Cell Biology: Cytoskeleton, Endocytosis, Cell Cycle, and Apoptosis

What are the three primary components of the cytoskeleton?

Intermediate filaments, microtubules, and actin filaments (microfilaments).

Which cytoskeletal component provides mechanical strength and is not involved in active movement?

Intermediate filaments.

What is the structural composition of intermediate filaments?

Elongated proteins forming coiled-coil dimers, which associate into tetramers and stack into rope-like filaments.

What is a key structural difference between intermediate filaments and the other two cytoskeletal components?

Intermediate filaments lack polarity and do not use nucleotide hydrolysis for assembly.

What is the function of nuclear lamins?

They form the nuclear lamina to provide structural support to the nucleus and anchor chromatin and nuclear pore complexes.

What are the subunits of microtubules?

Alpha-tubulin and beta-tubulin heterodimers.

What is the primary microtubule organizing center (MTOC) in animal cells?

The centrosome.

What is dynamic instability in microtubules?

The rapid switching between phases of growth and shrinkage.

How does the GTP cap stabilize a microtubule?

It prevents depolymerization; if GTP hydrolysis catches up to the growing tip, the cap is lost and the microtubule shrinks.

What is the function of microtubule capping proteins?

They bind to microtubule ends to prevent both growth and depolymerization, stabilizing the structure.

What is actin treadmilling?

A steady-state process where actin monomers are added at the plus end at the same rate they are lost from the minus end.

Which protein complex is responsible for nucleating branched actin filament networks?

The Arp2/3 complex.

In which direction does myosin typically move along actin filaments?

Toward the plus (barbed) end.

What are the two motor proteins that move along microtubules?

Kinesin and dynein.

Which motor protein is responsible for retrograde transport toward the minus end of microtubules?

Dynein.

How do kinesin and dynein position the ER and Golgi?

Kinesin pulls the ER toward the cell periphery (plus ends), while dynein pulls the Golgi toward the nucleus (minus ends).

What energy source powers the movement of motor proteins?

ATP hydrolysis.

What is the first step in muscle contraction after an action potential reaches the neuromuscular junction?

The motor neuron releases acetylcholine (ACh) into the synapse.

What is the role of T-tubules in muscle contraction?

They conduct the action potential deep into the muscle fiber to trigger calcium release from the sarcoplasmic reticulum.

What does calcium bind to in order to initiate muscle contraction?

Troponin.

What happens when calcium binds to the troponin-tropomyosin complex?

Tropomyosin moves out of the way, exposing the myosin-binding sites on actin.

What is the 'power stroke' in muscle contraction?

The release of inorganic phosphate (Pi) causing the myosin head to pivot and pull the actin filament.

What causes the myosin head to detach from actin after the power stroke?

The binding of a new ATP molecule.

Which cytoskeletal component is involved in the formation of the mitotic spindle?

Microtubules.

What is the primary difference in energy usage between actin and microtubules?

Actin uses ATP hydrolysis, while microtubules use GTP hydrolysis.

Which motor protein is associated with muscle contraction?

Myosin II.

What is the primary role of calcium in muscle contraction?

It acts as a regulatory switch that binds to troponin, allowing actin to be exposed for myosin binding.

What happens to a muscle when the action potential stops?

Calcium is pumped back into the sarcoplasmic reticulum by Ca²⁺-ATPase pumps, and troponin-tropomyosin re-blocks actin.

Why does rigor mortis occur after death?

ATP is depleted, preventing the myosin head from detaching from actin.

What is the primary function of organelles in a cell?

To compartmentalize different chemical reactions, allowing incompatible processes to occur simultaneously.

What is the endomembrane system?

A network of membrane-bound organelles that work together to synthesize, process, and transport proteins and lipids.

What are the three main protein sorting mechanisms?

Signal sequences, transport vesicles, and nuclear import/export signals.

Which organelles require proteins to be threaded through translocons while unfolded?

