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194 Cards in this Set
- Front
- Back
Does the cytoskeleton have a large or small surface area?
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large
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Which has a greater surface are, internal membranes or the plasma membrane and how much greater?
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internal membranes, 10x
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True or False. There is a strong correlation between size of genome and complexity of organism.
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false, there is no correlation
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Which 2 domains of life have the smallest genomes?
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bacteria and archaea
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How is genome size measured?
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in nucleotide pairs of DNA per haploid genome
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True or False. The fern has one of the largest genomes.
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True
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True or False. Mammals and reptiles have about the same range of genome size.
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True
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How many bps are in the human genome?
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3 billion bp
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How many times bigger is the human genome than a bacterial genome?
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1000x
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Which technique can be used to identify family members?
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Sequence aligment/conservation
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The conserved stretches shown in the sequence alignment/conservation example allowed for ____________________ to be searched for in databases.
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SH2 domains
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True or False. The Beta hemoglobin subunit is highly conserved.
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True
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T or F. Globins diverged recently in history.
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False. They diverged early on and have been evolving and accumulating changes in parallel.
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What is the end result of alternative splicing?
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generates multiple transcripts of the same gene aka isoforms, increases diversity
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Do males or females posses exon 3 of the sxl gene?
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males
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Sxl undergoes ____ regulation and transformer undergoes ____ regulation
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auto; cross
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Who coined the term 'gene?'
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Wilhelm Johanssen
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What did Morgan determine?
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genes are on chromosomes
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What did Beadle and Tatum propose?
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one gene, one enzyme
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What did Roberts and Sharp discover?
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one gene can make several proteins
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Name the 4 functions of proteins discussed in the intro lecture.
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1 - cell division
2 - mechanical stability 3 - adhesion between cells 4 - cell death |
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Which dye allows for the visualization of dying cells between developing digits?
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acridine orange (dying cells are more leaky)
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TUNEL allows for the visualization of duing cells by labelling ______.
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DNA
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Name the 5 types of covalent modifications discussed in class.
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1 -phosphorylation
2 - glycosylation 3 - acetylation 4 - ubiquitinylation 5 - sumoylation |
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True or False. Phosphate groups are neutral.
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False. They are negatively charged.
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Protein kinases _________ a phosphate group and protein phosphatases ________ a phosphate group.
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add; remove
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T or F. Phosphorylation can both activate and deactivate proteins.
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True
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Describe glycosylation. Which types of proteins are often glycosylated and why?
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- proteins modified through addition of sugar chains
- cell surface proteins, secretory proteins |
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Name the 2 types of glycosylation.
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1) N- linked
2) O-linked |
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How does acetylation affect DNA?
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DNA more accesible upon acetylation
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How many a.a.s long is ubiquitin?
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76 aa
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What is E1? (ubiquitination)
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ubiquitin activating enzyme
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What is E2? (ubiq)
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ubiquitin-conjugating enzyme
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What is E3 (ubiq) and what does it bind to?
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ubiquitination ligase; E2
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How does the ubiquitin E1E2E3 complex modify proteins?
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puts a flag on proteins destined to die
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What does SUMO stand for
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Small Ubiquitin-like MOdifier
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How many SUMO conjugating enzymes are there?
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1 --> UBC9
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Which type of filaments are sumoylated?
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IFs
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Which units are cells, organelles and molecules usually measured in?
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um, nm, nm
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Name the 4 types of light microscopy?
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1 - bright field
2 - phase contrast 3 - differential interference contrast (DIC) 4 - dark field |
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How does DIC generate contrast? What happens to the ray of light? What are phase differences transformed into?
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- by exploiting phase differences
- split in two beams - amplitude differences |
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What takes longer to prepare, SEM or TEM?
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TEM
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How does the immunogold method of EM work?
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antibody linked to colloidal gold particles, high density where proteins located
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T or F. Resolution is proportional to wavelength.
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False. Resolution is inversely proportional to wavelength.
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T or F. Fluorescence microscopy can be used to visualize fixed specimens.
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True. As well as live specimens
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Which has better resolution, conventional or confocal fluorescence microscopy?
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confocal
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What's a problem with confocal fluorescence microscopy and how can it be improved?
