what is the advantage of CD\nover crystallization in studying protein\nif possible, plx explain also the rational \nof using CD to study protein aggregation \nlike what data to collect and how to analyze
128228
Circular dichroism (CD), is the differential absorption of left- and right-handed circularly polarized light. It is a form of spectroscopy used to determine the optical isomerism and secondary structure of molecules.\n\nAt a given wavelength,\n\nΔA = (AL − AR) \nwhere ΔA is the difference between absorbance of left circularly polarized (LCP) and right circularly polarized (RCP) light (this is what is usually measured). It can also be expressed as:\n\nΔA = (εL − εR) C l \nwhere εL and εR are the molar extinction coefficients for RCP and LCP light, where C is the molar concentration and l is path length.\n\nThen\n\nΔε = (εL − εR) \nis the molar circular dichroism. This is what is usually meant by the circular dichroism of the substance.\n\nAlthough ΔA is usually measured, for historical reasons most measurements are reported in degrees of ellipticity.\n\nThe molar ellipticity is:\n\n[θ] = 3298Δε. \nIn general, this phenomenon will be exhibited in absorption bands of any optically active molecule. As a consequence, circular dichroism is exhibited by biological molecules, because of the dextrorotary (e.g. some sugars) and levorotary (e.g. some amino acids) molecules they contain. Noteworthy as well is that secondary structure will also impart a distinct CD to their respective molecules. Therefore, the alpha helix of proteins and the double helix of nucleic acids have CD spectral signatures representative of their structures.\n\nCD is closely related to the optical rotary dispersion (ORD) technique, and is generally considered to be more advanced. CD is measured in or near the absorption bands of the molecule of interest, while ORD can be measured far from these bands. In principle these two spectral measurements can be interconverted through an integral transform, if all the absorptions are included in the measurements.\n\nThe ultraviolet CD spectrum of proteins can predict important characteristics of their secondary structure. CD spectra can be readily used to estimate the fraction of a molecule that is in the alpha-helix conformation, the beta-sheet conformation, the beta-turn conformation, or some other (random) conformation. These fractional assignments place important constraints on the possible secondary conformations that the protein can be in. CD cannot, in general, say where the alpha helices that are detected are located within the molecule or even completely predict how many there are. Despite this, CD is a valuable tool, especially for showing changes in conformation. It can, for instance, be used to study how the secondary structure of a molecule changes as a function of temperature or of the concentration of denaturing agents. In this way it can reveal important thermodynamic information about the molecule that cannot otherwise be easily obtained. Anyone attempting to study a protein will find CD a valuable tool for verifying that the protein is in its native conformation before undertaking extensive and/or expensive experiments with it. Also, there are a number of other uses for CD spectroscopy in protein chemistry not related to alpha-helix fraction estimation. s\n\nCD spectroscopy is usually used to study proteins in solution, and thus it complements methods that study the solid state. This is also a limitation, in that many proteins are embedded in membranes in their native state, and solutions containing membrane structures are often strongly scattering. CD is sometimes measured in thin films.\nCD has also been studied in carbohydrates, but with limited success due to the experimental difficulties associated with measurement of CD spectra in the vacuum ultraviolet (VUV) region of the spectrum (100-200 nm), where the corresponding CD bands of unsubstituted carbohydrates lie. Substituted carbohydrates with bands above the VUV region have been successfully measured.\n\nMeasurement of CD is also complicated by the fact that typical aqueous buffer systems often absorb in the range where structur
589501
Advantage: many chekpoint allow for a very fine tuning of the hormone response as each steps is another way to control the hormone output.\n\nDisadventage: hell of a lot harder to study in a lab, believe me!
