Polymer Dynamics and Actin Filament Quiz

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Questions and Answers

What determines the equilibrium constant for the association of a polymer?

The ratio of the rate constants for association (kon) and dissociation (koff) determines the equilibrium constant.

How do the growth rates of the plus and minus ends of a polymer compare when C > Ca?

Both ends grow when C > Ca, with the plus end growing faster than the minus end if kon for the plus end is higher.

What happens to both ends of a polymer when C < Ca?

When C < Ca, both ends of the polymer shrink, as the subunits are lost at both ends.

What is the effect of nucleotide hydrolysis on the binding affinity of subunits in a polymer?

Nucleotide hydrolysis reduces the binding affinity of subunits, making dissociation more likely. Signup and view all the answers

Identify the forms of actin and tubulin that primarily add to and leave the filament.

The T form (carrying ATP or GTP) typically adds to the filament, while the D form (carrying ADP or GDP) usually leaves. Signup and view all the answers

What is the significance of the identical AG for subunit loss at both ends of a polymer?

The identical AG indicates that the energy cost of subunit loss is the same, regardless of whether it occurs at the plus or minus end. Signup and view all the answers

Explain the relationship between nucleotide hydrolysis and polymerization in the context of actin and tubulin.

Nucleotide hydrolysis facilitates polymerization by allowing subunits to have a reduced binding affinity, leading to dynamic stability. Signup and view all the answers

In a simple polymerization reaction, how do kon and koff behave at both ends of the polymer?

In a simple polymerization reaction, kon and koff may differ in their rates, but their ratio must be identical at both ends of the polymer. Signup and view all the answers

What is the process called when the plus end of an actin filament grows while the minus end shrinks?

Treadmilling. Signup and view all the answers

Which chemical stabilizes actin filaments by binding along their structure?

Phalloidin. Signup and view all the answers

How does Cytochalasin B affect actin filaments?

It depolymerizes actin by capping the filament plus ends. Signup and view all the answers

What role does the Arp2/3 complex play in actin filament dynamics?

It nucleates assembly to form a branched network. Signup and view all the answers

Name one function of tropomodulin in actin filaments.

It prevents assembly and disassembly at the minus end. Signup and view all the answers

What is the mechanism of action for nocodazole?

It depolymerizes microtubules by binding to tubulin subunits. Signup and view all the answers

Which protein binds ADP-actin filaments and accelerates their disassembly?

Cofilin. Signup and view all the answers

What is the primary function of gelsolin in relation to actin filaments?

It severs filaments and binds to the plus end. Signup and view all the answers

Describe the effect of taxol on microtubules.

Taxol stabilizes microtubules by binding along their filaments. Signup and view all the answers

How does thymosin affect actin filament assembly?

It binds actin subunits and prevents their assembly. Signup and view all the answers

What is the role of the Arp2/3 complex in actin dynamics?

The Arp2/3 complex promotes the nucleation of new actin filaments, facilitating actin polymerization. Signup and view all the answers

How do actin-binding proteins contribute to cellular function?

Actin-binding proteins regulate the assembly, organization, and dynamics of actin filaments, impacting various cellular processes. Signup and view all the answers

Explain the significance of the 'plus end' and 'minus end' in actin filaments.

The 'plus end' is the site where actin monomers are added rapidly, while the 'minus end' is where disassembly occurs. Signup and view all the answers

What might be the implications of having unrecognized actin-associated proteins in cells?

Unrecognized actin-associated proteins could play critical roles in actin regulation and cellular processes that remain to be discovered. Signup and view all the answers

Describe the function of nucleation-promoting factors (NPFs).

Nucleation-promoting factors assist in activating the Arp2/3 complex to initiate the formation of new actin filaments. Signup and view all the answers

What is the overall effect of Arp2/3 complex activation on actin filament structure?

Activation of the Arp2/3 complex results in the formation of branched actin filament networks, increasing the filaments' density. Signup and view all the answers

How does the presence of accessory proteins influence actin filaments?

