law
J= P X (C2-C1)
J= flux; P= permeability; (C2-C1)= concentration gradient.

Charged Solute
For charged solute such as ions, etc.. they diffuse down the lipid bilayer very
poorly. The charge that they possess, either +ve/-ve causes them to be repelled from similar
charges. Their charge also causes them to bind to water molecules thus becoming quite
large.For charge solute, we have to also take account that when they move down their
concentration gradient, they create membrane potential.

Equilibrium state for a charged solute is when the membrane potential exactly
balances the concentration gradient.
To measure the membrane potential required to reach equilibrium:
- Nerst equation
E= (RT/ZF) ln ( (C in)/(C out) )

E= membrane potential; R= Gas constant; T= Absolute temp; F= Faraday

constant

Examples of Simple Diffusion

Carbon Dioxide
Carbon dioxide is a small molecule that can be dissolved into water. If you’ve ever
enjoyed a bubbly soda, you know this. However, you might not know that the same
mechanism is transporting the carbon dioxide that your cells create into your bloodstream
and out of your body via your lungs. Carbon dioxide is small enough to move through
simple diffusion through your tissues and out of your body. If you hold your breath for a
short time, you will begin to feel a burning “desire to breathe”. This is caused by the
accumulation of carbon dioxide in sensitive nerve tissues in your bloodstream, lungs and
brain. When you begin to breathe again, the carbon dioxide diffuses out of your system.
Many gases are able to do this through your lungs including oxygen, nitrogen, and many
others in the atmosphere.

Bacteria
Being the simple organisms they are, bacteria have no way to intake nutrients other
than diffusing them across the cell membrane. While they do use facilitated diffusion to
transport most nutrients, they rely on simple diffusion to deliver oxygen, water and small
nutrients to the cytoplasm. Within their cells, there are no specialized organelles to hold or
transport substances, so bacteria rely on the simple diffusion of material within their cells
to ensure materials are present for the reaction that control their life processes.

Surface Tension
Surface tension is the energy, or work, required to increase the surface area of a
liquid due to intermolecular forces. Since these intermolecular forces vary depending on
the nature of the liquid (e.g. water vs. gasoline) or solutes in the liquid (e.g. surfactants like
detergent), each solution exhibits differing surface tension properties. Whether you know
it or not, you already have seen surface tension at work. Whenever you fill a glass of water
too far, you may notice afterward that the level of the water in the glass is actually higher
than the height of the glass. You may have also noticed that the water that you spilled has
formed into pools that rise up off the counter. Both of these phenomena are due to surface
tension.

Molecular Perspective

In a sample of water, there are two types of molecules. Those that are on the outside,
exterior, and those that are on the inside, interior. The interior molecules are attracted to all
the molecules around them, while the exterior
molecules are attracted to only the other surface
molecules and to those below the surface. This
makes it so that the energy state of the molecules
on the interior is much lower than that of the
molecules on the exterior. Because of this, the
molecules try to maintain a minimum surface
area, thus allowing more molecules to have a
lower energy state. This is what creates what is
referred to as surface tension.

The water molecules attract one another due to the water's polar property. The
hydrogen ends, which are positive in comparison to the negative ends of the oxygen cause
water to "stick" together. This is why there is surface tension and takes a certain amount of
energy to break these intermolecular bonds. Same goes for other liquids, even hydrophobic
liquids such as oil. There are forces between the liquid such as Van der Waals forces that
are responsible for the intermolecular forces found within the liquid. It will then take a
certain amount of energy to break these forces, and the surface tension. Water is one liquid
known to have a very high surface tension value and is difficult to overcome.

Surface tension of water can cause things to float which are more dense than water,
allowing organisms to literally walk on water (Figure 2). An Examples of such an
organisms is the water strider, which can run across the surface of water, due to the
intermolecular forces of the molecules, and the force of the strider which is distributed to
its legs. Surface tension also allows for the formation of droplets that we see in nature.

