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203 Cards in this Set
- Front
- Back
Eucaryotic cells contain protein fibers that are involved in what?
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-establishing cell shape
-providing mechanical strength - cell movement - chromosome separation - intracellular transport of organelles |
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Protein fibers form the cytoskeleton and there are 3 types ..
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- Actin filaments (also called microfilaments)
- Intermediate filaments - Microtubules |
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Some functions of actin filaments are:
|
- to provide mechanical strength to the cell by forming a band under the plasma membrane
- link transmembrane proteins to cytoplasmic proteins form contractile ring during cytokinesis in animal cells cytoplasmic streaming - generate locomotion in cells such as white blood cells and amoeba - Interact with myosin to provide force of muscular contraction |
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What type of activities do Microtubules participate in through out the cell?
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Most involve motion that
is provided by protein “motors” that use ATP. They determine the positions of membrane-enclosed organelles and direct intracellular transport. The migration of chromosomes during mitosis and meiosis takes place on microtubules that make up the spindle fibers. |
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What do intermediate filaments do?
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provide mechanical strength and resistance to shear stress.
|
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What are the different filaments and their functions?
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-Keratins: are found in epithelial cells, hair and nails
-Nuclear lamins: form a meshwork that stabilizes the inner nuclear membrane -Neurofilaments: strengthen the long axons of neurons -Vimentins: provide mechanical strength to muscle and other cells |
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Defective keratins lead to what?
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epidermolysis bullosa simplex disorder
|
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The tubulin and actin subunits assemble head-to-tail to create what?
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polar filaments
|
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What is the limiting step in the formation of a cytoskeletal polymer?
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Nucleation
|
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Microtubules and actin filaments have two distinct ends that do what?
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grow at different rates
|
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What are consequences of nucleotide hydrolysis by tubulin and actin?
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Filament treadmilling and dynamic instability
|
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What occurs at intermediate concentrations of free subunits?
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Treadmilling
|
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Nucleation is catalyzed by a complex of proteins that includes what?
|
actin-related proteins (ARPs
|
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The ARP complex nucleates actin filament growth how?
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-from the (-) end, allowing rapid elongation at the (+) end
-The ARP complex can also attach to the side of another actin filament while remaining bound to the (-) end of the filament that it has nucleated |
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When is the ARP complex nucleated filaments more efficiently?
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when it is bound to the side of a preexisting actin filament resulting in a filament branch that grows at a 70° angle relative to the original filament
|
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How is actin elongation mediated?
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formins
|
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How is Filament elongation is modified?
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by proteins that bind to the free subunits
|
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What is a special protein that binds to actin?
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Thymosin
- Actin monomers bound to thymosin are locked where they cannot associate with either the (+) end or (-) end of the actin filament. |
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How do cells recruit actin monomers from this sequestered pool and use them for polymerization?
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Recruitment depends on another monomer-binding protein profilin.
|
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What is profilin?
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Profilin binds to the face of actin opposite the ATP-binding cleft.
|
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What is Actin-profilin?
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Actin-profilin can bind to the plus end of the actin filament but is unable to bind to the minus end.
|
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Proteins that bind to the sides of actin filaments can either ..
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stabilize or destabilize them
|
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Tropomyosin stabilizes actin filaments by binding simultaneously to what?
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seven adjacent actin subunits in one protofilament This prevents other proteins from binding to actin
|
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What destabilizes actin filaments by forcing it to twist a little more tightly?
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Cofilin
|
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What organizes assemblies of actin filaments?
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Cross-linking proteins
|
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Polymerization of tubulin nucleated by what?
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g-tubulin ring complexes
|
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Actin-based motor proteins are members of what super family?
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myosin
|
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What Are Two Types of Microtubule Motor Proteins?
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Kinesins and Dyneins
|
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The Structural Similarity of Myosin and Kinesin Indicates what?
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a common evolutionary origin
|
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Motor Proteins Generate Force by what?
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Coupling ATP Hydrolysis to Conformational Changes
|
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Motor Proteins Mediate what?
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the Intracellular Transport of Membraneenclosed Organelles
|
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The Cytoskeleton Localizes what?
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Specific RNA Molecules
|
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Cells regulate what?
