BIOCHEMISTRY

The Nature of
Biochemistry

Biochemistry is the study of compounds, chemical

reactions, and molecular interactions that are

involved in the production, maintenance and
reproduction of living organisms. Biochemistry will
serve as a central component of all the health
sciences, including microbiology , genetics,
physiology, nutrition, medicine, dentistry and nursing.

Biochemistry deals with the study of the

chemistry of living organism. It deals with the

application of the principles and method of
chemistry to the field of biology and
physiology.
It is the language of biology basic to the
understanding of the different phenomena
both in biological and medical sciences.
It is concerned with the physico chemical
processes underlying digestion, absorption,
circulation, respiration, metabolism, growth
and reproduction.

Processes occurring under normal conditions

are physiological hence the term

Physiological Chemistry. Those occurring
under abnormal conditions are Pathological
they fall under Clinical Biochemistry

Growing biochemistry knowledge will set the place in

the search for the prevention and treatment of heart

disease, cancer, genetic disease, nutritional
deficiencies, infectious diseases, and other health
disorders. Present biochemistry knowledge has come
up with mechanisms on how oncogenes convert
normal cells into tumor cells, how enzymes catalyze
chemical reactions, how cholesterol contributes to
heat disease, how aspirin lowers body temperature,
and how AZT inhibits the growth of the AIDS virus.

In summer, 2001, Associate Editor Gunjan Singha of

Flash Forward magazine and co-director of a

program in Genomics, Ethics and Society at
Stanford University and who sits on an advisory
committee on human cloning for the state of
California when will we clone human.

Broad/Scope Scientific Discipline

A. Biochemistry is the study of the structure, composition,

and chemical reactions of substances in living systems.

B.

Biochemistry emerged as a separate discipline when

scientists combined biology with organic, inorganic, or
physical chemistry and began to study such topics as how
living things obtain energy from food, the chemical basis of
heredity, and what fundamental changes occur in disease.

C.

Biochemistry includes the sciences of molecular biology;

immunochemistry;
neurochemistry;
and
bioinorganic,
bioorganic, and biophysical chemistry.

Range of Application
Biochemistry

is applied to medicine, dentistry, and

veterinary medicine. In food science, biochemists research
ways to develop abundant and inexpensive sources of
nutritious foods, determine the chemical composition of
foods, develop methods to extract nutrients from waste
products, or invent ways to prolong the shelf life food
products. In agriculture, biochemists study the interaction of
herbicides with plants. They examine the structure-activity
relationships of compounds, determine their ability to inhibit
growth, and evaluate the toxicological effects on surrounding
life.

Biochemistry spills over into pharmacology,

physiology, microbiology, and clinical chemistry.

In these areas, a biochemist may investigate the
mechanism of a drug action; engage in viral
research; conduct research pertaining to organ
function; or use chemical concepts, procedures,
and techniques to study the diagnosis and
therapy of disease and the assessment of health.

Branches of Biochemistry

Biochemistr
y
Living
Organism

Biomolecules

Complex
Polysaccharid
es
Polynucleotid
es
Proteins
Lipids
Membranes

Simple
Carbohydrate
s

Nutrients

Kingdoms

Energy

Morphology
Cells

Nucleotides
Amino acids
others
Organelles

Eukaryotic

Prokaryotic

Complex

Simple cells

Nuclear/boun
d DNA

Cytoplasm
DNA

Chemical Composition of Living

Matter
The tissues are made up of about 70 % to

90% and 10% to 30% solids. Of the solids !%

is organic and the rest are organic substances.
WATER- component is found partly in the free
state, that is capable of passing from one cell
to another, this passage is governed by the
physical laws Osmosis and Diffusion. The
amount of fixed water in the tissues varies
with their function activities. Tissue with
greater physiological activity have greater
amount of water.

The inorganic substances are up of sodium,

potassium etc.
The organic substances such as

carbohydrates, lipids, and proteins.

Attributes of Life

Some characteristics of Living Things that ensure survival are:

ADAPTATION

- Or the presence of body structure that make living

things
fit to live in its habit.
GROWTH AND REPAIR
- Growth is the ability to add new tissue, while repair
if
the ability to replace damage parts.
REPRODUCTION
- Or the ability to beget offspring, ensure propagation
and continuance of the species.

METABOLISM

- Or the biological and chemical activities or functions

that provide energy. Constructive metabolism is call
anabolism, while destructive metabolism is catabolism
COMPLEXITY AND ORGANIZATION
- Complexity refers to elaborate structures needed to
carry out laborious functions like metabolism.
Organization is putting the different body structure into
order, so that the organism can function effectively and
efficiently.

