NO.

11

1. Golgi apparatus :
Itisadenselystainedreticularstructuresnearthenucleus.Theyconsistofmany
flatdiscshapedsacorcisternae.Thesearestackedparalleltoeachother.The
golgicisternaeareconcentricallyarrangednearthenucleuswithdistinctconvex
cisortheformingfaceandconcavetransormaturingface.Thecisandtransface
oftheorganellesareentirelydifferentbutinterconnected.
Thegolgiapparatusprincipallyperformthefunctionofpackagingmaterialstobe
deliveredtotheintracellulartargetsorsecretedoutsidethecell.Materialstobe
packagedintheformofvesiclesfromERfusewiththecisfaceofgolgiapparatus
andmovetowardsthematuringfacethatswhythegolgiapparatusremainsclose
relatedtoER.AnumberofproteinssynthesizedbyribosomesonERare
midwifedinthecisofthegolgiapparatusbeforetheyarereleasedfromtheirtrans
face.
Thegolgiisimportantsiteofformationofglycoproteinsandglycolipids.Sothey
areprominentinthecellsthatsarespecializedforsecretionofglycoproteinsuch
asgobletcellsofintestinalepitheliumwhichsecretelargeamountsof
polysaccharidesreachthemucousintothegut.
The oligosaccharide processing steps occur in an organized
sequence in the Golgi stack, with each cisterna containing a
characteristic abundance of processing enzymes. Two broad
classes of N-linked oligosaccharides, the complex
oligosaccharides and high-mannose oligosaccharides are
attached to mammalian glycoproteins . The Golgi apparatus
confines the heaviest O-linked glycosylation of all mucins the
glycoproteins in mucus secretion and on proteoglycan core
proteins, which it modifies to produce a proteoglycan [a
compound consisting of a protein bonded to
mucopolysaccharide groups, present especially in
connective tissue] .
Many of the proteoglycans are secreted and become components
of extracellular matrix
The presence of oligosacchaides tends to make a protein more
resistant to digestion by proteolytic enzymes
Oligosaccharides on cell-surface proteins provide the cell with a
protective coat
The mucus coat of lung and intestinal cells protects against
many pathogens
The recognition of sugar chains by lectins in the extracellular
environmnet is important in many developmental processes and
in cell-cell recognition and cell adhesion
According to the vesicular transport model, the Golgi apparatus is a
relatively static structure, with its enzymes held in place , while the
molecules in transit move through the cisternae in sequence,
carried by transport vesicles. A retrograde flow of vesicles retrieves
escaped ER and Golgi proteins and returns them to preceding
compartments . Cisternal maturation model views the Golgi as a
dynamic structure in which the cisternae themselves move .
The vesicular transport model and the cisternal maturation models
are not mutually exclusive .
Evidence suggests that transport may occur by a combination of the
two mechanisms . Proteins are returned by golgi apparatus by
retrograde or retrieval transport in COPI-coated vesicles [ COPI is a
protein complex that coats vesicles transporting proteins from the
cis end of the golgi complex back to the RER , this transport called
Retrograde transport ]

2. Oogenesis: it is the process of formation of a mature female

gamete . Oogenesis is initiated during the embryonic development
stage when a couple of million gamete mother cells [oogonia] are
formed within each fetal ovary no more oogonia are formed and
added after birth. Oogonia develop from primordial germ
cells(PGCs) that migrate into developing gonads early in
embryogenesis.
These cells start division and enter into prophase-1 of the meiotic
division and get temporaily arrested at that stage primary oocytes .
each primary oocytes then gets surrounded a layer of granulosa
cells and is called the primary follicle. Large number of these
follicles degenerate during the phase from birth to puberty .
Therefore at puberty only 60,000-80,000 each ovary. The primary
follicles get surrounded by more layers of granulosa cells and a new
theca and are called secondary follicles. Then it soon transforms
into a tertiary follicles which is characterized by a fluid filled cavity
called antrum.
The theca layer is organized into an inner theca interna and an
outer theca external , at this stage that the primary oocytes within
the tertiary follicle grows in size and completes its first meiotic
division. It is an unequal division resulting in the formation of a large
haploid secondary oocyte and tiny first polar body. The secondary
oocyte retains the bulk of the nutrient rich cytoplasm of the primary
oocyte. The tertiary follicle further changes into the mature follicle
or grafiaan follicle.
The secondary oocyte form a new membrane called zona pellucida
surrounding it. The graafian follicle then ruptures to release the
secondary oocyte fromthe ovary.

3.Peroxisomes:
Peroxisomes are surrounded by only a single membrane, they dont
contain DNA or ribosomes
They contain oxidative enzymes, such as catalase and urate
oxidase
Peroxisomes are major sites of oxygen utilization
Peroxisomes usually contain one or more enzymes that use
molecular oxygen to remove hydrogen atoms from specific
organic substrates in an oxidation reaction that produces
hydrogen peroxide RH2 + O2 R +2H2O2
Catalase uses hydrogen peroxydase to oxidase a variety of other
substrates including phenols, phormic acid, formaldehyde and
alcohol by the peroxidation reaction : H2O2 + RH2 R + 2H2O
This type of oxidation reaction is particularly important in liver
and kidney cells, where peroxisomes detoxify various toxic
molecules
When excess hydrogen peroxide accumulates in the cell,
catalase converts it to water. A major function of oxidation
reactions performed in peroxisomes is the breakdown of fatty
acid molecules . This process called oxidation shortens the
alkyl chains of fatty acids sequentially in blocks of two carbon
atom at a time, converting the fatty acids to Acetyl CoA . An
essential biosynthetic function of peroxisomes is to catalyse the
first reactions in the formation of plasmalogens, which are the
most abundant class of phospholypids in myelin.
Thats why peroxisomal disorders lead to neurological disease.
A specific sequence of three amino acids (Ser-Lys-Leu) located at
the C terminus of many peroxisomal proteins functions as an
import signal
Other peroxisomal proteins contain import signals at the N
terminus
At least 23 distinct proteins called peroxins participate in the
import process which is driven by ATP hydrolysis
A complex of at least 6 different peroxins form a membrane
translocator . The importance of the import process and of
peroxisomes is demonstrated by the inherited human disease
Zellweger Syndrome, in which a defect in importing proteins into
peroxisomes leads to a profound peroxisomal deficiency.
Individuals whose cells contain such empty peroxisomes have
severe abnormalities in the brain, liver and kidnays and they die
soon after birth. New peroxisomes are thought to arise from pre-
existing ones by organelle growth and fission