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motor protein function
|
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The cytoskeleton and cell behavior causes what to happen in muscles?
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muscle contraction is a burst of calcium while Sliding of Myosin II and Actin Filaments Causes Muscles to Contract
|
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Cilia and Flagella Are Motile Structures Built from what?
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Microtubules and Dyneins
|
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Construction of the Mitotic Spindle Requires
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Microtubule
|
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Actin Polymerization Drives
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Plasma Membrane Protrusion
|
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Cell Adhesion and Traction Allow Cells to move how?
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Pull Themselves Forward (sticking to wall of vessel and exiting areas of infection or inflammation)
|
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Which family causes Major Rearrangements of the Actin Cytoskeleton?
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Rho protein family
|
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Extracellular Signals Can Activate how many Rho Protein Family Members?
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3!
|
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What Can Dictate the Direction of Cell Migration?
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External signals
|
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Dyneins are a family of
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minus-end directed microtubule motors
|
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Two major families of dyneins
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cytoplasmic dyneins and axonemal dyneins
|
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Cytoplasmic dyneins are found in all eucaryotic cells and are important for what?
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vesicle trafficking and localization of the Golgi apparatus near the center of the cell
|
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Axonemal dyneins are highly specialized for what?
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rapid and efficient sliding movement of microtubules that drive the beating of cilia and flagella and negatively charged
|
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What do dyneins require to associate with membrane-enclosed organells?
|
a large number of accessory proteins
|
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Ion concentration differences across the lipid bilayer are useful for 4 things:
|
1) Driving various transport processes
2) Conveying electrical signals in electrically excitable cells 3) Making most of the cell’s ATP 4) Cell signaling |
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The rate at which a molecule diffuses across a synthetic lipid bilayer depend on its ..
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size and solubility
|
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Complete the statement:
The smaller the molecule and the less polar it is, the ... |
the more rapidly it diffuses across the
bilayer |
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What are the 2 main classes of membrane transport proteins?
|
Transporters and channels
|
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What do transporters do?
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bind to a specific solute and undergo a series of conformational changes
|
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What does a channel do?
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interact with the solute much more weakly
form aqueous pores transport at a faster rate |
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How do solutes cross membranes?
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either active or passive transport
|
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AcActive transport goes against...
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the concentration gradient
|
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Electrochemical gradients do what 2 thing?
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combines membrane potential & the concentration gradient
|
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A conformational change in a transporter could mediate
|
the passive transport of a solute
|
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Cells carry out active transport in three main ways:
|
(1) Coupled transporters couple the uphill transport of one solute
across the membrane to the downhill transport of another. (2) ATP-driven pumps couple uphill transport to the hydrolysis of ATP. (3) Light-driven pumps, found mainly in bacteria and archaea, couple uphill transport to an input of energy from light. |
|
ion-driven transporters mediate
|
secondary active transport
|
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ATP-driven transporters mediate
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primary active transport
|
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Three types of transporter-mediated transport
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1) Uniports
2) symports 3) antiports are all used for both passive and active transport |
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Coupled transport involves...
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either the simultaneous
transfer of a second solute in the same direction (symporters) or the transfer of a second solute in the opposite direction (antiporters) |
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The glucose-Na+ symport protein uses the electrochemical Na+ gradient to drive what?
|
the import of glucose
|
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The active transport of many sugars and amino acids into bacterial cells is driven by what?
|
the electrochemical H+ gradient across the
plasma membrane |
|
During the transport cycle, some of the helices undergo what kind of motion?
|
sliding motions causing them to tilt
|
|
An asymmetric distribution of carrier proteins underlies the transcellular transport of solutes... meaning what?
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You don’t have an equal number of proteins in the cell which allows the gradient to exist, if equal gradient wouldn’t be forcing ion drive. Asymmetrical allows transcellular transport.
|
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what are the 3 classes of ATP-driven pumps?
|
P-type pump
F-type pump ABC transporter |
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what does the p-type pump do?
|
relies on the hydrogen, potassium, sodium or calcium can be outside causing the gradient getting a phosphorous attachment or attachment. ATP converting to ADP with phosphorous converting to the pump.
|
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What does the F-type pump do?
