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Cell Bio Test #4
The cytoskeleton, intracellular transport, cell motility, DNA, the cell cylce
| Question | Answer |
|---|---|
| What is the cytoskeleton? | the skeleton of the cell composed of microtubules, microfilaments, and intermediate filaments |
| microtubule characteristics | -long hollow tubes -largest cytoskeleton component (25 nm) -used for long-range transport -inherent polarity -composed of a and B tubulin monomers -2 main types: cytoplasmic and axonemal |
| Formation of microtubule Step #1 | a and B tubulin monomers associate into heterodimers |
| Formation of microtubule Step #2 | heterodimers associate into 13 protofilaments |
| Formation of microtubule Step #3 | protofilaments associate into tube |
| cytoplasmic microtubule utilization | -cell shape and morphology -cell division (mitotic spindle) -long-range intracellular transport |
| axonemal microtubule utilization | -cellular movement -found in cilia, flagella |
| What does the colchicine binding domain do? | prevents assembly/addition to microtubule |
| What does acetylation do? | makes microtubules more stable |
| What does tyrosination do? | makes microtubules more dynamic |
| 1 microtubule polymer | singlet |
| 2 microtubule polymers | doublet |
| 3 microtubule polymers | triplet |
| The lag phase of microtubule polymerization/assembly is ___. | slow |
| Lag phase process | a and B dimers -> heterodimers -> oligomers -> nucelation begins |
| The elongation phase of microtubule polymerization/assembly is ___. | fast |
| Elongation phase process | oligomers -> protofilaments -> microtubule by adding a and B to both ends |
| What is the plateau phase of microtubule polymerization/assembly? | microtubule is stable with growth/polymerization and shrinking/depolymerization on both ends |
| What is critical concentration? | -basically equilibrium -[free tubulin subunits] at which the addition and subtraction is equal at both ends of the microtubule |
| The plus end | faster growing |
| The minus end | slower growing; loses more than the plus end |
| What is treadmilling? | when the loss at the - end and addition at the + end makes it look like the microtubule is moving |
| high [free tubulin] | -GTP subunits are added to plus end -> formation of GTP cap -GTP cap promotes growth/polymerization |
| low [free tubulin] | -GTP is hydrolyzed -GTP cap is depleted -> GDP-rich microtubule -catastrophe -possible rescue |
| What is catastrophe? | when the microtubule begins to dissasemble: protofilaments peel apart and break off |
| What is rescue? | rapid growth after catastrophe |
| This is the microtubule organization center/where all microtubules radiate from, also called the centrosome. | MTOC |
| These are always in pairs in the centrosome and are where new microtubules grow from. | centrioles |
| This acts like the centrioles. | y tubulin |
| What do Tan subunits do? | bundle microtubules within axons |
| What is a + TIP? | a tip interacting protein that interacts with the + end of microtubules |
| What can + TIPs do? | mark growing + ends of microtubules |
| What are examples of + TIPs? | EB1, CLIP-170 |
| What is MCAK? | a motor protien that binds the the + end and promotes catastrophe |
| What are katanins? | proteins that promote dis-assembly by cutting microtubules |
| Characteristics of microfilaments | -smallest cytoskeleton component (7 nm) -inherent polarity -made of 2 polymers of actins |
| Roles of microfilaments | -muscle contraction -cell locomotion -cytokinesis -cytoplasmic streaming -cell shape |
| Structure of microfilaments | 2 polymers of G-actin monomers in F-actin chains twisted into one strand |
| Which end of microfilaments grows faster? | barbed/+ end |
| Which end of microfilaments grows slower? | pointed/- end |
| Drugs that prevent addition to + ends of microfilaments | Cytochalasin D, Latrunculin A |
| Drugs that stabilize microfilaments | Phallodin |
| Which type of microfilament network is involved in contraction? | contractile bundles |
| Which type of microfilament forms a mesh network to stabilize the cell? | gel |
| Which type of microfilament network helps with cell movement? | parallel bundles |
| This type of actin-binding proteins can promote or prevent polymerization of microfilaments. | polymerization proteins |
| These are types of polymerization proteins that prevent polymerization of microfilaments. | Profilin, Thymosin B |
| These are types of polymerization proteins that promote polymerization of microfilaments. | ADF, Cofilin |
| This type of actin-binding proteins help stabilize microfilaments. | capping proteins |
