Biochemistry of Cell

Dr. Rabbiah Manzoor Malik

Cell:
 Cells are the structural and fundamental units of
all
living organisms.
 They are functional entities, each of which is
enclosed by a semi-permeable membrane

 Despite their immense diversity of sizes, shapes and

capacities, living cells are also remarkably similar.

 There are two basic forms of cell: Prokaryotic and
Eukaryotic.
 The cell structure is studied under the
following:
• Cell membrane (Biological membrane) OR plasma
membrane.

• Cytoplasm • Golgi Body

• Endoplasmic reticulum • Lysosomes.

• Cyto-Skeleton • Peroxisomes

• Mitochondria • Nucleus.

• Ribosomes
(II) CYTOPLASM:
 The gelatinous fluid portion filling the cell is
called cytoplasm.

 Cytoplasm keeps the cell structures in their

proper places.

 The cytoplasm of eukaryotic cells have an

extensive membrane system and an intricate
supportive network of proteinaceous fibers and
filaments called the cytoskeleton.
 Whereas the cytoplasm of prokaryotes has a
uniform, grainy appearance except for inclusion
bodies i.e.
 Large granules that contain organic or inorganic
substances e.g. reservoirs of glycogen, fats, or
polyphosphates.
 The cytoplasm also called cytosol & perform the
following important functions:
 Synthesis of Proteins.
 Glycolysis.
 Gluconeogenesis
 Pentose Phosphate systems.
 Fatty acid biosynthesis.
X). NUCLEUS
 The nucleus surrounded by nuclear
envelope consisting of inner and outer
nuclear membrane. The nucleus consists of
nucleoplasm a material rich in DNA. All of
the DNA is held in a fibrous network of
chromatin fibers.
 The chromatin fibers composed of DNA
and DNA packaging proteins known as
histones. The nuclear envelope have
nuclear pores through which pass most of
the molecules that enter and leave the
nucleus.
 The nucleus is now known to perform two
critical functions. First , it contains the cells
hereditary information. Second, the nucleus
exerts a profound influence over all cellular
metabolic activities.

 When nuclei are stained with certain

dyes , one or more spherical structures
called nucleoli (sing: nucleolus) become
visible . The nucleolus, where the cell’s
ribosomes are assembled ,the site for RNA
synthesis.
 Most cells have single nucleus.

 Hepatocytes, parietal cells of stomach and

cardiac myocytes contain two nuclei.

 Osteoclasts contain many nuclei.

 Anucleated cell i.e without nucleus e.g

R.B.C & platelets.
VI).RIBOSOMES.
 Ribosomes are complex structures
containing two irregularly shaped subunits of
unequal size. The ribosomes are RNA/Protein
complexes of about 20 nm diameter. They
synthesize protein for cell.
 The ribosomes are of similar shape and
perform the similar function in eukaryotes
and prokaryotes but the eukaryotic
ribosomes are larger and more complex.
 Ribosomes are ribonucleoprotein particles some
occur as free form as monoribosomes and some
are associated with mRNA as polysomes and
some are associated with RER.
 They are composed of almost entirely of RNA and
proteins, with small amounts of polyamines such
as spermidine and metal ion such as magnesium.
 The ribosomes are isolated by centrifugation and
the rate at which they sediments in a centrifugal
field is called as svedberg units (S). The bacterial
(Prokaryotic) mitochondrial and chloroplast
ribosomes are of 70S
 70S 50 S + 30 S (Subunits).
 Whereas the eukaryotic ribosome’s are of 80S &
some what larger then prokaryotic ribosome.

 80S 60 S + 40 S (Subunits).

 Ribosomes are complex structures containing two

irregularly shaped subunits of unequal size.

 The ribosomes are RNA/Protein complexes of about

20 nm diameter. They synthesize protein for cell.
 Prokaryotic ribosomes contain three types of rRNA
molecules with sedimentation coefficients of 16, 23,
and 5S.

The 30S ribosomal subunit contains the 16S rRNA

complexed with proteins.

The50S ribosomal subunit contains the 23S and 5S

rRNAs complexed with proteins.