4. Hsp60 , Hsp70 : Heat shock protein 60 is a mitochondrial chaperonin that is

typically held responsible for the transportation and refolding of proteins from the
cytoplasm into the mitochondrial matrix. In addition to its role as a heat shock protein,
HSP60 functions as a chaperonin to assist in folding linear amino acid chains into their
respective three-dimensional structure.
Stresses such as temperature, concentration imbalance, pH change, and toxins can all
induce heat shock proteins to maintain the conformation of the cells proteins. HSP60
plays an important role in the transport and maintenance of mitochondrial proteins as
well as the transmission and replication of mitochondrial DNA and also as heat shock
protein. HSP60 possesses two main responsibilities with respect to mitochondrial protein
transport. It functions to catalyze the folding of proteins destined for the matrix and
maintains protein in an unfolded state for transport across the inner membrane of the
mitochondria. The hydrophobic portion HSP60 is responsible for maintaining the
unfolded conformation of the protein for transmembrane transport. HSP60 binds to
incoming proteins and induces conformational and structural changes.HSP60 is also
capable of distinguishing between proteins designated for export and proteins destined to
remain in the mitochondrial matrix by looking for an amphiphilic alpha-helix of 15-20
residues. HSP60 is involved in the replication and transmission of mitochondrial DNA.
The cytoplasmic HSP60 forms a complex with proteins responsible for apoptosis and
regulates the activity of these proteins. The cytoplasmic version is also involved in
immune response and cancer.HSP60 influence apoptosis in tumor cells which seems to be
associated with a change in expression levels.

HSP 70s : The 70 kilodalton are heat shock proteins. The Hsp70s are
an important part of the cell's machinery for protein folding, and help
to protect cells from stress.
When not interacting with a substrate peptide, Hsp70 is usually in an
ATP bound state. Hsp70 by itself is characterized by a very weak
ATPase activity, such that spontaneous hydrolysis will not occur for
many minutes. As newly synthesized proteins emerge from the
ribosomes, the substrate binding domain of Hsp70 recognizes
sequences of hydrophobic amino acid residues, and interacts with
them. This spontaneous interaction is reversible, and in the ATP bound
state Hsp70 may relatively freely bind and release peptides. However,
the presence of a peptide in the binding domain stimulates the ATPase
activity of Hsp70, increasing its normally slow rate of ATP hydrolysis.
When ATP is hydrolyzed to ADP the binding pocket of Hsp70 closes,
tightly binding the now-trapped peptide chain.
By binding tightly to partially synthesized peptide sequences
(incomplete proteins), Hsp70 prevents them from aggregating and
being rendered nonfunctional. Once the entire protein is synthesized, a
nucleotide exchange factor stimulates the release of ADP and binding
of fresh ATP, opening the binding pocket. The protein is then free to
fold on its own, or to be transferred to other chaperones for further
processing.
Hsp70 also aids in transmembrane transport of proteins, by stabilizing
them in a partially folded state.
Hsp70 proteins can act to protect cells from thermal or oxidative
stress. These stresses normally act to damage proteins, causing partial
unfolding and possible aggregation. By temporarily binding to
hydrophobic residues exposed by stress, Hsp70 prevents these
partially denatured proteins from aggregating, and allows them to
refold.
Hsp70 seems to be able to participate in disposal of damaged or
defective proteins. Interaction with CHIP (Carboxyl-terminus of Hsp70
Interacting Protein)an E3 ubiquitin ligaseallows Hsp70 to pass
proteins to the cell's ubiquitination and proteolysis pathways.
Finally, in addition to improving overall protein integrity, Hsp 70
directly inhibits apoptosis.

NO.12

1. Apoptosis : The number of cells is tightly regulated - by

controlling the rate of cell division and by controlling the rate of cell
death
If cells are no longer needed, they commit suicide by activating
an intracellular death program
This process is called programmed cell death or apoptosis
Intracellular machinery, responsible for apoptosis are caspases
C for cysteine at their active site and asp for aspartic acid which
they cleave on their target proteins
They are synthesized as inactive procaspases which are
activated by proteolytic cleavage

Their is two types of procaspases :

1.Initiator procaspases
2.Executioner procaspases

Target proteins: nuclear lamina, components of the cytoskeleton,

cell-cell adhesion proteins
 Cells dying by apoptosis undergo chatacteristic morphologic
changes: They shrink and condense, cytoskeleton collapses, the
nuclear envelope disassembles, the nuclear chromatin condenses
and breaks up into fragments. The cell surface often blebs and
breaks up into membrane-enclosed compartments called apoptotic
bodie . Macrophages rapidly engulf them before they can spill their
contents . In this way, the cell dies neatly and is rapidly cleared
away without causing a damaging inflammatory response.
When the cell receives a signal to undergo apoptosis the initiator
procaspases are brought into close proximity in activation
complexes
They have caspase recruitment domains and they cleave each other
and activate executioner procaspases . The two best signaling
pathways that leading to apoptosis in mammalian cells are called
the extrinsic pathway and the intrinsic pathway.

