Term
| cell size- linear vs. volume |
|
Definition
limiting factor of cell size is surface area
* eukaryotes solved by having membranous internal organelles |
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Term
| cytoskeleton- Eukaryotes vs. Prokaryotes |
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Definition
| although prokaryotes don't have microtubules, actin filaments, and intermediate filaments--> they have homologous cytoskeletal structures |
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Term
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Definition
| light source passes through condenser through specimen- through objective lens and through occular (two lens system) |
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Term
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Definition
= 0.61(lambda)/ n sin ø
lambda=wavelength
n=refractive index of medium separating specimen from objective and condenser
ø-half the angular width of cone of rays from specimen (sinø- max of 1) |
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Term
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Definition
| need dyes to see parts of cell- inside has similar refractive index as water |
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Term
Dyes-
Sudan Black
Silver Nitrate
Hematoxylin
Eosin |
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Definition
sudan black- lipids and cholesterol(fingerprints)
silver nitrate- internal organelles (golgi)
hematoxylin- + binds - (nucleic acids, DNA)
eosin- - binds +
**often have to be dead to stain |
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Term
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Definition
| optical tricks (lighting from the sides) allows you to visualize cells without staining (so they can be alive) |
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Term
| Antibodies for visualization |
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Definition
primary antibody binds to target molecule- secondary marked antibody binds to 1º antibody
when labelled with a fluorophore- cimmunofluorescence |
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Term
|
Definition
| beam splitting mirror lights specimen with excitation wavelength- transmits light emitted from flurophore |
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Term
| GFP- jellyfish flurophore |
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Definition
| can be incorporated into host DNA- makes a protein that fluoresces. (can be attached to target protein) |
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Term
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Definition
| demonstrated flexibility of membrane. can be used to calculate force to move things in a cell |
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Term
|
Definition
gives resolution ~0.1 nm.
(TEM)- sectioned
(SEM)- surface
must be dead- fixed and stained |
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Term
| Building blocks of the Cell |
|
Definition
sugars-> make polysaccharides
fatty acids-> make fats, lipids, membranes
amino acids-> make proteins
nucleotides-> make nucleic acids, RNA, DNA |
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Term
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Definition
| monosaccharides condense (lose H2O) creates disacchardes- hydrolysis consumes water to reproduce monosaccharides |
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Term
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Definition
| condensation reaction between glucose and galactose- lactose intolerence happens when monosaccharides can't be reproduced |
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Term
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Definition
amino group- alpha carbon - carboxyl group
-R Group
NH2-C-COOH -->ionized form +NH3-C-COO- |
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Term
| protein and protein folding |
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Definition
proteins- polymers of amino acids joined by peptide bonds O=C-N-H
folding of the protein is dependent on charges of R group (can be acidic, basic, non-polar, uncharged polar) |
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Term
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Definition
| cAMP phosphorylated by ATP and acetyl Co-A. energy from sunlight or food add an inorganic phosphate --> ATP |
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Term
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Definition
uses deoxyribose instead of ribose (no OH group on 2' C)
Nitrogenous Bases-
Adenine, Guanine, Thymine, Cytosine |
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Term
|
Definition
| DNA replication- transcription to RNA- translation to protein |
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Term
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Definition
| have both hydrophilic and hydrophobic ends |
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Term
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Definition
| hydrophilic carboxylic acid head, hydrophobic hydrocarbon tail |
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Term
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Definition
| one tail- cone shaped- congregate as spherical micelle |
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Term
|
Definition
3 hydrocarbon tails connected by glycerol
H
I
H2C-C-CH2
I I I
Carboxylic Ends of fatty acids |
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Term
| fats vs. oils (saturated vs. unsaturated) |
|
Definition
saturated with Hydrogens, pack tightly
unsaturated- packing broken up with C=C bonds |
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Term
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Definition
| breaking and reforming of C=C bonds can be carcinogenic |
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Term
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Definition
| made of fatty acids- carboxylic acids mix with water, hydrocarbon tails with oils |
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Term
|
Definition
2 fatty acid tails, glycerol, phosphate group
makes bilayer in water- energetically favorable to form sphere |
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Term
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Definition
self-healing to keep hydrophobic tails from being exposed to aqueous environment
*in oil and water phospholipids form monolayer |
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Term
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Definition
| saying that there is diffusion of phospholipids in membrane- there would be a disposition to homogeneity |
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Term
|
Definition
based on length of tails, number C=C bonds, which polar head groups, and amount of cholesterol in membrane
move by
-laterally diffusing
-rotating
-flexing (back and forth) |
|
|
Term
| molecular segregation- phospholipids |
|
Definition
-structural interactions(kinkedness)
-hydrophobic length mismatches
-polar head group interactions
-interactions with membrane proteins
*form microdomains |
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Term
| Synthesizing Phosphatidic Acid |
|
Definition
Acyl-CoA synthetase adds to fatty acid-> acyl Co-A fatty acid
Glycerol kinase adds to Glycerol -> gylcerol-3-phosphate
2 Acyl-CoA Fatty Acids embed in cytosolic leaf of ER--> Acyl transferase joins two and adds glycerol-3-phosphate making phosphatidic acid in cytosolic leaf of ER |
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Term
| synthesizing phospholipids |
|
Definition
phosphatase dephosphorylates phosphatidic acid-> diacylglycerol
CDP carrier molecule brings polar head group
(choline, ethanolamine, serine, inositol)
*all are synthesized using head group specific phosphotransferases (ex// choline phosphotransferase) |
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Term
| control points in phospholipid variation |
|
Definition
1) what fatty acids are made? (chain length)
2) which acyl-transferases become active? (which fatty acids are inserted in ER membrane)
3) which head group transferase is activated? (which group is added?)