| This is a type of capping protein that binds to the barbed/+ end to help stabilize microfilaments. | CapZ |
| These are types of capping proteins that bind to the pointed/- end to help stabilize microfilaments. | Tropomodulins |
| This type of actin-binding proteins cuts microfilaments. | severing proteins |
| This is a type of severing protein that cuts caps. | gelsolin |
| This type of actin-binding proteins make microfilament mesh works. | crosslinking protiens |
| This is a type of crosslinking protien that brings filaments together into a network. | filamin |
| This type of actin-binding proteins bundle microfilaments into contractile or parallel bundles. | bundling proteins |
| Examples of bundling proteins | facin, a-actin |
| This type of actin-binding proteins link microfilaments/actin to the plasma membrane. | anchoring proteins |
| This type of anchoring protein runs along the edge of the plasma membrane inside the cell. | spectrin |
| Other examples of anchoring proteins | ankyrin, Band 4.1 |
| This type of actin-binding proteins form branches off existing microfilaments which can stimulate cell movement. | branching proteins |
| Types of branching proteins | Arp 2/3, WASP |
| Arp + G-actin + WASP | Arp 2/3 complex |
| Process of promoting branch growth in microfilaments | WASP + Arp 2/3 -> activated complex -> nucleation/growth of branch |
| What are the Rho family GTPases involved in? | binding and redulating actin-binding proteins |
| Examples of Rho family proteins | Rho, Rac, Cdc42 |
| Rho family process | Cdc42 -> WASP -> Arp 2/3 -> branch nucleation |
| Intermediate filament characteristics | -intermediate sizes (8-12 nm) -can be made of different types of proteins -made up of 8 protofilaments joined end to end with staggered overlaps -stable/don't grow |
| Types of intermediate filaments | keratins, vimentin, neurofilaments, nuclear lamins |
| What do keratins make up? | hair, feathers, skin, nails, horns, etc. |
| What is vimentin used for? | cell shape |
| What are neurofilaments used for? | axon structural support |
| What are nuclear lamins do? | compose the nuclear envelope |
| Assembly of intermediate filaments | dimers -> tetramers -> 8 protofilament -> intermediate filament |
| Intracellular transport is ___-___, or ____ ____. | ATP-dependent, active transport |
| Microtubule-based motility is ____ ____. | long range |
| What are the types of microtubule motor proteins? | kinesins, dyneins |
| Actin (microfilament)-based motility is ___ ___. | short range |
| What is the microfilament motor protein? | myosin |
| Microtubule motor proteins are also called ____ because they can hydrolyze ATP, or ____. | ATPases, enzymes |
| Dyneins | always move towards - ends of microtubules |
| What are the types of dyneins? | cytoplasmic, axonemal |
| Kinesins | can move towards - or + ends of microtubules |
| This type of kinesin moves its cargo only towards the + ends of microtubules. | kinesin 1 |
| This type of kinesin moves its cargo only towards - ends of microtubules, and it is also involved in mitosis and meiosis. | kinesin 14 |
| What are the main functions of microtubule motor proteins? | -axonal transport -form spindle in mitosis -vesicle movement -viral trafficking -microtubule sliding -structure |
| What is the basic structure of kinesin? | -2 heavy chains dimerized together form basis of the motor -2 light chains dimerized and bound to heavy chains form tail domain |
| This domain of kinesin is the "walking" part where ATP binds and is hydrolyzed so the kinesin can bind to the microtubule. | motor domain |
| This kinesin domain in involved in cargo binding. | tail domain |
| What is the basic structure of dynein? | -2 heavy chains dimerized -intermediate chains -motor domain -dynactin |
| What does dynactin do? | it binds to actin |
| What is anterograde transport? | cell body -> |
| What is retrograde transport? | cell body <- |
| What is the 9 + 2 axonemal arrangement? | a central pair of microtubules surrounded by 9 outer doublets |
| What do the radial spokes do in the axoneme? | they connect the doublets to the central pair |
| This structure in the axoneme slides the microtubules against each other which allows the movement of cilia or flagella. | dynein arms |
| THis structure in axonemes anchors the microtubules in a central point. | basal body |
| What is situs inversus viscerum? | a ciliopathie where all organs are reversed in the body |
| These are types of disorders caused by defects in cilia or flagella. | ciliopathies |
| What is Kartageners triad/syndrome? | a ciliopathie with 50% organ reversal |
| What are types of ciliopathies caused by deffects in the dynein arms? | male sterility, situs inversus viscerum, and Kartageners triad/syndrome |