Extrinsic pathway : Cells can also activate their apoptosis

program from inside the cell, usually in response to injury or other
stresses, such as DNA damage or lack of oxygen, nutrients, or
extracellular survival signals. Whereas, The intrinsic pathway : of
apoptosis depends on the release into the cytosol of mitochondrial
proteins that normally reside in the intermembrane space of these
organelles

Human disorder in which execessive numbers of cells undergo

apoptosis are heart attacks and strokes , many cell die by necrosis
due to ischemia, but some of them die by apoptosis
Whereas decreased apoptosis contributes to many tumors and
cancers

3. lysosomes : Lysosomes are membrane-enclosed compartments

filled with soluble hydrolytic enzymes. Lysosomes contain about 40
types of hydrolytic enzymes, including proteases, nucleases,
glycosidases, lipases, phospholipases, phosphatases and sulfatases .
All are acidic hydrolases . Most of the lysosomal membrane proteins
are highly glycosylated, which helps to protect them from the
lysosomal proteases in the lumen . A vacuolar H ATPase in the
lysosomal membrane uses the energy of ATP hydrolysis to pump H
into the lysosome, thereby maintaining the lumen at its acidic pH
The heterogenity of lysosomal morphology reflects the wide
variety of digestive functions that acid hydrolases mediate:
Breakdown of intra- and extracellular debris
The destruction of phagocytosed microorganisms
 The production of nutrients for the cell

A route that leads outwards from the ER via the Golgi apparatus
delivers most digestive enzymes
At least three paths from different sources feed substances into
lysosomes for digestion
The best studied of these paths is endocytosis
Endocytosed molecules are initially delivered in vesicles to early
endosomes
Here the endocytosed materials first meet lysosomal hydrolases
Lysosomes are meeting places where several streams of
intracellular traffic converge
Some of the ingested molecules are selectively retrieved and
recycled to the plasma membrane
Others pass on into late endosomes
Mature lysosomes form by a maturation process from late
endosomes

o All cell types use a second degradation pathway to dispose of

obsolete parts of the cell itself - a process called autophagy
o The process begins with the enclosure of an organelle by a
double membrane of unknown origin, creating an
autophagosome which fuses with a lysosome
o In addition to maintaining basic cell functions in balance and
helping to dispose of obsolete parts, autophagy also has a role in
development and health
o The third pathway that brings materials to lysosomes for
degradation is found mainly in cells specialized for the
phagocytosis of large particles and microorganisms
o Such professional phagocytes (macrophages and neutrophils)
engulf objects to form a phagosome, which is then converted to
a lysosome

Lysosomal hydrolases and membrane proteins are co-

translationally transported into the ER and then transported
through the Golgi apparatus to the TGN
The transport vesicles bud off from TGN
These vesicles incorporate the lysosomal proteins
Lysosomal hydrolases carry a unique marker in the form of
mannose-6-phosphate (M6P) groups
Transmembrane M6P receptor proteins recognize the M6P groups
The receptor proteins bind to lysosomal hydrolases and to
adaptor proteins in assembling clathrin coats
In this way, they help package the hydrolases into clathrin-
coated vesicles that bud from the TGN
 Genetic defects that affect one or more of the lysosomal
hydrolases cause a number of human lysosomal storage diseases
These defects result in an accumulation of undigested
substrates in lysosomes with severe pathological consequences,
most often in the nervous system
In Hurlers disease, the enzyme required for the breakdown of
certain types of glycosaminoglycan chains is defective or missing
The most severe form of lysosomal storage disease is a very rare
disorder, called inclusion-cell disease (I-cell disease)
In this condition almost all of the hydrolytic enzymes are missing
from the lysosomes of fibroblasts
I-cell disease is due to a single gene defect and is recesive
All the hydrolases missing from the lysosomes are found in the
blood
The missorting has been traced to a defective or missing GlcNAc-
phosphotransferase
Lysosomes in some cell types, such as hepatocytes, contain a
normal complement of lysosomal enzymes, implying that there is
another pathway for directing hydrolases to lysosomes
The nature of this M6P-independet pathway is unknown

4. Synaptonemal Complex :

It is a protein structure that forms between homologous chromosomes

(two pairs of sister chromatids) during meiosis and is thought to
mediate chromosome pairing, synapsis, and recombination. It is
currently thought that the SC functions primarily as a scaffold to allow
interacting chromatids to complete their crossover activities. The
synaptonemal complex is a tripartite structure consisting of two
parallel lateral regions and a central element.

Three specific components of the synaptonemal complex have been

characterized: SC protein-1 (SYCP1), SC protein-2 (SYCP2), and SC
protein-3 (SYCP3). In humans, the SYCP1 gene is on chromosome 1p13;
the SYCP2 gene is on chromosome 20q13.33; and the gene for SYCP3
is on chromosome 12q.
"tripartite structure" is seen during the pachytene stage of the first
meiotic prophase, both in males and in females during gametogenesis.
Previous to the pachytene stage, during leptotene, the lateral elements
begin to form and they initiate and complete their pairing during the
zygotene stage. After pachytene ends, the SC usually becomes
disassembled and can no longer be identified.

Formation of the SC usually reflects the pairing or "synapsis" of

homologous chromosomes and may be used to probe the presence of
pairing abnormalities in individuals carrying chromosomal
abnormalities, either in number or in the chromosomal structure. The
sex chromosomes in male mammals show only "partial synapsis" as
they usually form only a short SC in the XY pair. The SC shows very
little structural variability among eukaryotic organisms despite some
significant protein differences. In many organisms the SC carries one or
several "recombination nodules" associated to its central space.
These nodules are thought to correspond to mature genetic
recombination events or "crossovers".

In cell development the synaptonemal complex disappears during the

late prophase of meiosis I.

synaptonemal complexes can be affected and damaged by chemical

exposure, specifically by toxins like bisphenol A

NO.13

1.Meiosis : Haploid germ cells arise from a special kind of cell division
in which the number of chromosomes is precisely halved
. At the beginning of meiosis, the chromosomes have replicated their
DNA and the two copies are tightly bound together by cohesin
complexes along their entire length and are called sister chromatids. A
single round of DNA replication is followed by two successive rounds of
chromosomes segregation

In division I of meiosis the duplicated paternal and maternal

homologs pair up along side each other and exchange genetic
information through the process of genetic recombination
 Then they line up at the equator of meiotic spindle, after which
the duplicated homologs are pulled apart and segregated into
the two daughter cells
Only in division II of meoisis, which occurs without further DNA
replication, are the sister chromatids pulled apart and
segregated to produce haploid daughter cells
Each diploid cell that enters meiosis produces four haploid cells,
each of which inherits either the maternal or the paternal copy of
each chromosome but not both

