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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is there any process to detect methane chimicaly? [closed]

Dear collegues, I want to know if is there any process to detect methane chimicaly? I want to detect the methane released by archaea with a chemical process.
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What is the main contributor of the color of honey? [closed]

I was told that the color of honey contains so much chemistry and that was interesting to me and after doing a couple of research I found that the color of honey depends on the presence of plant ...
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Why is methyl parathion less toxic than ethyl parathion?

According to the PubChem pages on ethyl parathion and methyl parathion (pages 11 and 12 of the toxicity section, respectively), methyl parathion is significantly less toxic than ethyl parathion. The ...
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Hydrolysis of phosphoryl-oximes

When acetylcholinesterase that has been inhibited by an organophosphorus compound is reactivated by an oxime, a phosphoryl-oxime is formed, which is then somehow hydrolyzed in the blood. One study ...
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1answer
38 views

Can aged acetylcholinesterase be reactivated?

it is a well-known fact that certain phosphorus compounds can inhibit the enzyme acetylcholinesterase, and that the treatment of poisoning with such compounds is administration of atropine and some ...
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1answer
25 views

How does sodium rosinate enhances lathering property? [closed]

Why don't we use sodium carbonate or sodium stearate? What does sodium rosinate contain that the other two don't?
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1answer
38 views

Multiday lab courses in classic chemistry [closed]

This time of the year I usually get some extra income I can use on interesting courses. Usually rescue or sport courses. However, I also have a master degree in chemistry, and would like to spend some ...
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94 views

Interaction of trifluoroacetates with acetylcholinesterase

There exists a substance called TMTFA, or 3-(N,N,N-Trimethylammonio)-2,2,2-trifluoroacetophenone. It is known for being able to inhibit acetylcholinesterase at femtomolar concentrations. The TMTFA-...
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1answer
99 views

Who was C.H. Kao?

I am editing a Wikipedia article about the Chen-Kao reaction that is used to identify ephedrine, but I am unable to find biographical info on C. H. Kao: K.K. Chen and C.H. Kao - Ephedrine and ...
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1answer
54 views

Finding the sensitivity of zero-order ultra sensitivity and its parameter dependence

I am provided a one-dimensional reaction system showing zero-order ultra sensitivity. $$\ce{X_1 ->[f_1] X_2}, \quad \quad \quad \ce{X_2 ->[f_2] X_1}$$ The reaction rate function is the reduced ...
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Why are carbamates capable of inhibiting acetylcholinesterase?

Certain carbamate compounds, such as the insecticide carbaryl or the Edgewood carbamates such as EA-3990, can inhibit the enzyme acetylcholinesterase. Unlike organophosphorus compounds, however, they ...
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Dispersity of synthetic DNA [closed]

Recently I was reading an article about DNA nanostructures and I was wondering-- I know that DNA in living systems is monodisperse, but when we make DNA synthetically, is it truly monodisperse or ...
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What exactly makes a carbon atom “α” in a protein residue?

I'm a computer scientist and have no biochemical background, but was working on a project recently that had me going through a lot of protein residues for one reason or other. Feel free to correct me ...
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Prostaglandin Nomenclature

Prostaglandins are lipid substances derived from fatty acids, which act as powerful biochemical regulators. In Wade's Organic Chemistry, they indicate that there are several families of ...
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1answer
41 views

Meaning of hydrogen bonds for life [closed]

Why are hydrogen bonds so important for life? Or more generally asked: Why is water so important for life / biological systems? Or maybe again in other words: Why does especially water provide this ...
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1answer
29 views

Preferred IUPAC name of Protoporphyrin IX

I was looking up protoporphyrin IX and was surprised to find that no two websites gave the same IUPAC name for the compound. Here are some examples: 3,3'-(7,12-Diethenyl-3,8,13,17-...
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How does the pKa of a neutral molecule inform the protonation state of its positively charged molecule?

Let's say we have some neutral molecule A and its protonated form, A+. The pKa of molecule A is known, but we do not know the pKa of molecule A+. Can the pKa of molecule A+ be determined only knowing ...
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Calculate amount of enzyme needed for in vitro phosphorylation?

