# Cell Bio Presentation Topics:

## 1. What is apoptosis?
Apoptosis is a form of programmed cell death, or “cellular suicide.” It is different from necrosis, in which cells die due to injury.

Apoptosis is an orderly process in which the cell’s contents are packaged into small packets of membrane for “garbage collection” by immune cells.

Apoptosis removes cells during development, eliminates potentially cancerous and virus-infected cells, and maintains balance in the body.

apoptosis is tidy and splits the cell into little parcels that can be taken up and recycled by other cells, as opposed to necrosis, which is messy and causes an immune response of inflammation.

In this process, cells shrink and develop bubble-like protrusions (or blebs) on their surface.

The DNA in the nucleus gets chopped up into small pieces, and some organelles of the cell, such as the endoplasmic reticulum, break down into fragments.

In the end, the entire cell splits up into small chunks, each neatly enclosed in a package of membrane.

These chunks then release signals that attract debris-eating (phagocytic) immune cells, such as macrophages. Also, the fragments of the dying cell display a lipid molecule called phosphatidylserine on their surface. Phosphatidylserine is usually hidden on the inside of the membrane, and when it is on the outside, it lets the phagocytes bind and "eat" the cell fragments.

Why do cells undergo apoptosis?

Basically, apoptosis is a general and convenient way to remove cells that should no longer be part of the organism.

Some cells need to be “deleted” during development – for instance, to whittle an intricate structure like a hand out of a larger block of tissue.

Some cells are abnormal and could hurt the rest of the organism if they survive, such as cells with viral infections or DNA damage.

Cells in an adult organism may be eliminated to maintain balance – to make way for new cells or remove cells needed only for temporary tasks.
## 2. What is necrosis?
Necrosis a passive process, is death of a circumscribed area of plant or animal tissue as a result of disease or injury.

Necrosis is a form of premature tissue death, as opposed to the spontaneous natural death or wearing out of tissue, which is known as necrobiosis.

Necrosis is further distinguished from apoptosis, or programmed cell death, which is internally regulated by cells, plays a critical role in embryonic development, and serves as a protective mechanism against disease and other factors.

Cells undergo necrosis when they are damaged by harmful factors (such as injury or toxic chemicals), they usually “spill their guts” as they die. Because the damaged cell’s plasma membrane can no longer control the passage of ions and water, the cell swells up, and its contents leak out through holes in the plasma membrane. This often causes inflammation in the tissue surrounding the dead cell.

It may follow a wide variety of injuries, both physical and biological in nature. Examples of physical injuries include cuts, burns, bruises, oxygen deprivation (anoxia), and hyperthermia. Biological injuries can include immunological attack and the effects of disease-causing agents.

Early cellular signs of necrosis include swelling of the mitochondria, a process that impairs intracellular oxidative metabolism. Later, localized densities appear, with condensation of genetic material.

Cytoplasmic organelles are disrupted, and affected cells separate from neighbouring cells. The dissolution of lysosomes, which normally house hydrolytic enzymes, leads to intracellular acidosis.

The nucleus swells and darkens (pyknosis) and eventually ruptures (karyolysis).

The outer membrane of the cell also ruptures, resulting in a loss of ion-pumping capacity and a rapid flow of sodium and calcium ions into the intracellular environment, resulting in osmotic shock (a sudden shift in intracellular and extracellular solute concentrations).
## 3. Mention major three differences between apoptosis and necrosis.

## 4. Name any three major features of apoptosis.

## 5. What are the different pathways of apoptosis? Are both the pathways interrelated?
Two different pathways work on different mechanisms to achieve apoptosis. Both of these pathways converge at the same terminal pathway, which results in the sequential degradation of cellular organelles.
The intrinsic or mitochondrial pathway
• The intrinsic pathway that initiates apoptosis involves a series of non-receptor-mediated processes that produce intracellular signals and act directly on targets within the cell.
• This pathway involves mitochondrial-initiated events.
• Different factors cause changes in the inner mitochondrial membrane that causes the opening of the mitochondrial permeability transition (MPT) pore and release of pro-apoptotic proteins from the intermembrane space into the cytosol.
• It consists of cytochrome c that binds and activates Apoptotic protease-activating factor – 1(Apaf-1) as well as procaspase-9, forming a protein complex termed, apoptosome.
• The apoptosome cleaves the procaspase into the active form, caspase 9, which further cleaves and activates procaspase into the effector caspase 3.

