CHAPTER ONE

INTRODUCTION TO BIOCHEMISTRY
 Introduction

What are the basic activities of living organisms?

1. Maintenance of the individual

2. Perpetuation of the species

To maintain an organism:
There must be synthesis of new molecules to replace the
degraded and outdated molecules.
Cells obtain energy from biological fuels for various cellular
function.
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Introduction …

To perpetuate the species:

There is storage and transmission of genetic information from
generation to generation at molecular level.
Genetic macromolecule, DNA is replicated to give daughter
DNA that passes to the offspring.
In an organism DNA is also transcribed in to RNA and then
RNA is translated to proteins of variable uses.
Is biochemistry helps to understand the activities of life at
molecular
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What is biochemistry?
Biochemistry can be defined as the science of the
chemical basis of life (Greek bios “life”).
The science of the chemical constituents of living cells
and of the reactions and processes they undergo.
The science concerned with the various molecules that
occur in living cells and organisms and with their
chemical reaction.

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 Anything more than a superficial comprehension of life –

in all its diverse manifestation - demands a knowledge of

biochemistry.

By this definition, Biochemistry encompasses large areas

of cell biology, molecular biology, and molecular

genetics.

The aim of biochemistry is to describe & explain all

biochemical processes of living cells in molecular terms.

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 The major objective of biochemistry is the complete

understanding of all biochemical processes associated

with living cells at the molecular level.

To achieve this objective, biochemists have sought to

isolate the numerous molecules found in cells, determine

their structures, and analyze how they function. Many

techniques have been used for these purposes.

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 Health depends on

 a harmonious balance of biochemical reactions occurring

in the body, and

 Disease reflects

 abnormalities in biomolecules, biochemical reactions, or

biochemical processes ; this is the main concern of

medical biochemistry.
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The scope of biochemistry

The knowledge and skills of biochemistry is applied in a

number of areas.

Genetics – the biochemistry of nucleic acids

Physiology – study of normal body function

Pharmacology and pharmacy – for designing of therapeutic

drugs, the metabolism of drugs .

Toxicology – to understand toxic effect of metabolites and

xenobiotics
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The scope of biochemistry…

Pathology (the study of disease) – e.g., inflammation, cell injury

and cancer. Each pathologic condition has biochemical basis.

Microbiology, zoology and botany

Medicine – the understanding and maintenance of health and

effective treatment of diseases.

Public health

Nutrition and preventive medicine

Agriculture and biotechnology

In forensic medicine
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Two categories of biochemistry
Descriptive biochemistry: deals with qualitative and
quantitative nature (character, complexion & makeup) of
molecules in the living cells.

Major Molecules in humans include: Water, Macromolecules

(Carbohydrates, Proteins, Lipids and Nucleic acids) and Micro
molecules which include Vitamins & Minerals.

Dynamic biochemistry: deals with reactions and mechanisms

of reactions in the living cells.
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 The Biomolecular Hierarchy

Atoms/ elements

Simple Molecules (are the Units for Building Complex

Structures)

Metabolites and Macromolecules

Organelles

Membranes

The Unit of Life is the Cell

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carbon DNA organelle cell
atom molecule tissue

biosphere

ecosyste
m
organ

organ
system

communit organism
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y
Figure: structural hierarchy in the molecular organization of Cells. For example the nucleus is an
organelle containing several Types of supramolecular complexes, including chromosomes.

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 Elemental Composition of the living system

More than 99% of the elements in animals’ bodies are

accounted for by four elements, carbon, hydrogen, oxygen,
and nitrogen. Most of the H and O occur as H2O, which
alone make 60-70% of cell mass.

These elements are the major constituents of organic

molecules, called biomolecules, on which most living
organisms depend.

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The second biologically important group of elements, which
account only about 0.5% of the body mass, are the seven
essential mineral elements.

These elements include sodium, potassium, calcium,

magnesium, chlorine, sulfur and phosphorus.

Sulfur and phosphorus are also components of some

biomolecules.

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The chemical components of cells

Water

Water accounts for about 60-70% of the weight of the cell.

Other cellular constituents are either dissolved or suspended
in water.

Organic Compounds/Biomolecules

They are nucleic acids, proteins, polysaccharides

(carbohydrates) and lipids.

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• Proteins accounts 10-20% of the weight of the cell.