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allows the phosphorous to drive the hydrogen into the pump itself. These require the phosphorous to change the shape of the pump allowing for hydrogen to flow totally driven by phosphorous
|
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What does the ABC transporter do?
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requires two ATP molecules pushing the molecule out against the gradient and the abc transporters are forcing the gradient in the opposite direction
|
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where does the p-class pump occur?
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-plasma membrane of plants, fungi, bacteria (H+ pump)
-plasma membrane of higher eukaryotes (Na+/K+pump) -Apical plasma membrane of mammalian stomach (H+/K+ pump) -plasma membrane of all eukaryotic cells (Ca2+ pump) -Sarcoplasmic reticulum membrane in muscle cells (Ca2+ pump) |
|
Where does the F-class proton pump occur?
|
-Bacterial plasma membrane
-Inner mitochondrial membrane -Thlakoid membrane of chlorplast (similar to the mitochondria that drives the oxidative phosphorylation Hydrogen ions that drive the motor in the F-pump to ADP to ATP) |
|
V-Class proton pump occurs where?
|
-Vacuolar membranes in plants, yeast and other fungi
-Endosomal and lysosomal membranes in animal cells -Plasma membrane of osteoclasts and some kidney tubule cells |
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Where does the ABC superfamily occur?
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-Bacterial plasma membranes
(amino acid, sugar and peptide transporters) -Mammalian plasma membranes (transporters of phospholipids, cholesterol and other small molecules) |
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How have structures of the Ca2+ pump been determined?
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x-ray crystallography
|
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What is the structure and function of Ca2+ pump?
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Without the release of calcium you wont have muscle movement or immune response. A burst of calcium allows for the release of inflammatory mediators into tissue. Calcium is the last ion that has to move into or out of the cell for a muscle contraction to take place. 10-20years of work to figure out all this information.
|
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What kind of pump is the Na+-K+ pump?
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P-type transport ATPase
|
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What and how many ions go in and out of the Na+-K+ pump?
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3 ions of sodium going into the pocket and 2 potassium's going out
|
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The Na+ - K+ pump is required to maintain what?
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osmotic balance and stabilize cell volume
|
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Where does the ATPases belong to?
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ABC transporter superfamily
|
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A typical ABC transporter consists of four domains
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two highly hydrophobic domains and two ATP-binding catalytic domains
|
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ATP binding leads to dimerization of ...
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the two ATP-binding domains and ATP
hydrolysis leads to their dissociation. |
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How fast can Ion Channels transport?
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100 million ions per second
greater than that mediated by a carrier protein |
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What are some of the ion channel functions?
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-control the pace of the heart
-regulate the secretion of hormones into the bloodstream -generate the electrical impulses underlying information transfer in the nervous system |
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Ion channels are..
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Ion selectivity
|
|
Ions fluctuate between ...
|
open and closed states (gated)
|
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What are the Ion channels specific substrates?
|
potassium
sodium calcium chloride channels permit only their namesake ions to diffuse through their pores |
|
The ability of channels to discriminate among ions is called
|
Ion selectivity
|
|
What is the atomic radius of potassium compared to Sodium?
|
The atomic radius of K+ is 1.33 Å and that of Na+ is 0.95 Å
With only this difference to work with. K+ channels manage to select for the K+ ion over the Na+ ion by a factor of more than 1000. |
|
What is Ion channel Gating?
|
Ion channel gating refers to opening and closing of the ion conduction pore in response to a specific stimulus.
|
|
What are the different ion gating channels?
|
ligand-gated channels (intracellular & extracellular)
voltage-gated channels mechanically gated channels |
|
Define membrane potential
|
difference in electrical charge on the two sides of a membrane as a result of active electrogenic pumping and passive ion diffusion
|
|
The equilibrium condition, in which there is no net flow of ions across the plasma membrane defines the
|
resting membrane potential
|
|
What equation expresses the equilibrium condition quantitatively about resting membrane potential?
|
Nernst equation
|
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What amino acids are responsible for potassium selectivity?
|
Potassium channels are tetramers of identical subunits in which specific "signature sequences" are the amino acids responsible
|
|
The signature sequence is conserved in all potassium channels throughout nature and forms a structural unit
called the .. |
selectivity filter
|
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In the vestibule (talking about K+ specificity of the selectivity filter in a K+ channel) ions are...