Extrinsic or death receptor pathway
• The extrinsic pathway initiates apoptosis involves transmembrane receptor-mediated interactions.
• These interactions take place between ligands and their corresponding death receptors
• Upon ligand binding, cytoplasmic adapter proteins are activated, which causes the receptors to exhibit death domains.
• The binding of FasL to FasR results in the activation of the adapter protein FADD
• These events cause the dimerization of the death effector domain, causing FADD to bind with procaspase-8.
• As a result of the binding, a death-inducing signaling complex (DISC) is formed, resulting in the auto-catalytic activation of procaspase-8.
• Once caspase-8 is activated, the terminal phase or execution phase of apoptosis is triggered.
## 6. How procaspases get activated?
Caspases are produced as inactive precursors known as procaspases, which are subsequently cleaved to create active enzymes, often by other caspases, in a proteolytic cascade.
Procaspases are the inactive precursors to caspases. They are activated by cleaving specific aspartic acids. It has 3 parts- larger subunit, smaller unit (Carboxylic group) and the amino group. The procaspase is cleaved into two subunits, the funnel part that is amino side is called pro domain after activation and the other two parts form a dimer. Two of these dimers combine to form the activated caspase. This process is activated by already active caspases.
In particular, a number of macromolecular protein complexes, in which the activation of the initiator (or apical) procaspases (caspases-2, -8, -9, -10) occurs, are formed upon induction of the apoptosis signal. In turn, initiator caspases cleave and activate the effector cysteine proteases (caspases-3, -6, -7), which leads to the fulfillment of the cell death program formed upon induction of the apoptosis signal.
## 7. What is caspase cascade?
An important step in apoptosis is the activation of a series of enzymes called caspases.
Caspases are a family of 12 cysteine proteases that act in concert in a cascade triggered by apoptosis signaling. The culmination of this cascade is the cleavage of a number of proteins in the cell, followed by cell disassembly, cell death, and, ultimately, the phagocytosis and removal of the cell debris.
There are primarily 2 pathways of the caspase cascade during apoptosis:
1. Intrinsic apoptotic pathway wherein mitochondrial cytochrome c is released during times of cellular stress. This binds to a molecule Apaf1 and leads to formation of caspase activating miltiprotein complex called apoptosome. Then initiator casespases like caspase-9 are activated which then cleave and activate other executioner caspases.
2. Extrinsic apoptotic pathway which is activated by extracellular ligands via cell surface death receptors. A multiprotein Death Inducing Signalling Complex (DISC) is formed that recruits and activates pro-caspases leading to activation of death domain complexes & interactions which then activates Caspase-8 leading to activation of executioner caspases.
## 8. What is the importance of Apaf1?
The apoptotic protease activating factor 1 (Apaf1) is the main component of the apoptosome, and a crucial factor in the mitochondria-dependent death pathway. It is the core of the apoptosome, which is formed upon triggering of the mitochondrial apoptotic pathway. Apaf1 loss induces centrosome defects that impair centrosomal microtubule nucleation and cytoskeleton organization. This, in turn, affects several cellular processes such as mitotic spindle formation, cell migration and mitochondrial network regulation. As a consequence, Apaf1-depleted cells are more fragile and have a lower threshold to stress than wild-type cells. It is theorized that the apoptosome may induce caspase-9 dimerization and subsequent autocatalysis. The apoptosome binds and cleaves Procaspase-9 protein, releasing its mature, activated form Activated caspase-9 stimulates the subsequent caspase cascade that commits the cell to apoptosis.
## 9. How can you describe cell cycle?
A cell cycle is a series of events that takes place in a cell as it grows and divides. A cell spends most of its time in what is called interphase, and during this time it grows, replicates its chromosomes, and prepares for cell division. The cell then leaves interphase, undergoes mitosis, and completes its division. The resulting cells, known as daughter cells, each enter their own interphase and begin a new round of the cell cycle.
Cell cycle has different stages called G1, S, G2, and M. G1 is the stage where the cell is preparing to divide. To do this, it then moves into the S phase where the cell copies all the DNA. So, S stands for DNA synthesis. After the DNA is copied and there's a complete extra set of all the genetic material, the cell moves into the G2 stage, where it organizes and condenses the genetic material, or starts to condense the genetic material, and prepares to divide. The next stage is M. M stands for mitosis. This is where the cell actually partitions the two copies of the genetic material into the two daughter cells. After M phase completes, cell division occurs and two cells are left, and the cell cycle can begin again.
## 10. What is the importance of G0 phase?
It is quite important in cell cycle. It is also known as the resting phase. After entering the G0 phase, a cell can either enter the whole cell cycle, or spend some time in G0 phase. This G0 phase is not a death phase, it is a temporary resting phase. Here neither division nor apoptosis takes place. Certain cells in humans enter G0 phase and then spend their entire life in it, like neurons, heart muscles. The G0 phase can be excited by extracellular signals from mitogen.

