Bio 2 Exam 2

-Give the cell its shape, strength and ability to move.

- Important in adapting to changes in environment, cell to cell communication, and to rearrange internal components during cell division.

Actin filaments-determine the shape of the cell's surface and are necessary for whole cell locomotion; they also drive the pinching of one cell into two

Microtubules- determine the position of membrane enclosed organelles, direct intracellular transport, and form the mitotic spindle that segregates chromosomes during cell division.

intermediate filaments- provide mechanical strength

actin filaments= actin subunits which are compact and globular

Microtubules= tubulin subunits which are compact and globular

intermediate filaments= made up of smaller subunits that are elongated and fibrous

yes, they even have homologs of the the subunits that help control shape and division

The rate limiting step in formation of actin filaments.

Subunits must first assemble into an initial aggregate or nucleus, that is stabilized by multiple subunit-subunit contacts and can then elongate rapidly by the addition of more subunits

-Allows the cell to rapidly modify cytoskeletal structure and function under different conditions

-In cells such as mature neurons or epithelial cells that do not turn over (regenerate)

- The actin bundles in the inner ear must remain stable for the entire lifetime of the animal since they do not have turn over.

Important to provide both strength and adaptability in a microtubule

- They are linear strings of subunits joined end to end and they associate with one another to form a hollow cylinder which is a microtubule.

FtsZ- (A homolog of tubulin) which can polymerize into filaments and assemble into a z ring at the site where the septum forms druing cell division. They are thought to generate a bending force that drives the membrane invagination which is necessary to complete cell division.

-assemble head to tail to form a right right handed helix

-all subunits face in the same direction forming a slower growing minus end (pointed end) and a faster growing plus end (barbed end)

Critical concentration- The concentration of free subunits left in solution at the point where dissociation=association

-The cell takes advantage of the nucleation requirement: it uses special proteins to catalyze filament nucleation at specific sites, thereby determining the location at which new actin filaments are assembled

- Minus end is slower growing (pointed end)

-Plus end is faster growing (barbed end)

-equilibrium constant must be the same for addition of subunits on either end of the polymer

-Tredmilling is when the subunits undergo a net assembly and net disasembly at an identical rate. The polymer maintains a constant length even though there is a net flux of subunits through the polymer.

- occurs when Cc(minus end) is greater than the Cc(plus end)

Important is antibiotic resistance.

Actin: Actin, smallest, two strands, yes, Yes-ATP, Atp hydrolysis

Microtubules: Tubulin, largest, hollow cylinder, yes, yes-GTP, GTP hydrolysis

Intermediate filaments-Varies, between, ropelike fibers, non polar, no, less known

-(actin homolog) found mainly in rod or spiral shaped cells where they assemble to form dynamic patches that move along the length of the cell.

-contribute to cell shape by acting as a scaffold to direct synthesis of the peptidoglycan cell wall.

-Half lives of a few minutes and nucleotide hydrolysis accompanies the polymerization process.

(Bacterical actin homolog)-assembles into filaments that associate at each end with a copy of the plasmid and growth of the ParM filaments pushes the replicated plasmid copies apart.

- encoded by a gene on certain bacterial plasmids that also carry genes responsible for antibiotic resistance and cause the spread of multidrug resistance in epidemics.

nucleates assembly to form a web and remains associated with the minus end

-nucleate the growth of straight unbranched filaments that can be cross-linked by other proteins to form parallel bundles.

-actin monomers bound to thymosin are in a locked state and cannot associate with either plus or minus ends of actin filaments and can neither hydrolyze nor exchange their bound nucleotide

- Binds to the face of the monomer that would normally associate with the filament minus end, while leaving exposed a spot on the monomer that binds to the plus end. A conformational change occurs so the profilin falls off leaving the actin filament one subunit longer

-Caps actin filaments at their minus end, most commonly after actin filament has been treated with tropomyosin

binds ADP-actin filaments, accelerates disassembly

-binds along the length of the actin filaments, forcing the filament to twist a little more tightly. The stress weakens the contacts between subunits makes them easier to break

-Prefers to bind to ADP bound actin so it usually breaks down older cells.

