BIOCHEMISTRY &

MEDICINE
Biochemistry
— Application of chemistry to study of
biological processes at cellular & molecular
level
OR
— Study of chemical constituents of living cells
& of reactions & processes they undergo
ü Cellular biology

ü Molecular biology
ü Molecular genetics
— Cell is the structural unit of living system

— Major objective is to understand the

chemical processes associated with living
cell, at the molecular level
THE CELL
— Cell is the fundamental unit of life &
building block of all organisms
— All organisms are composed of cells
— Smallest unit of life
— Human body have more than 10 trillion
cells
In human body, there are 200 different
types of cells
Modern Cell Theory
— Modern cell theory, based on the work of
scientists Theodor Schwann and Matthias
Schleiden in 1839, states that:
ʺAll living things are made up of
microscopic, functional units called
cellsʺ
— All living organisms are composed of one
or more cells
— Cell is the most basic unit of life

— All cells arise from pre-existing cells

— All basic chemical & physiological
functions are carried out inside the cells

— Cell activity depends on the activities of

sub-cellular structures within the cell
(organelles, nucleus, plasma membrane)

— The cell contains hereditary information

(DNA) which is passed on from cell to
cell during cell division
Characteristics of Cell

— A surrounding membrane
— Protoplasm – cell contents in thick fluid
— Organelles – structures for cell function
— Control center with DNA
— Protoplasm:
Different substances that make up the cell
ü Water
ü Electrolytes
ü Proteins
ü Lipids
ü Carbohydrates
— Water:
70-85%, cellular chemicals dissolved in
water
— Ions:
Provide inorganic chemicals for various
reactions
K, Mg, HCO3, PO4,
—Proteins:
10-20% of cell mass

ü Structural proteins
Fibrillar proteins
ü Functional proteins
enzymes
— Lipids:
2% of cell mass, insoluble in water
Provides barrier for various cell
compartments

ü Phospholipids
ü Cholesterol
— Carbohydrates:
ü 1% of total cell mass
ü role in nutrition
ü Stored as glycogen
Cytoplasm
— Jelly-like fluid that fills a cell
— Mostly water (80%) and salt
— Cytoplasm contains all organelles and cell
parts
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Biological significance
— Cytoplasm is responsible for giving a cell its shape. It
helps to fill out the cell and keeps organelles in their
place

— Cytoplasm contains molecules such as enzymes which

are responsible for breaking down waste and also aid in
metabolic activity

— It helps movement of the cellular materials around the

cell through a process called cytoplasmic streaming

— Cytoplasm also constitutes numerous salts and is a very

good conductor of electricity
Cytoskeleton
— Provides shape and structure
— Helps move organelles around the cell
— Made of three types of filaments
Consists of large number of proteins in the
form of:
— Microfilaments: mostly actin filament,
involved in muscular contraction

— Intermediate filaments: consist of Keratin,

desmin and neurofilaments

— Microtubules: cylindrical structures made up

of alpha and beta tubulins. Involve in cell
organelle movement
Types of Cells
— 2 types of cells exist in nature

vProkaryotic cells
vEukaryotic cells
Prokaryotic Cells
— Derived from greek word i-e Pro-before
& karyon-nucleus
— The prokaryotes are represented by
bacteria (eubacteria and archaebacteria).
— These are almost all small unicellular
organisms only a few microns (10–6 m) in
size
Characteristics of Prokaryotic Cell
— Minimum internal organization
— Smaller in size
— Does not have membrane bound organelles
— Genetic material is not enclosed by nuclear
membrane
— In prokaryotes, DNA is ring shaped, much
shorter (up to 5106 bp), & located in the
cytoplasm
— DNA is not complexed with histones
— Cell divides by binary fission
Eukaryotic Cells
— Greek: Eu- true & karyon-nucleus
— The eukaryotes include fungi, plants, and
animals
— Comprise both unicellular and
multicellular organisms
— Larger in size
Characteristics of Eukaryotic Cell
— Considerable degree of internal structural
organization
— Large number of distinctive membrane
enclosed organelles
— Nucleus is the site for informational
components, known as Chromatin
— Reproduction involve mitosis & meiosis
— Mitochondria provides the respiratory
site
— The eukaryotic cell is subdivided by
membranes. On the outside, it is enclosed by
a plasma membrane
— Inside the cell, there is a large space
containing numerous components in
solution—the cytoplasm
— Additional membranes divide the internal
space into compartments
— Well defined compartments of this type are
known as organelles
Comparison b/t Eu & Prokaryotes
Organization of Cell
Organelles
— Organelles are the complex intracellular
locations where processes for eukaryotic
cellular life occurs
— Most are membrane enclosed
— Together with cytosol, they form the
cytoplasm
— Don’t float freely, rather
interconnected & joined by framework
established by proteins of cytoskeleton
— Organelles involved in protein
processing:
ü Nucleus
ü Ribosomes
ü Endoplasmic reticulum
ü Golgi complex