The restriction point decision is influenced by:
• Growth Factors
• Nutrients
• Cell Size
• DNA Damage
Proto-oncogenes -> encourage cell division.
Tumor-suppressor genes (p53) -> discourage cell division.
If the cell division is not controlled, it can lead to a tumors.
P53 gene decides if DNA is healthy or damaged. If damaged, it can activate other proteins to repair it (not sure if it’s in G0), or apoptosis if the damage is severe.
## 11. What is cyclin?
Cyclin is one of the major proteins involved in the regulation of cell cycle. It helps to direct CDKs to the target proteins. There are different types of cyclins:
1) Cyclin D: it comes in early G1 phase and its activity diminishes by the end of mitosis
2) Cyclin E: it comes out in middle of G1 phase & starts diminishing in the middle of the S phase.
3) Cyclin A: comes out at the end of G1 phase, diminishes at the onset of mitosis.
4) Cyclin B: starts at the onset of S phase and diminishes by the middle of mitosis.
## 12. What is the importance of cyclin-cdk complex?
A cyclin dependent kinase complex or cyclin-CDK is a protein complex formed by the association of an inactive catalytic subunit of a protein kinase, CDK, with a regulatory subunit, cyclin. It is a major control switch which causes transitions such as G1-->S/G2-->M. Concentration of this protein decides whether the cell will enter into the next phase or not.
Distinct cyclins partner with distinct CDKs to trigger different events of the cell cycle.
for eg (Mitotic cyclin or M cyclin) and M-cdk triggers the mitotic machinery
S cyclin and S-cdk triggers DNA replication machinery
Previous topics
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## 1. Phospholipids and glycolipids
- Phopholipds and glycolipids as the name suggests are classes of lipids which are definied as "organic compounds that contain hydrogen, carbon, and oxygen atoms, which forms the framework for the structure and function of living cells.”

#### <ins>Phospholipids</ins>:

**Definition:** Phospholipid structure consists of glycerol- a 3carbon polyalcohol acting as a backbone for the phospholipid, 2 fatty acids attached to the glycerol & a phosphate group attached to the glycerol.
- The structure is somewhat like the victory or V sign you make with the two fingers representing the fatty acids and your circular hand representing the hydrophillic head made up of glycerol to which phospohate group is attached.
- The fatty acids are nonpolar chains of Carbon and Hydrogen and this nonpolar nature makes them hydrophobic aka 'water-fearing' whereas the phosphate group is polar and hydrophilic aka 'water-loving'.

#### <ins>Glycolipids</ins>:

**Definition:** Glycolipids are somewhat similar to phospholipids but unlike phospholipid, mostly their backbone is formed by non-polar sphingosine instead of glycerol although glycerol glycolipids do exist. Their polar head contains a sugar unit(glucose & galactose) instead of a phosphate group.

They are often found on the outer surface of membranes, where they play a
role in cell recognition.

Some glycolipids are glycerol based, and others are derivatives of
sphingosine and are therefore called glycosphingolipids.

- The cell membrane is made up of mostly Phospholipds along with glycolipids and cholesterol, forming a bilayer structure called sandwich model.