Hydrolysis
Hydrolysis is a reaction involving the breaking of a bond in a molecule using water.
The reaction mainly occurs between an ion and water molecules and often changes
the pH of a solution. In chemistry, there are three main types of hydrolysis: salt hydrolysis,
acid hydrolysis, and base hydrolysis.

Salt Hydrolysis

In water, salts will dissociate to form ions (either completely or incompletely

depending on the respective solubility constant, Ksp Ksp. For example:
NH4Br(s)→NH+4(aq)+Br−(aq)(1)(1)NH4Br(s)→NH4(aq)++Br(aq)−

Here, the salt NH4BrNH4Br is put into water and dissociates

into NH+4NH4+ and Br−Br−.

There are four possible mechanisms of forming salts:

1. If the salt is formed from a strong base and strong acid, then the salt solution is
neutral, indicating that the bonds in the salt solution will not break apart (indicating
no hydrolysis occurred) and is basic.
2. If the salt is formed from a strong acid and weak base, the bonds in the salt solution
will break apart and becomes acidic.

3. If the salt is formed from a strong base and weak acid, the salt solution is basic and
hydrolyzes.

4. If the salt is formed from a weak base and weak acid, will hydrolyze, but the acidity
or basicity depends on the equilibrium constants of Ka and Kb. If the Ka value is
greater than the Kbvalue, the resulting solution will be acidic and vice versa.

Acid Hydrolysis

Water can act as an acid or a base based on the Brønsted-Lowry acid theory. If it
acts as a Bronsted-Lowry acid, the water molecule would donate a proton (H+), also written
as a hydronium ion (H3O+). If it acts as a Bronsted-Lowry base, it would accept a proton
(H+). An acid hydrolysis reaction is very much the same as an acid dissociation reaction.

CH3COOH+H2O⇌H3O++CH3COO−(2)(2)CH3COOH+H2O⇌H3O++CH3COO−
 In the above reaction, the proton H+ from CH3COOH (acetic acid) is donated to
water, producing H3O+ and a CH3COO-. The bonds between H+ and CH3COO- are broken
by the addition of water molecules. A reaction with CH3COOH, a weak acid, is similar
to an acid-dissociation reaction, and water forms a conjugate base and a hydronium ion.
When a weak acid is hydrolyzed, a hydronium ion is produced.

Basic Hydrolysis

A base hydrolysis reaction will resemble the reaction for base dissociation. A
common weak base that dissociates in water is ammonia:

NH3+H2O⇌NH+4+OH−(3)(3)NH3+H2O⇌NH4++OH−

In the hydrolysis of ammonia, the ammonia molecule accepts a proton from the
water (i.e., water acts as a Bronsted-Lowry acid), producing a hydroxide anion (OH-).
Similar to a basic dissociation reaction, ammonia forms ammonium and a hydroxide from
the addition a water molecule.

Use of Hydrolysis in the "Real World"

In nature, living organisms are only able to live by processing fuel to make energy.
The energy that is converted from food, is stored into ATP molecules (Adenosine
Triphosphate). Life requires many processes in order to sustain itself such as cellular
respiration, respiration, muscle contraction, distribution of hormones, transmittance of
neuro-transmitters in the brain, etc. All of these important processes require an input of
energy. To distribute this energy, the energy from the ATP molecules must be released. To
release the energy stored in the bonds of ATP molecules, hydrolysis must occur to break a
phosphate group off of an ATP molecule, thus releasing energy from the bonds. ATP now
becomes ADP (Adenosine Diphosphate) from losing a phosphate group through
hydrolysis.

Sodium-Potassium Ion Exchange

What is the purpose of pumping sodium and potassium across a membrane? The
sodium potassium pump is a well understood example of active transport. Sodium and
potassium ions are pumped in opposite directions across the membrane building up a
chemical and electrical gradient for each. These gradients can be used to drive other
transport processes. In nerve cells the pump is used to generate gradients of both sodium
and potassium ions. These gradients are used to propagate electrical signals that travel
along nerves. Therefore the action of nervous tissue requires ATP to generate resting
potentials. Poisons that disable the pump prevent proper functioning of the nervous system.