• Nucleic acids account 7-10% of the cell weight.

• Polysaccharides usually account for 2-5% of the cell

weight.
• About 3% of cell weight is due to lipids.

• Lipids content may be higher in adipocytes or fat cells.

• Proteins may account more of cell weight in cells like

erythrocytes.
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Other low molecular weight organic compounds may account
for 4% of cell weight. They are monosaccharaides, amino
acids, fatty acids, purine and pyrimidine nucleotides, peptides,
hormones, vitamins and coenzymes.

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Inorganic Compounds

Inorganic compounds account for the rest of the cell weight.

They are cations like sodium, potassium, calcium,

magnesium, copper, iron and anions like chloride,
phosphate, bicarbonate, sulfate, iodide and fluoride.

They exist as electrolytes (sodium ion) and compounds

( calcium phosphate in bone) in the living system

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 Biochemical reactions in the living system

Metabolism: the sum total of chemical reactions in the living

cell/organism.

Can be of two type

1. Catabolism: break down or degradation reactions

Examples: digestion, oxidation of glucose…

2. Anabolism: Synthetic reactions

Examples: Synthesis of proteins, nucleotides…

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Biochemical reactions in the living system…

Metabolic errors: abnormalities in metabolism.

Inherited and acquired type

Waste products: inevitable waste products are produced

when biochemical reactions are undergoing in the living
system.

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 Anabolic

Building blocks Macromolecules

– Simple sugars – Polysaccharides
– Amino acids – Proteins /peptides
– Nucleotides – RNA or DNA
– Fatty acids – Lipid/fats

Catabolic

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Metabolism of dietary components

In order to survive, humans must meet two basic metabolic

requirements:

 we must be able to synthesize everything our cells need that is

not supplied by our diet, and

 we must be able to protect our internal environment from toxins

and changing conditions in our external environment.

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 Metabolism of dietary components…

• In order to meet these requirements, we metabolize

our dietary components through four basic types of
pathways:
 fuel oxidative pathways,

 fuel storage and mobilization(utilization) pathways,

 biosynthetic pathways, and

 detoxification or waste disposal pathways.

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Figure: General metabolic routes for dietary components in the body

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 Role of biochemistry in medicine and other health
sciences
Biochemistry helps to understand the biochemical changes and
related physiological alteration in the body. Pathophysiology of
any disease is studied through biochemical changes. Example

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Role of biochemistry…
In the present scenario, many people rely in taking
multivitamin and minerals for better health. The
function and role of vitamins and minerals are best
described by biochemistry.
There are many disorders due to hormonal imbalance
especially in women and children. The formation,
role of hormones and disorders in due to deficiency
or excess of hormones are best studied by
biochemistry.
To determine health effects of toxins and pollutants.

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 Role of biochemistry…
Almost all the diseases or disorders have some biochemical
involvement. So the diagnosis of any clinical condition is easily
possible by biochemical estimations.

Examples:

1. In kidney disorders and chemotherapy treatment urine test is used to

understand the extent of excretion of drugs or other metabolites, the
change in pH, the color of urine etc.

2. In diabetes blood glucose level test helps to understand the severity

of diabetes disorders. Biochemical test for ketone bodies in urine also
indicate the stage of diabetes.
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 Role of biochemistry…
3. Liver function tests help to understand the type of disease or

damage to the liver, the effect of any medication on liver.

4. Evaluation of blood cholesterol level and lipoproteins help
to understand the proneness of the patient to cardiovascular
disease.
Thus importance of biochemical tests is to help to monitor
the patient health condition regularly during the treatment.

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Role of biochemistry…

Biochemistry gives an idea of the composition of drugs and

their chance of degradation.
It also gives an idea how drugs are metabolized by many
biochemical reactions in the presence of enzymes. This helps to
avoid drugs with poor metabolism or those with excessive side
effects from being prescribed or dispensed to patients.
Biochemical tests help to fix the specific half life or time of
expiry of drugs.
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Role of biochemistry…
For maintenance of health, optimum intake of many
biochemicals like vitamins, minerals, proteins, essential
fatty acids, water etc… is necessary.
Biochemistry gives an idea of what we eat i.e. it’s
components and possible alteration due to their deficiency
or excess. Helps to understand the importance of
biomolecules to health.
The nutrient value of food materials can also be determined
by biochemical tests.
Helps Physician to prescribe limited usage of certain foods
like excess sugar for diabetics, excess oil for heart problem
prone patients etc.