|
hydrated
|
|
Dehydration of the K+ ions require..
|
energy
which is precisely balanced by the energy regained by the interaction of the ion with the carbonyl oxygens that serve as surrogate water molecules |
|
Who won the chemistry nobel prize in 2003?
|
Roderick MacKinnon for discoveries concerning channels in the cell membrane
|
|
Shape of the channels mimics what?
|
the shape of the ion (ex: potassium ion for potassium channel)
|
|
A marvelous electrostatic feature of the potassium channel is a cavity of...
|
water half way across the membrane with specifically oriented a helices.
|
|
The cavity of water design reduces what and causing what to happen?
|
This design reduces the dielectric barrier, that is, the energetic cost of moving an ion from the high-dielectric environment of water to the low-dielectric membrane, and thereby supports a high ion throughput
|
|
What is voltage sensing?
|
Conformational changes underlying voltage sensing in KvAP are large and involve movements of arginine residues through the membrane, near the protein lipid interface
|
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Aquaporins are permeable to ..
|
water but impermeable to ions
|
|
Aquaporins play a key role in...
|
in cellular water homeostasis in humans, animals, and plants. These water channel proteins associate as tetramers. Each aquaporin contains a single 28-Å-long cylindrical pore that supports a string of nine hydrogen-bonded water molecules in single file.
|
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The structure of aquaporins needs what?
|
more alpha than beta sheets to protect the structure
|
|
How many and what type of atoms are lined in the aquaporin?
|
a row of 8 carbonyl oxygen atoms that can accept hydrogen bonds from the queue of water molecules
|
|
because the rest of the pore is lined with mostly hydrophobic amino acids, "water-pore interactions are kept to a minimum," allowing water to rush through each pore at a rate of...
|
3 x 10 (raised) 9 molecules per second.
|
|
a pair of asparagine residues as well as the dipole moments of short a-helices would force water to do what?
|
to flip near the pore's center. This forced reorientation breaks the continuous chain of hydrogen-bonded waters and prevents protons from "hopping" along the hydrogen-bond network.
|
|
What does a proton block do?
|
keeps hydrogen from moving across the membrane
|
|
Unlike gramicidin A, an antibiotic peptide that kills bacteria by forming pores in their cell membranes, aquaporins must not leak protons. Doing so would disturb what?
|
the delicate balance of charge across cell membranes that underlies cellular function
|
|
how do aquaporins manage to do what gramicidin A can't?
|
Near the center of the aquaporin pore, hydrogen bonds from a pair of asparagine residues (as well as the pull of nearby a-helix dipoles) reorient the central water molecule, preventing it from accepting a proton from nearby water molecules.
|
|
Recent results indicate that the main barrier to proton transfer is not caused by interruption of the hydrogen-bonded water chain, as had previously been speculated, but rather ....
|
by an electrostatic field created by the a-helix dipoles in the NPA region.
|
|
Voltage-gated cation channels generate action potentials in electrically excitable cells which are what 4?
|
- neurons
- muscle cells - endocrine cells - egg cells |
|
Action potentials are the direct consequence of ...
|
the properties of voltage-gated cation channels
|
|
Invention of patch-clamp allowed us to understand what?
|
if you don’t hit thresh hold you wont get an action potential, you need enough energy to open up the gate
|
|
transmitter-gated ion channels convert chemical signals into ...
|
electrical signals at chemical synapses
|
|
Three conformations of the acetylcholine receptor
|
occupied and open
occupied and closed (inactive) unoccupied and closed |
|
What do genes code for?
|
MRNA and eventually amino acids and those amino acids become proteins
|
|
How are cells and bodies made from the instructions in DNA?
|
DNA to Proteins to Cells to an organism
|
|
The Central Dogma of DNA to protein is:
|
DNA, transcription to RNA, translation to Protein to get the trait
|
|
To get from the chemical language of DNA to the chemical language of proteins requires 2 major stages:
|
transcription and translation
|
|
Each disease (phenotype) is caused by non-functional gene product, some diseases are:
|
lack of an enzyme
Tay sachs PKU albinism |
|
Who discovered that genes act by regulating definite chemical events?