Gives approx 1000 different lipids in a eukaryotic cell |
|
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Term
|
Definition
palmitic acid (16 C)
-palmitoleic
stearic acid (18 C)
-oleic, linoleic
* all are in synthesized in 2C increments (12-20) |
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Term
|
Definition
charged,
precursor for phosphatidlycholine(most common), and sphingomyelin |
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Term
|
Definition
|
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Term
|
Definition
| terminal amine, uncharged polar |
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Term
|
Definition
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|
Term
| phospholipids in membranes |
|
Definition
different amounts of each are in different cell types
many can undergo alterations to become another type
(ex// phosphatidyl-ethanolamine can be methylated to become phosphatidlycholine
phosphatidyl-serine can be decarboxylated to form phosphatidyl-ethanolamine) |
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Term
|
Definition
| phospholipids only grow on ER cytosolic leaf- Must be flipped to ER lumenal leaf. |
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Term
|
Definition
ER scramblase- nonspecificallly flips phospholipids to lumenal leaf
flippase then specifically flips PS and PE back to cytosolic leaf |
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Term
| membrane leaf composition |
|
Definition
PI, PS, and PE are present on the cytosolic face. PC and glycoproteins are on the lumenal or extra-cellular leaf
* most negatively charged phospholipids are on cytosolic leaf |
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Term
|
Definition
phospholipids are moved between organelles by vesicle budding, fission, and fusion. Those that do not contact vesicles(mitochondria and chloroplasts) are often directly contacted to ER.
*drugs can block vesicles, don't block organelle growth- therefore they probably contact ER directly |
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Term
|
Definition
cytosol- cell contents separate from organelles
cytoplasm- cytosol and organelles |
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Term
| regulating membrane fluidity |
|
Definition
1) higher and more C=C make harder to freeze
2) shorter tails- less interaction between phospholipids- more fluidity
3) cholesterol- makes membranes less deformable, but less able to freeze |
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Term
|
Definition
ER site of sterol synthesis, hydrophobic tail, small polar head group.
contributes to hydrophobic environment inside bilayer- decreases h20 intake |
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Term
| evidence for fluid mosaic model |
|
Definition
| fusion of mouse and human cell- proteins mix |
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Term
|
Definition
| longer saturated hydrophobic regions(sphingomyelin), and GPI-linked proteins (important for signaling) |
|
|
Term
|
Definition
allow transport of lipid rafts to other places in cells-transcytosis
or to other organelles-endocytosis
(ex// gut side to blood side of gut cell) |
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Term
|
Definition
| cleaves phospholipids at specific places-- can form molecules important in cellular signaling |
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Term
|
Definition
| cleaves PI or PC to create arachidonic acid-> which can be modified later to make prostaglandins |
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|
Term
|
Definition
storehouse in membranes- can come from phosphoatidylinositol or phosphatidly choline.