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In the future, Biochemistry may provide answers for:

Obesity solutions/weight reduction

A cure for diabetes and many other diseases, more accurate

diagnosis, better treatment of infection.

Increased life expectancy with slower ageing

synthetic organs and tissues for transplant, and a whole array

of other potential paths that Biochemistry could take.

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2. Cell and sub cellular Fractionation

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Biochemical studies at different level

Stage Examples of study

1. Whole organism Systems: respiration, circulatory etc..
2. Organ Control /function of an organ

3. Cells Biosynthesis, secretion of proteins...

4. Membrane transport, energy metabolism…

5. Organelle specialised organelle metabolism

6. Cell supernatant Enzyme activity...

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Introduction to Cell
Cell is the basic functional and structural unit of all forms
of life in which different biochemical reactions takes place
at mild physiological condition.
On the basis of differences in cell structure, all life forms
are divided into two major classes.
Prokaryotes are simple cells and in most cases, individual
cell itself is the organism. They lack membrane bound
organelles.
Examples for prokaryotes are bacteria, primitive green algae
and archae.
Eukaryotes: They have membrane bound organelles.
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They include plants, animals, fungi, protozoa, and true algae.
Introduction to Cell…

The cells of humans and other animals are eukaryotes

(eu, good; karyon, nucleus) because the genetic
material is organized into a membrane-enclosed
nucleus.
In contrast, bacteria are prokaryotes (pro, before; karyon,
nucleus); they do not contain nuclei or other organelles
found in eukaryotic cells.
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Eukaryotic cell structure and function
A eukaryotic cell is surrounded by a plasma membrane,
has a membrane bound nucleus and contains a number
of other distinct sub-cellular organelles.
In eukaryotes, cells aggregate to form tissues or organs
and these are further organized to form whole organism.
In humans, eukaryotic cells exist in large number of sizes
and shapes to perform varieties of functions.
Organelles (such as the nucleus, mitochondria,
lysosomes, and peroxisomes) are also surrounded by a
membrane system that separates the internal compartment
of the organelle from the cytosol.

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 The function of these membranes is to collect or
concentrate enzymes and other molecules serving a
common function into a compartment with a localized
environment.
Each organelle has different enzymes and carries out
different general functions.
 For example, Lysosomes contain hydrolytic enzymes that
degrade proteins and other large molecules.
 The nucleus contains the genetic material and carries out.
gene replication and transcription of DNA

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 Different cell types differ quantitatively in their organelle
content, or their organelles may contain vastly different
amounts of a particular enzyme, consistent with the
function of the cell.
For example, liver mitochondria contain a key enzyme
for synthesizing ketone bodies, but they lack a key
enzyme for their use. The reverse is true in muscle
mitochondria.
Thus, the enzymic content of the organelles varies
somewhat from cell type to cell type.

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Fig. Common components of human cells
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Cell Membrane(plasma membrane )
The cell membrane is a lipid bilayer that serves as a
selective barrier; it restricts the entry and exit of
compounds.
Envelops the cell, separating it from the external
environment; maintaining the correct ionic composition and
osmotic pressure of the cytosol.
It is impermeable to most substances but within the plasma
membrane, different integral proteins facilitate the
transport of specific compounds by energy-requiring
active transport, facilitated diffusion, or by forming pores
or gated-channels.

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 Cell membrane is involved in communicating with other
cells, in particular through the binding of ligands
(small molecules such as hormones, neurotransmitters,
etc.) to receptor proteins on its surface. The transporters
and receptors in cell membrane control communication
of the cell with the surrounding milieu(environment).
It is also involved in the exocytosis (secretion) and
endocytosis (internalization) of proteins and other
macromolecules. E.g. Exocytosis of hormones from
endocrine cells; Endocytosis of foreign substance by
phagocytic cells.

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 The selective permeability of cell membrane is
responsible for the maintenance of internal environment of
the cell and for creating potential difference across the
membrane.
The variable carbohydrate components of the glycolipids
on the cell membrane surface function as cell recognition
markers. For example, the A, B, or O blood groups are
determined by the carbohydrate composition of the
glycolipids.
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 Cell membrane surface glycolipids may also serve as
binding sites for viruses and bacterial toxins before
penetrating the cell.
The modification of the cell membrane results in
formation of specialized structures like axon of
nerves, microvilli of intestinal epithelium and tail of
spermatids.

