Question No.1:
Discuss the biochemical basis for regulation of cell cycle at G1-S
checkpoint, M checkpoint and G2 Checkpoint. Also give their schematic
illustrations?
Answer:
The
cell cycle in eukaryotic cell is performed in phases, ie G-1 Phase, S-phase,
G-2 Phase and then mitosis. The proceeding of cell cycle, from one phase to
another phase is dependent on regulators. A checkpoint exists between the
boundaries of phases, that check all the functions (that need to be completed
in given phase) are properly completed or not. Checkpoint is controlled by
specific biochemical regulators which are proteinous in nature.
BIOCHEMICALS
INVOLVED:
Cyclin dependent kinases (CDKs) are the enzymes that phosphorylate
(attach phosphate groups to) specific target proteins, when attached to
specific cyclin. The proteins phosphorylated by Cdks are involved in advancing the
cell to the next phase.
The cyclins varies, according to phase. In general, Cdk levels
remain relatively constant across the cell cycle, but Cdk activity and target
proteins change as levels of the various cyclins rise and fall. Cdks must also
be phosphorylated on a particular site in order to be active, and may also be
negatively regulated by phosphorylation of other sites. The concentrations of cyclin
fluctuate and determine when Cdk/cyclin complexes form. The different cyclins
and Cdks bind at specific points in the cell cycle and thus regulate different
checkpoints.
CHECKPOINTS:
1.
G1/S Checkpoint:
The G1/S checkpoint determines whether all conditions are
favorable for cell division to proceed. In addition to adequate reserves and
cell size, there is a check for genomic DNA damage at the G1 checkpoint. A
cell that does not meet all the requirements will not be allowed to progress
into the S phase. The cell can halt the cycle and attempt to remedy the
problematic condition, or the cell can advance into G-0 and await further
signals when conditions improve.
Biochemical Phenomena: In G1/S
Checkpoint, the classical model of cell cycle control indicates that E-type
cyclins and Cdk2 or Cdk1 regulate events in the early G1 phase. In this
phase the Cyclin-E concentration is high and combines with CDKs to phosphorylate
the target protein that initiate S-phase. The cyclin E-Cdk2 complex is required
for S phase initiation.
2.
G2 Checkpoint:
G2 checkpoint is to
ensure that all of the chromosomes have been replicated and that the replicated
DNA is not damaged. If the checkpoint mechanisms detect problems with the DNA,
the cell cycle is halted, and the cell attempts to either complete DNA replication
or repair the damaged DNA.
Biochemical Phenomena: In G2
Checkpoint, if detected DNA damage this leads to the activation of the p53
transcription factor. The main function of p53 is to induce cell cycle arrest
at the G2 phases and initiate DNA repair. It activates gene expression of DNA
repair genes such as P53R2. p53 can also induce apoptosis as a last
resort, if the damaged DNA cannot be repaired, by inducing expression of
apoptotic genes such as BAX . Since it plays such an important
role in preventing the continued cell cycle progression of cells with mutated
DNA.
If no DNA damage is detected, the cyclin-A is in abundance
and binds with CDKs (cdk1 and cdk2), Cyclin A together with Cdk1 or Cdk2
regulates the completion of the S phase and entry into mitosis.
3.
M Checkpoint:
The M checkpoint occurs near the end of the metaphase stage of
karyokinesis. This is also known as “spindle checkpoint”, because it determines
whether all the sister chromatids are correctly attached to the spindle
microtubules. Because the separation of the sister chromatids during anaphase
is an irreversible step, the cycle will not proceed until the kinetochores of
each pair of sister chromatids are resolutely anchored to at least two spindle
fibers arising from opposite poles of the cell.
Biochemical Phenomena: In M Checkpoint, Cyclins- B1 and B2 interact with Cdk1 in the M checkpoint to form the “maturation-promoting factor (MPF)”, the MPF complexes add phosphate tags to several different proteins in the nuclear envelope, resulting in its breakdown (a key event of early M phase), and also activate targets that promote chromosome condensation. promote mitotic spindle assembly and finally, cell division.
CONCLUSION:
The cyclins are the proteinous molecules that binds with “Cyclin
dependent kinases” to form complexes, which acts as ON-OFF switch for target
proteins that are required in upcoming phases. Complexes activate target
proteins, by its phosphorylation.