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light converges at a small point, use a computer to scan through each plane, store info and generate 3-D image
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Is deconvolution imaging a type of microscopy?
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No, its a ghetto version of confocal but its technically just a software program
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What does FRET stand for?
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Fluorescence Resonance Energy Transfer
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Which type of microscopy for visualizing protein-protein interactions?
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FRET
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How is the FRET signal in budding yeast obtained?
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by exciting CFP but recording fluorescence from YFP, get superimposed image
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What does FRAP stand for?
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Fluorescence Recovery After Photobleaching
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How does AFM work?
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fine tip moves up and down, scans object, looks at repulsion and attraction of atoms
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Which type of indicators are used for FRET?
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fluorescent protein-based Ca2+ indicators
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Rank the cytoplasmic fibers/filaments in order of diameter.
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MT > IF > AF
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What are AFs assembled from?
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actin monomers
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What are MTs assembled from?
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dimeric subunits of alpha and beta tubulin
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What are IFs assembled from?
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large diverse family of proteins including lamins and keratins
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Are MTs, IFs or AFs responsible for stability?
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IFs
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Do MTs, IFs or AFs receive and transmit signals?
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AFs
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Do MTs, IFs or AFs interact with transport molecules, motor proteins and are involved in chromosome segregation?
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MTs
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Do MTs, IFs or AFs determine the shape of the cell's surface and are necessary for locomotion?
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AFs
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Do MTs, IFs or AFs determine the positions of organelles?
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MTs
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Are MTs, IFs or AFs polar?
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MTs and AFs
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Do MTs, IFs or AFs connect to desmosomes?
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IFs
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Do MTs, IFs or AFs include filopodia and lamellipodia?
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AFs
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Are MTs, IFs or AFs involved in cytokinesis?
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AFs
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Are MTs, IFs or AFs involved in the assembly of the mitotic spindle?
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MTs
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Do MTs, IFs or AFs form the nuclear envelope?
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IFs
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Are cilia and flagella composed of MTs, IFs or AFs ?
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MTs
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Are hairs and fingernails composed of MTs, IFs or AFs ?
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IFs
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What happens to platelets when an injury occurs?
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large spread lamellipodium (AF), dramatic shape change due to myosin II mediated contraction, trying to sense environment to see where signal is coming from and migrate towards site of injury
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Are MTs, IFs or AFs involved in the formation of a bud in yeast? Where is the concentration the highest?
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AFs; where pinching is occurring
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Are axons and dendrites filled with MTs, IFs or AFs ?
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MTs
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Is the cortex of the axon lined with MTs, IFs or AFs ?
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AFs
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Are neurofilaments a specialized form of MTs, IFs or AFs ?
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IFs
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Do developing growth cones in neurons utilize MTs, IFs or AFs for extensive branching?
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AFs
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True or False. Actin and tubulin are present in all eukaryotic cells.
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True
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About how many isoforms of actin are there invertebrates?
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~3
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About how many isoforms of alpha and beta tubulin are there in vertebrates?
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~6
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True or False. Yeast and human tubulin are very similar.
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True
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What is the function of accessory proteins?
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catalyze nucleation of filaments, cross-link filaments, link filaments to other cell components, act as motor proteins
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What is the diameter of AFs?
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5-9 nm
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What's another name for AFs?
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microfilaments
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Describe the shape of AFs.
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two-stranded helical polymers of actin; bead-like structure
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What is the MW of an actin monomer?
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42 kD
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How many actin genes to humans have?
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6
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What are the 3 isoforms of actin called?
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alpha, beta, gamma
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Where are AFs often nucleated?
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at the plasma membrane
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When was the crystal structure of AFs solved?
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1990
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How many subdomains does monomeric actin contain?
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4
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True or False. Actin can bind ATP but not hydrolyze it.
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False. It can bind and hydrolyze ATP to ADP.
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True or False. Before polymerization, each actin monomer is bound to ATP.
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True.
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How many protofilaments are in one MT and how are they arranged?
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13; in a circular pattern
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What is the diameter of MTs?
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24 nm
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True or False. Alpha and beta tubulin subunits can bind and hydrolyze GTP.
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False. Both can bind to GTP but alpha is bound tightly and cannot be hydrolyze like beta.