— Others include:
ü Mitochondria
ü Lysosomes
ü Peroxisomes
NUCLEUS
— All eukaryotic cells except mature
erythrocytes contain nucleus, which
contains hereditary information in the
form of DNA
— Average diameter of the nucleus is 10µm
— 10% of the total cell volume
— Dense, roughly spherical organelle
Structure of Nucleus
ü Nuclear envelope

ü Nuclear pores
ü Nuclear lamina

ü Nucleoplasm

ü Nucleolus

ü Chromatin
— Nuclear Envelope:
ü Outer most structure of nucleus
ü Double –layered phospholipid membrane
ü The outer layer of the membrane is
connected to the endoplasmic reticulum
ü A fluid-filled space or perinuclear space
is present between the two layers of a
nuclear membrane
— Nuclear pores:
ü Pores in the nuclear membrane, that
permit transfer of material between
cytoplasm & nucleus
ü Sites for exchange of large molecules
(proteins and RNA) between the nucleus
and cytoplasm
— Nucleoplasm:
ü Gelatinous substance within the nuclear
envelope, karyoplasm
ü This semi-aqueous material is similar to
cytoplasm and is composed mainly of water
with dissolved salts, enzymes, and organic
molecules suspended within
ü The nucleolus and chromosomes are
surrounded by nucleoplasm, which functions
to cushion and protect the contents of
the nucleus
— Nucleoplasm also supports the nucleus
by helping to maintain its shape

— Provides a medium by which materials,

such as enzymes and nucleotides (DNA &
RNA subunits), can be transported
throughout the nucleus
— Nuclear lamina:
ü Protein scaffolding of nucleoplasm that is
composed of intermediate filaments

ü Forms association between DNA & inner

nuclear membrane
— Nucleolus:
ü Dense, spherical-shaped structure present
inside the nucleus

ü Some of the eukaryotic organisms have

nucleus that contains up to four nucleoli
ü Indirect role in protein synthesis by
producing ribosomes

ü Nucleolus disappears when a cell

undergoes division and is reformed after
the completion of cell division
— Chromatin:
ü Chromosomes are present in the form of
strings of DNA and histones called
chromatin
ü Hetrochromatin: It is a highly condensed,
transcriptionally inactive form, mostly
present adjacent to the nuclear membrane
ü Euchromatin: is a delicate, less condensed
organization of chromatin, which is found
abundantly in a transcribing cell
Nuclear Transport:
— Karyopherins are group of proteins,
facilitate the movement of molecules
between cytoplasm & nucleus
— This transport is mediated through
nuclear pores
— Two types of karyopherins
ü Importins
ü Exportins
Nuclear/ Genomic DNA
— Deoxyribonucleic acid (DNA) is located
in the nucleus
— Repository of genetic information
— It presents as DNA- protein complex
called Chromatin, which is organized into
chromosomes
Functions of Chromatin
— To pack DNA into a smaller volume to fit
in the cell in the form of nucleosomes
— To reinforce the DNA macromolecule to
allow mitosis
— To prevent DNA damage
— To control DNA replication and gene
expression
— The primary protein components of
chromatin are histones that compact
the DNA
 Biomedical Importance
— Controls the heredity characteristics of an
organism
— Stores heredity material in the form of DNA
— It is responsible for protein synthesis, cell
division, growth and differentiation
— Stores proteins and ribonucleic acid (RNA)
— Site for transcription
— Nucleolus produces ribosome and are
known as protein factories
— Aids in exchange of DNA and RNA
(heredity materials) between the nucleus
and the rest of the cell