Duplicated meiotic prophase chromosomes initially appear as

long threadlike structures in which sister chromatids are tightly
glued together and appear as one
In prophase the homologs begin to associate along their length
in a process called pairing
As prophase progresses homologs become more closely
juxtaposed, forming a four-chromatid structure called a bivalent

Two kinds of genetic reassortment have occurred during meiosis

One kind of reassortment is the consequence of the random
distribution of the maternal and paternal homologs between the
daughter cells at meiotic division , as a result of which each
gamete acquires a different mixture of maternal and paternal
chromosomes
The second kind of reassortment is chromosomal crossing-over
During crossing-over fragments are exchanged between the two
nonsister chromatids in a reciprocal fashion by a process known
as genetic recombination
Two duplicated homologs that form each bivalent are seen to be
physically connected at specific points
Each connection called a chiasma corresponds to a crossover
between two non-sisiter chromatids

Crossovers between sex chromosomes X and Y are possible

because of a small region of homology between them
The two chromosomes pair and cross over in this region at
Prophase
The chiasmata resulting from this genetic recombination keep
the X and Y chromosomes connected on the spindle so that only
two types of sperm are normally produces

Prophase is divided into five stages: leptotene, zygotene,

pachytene, diplotene and diakinesis
At leptotene homologs condense and pair and genetic
recombination begins
 At zygotene the synaptonemal complex begins to assemble;
assembly initiates at sites where the homologs are closely
associated and recombination events are occurring
At pachytene the assembly process is complete and homologs
are synapsed along their entire lengths
Desynapsis begins at diplotene with the disassembly of the
synaptonemal complexes and the condensation and shortening
of chromosomes
At this stage individual crossover events between non-sister
chromatids can be seen as interhomolog connections called
chiasmata
Homologs are now ready to begin the process of segregation
Prophase ends with diakinesis

MEIOSIS-1 :
Prophase 1: Each chromosome duplicates and remains closely
associated. These are called sister chromatids. Crossing-over can
occur during the latter part of this stage.
Metaphase 1: Homologous chromosomes align at the equatorial
plate.
Anaphase 1: Homologous pairs separate with sister chromatids
remaining together.
Telophase 1: Two daughter cells are formed with each daughter
containing only one chromosome of the homologous pair.

MEIOSIS-2 :
Prophase 2: DNA does not replicate. Spindle apparatus forms.
Metaphase 2: Chromosomes align at the equatorial plate.

Anaphase 2: Centromeres divide and sister chromatids migrate

separately to each pole.

Telophase 2: Cell division is complete. Four haploid daughter cells

are obtained.

2. Zellweger syndrome : peroxisomes is demonstrated by the

inherited human disease Zellweger Syndrome, in which a defect in
importing proteins into peroxisomes leads to a profound peroxisomal
deficiency

Zellweger syndrome is one of three peroxisome biogenesis

disorders which belong to the Zellweger spectrum of peroxisome
biogenesis disorders (PBD-ZSD).[4] The other two disorders are neonatal
adrenoleukodystrophy (NALD), and infantile Refsum disease (IRD).[5]
[6]
Although all have a similar molecular basis for disease, Zellweger
syndrome is the most severe of these three disorders.[7]
Zellweger syndrome is associated with impaired neuronal migration,
neuronal positioning, and brain development.[4] In addition, individuals
with Zellweger syndrome can show a reduction in central nervous
system (CNS) myelin (particularly cerebral), which is referred to
as hypomyelination. Myelin is critical for normal CNS functions, and in
this regard, serves to insulate nerve fibers in the brain. Patients can
also show postdevelopmental sensorineuronal degeneration that leads
to a progressive loss of hearing and vision.[4]
Zellweger syndrome can also affect the function of many other organ
systems. Patients can show craniofacial chondrodysplasia
punctata (punctate calcification of the cartilage in specific regions of
the body), eye abnormalities, and renal cysts.

Zellweger syndrome is an autosomal recessive disorder

caused by mutations in genes that encode peroxins, proteins required

for the normal assembly of peroxisomes. Most commonly, patients
have mutations in
the PEX1, PEX2, PEX3, PEX5, PEX6, PEX10, PEX12, PEX13, PEX14, PEX1
6, PEX19, or PEX26 genes.[8] In almost all cases, patients have
mutations that inactivate or greatly reduce the activity of both the
maternal and paternal copies of one these aforementioned PEX genes.
As a result of impaired peroxisome function, an individual's tissues and
cells can accumulate very long chain fatty acids (VLCFA) and branched
chain fatty acids (BCFA) that are normally degraded in peroxisomes.
The accumulation of these lipids can impair the normal function of
multiple organ systems, as discussed above. In addition, these
individuals can show deficient levels of plasmalogens, ether-
phospholipids that are especially important for brain and lung function.

3. Regeneration :, regeneration is the process of renewal,

restoration, and growth that makes genomes, cells, organs, organisms,
and ecosystems resilient to natural fluctuations or events that cause
disturbance or damage. Every species is capable of regeneration, from
bacteria to humans. Regeneration can either be complete where the
new tissue is the same as the lost tissue, or incomplete where after
the necrotic tissue comes fibrosis. At its most elementary level,
regeneration is mediated by the molecular processes of DNA synthesis.
Regeneration refers to the morphogenic processes that characterize
the phenotypic plasticity of traits allowing multi-cellular organisms to
repair and maintain the integrity of their physiological and
morphological states. Above the genetic level, regeneration is
fundamentally regulated by asexual cellular processes. Regeneration is
different from reproduction. For example, hydra perform regeneration
but reproduce by the method of budding.
Tissues and organs
"Regenerative strategies include the rearrangement of pre-existing
tissue, the use of adult somatic stem cells and the dedifferentiation
and/or transdifferentiation of cells, and more than one mode can
operate in different tissues of the same animal. Dedifferentiation of
cells means that they lose their tissue-specific characteristics as
tissues remodel during the regeneration process. Transdifferentiation of
cells is when they lose their tissue-specific characteristics during the
regeneration process, and then re-differentiate to a different kind of
cell.