I have 100 micrograms of STAT1 and its molecular weight is 90 kDa. I calculated the number of moles to be 1 nmoles. The specific activity of JAK1 (the kinase) is 110 nmoles of phosphate per minute per ...
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What question could be answered by “because the metabolites in the cell are in ionized form” in the topic of anaerobic metabolism?

I know it might sound a bit absurd, but my teacher gave us some "answers to question", that is, given one answer, write at least one question the answer to which is the given one. I've solved most of ...
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1answer
71 views

How can I model cellular membranes in terms of topology?

I'm reading from Principles of Physical Biochemistry by Kensal E van Holde (1998-01-06) in order to review some biochemistry and work my way toward a more mathematical approach to understanding ...
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1answer
45 views

What is the rate expression for decomposition of $\ce{H2O2}$ in the presence of a catalyst?

What is the rate expression for decomposition of $\ce{H2O2}$ in the presence of a catalyst? As far as I know for catalase, it is like this: $$\ce{Rate = k[H2O2][Catalase]}$$ I don't know what it is ...
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4answers
236 views

Why do so many biochemical reactions require enzymes?

Studying biochemistry as part of the Great Courses, I am struck that all 10 steps in glycolysis require an enzyme. I’d have thought that evolution would have selected for a “simpler” pathway with ...
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Where does the beta notation come from in the alpha 1,2 beta glycosidic bond (in sucrose)? [duplicate]

I am confused as to where the beta is coming from (in the alpha-1,2-beta glycosidic bond in sucrose). I understand that the alpha is from the anomeric carbon of the glucose, but I don't see how the ...
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1answer
45 views

How do “basic” amino acids (lysine, arginine) act as base under physiological conditions? [closed]

Why do we consider amino acids with high side chain pKa's basic, yet with a higher pKa, less of the amino acid will exist in basic form at equilibrium compared to acid form at physiological pH? What ...
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35 views

Measuring Testosterone Levels Using ELISA [closed]

I am new to this topic so please be patient. I am looking to understand ELISA better and how one may attempt to not only detect but measure the total calculated level present in a sample. I would ...
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2answers
104 views

How to experimentally determine the elemental composition in fingernails?

I am doing a project in my highschool about analysing C/N and C/S ratio of finger nails of various ages and sexes. Please suggest me a way to do this. I don't know where to start, I know the various ...
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A question about potential difference across a membrane

Membrane potential of living cells arising from the difference of concentration of ions on both sides of the membrane, but why didn't someone use selective polymers as AEM (Anion Exchange Membrane) ...
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1answer
79 views

Periodate oxidation of sugars

When Methyl D-glucopyranoside is treated with $\ce{HIO4}$, what is the amount of $\ce{HIO4}$ (in moles) consumed per mole of the sugar? I have studied that $\ce{HIO4}$ oxidises only those vicinal ...
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How is presupposition of the order of reaction justified in Michaelis-Menten model?

from what I have understood, to derive Michaelis-Menten equation, we first suppose that $\ce{E + S <=>[k_1][k_{-1}] ES->[k_2]E + P }$ and make the 'steady-state assumption', that $k_1[E][S]=...
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51 views

Does ADP + P => ATP produce water?

ADP + P has one oxygen and two hydrogen more atoms than ATP. Are these atoms released as water in the reaction ADP + P => ATP? To balance the equation, would ADP + P => ATP + H2O be more correct?
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Collagen digestion

As far as I know, pepsin is used very often in collagen solutions extraction. Since it only cleaves the telopeptides and leaves the triple helix chains of the collagen intact. I was wondering if there ...
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1answer
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What is a secondary shell in an enzyme?

I've searched the internet for a definition of what the different shells in enzymes/proteins are and haven't found a good answer. This Nature article, which is about an enzyme that catalyzes Kemp ...
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1answer
99 views

What is “dithreitol”?