Mitochondria, peroxisomes, and the ER.

How can scientists prove a signal sequence is sufficient for protein targeting?

By performing a signal sequence swap experiment, where the sequence is attached to a protein that normally goes elsewhere.

What is the function of the nuclear pore complex (NPC)?

It allows selective transport of molecules between the nucleus and the cytoplasm.

What determines if a molecule can passively diffuse through the nuclear pore?

Size; molecules smaller than 40 kDa can diffuse passively.

What is a Nuclear Localization Signal (NLS)?

A stretch of positively charged amino acids that signals a protein to be transported into the nucleus.

What is the role of importins in nuclear transport?

They recognize and bind to NLS sequences on cargo proteins to facilitate their transport into the nucleus.

What triggers the release of cargo from an importin inside the nucleus?

Binding of Ran-GTP to the importin.

What is the function of Ran-GEF?

It is located in the nucleus and converts Ran-GDP to Ran-GTP.

What is the function of Ran-GAP?

It is located in the cytoplasm and converts Ran-GTP to Ran-GDP.

How do exportins function in nuclear export?

They bind to cargo only when Ran-GTP is present in the nucleus and release it in the cytoplasm when Ran-GAP converts GTP to GDP.

What is the purpose of an immunoprecipitation (IP) experiment?

To pull down a specific protein from a cell lysate using an antibody to determine if it interacts with other proteins.

What does a co-immunoprecipitation (co-IP) suggest?

That two proteins physically interact or are part of the same protein complex.

What is a reciprocal IP?

Testing that pulling down protein B also pulls down protein A, used as a control in interaction studies.

What is the role of the Signal Recognition Particle (SRP)?

It recognizes the ER signal sequence on a nascent protein, pauses translation, and escorts the ribosome to the ER membrane.

What happens to the signal sequence of a soluble protein after it enters the ER lumen?

It is cleaved off.

How do single-pass transmembrane proteins anchor in the ER membrane?

A hydrophobic stop-transfer sequence halts translocation and causes the protein to exit the translocon laterally into the bilayer.

What is the sliding filament theory?

The process where actin and myosin filaments slide past each other to shorten the sarcomere during muscle contraction.

What is the difference between endocytosis and exocytosis?

Endocytosis brings molecules into the cell, while exocytosis moves molecules out of the cell.

What is the structural feature of the nuclear pore that creates a selective hydrophobic barrier?

Intrinsically disordered FG-repeat nucleoporins.

What is the result of mutating the NLS of a nuclear protein?

The protein will fail to enter the nucleus and will remain in the cytoplasm.

What signal keeps a protein in the ER lumen?

The KDEL sequence.

Which vesicles transport proteins from the ER to the Golgi?

COPII vesicles.

What is the function of COPI vesicles?

Retrieval transport from the Golgi back to the ER.

What protein coat is primarily associated with endocytosis?

Clathrin.

Which motor proteins transport vesicles along microtubules?

Kinesin and dynein.

What is the role of v-SNAREs and t-SNAREs?

They bind together to mediate membrane fusion between a vesicle and its target.

What is the primary function of the cis-Golgi?

The entry face that receives COPII vesicles from the ER.

What is the primary function of the trans-Golgi?

The exit face that sorts proteins to their final destinations.

How does constitutive secretion differ from regulated secretion?

Constitutive is a default, continuous pathway; regulated requires a specific signal like Ca2+ influx.

What is exocytosis?

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

What are the three main types of endocytosis?

Phagocytosis, pinocytosis, and receptor-mediated endocytosis.

What mechanism drives phagocytosis?

Actin polymerization to extend pseudopods around a target.

What is the primary characteristic of pinocytosis?

It is a non-selective process of sampling extracellular fluid.

What is the function of an early endosome?

A sorting station that decides the fate of internalised cargo.

How are receptors recycled in the endosomal pathway?

They are sorted into tubular extensions of the early endosome and returned to the plasma membrane.

What is the pH range of a late endosome?