146278
Inside our cells -it is a blind, mute and deaf world of roaming/floating molecules! Molecules (including the macromolecules like proteins) wonder almost aimless but can have influence on each other -like, breaking or joining others. But these interactions have to specific. The specific contact and the influence on each other is possible only due to the compatibility in the physico-chemical features on their surfaces, which are directly dependent on the structure.\n\nIt is the proteins that carry out most of the functions in cells. Hence, protein structure is very important for cell function. Because actin is such a basic structural protein and cytochalasin B can interact with it (and affect it), their interactions seem influence activities in different cells and events like fertilization and immune functions. You can look up for literature on this aspect.\n\nI am quoting one abstract from the NCBI's PubMed database (Journal -Biochim Biophys Acta. 1980 Dec 16;626(2):494-500.; PMID: 6894243)of research work by  Maruyama K, Hartwig JH &Stossel TP.:\n\nCytochalasin B and the structure of actin gels. II. Further evidence for the splitting of F-actin by cytochalasin B.\nCytochalasin B decreased the flow birefringence and s20,w and increased the extinction angle of actin filaments in salt solutions favoring polymerization of the protein. These changes occurred without a detectable increase in the equilibrium actin monomer concentration determined by a radioassay. These results complement earlier observations indicating that cytochalasin B shortens actin filaments without net depolymerization. Analyzed in terms of Flory's classical network theory, this shortening accounts for the marked effect of cytochalasin B in dissolving the gel structure of F-actin crosslinked by actin-binding protein concentrations near the critical concentration for incipient gelation. Cytochalasin B decreased the annealing rate of low concentrations of actin filament fragments prepared by sonic disruption. The result is consistent with the idea that cytochalasin B binds to the ends of actin filaments, and may explain how cytochalasin B causes filament shortening.
131912
do you mean interactions BETWEEN nucleic acids and proteins?  If so there's a lot of ways you can study that - you can do a footprint analysis - digest the nucleic acid in the presence of the protein and see what piece gets protected to see where the protein binds if you know the identity of the two interacting molecules.  If you don't know their identity you can try a gel-shift assay where DNA will move at different rates on a gel in the presence and absence of various proteins.  If you know the protein but not the DNA you can try an affinity column with the protein immobilized and then try to determine which DNA sequences bind.  You can also try to determine the crystal structure of a co-crystal if you have a lot of the two materials.  good luck!
496789
Alanine (Ala) also 2-aminopropanoic acid is a non-essential α-amino acid. It exists as two distinct enantiomers - L-alanine and D-alanine. L-alanine is one of the 20 amino acids most widely used in protein synthesis, second to leucine, accounting for 7.8% of the primary structure in a sample of 1,150 proteins [1]. D-alanine occurs in bacterial cell walls and in some peptide antibiotics.\n\nStructure\nThe α-carbon atom of alanine is bound with a methyl group (-CH3), making it one of the simplest α-amino acids with respect to molecular structure and also resulting in alanine being classified as an aliphatic amino acid.\n\n\nSynthesis\nAlanine is most commonly made by transfer of an amine group to pyruvate. Because transamination reactions are readily reversible, alanine can be easily formed from pyruvate and thus has close links to metabolic pathways such as glycolysis, gluconeogenesis, and the citric acid cycle.\n\n\nFunction\nThe methyl group of alanine is very non-reactive, and is thus rarely directly involved in protein function. However, alanine can play a role in substrate recognition or specificity, particularly in interactions with other non-reactive atoms such as carbon.\n\nIt goes through alanine cycle to generate glucose from protein.\n\n\nSources\nAny protein containing food such as meat, poultry, fish, eggs, and dairy products are rich in alanine.
341429
The answer is A of course. The other answers doesn't make sense.  They are referring to the ....lysosomes.... ok. Ribosomes synthesize proteins for the cell.
423162
is this your school homework,  are there suppossed to be other questions before these because my computer shows them starting from No. 4.\nnway,\n4.  filter the solution while still hot because as the soltion cools crystallization occurs, and you will nloose your product on the fiolter paper.\n5. crystallization can be induced by reduction in temperature i.e put in an ice bath or you can use a technique called seeding where you put a few crystals of the expected substance in the solution, the other method is to increase the concentration of the solution by evaporating it, to saturation point, ensure you do not evaporate it dry.\n6.i do not know what you started with so i can not tell.\n7.slow cooling will definately give bigger crystalls.\n8.sodium chloride reacts with silver nitrate to form a white precipitate, actually silver nitrate solution is used to analyse NaCl in industrial setting.\n\nope you will find these information sufficient.