— Regulates the integrity of genes and gene

expression
Progeria / Hutchinson-Gilford
syndrome
— Autosomal dominant trait
— A rare condition characterized by
premature ageing beginning in very
early life and ending in premature death

— Child appear normal at birth

— Life expectancy is 13-14 years
—Biochemical causes:
ü Mutation in lamin A (LMNA) gene
(present in nuclear lamina, maintains
structural integrity of nuclear scaffold)

ü Gene mutation forms an abnormal form

of the lamin A protein called progerin is
produced and makes cells unstable
RIBOSOMES
— Cellular machinery for protein synthesis
— It consist of proteins (40%) & ribosomal
RNA (r RNA) (60%)
— Ribosomes are tiny particles about 200 Ã
— Found within the cytoplasm, either free or
attached to ER
Structure of Ribosomes
— It consist of 2 subunits
— Larger subunit
— Smaller subunit
— Larger subunit contains 3 r RNA
molecules & close to 50 proteins
— Small consist of one r RNA & close to 30
proteins
— On an average in a mammalian cell there
can be about 10 million ribosomes
— Prokaryotes have 70S
ribosomes each subunit
consisting of small subunit
(30S) and the large subunit
(50S)

— Eukaryotes have 80S

ribosomes each consisting
of small (40S) and large
(60S) subunit

— The catalytic activity of

the ribosome is carried
out by the RNA, the
proteins reside on the
surface and stabilize the
structure
 Biomedical Importance

— They assemble amino acids to form

specific proteins
— Ribosomes reads the m RNA
sequence & translates the genetic
code into specified string of A.A
— In the cytoplasm, the two subunits of
ribosomes are bound around the polymers
of mRNA; proteins are then synthesized
with the help of transfer RNA
ENDOPLASMIC RETICULUM
— Continuous membrane system that forms
a series of flattened sacs within
the cytoplasm of eukaryotic cells
— Serves multiple functions, being important
particularly in the synthesis, folding,
modification, and transport
of proteins
— All eukaryotic cells contain an
endoplasmic reticulum (ER)
— Varying in shape, size &
amount ER extends
from cell membrane,
coats nucleus,
surrounds
mitochondria &
appears to connect
directly to golgi

— The membrane &

aqueous channels they
enclose are called
cisternae
Types of ER
— Rough ER (rough surface b/c of attached
ribosomes)
— Smooth ER

vIn muscle it is known as Sarcoplasmic

Reticulum
Rough ER
— It plays a central role in the synthesis and
export of proteins
— Synthesized proteins are modified
— Protein glycosylation also occurs in RER
— It also plays role in synthesis of
membrane lipids
Smooth ER
— Smooth ER refers to the portion on which
ribosomes are not attached
— Protein modification occurs in SER
— Important role is the synthesis
of phospholipids and cholesterol, which
are major components of the plasma and
membranes
— Calcium triggers the contraction of muscle
cells. Calcium ions are released from the SER
— In liver cells, the SER is specialized for the
detoxification of various compounds

— Liver SER contains a number of enzymes

called cytochrome P450, which catalyze the
breakdown of carcinogens and other
organic molecules

— In cells of the adrenal glands and gonads,

cholesterol is modified in the SER at one
stage of its conversion to steroid hormones
GOLGI APPARATUS
— The Golgi complex is the site of the
modification, completion & export of
secretory proteins and glycoproteins
— It was first described by the Italian
cytologist Camillo Golgi in 1898