Approximately 5.5.

What enzyme maintains the acidic pH of lysosomes?

V-type H+-ATPase (vacuolar proton pump).

Why do lysosomal enzymes not degrade the lysosome itself?

They require a low pH to be active and the lysosomal membrane is protected by a heavy glycocalyx.

What is the address label for lysosomal hydrolases?

Mannose-6-phosphate (M6P).

Where are lysosomal hydrolases tagged with M6P?

In the cis-Golgi.

What happens to ligands in the early endosome?

The low pH causes them to dissociate from their receptors.

Which Rab protein is a marker for early endosomes?

Rab5 (and EEA1).

Which Rab protein is a marker for late endosomes?

Rab7.

What is the primary role of lysosomes?

To serve as the cell's primary degradation compartment for macromolecules.

What happens to the clathrin coat after a vesicle pinches off?

It is shed before the vesicle becomes an early endosome.

What is the result of the maturation of a late endosome?

It fuses with or matures into a lysosome.

What is the primary function of the LDL receptor in cholesterol metabolism?

It acts as a sensor and transport protein that regulates the cell's cholesterol economy via receptor-mediated endocytosis.

What are the two pathways cells use to acquire cholesterol?

Endogenous synthesis via the HMG-CoA reductase pathway and the LDL receptor pathway.

How do normal cells respond to high levels of external LDL?

They suppress HMG-CoA reductase to stop internal synthesis and downregulate LDL receptor expression.

What is the genetic cause of Familial Hypercholesterolemia (FH)?

A mutation in the LDL receptor gene resulting in defective or absent LDL receptors.

Why do FH patients experience runaway cholesterol biosynthesis?

Because cells cannot internalize LDL, they fail to detect intracellular cholesterol and thus never suppress HMG-CoA reductase.

What is the primary difference between membrane-bound organelles and condensates?

Membrane-bound organelles use lipid bilayers for boundaries, while condensates form via phase separation without a membrane.

What physical process drives the formation of cellular condensates?

Liquid-liquid phase separation (LLPS).

How is permeability controlled in condensates?

Through selective partitioning based on interaction affinity rather than specific transporters.

What is a key dynamic difference between condensates and membrane-bound organelles?

Condensates are highly dynamic, with components exchanging rapidly with their surroundings.

What are three characteristics of a liquid condensate?

Free internal diffusion, defined interface/surface tension, and the ability to fuse with other droplets.

How do solid/amyloid aggregates differ from liquid condensates?

Molecules in solids are locked in place, show no internal diffusion, and do not exchange components with surroundings.

What does FRAP stand for in cell biology?

Fluorescence Recovery After Photobleaching.

What does rapid fluorescence recovery in a FRAP experiment indicate?

The material is a liquid, where molecules are diffusing freely into the bleached zone.

What does a lack of fluorescence recovery in a FRAP experiment indicate?

The material is a solid or gel, where molecules are immobile.

What is the mechanistic concept of multivalency in protein phase separation?

Proteins have multiple weak interaction sites that, when combined, provide enough total energy to drive phase separation.

What are IDRs in the context of protein structure?

Intrinsically disordered regions that lack fixed structure and facilitate transient contacts.

What types of weak interactions drive the formation of condensates?

Pi-pi stacking, cation-pi interactions, and other transient, low-affinity contacts.

What do FG-Nups form within the nuclear pore complex?

A hydrogel-like condensate that acts as a selective barrier.

Who won the Nobel Prize for discovering receptor-mediated endocytosis of LDL?

Brown and Goldstein.

What happens to LDL once it is internalized via receptor-mediated endocytosis?

It is delivered to lysosomes where it is hydrolyzed to release free cholesterol.

What is the main symptom of Familial Hypercholesterolemia?

Dramatically elevated blood LDL cholesterol levels.

Why are condensates considered 'functional' in normal biology?

They allow for rapid, dynamic organization of cellular components without the need for permanent membrane structures.