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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23 views

Function of sodium amalgam and CO2 in formation of aldohexose

There is this following conversion in my book: $$\gamma-\text{Lactone}\ce{->[Na/Hg +CO2]}\text{Aldohexose}$$ I'm not sure how this reaction takes place. I searched for mechanisms and couldn't ...
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1answer
125 views

Why are Tyrosine and Tryptophan considered hydrophobic?

Since Tyrosine and Tryptophan are amino acids, their polarity is determined on their side chains or R groups. If their R groups are polar, the amino acid is polar. Both Tyrosine and Tryptophan are ...
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Three-dimensional structures of molecules are important. Explane protein structures which kind of bonding are important for relevant structures [closed]

Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers – specifically polypeptides – formed from sequences of amino acids, the monomers ...
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1answer
77 views

Why is the overall change in entropy of Photosynthesis positive? [closed]

Net Reaction: $$\ce{6CO2(g) +6H2O(l) -> 6O2(g) + C6H12O6(aq)}$$ The net reaction shows that 12 moles become 7 moles; 6 of gas,and 1 complex molecule. This implies a decrease in entropy over the net ...
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96 views

Which solvent is good for using SU-8 particle in Optical tweezers?

I'm studying Optical tweezers. I've used Polystyrene for samples. Nowadays, I've got SU-8 pillar. I wanna use that for sample, but its density is heavier than water. I can't use that. So I wanna know ...
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5k views

Why does the reduction of NAD+ to NADH change the absorbance so much, and cause fluorescence?

This is an updated question: I don't have a very strong background in biophysics, but I want to understand the theory behind $\ce{NAD+}$ and $\ce{NADH}$ absorbance and fluorescence. Background: I ...
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1answer
41 views

Why is PLGA so expensive in comparison to PLA?

A Google search has lead me to believe that PLGA goes for anywhere between 8 USD and 100 USD per gram. Meanwhile, for PLA (3d printer grade), prices float around 50-100 USD per kilogram. I understand ...
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36 views

Relation between Gibbs free energy and the order of a reaction

I was reading a biophysics book and at the chapter for membranes it was talking about the melting of the lipid bilayer. Now I don't know much about this topic but this phrase strikes me as kind of odd:...
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Polar vs. ionic bond strength - can we put a ball-park number on it? [closed]

It will depend on the context of course, but ball-park? Let's say, in terms of charge, if a Na+ ion has by definition a charge of +1, what is the partial positive charge on a water molecule? A 10th, ...
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Synthesis question: Using reductive amination to form pyrrolidine

What molecule results from treating 4-oxopentanal with $\ce{NH4Cl}$ and $\ce{NaCNBH3}$? Why? Is this a good, high yield reaction? I believe that pyrrolidine is formed because amination will convert ...
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1answer
56 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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29 views

What specific toxins are formed during deep frying? And how (chemically) do they attack the body cells? [closed]

From what I understand, deep frying causes the oxidation of lipids into advanced lipid oxidation products. When these are consumed and metabolized by the body, they release ROS or free radicals which ...
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1answer
44 views

What is the mechanism of AChE inhibition by Onchidal?

A naturally-occuring neurotoxin, called Onchidal, produced by a species of sea slug acts as an irreversible inhibitor of acetylcholinesterase. The structure of Onchidal is presented below: How and ...
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What is “protein redox conformation”?

From an article by Frye et al. [1]: Reduced glutathione (GSH) is the major intracellular redox buffer and is essential in free radical scavenging, redox homeostasis, maintenance of protein redox ...
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226 views

How can I properly calculate the isoelectric point (pI) of amino acids?

The following amino acid is called lysine. I was asked to calculate its isoelectric point, with the given $\mathrm pK_\mathrm a$ values. I've searched a lot, and the most helpful post that I found ...
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1answer
130 views

Why is the 1,6 linkage in Amylopentin an alpha link and not a Beta link? [closed]

The alpha link as I have understood it means that the $\ce{OH}$ molecules which make up the glycosidic bond lie on the same side of(above/ below) the plane and for beta, one lies above the plane and ...
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How were urolithins discovered and named?

Urolithin is a product of the degradation of ellagic acid by gut flora and has significant biological activity. (Wikipedia) I am curious as to how it was discovered but cannot find the story. Although ...
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1answer
84 views

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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3k views

Reaction of glucose with 2,4-dinitrophenylhydrazine (DNPH)

In its open-chain form, glucose possesses an aldehyde group; however, glucose does not test positive with 2,4-dinitrophenylhydrazine (which typically forms a yellow/orange/red precipitate with ...
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1answer
72 views

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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24 views

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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46 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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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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ATP break down and energy release?

I have a very basic question. Energy is absorbed to break bonds. Bond-breaking is an endothermic process. Energy is released when new bonds form. Bond-making is an exothermic process. But ATP breaks ...
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1answer
26 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
325 views

Why do many organic halogen compounds smell or taste sweet?

Is it just coincidence that many organic halogen compounds (especially chlorinated ones) tend to either taste or smell sweet? Examples include dichloromethane, vinyl chloride, chloroform, and ...
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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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1answer
128 views

Why is there no effective alternative to metal salts in antiperspirants?

Metal salts, especially aluminum compounds are used in antiperspirants to prevent sweating. I found out aluminum chloride hexahydrate, which is found in most antiperspirants, undergoes an acid-base ...
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1answer
102 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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2answers
80 views

Measuring a high Michaelis constant using fluorescence

We have the task of measuring kinetic parameters of an oxidase reaction that has a $K_M$ of about $2 \,\text{mM}$. For that, we want to use a fluorescence assay based on Amplex Red. The latter is a ...
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228 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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1answer
5k views

Should β-mercaptoethanol and anything that touches it be handled only under fume hoods for safety aspects?

Background: I recently started in a lab that regularly uses β-mercaptoethanol (βME) for protein purification. I know that the chemical is an irritant for the lungs if inhaled (mucus membranes), ...
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1answer
76 views

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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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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23 views

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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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
61 views

Production of Succinic Acid from Crude Glycerol using Fermentation

So I am writing a short paper on how one can produce Succinic acid from glycerol. I have to find a microorganism which can do that. I have found the following microorganism, which are traditionally ...
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1answer
48 views

EtG formation outside the liver

Ethyl glucuronide (EtG) is formed by conjugation with glucuronic acid catalyzed by the enzyme UDP-glucuronosyltransferase. My question: Is it possible for EtG to form spontaneously in a urine sample ...
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2answers
106 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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2answers
54 views

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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13k views

How is chlorophyll made in plants?

I've been studying photosynthesis and something made me think about how chlorophyll itself is made in plants.How exactly is it formed ?
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43 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
766 views

How do I know that an acid and conjugate base are present in equimolar amounts?

Acetylsalicylic acid is a molecule in several popular drugs such as Magnyl and aspirin. It has a $\mathrm{p}K_\mathrm{a}$ of 3.5. I'm about to calculate the $\mathrm{pH}$ of a $\pu{0.010 M}$ solution ...
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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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27 views

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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Betaine HCl stomach pH

It seems betaine HCl is often recommended for those suffering from "low stomach acid" -- which, as I understand, is having too high stomach pH for proper digestion (especially for proteolysis via ...
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1answer
82 views

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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4answers
240 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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34 views

Can you discriminate a monooxygenase from other enzymatic mechanisms by the requirement of NADPH?

I am working on a project about CYPs 450. It seems that most of them function as monooxygenases but there are other categories as well. Assuming that the question makes sense, is it correct to say ...

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