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.

Filter by
Sorted by
Tagged with
0
votes
1answer
101 views

Plastic: Reputable Publications

I would just like some reputable textbooks and or publication companies that have extensive research on plastics, as, for example, dealing with life cycles of plastics, degradation factors, effect on ...
3
votes
1answer
302 views

Michaelis Menten derivation for 2 enzyme substrates

We know the Michaelis Menten derivation for the following reaction: $$\ce{E + S <=> ES -> E + P}$$ However, what if the reaction took place in a different scenario whereby: $$\ce{E + S <...
3
votes
1answer
263 views

Best way to dissolve and consume cysteine HCl monohydrate powder

Does cysteine break down in filtered water? Should this made more acidic? If I mix cysteine powder in juice (something acidic maybe), does it remain at cysteine? It seems that it can oxidize into ...
1
vote
1answer
550 views

Why do we need to incubate this system for 18 hours at 60 degrees Celsius?

I am conducting a bio-chemistry related experiment and I have been unable to understand a step which is commonly performed. The procedure that is confusing me is outlined in the supporting information,...
2
votes
1answer
183 views

Does tolerance to alcohol affect blood/breath alcohol levels?

When blood / breath alcohol levels are taken to determine how intoxicated a person is, does it depend on their tolerance ? i.e. If you had two people of identical age, weight, fitness, etc. person A,...
16
votes
2answers
821 views

Why do chalcogens (Group VI) stink so badly?

For more fun with Dr. Derek Lowe, see this for a primer: Things I Won't Work With - Carbon Diselenide. The short of it is that we carbon-based life forms generally like oxygen. However, move just one ...
3
votes
3answers
9k views

Homemade preservative for natural aloe-vera gel?

I suppose this question can be extrapolated to food in general, but it is the case that I would like to know if there are any methods that would help me to keep the aloe gel fresh, i.e. avoiding it to ...
3
votes
2answers
941 views

Recreational drugs by half life

I am interested in the Biological Half Life of substances. In the previous wikipedia link, I've already found the half lives of common pharmaceutical products. I can't seem to find similar data for ...
1
vote
1answer
186 views

What metabolite intermediate will accumulate in a mammalian cell-free extracts capable of glycolysis if lactate dehydrogenase is inhibited?

I know the reaction proceeds as follows: Pyruvate accepts the electrons from NADH to form lactate. What would be the intermediate in this reaction? Would it be NADH or NAD+?
6
votes
1answer
1k views

Is it possible to separate salt from food, or at least convert it into something that doesn't taste salty?

A couple months ago, one of my room mates accidentally used a cup of salt to make apple crumble. She asked if there was any way to separate it, probably because I had recently reduced the acidity of a ...
5
votes
1answer
172 views

What are the factors controlling the fate of post-adhesed volatile molecules of the olfactory epithelium?

What happens to volatile molecules that reach the main olfactory epithelium in the nasal cavity after they bind and the neural stimulus fades? To what extent do such factors as receptor kinetics and ...
2
votes
1answer
47 views

Which mutated enzymes act as better drugs than their non-mutated form?

Is there an enzyme which is used as a drug (let it be called version $A$) and a mutated version of it ($M$), where the activity of $M$ was found to be higher than $A$? Any references on such a case ...
3
votes
2answers
3k views

How can I control the oxygen in an erlenmeyer flask in a bioprocess?

I need to control oxygen in a erlenmeyer flask in a bioprocess. I need to remove overall oxygen in a erlenmeyer flask, and after I need to add oxygen in controlled amounts to a culture in a shaken ...
2
votes
1answer
93 views

Aflatoxin versus Benzene, permissible levels

Alfatoxin and benzene are carconogenic, and this is the major concern for low, chronic doses. They are regulated to the few parts per billion level in food. However, according to http://toxnet.nlm.nih....
2
votes
1answer
394 views

Impact of detergent on internal living tissue?

There was some spirited debate between the members of my chemistry lab today about the theoretical consequences of ingesting a large amount of the detergent Triton X-100 at a 100% concentration. The ...
4
votes
1answer
105 views

How can you estimate how much of a substance will dissolve in a given lipid?

How can you estimate how much of a substance with a known partition coefficient and other physical/chemical data regarding the substance will dissolve in a given lipid? In particular I would like to ...
4
votes
1answer
3k views

How is the time for a test tube in a centrifuge determined?

I came across some hairy math that's used for analytical centrifugation, mostly for things like determining the sedimentation rate for liquids. However, what I don't understand is how someone ...
9
votes
2answers
3k views

Is formaldehyde a carbohydrate?

Formaldehyde has the formula $\ce{CH2O}$, and the ratio of atoms in a simple carb is $\ce{1C:2H:1O}$. This fits the formula of formaldehyde. When I researched this, I found some sources saying that ...
2
votes
0answers
70 views

Determine max of 2 parameter functions

I have 12 experimental tables with OD(substrate concentration, time), where OD is optical density and one table with $\mu$ (substrate), where $\mu$ is growth speed. OD and $\mu$ are functions. The ...
1
vote
2answers
702 views

What is the oxidation state of Calcium in teeth?

What is the oxidation state of Calcium found in human teeth?
7
votes
2answers
2k views

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 ...
7
votes
2answers
10k views

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 ...
2
votes
1answer
1k views

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 ?
3
votes
1answer
9k views

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 ...
8
votes
2answers
2k views

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 + ...
7
votes
2answers
713 views

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 ...
49
votes
1answer
9k views

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
votes
1answer
443 views

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
votes
3answers
3k views

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
votes
1answer
2k views

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 ...
22
votes
1answer
2k views

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)
13
votes
1answer
184 views

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/...
16
votes
1answer
1k views

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 ...
21
votes
3answers
2k views

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 ...
6
votes
2answers
714 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 ...
25
votes
1answer
941 views

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). ...
20
votes
1answer
10k views

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 ...
22
votes
2answers
314 views

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?