Cytoskeleton and Muscle Contraction: BMB 252 Exam 2 Practice, Exams of Biomechanics

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BMB 252 EXAM 2 PRACTICE QUESTIONS AND

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What kinds of filaments does the cytoskeleton consist of? - SOL intermediate filaments microtubules actin filaments Which type of filaments line the nucleus? - SOL Intermediate filaments line the inner face of the nuclear envelope providing mechanical structure Which type of filaments line the plasma membrane? - SOL Actin filaments are a layer under the plasma membrane providing for strength and shape of the lipid bilayer Which types of filaments make the mitotic spindle? - SOL microtubules Which type of filaments make the contractile ring in cell division? - SOL Actin filaments What are the advantages of having filaments vs. protofilaments? - SOL Filaments have higher thermal stability a single Protofilaments is thermally unstable multiple protofilaments are thermally stable What is nucleation? - SOL formation of a new filament from the subunits; need proteins to help which filament helps to change the shape of a cell when it moves? - SOL actin filaments are necessary for cell movements A filament is most likely to disassemble ___ - SOL by subunits breaking off at the end

Which end is more dynamic: plus or minus? - SOL plus end adds and loses subunits faster Which filament can bind and hydrolyze ATP? - SOL Actin filaments Which form of subunit: ATP- or ADP-bound is easier to dissociate? - SOL ADP-bound are easier to dissociate Which end: plus or minus will most likely have ATP form of the subunit? - SOL plus end What is treadmilling? Which end grows and which end shrinks in treadmilling? - SOL Treadmilling- when the plus end grow and the minus end shrinks at the same rate so the length of the filament (actin or microtubules) stays the same Where are the actin filaments nucleated? - SOL at or near plasma membrane What is the cell cortex? - SOL layer beneath cell membrane, the actin filaments in the cortex determine the shape and movement of the cell surface What protein complexes can promote actin filaments nucleation? - SOL ARP complex (actin related proteins) and formins What kind of actin assembly is nucleated by each of those complexes? - SOL ARPS- formation of branched structures formins- formation of straight, non-branched actin filaments (which can form parallel bundles) At which end do ARPs nucleate actin? - SOL nucleate at minus end so that the plus end can still grow How are the branched structures formed by actin filaments? - SOL attach to the side of actin filaments ARPs are associated with the structures at the leading edge of the migrating cells

How do formins promote actin nucleation? - SOL they catalyze the straight, unbranched actin filaments, which can form parallel bundles How is the subunits pool kept in the cell? What is the mechanism of its regulation? - SOL one protein locks actin monomers in the state when they can't bind to filaments another protein allows actin monomers addition to the chains which of the following helps to organize the contractile ring in mitosis? ARPs Formins - SOL formins What is the source of energy for motor proteins movement? - SOL energy from ATP hydrolysis What kind of cargo can motor proteins move? - SOL membrane-enclosed organelles golgi stacks secretory vesicles RNA What are the three kinds of motor proteins? Which filaments do they use for movement? - SOL Myosins- actin filaments kinesins- microtubules dyneins- microtubules which type of cytoskeletal filaments is not associated with motor protein movements? - SOL intermediate filaments What kind of structure does myosin II have? - SOL 2 heavy chains plus 2 light chains heavy chains have globular head domains (ATPases) and extended coil- coil domain (for dimerization) Which domain of myosin motor proteins is common for all of them? - SOL motor domain