| What are types of ciliopathies linked to basal body or cilia genes? | BBS, PKD, and polydactyly |
| What are sarcomeres? | segments that make up myofibrils |
| What are myofibrils? | muscle cells |
| This part of the sarcomere is made up of actin. | thin filaments |
| This part of the sarcomere is made up of myosin. | thick filaments |
| What are Z lines? | the edges of a sarcomere that define it, barbed ends |
| What is the A band? | the length of a thick filament |
| What is the H zone? | the area between thin filaments in a sarcomere |
| What is the M line? | it runs directly down the center of a sarcomere to hold the thick filaments together |
| What is the I band? | the area between two A bands |
| What is the bare zone? | the area on a thick filament with no myosin |
| What does the protein tropomyosin do? | it helps stabilize actin |
| What makes up the troponin complex? | TnI, TnC, and TnT |
| What is cross bridge formation? | when myosin forms a "bridge" with actin using power from ATP hydrolysis |
| Contraction relying on ATP hydrolysis step #1 | cross bridge formation |
| Contraction relying on ATP hydrolysis step #2 | power stroke ADP release |
| Contraction relying on ATP hydrolysis step #3 | ATP binds myosin and myosin becomes detached from actin |
| Contraction relying on ATP hydrolysis step #4 | ATP hydrolysis |
| low [Ca +2] | relaxed state where troponin complex and tropomyosin block actin from binding myosin |
| high [Ca +2] | contracted state where Ca +2 binds to TnC and allows actin and myosin to bind |
| This is the space/meeting place between a neuron and a motor cell. | neuromuscular junction |
| This is the are of muscle near the neuron. | motor end plate |
| What is the sarcolema? | where the motor end plate meets the neuron |
| What is the T tubule system? | tubes that allow the action potential to continue from nerves to myofibrils |
| What is the sarcoplasmic reticulum? | muscle form of the ER that stores Ca +2 |
| What is the 5' end structure? | free phosphate group on 5' carbon |
| What is the 3' end structure? | free OH group on 3' carbon |
| How many H-bonds are between A and T? | 2 |
| How many H-bonds are between C and G? | 3 |
| What is B DNA? | typical double helix form |
| What is Z DNA? | appears under special conditions; longer, stretched out |
| What is A DNA? | appears under special conditions; shorter |
| When is DNA supercoiled? | for storage |
| These enzymes can uncoil DNA or unwind the helix. | topoisomerases |
| These are the basic chromatin units. | nucleosomes |
| DNA wraps around theses to form nucleosome beads. | histones |
| These form the histone octamer (one bead). | H2A, H2B, H3, and H4 |
| This interacts with linker DNA between beads. | H1 |
| These are packaged into chromatin. | nucleosomes |
| What is euchromatin? | the looped domains of chromatin |
| What does chromatin condense into? | chromosomes |
| This is euchromatin coiled tightly together. | heterochromatin |
| This is made up of nucleoporins. | nuclear pore complex |
| These line the inside of the nuclear pore complex and help larger molecules enter and exit the nucleus. | transporter proteins |
| What is NLS? | nuclear localization signal |
| What does importin do? | escorts NLS-labeled proteins to nucleus |
| What is NPC? | nuclear pore complex |
| What is Ran? | a monomeric G protein |
| What is GEF? | guanine nucleotide exchange factor |
| What is GAP? | a GTPase activating protein |
| Import to nucleus step #1 | importin recognizes NLS and binds to it on the protein |
| Import to nucleus step #2 | importin escorts protein into nucelus |
| Import to nucleus step #3 | Ran-GDP -> GTP |
| Import to nucleus step #4 | Ran-GTP (activated) interacts with importin and NLS protein is released in nucleus |
| Import to nucleus step #5 | Ran-GTP escorts importin out into cytoplasm |
| Import to nucleus step #6 | GAP -> GTP hydrolysis releases importin into cytoplasm |
| Import to nucleus step #7 | NTF2 escorts Ran-GDP back into nucelus |
| Export from nucleus step #1 | Ran-GDP -> GTP (activated) |
| Export from nucleus step #2 | Ran-GTP binds exportin |
| Export from nucleus step #3 | Ran-GTP-exportin binds protien with NES |
| Export from nucleus step #4 | transport of NES out of nucelus |
| Export from nucleus step #5 | GAP -> GTP hydrolysis (inactivates Ran) |
| Export from nucleus step #6 | exportin and NES are released |
| Export from nucleus step #7 | NTF2 escorts Ran-GDP back into nucleus |
| Export from nucleus step #8 | exportin goes back into nucleus |
| What does exportin do? | it escorts NES-labeled proteins out of the nucleus |