*has four unconjugated double bonds |
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Term
|
Definition
-inflammation response (especially arthritis and psoriasis)
-pain and fever
-blood pressure regulator
-blood clotting inducer
-labor inducer
*acts like a paracrine hormone
often binds g-protein-coupled receptors
effects mediated by intracellular cAMP response
local mediators |
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Term
|
Definition
| carbons 8-12 of arachidonic acid been cyclized |
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Term
| cycloxygenases (prostaglandin synthase) |
|
Definition
| cyclizes and oxygenates arachidonic acid to prostanoic acid |
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Term
|
Definition
| 2 production peaks= more than one synthase |
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|
Term
|
Definition
non-steroidal anti-inflammatory
*act by blocking COX fxn |
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Term
|
Definition
| modifies cox1 and cox2 by acetylating serine in active site (also blocks unwanted clotting-heart) |
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Term
|
Definition
| weakly binds cox3- no significant anti-inflammatory response |
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Term
|
Definition
| competitive inhibitor for COX binding site |
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|
Term
|
Definition
cox 1 has good roles
-platelet and microphage fxn
-mucus formation (ulcers- too much ibuprophen)
-hematopoiesis (generation of blood cells)
cox2- mostly inflammatory response
-may contribue to cancer cell growth |
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Term
|
Definition
| inserts itself into membranes- associations between caveolin proteins-> caveolae |
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Term
|
Definition
1º- string of amino acids with R groups
2º-alpha helices and beta sheets stabilized by H-bonds
R groups can effect hydrophobicity or philicity (sides or sheets, outside or inside of helix) |
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|
Term
| integral membrane proteins |
|
Definition
often pass through membrane with alpha helix- hydrophobic R groups
ex// glycine -H
phenylalanine- CH2-ring
leucine- CH2-CH-(CH3)2
Isoleucine- CH-CH2-CH3
I
CH3
serine, tyrosine
Can also be Beta Barrels, or single leaf associated |
|
|
Term
|
Definition
| try 'pushing' 10AA regions of protein through membrane to see how much energy it takes- more energy=hydrophobic region |
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Term
| asymmetries of protein reactions relative to bilayer |
|
Definition
often the cytosol is a reducing environment- Sulfide is reduced to -SH
outside the cell sulfide usually formed disulfide bonds(helps folding) |
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Term
| membrane associated proteins |
|
Definition
can also be lipid-linked and peripheral, or associate via van der waals, ionic or H-bonding with membrane bound proteins
some can be modified or released for signalling and recruiting |
|
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Term
| myristyl and farnesyl anchors |
|
Definition
| regulated and reversible recruitment of proteins at membrane surface |
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Term
|
Definition
ionic- strip protein and make it charged
gentle- allow reformation of membrane with purified protein (ex// Na+/K+ pump) |
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Term
|
Definition
bleach one area once-
quantify immobile phase by the % of proteins not moving from bleached area
limitations- where is rescue coming from?
measures only mobile phase- how fast lipids move |
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|
Term
|
Definition
continually bleach one spot- measure another area
allows determination of non-mobile phase
demonstrates continuity of membrane |
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Term
| single phospholipid tracking |
|
Definition
| can label one or small number molecules with gold bead |
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Term
| proteins restricting lateral mobility |
|
Definition
self-congregating proteins, cytoskeletal elements, extracellular matrix (including glycocalyx)
ex// sperm cells (acrosomal membrane, PM, tail) |
|
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Term
| glycolipid and glycocalyx |
|
Definition
serine replaces glyerol- no phosphate = glycolipid
glycocalyx- cell coat comprised of oligosaccharide side chains from glycolipids and membrane proteins
*also protects against mechanical stresses |
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Term
| other formations of arachidonic acid |
|
Definition
elongase can add 2C to other cleaved phospholipids
B oxidation can also remove 2C at a time
*for both- desaturase is needed to form the 4 unconjugated double bonds |
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|
Term
|
Definition
hydrophobic molecules, small neutral non-polar molecules can diffuse through PM
some water can
organic molecules, ions, proteins need help |
|
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Term
|
Definition
K+ high inside cell
Na+ high outside cell
Cl- high outside cell
mg++ slightly higher outside
ca++ higher outside
H+ higher (more acidic) inside cell |
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|
Term
| membrane potential (and experiment) |
|
