What is the role of the endoplasmic reticulum (ER) in protein transport?

The ER synthesizes proteins and starts glycosylation; it plays a key role in folding and quality control.

What is the function of the Golgi apparatus in protein sorting?

It modifies, sorts, and packages proteins for delivery to various destinations.

What are microsomes used for in cell biology?

Microsomes are vesicle-like artifacts from the ER used in vitro to study protein import and processing.

How are ER-bound proteins different from membrane-bound proteins?

ER-bound proteins enter the ER lumen, while membrane-bound proteins embed in the membrane via transmembrane domains.

What are multiple spanning loops in membrane proteins?

Hydrophobic segments that cross the membrane multiple times, anchoring proteins into the lipid bilayer.

What is a signal sequence?

A short peptide that directs a protein to a specific location, such as the ER or mitochondria.

How can protein destination be changed?

By exchanging signal sequences to re-route proteins to different organelles.

How do proteins enter mitochondria?

Through a specialized import machinery that recognizes mitochondrial targeting signals.

What is the importance of N-glycosylation in the Golgi?

It modifies proteins for proper folding, stability, and sorting.

How are proteins targeted to lysosomes?

Via mannose-6-phosphate (M6P) tagging in the Golgi.

What is exocytosis?

The process where vesicles fuse with the plasma membrane to release contents outside the cell.

What role do adaptor proteins play in vesicle formation?

They help select cargo by linking it to the clathrin coat.

What does clathrin do?

Forms a scaffold that shapes the budding vesicle.

What is the function of dynamin in vesicle formation?

A GTPase that pinches the vesicle from the membrane.

Why is uncoating important in vesicular transport?

It allows vesicle fusion with the target membrane.

What is the role of Rab proteins?

They guide vesicles to the correct target by acting as molecular switches.

What do SNARE proteins do?

They mediate the fusion of vesicle and target membranes through specific pairing.

What is the SNARE zipper hypothesis?

SNAREs pull membranes together in a zipper-like fashion, facilitating fusion.

How is membrane size maintained?

Endocytosis and exocytosis balance membrane gain and loss.

How does botulinum toxin affect vesicle fusion?

It cleaves SNARE proteins, blocking neurotransmitter release and causing paralysis.

What is endocytosis?

The process where cells internalize molecules and particles by engulfing them in vesicles.

What are the types of endocytosis?

Includes receptor-mediated endocytosis, pinocytosis, and phagocytosis.

1. Receptor-Mediated Endocytosis

• The cell takes in specific molecules (like cholesterol or hormones).
• These molecules bind to special receptors on the cell surface.
• The cell then forms a small bubble (vesicle) around them and pulls them inside.

2. Pinocytosis ("Cell Drinking")

• The cell gulps in fluid and small dissolved stuff from its surroundings.
• It doesn’t choose what to take in—just grabs a bit of everything.
• Happens all the time in many cells.

3. Phagocytosis ("Cell Eating")

• The cell swallows big things, like bacteria or dead cells.
• The cell wraps around the particle and forms a big bubble (called a phagosome).
• That bubble then fuses with a "stomach" part of the cell (lysosome) to break it down.

What determines the destination of endocytic vesicles?

Signals and Rab proteins guide vesicles to lysosomes or recycling endosomes.

What is transcytosis?

Transport of materials across a cell, combining endocytosis and exocytosis.

What are the types of exocytosis?

Constitutive (continuous) and regulated (stimulus-triggered, e.g., insulin release).

1. Constitutive Secretion (Continuous)

• Happens all the time.
• The cell constantly makes and sends out proteins (like collagen or membrane proteins).
• No special signal is needed.
• Common in all cells to maintain the cell’s surface and surroundings.

Ex: A fibroblast secreting collagen for the extracellular matrix.

2. Regulated Secretion (Stimulus-Triggered)

• Only happens when triggered by a signal (like a hormone or nerve impulse).
• Proteins are stored in vesicles inside the cell.
• When a signal arrives, vesicles fuse with the membrane and release their contents.

Ex: Insulin is released from pancreatic cells only when blood sugar rises.

What is the role of secretory vesicles in exocytosis?

Store and release proteins upon receiving a signal.

How does exocytosis differ in polarized cells?

It is directionally targeted (apical vs. basolateral).

1. Apical Surface

• Faces the lumen (the inside of a tube or organ, like the gut or airway).
• It’s the "top" of the cell.
• Often specialized for absorption or secretion.
• May have microvilli or cilia.

