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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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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98 views

Does this cycle of reactions appear in nature?

Does anyone know a real-world example of a cycle exactly like this: or in other words, this: $$\begin{array}{ccc} \ce{A + C1 -> C2}\\ \ce{X + C2 -> C3}\\ \ce{C3 -> B + C4}\\ \ce{C4 -> Y +...
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209 views

Solve this chemical or biological mystery

I hope this is the best place to pose this unique question. Please forgive me if it's not. I went into a closet to get a prescription medication that was filled about a year ago. The label on the ...
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45 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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97 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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249 views

Why do nitrogen molecules not act as ligands in haemoglobin?

Nitrogen molecules $(\ce{N2})$ have lone pairs, which, as far as I know, is the property of oxygen molecules $(\ce{O2})$ that allows them to act as ligands bonding to iron in haemoglobin in the blood. ...
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32 views

Fatty Acid synthesis - enzymes that vertebrates cannot make

In the fatty acid elongation and desaturation reactions, how are enzymes that insert double bonds after the 9th carbon different from those that insert at the 9th or before? Vertebrates (at least ...
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280 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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998 views

Selective sorption of toxins by polymethylsiloxane polyhydrate

Polymethylsiloxane polyhydrate (PMSPH) is used as enterosorbent for a couple of decades (nowadays under the trademark "Enterosgel"), intended for binding in the gastrointestinal tract and excretion of ...
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3k views

Why does NADH have 2 peaks in its absorption spectrum but NAD+ has only one?

From what I understand, in general aromatic rings absorb UV radiation. Looking at the structures of NAD+ and NADH, I see one aromatic ring that is common in both (the lower one due to adenine), which ...
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90 views

Phlorizin content in grapes

I work in a winery and we have some problems about a new process involving phlorizin. We know that phlorizin is the major dihydrochalcone found in apples. I have been reading that this compound is ...
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2k views

What methods could be used to preserve scorpion venom?

As extracting scorpion venom goes, how would one most effectively store and preserve the venom for future research? My thoughts are lyophilization, however I am not sure that would be the best of all ...
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108 views

Catalyzation in Carbonic Acid

I understand the basics of carbonic acid + 1 kcal breaking down into water and carbon dioxide. However, my professor wants me to draw an energy map showing the catalyst in human blood reducing the ...
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57 views

Synthesis of tripeptide using Merrifield peptide synthesis procedure - Inclusion of asparagine

I am supposed to synthesize tripeptide, $\mathrm{Ala-Asn-Phe}$, using Merrifield peptide synthesis procedure. Accordingly, I have done followings: Attached protected $\mathrm{Phe}$ as the first ...
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56 views

Thyroid peroxidase - can atomic iodine serve as iodinating agent?

McMurry's Organic Chemistry (7th Ed.) states, that Tyrosine is iodinated by mechanism of electrophilic aromatic substitution and the iodinating agent is $\ce{I+}$ or $\ce{HIO}$ formed by thyroid ...
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52 views

Is there a model for (quality of) two-component-polymerization (dependent on e.g. concentration)?

Sadly my chemistry background is only from high school (I'm a roboticist), but I try my best to explain the problem: Situation: Lets say I have two water based solutions/suspensions. One contains ...
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241 views

What are the chemical similarities between gallium and barium?

I am analyzing nutrient concentrations in wood, and I have found that in all my samples the distribution of gallium and barium are closely related. As a related phenomenon, the presence of these ...
4
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551 views

Calculating volume ethanol in an fermented aqueous solution of sucrose, water, and ethanol

I've been working on a biology experiment where I calculate the fermentation yield of yeast under various light induced stress responses inhibiting the translation of various fermentation enzymes. My ...
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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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158 views

Why dried, closed coconuts go through carbonation?

Some dried, closed coconuts go through carbonation: The white meat of the coconut becomes disintegrated and smeary The liquid becomes carbonated with a bit sour-salty tasted coconut water (which ...
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80 views

When the present state of knowledge concerning central noradrenergic transmission was established?

Some time ago I began to search for descriptions of the mechanisms responsible for the regulation of noradrenergic transmission in the central nervous system of man and to my great surprise the most ...
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104 views

Calculating amino acid mol/mol ratios

I am trying to understand how the authors calculated the TRP/LNAA (mol/mol) ratios in Table 1 in this paper. For example, when I calculate the TRP/LNAA (mol/mol) ratio for HPROT, I get 0.14 instead ...
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61 views

Formating chemical equations for proteins binding in multiple configurations

I am working on problems involving protein-protein binding, particularly ones in which two proteins may bind in two or more configurations, and where some of the resultant structures may also bind ...
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757 views

How to measure the amount of lactose in milk/dairy using high school lab equipment?