Definition
K+ channels through synthesized membrane
K+ moves down concentration gradient, like charge repulses like, K+ moves back across (to equilibrium). relative higher Cl- on other side line up along membrane, K+ on opposite side = membrane potential |
|
|
Term
|
Definition
concentration plus membrane potential gradient
resting K+ chanels and K+/Na+ ATPase channels mostly responsible for human cell resting potential |
|
|
Term
|
Definition
channels-pores
carriers-alternate solute bound conformations |
|
|
Term
|
Definition
-requires conformational change
-no direct communication
-very selective
-slow |
|
|
Term
|
Definition
-weak interactions
-fast
-direct communication
-conformational change(closed or open) |
|
|
Term
| carrier proteins- enzyme rate |
|
Definition
V-max is where rxn rate levels off with increase in substrate concentration
Km- @ 1/2 vmax, concentration-> lower km means tighter binding to substrate
*same vMax has to be same Km |
|
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Term
|
Definition
| facilitated diffusion, moves according to concentration gradient-> passive transport |
|
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Term
|
Definition
carrier-mediated(facilitated diffusion)-passive
pumps require energy- active transport
*against concentration gradient |
|
|
Term
|
Definition
high concentration of inorganic counter ions- too much osmolarity causes lysis of cell
pumps regulate ion concentration-osmolarity |
|
|
Term
|
Definition
regulates osmolarity
major player in keeping Na+ gradient |
|
|
Term
|
Definition
often Na+ is coupled to another molecule- Na+ gradient drives the carrier
in yeast and prokaryotes this is replaced by an H+ pump |
|
|
Term
|
Definition
driven by ATP- autophosphorylation cuases conformational change pumping 3 Na+ out of cell and 2 K+ into cell {electrogenic}
*this maintains the Na+/K+ disequilibrium |
|
|
Term
| other stuff about Na+/K+ pump |
|
Definition
ouabain- inhibits ATPase activity-> cells burst
digoxin-heart meds. low amnts reduce Na+ removal, indirectly causes Ca++ influx (Na+/Ca++ antiporter)- Ca++ helps muscle contractility |
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Term
|
Definition
| reversible- can make ATP if electrochemical gradients reversed |
|
|
Term
|
Definition
tetramer- 2.5 transmembrane domain with P loop(necessary)- some have 6.5 TMD but conserved 2.5 area
K+ moves out of cell according to gradient
main source of membrane potential (Cl- inside) |
|
|
Term
| K+ resting channel mechanism |
|
Definition
has vestibule- 'waiting area' that in effect shortens the membrane
carbonyl groups from amino acids of protein act like hydration residue to move K+ through channel
*Thr, X, Gly, Tyr, Gly (inside to out)
when internal membrane is + charged, K+ channel closes |
|
|
Term
|
Definition
Na+/Glucose symporter
Na+/K+/Cl- symporter
Na+/Ca++ antiporter
Na+/Mg++ antiporter |
|
|
Term
|
Definition
Na+ binds, making site for glucose to bind. glucose binds, conformational change switches open side of protein. Na+ release drives glucose release
2 Na+(down), 1 glucose(up gradient) |
|
|
Term
| gut cell- glucose transporters |
|
Definition
Na+/glucose symport from intestinal side. passive trancytosis of glucose to basal lateral domain- where Na+/K+ pump active to maintain disequilibrium driving Na+/glucose pump
*tight junctions important for gradient and asymmetry of pumps |
|
|
Term
| other glucose transporters |
|
Definition
important in moving glucose to astrocytes(across blood/brain barrier)- where it can be made into something functional for brain
*defects can cause seizures, diabetes, developmental defects |
|
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Term
|
Definition
| hydrolyze ATP to drive conformational change |
|
|
Term
|
Definition
| generate ATP as byproduct (often turbine/rotor-like carriers, lollipop-like) |
|
|
Term
|
Definition
drugs and immunity-2 AtpBindingCassetes, 6 transmembrane domains(dimerize, or one protein 12 TMD)
substrate binding forms ATP site
Functionally very diverse(ions, AA's, etc.)
Eukaryotes-mostly export |
|
|
Term
| V-type example (eukaryotes) |
|
Definition
inner mitochondrial membrane- e- transport chain drives H+ pump- H+ gradient drives ATP synthase
gradient turned into mechanical energy (10-14H+ per turn, 4H+=1 ATP) |
|
|
Term
|
Definition
also important for endosomes and organelles with lower acidity than cytosol
-acidify urine
-osteoclast bone breakdown
-maintain pH(macrophage) |
|
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Term
|
Definition
| move by rotor-like motion. could be V-type pump that moves it. also reversible |
|
|
Term
|
Definition
cancer cells mutate to get around medications
(decrease intake, comparmentalization, repair DNA, change membrane protein, increased or altered drug targets)--> ABC efflux pumps
MDR1 pumps out entire class of hydrophobic drugs |
|
|
Term
| TAP immunological response |
|
Definition
ABC transporter on ER membrane
recruits ATP- pulls peptides into ER (from broken up virus). MHC binds, presents to outside of cell for T-cell response |
|
|
Term
|
Definition
CFTR moves Cl- into cell- regulates ENac Na+ intake
when CFTR is inhibited, Na+ not taken up- thick extracellular fluid=CF |
|
|
Term
|
Definition
cholera toxin attaches to digestive system- hyperactivates cAMP-> activates Protein Kinase A(PKA) turns on CFTR
*instead of thick fluid, watery diahrrea |
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