Questions tagged [biochemistry]

This tag is for questions concerning biochemical methods (e.g. electrophoresis) or those concerning biochemical mechanisms or research. Do not use this tag if your question is merely about compounds often used in areas related to biochemistry or associated with these. These may fall under organic chemistry or the appropriate compound’s functional groups’ tags.

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Why is tin(II) fluoride more effective in turning apatite into fluorapatite?

In more powerful toothpastes, like Crest Pro-Health, stannous fluoride is used in place of sodium fluoride. According to Wikipedia: Stannous fluoride converts the calcium mineral apatite into ...
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Why does milk flake?

While drinking milk (or better 'while seeing the milk I'm gonna drink') a question came up to my mind: Why does the milk sometimes flake, even if not in contact with some other substances? I guess ...
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Are there ways to predict which chemicals will kill certain bacteria?

Are there ways to compute what chemicals kill a give bacteria but not another given bacteria ? Does that help much to make medication ?
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1answer
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Can acidic conditions break disulfide bonds

I am denaturing a protein using organic solvent and acid (49:49:2% water:methanol:acetic acid), but I want to maintain the disulfide bonds. My chemistry knowledge isn't good but disulfides are broken ...
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Why do lipids in a cell hydrolyze into glycerol and fatty acids?

Most Lipids in a cell have ester bonds (made up of glycerol and fatty acids). I have learned in my chemistry class that we can hydrolyze an ester by simply adding water to it. $$\ce{CH3COOCH2CH3 + ...
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Cyanogenic glycosides and HCN

I'm researching cyanide for a biology project and noted that one of the largest sources of carbohydrates in the tropics is the cassava root -- which I previously researched as a food that contains a ...
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1answer
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Why does menthol (e.g. peppermint) feel cool to the tongue?

Especially when drinking water after the fact, mint can give a sharp cold sensation inside one's mouth. What process causes the sensation to occur?
8
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1answer
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What is the timescale of disulfide bond formation?

What is the timescale of disulfide bond formation in a given protein? What influences it? Finally, how does one actually measure it? From what I understand, the reduction and oxidation of bonds ...
9
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3answers
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What causes the DNA fragments to stop moving in gel electrophoresis?

I'm currently studying VCE BioChemistry, and we're studying the separation of DNA strings of different lengths via gel electrophoresis. (This involves having 'clumps' of DNA at one end of a gel ...
15
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1answer
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What is Cβ (C-beta) deviation?

Molprobity and some other protein structure validation tools report a Cβ deviation statistic and offer plots for it (example below). Apparently if the Cβ is greater than 0.25 Å, some ...
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1answer
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What software is used to generate the PDB molecule of the month images?

What software does the PDB use to generate these "cel-shaded" protein models with outlines around foreground atoms? (Leptin: May 2012 Molecule of the Month by David Goodsell)
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What are the border definitions in the Ramachandran plot?

I've heard some people mention that this or that program isn't "up to date" with respect to the borders used in the Ramachandran plots to classify φ/ψ as being in the most favorable/acceptable/...
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Why does the sulfone ring in tazobactam open when the lactam is hydrolyzed?

One of the drugs I work with is a beta-lactam (4-membered ring with an amide bond) fused to a sulfone ring, tazobactam. It's relatively stable in water; the lactam is not significantly hydrolyzed ...
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What are known examples of drugs that racemize/stereoconvert in vivo, and how are they converted?

It is known that although only the (S)-enantiomer of the infamous sedative thalidomide possesses teratogenic properties, it is not very useful to administer the pure (R)-enantiomer since it is ...
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725 views

Molecular explanation of the Hofmeister Series

The Hofmeister Series is a useful metric in understanding how to precipate proteins. However, wikipedia and many other source indicate that the order of the series is rather empirical. I'm curious ...
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How can I determine if there are π-π interactions between an amide and an aromatic ring in a protein?

In a crystal structure I've determined, a triazole ring on my ligand appears to be stacking with a tyrosine (top in picture): However, there is also an amide, courtesy a glutamine, near it (bottom). ...
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1answer
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Side reactions of NHS Chemistry

N-Hydroxysuccinimide (NHS) chemistry is commonly used in chemical biology to react with primary amines like lysine and the N-terminus of proteins. I was curious how labile NHS esters are to other ...
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What is a good method to measure the redox potential of a cellular system?

I know how to measure the concentration of free thiols, which is reflective of the redox-potential of cellular compartment such as the cytoplasm or a lysosomes. What other methods exist?

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