|
George Beadle and Edward Tatum
(1941:1958) |
|
what is made in nucleus?
|
replication of DNA
ribosomes RNA, TRNA, SRNA in addition to the reading of genes |
|
when making mRNA the transcribed DNA strand =...
|
template strand
|
|
when making mRNA UNtranscribed DNA strand=..
|
coding strand
|
|
Transcription requires what enzyme?
|
RNA polymerase making the bubble which creates the strand 5'to 3'
|
|
How many RNA polymerases are there?
|
3!
|
|
what does RNA polymerase 1 do?
|
-only transcribes rRNA genes
-makes ribosomes |
|
What does RNA polymerase 2 do?
|
transcribes genes into mRNA
|
|
what does RNA polymerase 3 do?
|
only transcribes tRNA genes
|
|
DNA to protein we are actually using what?
|
RP2
|
|
What is the promoter region?
|
binding site before beginning of gene
|
|
in promoter region is what?
|
TATA box
-thymine and adenine sequence that tells the binding proteins that this is the promoter region |
|
TATA bos does what?
|
binding site for RNA polymerase & transcription factors
|
|
what is the enhancer region?
|
binding site far upstream of gene
-turns transcription on high |
|
What does the initiation complex include?
|
transcription factors that bind to the promoter region
-trigger the binding of RNA polymerase to DNA |
|
exons=
|
the real gene
expressed/coding DNA |
|
introns=
|
the junk
in between sequence |
|
What does mRNA spicing do?
|
edit out introns
|
|
primary transcript in mRNA splicing = what?
|
pre-mRNA
|
|
When and by who were the discovery of introns/exons?
|
1977 & 1993
Richard Roberts Philip Sharp |
|
If an error occurs in splicing what happens?
|
a single base added or lost throws off the reading fram
|
|
What are snRNPs?
|
small nuclear RNA
|
|
What is a spliceosome?
|
several snRNPs
recognizes splice site sequence which can cut and paste genes |
|
How does mRNA code for proteins?
|
it reads in sets of 3 (Codon then translated into amino acid)
|
|
What code is a start codon?
|
AUG
|
|
what codes is/ are a stop codon?
|
UGA
UAA UAG |
|
What aids in the loading tRNA bond?
|
Aminoacyl tRNA synthetase
|
|
Are ribosomes an organelle or enzyme?
|
Ribosomes are both an organelle and enzyme: not surrounded by membranes, function like an organelle but act like a protein.
|
|
What are the different Ribosome sites?
|
A-site
P-site E-site |
|
What does the A-site do?
|
aminoacyl-tRNA site
|
|
what does the P-site do?
|
peptidyl-tRNA site
|
|
What does the E-site do
|
exit site
|
|
What 3 steps are needed to build a polypeptide?
|
Initiation
Elongation Termination |
|
What is the purpose of protein targeting?
|
signal peptide (address label)
|
|
What do prokaryotic genes contain?
|
DNA in cytoplasm
circular chromosomes naked DNA NO introns |
|
What do eukaryotic genes contain?
|
DNA in nucleus
linear chromosomes DNA wound on histone proteins introns vs. exons |
|
Transcription and translation are what in bacteria?
|
simultaneous!
- while ribosomes read mRNA as its transcribed |
|
What is the difference between prokaryotes & eukaryotes in translation?
|
Time and physical separation between processes
(Eukaryotes takes ~1hr from DNA to protein) |
|
What are the modes of cell signaling?
|
Direct cell-cell signaling
Signaling by secreted molecules signaling molecules |
|
What are the signals secreted by molecules?
|
Endocrine:
- distant signaling ex: estrogen Paracrine: -act on neighboring target cells ex: neurotransmitters Autocrine: -self signaling molecules ex: T cells |
|
What are the classes of signaling molecules?
|
Hydrophobic
neurotransmitters peptide signaling molecules eicosanoids |
|
which signaling molecules are use membrane receptors?
|
Neurotransmitters
peptide signaling molecuels eicosanoids |
|
What do hydrophobic signaling molecules do?