275520
put simply its complete bullshit... lol, solidification is just the slowing of atoms/molecules, sonce light ALWAYS (dont even go tehre with the whole medium thing, its always) travels at teh same speed... like i said before solidified light is bs. :-)
183346
1D NMR spectra can be too complex for interpretation, especially in the case of protein analysis for most of the signals heavily overlap.  By introduction of an additional dimension, the spectra can be simplified and further information is obtained.\n\n.
173494
So many questions zapped in one, eh?\n\nOk, let me answer them one by one. First let us talk about Enzymes in general.\n\n1] Enzymes-\n\nStructures.\nThe enzymes can have different structures as there are too many functionally and structurally different enzymes. You can view and study the structures from the online Enzyme Structure Database. Here is the link-\nhttp://www.biochem.ucl.ac.uk/bsm/enzymes/\nhttp://www.cartage.org.lb/en/themes/sciences/lifescience/GeneralBiology/Biochemistry/Enzymes/Classification/Classification.htm\nFor further such web-pages, refer to the links listed here-\nhttp://www.google.com/search?hl=en&lr=&q=enzymes+structure&btnG=Search\n\nMode of Working.\nThe enzymes usually work by the "Lock and key" mechanism. They recognise the substrate and attatch to them. Thereafter, they change the substrate to the product and release it and remain unchanged in the process.\n\nHere are links with pictures and graphs that you might find useful-\nhttp://www.biologycorner.com/bio3/notes-enzymes.html\n\nLatest Research-\n1] http://www.sciencepages.co.uk/keystage4/GCSEChemistry/enzymeslinks.php\n2] http://www.google.com/search?hl=en&lr=&q=enzymes+research&btnG=Search\n3] http://www.musclemass.com/digestive_enzymes.html\n4] http://www.valleyenzymes.com/\n\n=========== ============ ============\n\n2- Amylases\n\nStructure\nTheir structures can also be found in the database here-\nhttp://www.biochem.ucl.ac.uk/bsm/enzymes/ as they are also enzymes. Here are a few more links that you might find useful-\n1] http://content.febsjournal.org/cgi/content/abstract/269/2/397\n2] http://www.google.com/search?hl=en&q=amylases+structure&btnG=Google+Search\n3] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=4196183&dopt=Abstract\n\nMode of action.\nSimilar to Enzymes. Here are a few more useful links-\n1] http://www.google.com/search?hl=en&q=amylases+working&btnG=Google+Search\n2] http://www.classofoods.com/page1_4.html\n3] http://www.realbeer.com/jjpalmer/ch14.html\n\nLatest Research.\n1] http://www.findarticles.com/p/search?tb=art&qt=Amylases+%2F+Research\n2] http://www.google.com/search?hl=en&q=amylases+research&btnG=Google+Search\n3] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=13835834&dopt=Abstract\n\n========= =========== ============\n\n3- Glucoamylases\n\nStructures.\nSee the database again-\nhttp://www.biochem.ucl.ac.uk/bsm/enzymes/\n\nA few more specific links are-\n1] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10491121&dopt=Abstract\n2] http://peds.oxfordjournals.org/cgi/content/abstract/7/3/393\n3] http://www.public.iastate.edu/~pedro/papers/coutinho94a.html\n4] http://www-hasylab.desy.de/science/annual_reports/2005_report/part2/contrib/72/14454.pdf  \n5] http://www.google.com/search?hl=en&q=glucoamylases+structure&btnG=Google+Search\n\nMode of Action\nSee Enzymes again. Some more specific links can be found here-\nhttp://www.google.com/search?hl=en&q=glucoamylases+working&btnG=Google+Search\n\nResearch.\nHere are some awesome pages-\n1] http://www.enzymestuff.com/conditionceliac.htm\n2] http://www.chemweb.com/journals?type=issue&jid=07349750&iid=00240001\n3] http://www.google.com/search?hl=en&q=glucoamylases+research&btnG=Google+Search\n4] http://www.bb.iastate.edu/FacultyResearchFolder/Robyt/Research.html\n5] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10767433&dopt=Abstract\n6] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2116499&dopt=Abstract
115581
label the known protein with a radioactive isotope, or better yet, maybe you could label the protein with a flourescent dye (dont know how, its beyond my expertise) and where ever the protein binds on the receptive cell may be what you're looking for.  but i dont know of any assays per se for it.