Accessory proteins can stabilize actin filaments, promote their polymerization, or regulate their disassembly. Signup and view all the answers

Why is it important that cells contain a diverse array of actin-binding proteins?

A diverse array of actin-binding proteins allows cells to adapt their cytoskeleton to various functions and environmental changes. Signup and view all the answers

What are the key differences in the projection arms of MAP2 and tau?

MAP2 has a long projecting arm, while tau possesses a shorter projection arm. Signup and view all the answers

How does augmin contribute to microtubule formation in cells?

Augmin nucleates new microtubules with a low branching angle from a tubulin ring complex. Signup and view all the answers

What role do catastrophe factors like kinesin-13 play in microtubule dynamics?

Catastrophe factors such as kinesin-13 promote microtubule depolymerization by binding to their ends and pulling them apart. Signup and view all the answers

What effect does XMAP215 have on microtubule growth?

XMAP215 promotes rapid microtubule polymerization by binding tubulin dimers and delivering them to the microtubule plus end. Signup and view all the answers

How does the presence of EB1 protein indicate microtubule growth?

EB1 is associated with the microtubule tip when the microtubule is growing. Signup and view all the answers

What happens to EB1 when a microtubule undergoes a catastrophe?

EB1 is lost from the microtubule tip during a catastrophe. Signup and view all the answers

What consequences does the depletion of augmin have on plant growth?

Depletion of augmin severely stunts plant growth. Signup and view all the answers

What is the significance of the regular spacing of microtubules observed in cells overexpressing MAP2?

The regular spacing results from the constant length of MAP2's projecting arms, which organizes microtubule bundles. Signup and view all the answers

What role does Cdc42-GTP play in establishing polarity in C. elegans?

Cdc42-GTP recruits its own GEF to the plasma membrane, creating a focal site of Cdc42 activity that contributes to symmetry breaking and polarization. Signup and view all the answers

How do PAR proteins contribute to the anterior-posterior polarity in the zygote?

PAR proteins localize to opposite ends, with Par-3 at the anterior and Par-2 at the posterior, establishing distinct cortical domains through mutual antagonism. Signup and view all the answers

What is the consequence of Rho GEF activity being reduced at the posterior end of the C. elegans embryo?

Reduced Rho GEF activity leads to decreased myosin levels and contractility, contributing to anterior PAR protein accumulation. Signup and view all the answers

Describe how Cdc42 influences actin filament assembly.

Cdc42 activates formin proteins, which nucleate actin filament assembly, crucial for vesicle transport towards the cell's plus ends. Signup and view all the answers

What contrasting effects do Rac and Rho have on actin organization?

Rac activation promotes the formation of protrusive actin networks in lamellipodia, while Rho activation leads to actin filament nucleation and increased contraction in stress fibers. Signup and view all the answers

How does the localization of PAR and Scribble proteins affect cellular polarity?

PAR proteins help assemble apical junctions, while Scribble defines the basolateral domain, and they are mutually antagonistic. Signup and view all the answers

What occurs to myosin II distribution in the unpolarized egg prior to fertilization?

Myosin II is uniformly distributed throughout the cortex, due to the uniform activation of Rho across the plasma membrane. Signup and view all the answers

Explain the role of myosin V in the context of actin filament transport.

Myosin V transports vesicles along actin filaments toward their plus ends, facilitating cargo delivery needed for bud growth. Signup and view all the answers

What role does ATP binding and hydrolysis play in the functioning of dynein during ciliary movement?

ATP binding and hydrolysis cause the linker domain of dynein to throw the head domain toward the microtubule minus end, leading to a power stroke that facilitates movement along the microtubule. Signup and view all the answers

Describe the primary function of axonemal dynein in the context of ciliary structure.

Axonemal dynein generates sliding forces between adjacent microtubule doublets, allowing for the bending and movement of cilia or flagella. Signup and view all the answers

How does the tail domain of axonemal dynein differ from its head domain in structure and function?

The tail domain is less conserved and is primarily responsible for binding to the A microtubule, while the head domain contains the motor activities for ATP hydrolysis and movement. Signup and view all the answers

What is the significance of the 8 nm step produced by dynein during its power stroke?