## 2. FRAP:
- Fluorescence recovery after photobleaching is a technique which is used to determine kinetics of diffusion through tissues or cells
- When fluorescent molecules are irradiated with light at the appropriate excitation wavelength for long periods of time, they undergo photobleaching (i.e., the irradiation induces the molecules to cease fluorescing).
- If a cell is exposed to intense light in only a small region, such bleaching results in a characteristic decrease in fluorescence. As unbleached molecules move into the bleach zone, the fluorescence gradually returns to normal levels.
- Such fluorescence recovery after photobleaching (FRAP) is therefore one useful measure of Fluorescence recovery after bleaching is a technique which is used to determine how fast molecules diffuse or undergo directed transport.
- It is basically quantifying mobility of molecules. It helps in understanding the dynamics of protein-protein interaction & cell signaling.
- An instrument used in this technique is fluorescence microscope equipped with light sources. With the help of this, we can actually visualize active transport across the cell membrane.

## 3. Sodium potassium pump
- It is an active transport mechanism which exchanges sodium ions for potassium ions across the plasma membrane of animal cells.
- What is an active transport mechanism? It is a process in which substances are moved or 'pumped' uphill i.e against a concentration gradient which requires expending energy often in the form of ATP to facilitate this process.
- It is an antiporter. The sodium-potassium pump system moves sodium and potassium ions against large concentration gradients. It moves two potassium ions into the cell where potassium levels are high, and pumps three sodium ions out of the cell and into the extracellular fluid.
- In this case the carrier proteins present on cell membrane bind with intracellular Na. In a process called phosphorylation, ATP changes conformation of the carriers proteins thus reducing its affinity for Na+ ions which diffuse out but increases its affinity for K+ ions which come and bind to it from outside the cell.
- The binding of K+ to the carrier proteins causes dephosphorylation of the protein which changes back to its original conformation which had a low affinity for K+ and thus K+ ions diffuse into the cells and the cycle repeats.
- This mechanism is very important for the functioning of nerve cells where it creates a voltage difference called membrane potential which is important for conducting the nerve impulses.

## 4. Transport of glucose across the cell membrane
Glucose which is a sugar is transported across the cell membrane in one of two ways :

1. **Facilitated Diffusion**:
- Facilitated diffusion is the spontaneous, passive movement of molecules across the cell membrane via the aid of specific transmembrane proteins
- Since glucose is a large molecule, it is difficult to be transported across the membrane through simple diffusion. Hence, it diffuses across membranes through facilitated diffusion, down the concentration gradient.
- This mechanism is used to transport glucose in erythrocytes(red blood cells) and most other tissues in your body.
- Glucose is transported across erythrocyte membranes by a uniporter, a type of facilitated diffusion protein

2. **Coupled Active transport**:
- Glucose is transported by active transport from the gut into intestinal epithelial cells
- Epithelial cells lining the gut need to bring glucose made available from digestion into the body and must prevent the reverse flow of glucose from body to gut. We need a mechanism to ensure that glucose always flows into intestinal cells and gets transported into the bloodstream, no matter what the gut concentration of glucose. Imagine what would happen if this were not so, and intestinal cells used facilitated diffusion carriers for glucose. Immediately after you ate a candy bar or other food rich in sugar, the concentration of glucose in the gut would be high, and glucose would flow "downhill" from the gut into your body. But an hour later, when your intestines were empty and glucose concentrations in the intestines were lower than in your blood and tissues, facilitated diffusion carriers would allow the glucose in blood and tissues to flow "downhill," back into the gut. This would quickly deplete your short-term energy reserves. Because this situation would be biologically wasteful and probably lethal, it is worth the additional energy cost of active transport to make sure that glucose transport is a one-way process.
- glucose-Na + symporter captures the energy from Na + diffusion to move glucose against a concentration gradient