The 30S and 50S ribosomal subunits Join to form

the 70S ribosome, which participates in protein
synthesis.
Cytoplasmic ribosomes in eukaryotes contain four
types of rRNA molecules of 18, 28, 5, and 5.8S

and the 60S ribosomal subunit contains the 28, 5, and

5.8S rRNAs complexed with proteins.

 The 40S ribosomal subunit contains the 18S rRNA

complexed with proteins.

In the cytoplasm, the 40S and 60S ribosomal subunits

combine to form the 80S ribosomes that participate in
protein synthesis.
 Mitochondrial ribosomes, with a sedimentation
coefficient of 55S, are smaller than cytoplasmic
ribosomes. Their properties are similar to those of the
70S ribosomes of bacteria.
III) ENDOPLASMIC RETICULUM:
 The endoplasmic reticulum (ER) is a system of
interconnected membranous tubules, vesicles, and
large flattened sacs, extended throughout the
cytoplasm of eukaryotic cells.

 The endoplasmic reticulum membrane encloses

an internal space called the endoplasmic reticulum
lumen or cisternal space.
 The endoplasmic reticulum membrane is in
structural continuity with the outer membrane of
the nuclear envelope and function as passage for
the transport of various molecules. There are two
types of endoplasmic reticulum:
a). Rough Endoplasmic Reticulum (RER):
•Numerous ribosomes are attached on the
cytoplasmic surface of the flattened sheets engaged
in protein synthesis.
b). Smooth Endoplasmic Reticulum (SER):
• Generally more tubular and lacks attached
ribosomes. Although the SER membranes are
continuous with those of RER but their physical
appearances may be significantly different.
Functions of SER include lipid synthesis and
biotransformation, a process in which water insoluble
organic molecules are prepared for excretion. Help in
hydroxylation of various chemicals (drugs) by
cytochrome P450 system in liver. SER also causes
elongation of fatty acid chain.
VII). GOLGI BODIES/APPARATUS.
 The golgi apparatus also known as the
golgi complex or golgi bodies,is a system of
stacked , membrane bounded, flattened
sacks involved in modifying, sorting and
packaging macro molecules for secretion or
for delivery to other organelles.

 The golgi apparatus in plant cell is called

dictyosomes.
 Small membranous vesicles containing
newly synthesized protein and lipid bud off
from the endoplasmic reticulum and fuse
with the golgi membrane.

 These molecules are transported from one

golgi apparatus sac to the next by vesicles,
where they are further processed by enzyme.
 Secretary product such as digestive enzyme or
hormones , are concentrated within secretary
vesicle also called secretary granules.

 which are formed by a process of budding off

from the membrane of golgi bodies.

 When a stimulus come the granules fuse with the

plasma membrane and release the secretary
products by exocytosis.
 The three compartments of golgi-complex are:
 Proximal:
Receive newly formed proteins and help in
posttranslational modification such as lipid addition
or phosphorylation.
 Medial:
More changes occur when proteins passes through
this central compartment.

 Distal:
In this, terminal sugars are added and final sorting
takes place.
VIII). LYSOSOMES
 Lysosomes found in all animal cells except
erythrocytes in varying numbers and types, the
lysosome, in general, is a rather large organelle
consisting of a membrane enclosing a matrix
containing about 30 to 40 hydrolytic enzymes.

 These enzymes are characterized by having acid

pH optima; acid phosphatase is used as a marker
enzyme for this organelle.
ENZYME GROUPS IN LYSOSOMES
 Ribonucleases

 Cathepsins (proteinase)

 Deoxyribonucleases

 Acid glycosidases

 Acid Phosphatases

 Sulfatases

 Lipases

 Phospholipases.
 LYSOSOMES
 They contain packets of enzymes
 These are minute bodies having diameter from
0.08-0.8 μ (app 0.4 μ)
 Surrounded by a lipoprotein membrane
 Found in all cells except erythrocytes
 pH is lower than that of cytosol around 5
 Acid Phosphatase is used as a marker enzyme
for this organelle
 LYSOSOMAL ENZYMES
 Proteolytic enzymes (proteases)
 Cathepsins
 Collagenase
 Elastase