Which type of myosin can transport cargo? - SOL myosin 5 carries cargo on actin filaments towards the + end Which type of myosin is responsible for the muscle contraction? - SOL myosin 2 Which conformation of myosin filament is responsible for the stiffness of death (rigor mortis)? - SOL myosin heads attached to the filament myosin II is a _____ cytoskeletal filament Motor protein - SOL Motor protein what are the steps of myosin movement - SOL myosin head attaches to actin ATP binds to myosin and the myosin head releases actin After ATP hydrolysis; the myosin head swings to the right myosin head binds again and phosphate is released (force-generating step/power stroke) ADP is released; myosin head returns to original conformation Which of the following is a cell: a muscle fiber or a myofibril? - SOL muscle fiber (made up of many myofibrils) which step is associated with the physical movement of myosin along actin (power stroke)? - SOL release of the phosphate (forces the power stroke) What is a sarcomere? - SOL contractile unit of a muscle fiber What forms the light and the dark bands of a sarcomere? - SOL dark bands-mostly composed of thick filaments of myosin II light bands- mostly composed of actin What is a function of the z-disc? - SOL is a place of attachment of actin filaments plus end. Which molecule functions as a molecular spring? - SOL protein titin

allows muscle fiber to return to its initial state which of the following is responsible for the dark bands appearance? - SOL myosin Which molecule can stabilize the actin filament or block its binding to myosin heads? - SOL tropomyosin Which calcium-binding protein regulates the tropomyosin position? - SOL troponin At which Ca concentration, low or high, does troponin pull tropomyosin and make it block myosin binding? - SOL low ca2+ In a resting muscle, protein complex troponin pulls tropomyosin from its normal binding groove into a position that interferes with myosin heads muscle contraction with high ca2+ environment - SOL in a contracting muscle, calcium concentration causes troponin to release tropomyosin. tropomyosin slides into a position that does not interfere with myosin binding myosin heads move along actin filament and muscle contracts What compartment is used as a source of calcium for muscle contraction? - SOL stored in the sarcoplasmic reticulum What system allows a signal from nerve to spread fast to reach each myofibril simultaneously? - SOL motor neurons transmits an action potential to muscle cells Which neurotransmitter spreads a signal from a motor nerve to a muscle cell? - SOL acetylcholine at the synaptic cleft What kind of receptor on a muscle cell does it interact with? What kind of effects does this interaction cause? - SOL nicotinic acetylcholine receptors ligand-gated ion channels and when bound to acetylcholine, they open and allow sodium to flow in and potassium ions flow out of muscle's cytosol

this process produces a local depolarization of the muscle cell and spreads into the T tubules Which ion is released from the T tubules? What is the effect of this? - SOL releases large amounts of calcium and initiates muscle contraction Which subunit of the tubulin can hydrolyze GTP? - SOL beta tubulin Which form of subunit: GTP or GDP bound is easier to dissociate? - SOL GDP since they are curved and lose their lateral connections GTP- straight GDP- curved Which end: plus or minus will most likely have GTP form of the subunit? - SOL plus GTP bound plus end is more likely to be stable and add more subunits What is dynamic instability? Catastrophe? Rescue? - SOL Dynamic instability is the state of constant addition or subtraction of subunits When the end has GTP, it will most likely add subunits. This is called rescue. When the end has GDP, it will most likely shrink. This is called catastrophe. which filament is the hardest to bend? microtubule actin intermediate filament - SOL microtubule Which protofilaments are more straight: that consist of GTP or GDP? Which of themdissociate easier? - SOL GTP filaments are straighter, more stable, and more likely to add subunits

Where are microtubules nucleated? At which end, plus or minus? What serves as atemplate for assembly of new tubulin subunits? - SOL nucleated at the microtubule organizing center (MTOC) at the minus ends the gamma-tubulin ring complex (gamma-TuRC) serves as the template What is the centrosome? Where is it located? - SOL microtubule organizing center near the nucleus the microtubules emanate from the centrosome in an astral conformation What is the centrosome composed of? - SOL a fibrinous centrosome matrix and two centrioles microtubules organizing center serves to ____ - SOL overcome a problem of inefficient nucleation of filaments What are the centrioles made of? - SOL bundle of modified microtubules Do all cells have centrioles? - SOL no, most plant cells and fungal cells do not Where are the microtubules nucleated in the absence of centrioles? - SOL microtubules organizing center alternating growing and shrinking of the plus end is called _____ dynamic instability treadmilling - SOL dynamic instability What is the function of the centrosome? - SOL Essential for movement of chromosomes during cell division; organization of microtubules in cytoskeleton How is the distance between microtubules regulated? Which proteins are responsible for it? - SOL Microtubule associated proteins (MAPs) bind to the sides of the microtubules and regulate how close two filaments can get to each other Proteins responsible are MAPs, MAP2, and tau.