-activated by high levels of cytosolic Ca2+. Interacts with the side of the actin filament and contains subdomains that bind to two different sites: One that is exposed on the surface if the filament and one that is hidden between adjacent subunits. Inserts into the gap to break the filament

-once the actin molecules have hydrolyzed their ATP, the binding of a plus end capping protein stabilized the filament at the plus end by rendering it inactive.

-Capping are the minus end is done by Arp 2/3 complex

-an elongated side binding protein that binds to six or seven adjacent actin subunits along each of the two grooves of the helical actin filament.

-It stabilizes and stiffens the filament but also prevents it from interacting with other proteins

cross link actin filaments into a parallel array. also determines which other molecules can interact with the crosslinked actin filaments

use structural changes in the atp binding sites to produce cyclic interactions within a cytoskeletal filament. each cycle of (atp binding, hydrolysis, and release) propels them forward in a single direction to a new binding site along the filament

an elongated protein formed from two heavy chains and two copies of each of two light chains. Each heavy chain has a globular head domain at its N terminus that contains the force generating machinery, followed by a long AA sequence that forms an extended coiled coil.

-Generates the force for muscle contraction

-Name given to the basic contractile elements of the muscle cell

- cylindrical structure often as long as the muscle cell itself

-consists of a long repeated chain of tuny contractile units called sarcomeres

-give the vertebrate myofribril its striated appearance

-each is formed from a miniature preciselt ordered array of parallel and partially overlapping thin and thick filaments

-composed of actin and associated proteins, attached at their plus ends to a z disc at each end of the sarcomere

bipolar assemblies formed from specific isoforms of myosin 2

a regularly spaced bundle located at each end of the sarcomere as an attachment site for rhe plus ends of actin filaments (thin filaments)

No, actin behavior is also regulated by accessory proteins

-Cell contains proteins called thymosin that make polymerization unfavorable so they need monomer binding proteins called profilin to bind and make polymerization more favorable.

Arp2/3 complex= stays attached to the minus end prevents subunit addition or loss to that end to allow rapid elongation at plus end. Creates a weblike structure

Formins= stays attached to the plus end of the filament while still allowing addition of new subunits to that end. Nucleate the growth of straight unbranched filaments.

- Occurs primarily at the plasma membrane/ Cell cortex

The use of tropomyosin, tropomodulin, and capping proteins affect elongation and stability.

The structural organization of different actin actin networks depend on specialized accessory proteins. They are assembled and maintained by bundling proteins: Crosslink actin filaments into a parallel array--Gel forming proteins: hold two actin filaments together at a large angle to each other thereby creating a looser meshwork

1. Myosin is attached to actin filament

2. ATP binds to myosin head causing the myosin head to detach form the filament

3. Conformational change cocks the myosin and hydrolysis occurs attaching the filament when myosin is cocked

4. Phosphate group is lost causing the power stroke

calcium influx triggers the opening of calcium release channels in the sarcoplasmic reticulum which leads to flooding of calcium into the cytosol which initiates the contraction of each myofibril. It then is pumped right back into the sarc retic. by an atp depending calcium pump within 30 msec letting the myofibrils relax

yes and MLCK is an example of motor protein regulation.

-Smooth muscle contraction

calcium bound calmodulin activates (myosin light chain kinase) thereby inducing the phosphorylation of smooth muscle myosin on one of its two light chains. When the light chain is phosphorylated, the mysosin head can interact with actin filaments and cause contraction. -dephosphorylation causing unattachment and relaxing of the muscle

-subunit of microtubules

- heterodimer formed from two closely related globular proteins a-tubulin and b-tubulin bound together by noncovalent bonds

Microtubule organization center

-microtubules are usually nucleated here because y tubulin is most enriched here

-nucleation depends on this process. Within the complex two accessory proteins bind directly to the y tubulin along with several other proteins that help create a spiral ring of y tubulin molecules, which serves as a template that creates a microtubule with 13 protofilaments

-A well defined MTOC in animal cells.