The article by Hu et al. [1] mentions a compound "dithreitol" in the Saliva Proteome Analysis section (emphasis mine): For the "shotgun" approach, saliva samples (1 mL) were pre-fractionated with ...
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1answer
58 views

Disinfectant production [closed]

One of my friends says that he made a disinfectant. These are the materials: 83% methanol isopropyl alcohol propylene glycol and the others are: citral, geraniol, linalool, dlimonene, l alpha ...
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1answer
179 views

CO2 kills humans. Does it also kill organisms? [closed]

CO2 kills humans. Does it also kill organisms? Does it also kill viruses?
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1answer
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Cadmium Selenide, Cadmium Sulfide, Cinnabar and Lead Oxide toxicity

I have a question about the toxicity of the pigments Cadmium Selenide (Cadmium Red), Cadmium Sulfide (Cadmium Yellow), Mercury Sulfide (Cinnabar or Vermillion) and Lead Oxide (Lead White). Not long ...
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1answer
24 views

How does one refer to the amino acids in a peptide?

Once a part of a peptide an amino acid is no longer an amino acid, so how do we refer to the part of the peptide that was once amino acid x?
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1answer
34 views

Esterification of Glycine

I came upon the following statement in a true/false question: Glycine can be esterified by an alcohol in the presence of inorganic acid Is this statement correct? Glycine contains the basic $\ce{-...
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71 views

Differences in efficacy of oxime reactivators in organophosphate poisoning

Compounds containing an oxime functional group, such as 2-PAM and obidoxime, are used in the treatment of poisoning with organophosphorus compounds. These oximes reactivate the enzyme ...
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1answer
72 views

How does gefitinib affect the EGFR(ecptor) and why is there relapse

Gefitinib has been shown to be an effective tyrosine kinase inhibitor in a fraction (~$10$%) of non-small cell lung cancer patients. These patients are characterized as having a mutation (usually a ...
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1answer
57 views

Can someone explain the article below? [closed]

This is the article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5611670/ I'm not a Chemist, so I can't understand the article very well. The conclusion states that the molecules tested should not ...
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223 views

AChE Aging time of organophosphorus compounds containing hydroxyl groups

Organophosphorus compounds are known to inhibit the enzyme acetylcholinesterase (AChE). This occurs when the OPC phosphorylates the serine-203 residue of the enzyme. If the enzyme is not reactivated ...
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25 views

When and how do mineral chelates separate in the body?

If one consumes an amino acid chelate such as iron bisglycinate, it is generally absorbed intact as far as I am aware. At some point, presumably the iron could be used for say hemoglobin synthesis and ...
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To get clear plasma out of a minute particle (such as fibrin), is it necessary to vortex sample before centrifugation? [closed]

I'm going to analyse plasma samples that contain a lot of fibrin. It is necessary to centrifuge the samples to be able to pipette the plasma. After the samples are centrifuged I can't vortex them ...
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1answer
61 views

How can subtilisin still function without its catalytic triad?

I read chapter 9 in the book Biochemistry (5th edition), by Berg, Tymoczko, and Stryer (provided in the NCBI site here). It describes the mechanism of action of the chymotrypsin enzyme. The catalysis ...
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Fed-Batch Titer Calculation

If the titer concentration is provided in g/L. Let us consider the following problem. Problem Lets say that titer concentration is X g/L, and using the titer concentration, the amount of water is ...
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1answer
38 views

Chemical Reaction for making Acetic Acid from Glycerol inside Fermenter

I have been trying to find a chemical reaction for the formation of acetic acid from glycerol. I have been searching different literature, but apparently the reaction can not be found. I was hoping ...
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1answer
51 views

Options to keep someone awake against their will? [closed]

I already asked this on Worldbuilding Stack, but they told me to ask here. It is for a RPG campaign. Are there any options that an evil person could use to keep someone awake against their will? Like ...
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1answer
59 views

How to derive the steady-state solution for simple two-step reaction with differential equations? [closed]

Consider this simple two step reaction, a variant of a Michaelis-Menten type of problem, where $\ce{A}$ and $\ce{B}$ reversibly bind to make $\ce{AB}$, and $\ce{AB}$ and $\ce{C}$ reversibly bind to ...
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53 views

Data-processing pipeline for protein x-ray crystallography: uncertain of terminology and order of procedures [closed]

Background: I am trying to get an overview of the data-processing pipeline for solving protein structures by x-ray crystallography, and in a very simple way understand what mathematical procedures are ...

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