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What happens when a GTP cap is present on a MT?
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growth is favored (dissociation less likely)
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Compare the dissociation rates of GTP and GDP tubulin dimers.
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GTP tubulin dimers have 4 times slower dissociation rate
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At which end of the MT is tubulin with bound GTP located?
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+ end
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Which end of AFs and MTs is the fast-growing end?
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+ end
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Is the + or - end also known as the barbed end?
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+
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What must occur in order for the + end to accept another subunit?
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back end must change conformation (become barbed)
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What must ocurr in order for the - end to accept another subunit?
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subunit must change conformation (become barbed)
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Does Kon or Koff depend on concentration of the monomer?
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Kon
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True or False. AF and MT subunits leave at a constant rate.
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True
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What are association and dissociation of AFs and MTs measured in?
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association - per mole per second
dissociation - per second |
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What is the critical concentration? (Cc)
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when rate of subunit addition equals rate of subunit loss
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T or F. K is inversely proportional to Cc.
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True
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What happens when C > Cc ?
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Kon will be high, polymerization will continue until C = Cc
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What happens when C < Cc?
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Kon will be low, dissociation will occur
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T or F. Cc = Kt/Kd
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False. Cc = Kd/Kt = Koff/Kon
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What is the Cc of the + end?
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0.1 um
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What is the Cc of the - end?
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0.6 um
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At which end is there a lower threshold?
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+ end
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What happens when the concentration of free monomers is intermediate between the Cc values for the - and + ends?
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The filament grows at the plus end wherease shrinks at the minus end --> treadmilling
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What is steady-state treadmilling?
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polymer maintains a constant length
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When does dynamic instability occur?
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When concentration of T subunits is low
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What is catastrophe?
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rapid shrinkage due to accidental loss of GTP cap
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What is rescue?
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rapid growth due to regain of GTP cap
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Is treadmilling preferentially observed in AFs or MTs?
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AFs
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Is dynamic instability preferentially observed in AFs or MTs?
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MTs
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What is the Cc of actin in a test tube?
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< 1 um
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What is the concentration of actin in the cell?
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50-200 um
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What prevents soluble actin monomers from polymerizing into filaments inside the cell?
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sequestering proteins
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What is the protein called that binds and sequesters actin monomers so they are not available for polymerization?
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Thymosin beta4
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What is the name of the protein that promotes filament assembly by binding acting monomer and making them available at the + end?
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profilin
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True or False. Profilin is one of the few actin-binding proteins that allows exchange of ADP for ATP.
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False. It is the only one
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What is the rate limiting step for AF polymerization?
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nucleation
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Where are AFs nucleate in eukaryotic cells?
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at the plasma membrane in the cell cortex
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What are the 3 classes of nucleator proteins?
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Arp2/3 complex, formins, spire
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T or F. Polymerization of AFs occurs more slowly in the presence of oligomers.
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False. More quickly.
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T or F. Arp2 and 3 proteins are very similar to actin.
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True
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How do Arp2 and 3 serve as a template for monomer addition?
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mimic barbed end of growing actin filament
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Where does nucleation of the AF occur?
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at the - end, allowing elongation at the + end
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What happens when the ARP complex binds to the side of a preexisting AF?
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filament branching
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AF branching occurs at what angle?
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70 deg
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How does the absence of nuclei affect AF elongation?
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delays elongation
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How many proteins is the Arp2/3 complex composed of?
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7
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T or F. Arp2 and 3 must be bound to ATP in order to initiate branching.
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True.
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What is a VCA domain and what is its role?
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- composed of an actin-bining, connecting and acidic region
- promotes nucleation and branching |
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Is the VCA domain necessary or sufficient for activation of Arp2/3?
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both
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The VCA domain containing protein is a member of which family?
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WASP family
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The 3 proposed model of how debranching occurs in the Arp2/3 complex consist of which 3 steps, but in different orders?
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- nucleation and elongation
- ATP hydrolysis of Arp2 (possibly Arp3 also) - VCA dissociation |
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Which domains of formins bind actin?
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FH2 domains
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Describe the structure of formins.
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form dimer that has hoop-shaped structure
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Which domains of spire bind to actin?