which of the following does not move across microtubules myosin kinesin dynein - SOL myosin Which proteins stabilize and destabilize microtubules and what is the mechanism? - SOL MAPs stabilize (grow) microtubules and catastrophe factors destabilize them Which proteins stabilize and destabilize actin and what is the mechanism? - SOL tropomyosin stabilizes and cofilin destabilizes What are the nuclear intermediate filaments? - SOL nuclear lamins line the interior of the nuclear envelope in all eukaryotic cells Make some examples of intermediate filaments involved in muscle, epithelial, and neural tissues. - SOL epithelial- keratin filaments (hair and nails) neural tissues- axons and glial cells muscle- desmin Which protein crosslinks intermediate filaments? - SOL plectin links intermediate filaments to each other, actin filaments, microtubules, and cell membrane structures What are the phases of cell cycle? - SOL G1, S, G2, M What happens during G1 - SOL cell grows and chromosomes replicate What happens during S phase - SOL DNA replication what happens during G2 - SOL cell growth and preparation for division what happens during m phase - SOL mitosis true or false: neuron cells do not divide - SOL false

true or false: mitosis is the longest stage of the cell cycle - SOL false mitosis=shortest synthesis=longest What are the stages of M-phase? - SOL prophase, prometaphase, metaphase, anaphase, telophase What is cytokinesis? - SOL division of the cytoplasm a part of cytokinesis happens during _____ M-phase mitosis all of the above - SOL all of the above starts during anaphase in mitosis Which phases are part of interphase? - SOL G1, S, G What is the name of resting phase? - SOL G0 - only phase in which cells can exit What is the name of a point in cell cycle when a cell commits to division? - SOL Restriction point during late G is cell cycle conserved? What is cell cycle control system for? - SOL the cell cycle is conserved in eukaryotes to provide a certain amount of time for each event and make sure the events occur in order Which stages of cell cycle will not start before a cell passes the checkpoint? - SOL G1 and G What are checkpoints and at what time during cell cycle do they take place? - SOL checkpoints to ensure the cell can divide properly start checkpoint (late G1)- is environment favorable and is DNA damaged?

late G2- is all DNA replicated and is environment favorable? Metaphase checkpoint- are the spindles properly assembled? At which stages of cell cycle do checkpoints for DNA damage take place? - SOL At the G2/M transition before entering mitosis What happens if a cell did not pass a checkpoint? - SOL apoptosis Do checkpoints generally operate through negative or positive signals? - SOL negative signals will half the cell cycle if it is not properly completed What are the key proteins responsible for cell cycle control system? - SOL cyclin and cdk (cyclin dependent kinase) cyclins go through cycles of synthesis and degradation The binding of which proteins activate Cdks? - SOL Cdks are activated when they bind cyclin. cdks activate other proteins by adding phosphate groups Does Cdk concentration change during cell cycle? - SOL Cdk concentration remains the same throughout the cell cycle. Does cyclin concentration change during cell cycle? - SOL cyclin concentration changes throughout the cycle Does Cdk activity change during cell cycle? - SOL Cdk activity DOES change during the cell cycle, depending on how much cyclin is available to activate it. What is the mechanism of activation of Cdk by cyclin? - SOL the binding of a cyclin removes the block from the active site of Cdk Cdk-activating kinase (CAK) can further increase Cdk what can addition of phosphate group do to the cyclin-Cdk activity? - SOL phosphorylation at a different location has inhibitory effects