Types of regeneration:
1. Physiological regeneration regeneration of dead, damaged or
exhausted cells and their components, which have died during
the life of an organism.
2. Reparational regeneration growth of damaged or amputated
body parts.
3. Pathologic regeneration proliferation of a completely different
types of cells instead of a damaged tissue.

Physiological regenartaion maintain homeostasis in the following way:

1) Tissues require mechanical strength that is provided by
extracellular matrix produced by fibroblasts.
2) All types of tissues and organs require blood supply for their
normal functioning that is provided by vessels lined with
endothelial cells.
3) All types of tissues require inervetion and contain nerve endings
and nerve cells.
4) All types of tissues contain immunocompetent cells that are
specialized in the defense of an organism against infection.

Mechanisms of physiological regeneration:

1) Constant renewal of cells and intracellular components by
utilization of old and emaciated structures, synthesis of new
macromolecules, formation of new functional complexes.
2) Renewal of cells constituting a particular type of tissue by the
following mechanisms: utilization of dead cells, proliferation of
new cells and substitution of utilized old cells, phagocytosis of
old cellular fragments.
3) Proliferation and differentiation of cells based on stem cells.
Reparational regeneration is characteristic to various organisms. The
ageing or damage to an organ may be caused by mechanical or
thermal traumas, toxic agents and so on. Renewal of the skin surface,
healing of fractures and wounds of internal organs are the examples.
Epithelization is the renewal of the epithelial surface in case of
superficial wounds.
Epimorphosis is the growth of removed organ from the surface of
the wound, example is the growth of lizards tail. Epimorphosis can be
atypic or heterotypic.
Morpholaxis - is the regenretaion of a whole organism on the bases
of a single organ.
Endomorphosis is the regeneration of the organ after the removal
of the part of it, for example regeneration of mammalian liver.
Compensatory hypetrophy if one organ is removed the other
grows in size to increase the function (kidney).
Hypetrophy is the increase in the size and hyperplasia is the
increase in the number of cells.

Humans
Liver
The human liver is one of the few glands in the body that has the
ability to regenerate from as little as 25% of its tissue. This is largely
due to the unipotency of hepatocytes. Resection of liver can induce the
proliferation of the remaining hepatocytes until the lost mass is
restored, where the intensity of the livers response is directly
proportional to the mass resected. For almost 80 years surgical
resection of the liver in rodents has been a very useful model to the
study of cell proliferation.
Kidney
Regenerative capacity of the kidney remains largely unexplored. The
basic functional and structural unit of the kidney is nephron, which is
mainly composed of four components: the glomerulus, tubules, the
collecting duct and peritubular capillaries. The regenerative capacity of
the mammalian kidney is limited compared to that of lower
vertebrates.
In the mammalian kidney, the regeneration of the tubular component
following an acute injury is well known. Recently regeneration of the
glomerulus has also been documented. Like other organs, the kidney is
also known to regenerate completely in lower vertebrates such as fish.
Some of the known fish that show remarkable capacity of kidney
regeneration are goldfish, skates, rays, and sharks. In these fish, the
entire nephron regenerates following injury or partial removal of the
kidney.
Heart
Several animals can regenerate heart damage, but in mammals
cardiomyocytes (heart muscle cells) cannot proliferate (multiply) and
heart damage causes scarring and fibrosis.
Intestinal epithelium has high ability of regeneration as it contains
stem cells which are located at the base of crypts, they proliferate and
differentiate into cylindrical cells.
Nerve tissue also has a good ability of regeneration while striated
muscles have some ability - that is intracellular regeneration and
constant renewal of muscle fibers. The proliferation of muscle cells
ceases by the end of the first year of living and the following increase
in size of muscles is determined by the thickening of muscle fibers that
is caused by hypertroph

4.Bcl-2 : Bcl-2 (B-cell lymphoma 2), encoded in humans by

the BCL2 gene, is the founding member of the Bcl-2 family of regulator
proteins that regulate cell death (apoptosis), by either inducing (pro-
apoptotic) it or inhibiting it (anti-apoptotic). Bcl-2 is specifically
considered as an important anti-apoptotic protein and is thus classified
as an oncogene.

Bcl-2 derives its name from B-cell lymphoma 2, as it is the second

member of a range of proteins initially described inchromosomal
translocations involving chromosomes 14 and 18 in follicular
lymphomas. Damage to the Bcl-2 gene has been identified as a cause
of a number of cancers, including melanoma, breast, prostate,chronic
lymphocytic leukemia, and lung cancer, and a possible cause
of schizophrenia and autoimmunity. It is also a cause of resistance to
cancer treatments.

The over-expression of the anti-apoptotic Bcl-2 protein in lymphocytes

alone does not cause cancer. But simultaneous over-expression of Bcl-2
and the proto-oncogene myc may produce aggressive B-
cell malignancies including lymphoma. In follicular lymphoma,
a chromosomal translocation commonly occurs between the fourteenth
and the eighteenth chromosomest(14;18) which places the Bcl-2
gene next to the immunoglobulin heavy chain locus. This fusion gene is
deregulated, leading to the transcription of excessively high levels of
Bcl-2. This decreases the propensity of these cells for undergoing
apoptosis.
Mammalian Bcl2 proteins regulate the intrinsic pathway of apoptosis
mainly by controlling the release of cytochrome c and other
intermembrane mitochondrial proteins into the cytosol. Some Bcl2
proteins are pro-apoptotic and promote apoptosis by enhancing the
release, whereas others are anti-apoptotic and inhibit apoptosis by
blocking the release.
Pro-apoptotic proteins are Bak and Bax they induce release of
Cytochrome from mitochondria. Other members of the Bcl2 family,
including Bcl2 itself can inhibit procaspase activation and apoptosis.
They block the ability of Bak and Bax to release cytochorme c from
mitochondria. Most animal cells make IAP proteins (Inhibitors of
Apoptosis), which inhibit activated caspases. Some also
polyubiquitylate caspases, marking the caspases for destruction in
proteasomes. Anti-IAPs are released from the mitochondrial
intermembrane space when the intrinsic pathway of apoptosis is
activated , blocking IAPs in the cytosol and thereby promoting
apoptosis. In summary, the combined activities of Bcl2, IAPs and anti-
IAPs determine the sensitivity of an animal cell to apoptosis-inducing
stimuli. With IAPs and anti-IAPs dominating in flies and Bcl2 dominating
in humans.

