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| 1. cell is simplest unit of life that can perform all the fundamental activities of life. 2. all living things are made up of cells. 3. all cells have essentially the same chemical composition. 4. all cells are derived from pre-existing cells. 5. cells contain heriditary information that is passed on during cell division |
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| overview of cell signaling |
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| signal-reception-(amplification)transduction-response |
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| location of steroid receptors |
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| in cytoplasm, once it is bound it leaves for transcription in nucleus |
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| separate internal from external enironment, generate and transform energy, concentrate macromolecules to increase reactivity, respond to environment, reproduce, defend itself, move |
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| steroid competition examples |
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| RU486( progesterone receptor) and tamoxifen (estrogen receptor) |
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| example of a spherical bacterica |
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| example of a rod-shaped bacteria |
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| amino acids for phosporylation |
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| tyrosine, serine, and throrine? sp. |
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| adenyl cyclase (target protein) |
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| activated cAMP (which is a secondary messenger |
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| makes inactive protein kinase A-- activate protein kinase A, note that cAMP is a allosteric regulator |
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| phoshporylase kinase substrate |
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| glycogen phosphorylase substrate |
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| glycogen and converts it to glucose |
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| bind to phosphotryrosinated proteins |
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| phosphorylated PI creates.. |
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| IP3 and DAG (which are secondary messengers) |
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| organism becomes symbiotic within another organism, like mitochondria or chloroplasts |
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| GTP exchange factor (GTP--GDP), activates Ras |
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| GTPase activating protein-deactivates Ras protein |
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| experiment: identify DNA as the genetic material |
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| smooth colonies of bacteria are more dangerous than rough because S bacteria have an additional polysaccaharide capsule that prevent immune detection. killing smooth bacteria and then mixing them with rough makes the rough dangerous. adding DNAase prevents this, showing DNA is the transformation mechanism. hershey and chase radioactively labeled DNA in phages and saw the DNA was transferred into bacteria, not proteins. |
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| carotenoids (450), chlorophyll a (650, 440) and chlorophyll b (640, 450-450) |
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| resonance energy transfer (RET) |
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| photopigments capture light and transfer energy to other photopigments ultimately to the rxn. center chlorophyll, antenna molecules |
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| what happens at reaction center |
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| chlorophyll donates electron to electron acceptor, charge separation |
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| enhanced yield with flashed of P680 nm, and P700 nm |
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| radius of strand - 1 nm. length of spiral - 3.4 nm. Length of base pair - .34 nm |
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| PSI-makes ATP but not NADPH |
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| adenine, guanine, cytosine, thymidine, uracil |
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| nucleotide component lacking phosphate, only sugar + base |
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| phosphodiester bond formation |
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| 3'hydroxyl attacks 5' phosphate. synthesis occur in 5' -> 3' direction |
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| most prevalent enzyme responsible for fixing CO2 in chloroplast stroma |
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| which is stronger - A-T base pair bond or C-G? |
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| C-G because they form a triple bond. A-T form a double bond. |
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| RuBP (rubisco) takes O2, 1, 3 phosphoglycerate used in calvin cycle |
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| gas exchange, consist of two guard cells that can change shape to create a pore when C02 concentration is low |
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| genes that code for position of things like arms, eyes. position on strand is related to position on body, so left side of strand could code for head and right strand for feet |
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| control points for calvin cycle |
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| pH increase starts enzymes for calvin cycle, shuts off in the dark to conserve ATP for other stuff |
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| mRNA, rRNA, tRNA, small rnas with varied functions |
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| why does ATP hydrolysis have a large delta G |
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| relief of electrostatic repulsion between phosphates and resonance stabilization of the phosphates |
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| atoms of life from most abundant to least |
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| h, c, o, then much lower are N, Ca & Mg, Na & K, others |
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| proteins, polysaccharides, nucleic acids, lipids (sort of) |
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| types of chemical interactions |
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| covalent, ionic, van der waals "weak", hydrogen bonds |
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| traps glucose in cells and commits it to glycolysis |