What are the mechanisms of Cdk activation? - SOL cyclin binds --> cdk activating kinase phosphorylates cyclin-cdk complex --> cdc phosphatase removes inhibitory phosphate and cdk becomes activated which of the following are true cyclin is always in a complex with Cdk there are both inhibitory and activating phosphates on a Cdk cyclin is a kinase that phosphorylates cdk none of the above - SOL there are both inhibitory and activating phosphates on a Cdk What does ubiquitin ligase do? - SOL adds ubiquitin chains which marks proteins for destruction What is anaphase promoting complex (APC)? - SOL an ubiquitin ligase that causes degradation of cyclins and deactivation of cdks The proteolysis of which cyclin can APC initiate? - SOL M cyclin Proteolysis by APC happens by ______ - SOL addition of ubiquitin chains that signal for a protein to be degraded by a proteasome Does APC activity change during cell cycle? - SOL Yes, it goes up and down depending on the stage of the cell cycle. when cyclin M-Cdk reaches a certain level, it activates its own destruction by Cdc20-APC and then can drop once cyclin is gone How is M-Cdk kept inactive until the start of mitosis? - SOL an inhibitory phosphate is attached What happens in S-phase? - SOL DNA replication Which cyclin-Cdk activation is needed for the S-phase events to take place? - SOL s-Cdk controls initiation Which protein occupies replication origin throughout the cell cycle? - SOL ORC (origin recognition complex)

What is the name of a helicase complex and when does it assemble at origin? - SOL Mcm helicase assembles during G What is pre-replicative complex? When does it assemble in cell cycle? - SOL preRC consists of ORC, Cdc6, and Mcm and assembles during G Which events prevent the assembly of pre-replicative complexes in S phase? - SOL Cdc 6 is phosphorylated, and disassembled from ORC which degrades ORC is phosphorylated and can't bind Cdc6 and Mcm anymore What is necessary for a cell to pass the G2 checkpoint? - SOL replication must be complete and no DNA damage What is the mechanism of M-Cdk inhibition until the cell passes the G checkpoint? Which phosphatase is involved? - SOL M-Cdk is inhibited by inhibitory phosphate till replication is complete cdc25 will removed the inhibitory phosphate What are the two processes of M-phase? - SOL mitosis and cytokinesis What are the stages of mitosis? - SOL prophase, prometaphase, metaphase, anaphase, telophase What happens to chromosomes at each stage of mitosis? - SOL prophase: chromosomes condense prometaphase: nuclear envelope breaks so chromosomes are able to attach to spindle microtubules metaphase: chromosomes are aligned at the equator of the spindle anaphase: sister chromatids separate to form 2 daughter chromosomes (opposite poles) telophase: nuclear envelope reforms around daughter chromosomes at spindle poles

What is the function of condensins? What is the function of cohesins? - SOL condensins helps chromosomes compact during prophase by forming rings around DNA loops cohesions hold the sister chromatids together by forming a ring around them At which stage does nuclear envelope disassemble? Chromosomes condense? Chromosomes align at the equator of a cell? Nuclear envelope reforms - SOL Disassembles during prometaphase chromosomes condense during prophase chromosomes align at the equator during metaphase nuclear envelope reforms during telophase Where do microtubules mostly nucleate in mammalian cells? - SOL Mostly form at centrosomes (MTOC) in animal cells What are the three types of microtubules assembly driving mitosis? - SOL astral, kinetochore, and interpolar Which motor proteins are responsible for pulling the poles to cell membrane? - SOL dyneins and kinesins Which motor proteins keep overlapping microtubules together? - SOL kinesins keep interpolar microtubules together Are microtubules stabilized or destabilized at prophase? Which proteins are responsible for that? - SOL Microtubules are destabilized at prophase, frequency of catastrophes increased