— It has a characteristic structure composed

of 5 to 8 flattened, disk-shaped,
membrane-defined cisternae
arranged in a stack
 Structure of Golgi
ü Cis: closest to the ER
ü Medial:
ü Trans: nearest to the
plasma membrane
v These faces are
biochemically distinct,
and the enzymatic
content of each
segment is markedly
different
 Functions of Golgi
— Cis portion helps in doing post-translational
modifications like glycosylation,
phosphorylation & proteolysis
— Trans golgi network sorts & packages
the newly synthesized & modified proteins
into distinct regions
— These bud off from the main golgi & form
structures called transport vesicles
— These secretory vesicles move to & fuse
with the plasma membrane, where the
contents may be expelled out of
membrane by exocytosis
MITOCHONDRIA
— Mitochondria are rod-shaped, spherical
or filamentous organelles

— Considered as the power generators of

the cell, converting oxygen and nutrients
into ATP
— Size: 0.5µm -1µm in diameter
— 1-10 µm in length
— Number varies in different cells, depending
upon its metabolic activity
— E-g mammalian liver cell contains 800-2500
mitochondria
— RBCs don't have mitochondria
Structure of Mitochondria
Outer membrane:
— Phospholipid & cholesterol

— Permeable to most ions and

molecules which can move from the
cytosol to inter membranous space
— Porins:
ü Protein channels, which allow movement
of molecules less than 10,000 mol. wt, to
freely diffuse across the membrane
— Inner Membrane:
ü Rich in proteins
ü Ratio of lipid to protein is 0.27:1 by
weight
ü Contains high amount of phospholipid
cardiolipin
ü Virtually impermeable to polar &
ionic substances
— It contains components of electron
transport system
— For the transport special carriers are
present e.g. adenine nucleotide
carrier(ATP –ADP transport)
— Highly convoluted so that a large number
of infoldings called cristae
— Intermembranous space:

ü Space between inner & outer membranes

ü Same ionic composition as that of cytosol
— Mitochondrial matrix:
ü Region enclosed by inner membrane
ü Contains enzymes of citric acid cycle
ü Enzymes of β-oxidation of fatty acids
ü Enzymes of amino acids oxidation
ü Some enzymes of urea and heme
synthesis
Mitochondrial DNA
— Mitochondrial DNA is the smallest
chromosome coding for 37 genes and
containing 16,569 base pairs
— It’s a maternal inherited
— Mitochondrial DNA is evolved from
circular genome of bacteria that were
engulfed by the early ancestors
of today's eukaryotic cell
— It constitute about 1% of the total cellular
DNA
— Mitochondria self replicates or
divides by fission
Mutation rate is high compare to
Nuclear DNA
Functions of mitochondria
— Generates energy in the form of ATP
— Mitochondria store calcium for cell
signaling activities
— Mediate cell growth
— Role in apoptosis
Function in cell survival
— Survival of eukaryotic cell depends upon
mitochondria
— During development, some cells must die
to allow organ formation
— Death of abnormal cells like virally
infected cells or cancerous cells is also
necessary
— When process of apoptosis is stimulated in
the cell, pro-apoptotic proteins insert into
mitochondrial membranes, forming pores
— A protein i-e Cytochrome c, leaves the inter-
membrane space of mitochondria through
the pores, thus entering the cytosol
— In cytosol cytochrome c stimulates a cascade
of events resulting in apoptotic death of the
cell
Mitochondrial Diseases
— More than 40 mitochondrial disorders
have been identified
— Resulting in reduced ability of
mitochondria to completely oxidize the
food sources
— Brain, heart, liver, skeletal muscles &
eyes are mostly affected
— Developmental delays, poor growth, loss
of muscle co-ordination & loss of vision
— Kearns-Sayre syndrome:
ü Rare disorder, caused by defective m
DNA
ü Caused by large deletion of m DNA
ü Paralysis of eye muscles
ü Degeneration of retina
— Leber Heritary optic neuropathy:
ü B/c of point mutation in m DNA
ü Causes blindness
ü Occurs primarily in young men
— Pearson Syndrome:
ü By deletion in m DNA
ü Affects bone marrow & pancreas
— Fatal infantile mitochondrial myopathy
and renal dysfunction ( cytochrome-c-
oxidase deficiency)
— MELAS (mitochondrial encephalopathy
lactic acidosis and stroke)
— Alzheimer’s disease, Parkinson’s
disease and Cardiomyopathies may
also result in part from decreased
mitochondrial function
Parkinsons disease
— Neurodegenerative
disorder
— Lack of dopamine
— Biochemical
causes:
ü Mitochondrial
damage
ü Oxidative stress
ü Protein misfolding &
their aggregation
LYSOSOMES
— Single membrane-enclosed organelles