The 8 nm step is crucial as it corresponds to the distance along the microtubule that dynein moves its cargo or induces bending in cilia and flagella. Signup and view all the answers

In what way does the arrangement of microtubules influence the function of dynein?

The arrangement of microtubules in structures like flagella provides the scaffolding necessary for dynein to exert forces, leading to effective bending and movement. Signup and view all the answers

How does the arrangement of dynein arms contribute to the function of sperm axonemes?

Dynein arms connect the A microtubule of one doublet with the B microtubule of an adjacent doublet, generating the necessary sliding force for movement. Signup and view all the answers

What occurs during the dynein power stroke when ATP is released?

Upon ATP and phosphate release, the linker domain undergoes a conformational change that pulls the tail and its attached microtubule toward the minus end. Signup and view all the answers

Explain the difference between axonemal dynein and cytoplasmic dynein in terms of their function.

Axonemal dynein primarily functions in the movement of cilia and flagella, while cytoplasmic dynein is responsible for transporting cargo like vesicles along microtubules. Signup and view all the answers

Study Notes

The Cytoskeleton

Cells need to organize themselves and interact mechanically with each other and their environment for proper function.
Cells need to be correctly shaped, physically robust, and properly structured internally.
Cells can change shape and move around.
Internal components of cells are continually rearranged to adapt to changing conditions.
This is due to the cytoskeleton structure composed of protein filaments: actin, microtubules, and intermediate filaments.

Function and Dynamics of the Cytoskeleton

Actin filaments control cell surface shape, and are necessary for whole-cell locomotion, and driving the pinching of one cell into two.
Microtubules specify the positions of organelles, direct intracellular transport, and form the mitotic spindle that segregates chromosomes during cell division.
Intermediate filaments provide mechanical strength.

Actin filaments

Actin filaments are helical polymers of the protein actin.
They have a diameter of 8nm.
They organize into linear bundles, two-dimensional networks, and three-dimensional gels.
They are highly concentrated in the cell cortex (just beneath the plasma membrane).

Microtubules

Microtubules are long, hollow cylinders made of the protein tubulin.
They have an outer diameter of 25 nm.
They are rigid compared to actin filaments.
They frequently have one end attached to a microtubule-organizing center (MTOC) called a centrosome.
Microtubules have a plus end (fast-growing end) and a minus end(slow-growing end).

Intermediate Filaments

Intermediate filaments are rope-like fibers with a diameter of 10 nm.
They are made of intermediate filament proteins, which form a large heterogeneous family.
The nuclear lamina is a meshwork of intermediate filaments just beneath the inner nuclear membrane.
Other types provide mechanical strength to cells.
They are essential for strengthening an entire epithelium.

Cytoskeletal Filaments- Dynamic but Stable Structures

Large-scale cytoskeletal structures can change or persist according to need.
The components that make up these structures are dynamic.
A rearrangement in a cell will require little extra energy when conditions change.
Actin filaments form cell-surface projections (e.g., filopodia, lamellipodia, pseudopodia) that allow cells to explore and move around.

Cytoskeletal Organization Associated with Cell Division

In cell division, actin cytoskeleton becomes polarized.
Microtubules form a bipolar mitotic spindle which aligns and segregates duplicated chromosomes.
Actin filaments form contractile ring at cell center to pinch the cell in half.

Neutrophil in Pursuit of Bacteria

Neutrophils rapidly re-assemble and disassemble actin cytoskeleton to change orientation and direct their movement within minutes.
The dense actin network in a pseudopod helps the neutrophil push towards bacteria.

Cytoskeletal Organization and Polarity

Epithelial cells that line organs like the intestine and lungs maintain a constant location, length, and diameter of microvilli and cilia over their entire lifetime.
Some cells (like hair cells in inner ears) have stable actin filaments that don't turn over.
Cytoskeleton is responsible for cellular organization and polarity (like top/bottom or front/back orientation of the cell).