• Stabilized during Interphase (MAPs) which motor proteins form poles connecting to the (-) ends - SOL dyneins What is microtubules behavior at each stage of mitosis? - SOL interphase: microtubules are long and stable, project to the cell wall

prophase: microtubules are destabilized, more of them are formed at centrosomes, spindle poles separate prometaphase: microtubules catch condensed chromosomes by kinetochore once the nuclear envelope breaks down metaphase: microtubules keep chromosomes attached to both poles through kinetochores. microtubules are pulled to both poles anaphase: chromosomes separate and move to the poles telophase: nuclear envelope reforms. Microtubules are back to interphase state At which stage does a checkpoint happen in mitosis? What is it for? - SOL metaphase checkpoint ensures that all chromosomes are attached to the spindle in a correct way anaphase will start only after all kinetochores are correctly connected to the spindle which microtubules assembly would be missing without centrosomes? - SOL Astral microtubule flux is a type of _____ treadmilling dynamic instability - SOL treadmilling What happens with M-Cdk after the checkpoint? - SOL The APC targets the mitotic cyclins for degradation, resulting in the inactivation of M-CdK complexes which initiates the start of anaphase What are the two movements of Anaphase: A and B? - SOL Anaphase A: microtubules shorten and pull separated chromosomes to the poles Anaphase B: poles move apart APC marks _____ for degradation

cyclin M separase condensins - SOL cyclin M In which species are there are no centrioles? - SOL fungi and plants When does centrosome duplicate? - SOL during S phase What does kinetochore bind to on DNA? - SOL spindles How do microtubules bind chromosomes? Which protein complex facilitates this binding? How does the cellular cytoplasm divide in plants? What is the name of new cell wall? Which structure guides its formation - SOL kinetochores bind them A midbody forms because a contractile ring forms made up of actin and myosin filaments in plants, a new cell wall (cell plate) forms between the 2 daughter cells cell plate formation is guided by phragmoplast (leftovers of overlapping microtubules between the poles) When does cytokinesis start? - SOL begins during anaphase and ends right after telophase What is midbody? - SOL region of remaining overlapping microtubules from central spindle helps complete cytokinesis Does the amount of actin and myosin filaments change during contraction of actin-myosin ring in cytokinesis? - SOL yes they both shrink as the ring tightens How are organelles dividing in mitosis? - SOL ER: cut in two and regenerated Mitochondria: separated randomly based on cell energy needs Golgi: fragmented in mitosis and moved to the spindle poles; reconstructed in telophase

How does the cell DNA set (1N, 2N etc.) change during meiosis? - SOL Begins at 2N After S phase, DNA is doubled and it becomes 4N After first division, there's 2 cells with 2N After second division, there's 4 cells with 1N Which chromosomes are homologous? - SOL a set of one maternal and one paternal chromosome that pair up with each other inside a cell during meiosis What are sister chromatids? - SOL 2 identical copies of DNA held together by a centromere What is the longest stage of meiosis? - SOL Prophase I how many of each chromosome are there in a cell that enters meiotic division I? - SOL one paternal and one maternal which chromosomes go to different daughter cells in mitosis? - SOL sisters (identical replication products) What happens in the prophase I? - SOL crossing over Which chromatids go to the different poles in anaphase one? - SOL pairs of sister chromatids go to different poles Which chromatids participate in the cross-over? - SOL All four sister chromatids (two identical copies) participate in the crossover. What holds homologue chromatids together in metaphase I? - SOL chiasmata How are the chromosomes connected along their length at meiotic metaphase II? - SOL cohesions How many chromosomes are there in human? - SOL 46 (23 pairs)

What is crossover? - SOL An exchange of genes between non-sister chromatids of homologous chromosomes (maternal and paternal) What is synaptonemal complex? - SOL The synaptonemal complex initially brings the homologous chromosomes together, facilitating crossover At which stage of meiosis do chiasmata form? - SOL Prophase I What are the stages of prophase I? When does synapsis occur? When do crossovers occur? - SOL leptotene- sister chromatids form visible strands within the nucleus zygotene-SYNAPSIS (coming together) of homologous chromosomes pachytene- tetrad of the chromosomes forms a bivalent. chromosomal crossovers form (chiasmata) diplotene- synaptonemal complex degrades and homologous chromosomes remain tightly bound at the chiasmata diakinesis- (resembles prometaphase of mitosis) nuclear membrane disintegrates into vesicles and meiotic spindle begins to form How does meiosis contribute to genetic variability? - SOL 1. maternal and paternal chromosomes are combined in different ways in gametes