 Nucleotides hydrolyzing enzymes (Nucleases)

 Ribonucleases
 Deoxyribonucleases

 Lipid hydrolyzing enzymes ( lipases)

 Phospholipases
 Fattyacid esterases
 LYSOSOMAL ENZYMES
 Carbohydrates splitting enzymes
(carbohydratases)
 Αlpha-glucosidase
 Βeta-glucosidase
 Hyaluronidase
 Aryl sulfatase

 Other enzymes
 Acid phosphatase
 Catalase
 Collectively, the lysosomal enzymes act on a number
of biopolymers.
 Thus, the proteases have a wide capacity for the
hydrolysis of proteins.
 The acid nucleases for RNA and DNA, and the acid
glycosidases for polysaccharides.
 A pH optima of these enzymes is around pH 5.
Obviously, the lysosomal matrix muxt be acidic for
the enzymes to be reactive.
 It is attractive to consider the lysosomal
membrane that has a high specific activity for
NADH dehydrogenase as serving as a hydrogen
ion pump.
 All the enzymes, other than the esterases and the
NADH dehydrogenase, are present as soluble
proteins in the matrix of the lysosome.
 In autophagic processes, cellular organelles such
as mitochondria and the endoplasmic reticulum
undergo digestion within the lysosome.
 The enzymes are active at postmortem autolysis.
 In the death of a cell, lysosomal bodies
disintegrate, releasing hydrolytic enzymes into
the cytoplasm with the result that the cell
undergoes autolysis.
 There is good evidence that in the metamorphosis
of tadpoles to frogs, the regression of the
tadpole’s tail is accomplished by the lysosomal
digestion of the tail cells.
 Bacteria are digested by white blood cells by
engulfment and lysosomal action.
 The acrosome, located at the head of the sperm,
is a specialized lysosome and is probably involved
in some manner in the penetration of the ovum by
the sperm.

 Finally, a number of hereditary diseases

involving the abnormal accumulation of complex
lipids or polysaccharides in cells of the afflicted
individual have now been traced to the absence of
key acid hydrolases in the lysosomes of these
individuals.
These are involved in intracellular and
extracellular digestion in three fundamental
ways.
 Digestion of food molecules or other substances
taken into the cell by endocytosis.
 Digestion of worn out or unnecessary cell
components.
 Breakdown of extracellular material.
 One genetic disorder in which a
lysosomal enzyme required to degrade
a specific complex lipid is defective in
lysosomal storage diseases and the
conditions is Tay –sachs disease.