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Question No.2:
Discuss biochemical pathways leading to mitochondrial basis of
cellular apoptosis?
Answer:
APOPTOSIS:
Apoptosis is referred to as “programmed” cell death because it
happens due to biochemical instructions in the cell’s DNA. Apoptosis is a
process that occurs in multicellular when a cell intentionally “decides” to die. This often occurs for the survival
of the whole organism, such as when the cell’s DNA has become damaged and it may become
cancerous.
PATHWAYS:
Apoptosis can be initiated by one of two pathways:
· Extrinsic(Cell Death due to external stimuli)
· Intrinsic(Cell death due to internal stimuli)
Let’s discuss (Biochemically) these both
pathways (Stepwise):
Extrinsic
In the “extrinsic” pathway to apoptosis, a signal is received from
outside the cell instructing it to commit programmed cell death. This may occur
if the cell is no longer needed, or if it is diseased.
· Step 1: The extrinsic pathway of apoptosis starts with a
signal molecule binding to a receptor on the outside of
the cell membrane. Two common types of chemical messengers that trigger
the extrinsic pathway to apoptosis are FAS and TRAIL. These molecules may be
excreted by neighboring cells if a cell is damaged or no longer needed. The receptor
proteins that bind to FAS and TRAIL are called “FASR” for “FAS Receptor” or
“TRAILR” for “TRAIL Receptor.”
When FASR and TRAILR encounter to their signal
molecule – sometimes called a “ligand” – they bind to it.
The binding process causes changes
to the receptor’s intracellular domain.
· Step 2: In response to the changes in the intracellular domain of TRAILR or
FASR, a protein inside the cell called FADD also changes.
FADD’s stands for “FAS-Associated Death Domain”
protein.
Once FADD has
been activated by changes to the receptor, it interacts with two additional
proteins, which go on to start the process of cell death.
· Step 3: Pro-caspase-8 and pro-caspase-10 (called as “the beginning of the
end”) are inactive proteins until they interact with an activated FADD. After
interaction with FADD, the parts of the proteins that keep them inactive are
“cleaved” or “cut” away.
Caspases-8 and
-10 disperse through the cytoplasm and trigger changes to several other molecules throughout the
cell, including messengers that start the breakdown of DNA after being
activated by the caspases.
· Step 4: Another inactive molecule called BID is transformed into tBID when
the activated caspases removes the part of BID that keeps the molecule
inactive. After BID is transformed into tBID, tBID moves to the mitochondria.
tBID activates the molecules BAX and BAK.
· Step 5: Activated BAX and BAK cause a condition known as “MOMP.” MOMP
stands for “mitochondrial outer membrane permeability.”MOMP is considered the
“point of no return” for apoptosis. The steps leading up to MOMP can be stopped
in their tracks by inhibitor molecules, but once MOMP has been achieved, the
cell will complete the death process. MOMP plays its key role in apoptosis by
allowing the release of cytochrome C into the cytoplasm.
· Step 6: Under normal circumstances, cytochrome C plays a key role in the
mitochondrial electron transport chain.
During MOMP, however, cytochrome C can escape the mitochondria and act as a
signaling molecule in the cell cytoplasm. Cytochrome-C in the cell cytoplasm forms
the ominous-sounding “apoptosome” a complex of proteins that performs the final
step to beginning cellular breakdown.
· Step 7: The apoptosome, once it is formed, turns pro-caspase-9 into
caspase-9. Just as with the activation of caspases-8 and -10, caspase-9 is able
to trigger further changes throughout the cell.
· Step 8: Caspase-9 performs several functions to promote apoptosis. Among
the most important is the activation of caspases-3 and -7.
· Step 9: Once activated, caspases-3 and -7 begin the breakdown of cellular
materials. Caspase-3 condenses and breaks down the cell’s DNA.
Intrinsic
The intrinsic pathway to apoptosis is triggered by stress or damage
to the cell. Factors include damage to its DNA, oxygen deprivation, and other
stresses that impair a cell’s ability to function.
· Step 1: In response to these damages or stresses, the cell “decides” that
its continued existence might be dangerous to the organism as a whole. It then
activates a set of proteins called “BH3-only proteins.”