NO.14

1. Oocytes and special mechanism to grow

An egg is the most remarkable of animal cells: once activated it

can give rise to a complete new individual within a matter of
days or weeks
No other cell in a higher animal cell has this capacity
Activation is usually consequence of fertilization fusion of an
egg with a sperm
An egg can give rise to every cell type in the adult organism
The eggs are giant single cells
They are typically spherical or ovoid, with a diameter of about
0.1 mm in humans
The egg cytoplasm usually contains nutritional reserves in the
form of yolk, which is rich in lipids, proteins and polysaccharides
and is often contained with a discrete structures called yolk
granules
The egg coat is another peculiarity of eggs
It is a specialized form of extracellular matrix consisting largely
of glycoproteins
In mammalian cells it is called the zona pellucida
 This layer protects the egg from mechanical damage and acts as
species-specific barrier for a sperm, admitting only those of the
same or related species

Eggs have special mechanisms for achieving their large size

One mechanism is to have extra gene copies in the cell
Most of the growth of the oocyte occurs after DNA replication,
when the diploid chromosome set is in duplicate
In this way, it has twice as much DNA available for RNA synthesis
as does an average somatic cell in the G1 phase of the cell cycle
Oocytes may also depend partly on the synthetic activities of
other cells for their growth
Yolk, for example, is usually synthesized outside the ovary and
imported into the oocyte
Nutritive help can also come from neighbouring accessory cells
in the ovary, such as folicle cells

2. ARF :
To balance the vesicular traffic to and from the compartments,
coat proteins must assemble only when and where they are
needed. Coat-recruitment GTPases control the assembly of
clathrin-coat on endosomes and the COPI and COPII coats on
Golgi and ER. Many steps in vesicular transport depend on
variety of GTP-binding proteins that control both the spatial and
temporal aspects of membrane exchange . They act as molecular
switches. There are Two classes of proteins regulate flipping:

1. Guanine-nucleotide-exchange factors (GEFs) activate coat-

recruitment proteins by catalyzing exchange of GDP to GTP

2. GTPase-activating proteins (GAPs) inactivate these proteins by

triggering the hydrolysis of the bound GTP to GDP

Coat-recruitment GTPases are members of family of monomeric

GTPAses . They include the ARf proteins which are responsible for
both COPI coat assembly and clathrin coat assembly at Golgi
membranes and the Sar1 protein which is responsible for COPII
coat assembly at the ER membrane. Coat-recruitment GTPases
are usually found in high concentration in the cytosol in an
inactive, GDP-bound state.
ADP Ribosylation Factors (ARFs) are members of the ARF family of GTP-
binding proteins of the Ras superfamily. ARF family proteins are
ubiquitous in eukaryotic cells, and six highly conserved members of
the family have been identified in mammalian cells. They function as
regulators of vesicular traffic and actin remodelling.

The small ADP ribosylation factor (Arf) GTP-binding proteins are major
regulators of vesicle biogenesis in intracellular traffic. Arf proteins cycle
between inactive GDP-bound and active GTP-bound forms that bind
selectively to effectors. The classical structural GDP/GTP switch is
characterized by conformational changes at the so-called switch 1 and
switch 2 regions, which bind tightly to the gamma-phosphate of GTP
but poorly or not at all to the GDP nucleotide. Structural studies of Arf1
and Arf6 have revealed that although these proteins feature the switch
1 and 2 conformational changes, they depart from other small GTP-
binding proteins in that they use an additional, unique switch to
propagate structural information from one side of the protein to the
other.

3.Cytochrome-C :
The cytochrome complex, or cyt c is a small heme protein found
loosely associated with the inner membrane of the mitochondrion. It
belongs to the cytochrome c family of proteins. Cytochrome c is a
highly water soluble protein, it is an essential component of
the electron transport chain, where it carries one electron. It is capable
of undergoing oxidation and reduction, but does not bind oxygen. In
humans, cytochrome c is encoded by the CYCS gene.

Functions:

Cytochrome c is a component of the electron transport chain in

mitochondria. The heme group of cytochrome c accepts electrons from
the bc1 complex and transfers electrons to the cytochrome oxidase
complex. Cytochrome c is also involved in initiation of apoptosis . Upon
release of cytochrome c to the cytoplasm, the protein binds apoptotic
protease activating factor-1 (Apaf-1).

Role in apoptosis:
Cytochrome c is also an intermediate in apoptosis, a controlled form of
cell death used to kill cells in the process of development or in
response to infection or DNA damage.

Cytochrome c binds to cardiolipin in the inner mitochondrial

membrane, thus anchoring its presence and keeping it from releasing
out of the mitochondria and initiating apoptosis. While the initial
attraction between cardiolipin and cytochrome c is electrostatic due to
the extreme positive charge on cytochrome c, the final interaction is
hydrophobic, where a hydrophobic tail from cardiolipin inserts itself
into the hydrophobic portion of cytochrome c.

During the early phase of apoptosis, mitochondrial ROS production is

stimulated, and cardiolipin is oxidized by a peroxidase function of the
cardiolipincytochrome c complex. The hemoprotein is then detached
from the mitochondrial inner membrane and can be extruded into the
soluble cytoplasm through pores in the outer membrane.

The sustained elevation in calcium levels precedes cyt c release from

the mitochondria. The release of small amounts of cyt c leads to an
interaction with the IP3 receptor (IP3R) on the endoplasmic
reticulum (ER), causing ER calcium release. The overall increase in
calcium triggers a massive release of cyt c, which then acts in the
positive feedback loop to maintain ER calcium release through the
IP3Rs. This explains how the ER calcium release can reach cytotoxic
levels. This release of cytochrome c in turn activates caspase 9, a
cysteine protease. Caspase 9 can then go on to activate caspase
3 and caspase 7, which are responsible for destroying the cell from
within.