|
passively diffuse across the cell membrane
ex: vitamin D3, steroid hormones thyroid hormone etc. - use intracellular receptors & function as activators or repressors of genes |
|
How do neurotransmitters carry signals?
|
between neurons to other target signals
-they are hydrophilic and bind to surface receptors |
|
What are 3 peptide signaling molecules?
|
peptide hormones
neuropeptides polypeptide growth factors |
|
Eicosanoids lipid signaling molecules include what?
|
prostagiandins
prostacyclin throboxanes leukotrienes |
|
Peptide signaling molecules have what kind of lifespan?
|
short lived
act in autocrine or paracrine pathways |
|
What are the 2 types of signaling receptors?
|
Intracellular
membrane integral |
|
what do kinases bond to ?
|
phosphate
|
|
Nuclear receptor superfamily has transcription factors that have domains for...
|
ligand binding
DNA binding modulate transcription Glucocorticoid receptors |
|
What is the purpose of hormone binding?
|
replaces HDAC with HAT and may alter the activity of the receptor
|
|
How many membrane-spanning alpha helices are in membrane receptors?
|
7
|
|
What is a G protein?
|
important class of membrane bound receptors that have conformational change and trigger signal cascade inside the cell as well as other numerous activities inside the cell
|
|
What do kinases move?
|
phosphate
|
|
How many receptors do humans have?
|
59
|
|
What do receptor protein- tyrosine kinases help do?
|
ligand binding and autophosphorylation of receptors
|
|
What mediates binding/activation of downstream signaling molecules in tyrosine kinases?
|
SH2 domains
|
|
What are some non-receptor protein-tyrosine kinases?
|
Cytokine receptor superfamily
and non-receptor protein tyrosine kinases ex: JAK janus protein tyrosine kinases |
|
What does ligand binding induce?
|
receptor dimerizaiton
|
|
What is intracellular signal transduction?
|
chain of reactions, transmits signals/cell surface --> intracellular targets
-First studied for epinephrine |
|
What takes place first in intracellular signal transduction?
|
breakdown of glycogen
|
|
What is the purpose of cyclic AMP?
|
a secondary messenger leading to the breakdown of glycogen
Regulates genes and Metabolic regulation |
|
cAMP signal transduction pathways:
- What are the 2 phophorylation downstream enzymes? |
Glycogen synthase (inactivated)
Phosphorylase kinase (activated) |
|
Where do cascading events end up?
|
promoter regions
|
|
What does CREB do?
|
neuronal development
memory differentiation proliferation cognition |
|
PLC stimulates hydrolysis of ...
|
pip2 to DAG and IP3 because DAG and IP3 are secondary messengers
|
|
what does IP3 regulate?
|
calcium
|
|
When is calmodulin activated?
|
When calcium is increased from an inactive state to an active state
|
|
What does calmodulin activate as it is phosphorylated?
|
protein kinases
metabolic enzymes ion channels transcription factors (CREB) |
|
MLCK (myosin light chain kinase) is activated by what?
|
calmodulin which will activate muscle
|
|
Getting calcium into the cell does what?
|
brings more calcium for a cascading event to take place
|
|
PIP3 targets a protein-serine/threonine kinase called ..
|
Akt and also binds protein kinase PDK1
|
|
Akt phosphorylates several target proteins, transcription factors, and other protein kinases
Transcription factors include members of the |
forkhead or FOXOX family which travel to the nucleus and then bind to the genes that inhibit cell proliferation
|
|
Conserved across eukarytoic cells are 3groups of MAP kinases which are..
|
Stimulus
Growth Factors Inflammatory cytokines (ERK, JNK and p38) |
|
3 classes of signaling proteins are
|
cyclic AMP
pI3 MAP kinase |
|
What does ERK regulate?
|
meiosis
mitosis cell proliferation and differentiation |
|
What are ligands?
|
growth factors
cytokines and viral infections carcinogenic chemicals |
|
ERK activation leads to ...
|
RAS to RAF to MEK to ERK and goes into the nucleus and tells the cell todo something
|
|
ERK goes to the nucleus and phosphorylates
|
Elk-1
|
|
ERK tells the nucleus what?
|
To grow and divide
|
|
RAF MEK and ERK are held together by ...
|
KSR scaffold
|