Hi! I am Komal Sankaran, M.Sc. Biotechnology (Pune University Gold Medalist, 2013), CSIR-NET SPM fellow (Jun- 2014, 4th rank), CSIR-NET- LS (Dec 2013, 2nd rank), DBT JRF category- I. Please contact if anyone is interested in Life Sciences CSIR-NET coaching in Pune (Khadki area). Email- komalsan91@gmail.com

1. LECTURE 1
CELL BIOLOGY
-By KOMAL SANKARAN

2.  Definition:
Apo- apart
Ptosis- to drop/ to fall
(Shedding of leaves from trees)
 For every cell there is a time to LIVE and a time to DIE!
 There are two main ways by which cells die-
> Cell Death by NECROSIS:
- Mechanical damage
- Exposure to toxic chemicals
- Lack of Oxygen
- Extremes of temperature
> Cell Death by APOPTOSIS:
- Internal signals
- External signals

3.  Apoptosis is a pathway of cell death that is induced by a tightly
regulated suicide program in which cells destined to die
activate a set of enzymes that degrade the cells’ own nuclear
DNA and nuclear and cytoplasmic proteins.
 Apoptosis was recognized in 1972 by the distinctive
morphological appearance of membrane- bound fragments
derived from cells.
 Apoptosis is often used as a synonym for ‘Programmed Cell
Death’ (PCD) but PCD is physiological death, occurs only during
Embryogenesis.
 Apoptosis is a functional death and is a good mechanism to
eliminate wasted, useless, unwanted or crippled cells.
 Thus, During Embryogenesis - PCD
Post- Embryonal Life - Apoptosis
 By contrast, Necrosis occurs mainly because of cell injury.
There is an increase in cell volume and the cell bursts!

4. Two distinct forms of cell death- Apoptosis and Necrosis.
Programmed cell death eliminates unwanted cells…

5.  Apoptosis occurs normally, both during embryogenesis and
throughout adulthood , and serves to eliminate unwanted,
aged or potentially harmful cells.
 It is also a pathological event when diseased cells become
damaged beyond repair and are to be eliminated.
> Apoptosis in Physiological situations:
 The programmed destruction of cells during embryogenesis,
organogenesis, developmental involution and morphogenesis.
 Cell loss in proliferating cell populations to maintain their
constant numbers (Homeostasis).
Development of toes Incomplete Apoptosis

6.  Morphogenesis (removal of excess cells).
 Elimination of potentially harmful or self-reactive Lymphocytes,
either before or after they have completed their maturation.
 Maintenance of organ size and function.
 Death of host cells that have served their useful purpose such
as, Neutrophils in an acute inflammatory response and
Lymphocytes at the end of an immune response.
 Involution of hormone- dependent tissues upon hormone
withdrawal.

7.  DNA damage due to radiations, anticancer drugs, hypoxia,
production of free radicals. Larger doses of same stimuli may
result in necrotic cell death.
 Accumulation of misfolded proteins in the E.R.  ER stress
Apoptosis.
 Pathological atrophy in parenchyma organs such as Pancreas,
Parotid glands, Kidneys, after duct obstruction.
 Cell death in certain infections, particularly viral infections in
which loss of infected cells is largely due to apoptosis that may
be induced by the virus (Adenovirus and HIV infections) or by
the host immune response (as in Viral Hepatitis).

8.  Cell shrinkage.
 Breakdown of Cytoskeleton.
 Packaging of organelles along with the Cytoskeleton.
 Pyknosis- Condensation of chromatin and its attachment to the
nuclear envelope.
 Fragmentation of DNA – Karyorrhesis.
 Breakdown of nucleus and formation of chromatin bodies or
nucleosomal units (small vesicles along with some fragmented
DNA).
 Extensive surface blebbing of the apoptotic cell (Cytoplasmic
Blebbing). Packaging of some of the chromatin bodies into
these blebs.
 Fragmentation into membrane bound Apoptotic bodies.
 Engulfment of the Apoptotic bodies by Tingible body
Macrophages. Phagosomes + Lysosomes  Phagolysosomes 
Degradation.