Filaments Assemble from Protein Subunits

Cytoskeletal filaments can span tens to hundreds of micrometers, but their subunits are very small (a few nanometers) in size.
Filaments assemble (polymerize), in much the same manner as a skyscraper is built using bricks.
Subunits are small enough to diffuse rapidly in the cytosol.
Actin filaments and microtubules are built from globular subunits (actin and tubulin), whereas intermediate filaments are from elongated fibrous subunits.

Filaments Assemble from Protein Subunits - Physical and Dynamic Properties

Cytoskeletal filaments in living cells are not simply assembled in a single file, but instead require structural reorganization.
Microtubules are built of 13 protofilaments and their subunits are tightly bound to their two neighbors that allows for strength and adaptability.
The loss or addition of a subunit at one end requires breaking fewer bonds than breaking one in the middle or splitting the filament entirely.

Accessory Proteins and Motors Act on Cytoskeletal Filaments

The cell controls length, stability, number and geometry of cytoskeletal filaments, and their attachments to other components.
Filament properties are mostly regulated by accessory proteins reacting to received signals.
These accessory proteins modify spatial distribution and dynamic behavior of the filaments.
They bind to filaments to determine assembly sites, regulate partitioning of proteins between filament and subunit forms, change kinetics of assembly and disassembly, and link to other cell structures.

Actin

Actin subunits are 375-amino-acid polypeptides that are extremely conserved among eukaryotes.
They carry a tightly bound molecule of ATP or ADP.
There are three isoforms (alpha, beta, gamma) of actin in vertebrates differing slightly in amino acid sequences and functions.

Actin Subunits Assemble Head-to-Tail

Actin subunits form a tight, right-handed helix of approximately 8nm called filamentous actin (F-actin).
Actin filaments are polar, meaning they have plus and minus ends with different functions and growth rates.
Accessory proteins frequently cross-link and bundle actin filaments, creating more rigid structures.

Nucleation Is the Rate-Limiting Step in the Formation of Actin Filaments

Actin subunits spontaneously bind to one another. However, the association is unstable until multiple subunit-subunit contacts stabilize the nucleus or initial oligomer.
Rapid elongation occurs by the addition of more subunits. This process is called filament nucleation.
Cells control their shape and movement by regulating the formation of actin filaments.

On Rates and Off Rates

Polymerization/ depolymerization of linear polymers like actin (filaments) and microtubules occurs by the addition or removal of subunits at the ends of the polymer.
Addition rate is given by the rate constant (kon)
Loss rate is given by the rate constant (koff)

Nucleation

Multiple contacts between adjacent subunits stabilize a helical polymer.
The process of polymerization begins with the formation of a small nucleus (trimer of actin or ring of multiple tubulin molecules).
Nucleation is relatively slow compared to elongation.
Pre-formed nuclei (also called fragments) can speed up polymerization.

The Critical Concentration

Critical concentration (Cc) is the subunit concentration at which the rate of subunit addition equals the rate of subunit loss.
At this equilibrium, the rate of subunit addition is proportional to the free subunit concentration.

Time Course of Polymerization

The lag phase represents the time required for nucleation.
Growth phase occurs when subunits attach to the exposed ends of the polymer, causing elongation.
Equilibrium state is reached when the growth by subunit addition is balanced by disassembly back to monomers.

Plus and Minus Ends

Actin filaments and microtubules have two ends that exhibit different growth rates (plus and minus ends).
The rate of addition at the ends differs, and this is associated with changes in subunit conformation.
The ratio of koff and kon is the same for both plus and minus ends of the polymer (for simple polymerization)

Nucleotide Hydrolysis

ATP binds tightly to an actin molecule.
Hydrolysis to ADP decreases binding affinity for neighboring subunits and promotes dissociation from filament ends.
The T form (with ATP) binds preferentially to the plus end; the D form (with ADP) departs from the filament primarily from the minus end.

ATP Caps and GTP Caps

A cap of ATP- or GTP-containing subunits favors growth over hydrolysis.
Loss of this cap initiates rapid disassembly of subunits.