REGULATION

- Or the ability to keep the functions under control

through the use of substances like hormones and
enzymes.
ALL
LIVING
ORGANISMS
POSSESS
A
CHARACTERISTIC SIZE AND SHAPE
- An ant can never become as big as elephant.
RESPONSIVENESS TO STIMULI OR SENSITIVITY
- Which is the ability to respond favorably or
unfavorably to its environment.

LOCOMOTION
- The ability to move on its initiative, under its control.
VARIATION AND CHANGE
- Which explain why no two organisms are exactly

alike(variation) and no organism remains unchanged

forever. Adaptation and evolution are mechanism of
change.
STEREOSPECIFIC
- The ability of certain molecules present in an organism
to interact with nature in a left-or-right-handed manner.

The Chemicals of Life

All living organisms are predominantly constructed

from carbon, oxygen, and hydrogen , together with

some organic elements like nitrogen, phosphorus,
and sulfur.
A. WATER
- all life forms, from the simplest bacteria to the
most complex multicellular plants and animals c
contain water. Human cells are composed of about
70% to 90% water that makes it an ideal medium for
sustaining life.

Water and its ionization products H+ and OH-

are important in determining the structure

and biological properties of macromolecules,
proteins, carbohydrates, lipds,nucleic acid,
enzymes and other cell components.

WATER
- Is more essential to life than is food.
- A person can live for several days or

months, even without food but dies with in

5 to 10 days without water. (Dehydration).
Water loss will kill for quicker than
starvation. Loss of body water to an extent
of 20% results to death.
- 60%-70% of the total body weight.

Functions
1. It is a universal medium in which the various chemical changes of

the body take place.

2. As a carrier it aids in digestion, absorption, circulation and
excretion.
3. It helps in the maintenance of the body temperature
4. Acts as a transporting medium for nutrients and all body
substances.
5. It plays an important part in mechanical functions, such as
lubrication of joints and the movement of the viscera in the
abdominal cavity.
6. It aids I elimination of waste products.

General Properties
A. Water has a unique properties
-has a boiling point
- freezing point
-heat of vaporization
-specific heat
- heat of fusion
- water tension( the forces of attraction
between
molecules in liquid water is relatively high)

b. Water has exception solvent properties

-the polarity and hydrogen bonding properties of
water molecule makes it a potent solvent for many
ionic compounds and neutral molecules.
c. Water properties altered by solutes
-4 properties of water (colligative properties)
a. freezing point
b. boiling point
c. vapor pressure
d. osmotic pressure

Water Component

1. Within the cells - Intracellular water

2. Outside the cell Extracellular water
a. Within the blood vessels Intravascular water
b. Between vascular spaces and the cell

Interstitial water

3. Smaller amounts are in CSF, Synovial fluid,

aqueous and vitreous humors.

Homeostasis
-

Balance water input an output

Unbalance of water content will result to edema or dehydration.
Thirst is being control by HYPOTHALAMUS
THRIST is a distinct physical sensation and a conscious demand
of water caused by extracellular dehydration.
- It is natures signal that liquid intake must increase.
- Water output is being controlled by the hormone VASOPRESSINPituitary Gland
- Release of this hormones decreases, water excretions by the kidney
by increasing the rate of water reabsorption from the tubules.

A.Water Intake
1. Fluids and beverages 1,200 ml- 1,500 ml
2. Daily water intake - 2,100 ml 2,800 ml
3. Daily output 1,850 ml 2,600 ml

A.Organs
1.KIDNEY - one liter, 15 ml of water is required to

dissolved 1 gm of solute.
2.SKIN 350 ml of water is lost daily through the
skin by diffusion. 450 ml 700 ml of water is lost
through skin.
3.LUNGS lung water goes out of the body as tiny
droplets in the expired air ( 350 ml)
4.FECES 150 ml , small amount of water is
usually lost daily through intestinal elimination.

Electrolytes
-Acid, base and salt under current process is
known as electrolytes in the process of
ionization.
a. POSITIVE IONS ( CATIONS)
1. Sodium

(Na+)
2. Potassium (K+)
3. Calcium (Ca+)
4. Magnesium (Mg+)

a. NEGATIVE IONS ( ANIONS)

1.
2.
3.
4.
5.

Chloride (Cl-)
Bicarbonate (HCO3 -)
Phosphate (PO4-)
Sulfate (SO4 -)
Ions of inorganic salts such as lactate pyruvate

- 150 mEq/L average sum of concentration of all

the cations in serum. This is balanced by 150

milliequivalents of anions.

Organic Compounds
1. Nucleic acid (DNA and RNA)
2. proteins
3. carbohydrates
4. fats and lipids

Inorganic Elements
1. Bulk elements (N,Na,Mg,P,S,Cl,K, and Ca)

required in relatively large amounts.