How can more molecules be transported into areas with high concentrations of the
molecule? Cells often need to create concentration gradients across membranes. The
concentration of a molecule is much higher on one side of the membrane than the other
when a concentration gradient exists. In order to create or maintain a concentration
gradient, individual molecules must be moved from an area of low concentration to an area
of high concentration. This cannot occur through passive diffusion, in fact diffusion will
cause the gradient to break down. Only active transport, which requires both specialized
transport molecules and the expenditure of energy can drive molecules up a concentration
gradient. The sodium potassium pump is an important and well understood example of
active transport.
Difference between Active and Passive
Transport
Active and passive transport are
biological processes that move oxygen,
water and nutrients into cells and remove
waste products. Active transport requires
chemical energy because it is the movement
of biochemicals from areas of lower
concentration to areas of higher
concentration. On the other hand, passive
trasport moves biochemicals from areas of
high concentration to areas of low
concentration; so it does not require energy.

Active Transport Passive Transport

Requires cellular energy. Does not require cellular energy.

It circulates from lower concentrated It circulates from the higher concentrated

areas to the higher concentrated areas areas to the lower concentrated areas

Involved in transporting all the soluble

Involved in transporting all the molecules
molecules including water, oxygen, carbon
including complex sugars, proteins, large
dioxide, monosaccharides, lipids, sex
cells, ions, etc.
hormones, etc.

Active transport is involved in the Passive Transport is involved in

transportation of different molecules in the maintaining the equilibrium level in the
cell. cell.

Active transport is a vital process. Passive Transport is a physical process.

It is highly selective. It is partly non-selective

It is a rapid process. It is a comparatively slow process.

Occurs in one direction. Occurs in bidirectional.

Affected by temperature. Not affected by temperature.

In passive transport carrier proteins are not

Active transport requires carrier proteins.
involved

This process reduces or stops as the level This process is not affected by the oxygen
of oxygen content is reduced. content.
 Metabolic inhibitors stop the active Metabolic inhibitors do not influence
transport. passive transport.

Endocytosis, exocytosis, cell membrane or Osmosis, diffusion, and the facilitated

the sodium-potassium pump, are different diffusion are different types of Passive
types of Active Transport. Transport.

Definition of Terms
Amino acid – An amino acid is an organic compound, and it serves as a building block for
proteins. Each amino acid contains an amino group and a carboxylic
acid group.

Dialysate – Dialysate is one of the two fluids used in dialysis. The term dialysate is
borrowed from physical chemistry and refers to fluids and solutes which have
crossed a membrane. The main function of the dialysate is to remove waste
material from the blood and to keep useful material from leaving the blood. The
dialysate is an aqueous solution containing isotonic concentrations of all the
components that are to remain in the blood, but none of the waste products.
Thus, the concentration of waste products is higher in the blood than the
dialysate. Therefore, waste products flow from the blood into the dialysate
faster than they return and the isotonic solution flows into the arterial blood to
maintain a proper solute concentration.
Peptide bond – A peptide bond is a chemical bond formed between two molecules when
the carboxyl group of one molecule reacts with the amino group of the other
molecule, releasing a molecule of water (H2O). This is a dehydration synthesis
reaction (also known as a condensation reaction), and usually occurs between
amino acids.

Salivary amylase ptyalin – enzyme in the saliva of humans that converts (breaks down)
starch into dextrin and maltose.

Uses of the ff. materials/chemicals in

Biochemical Processes
Silver Nitrate in Dialysis
It is used to test for the presence of chloride ions in a solution. When it is added to
a solution which contains chloride ions, silver nitrate will change color from clear to cloudy
white. (Salt is composed of sodium ions and chloride ions)
Sodium Chloride in Osmosis
Margarine in Surface Tension
Small intestine in Dialysis
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