## 5. Trans-membrane protein with example
- A transmembrane protein (TP) is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequently undergo significant conformational changes to move a substance through the membrane. They are usually highly hydrophobic and aggregate and precipitate in water.
- Most transmembrane proteins are anchored to the lipid bilayer by one or more hydrophobic transmembrane segments, one for each time the protein crosses the bilayer.
- In most cases, the polypeptide chain appears to span the membrane in an a-helical conformation consisting of about 20–30 amino acid residues, most—sometimes even all—of which have hydrophobic R groups. In some multipass proteins, however, several transmembrane segments are arranged as a beta sheet in the form of a closed beta sheet—the so-called beta barrel. This structure is especially prominent in a group of pore-forming transmembrane proteins called porins that are found in the outer membrane of many bacteria as well as chloroplasts and mitochondria.
- Such proteins cross the membrane either once i.e singlepass proteins or several times i.e multipass proteins.
- Singlepass membrane proteins have just one transmembrane segment with a hydrophilic carboxyl(C-) terminus extending on one side and hydrophilic amino(N-) terminus protruding on the other side. An example of singlepass protein is glycophorin, a prominent protein in the erthrocyte plasma membrane
- Multipass membrane proteins several membrane have several membrane segments ranging from 2 or 3 to 20 or more such segments.
- One of the best-studied examples of a multipass protein is bacteriorhodopsin, the plasma membrane protein that serves halobacteria as a proton pump

## 6. Dynamic instability:
- Tim Mitchison and Marc Kirschner proposed the dynamic instability model. This model presumes two populations of microtubules, one growing in length by continued polymerization at their plus ends and the other shrinking in length by depolymerization. The distinction between the two populations is that growing MTs have GTP bound to the tubulin at their plus ends, while shrinking MTs have GDP instead
- During this phenomenon, tubulin subunits will both associate and dissociate from the plus end of the protofilament
- A number of factors regulate the dynamics of microtubule formation however the primary determinant of whether microtubules grow or shrink is the rate of GTP hydrolysis
- Direct evidence for dynamic instability comes from observation of individual microtubules in vitro via light microscopy. An individual MT can undergo alternating periods of growth and shrinkage. When an MT switches from growth to shrinkage, an event called catastrophe, the MT can disappear completely, or it can abruptly switch back to a growth phase, a phenomenon known as microtubule rescue.
- The frequency of catastrophe is inversely related to the free tubulin concentration. High tubulin concentrations make catastrophe less likely, but it can still occur.
- When catastrophe does occur, higher tubulin concentrations make the rescue of a shrinking MT more likely. At any tubulin concentration, catastrophe is more likely at the plus end of an MT—that is, dynamic instability is more pronounced at the plus end of the MT due to Catastrophe-promoting proteins (catastrophins) which bind to plus ends of microtubules and promote dissociation of tubulin dimers. They may activate GTP hydrolysis or induce a curved protofilament conformation.
- Proteins that promote microtubule disassembly:
- Katanin: Severs microtubules, generating new plus ends that lack a stabilizing GTP cap, and minus ends that are not stabilized by being capped by g-ring complexes of the centrosome.
- KLP10A and related members of the Kin I subfamily of kinesins associate with uncapped
minus ends of microtubules at the spindle poles during mitosis.