-located near the nucleus and from which microtubules are nucleated at their minus ends so the plus ends point outward and continuously grow and shrink, probing the entire 3D volume of the cell.

-Embedded within the centrosome

- a pair of cylindrical structures arranged at right angles to each other in an L shaped configuration.

-With a large number of accessory proteins the centrioles organize the pericentriolar material where microtubule nucleation takes place.

binds to two tubulin heterodimers and prevents their addition to the ends of microtubules

-members of a family of kinesin related proteins known as catastrophe factors

made up of two subunits: a smaller subunit that hydrolyzes ATP and performs the actual severing and a larger subunit that directs katanin to the centrosome.

-proteins that bind to microtubules

-stabilize microtubules by binding along sides

-mediate the interaction of microtubules with other cell components

-binds free tubulin subunits and delivers them to the plus end, promoting microtubule polymerizations and simultaneously counteracting catastrophe factor activity

-remain associated with growing plus ends and can link to to other structures such as membranes

-Kinesin and dynein

-Kinesin moves towards the plus end while dynein moves towards the minus end

- Kinesin has two identical head and moves in a step by step motion not in a lever and powerstroke motion

Axoneme- composed of microtubules and their associated proteins, arranged in a distinctive and regular pattern. Core of cilia and flagella

primary cilia- a shorter non motile couterpart of cilia and flagella. it can be viewed as a specialized compartment or organelle that perdorms a wide range of cellular functions but share many structure features with cilia and flagella.

basal bodies- has a centriol in the center and anchors the motil and nonmotile cilia and flagella to the cell surface.

protofilaments are composed of ab-tubulin heterodimers stacked head to tail and then folded into a tube.

T form is bound to GTP and produces straight protofilaments

D form is bound to GDP and makes the protofilaments curved

-dynamic instability is the rapid intraconversion between a growing and shrinking state at a uniform free subunit concentration.

-occurs when the concentration is between what is needed for T form and D form so it switches back and forth.

- Important to remain dynamic so the cell can move, divide and maintain or correct its shape

Drugs such as taxol that binds to and stabilizes microtubules lead to a net increase in tubulin polymerization and is successful in threatment if tumors

no, also regulated by accessory proteins

Nucleated at the MTOC where y tubulin and other accessory proteins form a spirl y-TuRC which serves as a template to create a microtubule with 13 protofilaments

Maps affect the stability of microtubules against disassembly

-contain numerous proteins that bind to the ends and influence stability and dynamics

kinesin contains two identical globular heads

1) Both heads are normally ADP bound, once on head attaches to a microtubule ADP is released and ATP attaches in its place.

2)The neck zippers and throws the other head forward to attach at the next binding site which causes the first head to loose its phosphate and detach (over and over in a step by step motion)

Kinesin- Carries membrane enclosed organelles away from the cell body toward the axon terminal by walking toward the plus end of microtubules

Dynein- minus end directed microtubule motors. 1) is used for mRNA and organelle trafficking, for positioning the centrosome and nucleus during cell migration, and contruction of microtubule spindle in division.2) only found in eukaryotic organisms that have cilia and are used to transport material from the tip to the base of the cilia

The movement of cilia or flagellum is produced by the bending of its core (axoneme)

Yes, it varies

-an example of intermediate filaments, they form a meshwork lining the inner membrane of the nuclear envelope, where they provide anchorage sites for chromosomes and nuclear pores.

Septins are GTP binding proteins and serve as an additional filament system in all eukaryotes except terrestrial plants.

-One dimentional, they contain a core of long, bundled actin filaments.