Dynamic Instability

Microtubules and actin can alternate between growth and rapid disassembly—this is called dynamic instability.
GTP cap favors growth.
Loss of the GTP cap, initiates rapid depolymerization

Microtubules Undergo a Process Called Dynamic Instability

GTP hydrolysis, which occurs within the beta subunit, is accelerated when the tubulin subunits are incorporated into microtubules.
The energy of the phosphate bond hydrolysis is stored as elastic strain, making dissociation from the D form more favored (i.e. more negative) than in T form (with GTP).

Microtubules- Dynamic Instability- catastrophe and rescue

Microtubules can switch from periods of growth to periods of rapid disassembly (dynamic instability) by switching between the T form (GTP-bound) and the D form (GDP-bound).
Catastrophe is the transition from growth to depolymerization.
Rescue is the transition from depolymerization to growth.
Critical concentration is the concentration where subunit addition = subunit loss.

Protofilaments

Microtubules are built of 13 parallel protofilaments, each with a- and b-tubulin dimer.
These are tightly held together by hydrophobic interactions.
Tubulin subunits are arranged in staggered protofilaments, forming a hollow cylinder.
The addition and loss of subunits occurs almost exclusively at the ends of the microtubules.

Centrosome is a Prominent Microtubule Nucleation Site

Many animal cells contain a centrosome as the main microtubule organizing center (MTOC).
Centrosomes contain two centrioles arranged perpendicular to each other.
The y-tubulin ring complex (γ-TuRC) is involved in microtubule nucleation within centrosomes and other locations.

Microtubule Organization Varies Widely among Cell Types

The arrangement of microtubules varies amongst different cell types.
Cell type differences observed include nucleation sites (MTOC), which are either nuclear-related (e.g. higher-plants and some fungi) or distinct structures like centrosomes (e.g. animals), distributions throughout the cell, differences in microtubule density, and the presence/absence of centrioles.

Microtubule-Binding Proteins

Microtubule polymerization and dynamics are influenced by microtubule-associated proteins (MAPs).
A variety of proteins that control microtubule dynamics and attach to plus ends and minus ends are called microtubule plus end-binding proteins (+TIPs).
+TIPs bind to growing plus ends of microtubules.
They dissociate when microtubules begin to shrink (e.g., catastrophe events).

Tubulin-sequestering and Microtubule-severing Proteins

Sequestering and severing proteins greatly influence microtubule dynamics and stability.
Sequestering proteins and stathmin bind to tubulin dimers to prevent them from adding to the ends of microtubules.
Severing proteins break microtubules to increase the rate of depolymerization, but some fragments that result can initiate further growth

Microtubule Severing

Katanin destabilizes microtubules by severing filaments.
This generates many new ends which can either favor growth or promote rapid disassembly depending on the conditions.

MicroTubules – Summary

Microtubules are formed from a- and b-tubulin dimers (2 types of proteins)
They have GTP or GDP bound to β-tubulin, this influences the function, but not the structure.
Microtubules are continually polymerizing and depolymerizing; this is called dynamic instability.
Microtubules are involved in many different cellular functions, including intracellular transport, cell division, and maintaining cell shape.

Motor Proteins (Kinesins and Dyneins)

Kinesins are microtubule motors that typically move towards the plus ends.
Dyneins are microtubule motors that typically move towards the minus ends.
Motor proteins have many domains that drive their interaction with microtubules as they move. This is associated with ATP binding and hydrolysis.
Different types of kinesins and dyneins are associated with different cargoes (like organelles, membrane vesicles, etc.) depending on which cargo-binding sites are at the c-terminus of the dimer.

Sliding of Myosin II Along Actin Filaments

Muscle contraction is dependent on the sliding of myosin along actin filaments.
The contraction involves a series of events that take place in response to an action potential arriving at the muscle cell membrane.
Cardiac and smooth muscle differ in their structural organization and gene expression.

Actin and Myosin in Non-Muscle Cells

Myosin II drives contractility in a variety of nonmuscle cells.
Actin-myosin bundles also provide mechanical support by associating the cell with the extracellular matrix (ECM) or with neighboring cells.
The forces exerted are crucial for cell shape and movement, cell division (organizing the mitotic spindle) and for cellular morphogenesis during development (like in hair, nails, claws, and scales).