4.SRP and SRP-R:

The ER signal sequence is guided to the ER membrane by at least
two componnets:
A signal recognition particle (SRP), which cycles between the ER
membrane and the cytosol and binds to the signal sequence
SRP receptor in the ER membrane
SRP is a complex particle consisting of six different polypeptide
chains bound to a single small RNA molecule
 Signal sequences have eight or more non-polar amino acids at
their centre
Signal sequence binding site in SRP is a large hydrophobic pocket
lined by methionines
The SRP binds to the ER signal sequence as soon as the peptide
has emerged from the ribosome
This causes a pause in protein synthesis
Once formed, the SRP-ribosome complex binds to the SRP
receptor, which is an integral membrane protein exposed on the
cytosolic surface of the RER
This interaction brings the SRP-ribosome complex to membrane
translocator
The SRP and SRPreceptor are then released and the growing
polypepetide chain is transferred across the membrane

ER signal is recognized twice: first by an SRP in the cytosol and

then by a binding site in the ER translocator

Three ways in which single-pass transmembrane proteins become

inserted into the ER:
N-teminal ER signal sequence initiates translocation
Stop-transfer signal anchors the protein in the membrane after
the ER signal sequence has been released from the translocator
and has been cleaved off
The stop-transfer sequence is transferred into the bilayer by the
lateral gating mechanism, and it remains there as a single -
helical membrane-spanning segment

In other two cases, the signal sequence is internal

The internal signal sequence is recognized by an SRP, which
brings the ribosome to the ER membrane and serves as a start-
transfer signal that initiates the translocation
After release from the translocator, the internal start-transfer
signal sequence remains in the lipid bilayer as a single-
membrane-spanning helix

SRP: The Signal recognition particle (SRP) is a multimeric protein,

which along with its conjugate receptor (SR), is involved in targeting
secretory proteins to the rough endoplasmic reticulum (RER)
membrane in eukaryotes, or to the plasma membrane in
prokaryotes. SRP recognises the signal sequence of the nascent
polypeptide on the ribosome, retards its elongation, and docks the
SRP-ribosome-polypeptide complex to the RER membrane via the SR
receptor. SRP consists of six polypeptides and a single 300 nucleotide
7S RNA molecule. The RNA component catalyses the interaction of SRP
with its SR receptor. In higher eukaryotes, the SRP complex consists of
the Alu domain and the S domain linked by the SRP RNA. The Alu
domain consists of a heterodimer of SRP9 and SRP14 bound to the 5'
and 3' terminal sequences of SRP RNA. This domain is necessary for
retarding the elongation of the nascent polypeptide chain, which gives
SRP time to dock the ribosome-polypeptide complex to the RER
membrane.

SRP-R: The eukaryotic SRP receptor (termed SR) is a heterodimer of

SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-
binding domain,while the prokaryotic SRP receptor comprises only the
monomeric loosely membrane-associated SR-alpha homologue FtsY.
SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide
complexes to the translocon.SR-alpha binds to the SRP54 subunit of
the SRP complex. The SR-beta subunit is a transmembrane GTPase that
anchors the SR-alpha subunit (a peripheral membrane GTPase) to the
ER membrane.SR-beta interacts with the N-terminal SRX-domain of SR-
alpha, which is not present in the bacterial FtsY homologue. SR-beta
also functions in recruiting the SRP-nascent polypeptide to the protein-
conducting channel.

NO:15

1.Vesicle transport :

Every cell must eat, communicate with the world around it, and
quickly respond to changes in its environment
Through the process of exocytosis, the biosynthetic-secretory
pathway delivers newly synthesized proteins, carbohydrates and
lipids to either the plasma membrane or the extracellular space
By the converse process of endocytosis cells remove plasma
membrane components and deliver them to internal
compartments called endosomes, from where they can be
recycled to the same or different regions of the plasma
membrane or can be delivered to lysosomes for degradation
Cells also use endocytosis to capture important nutrients, such
as vitamins, lipids, cholesterol, and iron

Proteins travel by means of numerous membrane-enclosed transport

containers ;
 Some of these containers are small spherical vesicles, while
others are larger irregular vesicles or tubules formed from the
donor compartment

The term transport vesicle is used to apply to all forms of these

containers

Transport vesicles continually bud off from one membrane and

fuse with another, carrying membrane components and soluble
molecules, which are referred to as cargo

2.p53 and Rb :

P53 : is a tumor suppressor protein. It is crucial in multicellular

organisms where it regulates the cell cycle, thus functions as tumor
suppressor that is involved in preventing cancer.
P53 has many mechanisms of anticancer function and plays role in
apoptosis, genomic stability, inhibition of angiogenesis.
It can activate DNA repair proteins when DNA has sustained
damage
It can induce growth arrest by holding the cell cycle at G1/S
regulatory checkpoint on DNA damage recognition. If it holds the
cell here for long enough, the DNA repair proteins will have time
to fix the damage and the cell will be allowed to continue cell
cycle.
It can initiate apoptosis, if DNA damage proves to be irreparable.

If P53 gene is damaged, tumor suppression is severely reduced. More

than 50% of human tumors contain a mutation or deletion. In healthy
humans P53 is continuousely produced and degraded in the cell.

Rb : [ retinoblastoma protein] is a tumor suppression protein. One

function is to prevent cell growth by inhibition of the cell cycle
progression until a cell is ready to divide. Rb protein prevents the cell
from replication of damaged DNA by preventing its progression along
the cell cycle through G1 into S. Rb protein binds and inhibits
transcription factors of the E2F family.

3.MPF [cyclin B] :
Cyclin B MPF is a mitotic cyclin. The amount of cyclin B and the
activity of cyclin B-Cdk complex rise through the cell cycle until
mitosis, where they fall abruptly due to degradation of cyclin B. the
complex of Cdk and cyclin B is called MPF mitosis promoting factor.
Cyclin B is necessary for the progression of the cells into and out of M
phase of the cell cycle.