— Contain an array of enzymes capable of

breaking down all types of biological
polymers

— Formed from regions of golgi complex

— Discovered by Christian de Duve in 1955

— Present in all animal cells except

erythrocytes
— Function as the digestive system of
the cell, serving both to degrade material
taken up from outside the cell and to
digest obsolete components of the cell
itself
— Visualized as dense spherical vacuoles
— Considerable variation in size & shape
— Acid Hydrolases with a PH of 5

— More than 50 different enzymes

— Acid phosphatase is used as marker

enzyme for this organelle

— Autophagy:
Cells own unwanted cytoplasmic material
enclosed in a membranous vacuole,
becomes fused with lysosome. The enzymes
perform hydrolytic digestion
— Heterophagy:
Hydrolytic digestion of exogenous material
taken up by cell
Lysosomal Storage Diseases
— Caused by defect in acid hydrolases

— Absence of acid hydrolase leads to

accumulation of particular macromolecule

— Storage occurs instead of degradation or

recycling
vAn exception is the I-cell disease, in
which acid hydrolase does not traffic
properly to the lysosome
Lysosomal storage diseases
— Inclusion cell (I- cell) disease

— Sphingolipidoses (Guacher’s and Niemann-Pick disease)

— Gangliosidosis (Tay-Sachs, Leulodystrophies)

— Mucopolysaccharidosis (Hunter Syndrome and Hurler

disease)

— Glycoprotein storage disease

— Mucolipidosis
I-cell disease
— Deficient phosphotransferase
— Acid hydrolases are absent in lysosomes
— Large inclusion bodies in cells
— Lysosomal enzymes in patients plasma &
urine
— s/s: skeletal abnormalities, restricted joint
movement, coarse facial features & severe
psychomotor impairment
Mucopolysaccharidosis:
— Hurler & Hunter syndrome

— Hearing loss
— CNS damage

— Children with hurler syndrome usually

stop developing between 2-4 years of age
Farber disease:
— Acid ceramidase deficiency

— Accumulation of ceramides
— Painful & progressive joint deformity

— Fatal within 1st year of life

Tay Sachs disease:
— Mostly seen in Jewish population
— 1/3600 live births
— Accumulation of gangliosides in the brain
— Blindness, seizures & muscle weakness
— Infantile form is most common variant
— Symptoms appear at 6 months & death
occurs by the age of 4 years
Gaucher Syndrome:
— Most common lysosomal storage disease
— Accumulation of glucocerebrosides
— Hepato-spleenomegaly
— Osteoporosis of long bones
— Infantile form is most severe with
neurological impairment & death occurs
by age of 3
— ERT is available
PEROXISOMES
— Small, oval or spherical in shape

— Formed from SER

— Have a single membrane
— Prominent in leukocytes and platelets
— Contain oxidative enzymes;
• Catalase
• Amino acid oxidase
• Uric acid oxidase
Biomedical Importance
— Detoxification of H2O2 (Catalases)

— Break lipids, particularly LCFAs (Fatty acyl

coA synthetase)

— Breakdown of purines (AMP & GMP)

— Myelin synthesis

— Hepatic peroxisomes synthesize bile acid

& cholesterol
Diseases of Peroxisomes
— Zellweger Syndrome:
(cerebrohepatorenal syndrome)
— Defect in transport of peroxisomal
enzymes into peroxisomes in liver, kidney
& brain
— Accumulation of very long chain
fatty acids mostly in the brain
— Survival rate is not more than 6 months
of age
Refsum”s disease:
— Rare neurological disorder
— Accumulation of phytanic acid in cells
— Impaired alpha oxidation of
branched cain fatty acid
— Causes numbness of hands & feet
Adrenoleukodystrophy:

— X-linked disease
— Characterized by deterioration of myelin
sheath of neurons, owing to failure of
fatty acid metabolism