## 7. Actin tread-milling
- Actin filaments may undergo treadmilling, in which filament
length remains approximately constant, while actin monomers
add at the (+) end and dissociate from the (-) end. This has been
monitored using brief exposure to labeled actin monomers.
- Actin treadmilling is a term that describes how individual pieces of actin are shuffled to move the entire cell around in an environment. Unlike our skeleton, the pieces of the cytoskeleton don’t stay in the same location. While our arm bones will always be connected to each other in the same order, the pieces that make up the cytoskeleton will move around relative to each other.
- Actin filaments are polar, meaning they have a direction. This is similar to magnets, which have a north end and a south end. The minus end of the actin filament is considered the back, and the plus end is the front. When a cell needs to move somewhere, the piece of actin from the minus end will detach and move to the front of the plus end. This will happen over and over to help, resulting in the cell being pushed forward. As new pieces of actin are moved to the front of the line, the cell membrane is forced to move forward. The result is the cell creeping along.
- Actin treadmilling is a convenient way for cells to move. It requires little energy, and because the cell is constantly recycling actin units, it doesn’t require the cell to have lots of extra proteins.
- This treadmilling reaction or disparity of the apparent affinity of the two ends for monomers is caused by a continuous hydrolysis of adenosine triphosphate occurring during the association of a monomer with a filament end
## 8. Formation of microtubule
Microtubules are the largest of the cytoskeletal elements
- Microtubules can grow as long as 50 micrometres and are largest of the cytoskeleton structure. They are highly dynamic.
- They are formed by the reversible polymerization of a dimer of two globular proteins, alpha and beta tubulin into protofilaments that can then associate laterally to form a hollow tube, the microtubule.
- The most common form of a microtubule consists of 13 protofilaments in the tubular arrangement. The first stage of formation is called "nucleation". The process requires tubulin, Mg²⁺ and GTP and also proceeds at 37^oC.
- A critical step in the formation of MTs is the aggregation of tubulin dimers into clusters called oligomers. These oligomers serve as “nuclei” from which new microtubules can grow, and hence this process is referred to as nucleation. Once an MT has been nucleated, it grows by addition of subunits at either end, via a process called elongation.
- This stage is relatively slow a period referred to as the *lag phase* of MT assembly. Until the microtubule is initially formed. In the cell itself, microtubules are formed in an area near the nucleus called the "aster". This is also called the Microtubule Organizing Center (MTOC).
- The elongation phase of MT assembly that is the addition of tubulin dimers—is relatively fast compared with nucleation Eventually, the mass of MTs increases to a point where the concentration of free tubulin becomes limiting. This leads to the plateau phase, where MT assembly is balanced by disassembly.

## 9. 9+2 rule:
- The 9 + 2 arrangement refers to how the microtubules are organised in structures such as the flagella and cilia.
- Flagella and cilia of eukaryotic cells possess a cytoskeleton at core. It is termed axoneme. Regardless of the organism or cell type, the axoneme is about 0.25 μm in diameter, but it varies greatly in length, from a few microns to more than 2 mm and is made of microtubules.
- The axonemes of the cilia used for propulsion and flagella have a characteristic “9 + 2” pattern
- Each cilium (or flagellum) is made of a cylindrical array of 9 evenly-spaced microtubules, each with a partial microtubule attached to it. 2 single microtubules run up through the center of the bundle often called the central pair, completing the so-called "9+2" pattern.
- The entire assembly is sheathed in a membrane that is simply an extension of the plasma membrane
- This characteristic “9 + 2” arrangement of microtubules is seen when the axoneme is viewed in cross section with the electron microscope
- The nine outer doublets of the axoneme are thought to be extensions of two of the three subfibers from each of the nine triplets of the basal body. - Each outer doublet of the axoneme therefore consists of one complete MT, called the A tubule, and one incomplete MT, the B tubule . The A tubule has 13 protofilaments, whereas the B tubule has only 10 or 11. The tubules of the central pair are both complete, with 13 protofilaments each.

## 10. Involvement of motor protein in cell cytoskeleton
- Motor protein is protein that uses energy derived from ATP to change shape in a way that exerts force and causes attached structures to move; includes three families of proteins (myosin, dynein, and kinesin) that interact with cytoskeletal elements (microtubules and microfilaments) to produce movements.
- Motor proteins are the driving force behind muscle contraction and are responsible for the active transport of most proteins and vesicles in the cytoplasm.
- They are a class of molecular motors that are able to move along the surface of a suitable substrate, powered by the energy gained from the hydrolysis of ATP.
- Motor proteins utilizing the cytoskeleton for movement fall into two categories based on their substrate: microfilaments or microtubules. Actin motors such as myosin move along microfilaments through interaction with actin, and microtubule motors such as dynein and kinesin move along microtubules through interaction with tubulin.
- Microtubule Associated Motors recognize the polarity of the MT, with each motor protein having a preferred direction of movement. At present, we are aware of two major families of MT motors: kinesins and dyneins in which dyneins moves cargo to the minus ends of the MT's while kinesins move cargo to the plus end.
- Microfilament -Associated Motors a class of proteins called Myosins are involved which function for Endocyctosis; Motion of membranes along MFs; endocytosis Slides MFs in muscle and other contractile events such as cytokinesis, cell migration. They are also involvd in Vesicle positioning and trafficking.