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Figure: Basic structure of an animal cell membrane.

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Cytoplasm
The cytoplasm of the cell is the portion of the cell between
the cell membrane and the nucleus.
The cytosol is solution part of the cytoplasm not
included within any of the subcellular organelles.
It is a major site of cellular metabolism like glycolysis ,
gluconeogenesis, the pentose phosphate pathway and
fatty acid synthesis.
The cytosol is not a homogeneous ‘soup’ but has within it
the cytoskeleton, a network of fibers criss-crossing through
the cell that helps to maintain the shape of the cell.

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Cytoskeletons
These are filament like structures made up of proteins
present in cytoplasm. Non-muscle cells perform
mechanical work with these intracellular network of
proteins.
These cytoskeletons are involved in the maintenance of
cell shape, cell division, cell motility, phagocytosis,
endocytosis and exocytosis.
Microfilaments (8 nm in diameter): Actin polymers
form the thin filaments (also called microfilaments).
It form a network controlling the shape of the cell and
movement of the cell surface, thereby allowing cells to
move, divide, engulf particles, and contract. Actin is
present
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in all living cells. Tewekel R 48
Microtubules (30 nm in diameter): Microtubules,
cylindrical tubes composed of tubulin subunits, are
present in all nucleated cells and the platelets in blood.
They are responsible for the positioning of organelles in
the cell cytoplasm and the movement of vesicles, including
phagocytic vesicles, exocytotic vesicles, and the transport
vesicle. They also form the spindle apparatus for cell
division.

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A variety of human cells have cilia and flagella, hair like
projections from the surface that have a stroke like
motion. These projections contain a flexible organized
array of microtubules.
Dendrites, axons of nerve cells and sperm cells contain
microtubules. The sperm cell moves with the help of
flagellum, a microtubule.
Intermediate Filaments (10 nm in diameter): Are
composed of fibrous protein polymers that provide
structural support to membranes of the cells and
scaffolding for attachment of other cellular components
(e.g., epithelial cells have cytokeratins, and neurons have
neurofilaments). These provide an internal network that
helps support the shape and resilience of the cell.
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Cytoplasmic organelles
1. Mitochondria
Mitochondria :has an inner and an outer membrane
between which is the inter-membrane space.
Are the second largest structures in the cell.
Generally mitochondria are ellipsoidal in shape and can
assume variety of shapes.
The outer membrane contains pores made from proteins
called porins and is permeable to molecules with a
molecular weight up to about 1000 g/mole.
The inner membrane, which is considerably less
permeable, has large foldings called cristae which
protrude into the central matrix.
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 The inner membrane is the site of oxidative
phosphorylation and electron transport involved in ATP
production.
The central matrix is the site of numerous metabolic
reactions including the citric acid cycle and fatty acid
breakdown.
Within the matrix is found the mitochondrial DNA; can
reproduce by replicating their DNA and then dividing in
half.
Although nuclear DNA encodes most of the enzymes
found in mitochondria, mitochondrial DNA encodes
some of the subunits of the electron transport chain
proteins and ATP synthase.
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Mutations in mitochondrial DNA result in a number of genetic
diseases that affect skeletal muscle, neuronal, and renal tissues.
They are implicated in aging.
The number of mitochondria ranges from 1-100 per cell
depending on type of cell and its function. Several factors
influence the size and number of mitochondria in cells.
Exposure to cold increases mitochondria by 20-30% in liver cells.
In highly metabolically active cells mitochondria are more and large.
Location of mitochondria in cell also depends on types and functions
of cell. In liver cell mitochondria are scattered. In muscles they are
parallely arranged.
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 Figure: The Structure Mitochondria

This organelle processes energy for a cell.

It makes ATP. (ATP = energy)
Involved in cellular respiration.

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2. Ribosomes

Synthesizes proteins/site of
translation.
Present in the cytoplasm.
Present with Rough ER.
Consists of protein and rRNA.
Ribosome & associated
molecules are termed as
translational apparatus

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3. Peroxisomes
Are also small vesicles surrounded by a single membrane. They

are also called as micro bodies

Contain enzymes that degrade fatty acids and amino acids.