Ex: In the intestine, the apical side absorbs nutrients from food.

2. Basolateral Surface

• Faces the bloodstream or underlying tissue.
• It’s the "bottom and sides" of the cell.
• Involved in transporting substances into the body or passing signals.

Ex: In the intestine, the basolateral side passes nutrients into the blood

What are lipid rafts and their role in exocytosis?

Cholesterol-rich membrane microdomains that sort proteins in the Golgi.

How does exocytosis work in neurons?

Involves SNARE-mediated fusion of synaptic vesicles to release neurotransmitters.

What is apoptosis?

Programmed cell death involving cell shrinkage, blebbing, and phagocytosis of apoptotic bodies.

What is necrosis?

Accidental cell death causing swelling, lysis, and inflammation.

What is anoikis?

Apoptosis triggered by detachment from the extracellular matrix.

What organelles are involved in apoptosis?

Mitochondria (cytochrome c), nucleus (DNA fragmentation), plasma membrane (PS flipping).

What are caspases?

Proteases that execute apoptosis by cleaving cellular components.

Know the differences between casp 3, 7, 6, 8, 9 and 1

Caspase-3: Executioner

• Activated by: Caspase-8 (extrinsic) or Caspase-9 (intrinsic)
• Role: Cleaves many structural and repair proteins → DNA fragmentation, membrane blebbing, cell shrinkage.
• Key point: “Main executioner” in apoptosis.

Caspase-7: Executioner

• Activated by: Caspase-8 or Caspase-9
• Role: Overlaps with caspase-3, but particularly efficient at cleaving PARP (DNA repair enzyme).
• Key point: Backup executioner to caspase-3, but can compensate if caspase-3 is absent.

Caspase-6: Executioner (late stage)

• Activated by: Caspase-3
• Role: Breaks down nuclear lamins and other nuclear proteins, causing nuclear envelope breakdown in apoptosis.
• Key point: “Clean-up crew” for the nucleus.

Caspase-8: Initiator

• Activated by: Death receptor signaling (Fas, TNF receptor, TRAIL) → DISC complex.
• Role: Activates executioners (3, 7) and can activate the intrinsic pathway via Bid cleavage (links pathways).
• Key point: Starts extrinsic apoptosis.

Caspase-9: Initiator

• Activated by: Intrinsic (mitochondrial) pathway → cytochrome c + Apaf-1 + dATP → apoptosome.
• Role: Activates executioners (3, 7).
• Key point: Starts intrinsic apoptosis.

Caspase-1: Inflammatory

• Activated by: Inflammasomes (e.g., NLRP3, AIM2).
• Role: Cleaves pro–IL-1β and pro–IL-18 into active cytokines; can trigger pyroptosis.
• Key point: Not for apoptosis — drives inflammation and pyroptotic cell death.

Quick Mnemonic

• "I Eat I Eat, Then I Burn"
• Intrinsic → 9 (initiator) → 3/7/6 (executioners)
• Extrinsic → 8 (initiator) → 3/7/6
• Burn (inflammation) → 1

What is phosphatidylserine flipping?

Externalization of PS on apoptotic cells to signal macrophages for phagocytosis.

How is apoptosis measured?

Annexin V detects PS exposure; PI stains necrotic cells with damaged membranes.

What triggers the extrinsic apoptosis pathway?

Death ligands (e.g., FasL) binding to death receptors (e.g., Fas/CD95).

1. Fas ligand monomer found on cell surface

2. Intracellularly bind FADD

3. Monomers become Trimers

4. Trimers bind Fas Ligand on another (T-cytotoxic) cells

5. Intracellularly caspase 8 clusters and binds to Fas receptors

6. Caspase 8 becomes activated by the DISC (Death inducing signaling complex)

7. Caspase 8 activates caspases 3, 6 and 7 and Bid

8. Effector caspases cause death

9. Bid induces intrinsic cell death pathway

Difference between Bcl-2 Family Proteins: Bcl-2, Bcl-x_L, Bax, Bak, Bad and Bid.

1. Anti-apoptotic (protect the cell, stop death)

• Bcl-2 – Blocks Bax/Bak so mitochondria don’t leak.
• Bcl-xL – Same job as Bcl-2, extra backup guard.

2. Pro-apoptotic effectors (cause death directly)

• Bax – When turned on, makes holes in mitochondria.
• Bak – Same as Bax, already attached to mitochondria.