2. exchange of genes between paternal and maternal chromosomes If an organism has 3 pairs of chromosomes, how many gametes can it produce (without taking crossovers into account)? - SOL 2^n (n=number of chromosomes) 2^3=8 different gametes What would be the problem with meiosis in an organism that has reduced frequency of cross-overs? - SOL There would be decreased genetic variation and the homologous chromosomes might break up before they line up along the cell equator in Metaphase I

What are the major classes of signaling molecules that regulate organ sizes? - SOL Mitogens: stimulate cell division by triggering G1 Cdk/ S Cdk Growth factors: stimulate cell growth (an increase in cell mass) survival factors: suppress cell death (apoptosis) Growth factors mostly activate __________ GPCR or RTK - SOL RTK What is mitogen? What would happen with the cell in the absence of mitogens? - SOL Mitogens stimulate G-Cdk and/S-Cdk. In the absence of this signal, cell division is blocked. What is intrinsic control over cell cycle? - SOL cyclins and checkpoints which of the following is a cancer suppresser myc G1-Cdk Rb - SOL Rb What is the function of Myc? - SOL Myc is a transcription regulatory protein If it is overexpressed, uncontrolled division can occur, making it an oncogene. What is the name of an activator of the majority of S-phase gene? - SOL G1-Cdk phosphorylates Rb, causing it to dissociate from E2F, leading to progression into S. What is the name of an inhibitor of the above activator? In which phase of the cell cycle would the cells be if the inhibitor was present? - SOL Rb is the inhibitor of E2F. If this inhibitor was present, the cell would be stuck in G1. At which checkpoint does P53 play a role? - SOL late G

is concentration of P53 high or low in the absence of DNA damage? - SOL low What is the mechanism of P53 activation? - SOL Phosphorylation of p blocks its binding to Mdm p53 accumulates to high levels and stimulates transcription of the gene that encodes the CKI protein p The p21 binds and inactivates G1/S-Cdk and S-Cdk complexes arresting the cell in G1. What gene does P53 activate? - SOL p21 gene at the regulatory region What is the function of a protein, expressed from P21 gene? - SOL G1-Cdk and S-Cdk inhibitor what is programmed cell death called? - SOL apoptosis Which of the following is a gene regulatory protein P P G1-S Cdk - SOL p What is the difference between apoptosis and necrosis? - SOL apoptosis is a programmed cell suicide necrosis is when a cell bursts and leads to apoptosis which checkpoint mostly protects us from cancer? - SOL late G What intracellular machinery is responsible for apoptosis? - SOL procaspases can be activated by active caspases which can cleave multiple substrates and cause apoptosis Are caspases synthesized in response to an apoptosis signal, or does the cell have a stock ofthem? - SOL cells have caspases stocked How is the caspases stock kept inactive? - SOL They constantly receive suppressing signals.

How are the first caspases activated in apoptosis? - SOL Extracellular signal promotes aggregation of procaspases at the cell surface. Procaspases start to cleave each other when they are aggregated (induced proximity) How are procaspases brought together in the extrinsic apoptotic pathway?

• SOL extracellular signal promotes aggregation of procaspases at the cell surface Which mitochondrial protein is released in the cytoplasm during the intrinsic pathway of apoptosis? - SOL cytochrome C What is the mechanism of bringing procaspases together in the intrinsic pathway? - SOL Procaspases are triggered by induced proximity, procaspases are forced together cleaving each other. They are brought together by cytochrome C which leads to the apoptosis wheel.