11.  Withdrawal of positive signals:
1) The survival of most cells requires that they receive
continuous stimulation from other cells. Eg:
- Growth Factor for Neurons
- Interleukin -2 (IL-2), an essential factor for the mitosis of
lymphocytes.
 Receipt of negative signals:
1) Increased levels of oxidants within the cell.
2) DNA damage by agents like
- UV light - Free Radicals
- X- rays - Chemotherapeutic Drugs
3) Accumulation of misfolded proteins in the ER.
4) Binding of Death Activators to specific receptors on the cell
surface. Eg:
- Tumor Necrosis Factor- alpha (TNF- α) to TNF receptor.
- Lymphotoxin (TNF-β) also to the TNF receptor.
- Fas ligand (FasL) to a cell surface receptor named Fas.

12. There are 3 major pathways by which Apoptosis takes place-
 Intrinsic Pathway (Mitochondrial Pathway)
 Extrinsic Pathway
 T cell mediated granzyme pathway.
> Extrinsic pathway is mediated by Extracellular stimuli like-
- Cytokines, Toxins,
Ions, Hormones, Growth Factors..
- Some infections, damage, injury, energy deficiency etc. may
also trigger Apoptosis.
> Intrinsic pathway is mediated by Intracellular stimuli like-
- Nutrient depletion,
- Increase in temperature of the cell,
- Inc. in Ca^2+ conc. beyond limit,
- Viral infections etc.

13.  A specific feature of apoptosis is the activation of several
members of a family of cysteine proteases named caspases.
 The “c” refers to a cysteine protease (i.e., an enzyme with
cysteine in its active site), and “aspase” refers to the unique
ability of these enzymes to cleave after aspartic acid residues.
 Expressed as zymogens (procaspases) that have three
domains: an N-terminal prodomain that is proteolytically
excised on activation, followed by sequences comprising the
active enzyme’s α and β subunits that are proteolytically
separated on activation.
 The presence of cleaved, active caspases is a marker for cells
undergoing apoptosis.
 Activation of Caspases

14. Procaspase activation during apoptosis
Apoptosis depends on an intracellular proteolytic cascade that is
mediated by caspases

15.  12 types of Caspases have been identified in humans.
 Two types of apoptotic caspases-
 Initiator caspases (Ex: CASP2, CASP8, CASP9 & CASP10):
- Cleave inactive pro-forms of effector caspases thereby
activating them. Have long N-terminal domain.
- Caspases 2 & 9 contain Caspase Recruiting Domain (CARD) that
promotes interaction with certain scaffolding and regulatory
proteins.
- Caspases 8 & 10 contain Death Effector domains, through which
they bind to DEDs on the target adaptor proteins.
 Executor caspases ( Ex: CASP3, CASP6, CASP7):
- Have little to no N-terminal domains.
- Cleave other protein substrates within the cell to trigger the
apoptotic pathway.
 Caspases 1, 4 & 5 don’t participate in apoptosis. They are
Inflammatory caspases.

16. Extrinsic Pathway
Death Ligand
Death Receptors
Caspases
Cell Death

17. Intrinsic Pathway
Mitochondria
Cytochrome C
Apoptosome Complex
Caspases
Cell Death

18.  Mediated by extracellular stimulus.
 Different pathways activated for different kinds of signals. Ex;
cytokine pathway activated due to release of TNF ( a cytokine).
 TNF receptor is a cell surface transmembrane receptor with an
extracellular ligand binding domain, an intermediate
transmembrane domain and a cytoplasmic domain.
 The cytoplasmic domain is an 80aa domain called the Death
domain or TRADD ( TNF Receptor Associated Death Domain).
Recognition of TNF by TNF receptor activates this domain.
Activation leads to initiation of the apoptotic pathway.
 Then an Intermediate membrane protein adaptor protein comes
and binds to TRADD.
 Procaspase 8 joins this complex and this entire complex of
proteins is known as the Death Induced Signaling Complex (DISC)
 Proteolytic cleavage of Procaspase 8 converts it into active
CASP8.
 This in turn, activates Caspase 3 which causes the changes
associated with apoptosis. (Effector caspase)