At the end of S phase the phosphatase cdc25c dephosphorylates

tyrosine15 and this activates the cyclin B/CDK1 complex. Upon
activation the complex is shuttled to the nucleus where it serves to
trigger for entry into mitosis.[4] However, if DNA damage is detected
alternative proteins are activated which results in the inhibitory
phosphorylation of cdc25c and therefore cyclinB/CDK1 is not activated.
In order for the cell to progress out of mitosis, the degradation of cyclin
B is necessary.[5]

The cyclin B/CDK1 complex also interacts with a variety of other key
proteins and pathways which regulate cell growth and progression of
mitosis. Cross-talk between many of these pathways links cyclin B
levels indirectly to induction of apoptosis. The cyclin B/CDK1 complex
plays a critical role in the expression of the survival signal survivin.
Survivin is necessary for proper creation of the mitotic spindle which
strongly affects cell viability, therefore when cyclin B levels are
disrupted cells experience difficulty polarizing.[6] A decrease in survivin
levels and the associated mitotic disarray triggers apoptosis via
caspase 3 mediated pathway.

Cyclin B plays in integral role in many types of

cancer. Hyperplasia (uncontrolled cell growth) is one of the hallmarks
of cancer. Because cyclin B is necessary for cells to enter mitosis and
therefore necessary for cell division, cyclin B levels are often de-
regulated in tumors. When cyclin B levels are elevated, cells can
enter M phase prematurely and strict control over cell division is lost,
which is a favorable condition for cancer development. On the other
hand, if cyclin B levels are depleted the cyclin B/CDK1 complex cannot
form, cells cannot enter M phase and cell division slows down. Some
anti-cancer therapies have been designed to prevent cyclin B/CDK1
complex formation in cancer cells to slow or prevent cell division. Most
of these methods have targeted the CDK1 subunit, but there is an
emerging interest in the oncology field to target cyclin B as well.

4.Cystic fibrosis :

Cystic fibrosis (CF) is a genetic disorder that affects mostly the lungs,
but also the pancreas, liver, kidneys, and intestine.[1][2] Long-term
issues include difficulty breathing and coughing up mucus as a result of
frequent lung infections. Other signs and symptoms may include sinus
infections, poor growth, fatty stool, clubbing of the fingers and toes,
and infertility in males. Different people may have different degrees of
symptoms. CF is inherited in an autosomal recessive manner. It is
caused by the presence of mutations in both copies of the gene for
the cystic fibrosis transmembrane conductance regulator (CFTR)
protein. Those with a single working copy are carriers and otherwise
mostly normal. CFTR is involved in production of
sweat, digestive fluids, and mucus. When CFTR is not functional,
secretions which are usually thin instead become thick. The condition
is diagnosed by a sweat test and genetic testing. Screening of infants
at birth takes place in some areas of the world.

No cure for cystic fibrosis is known. Lung infections are treated

with antibiotics which may be given intravenously, inhaled, or by
mouth. Sometimes, the antibiotic azithromycin is used long term.
Inhaled hypertonic saline and salbutamol may also be useful. Lung
transplantation may be an option if lung function continues to
worsen. Pancreatic enzyme replacement and fat-soluble
vitamin supplementation are important, especially in the young. Airway
clearance techniques such as chest physiotherapy have some short-
term benefit, but long-term effects are unclear. The average life
expectancy is between 42 and 50 years in the developed world. Lung
problems are responsible for death in 80% of people with cystic
fibrosis.

CF is most common among people of Northern European ancestry and

affects about one out of every 3,000 newborns.About one in 25 people
is a carrier.[It is least common in Africans and Asians. It was first
recognized as a specific disease by Dorothy Andersen in 1938, with
descriptions that fit the condition occurring at least as far back as
1595. The name 'cystic fibrosis' refers to the
characteristic fibrosis and cysts that form within the pancreas.

NO:21

3.Kit mutation: Mast/stem cell growth factor receptor (SCFR),

also known as proto-oncogene c-Kit or tyrosine-protein kinase
Kit or CD117, is a receptor tyrosine kinase protein that in humans
is encoded by the KIT gene. Multiple transcript variants encoding
different isoforms have been found for this gene.

Function:
CD117 is a cytokine receptor expressed on the surface
of hematopoietic stem cells as well as other cell types. Altered forms of
this receptor may be associated with some types of cancer. CD117 is
a receptor tyrosine kinase type III, which binds to stem cell factor (a
substance that causes certain types of cells to grow), also known as
"steel factor" or "c-kit ligand". When this receptor binds to stem cell
factor (SCF) it forms a dimer that activates its intrinsic tyrosine kinase
activity, that in turn phosphorylates and activates signal transduction
molecules that propagate the signal in the cell. Signalling through
CD117 plays a role in cell survival, proliferation, and differentiation.

Role in cancer:

Activating mutations in this gene are associated with gastrointestinal

stromal tumors, testicular seminoma, mast cell
disease, melanoma, acute myeloid leukemia.

CD117 is a proto-oncogene, meaning that overexpression or mutations

of this protein can lead to cancer. Seminomas, a subtype of
testicular germ cell tumors, frequently have activating mutations in
exon 17 of CD117. In addition, the gene encoding CD117 is frequently
overexpressed and amplified in this tumor type, most commonly
occurring as a single gene amplicon. Mutations of CD117 have also
been implicated in leukemia, a cancer of hematopoietic progenitors,
melanoma, mast cell disease, and gastrointestinal stromal
tumors (GISTs). The efficacy of imatinib (trade name Gleevec), a CD117
inhibitor, is determined by the mutation status of CD117. When the
mutation has occurred in exon 11 (as is the case many times in GISTs),
the tumors are responsive to imatinib. However, if the mutation occurs
in exon 17 (as is often the case in seminomas and leukemia), the
receptor is not inhibited by imatinib. In those cases other inhibitors
such as dasatinib and nilotinib can be used.