Myosin Superfamily

Myosin is a protein family. The different types of myosin function in diverse ways.
Myosins consist of heavy chains that have a globular head domain at the N-terminus, where the force generating machinery lies.
The tail domains of the heavy chains typically associate to form a coiled-coil structure.
Myosin heads bind to actin and use ATP hydrolysis to create movement along the filament.

Myosin Generates Force

Binding and hydrolysis of ATP leads to a series of conformational changes in the myosin head that generates force as the neck linker reorientates to create the power stroke in each cyclical step.
The cyclic interaction between myosin and actin is crucial for force generation and is required for muscle contraction.

Actin Filament-Binding Proteins

Different proteins influence actin dynamics and organization.
Actin filaments can frequently be terminated or stalled at one end or the other.
+TIPs are actin filament-binding proteins that associate at the plus end during growth.

Dynamic instability of microtubules

Microtubules exhibit dynamic instability, which is the rapid switching between periods of growth and disassembly.
This is regulated by GTP hydrolysis on the beta-tubulin.
A GTP cap promotes the addition of tubulin subunits, and loss can initiate the depolymerization transition.

Primary Cilia and Signaling Functions

Primary cilia are nonmotile structures present in most animals cell types.
They have a microtubule core, basal body, etc., similar to motile cilia.
They are specialized for signaling, acting as sensory probes/detecting changes in the environment or as sensors for extracellular cues during development.

Intermediate filaments

Intermediate filaments (IFs) are the third major type of cytoskeletal proteins.
They are present in most metazoans (animals, nematodes, and mollusks) but not in animals with rigid exoskeletons.
They form a network in the cytoplasm that provides mechanical strength to tissues.

Intermediate Filaments and Other Cytoskeletal Polymers Summary

IFs provide mechanical strength to tissues.
They are composed of a-helical coiled-coil domains and each fiber includes eight parallel protofilaments.
Examples include keratin (in epithelial cells), vimentin-like subunits (in connective tissue, muscles, and neurons), and nuclear lamins (in the nucleus).
These fibers lack polarity, are resistant to stretch, resist compression, and remain stable throughout the cell cycle.

Septins

Septins are GTP-binding proteins that form filaments, rings and cages.
Play an important role in cellular compartmentalization.

Cell Polarity and Coordination of the Cytoskeleton

Cells have polarity that is governed by the cytoskeleton.
The cytoskeleton is involved in intracellular signaling, secretion, cell division and directing a migrating cell.
Polarity signals interact to generate structures with specific components at their top/bottom or front/back.
This regulation is vital for oriented cell division and development in a multicellular organism.

Small GTPases (Cdc42, Rac, Rho)

Small GTPases like Cdc42, Rac, and Rho are important in cell polarity and in modulating actin organization.
Rac-GTP leads to formation of actin networks (lamellipodia and pseudopodia).
Rho-GTP leads to formation of actin bundles (stress fibers).
These GTPases have opposing effects on actin and microtubules.

Cell Migration

Cells use actin-based protrusion.
Myosin II-based contraction at the rear helps move the cell. (e.g., mesenchymal, amoeboid, blebbing migration)

How Bacterial Pathogens Hijack the Host Cytoskeleton

Some bacteria use the host cell's cytoskeleton to move inside the cell.
The bacteria's ability to use host cell cytoskeleton is through utilizing the host cell's protein components and utilizing the host's intracellular transport mechanisms.

Other Cytoskeletal Polymers

Septins are GTP-binding proteins forming filaments; they are typically in rings or cages.
Involved in compartmentalization of membranes/cytoskeleton, often found in primary cilia.

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Description

This quiz explores the intricacies of polymer dynamics, focusing on the association and dissociation of actin and tubulin filaments. You will answer questions related to equilibrium constants, growth rates, nucleotide hydrolysis, and specific chemical effects on polymer stability. Enhance your understanding of how these processes impact cellular functions.