2. Trace elements (Fe,Zn,I)

The Cellular Basis of Life

Human body develops from union of
SPERM + OVUM=FIRST CELL OF HUMAN BODY
Group of cells
Tissues
Organs
Systems

Structure of Cell
Cell is a structural & functional unit of human body, capable of
carrying out functions of life independently.
Basic unit of life.
Nucleus
Cytoplasm
Cell Membrane

Functions of Cell
Production of Bio-Energy
- Storage
- Multiplication
- Specific function according to location

Functions of the Organelles

Plasma Membrane
All cells are surrounded by plasma membrane.
It separates the contents of the cells and its environment
and regulates the passage of molecules into and out of
the cell.

Cell Wall
The cell wall functions to support and protect the cell.
Plants have cell walls composed of cellulose; fungi have
walls composed of chitin.

 Nucleus
The nucleus contains DNA; it is the control center of the
cell because DNA contains instructions needed to
produce proteins that control metabolism and other cell
functions.

Cytoplasm
Is the material enclosed by the plasma membrane,
excluding the nucleus.

 Ribosomes
Synthesize protein accordingly. It also read the code in
mRNA.

Nucleolus
It is a structure within the nucleus where the ribosomal
subunits are produced.
This structure appears darker than the nucleus.

 Smooth Endoplasmic Reticulum

This is a membranous network that extends throughout the cell.
It produce lipid compounds such as phospholipids, steroids and
fatty acids.

Rough Endoplasmic Reticulum

The rough appearance is due to the presence of ribosomes on
the membrane.
This serves as the transport channel or network of molecules
such as protein and hormones from the inside to outside of the
cell.

 Golgi Complex/Golgi Body/Golgi Apparatus

It is a stack of 3 to 20 flattened, slightly curved saccules
which appear like a stack of pancakes.

Lysosomes
These are membrane-bound vesicles containing hydrolytic
digestive enzymes produced by the Golgi Complex.
They fused with other vesicles formed around the material
the has entered the cell, allowing the digestion of the
vesicle contents.

 Peroxisomes
These are vesicles that contain enzymes which oxidize
(remove hydrogen) from a variety of different compounds
and pass the hydrogen to oxygen.

Vacuoles
It is a membranous sac similar to but larger than
vesicles.
This structure stores water and dissolved substances.

 Chloroplasts
It is the site of photosynthesis in the plants.

Mitochondria
It is the powerhouse of the cell where ATP, the energy
currency of the cell is produced.

Cytoskeleton
- It is a network of protein molecules that provides the

 Microtubules
The structure responsible for the movement of cilia and
flagella.
They also move the chromosomes during cell division.

Cilia and Flagella

These are hair-like structures projecting from the cell for
cell movement.

 Centrioles and Centrosome

They are involved in the formation of microtubules.

Actin Filaments (Microfilaments)

Actin filaments are important for muscle contraction.

Tissues

Tissue is a cellular organizational level

intermediate between cells and a complete
organism. A tissue is an ensemble of cells, not
necessarily identical, but from the same origin,
that together carry out a specific function. Organs
are then formed by the functional grouping
together of multiple tissues. The study of tissue is
known as histology or, in connection with disease,
histipathology.

Classification of Tissues
Connective Tissue
Muscular Tissue
Nervous Tissue
Epithelial Tissue

Systems

Muscular System
Skeletal System
Digestive System
Respiratory System
Circulatory System
Excretory System
Reproductive System (Male & Female)
Nervous System
Endocrine System

Physical Chemistry
Biochemistry dealing as it does with the

chemistry of living matter, requires the

knowledge of physical chemistry and possibly
all other branches of chemistry for he proper
understanding of the biochemical processes.
The important physicochemical phenomena is
essential and necessary.

COLLOIDAL STATE OF
MATTER
The old method of grouping substances
into colloids and crystalloids was base
upon the ability of the substances to pass
through parchment membrane. Those that
diffuse readily through such membrane
were called CRYSTALLOIDS, while those
which do not were termed COLLOIDS.

General Properties
1. Filtrability

-The particles of colloids solution can pass

through ordinary filter paper but not through
parchment membrane.
2. Negligible osmotic pressure
- colloidal solution have negligible osmotic
pressure. They possess the same vapor
pressure, boiling and freezing points as those of
pure solvents. The particle in a colloidal solution
is comparatively small.

3. Tyndall phenomenon
-colloidal solution manifest the tyndall effect.
That is , the path of a powerful beam of light
through a colloidal solutions appears strongly
luminous when viewed at right angle.
4. Brownian movement
- the suspended particles of colloidal
solutions are observed to be continuous, rapid
vibratory motion. This is attribute to the
incessant bombardment of the particles of the
solute by the movement of solvent.

5. Electrical charges
- colloidal particles especially suspensoids
are electrically charged, the charge being
distributed over the surface of the entire
particle. The migration of particles either to
positive and negative poles of an electricalfield is called ELECTROPHORESIS.
6. Surface tension
-the total surface area presented by colloidal
particles is enormous compared to those of
suspension.

