molbio questions

Flexibility-intermediate filaments> microtubules>

actin Strength-intermediate filaments> actin> microtubules

Vectorial trafficking guidance; microtubules and actin are vectorial due to asymmetry of molecular assembly; intermediate filaments are not polarized that way.

Turnover-Microtubules and actin can turn over very fast; intermediate filaments are not at dynamic.

Ability to gel: Any filament that can be crosslinked gels, so in principle all of them can, though actin meshworks are more often associated with gel-ing.

The triphosphate form is necessary to polymerize at plus and minus ends, the hydrolysis is used to create (and store) internal structural stress in the filament. Thus, hydrolysis is not coupled directly to assembly or disassembly.

The purpose is to drive the rapid depolymerization of the filament upon exposure of ‘uncapped ends’ by depolymerization from ends of from breakpoints in the middle of the filament.

Dynamic instability describes the polymerization dynamics of microtubules. The length of the microtubules in dynamic as it elongates and shrinks, the microtubule ends are unstable as they loose their cap to slow monomer incorporation or to factors that tease off the ends such as catastrophins. The dynamic equilibrium is advantageous because it keeps the microtubule cytoskeleton poised to change shape and re-arrange at any point in time in response to extracellular or intracellular cues.

The purpose of nucleation is to speed up the assembly of filaments, which is much slower otherwise due to slow kinetics of monomer assembly into a polymer initiation complex. Microtubule nucleation occurs at centrosomes and basal bodies, nucleated by gamma tubulin. Actin nucleation occurs at locations where Arp2 and Arp3 are located. Other locations are also possible. Regulation is needed to achieve organization of the cytoskeleton, otherwise it would be a web of filaments, rather than a highway for traffic or system for directional membrane projections. Gamma tubulin, and Arp2/3 complex structurally resemble microtubule and actin filaments, respectively, that is now they accomplish nucleation, by provided a ‘polymer’ template.

Depending on the severity of the down-regulation, the actin cytoskeleton may be reduced in complexity (less filaments), or may depolymerize altogether if the actin monomer concentration falls below the critical concentration for polymer assembly at both ends of a filament. Since actin polymers are constantly being replenished at both ends and actin filaments are often replaced, the reduced monomer concentration would quickly change the dynamics of polymerization leading to shorter, less stable filaments.

Two key structural features are 1) a motor domain with the ability to utilize the energy of ATP hydrolysis to change the structure of the molecule; and 2) a tail domain with the ability to attach to a cargo or scaffold. The source of energy is ATP and it is harvested upon 1) binding, 2) hydrolysis, 3) release of phosphate, and 4) release of ADP. The activity of a motor protein can be regulated by phosphorylation or sequestration. A phosphate on the head can regulate the ATPase activity of the motor; a phosphate on the tail can modulate the ability to interact with scaffolds or cargo.

They follow structural cues on the tubulin filaments. Specifically, microtubules are composed of alpha and beta tubulin heterodimers that assemble head to toe with polarity. The motors can recognize structural features that result as a consequence.

The fixed anchor points convert the sliding motion of microtubules (that results from motor activity) into bending motion. By physically preventing the gliding, the shift in position of one filament against the other causes torsion stress that is converted to curvature. Microtubules are flexible enough for this sort of bend.

They stand for gap #1 and gap #2; these are periods of time when the cell monitors: in G1 external signals such as nutrient availability, signals to proliferate or not, cell size, etc; and in G2 internal signals such as are the centrioles duplicated, has the DNA been duplicated, etc.

It is extended by several mechanisms that act on cyclins or cyclin-CDK complexes. First, the synthesis of cyclin is lowered at the gene expression level. Second, cyclin can be targeted for degradation via the proteasome pathway; and third, a cyclin-CDK inhibitor (CKI; p27; sic1) can cover the active site of CDK.

The most vectorial steps in the cell cycle are those that involve proteolysis, as it is terminal. Cyclin proteolysis at various stages of the cell cycle drives the transition between each stage to the next (M>G1; G1>S; S>G2: G2>M).

They are E3 ubiquitin ligases; they serve as adaptors between substrates and the ubiquitination machinery. They function to target proteins for degradation such as cyclins and securin (APC) and CKIs (SCF).

The memory is achieved at the level of the ORC complex, when it has a phosphate on (added by S-CDK) it cannot bind Cdc6 and thus cannot initiate re-melting of the origin and recruitment of Mcms. The phosphate on the ORC added after Cdc6 is phosphorylation, which targets it for degradation.

The checkpoint is monitored in part by Mad2, which binds to unattached kinetochores and sends some sort of signal that delays onset of anaphase. One unattached kinetochore is sufficient to delay anaphase. The physical attachment of the microtubules at kinetochores or the tension of the microtubules is being monitored.

MPF contains an M-CDK complex (M-cyclin with CDK). It can by pass protein synthesis because the protein synthesis is needed only to make cyclin in the initial cell cycles of the Xenopus embryo.

It is a proteolysis cascade where activation of one protease (from pro-caspase to caspase) leads to activation of others, which in turn activate even more caspases. It is initiated by the aggregation of pro-caspases, which is induced by adapter proteins.

The cells go apoptotic (i.e. they commit suicide) as part of a development program or as part of general tissue maintenance. The advantage of doing so is that the cell contents are not spilled into the cellular environment, thus not harming neighboring cells, as happens after necrosis.

They stop dividing because a cell cycle checkpoint control (at DNA duplication) tells the cells that the telomere sequences are too short or have not replicated appropriately. This is due to the fact that telomere sequences get shorter after each cell cycle. Tissue culture cells can be cultured for longer if the telomerase is somehow re-activated to produce longer telomeres or to maintain an appropriate length of existing telomeres.

The position is determined by the location of ‘overlap microtubules’ of the mitotic spindle. It ensures vectoriality because it cannot form until the mitotic spindle has assembled and the chromosomes have moved apart.

In the contractile ring there is actin in the form of filaments and myosin motors in the form of polymers.

Contraction is initiated by a calcium spike, which removes troponin C, which in turn destabilizes tropomyosin (the molecule bound to actin filaments that blocks access of myosin). In that way is it similar to muscle contraction.