3. Pro-apoptotic BH3-only (signal death, remove the guards)

• Bad – Handcuffs Bcl-2/Bcl-xL so Bax/Bak can work.
• Bid – Gets cut by caspase-8, tells Bax/Bak to make holes.

Quick picture in words:

• Bcl-2 & Bcl-xL = guards
• Bax & Bak = hole punchers
• Bad & Bid = take away the guards’ weapons so the hole punchers can work

What is the intrinsic apoptosis pathway?

Triggered by internal signals like DNA damage, involving mitochondria and Apaf1.

1. Mitochondria form a death inducing pore (mitochondrial permeability transition pore)

2. Membrane potential decreases

3. Bid binds bax and bak→ produces another pore on mitochondria

4. Cytochrome c, AIF, Smac and endonuclease Gare released

5. Cyt c binds Apaf1

6. Aggregation of Apaf1 causes apoptosome to form

7. Activates caspase 9

8. Apoptosis

What are other types of programmed cell death?

Autophagy, necroptosis (caspase-independent), and pyroptosis (inflammatory).

1. Autophagy ("self-eating")

• The cell cleans itself up by breaking down old or damaged parts.
• Helps the cell survive during stress (like starvation).
• Too much autophagy can lead to cell death, but it starts as a survival method.

2. Necroptosis

• A type of planned cell death, but it happens without caspases (a type of death enzyme).
• The cell bursts open, spilling its contents.
• Causes inflammation in the area.
• Often used when viruses block normal cell death.

3. Pyroptosis

• A fiery, explosive type of cell death.
• Happens in response to infections.
• The cell swells and bursts, sending out inflammatory signals.
• Helps the immune system fight pathogens.

Diseases that can be caused by apoptosis

Cancer

• Hallmark of cancer cells is resistance to apoptosis
• Bcl-2 (Non-hodgkins lymphoma)
• PTEN (breast cancer)

Autoimmune Diseases

• Systemic lupus erythematosus, Rheumatoid arthritis
• Self reactive cells have escaped programmed cell death

Neurological Disorders

Alzheimer, Parkinson, Huntington, ALS, Stroke

Cardiovascular Disorder

Ischemia, Heart failure

Viral and Bacterial infectious diseases

What is signal transduction?

Conversion of extracellular signals into intracellular responses.

What are common signaling types?

Autocrine, paracrine, gap junction, and endocrine.

1. Autocrine Signaling

• The cell talks to itself.
• It releases a signal that binds to its own receptors.
• Common in immune cells and during development.

Ex: A T cell releasing a signal to boost its own activity.

2. Paracrine Signaling

• The cell talks to nearby cells.
• Signals travel only a short distance.
• Used for local communication.

Ex: A nerve cell releasing neurotransmitters to a neighbor.

3. Gap Junctions

• Direct connection between two cells.
• Tiny channels let ions and small molecules pass back and forth.
• Fast and two-way communication.

Ex: Heart cells use gap junctions to coordinate beating.

4. Endocrine Signaling

• The cell sends a signal through the bloodstream to faraway cells.
• Usually involves hormones.
• Slower, but long-lasting.

Ex: The pancreas releases insulin, which affects many cells in the body.

What are molecular switches?

Phosphorylation (kinases/phosphatases) and GTP-binding (GTPases) toggle activity.

What are nuclear receptors?

Intracellular receptors for hydrophobic ligands; regulate gene expression upon binding DNA.

What are G protein-coupled receptors (GPCRs)?

Membrane receptors with 7 transmembrane domains; activate G proteins upon ligand binding.

What is the role of Gα subunits?

Gs ↑cAMP, Gi ↓cAMP, Gq activates PLC-β, Gt triggers vision pathway.

What are second messengers in signaling?

cAMP, IP3, DAG, and Ca²⁺ relay signals from receptors to cellular targets.

What are receptor tyrosine kinases (RTKs)?

Enzyme-linked receptors that autophosphorylate and activate downstream pathways like MAPK and PI3K.

What is the JAK

STAT pathway?/ Cytokine binding activates JAK, which phosphorylates STAT to regulate gene transcription.

What is the role of Toll-like receptors (TLRs)?

Detect PAMPs, activate NF-κB, and trigger immune responses.

What is ion channel signaling?

Ion flow through ligand- or voltage-gated channels alters membrane potential (e.g., Na⁺ in action potentials).