 Symptoms of disease include severe

mental retardation and death before
the age of 5 years.
 Biomedical Importance
 All the enzymes, other than the esterases and the NADH
dehydrogenase, are present as soluble proteins in the
matrix of the lysosome
 In autophagic processes cellular organalles such as
mitochondria and the endoplasmic reticulum undergo
digestion within the lysosome
 In the death of cell lysosomal bodies disintegrate releasing
hydrolytic enzymes into the cytoplasm with the result that the
cell undergoes autolysis
 Bacteria are digested by WBCs by engulfment of the bacteria
and lysosomal action
 The acrosome located at the head of the spermatozoa is
specialized lysosome and is probably involved in some way in
the penetration of ovum by sperm
 Lysosomal Storage diseases
 A number of hereditary diseases involving
the abnormal accumulation of complex
lipids or polysaccharides in cells of the
afflicted individual have now been traced to
the absence of key acid hydrolases in the
lysosomes of these individuals
These are involved in intracellular and extracellular
digestion in three fundamental ways.
 Digestion of food molecules or other substances
taken into the cell by ndocytosis.
 Digeston of worn out or unnecessary cell
components.
 Breakdown of extracellular material.
 Mitochondria
 Mitochondria are cell’s power sources
 They are distinct organelle with two membranes
 Usually they are rod shaped , however they can
be round
 Outer membrane limits the organelle
 The inner membrane is thrown into folds or
shelves that project inward, these are called
”cristae”
Outer Mitochondrial Membrane
 The outer membrane is freely permeable to
most ions and small molecules which can
move freely from cytosol into the
intermembranous space and also in reverse
direction
 This transport occurs by the presence of
channels in the outer membrane formed by
integral proteins called PURINS
 Intermembranous space
 The space between the outer and inner
membranes is known as the Intermembranous
space
 As the outer membrane is freely permeable to
small molecules the intermembranous space
has about the same ionic composition as the
cytosol
Inner Mitochondrial Membrane
 It is a specialized structure
 It is highly convulated to increase the surface
area
 These convultions are called cristae
 It contains the assembly for electron transport
chain which consists of loops of alternating
hydrogen and electron carriers (complex I, II,
III & IV)
 Mitochondrial Matrix
 The region enclosed by the inner membrane is known
as the Mitochondrial Matrix
 The enzymes responsible for the citric acid cycle and
fatty acid oxidation are located in matrix
 It also contains several strands of circular DNA
encoding for almost 13 proteins
 It contains ribosomes and enzymes required for
biosynthesis of the proteins coded in the
mitochondrial genome
 A large number of proteins more than 900 have extra
mitochondrial origin, which are encoded by nuclear
gene and synthesized by cytoplasmic ribosomes
 Mitochondrial Matrix
 The entry of these proteins into mitochondria
is quite complex
 These proteins are bound by specialized
proteins called chaperons proteins in cytosol
 First these are taken to the receptors on the
exterior surface of the mitochondria
 Finally specialized translocation mechanism
transport them into the mitochondria
 Mitochondrial Matrix
 Many enzymes associated with carbohydrates, fatty
acids and nitrogen metabolism are located within the
Mitochondrial Matrix
 Enzymes of electron transport chain and oxidative
phosphorylation are also located in different areas of
mitochondria
 They are specialized for the rapid oxidation of NADH
and FADH2 produced in the reactions of glycolysis,
citric acid cycle and oxidation of fatty acids
 The energy produced is stored as ATP
 Clinical Aspects
 A disease known as Luft’s disease involves
mitochondrial energy transduction
 Mitochondrial DNA can be damaged by free
radicals
 Degenerative disorders like Parkinson’s
disease, cardiomyopathy have a component of
mitochondrial damage
 PEROXISOMES
 Peroxisomes are small spherical
membranous organelles that contain
oxidative enzymes that generate and destroy
hydrogen per oxide (H2O2).

H2O2 + AH2 Peroxidase 2H2O + A

2H2O2 Catalase 2H2O + O2

O-2 + O-2 SUPER OXIDE H2O2 + O2

DISMUTASE
 This process is especially important in liver and
kidney cells, which have an important detoxifying
role in animal bodies.

 Lysosomes, peroxisomes, and glyoxysomes

(specialized peroxisomes found in some plant cells)
are some times referred to collectively as micro
bodies.
Peroxisomes are also involved in;
 Oxidation of ingested ethanol
 Purine oxidation
 β-oxidation of long-chain fatty acids
 Degradation of certain amino acids by
Amino Transferases
 Cytoskeleton
 The cytoskeleton is similar to the lipid bilayer in that it
provides the interior structure of the cell the way the lipid
bilayer provides the structure of the cell membrane
 Often, cell will reorganize its intracellular components,
leading to change in its shape. The cytoskeleton is responsible
for mediating these changes
 By providing tracks with its protein filaments the cytoskeleton
allows organelles to move around within the cell
 In addition to facilitating intracellular organelle movement, by
moving itself the cytoskeleton can move the entire cells in
multi-cellular organisms
 In this way the cytoskeleton is involved in intercellular
communication
 Cytoskeleton
 The cytoskeleton is unique to eukaryotic cells
 It is a dynamic three dimensional structure that fills
the cytoplasm
 The structure acts both as muscle and skeleton for
movement of cellular parts and cell and stability
 The long fibers of the cytoskeleton are polymers of
subunits of protein molecules
 It is composed of three types of protein fibres
 Microfilaments
 Microtubules
 Intermediate filaments
microfilaments