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| key glycolysis enzyme, makes fructose 1, 6 biphosphate, negative feedback ATP and citrate |
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| basis of base pairing in DNA? |
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| functions of carbohydrates |
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| source of energy to fuel cells, structure (cellulose), recognition (receptors, ligands, cell interactions), intracellular traffickinh |
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| general formula for a carbohydrate |
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| substrate level phosphorylation |
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| enzyme does the work to produce ATP (ex. pyruvate kinase takes PEP to make pyruvate) |
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| different configuration of hydroxyl groups |
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| acts on substrate, removes C02 and takes into coenzyme A, and produces acetyl CoA |
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| what starts the krebs cycle? |
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| glycosidic bond formation |
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| dehydration/condensation reaction |
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| branching in polysacharides |
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| glycogen > starch > cellulose (linear) |
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| couples the electron transport to ATP synthesis |
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| molecule with both polar and nonpolar ends, e.g. fatty acids |
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| oxidative phosphorylation-34, glycolysis- 2, krebs cycle-2 |
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| regulation of citric acid cycle |
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| inhibited by ATP, acetyl CoA and NADH (conversion to acetyl CoA): various points regulated by ATP and NADH |
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| three fatty acids + glycerol |
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| how is citric acid cylce integrated with other aspects of metabolism |
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| citrate-fatty acids+sterols, a-ketoglurarate-purines, succinyl CoA-heme+porphyrins+chlorophyll, oxaloacetate-amino acids+purines+pyrimidines |
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| triglycerides/trialcylglycerols (TAGs) |
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| are kinks in hydrocarbons bad or good for your health? |
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| good - this is why trans unsaturated fats are worse than cis and why saturated are worse than unsaturated |
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| proximity of substrates, positioning, stabilizing intermediates, acting like acids/bases, covalent catalysis, metal ion catalysis, prosthetic group catalysis |
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| two fatty acids and a phosphate group (could be amino acid side chain) attached to glycerol |
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| binds to polysaccharide and catalyzes its cleavage |
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| ligand can bind to protein and induce change in shape, not at active site though |
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| hypdrophobic interactions between non-polar substance are driven by the increase in entropy when the solvent cages combine, allowing water to be more disordered |
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| single lipid layer, not a biological membrane |
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| a type of allosteric regulation |
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| changes membrane fluidity. Increases fluidity at low temperature and decreases fluidity at high temperature. |
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| drugs that lower serum cholesterol by inhibiting an early enzyme in the cholesterol formation pathway |
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| inactive precursors to proteases |
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| prosthetic and coenzymes, coenzymes are reversible and prosthetic are stable parts of enzymes |
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| bind and hydrolyze GTP, can bind to and regulate the activity of other enzymes |
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| how many standard amino acids are there? how many are essential? |
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| co factors that add chemical functionality to enzymes |
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| pumping molecules across membranes, making or breaking macromolecules, motility, maintaining temperature, cell growth and division, signaling etc. |
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| positively charged amino acids |
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| special kink inducing amino acids* |
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| trans ships vesicles and the cis side receives: cell secretions are packages in the secretory vesiclesa the the golgi apparatus |
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| negatively charged amino acids |
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| uncharged polar amino acids |
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| ala, gly, val, leu, ile, pro, phe, met, trp, cys |
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| aromatic r group amino acids |
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| phenylalanine, tyrosine, tryptophan |
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| specific v-snare on vesicles and t-snare on golgi or cell membrane, this is the mechanism by which vesicles know where to go |
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| secondary structure (protein) |
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| formation of alpha helices and beta pleated sheets, stabilized by hydrogen bonding between peptide groups along the peptide backbone |
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| contain hydrolytic enzymes after budding off the golgi apparatus; capable of autophagy and phagocytosis (ingestiong of food or microbes into vessicles that then fuse with lysosome for digestion |
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| taking up small regions of cell membrane and forming vesicle |
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| membrane bound organelles that help direct enodcytosis material reach the lysosomes-they are recycled |
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| loads the correct amino acid on a tRNA |