| What is the nuclear matrix? | it's the nucleoskeleton composed of fibers that extend from lamina into the nucleus, and is involved in nuclear organization |
| What is the nuclear lamina? | it is a meshwork of lamins (intermediate filaments) that is structural support for the nuclear envelope |
| What are chromosome territones? | they are discrete locations where specific chromosomes reside within the nucleus |
| What is the nucleolus? | the spot where DNA and RNA are concentrated within the nucleus |
| What is denaturation? | the separation of DNA strands caused by an increase in temperature or pH |
| What is Tm? | melting temp dependent on G-C content |
| What is renaturation? | the nucleation and zipping up of DNA strands |
| This part of the cell cycle makes up most of the cell cycle where the cell is preparing for mitosis, and it is made up of the G1, G2, and S phases. | interphase |
| This part of the cell cycle is the division of the cell. | M phase |
| This is the nuclear division of somatic cells. | mitosis |
| This is where the old DNA strand is being taken apart and new strands are being added. | replication fork |
| What are the iniator proteins that bind to replication origins to start DNA replication? | ORC, MCM, helicase loaders |
| What does DNA helicase do? | it unwinds DNA for replication |
| What does DNA gyrase do? | it is a topoisomerase that unwinds supercoiled DNA (caused by DNA unwinding) by cutting |
| These are single stranded binding protiens that prevent rewinding. | SSB |
| This makes an RNA primer. | primase |
| This adds nucleotides to the RNA primer 5'->3'. | DNA polymerase III |
| This removes the RNA primer at the end of replication and replaces it with DNA. | DNA polymerase I |
| This links DNA fragments. | DNA ligase |
| DNA replication step #1 | initiator protien binds to mark the beginning of replication |
| DNA replication step #2 | DNA helicase binds and begins to unwind DNA while DNA gyrase follows it to relax the unwound strands and SSB keeps the strands stable |
| DNA replication step #3 | primase binds and makes an RNA primer so nucleotides ban be added by DNA polymerase |
| DNA replication step #4 | DNA polymerase III and a clamp protein start adding nucleotides to the leading strand |
| DNA replication step #5 | primase binds to make the first RNA primer for the lagging strand |
| DNA replication step #6 | lagging strand synthesis begins in the opposite direction of the leading strand |
| DNA replication step #7 | more RNA primers are made at other points DNA to continue lagging strand synthesis |
| DNA replication step #8 | DNA polymerase I removes the RNA primers and adds DNA to the gaps left by the primers |
| DNA replication step #9 | DNA ligase seals any gaps between lagging strand fragments (Okazaki fragments) |
| What are Okazaki fragments? | the new DNA fragments produced by the lagging strand |
| What are telomeres and what do the do? | they are the non-coding TTAGGG sequence repeated to prevent gene loss |
| What does telomerase do? | it adds telomere sequence to chromosomes |
| What happens during G1 and G2? | cell growth |
| What happens during S phase? | DNA synthesis |
| What are the steps of mitosis (M phase)? | prophase, prometaphase, metaphase, anaphase, telophase, cytokinesis |
| What happens during prophase? | the spindle forms, chromatin condenses into chromosomes, and the nucleolus breaks down |
| What happens during prometaphase? | the nuclear envelope breaks down, the centrioles go to opposite poles, and the chromosomes attach to the spindle |
| What happends during metaphase? | the chromosomes line up in the middle of the cell along the metaphase plate |
| What happens during anaphase? | sister chromatids separate |
| What happens during telophase? | the nuclear envelope reforms, nucleoli start to reappear, the chromosomes condense back into chromatin, and the spindle breaks down |
| What happens during cytokinesis? | the cytoplasm of the parent cell is divided between the new daughter cells |
| These are short microtubules located at the centrosome and involved in positioning the spindle. | astral microtubules |
| These microtubules physically attach to the kinetichores of sister chromatids. | kinetochore microtubules |
| These microtubules are part of the spindle that do not attach to chromosomes, but instead overlap and attach to each other by mitotic motors to push the chromosomes to the opposite ends of the cell during anaphase. | overlap microtubules |
| These are enriched in attachment protiens and have motors used in anaphase. | kinetochores |
| What do microtubule motors do? | attach the spindle to the cell cortex, involved in chromosome movement and pushing the microtubules apart during anaphase |
