BabcockHall

Exothermic and endothermic refer to enthalpy. But spontaneous and nonspontaneous refer to Gibbs' free energy. It is important not to confuse the two.

That is the trouble with common names; they can be a little misleading at times. Did you find these links? http://en.wikipedia.org/wiki/Neoendorphin http://en.wikipedia.org/wiki/Endorphin

By nutrient, may I assume that you are including protein in the diet? Amino acids are needed because the body has no way to store nitrogen. Why would it be preferable to consume one's calories in the form of alcohol, as opposed to carbohydrates?

Lysing the cells is usually done mechanically. The acids may or may not have something to do with separating the histones from DNA, but I am just speculating. Do you have some good books on protein purification (Scopes, Suelter, etc.)? Those are extremely valuable.

Was the sample a mixture of proteins or a single protein? Saving that fraction is always a good idea.

Generally one wants to keep the volume of sample low, perhaps around 3% of the column volume for best separation. As the volume increases, the resolution should fall, all else held equal. The buffer in the void volume might possibly have small molecules that contain chromophores (I am just speculating). This establishes a kind of baseline for absorbance values as one's peak elutes.

One generally tries to keep the volume of the sample in a gel filtration minimal for the best separation between two proteins. However, for protein desalting, the volume of the sample is a little less critical. I am not familiar with the type of column you are using. However, if you kept the sample volume < 10% of the column volume, that would probably work, depending on how complete the desalting has to be. I often test my desalting columns using a colored small molecule, such as riboflavin phosphate, to check the efficiency of separation.

Hello Everyone, Does anyone know how quickly the reagents for silver staining SDS PAGE gels for proteins go bad? We have a kit that is 3-4 years old. The kits are pricey, most likely due to the silver itself, so we would prefer not to replace it unless it is necessary. If one reagent is likely to go bad, can we just replace that one? We have experience in our lab with ordinary SDS PAGE, but silver staining is new to us.

Also, the apparent pKa of Tris is dependent on ionic strength. Therefore, your calculation of how much HCl to use, is just an approximation.

I am very short on time today, but this calculation does not look correct. 1 M Tris means the total concentration of Tris in all forms: [HA] + [A] = 1.0 M. EDT Now that I look at it again, it seems to me that you have correctly taken the point I made above into account.

It is very difficult to figure out what question you are posing from what you just wrote. The chemistry by which methionine is converted into homocysteine refers solely to the L-isomer. I am not sure what you mean by a D-amino group.

IIRC D-amino acid oxidase is one enzyme that degrades D-amino acids in mammals. http://www.ncbi.nlm.nih.gov/pubmed/21956578

Some hormones bind to proteins that bind to DNA and stimulate or inhibit transcription. That is generally true of steroid hormones and also of thyroid hormones. I am not sure of their routes of degradation.

The unfolding and refolding of ribonuclease by adding and then removing urea also included breaking and reforming disulfide bonds. Whether or not they reform with the correct pairings is an interesting part of the Anfinson experiment. One needs an oxidizing agent to reform them from sulfhydryl groups. From what I know you are correct about this being a case-by-case question.

@OP, Are you talking about breaking disulfide bonds or some other type of bond? Some proteins are capable of reversible denaturation but not all proteins are. Another experimental variable is concentration (this is very important in urea denaturation, but I am not certain about heat denaturation). In vivo molecular chaperones can aid in the refolding process.

I don't have time to do this topic justice today. However, I can give you a few quick thoughts. Thermogenesis is associated in some animals with brown adipose tissue (p. 917); adipose that has mitochondria. The energy that is ordinarily used to make ATP is used to generate heat instead. See p. 736 in Nelson and Cox, Biochemistry, 5th ed. I am not sure how to answer your second question. Lipogenesis literally means synthesis of lipids, which certainly includes fatty acids, TAGs (triglycerides), and cholesterol. Certainly humans are capable of synthesizing fatty acids from acetyl CoA.

Well for starters, muscle tissue is unresponsive to glucagon; therefore, covalent regulation of glycogen phosphorylase does not depend on this hormone. I am hesitant to call either the a form or the b form the default state. They interconvert. Liver glycogen phosphorylase is under the control of glucagon. Try Nelson and Cox's textbook.

There are many signal transduction cascades that might be what you want. Blood coagulation and complement (immunochemistry) both use serine proteases in the cascade. Trimeric Gq proteins work through phospholipase C and protein kinase C. However, these are not developmental cascades, which you said were of special interest. What about the binding of growth factors to RTKs through ras p21 (just before the MAP kinase cascade)? Or the JAK-STAT pathway that brings about maturation of erythrocytes? Clonal selection in the immune system might be a place to look, also.

I sometimes think that I have fewer clogging issues when I use celite versus when I use just fritted glass. I have not rigorously studied this, however.

Stay away from E-64 and leupeptin. Look into regenerating cysteine protease activity after treatment with PMSF. I think dithiothreitol will work, but I don't have a citation.

What's wrong with the MAP kinase cascade? I am not sure why you are posting this question in homework help. Is this homework or research?

The explanation may have some truth in it, but I have to wonder whether or not the whole story is exactly what they imply. The interactions among the bases in ds DNA is not classically hydrophobic in nature, if I recall what I read in Voet and Voet correctly. Of course, the interactions between aromatic groups on the membrane with the bases of DNA or RNA might still be hydrophobic, but this should ideally be demonstrated.

I once lyophilized protein that had been dialyzed against 1 mM hydrochloric acid. I followed the lyophilization with complete hydrolysis of the protein. Perhaps 1 mM hydrochloric is not suitable for your protein, in which case ammonium formate sounds reasonable.

It does not seem to me that you have provided enough information to answer the problem.

Do we know whether this protein has a single alpha helix as the transmembrane domain, or are there multiple alpha helices? A few proteins have beta transmembrane domains also, but perhaps we can ignore them. I think your answer might be backwards.