· Step 2: BH3-only proteins are a class of proteins including several pro-
and anti-apoptosis proteins. Apoptosis can be encouraged or discouraged,
depending on which BH3-only proteins are activated or expressed.
Pro-apoptotic BH3-only proteins activate BAX
and BAK (the same proteins that are activated by tBID after it is created
through the extrinsic pathway to apoptosis).
{After
this step, the pathway follows the same steps as in extrinsic.}
· Step 3: Activated BAX and BAK cause a condition known as “MOMP.” MOMP
stands for “mitochondrial outer membrane permeability.” MOMP release of cytochrome C into the
cytoplasm.
· Step 4: Under normal circumstances, cytochrome C plays a key role in the
mitochondrial electron transport chain.
During MOMP, however, cytochrome C can escape the mitochondria and act as a
signaling molecule in the cell cytoplasm. Cytochrome-C forms “apoptosome” .
· Step 5: The apoptosome, once it is formed, turns pro-caspase-9 into
caspase-9. Caspase-9 is able to trigger further changes throughout the cell.
· Step 6: Caspase-9 performs several functions to promote apoptosis. Among
the most important is the activation of caspases-3 and -7.
· Step 7: Once activated, caspases-3 and -7 begin the breakdown of cellular
materials. Caspase-3 condenses and breaks down the cell’s DNA.
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Question No.3:
Based on available literature, discuss, how the chloroplast model
can be used for production of green energy?
Answer:
First let’s discuss how the chloroplast works and how it converts
energy from sunlight into chemical energy.
CHLOROPLAST:
Photosynthesis takes place in the
chloroplast. Photosynthesis is a process used by plants and some other
organisms to convert light energy into chemical energy. In
plants, "light" reactions occur within the chloroplast thylakoids,
where the chlorophyll pigments is present. When light energy reaches the
pigment molecules, it energizes the electrons within them, and these electrons
are shunted to an electron transport chain in the thylakoid membrane. Every
step in the electron transport chain then brings each electron to a lower
energy state and harnesses its energy by producing ATP and NADPH. Meanwhile,
each chlorophyll molecule replaces its lost electron with an electron from
water; this process essentially splits water molecules to produce oxygen. Once
the light reactions have occurred, the light-independent or "dark"
reactions take place in the chloroplast stroma. During this process, also known
as carbon fixation, energy from the ATP and NADPH molecules generated by the
light reactions drives a chemical pathway that uses the carbon in carbon
dioxide (from the atmosphere) to build a three-carbon sugar called
glyceraldehyde-3-phosphate (G3P). Cells then use G3P to build a wide variety of
other sugars (such as glucose) and organic molecules. The products of these
reactions are then transported to other parts of the cell, to satisfy the
metabolic demands of the cell. In plants, some sugar molecules are stored as
sucrose or starch.
In short the light energy is used to initiate
electron flow, and the energy by this electron flow is utilized for the
preparation of glucose (containing chemical energy).
GREEN ENERGY:
Green
energy comes from natural sources such as sunlight, wind, rain, tides, plants,
algae and geothermal heat. These energy resources are renewable, meaning
they're naturally replenished. They are environment friendly because they don’t
pollute the environment.
CHLOROPLAST
MODEL USED FOR PRODUCTION OF GREEN ENERGY:
We can construct a structure like chloroplast that contains elements (semi-conductors) that easily emits electrons when light hints its surface. The electrons will then flow from higher concentration to lower concentration. The electrons flow is initiated by sunlight. The flow of these electrons can produce electric current. Such electrical energy produced, is called as Solar Energy, which is form green energy and such apparatus is known as photovoltaic cell. This may also be called as “Artificial Photosynthesis”.
PRACTICAL USE:
Solar
panel contains photovoltaic cells (working same as chloroplast) that covert
light energy into electrical energy. Solar panels are used worldwide for the
production of green energy.
Researchers
at the University of British Columbia, Canada, have co-opted genetically
engineered E. coli bacteria that use dye to convert light into energy in order
to create a so-called “biogenic” solar cell (a cell made of living
organisms). The
researchers coated the bacteria with a mineral to act as a semiconductor.
Their aim was to ensure that these new solar cells could continue to operate not only in bright but also in dim light. Solar powers of the near future could operate at far higher efficiency in cloudy regions of the world.
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