A byproduct of these degradation reactions is hydrogen peroxide,

which is toxic to the cell. The presence of large amounts of the

enzyme catalase in the peroxisomes rapidly converts the toxic

hydrogen peroxide into harmless H2O and O2.

The enzymes of H2O2 catabolism present in peroxisomes are

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Figure: Types of reactions in peroxisomes.

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 Peroxisomes function in the oxidation of very long
chain fatty acids (containing 20 or more carbons) to
shorter chain fatty acids, the conversion of cholesterol to
bile acids, and the synthesis of ether lipids called
plasmalogens.
Peroxisomal Diseases. Peroxisomal diseases are caused
by mutations affecting either the synthesis of functional
peroxisomal enzymes or their incorporation into
peroxisomes.
Zellweger’s syndrome is caused by the failure to
complete the synthesis of peroxisomes (read about this
syndrome)
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4. Lysosomes
Lysosomes are called as ‘Suicide bags’ of the cell, which are

found only in animal cells, have a single boundary membrane.

The internal pH of these organelles is mildly acidic (pH 4–5), and

is maintained by integral membrane proteins which pump H ions

into them.

The lysosomes contain a range of hydrolases that are optimally

active at this acidic pH (and hence are termed acid hydrolases) but

which are inactive at the neutral pH of the cytosol and extracellular

fluid.
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These enzymes are involved in the degradation of host and foreign

macromolecules into their monomeric subunits; proteases degrade

proteins, lipases degrade lipids, phosphatases remove phosphate

groups from nucleotides and phospholipids, and nucleases degrade

DNA and RNA.

Lysosomes are involved in the degradation of extracellular

macromolecules that have been brought into the cell by endocytosis

as well as in the degradation and recycling of normal cellular

components.
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Figure: Lysosomal reactions

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Lysosomal enzymes are involved in bone remodeling and
intracellular digestion.
Disease, shock or cell death causes rupture of lysosomes
and release of enzymes.
Lack of one or more of lysosomal enzymes cause
accumulation of materials in the cell resulting in lysosomal
storage diseases.

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Cytomembranes
There is an extensive network of membranes in the
cytoplasm. These membranes are called as
cytomembranes.
They are divided into endoplasmic reticulum and golgi
complex or apparatus.
The endoplasmic reticulum is further subdivided into
rough endoplasmic reticulum (RER) and smooth
endoplasmic reticulum (SER).
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Rough Endoplasmic Reticulum

It is continuous with outer nuclear membrane. The

cytoplasmic surface of rough endoplasmic reticulum is
coated with ribosomes. Membrane enclosed channels
of endoplasmic reticulam are called cisternae.

Functions

Ribosomes and RER are involved in protein synthesis.

Protein synthesized, enters cisternae and later extruded.

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Smooth Endoplasmic Reticulum

It is continuous with RER. It differs from RER by the

absence of ribosomes. When isolated SER is called as
microsomes (small vesicles).

SER of intestinal cells is involved in formation of

triglycerides.

In the adrenal cortex, SER is the site of steroid formation.

Cytochrome P450 dependent monooxygenases are present in

liver cell SER for drugs metabolism.

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Golgi Apparatus

Golgi apparatus - a system of flattened membrane-bound sacs,

is the sorting and processing center of the cell.

Membrane vesicles from the RER, containing membrane and

secretory proteins, fuse with the Golgi apparatus and release

their contents into it.

On transit through the Golgi apparatus, further

posttranslational modifications to these proteins take place

and they are then sorted andTewekel

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R into different vesicles.
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These vesicles bud off from the Golgi apparatus and are
transported through the cytosol, eventually fusing either
with the plasma membrane to release their contents into
the extracellular space or with other internal organelles
(e.g. lysosomes).
Exocytotic vesicles release proteins into the extracellular
space after fusion of the vesicular and plasma
membranes.
Exocytotic vesicles containing hormones also may
contain proteases that cleave the prohormone at a specific
site.

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 Golgi Complex
The protein packaging and
transport center of the cell.
Has incoming and outgoing
vesicles.
Incoming vesicles pick up proteins
from RER for post-translational
modification.
Proteins for different target are
leaving the complex by outgoing
vesicles.