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| creating a protein from a RNA sequence |
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| primary sequence (protein) |
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| order of amino acids, stabilized by peptide bonds |
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| tertiary sequence (protein) |
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| overall three-dimensional shape of a polypeptide, stabilized by bonds and other interactions between R-groups or between R-groups and the peptide backbone |
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| oxidize substrates to form H2O2, breakdown of fatty acides, new peroxisomes created by growth and division of preexisitng peroxisomes, protein components come from cytoplasm |
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| outer membrane, inner membrane (cristae are the folds in this membrane), matrix-region inside inner membrane |
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| quaternary structure (protein) |
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| shape produced by combinations of polypeptides, stabilized by bonds and other interactions between R-groups, and between peptide backbones of different polypeptides |
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| chloroplast, cell wall, plasmodesmata, central vacuole/tonoplast, lack centrioles |
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| right handed, periodicity of 3-4 amino acids |
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| made of tubulin, centrioles are bundles of microtubules, pull chromosomes apart during cell divions, shape and support cell |
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| interactions that determine the tertiary structure of proteins |
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| hydrogen bonding of side chains, van der waals interactions, disulfide bond, ionic bond |
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| made of actin, myosin;they interact to cause movement, 3D network in extracellular space, cytoskeleton and movement |
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| domains are regions of a protein which fold into a discrete structure and usually serve a specific purpose |
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| motor protein that walks along a microtubule |
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| keratin, desmosomes, cell strenght and cytoskeleton |
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| axoneme-body of flagellum made up of microtubules in the "9+2" manner, different from prokaryotic in structure and everything! |
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| in extracellular matrix, made up of three chains that wind around eachother, helical fiber helps so cells can stick together* |
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| interactions of membrane protein noncovalent but high affinity [zipper] |
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| adhesion, use keratin and other specific proteins to tether cells together (found in epithelial and muscle) |
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| create gaps that connect plant cell |
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| create gaps that connect animal cells |
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| consists of catabolism and anabolism |
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| adds electrons from some reduced cofactors |
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| uses water to a cleave a molecule |
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| active group of CoA, this sulfur containing group |
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| final electron acceptor in oxidative phosphorylation |
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| locations of cellular respiration stages |
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| glycolysis-cytoplasm, krebs/citric acid cycle-matrix, o. phosphorylation-cristae |
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| typical weight of amino acid |
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| create different chemical environments, impose order to events, allow functional complexity |
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| scanning electron microscopy |
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| transmission electron microscopy |
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| flat picture, like a cross section |
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| chromatin, nucleoli, nuclear pores, double layer membrane |
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| ionic, van der waals, hydrophobic and hydrogen bonding interactions |
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| darker, inactive, tightly packed |
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| synthesis of lipids, carb metabolism, detoxification |
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| site of synthesis of membrane bound or secreted proteins |
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| R + L in equil. with RL ; reactants over products |
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| nuclear membrane, ER, golgi complex, lysosomes, endosomes |
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| for both control and experiment, reduce to break covalent bonds and then add urea to break van der waals. If you remove urea and then oxidize, 3d structure reforms and then S-S bonds mostly reform correctly. If you oxidize first, covalent bonds form incorrectly and protein misfolds. |
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| 2 subunits, 4rRNA's, greater 50 proteins |
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| help refold misfolded proteins |
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| protein degradation, chops them into small peptides |
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| denature proteins by boiling in detergent, then add SDS to get uniform negative charge. Proteins migrate along gel only according to molecular weight. |
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| signal recognition particle receptor on the rough ER |
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| sequence a protein up to a small limit |
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| where does protein glycosylation |
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| in the Rough ER and Golgi |
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| used to determine protein sequence. Protein is cut out of a gel (purified), digested with trypsin, then sent through. Analyze results in computer |
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| a method to determine 3d shape of proteins and other macromolecules |
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