-formed by migrating growth cones of neurons and some types of fibroblasts

-formed by epithelial cells, fibroblasts and some neurons

-three dimensional and important for cells to cross tissue barriers, they also degrade the extracellular matrix which requires the delivery of vesicles containing matrix degrading proteases.

plasma membrane detaches locally from the actin cortex allowing the cytosol to rush in pushing the membrane outwards

ropelike fiber, Non polar (both ends are identicle), does not bind to ATP or GTP, and they are much more diverse.

Impart mechanical strength to tissues for the squishier animals

using proteins called plakins which are large and modular, containing multiple fomains that connect cytoskeletal filaments to each other and to junctional complexes.

They assemble into non polar filaments that form rings and cagelike structures which act as scaffolds to compartmentalize membranes into distinct domains, or recruit and organize the actin and microtubule cytoskeletons.

actin polymerization allows rapid elongation of actin filaments and it pushes the membrane out to form different types of protrusive structures.

actin filament protrusion forces are transmitted to the underlying substratum to drive cell locomotion. this must be coupled with myosin contraction for the movement to occur and fling forward.

1) S phase= cell growth and chromosome replication

2) M phase= chromosome segregation

3) cytokinesis= cell division

early in prophase two identical DNA molecules are gradually disentangled and condensed into pairs of rigid, compact rods

a commitment point near the end of g1- after calls pass this point they are committed to DNA replication, even if the ectracellular signals that stimulate cell growth and division are removed

(cyclin dependent kinase)- activity of these kinases rise and fall as the cell progresses through the cycle, leading to cyclical changes in the phosphorylation of intracellular proteins that initiate or regulate the major events of the cell cycle.

CDK regulator, they undergo a cycle of synthesis and degradation in each cell cycle (G1/s-cyclins, s-cyclins, and m-cyclins)

Wee1= protein kinase that inhibits CDK activity by phosphorylating at kinase active site

cdc25=phosphatase that dephosphorylates and increases cdk activity

CAK= CDK activating kinase; phosphorylates CDKs in cyclin-cdk complexes, activating the CDK

CKI- CDK inhibitor protein, primarily involved in control of G1 and S phases

APC/C= a member of the ubiquitin ligase family of enzymes- key regulator of the metaphase to anaphase transitions

SCF= ubiquitin ligase that ubiquitylates certain CKI proteins in late g1, helping to control the activation of s-cdks and dna replication and destruction of g1/s-cyclins in early s phase.

large complex of DNA helicases loaded onto the replication origin-initiating of DNA synthesis is permitted only at origins containing pre rc (licensing step)

origin recognition complex-binds to replication origins throughout the cell cycle

They collaborate withing the ORC to load the inactive DNA helicases around the DNA next to the origin. The resulting complec is the Pre RC

protein kinase-activated in s phase and helps drive origin activation by phosphorylating specific subunits of the DNA helicase

cdt1 inhibitor, allows cdt 1 to be active

large protein complex that holds sister chromatids togethers, they are deposited at many locations along the length of each sister chromatid as the dna is replicated in s phase.

M-CDK activation then triggers the progression through the G2/M transition and the events of early mitosis, leading to the alignment of sister chromatid pairs at the equator of the mitotic spindle.

the sister chromatids condense outside the nucleus

-mitotic spindle assembles between the two centresomes (which have been replicated and moved apart)

-starts abruptly with the breakdown of the nuclear envelope

-chromosomes attach to spindle microtubules via their kinetochores and undergo active movement

-Chromosomes are aligned at the equator

-the kinetochore microtubules attach sister chromatics to opposite poles of the spindle

sister chromatids separate to form 2 daughter chromosomes

-the kinetochore microtubules get shorter and the spindle poles move apart

-2 daughter chromosomes arrive at the poles of the spindle and decondense. A new nuclear envelope forms around each set

-five subunit protein complex, related to cohesin that holds sister chromatids together. forms a ringlike structure that uses the energy provided by ATP hydrolysis to promote the compaction and resolution of sister chromatids

to duplicate the vast amount of DNA in the chromosomes and then segregate the copies into two gentically identical daughter cells

Triggers the essential processes of the cell cycle; such as replication, mitosis, and cytokinesis

- "rotates" triggering essential processes when it reaches specific transitions .