19. Cell-surface death receptors activate the extrinsic pathway
of apoptosis
The extrinsic pathway of apoptosis activated through Fas death receptors

20.  Also called mitochondrial regulatory pathway.
 After receiving intracellular signals, there will be either;
- swelling in mitochondria to prepare pores in the membrane or
- increase in permeability in the mito. Membrane by the opening
of mitochondrial permeability transition pore (MPT)
 Two proteins leak out from the mitochondria into the
cytoplasm due to the opening of these pores-
- SMAC (Second Mitochondrial derived Activator of Caspase)
- Cytochrome c
 SMAC protein binds to IAPs (Inhibitor of Apoptosis Proteins)
present in the cytoplasm. IAPs inhibit apoptosis. Binding of
SMAC suppresses the activity of IAPs and due to this apoptosis
is initiated.
 Cytochrome c binds to a protein called Apoptotic Protease
Activating Factor (APAF).

21.  Now procaspase 9 joins the complex of APAF+ Cytc. Entire
complex called as Apoptosome.
 The apoptosome cleaves procaspase 9 converting it into
active caspase 9.
 Caspase 9 activates caspase 3 (Executioner caspase).
 Caspase 3 is responsible for all the changes associated with
apoptosis.
 Endonucleases are responsible for fragmentation of DNA .
Characteristic ‘Ladder pattern’ on gel
(DNA frag. of various sizes)
 How do macrophages recognize target apoptotic cells?
-There is expression of some particular protein markers like
Annexin-1, Calcineurin etc.
-The Phosphatidylserine residues that are usually present
towards the cytoplasmic side, flip and are exposed outside
the cell. Macrophages recognize these.

22. The intrinsic pathway of apoptosis depends on mitochondria

23. The three classes of Bcl2 proteins

24. The three major mammalian factions of the Bcl-2 family. The BH3-
only proteins (yellow) are essential initiators of apoptosis that
primarily antagonize their pro-survival relatives (blue), whereas
either Bax or Bak (red) is required downstream of Bcl-2.

25. The role of BH123 pro-apoptotic Bcl2 proteins (mainly Bax and Bak) in
the release of mitochondrial intermembrane proteins in the intrinsic
pathway of apoptosis

26. How pro-apoptotic BH3-only and anti-apoptotic Bcl2 proteins regulate
the intrinsic pathway of apoptosis

27. A proposed model for
the roles
of IAPs and anti-IAPs
in the
control of apoptosis in
mammalian cells

28. Three ways by which extracellular survival factors can inhibit apoptosis

29. TOO MUCH: Tissue atrophy
Neurodegeneration
Thin skin
etc
TOO LITTLE: Hyperplasia
Cancer
Atherosclerosis
etc
Accumulated oxidative damage?
(defective sensors, signals?
---> dysfunctional cells accumulate
hyperplasia (precancerous lesions)

30.  Neurons are post-mitotic (cannot replace themselves; neuronal stem cell
replacement is inefficient)
 Neuronal death caused by loss of proper connections, loss of proper
growth factors (e.g. NGF), and/or damage (especially oxidative damage)
 Neuronal dysfunction or damage results in loss of synapses or loss of cell
bodies (synaptosis, can be reversible; apopsosis, irreversible)
 PARKINSON'S DISEASE, ALZHEIMER'S DISEASE, HUNTINGTON'S DISEASE etc
Extracellular survival factors inhibit apoptosis in various ways

31. Apoptosis eliminates damaged cells
(damage => mutations => cancer)
Tumor suppressor p53 controls senescence
and apoptosis responses to damage
Most cancer cells are defective in apoptotic response
(damaged, mutant cells survive)
High levels of anti-apoptotic proteins
or
Low levels of pro-apoptotic proteins
===> CANCER

32. References:
1) The Cell
(Alberts)
A Presentation by Miss. Komal Sankaran.
2)