358234
Proteins were precipitated with an equal volume of 20% (w/v) trichloroacetic acid and washed three times with 4 ml of an ethanol/ethyl acetate mixture (1:1). Washings were achieved by mechanical disruption of pellets in the washing solution using a small spatula, and re-pelleting by centrifugation at 6000 g for 5 min. Finally, the precipitates were dissolved in 6 M-guanidine-HCl solution.Ref:Cell. Biochem. Func.(2006)24:79-85.
523747
i think that if you categorise it  under physics/biology/chemistry, you might get a better response.\n\nnevertheless:\n\nhttp://school.discovery.com/homeworkhelp/bjpinchbeck/bjscience.html
249729
Many of the orignal studies were based on mutations in bacteria which halt growth or have other phenotypes, where it was found that mutations could be labeled into several groups, and that if bacteria from different groups mated, then the phenotype is restored.  From this it was deduced that the mutations were in coding regions for proteins that exist in a network ie A to B to C, and usually proteins like A and B were in a complex.  Today its a large part of cell and molecular biology to figure out if proteins are in complexes, and what the complex does.  Its not necessarily important that A and B are in a complex, but what that complex does; since that is the proteni function in cells.  So if A and C are in a complex, the complex has a certain function.  if B and C are in a complex, then there is a different function.  Drug companies have been exploiting this type of knowledge for a long time, but what is more impt is the understanding of how proteins interact with other proteins, and how they regulate cellular functions.  Once this is understood, then drugs can be rationaly designed.  Even then, however, it's not possible to guarantee patient efficacy.  \n\nWe just had a great lecture by Gordon Mills, an expert in the PTEN protein pathway, and he talked about the dozens of drugs made against various members of this pathway, and noted that so far none of these drugs are effective in patients, although they work in the test tube and in mice.  So, drug discovery is a very difficult issue and takes billions of dollars for one drug to be delivered to market (and 10 years or more).
545217
okay I'm gonna try this. :-)\n\nImmunohistochemistry is a way to detect certain proteins that are in your body's tissues.\n\nIn kidney diseases, there may be abnormal proteins in the kidney that you'll want to look for.\n\nSo what happens is a scientific technician will take an extremely thin slice of kidney tissue, and treat it with "antibodies" to the abnormal (bad) protein.  \n\n[An antibody is something that will stick to a certain protein, they can be made to be very selective.  So there is a specially designed antibody that will find this bad protein and stick to it.]\n\nIn addition, this antibody has a "signal" stuck to it.  Normally it's some kind of fluorescent (shiny, hehe) dye.  After treating the sample with antibodies and getting them stuck to the abnormal proteins in the tissue, the technician will then perform a reaction that will activate the dye.  Then, the sample is put under a microscope, and the picture is analyzed for presence of this dye.  If the kidney is diseased and has the abnormal "bad" protein, there will be colored dye spots all over the picture.\n\nSo in short... kidney diseases can show abnormal (bad) proteins, scientists can make things ("antibodies") that stick to these bad proteins, and then these antibodies can be "activated" to light up the dye and reveal where the bad proteins (which they are sticking to!) are.\n\nIn theory, a normal kidney tissue sample would not show any fluorescence/lighting if they were looking for a "bad" protein.  Of course, "bad" protein is a huge generalization, and I'm just trying to simplify it into layman's terms. \n\nContact me if you have other questions, hope this helps!\n\n-IJ
389693
In SDS-PAGE you have the formation of a complex between SDS and proteins so that you have anegatively charged SDS molecule for approximately every two amino acids in the protein. This means that the protein-SDS complex will have a huge negative charge that will mask any charge of the protein itself and force the protein-SDS complex to move towards the positive electrode.\n\nI've never heard of the other thing you are mentioning. Could you expand on that? Hydrophobicity of what? DNA has a large negative charge due to its phosphate backbone and that's the reason it migrates during electrophoresis.
230434
"C" proteins is the correct answer.