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WH2 domains
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How to amoebas move?
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Move along cAMP concentration gradient (chemotaxis), exten filopodia
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What types of proteins are gelsolin and cofilin?
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AF severing proteins
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What do CapZ and tropomodulin do?
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stabilize AFs by capping ends
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What do CH-domains do?
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organize AFs into bundles and filaments
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Which are denser, filopodia or lamellipodia?
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filopodia
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What is the MW of gelsolin?
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87 kD
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What is the MW of cofilin?
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15 kD
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Which are arranged in parallel, bundles or networks of AFs?
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bundles
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True or False. Fimbrin is very flexible.
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False. Filamin is
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Crosslinking is facilitated by proteins that are members of which superfamily?
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C-H domain
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Name the 3 bundling proteins.
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- fimbrin
- alpha-actinin - villin |
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Name the 2 gel-forming proteins.
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- spectrin
- filamin |
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Which protein helps maintain the shape of RBCs?
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spectrin
|
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Which proteins are found in microvilli?
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villin & fimbrin
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Filamins clamp together 2 AFs at what angle?
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90 deg
|
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What does filamin facilitate?
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cell movement
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What happens when filamin is restored in malignant melanoma cells?
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form normal lamellipodia allowing them to crawl and metastasize
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Which end does CapZ bind to? Which end does tropomodulin bind to?
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+ end; - end
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The nucleation of AFs is catalyzed by _______ and _______. Binding of ARP complex to AF leads to ________________. Thymosin beta4 and profilin regulate ____________.
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Arp2; Arp3; branching; actin polymerization
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What does stathmin do?
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binds to MT subunits and makes them unavailable for polymerization
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Which type of tubulin is involved in nucleation of MTs?
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gamma
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T or F. Gamma tubulin is needed in much greater amounts than alpha and beta tubulin.
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False
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At which end does gamma tubulin bind?
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- end
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What is a common MTOC?
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centrosome
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What type of complexes cover centrosome?
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gamma-tubulin ring complexes
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Which end of the MT interacts with the MTOC?
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- end
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What helps position the centrosome at its centre?
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MTs
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T or F. Cell division cannot occur in the absence of centrosomes.
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False. Other cellular structures can be used as the MTOC (such as pericentriolar material, or PCM)
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T or F. Organelles can act as MTOCs.
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True. Ex. Golgi Complex
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Which type of proteins control assembly and dissasembly of MTs?
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MAPs
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Which proteins stabilize MTs?
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MAP1, MAP2, MAP4, Tau, gamma-TuRC, EB1
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Which are more spaced out, Tau or MAP2 bundles?
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MAP2 (due to longer arms)
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Where in neurons is MAP2 primarily found?
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dendrite
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T or F. Map4 is not found in neurons.
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False. IT is found in both neuronal and non-neuronal cells
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Where in the neuron is tau found?
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axons and dendrites
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T or F. Other MAPS can compensate the loss of Tau.
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True
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What happens when Tau is hyperphosphorylated?
|
tau misfolds, poor MT binding, low MT assembly activity, tangles/PHFs and NFTs accumulate, MTs less stable, reduced axonal transport along MTs, amount of normal tau reduced
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T or F. Misfolding of tau is due to hyperphosphorylation and not mutation.
|
True
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Which event is believed to lead to aggregation of tau?
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misfolding of a-beta species
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How do kinases and phosphatases play a role in hyperphosphorylation of tau?
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can be caused by increased kinase activity or decreased phosphatase activity
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Which proteins does hyperphosphorylated Tau sequester?
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normal tau, MAP1, MAP2
|
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Which proteins destabilize MTs?
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katenin (or stathmin), catastrophins
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What are +TIPS?
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+end tracking proteins, bind to + end of MTs, prevent premature catastrophes, promote MT growth, interact with CLIPS and CLASPS
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T or F. EB1 has a tip-tracking function.
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True
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Where on the MT does EB1 bind?
|
the seam (the weakest point of the MT)
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Which proteins can bring TIPs to the + end?
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motor proteins
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How many subunits is the Dam1 complex composed of?
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10
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How does the Dam1 complex help stabilize MTs?
|
form rings that surround MTs and slide, can bring in other MTs and form parallel bundles
|