-information about the completetion of cell cycle events as well as signals from environment can cause the control system to arrest the cycle at these transitions

1) Dependent on cyclins

2) CAK phosphorylates an AA near entrance of CDK active site which increases CDK activity

3) Binding of CKIs inactivate CDK

4) No inhibitory phosphates (wee1) but yes cdc25

-triggers the metaphase to anaphase transition

-the APC/C is the key regulator in this transition

-protein destruction leads to final stages of cell division

-can only occur once to prevent damaging effects of gene ampiflication

Initiation phase is divided into two parts/steps

1) occurs in late mitosis and early G1; pair of inactive DNA helicases are loaded onto ORC, forming the pre rc initiation of dna synthesis is permitted only at origins containing pre rc.

2) occurs in s phase; when dna helicases are activated, results in unwinding of dna and initiation of synthesis

-once the two helicases move out from the origin, that origin cannot be activated again until a new pre rc is formed at the end of mitosis

held together by cohesins

-cohesins are deposited along the length of each sister chromatid as dna is replicated in s phase

-results also in part from dna catenation, the intertwining of sister dna molecules that occurs when two replication forks meet during dna synthesis

interpolar: positive ends of microtubules that overlap in the midzone

Kinetochore: attach to the stister chromatids at their centromere

Astral: radiate outwards to the cell cortex to help position the spindle in the cell

Once per cell cycle

The shield over the scissors, inhibits separase

when activated they act as scissors which cut the cohesions to allow chromosomal segregation.

clevage furrow is the invagination of the membrane which depends until it pinches into two. This force doing this is driven by the contractile ring which fuctions with actin and myosin 2.

starts cytokinesis in plant cells by building a new cell call down the cortex

dynamic cytoskeletal filaments organized bu kinesins and dynein

The pericentriolar matrix (amorphous material the centromere consists of) nucleates a radial array of microtubules, with their fast growing ends pointing outwards and their minus ends connected to the centrosome.

Kinesin 5: Attaches at interpolar overlap sites and walks towards the positive ends pushing them past each other

Kinesin 14: minus bound, they cross link antiparallel interpolar and pull the poles together

Kinesin 4/10: links to the chromosome and brings it to the plus end to line it up by the equator

Dynein: minus bound, works on the atral. helps maintain location and shape

The microtubules are constantly changing throughout the cell cycle.

Interphase the microtubules are long while in metaphase and prometaphase their half decreases significantly.

-Controlled by MAPS that destabilize plus ends

-they attach at the kinetochore to kinesin 14, depends on ndc80 which links the kinetochore and microtubule together

sister chromatids are positioned back to back do it is unlikely that the kinetochore facing the other side will connect with the wrong microtubule.

If a mistake does happen this fix it with trial and error mechanisms

during metaphase; cohesiens resist the poles tension during the metaphase/anaphase transition APC/C complex targets securin for destruction which activates seperase which can cut the cohesins and allows the poles to pull the chromatids apart

APC/C targets secruin for destruction, which activates separase, which cuts cohesins, which allows chomosomal segregration to occur

This checkpoint makes sure the the cell does not go into anaphase unless the proper bi-orientation has been achieved.

-any kinetochore not properly attached sends out a signal that blocks cdc20/APC/C activation throughout the cell.

work together to form the contractile ring

a new cell wall is formed down the cortex by phargoplasts

in late m phase APC/C dependent cyclin destruction occurs deactivating CDK which triggers the late stages of mitosis, promotes cytokinesis, and enables a new cell cycle to start.

to suppress during g1 depends on an increased number of CKIs which when bound to CDK keeps it inactive