Classification
a. Emulsoids
b. Suspensoids

Emulsoids
Are lyophillic, having affinity for the solvent.
Forming gel and swell when contact with large

amount of water. (imbibition) plays an important

role in the normal state of the protoplasm.
Increased imbibition leads to increased retention
of fluid in the tissues producing edema. One
gram of plasma albumin can hold 18 cc of water.
When plasma proteins are lost as in
hemorrhage.
Influence by he temperature and hydrogen
concentration

Gels are made up of fibrillar structures

surrounded by dispersion medium. The

larger aggregates of colloidal particles
formed in the process of gel formation are
called MISCELLES. Gels are freely
permeable to non-colloidal ions and
molecules.
Peptization- dispersal of a solid into
colloidal state. (peptizing agent- water).

The gel however subsequently retracts giving

off the imbibe water, a process termed,

SYNERESIS. The retraction of blood coagulum
with the liberation of a straw colored fluid
(serum) is a good example.
Thixotropy- transformation of gel when
allowed to stand, after vigorously shaking
transformed to a sol.

Suspensoids
Are lyophobic ( no affinity for the solvent).
Exhibit Imbibition and Syneresis.
The colloidal state of suspensoids is rendered

more stable by the addition of emulsoids. The

latter produces a coating upon the surface of
the lyophobic particles preventing them from
coming contact with the electrolytes.

Comparison of True Solutions,

Colloidal Solutions and Suspension
True Solution

Colloidal Soln. Suspension

1. Size of
particles

1 milimicron or
less

1 to 100
milimicron

Above 100
milimicra to 1
mm

2.Diffusibility
and filtrability

Passes thru
membrane &
filters

Passes thru
filters but not
thru
membranes

Do not pass
thru either

3. Visibility

Not visible

Visible under
Visible with
ultramicroscope microscope or
naked eyed

4. Motion

Not visible

Brownian
movement

Settles down

5.Osmotic
pressure

High

Low

None

6.Tyndal

none

exhibits

none

a. Surface Tension

- the force by which the surface molecules

are held is called Surface tension.
- the stronger the attraction between
molecules, the greater is the surface tension.
- surface tension may be measured by the
use of a stalagmometer. This is a pipette of a
special design with a capillary tube ending ,
permitting a measured amount of liquid to flow
out drop by drop.

b. Adsorption
-accumulation of substances of the surface of
solid or liquid.
- the greater the surface of the adsorbing
agent the greater is the adsorption. It is
increased by a rise of pressure and diminished
by a rise in temperature.
-the process of adsorption brings substances
nearer each other, thus promoting chemical
reactions.

Chromatography
Is a technique used to separate and identify
the components of a mixture of substances.
Methods:
1. Adsorption chromatography

- this depends upon the use of solid

adsorbents which have specific affinities for
the adsorbed substances.

2. Ion exchange chromatography

- this is widely used for the separation of
amino acids. The synthetic resin used is either
anionic or cationic.
3. Countercurrent distribution method
- this is done by repeated distribution of a
solute between two miscible solution.
4. Partition Chromatography
-this method makes use of the principle of
countercurrent distibution.

5. Paper Chromatography
- one of the most ingenious methods of
utilizing partition chromatography is the
employment of paper as supporting medium.
6. Thin Layer Chromatography
7. Gel Filtration Chromatography
8. Gas Liquid Chrmatography

Emulsions
A dispersion of small drops of one liquid in
another liquid.
Types :
1.Emulsions in which oil is dispersed in water
known as the oil water type.
2. Emulsion in which water is dispersed in oil
known as the water oil type.

Viscosity
Liquid tends to flow due to its fluidity. The
resistance which a liquid offers to flowing is
viscosity. This varies greatly with different
liquids. The rate flow of a protein solution
through capillary tube by gravity or under
pressure is measured and compared with that
of the solvent alone.
Factors:
1. Temperature
2. Chemical nature
3. Colloids

4. Suspended particles cause and increase in

its viscosity.
Clinical correlations:
The viscosity of the blood is due to proteins,
emulsoids and corpuscles suspended in the
plasma.

Osmosis
Whenever two solutions of unequal

concentration are separated by a semipermeable membrane, the fluid tends to flow

from the side of low osmotic pressure to that a
higher osmotic pressure until an osmotic
equilibrium is reached.

Diffusion
Is the interpenetration of molecules between

two substances.t this occurs whenever the

solutes distributes itself in uniformly into the
solvent.

Dialysis
When two different solution are separated by

a membrane which allows the passage of the

crystalloids but not colloids, dialysis occurs. If
a mixture of crystalloids and colloids is placed
in a dializing bag and immersed in distilled
water the cyrtalloids pass out while the
colloids are left behind. This is utilized in the
purification of colloids from crytalloids
impurities and vice versa.