| What are the 3 main time pints within the cell cycle with high levels of regulation? | restriction point right after G0, between G2 and mitosis, and between metaphase and anaphase |
| What does the restriction point after G0 depend on? | GF, nutrients, cell size, and DNA damagme |
| What does the regulation point between G2 and mitosis depend on? | cell size, DNA damage, and DNA replication |
| What does the regulation point between metaphase and anaphase depend on? | chromosome-spindle attachment |
| What do cdks and cyclins do? | regulate the cell cycle |
| MPF driving cell cycle step #1 | cyclin levels increase -> cdk and cyclin associate into MPF |
| MPF driving cell cycle step #2 | inactivating kinase phosphorylates MPF |
| MPF driving cell cycle step #3 | activating kinase phosphorylates MPF |
| MPF driving cell cycle step #4 | phosphotase removes inactivating phosphates -> MPF activated |
| MPF driving cell cycle step #5 | positive feed back loop (increase in activated MPF -> more MPF activation) |
| MPF driving cell cycle step #6 | mitosis |
| What is APC? | anaphase-promoting complex |
| What does cohesion do? | holds sister chromatids together |
| What does separase do? | it's a protease that degrades cohesion |
| What does securin do? | inhibits chromatid separation |
| APC regulation of cell cycle #1 | APC activated |
| APC regulation of cell cycle #2 | APC targets securin for degredation |
| APC regulation of cell cycle #3 | separase degrades cohesin |
| APC regulation of cell cycle #4 | chromatid separation |
| APC regulation of cell cycle #5 | APC targets MPF to degrade cyclin (end of mitosis) |
| What is Rb? | it's a gene expression regulator |
| What is E2F? | its' a transcription factor |
| Restriction point step #1 | S phase genes are off during G1 because Rb and E2F are bound |
| Restriction point step #2 | growth factor -> receptor -> activates Ras pathway -> G1 cdk-cyclin synthesized |
| Restriction point step #3 | G1 cdk-cyclin targets Rb for phosphorylation |
| Restriction point step #4 | phosphorylized Rb dissociates from E2F |
| Restriction point step #5 | E2F transcribes S phase genes -> S phase proteins |
| What does damaged DNA lead to? | the phosphorylation of p53 |
| What does p53 do if the DNA is beyond repair? | it induces apoptosis |
| What does p53 do if the DNA can be repaired? | it arrests the cell to fix the DNA |
| What is apoptosis? | programmed cell death |
| What are EGF and PDGF? | growth factors that promote cell division by Ras pathway |
| What does activation of the Ras pathway do? | it activates the transcription of cell cycle genes |
| Apoptosis step #1 | apoptotic signal -> cell shrinks and chromatin condenses |
| Apoptosis step #2 | DNA fragments while the cell blebs |
| Apoptosis step #3 | phagocytosis |
| What is blebbing? | when apoptotic bodies (cell chunks) fall off a cell during apoptosis |
| What is meiosis? | when a diploid cell undergoes division into haploid cells |
| What is a homologous pair? | paternal and maternal chromosomes that match up |
| What happens in meiosis 1? | separation of homologous chromosomes |
| What happens in meiosis 2? | separation of sister chromatids, essentially mitosis |
| What happens during prophase 1? | same as mitosis prophase, except crossing over may occur at chiasmata and the synaptonemal complex attaches homologous chromosomes together |
| What are chiasmata? | sites where crossing over occurs |
| What happens during metaphase 1? | bivalents line up at the metaphase plate |
| What are bivalents? | chromosome pairs |
| What happens in anaphase 1? | homologous chromosomes separate |
| What happens in telophase 1? | the spindle breaks down and 2 haploid cells are formed with no homologous chromosomes |
| What does meiosis produce? | 4 haploid genetically similar daughter cells |
| What does mitosis produce? | 2 diploid genetically identical daughter cells |
| These are versions of a gene. | alleles |
| This is the location of an allele on a gene. | locus |
| This type of trait is seen most frequently. | dominant |
| This type of trait is seen less frequently. | recessive |
| This is the genetic makeup. | genotype |
| This is the physical appearance dictated by genotype. | phenotype |
| AA | homozygous dominant |
| aa | homozygous recessive |
| Aa | heterozygous |
| What is the Holliday junction? | where DNA strands cross over |
| What is branch migration? | when the Holliday junction moves |
| What does a horizontal cut produce? | mostly recombinant strands |
| What does a vertical cut produce? | all recombinant strands |
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