BabcockHall

I may not be picturing this accurately, but what about the air that comes in when one releases the vacuum? I would think that some kind of filter is necessary.

Hi DrP, Bleach solutions are particularly effective at removing DNA contamination, more so than acid (Prinz and Andrus, Biotechniques; see also the Promega guidelines). A speedvac is a slightly different beast than a rotary evaporator, but I do see some similarities. In both cases, releasing the vacuum seems as if it might be a crucial step. If there were airborne DNA, it could sneak in at that point.

On a discussion board about DNA sequencing I found this comment: "Instead of evaporating all of this, we bind it all to AMPure beads (2x cut), wash the beads once in 70% ethanol, dry them, and resuspend them in 10.5ul of hyb buffer. It takes all of 5 minutes, and no cross-contamination prone speedvac step!" I also found this comment elsewhere: "Particular care should be taken to avoid contamination of commonly used rotors. " From the context of the article, the author may have been referring to rotors used in organic precipitation of DNA or in post-precipitation drying of the pellet in a speed vac, but I am not sure. I also found ThermoScientific's literature about one low vacuum pump that was claimed to be hermetically sealed to prevent contamination. I am interested in the use of PCR in forensics. How much of a problem is contamination from other DNA during concentration in a speed vac? Is it the rotor that is the biggest problem, or is it aerosol DNA? How do people avoid it? Thank you.

A typical polypeptide or nucleic acid is a heteropolymer. Something like starch is a homopolymer (only glucose residues).

Lipids fall into a gray zone for me. They are big, but they are typically not as big as other biological macromolecules, such as proteins and RNA. I can't think of any that are polymers, exactly, although triacylglycerols have three fatty acyl groups. Cholesterol is not really a polymer in my mind, although perhaps some isoprenoids are.

An environmental chemist told me some years ago that glyphosate broke down relatively quickly in the environment. Given that glyphosphate is a phosphonate, I always found that a little surprising.

Thank you. We use it to induce protein overproduction and purify the protein.

Let's start with an easier question: Why do SN1 reactions have secondary isotope effects?

Isopropyl-beta-D-galactopyranoside (IPTG) is often advertised as being free of dioxane. How important is this? I understand that some strains of bacteria are inhibited by dioxane, but how severe is this problem?

"I know some enzymes work by catalytic action ,but are all enzymes merely catalysts? If so why do we need glands to constantly replenish them?" Enzymes may misfold or be damaged in some way. Also, the regulation of some enzymes is achieved partially by destroying them at one time and synthesizing them at another. HMG-CoA reductase comes to mind as one such enzyme. With respect to kinases and phosphatases, It is often the case that one is regulated to be highly active while the other is regulated to be relatively inactive. This is called reciprocal regulation, and it may be brought about by allosteric interactions or by reversible covalent modification.

For quick overviews, there are two books. One is PDQ Biochemistry, by Baker and Murray, and the other is Basic Concepts in Biochemistry, by Gilbert.

The only reference to the use of this group with which I am familiar was in the context of peptide synthesis, as opposed to the chemical modification of proteins. That having been said, I have not searched carefully, either. http://profiles.uonbi.ac.ke/ayusuf/publications/1-tetralinyl-group-asparagine-side-chain-protection-and-application-boc-solid-ph

You need to provide more information, and then it may be possible to help. What is your sample, and what is your goal? What kind of side chain do you wish to modify? (etc.)

If an ancestral glycogen catabolase simply broke down glycogen to run through glycolysis, then having the nucleophile be phosphate definitely confers an advantage. If this enzyme later became liver glycogen phosphorylase, then I can see why a glycogen hydrolase for liver might not have evolved. However, I have to wonder whether having two points of control (glycogen phosphorylase and glucose 6-phosphatase), might confer some ability to fine tune how much glucose gets created and from which of two sources (glycogen versus pyruvate and related glucogenic compounds). Just thinking out loud.

I don't believe that the question posed by the OP had anything to do with nonenzymatic hydrolysis (which would require an acidic environment) I think it was more along the lines of why is there no enzyme "glucose hydrolase" that would break glycogen down directly to glucose. There would still need to be a debranching enzyme, as CharonY pointed out.

Both glycogen phosphorylase and glucose 6-phosphatase are regulated enzymes, and the ability to regulate them independently may be important in some circumstances.

In some ways classifying on the basis of how the iron is coordinated makes sense. Of course, each type of coordination will have several functions. For example if we make a classification "heme iron proteins" we would have to include electron transfer proteins, oxygen transport proteins, and oxygen-using enzymes at the very least.

That is a very broad question, and it depends very much on the enzyme in question. Activity may be lost over time because the enzyme is oxidizing or degrading in some way. Also, if it adsorbs onto surfaces, you can lose some activity that way. The amount of buffer would not be my first place to look, but any calculations of activity would have to take into account differences in volumes from one experiment to the next.

Another way to think about NAD is to look at it as a hydride ion acceptor, a hydride ion being a proton and two electrons. NADH is a hydride ion donor. Likewise NADP is a hydride ion accepter, and it becomes NADPH. The original post has a typographical error with respect to NADP.

I don't know the answer, but I am happy to speculate. Although liver stores of glycogen can be converted into glucose and exported (this is obviously a major pathway), that is not its only possible fate. It can proceed through glycolysis or be converted into other carbohydrates, such as galactose. These are both more sensibly done through glucose phosphates.

Empirically aromatic carboxylic acids (benzoic acid and aspirin, for example) are not very soluble in water but are quite soluble in diethyl ether. Their conjugate base forms are quite soluble in water. This difference has a good deal of utility when trying to separate one molecule from another by extraction.

If two hydrogen atoms are in fast exchange, a single signal will appear at the weighted average of the chemical shifts of each one by itself.

A good place to start is protein modification books by Means and Feeney or by Roger Lundblad. N-hydroxysuccinimide esters are sometimes used to modify lysine residues in proteins. LInk.

LOL, I assumed that the Grignard would open the epoxide, but I managed not to see the question of ring size at all. I also have to wonder whether or not this is an error of some kind.

I would analyze it in terms of carbons that have a partial positive charge or a partial negative charge.