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Fig. The role of RER and Golgi complex for protein synthesis, post-
translational modification and sorting

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The digestive enzymes of pancreatic juice and insulin are
produced and released in this way.
Golgi apparatus helps in the formation of other sub-
cellular organelles like lysosomes and peroxisomes.
Golgi apparatus is involved in protein targeting. It directs
proteins to be incorporated into membranes of other sub-
cellular structures. It is also involved in glycosylation and
sulfation of proteins.

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Nucleus

Centre of the cell is nucleus. It is bounded by two

membranes. The two membranes fuse periodically to

produce nuclear pores. Exchange of material between

nucleus and rest of the cell occurs through nuclear pores.

Messenger ribonucleic acid (mRNA), proteins,

ribosomes, etc.] can move between the nucleus and the

cytosol.
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Nucleus…
Other proteins, for example those involved in regulating gene

expression, can pass through the pores from the cytosol to the

nucleus.

The outer nuclear membrane is often continuous with the rough

RER.

Within the nucleus the DNA is tightly coiled around histone

proteins and organized into complexes called chromosomes .

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Functions of the nucleus
Nucleus is the information centre of eukaryotic cell. More
than 90% of the cellular DNA is present in the nucleus. It
is mainly concentrated in the form of chromosomes.
Human cell contains 46 chromosomes. These
chromosomes are composed of nucleoprotein chromatin,
which consist of DNA and proteins histones. Some RNA
may also present in the nucleus.
In prokaryotes, the DNA is present as thread(strand) in
the cytosol.
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 Figure: The structure of cell nucleus

The control center of the cell. It

contains the DNA code for the cell
coiled into chromosomes.

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Nucleolus
It is visible under the light microscope ,it is the sub-region
of the nucleus which is the site of ribosomal ribonucleic
acid (rRNA) synthesis.
These are small dense bodies present in the nucleus. Their
number varies from cell to cell.
There is no membrane surrounding them. They are
continuous with nucleoplasm.
Nucleoplasm
It is also called as nuclear matrix. It contains enzymes
involved in the synthesis of DNA and RNA ( enzymes of
replication and transcription).

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Summary of major biochemical function of cell organelles

Organelles Major functions

Cell membrane Transport of molecules in and out of

cells
Intercellular adhesion and
communication
Signal transmission

Cytoplasm Enzymes of glycolysis

Fatty acid synthesis
Cholesterol synthesis etc
Golgi-apparatus Intra cellular sorting of proteins
Glycosylation reactions
Sulfation reactions
Peroxisomes Degradation of certain fatty acids &
amino acids
Production & degradation of H2O2
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Summary major biochemical function of cell organelles…
Organelles Major functions
Mitochondria Fatty acids oxidation
Citric acid cycle
Oxidative phosphorylation/ATP
formation etc..

Endoplasmic reticulum (ER) Membrane bound ribosome are a

major site of protein synthesis
Synthesis of various lipids
Metabolism of drugs
Nucleus Site of chromosome
Transcription…
Ribosomes Site of protein synthesis
Lysosomes Site of many acid hydrolases
(enzymes catalyzing degradative
reactions)
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Medical and biological importance of cell
Cells are mortal i.e., they have finite life span. In the body,
cells are formed and destroyed. So, cells are in dynamic
state.
Cell division and cell death are two opposite processes
required to maintain constant tissue volume (tissue
homeostasis).
Further cell death plays an important role in shaping
tissues and organs during development or during recovery
from injuries.
Cell death may occur due to several external factors .

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There are three types of cell death
Necrosis: It is also termed as cell murder. Cells undergo
necrotic death if
 cell membrane is damaged or
 due to decreased oxygen supply and
 if energy (ATP) production is blocked.
Apoptosis: This type of cell death occurs in tissue turnover.
Individual cells or groups of cells undergo this type of
death. Aged cells in the body are removed by apoptosis. It is
a genetically programmed cell death. In the initial stages of
apoptosis, cell shrinks, followed by fragmentation and
finally
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by phagocytosis. 83
• Atrophy: This type of cell death occurs in the absence
of essential survival factors. Survival factors required
by the cell are produced by other cells. Absence of
nerve growth factor leads to atrophy of nerves. It is
also genetically programmed cell death.

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