I am currently a high school student doing their Biology IB IA. For those who don't know, an IA is, in simple terms, an experiment that you design and execute yourself. My topic is "The effect of ...
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57 views

What component of the human DNA reacts with 4,5-benzo[a]pyrene oxide and 7,8-benzo[a]pyrene oxide to produce cancerous tumors

I read in an article that we have this enzyme called P450 that converts aromatic compounds into water soluble compounds that can be eliminated. This enzyme converts aromatic compounds into arene ...
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474 views

How do thiol groups act as reducing agents?

In my biochemistry practicals, we used reducing agents such as beta mercaptoethanol: and dithiothreitol (DTT) Both of these have S-H groups, and I am sure that these are involved in the reduction ...
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402 views

Why does the Michaelis-Menten constant decrease in the presence of non-competitive inhibitor?

Non-competitive inhibitors don't bind to the active sites of enzymes. However, in the presence of non-competitive inhibitors, the Michaelis-Menten constant is found to decrease. Why is this so?
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66 views

Questions about Genetic algorithm paper of Gilman and Ross

I want to reproduce an (old) biochemistry paper of Gilman and Ross, i.e. " Genetic algorithm selecetion of a regulatory structure that directs flux in a simple metabolic model." ( The following link ...
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572 views

Measuring reaction rates when reactants and products both have (different) molar extinctions at the chosen wavelenghth

In my Biochem labs we would always measure the consumption of NADH, and they always noted that it was useful that NAD+ had essentially no absorbance at 340 nm, which allowed us to directly relate ...
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514 views

The Health Effects of Alkaline Ionized Water?

I came across alkaline ionized water as my aunts bought a system called Kangen Water from Enagic Inc. The water produced by this system is claimed to contain smaller water clusters (4-6 molecules) ...
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64 views

Can one dichlorotriazine molecule form two bonds with cellulose?

In all the reactions I saw online, dichlorotriazine is shown to form only one bond with cellulose (example 1, example 2; paper). But cellulose has many potential sites for bonding. Can ...
3
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1answer
87 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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263 views

Why would ethanol or water give poor yields in a peptide deprotection hydrogenolysis?

A homework question asks: The following reaction was carried out using ethanol or water as solvents, but gave poor yields in both cases. Suggest why this might be the case and how these ...
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0answers
66 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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14 views

Oxidative phosphorylation analogue

Does the salt bridge in galvanic cells resemble the ATP pump in the inner mitochondrial membrane? And if yes than did someone use this pH difference in harvesting this energy?
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27 views

why do cone cells have broad responsivity spectra peaks?

My understanding of vision is that, although the cone cells in our eyes can detect three colors, there is enough overlap in the responsivity spectra (as shown here: https://en.wikipedia.org/wiki/...
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54 views

What's causing this dip in the FCS curve?

This is a fluorescence correlation spectroscopy measurement of light harvesting complexes. What could be causing the dip at 100 microseconds? Edit: The same thing was observed using fluorescence ...
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0answers
35 views

What do cannabinioids have in common structurally?

I'm looking at the wikipedia page for cannabinioids, and trying to find structural similarities between them. For plant based ones it's hard enough, the only similarity I could find seemed to be 6 ...
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0answers
30 views

How to determine charge of compounds in solution with many amphoteric functional groups?

I am curating a metabolic model that has compounds such as NADH/NADPH/Etc. that have multiple ionize-able hydrogens. Normally with amino acids there are only a few hydrogen with varying pKas that ...
2
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0answers
543 views

Chemistry of Benedict's Reagent

I want to understand what is the exact mechanism by which "enediols" reduce cupric to cuprous of Benedict's reagent. The principle of Benedict's test is that when reducing sugars are heated in ...
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0answers
44 views

Why there are just two Ramachandran angles in protein structure for two peptide bonds?

I really want to understand why there are just two ramachandran angles to understand the structure of the protein and why not three or many ? Can someone suggest some reference and explain this ?
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77 views

Calcium concentration in NMDARs e Nitric Oxide Synthase

My question is related to calcium $\ce{Ca^{2+}}$ concentration in NMDA receptors and nitric oxide synthase. I've found a very simple model that describes how the time change of calcium can be related ...
2
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0answers
417 views

How can I calculate the percentage of urea in animal feed?

I'am having some doubts in the calculation that concerns the urea percentage in animal feed using the method AOAC $967.07$ How can I calculate the urea percentage using the following data: The ...
2
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0answers
433 views

proteolysis - how to determine the partial or completeness of the cleavage reaction?

Though the question is about biomolecules, we agree the underlying functions, formation, degradation etc come down to chemistry, (then physics and maths). I am posting it here to receive an ...
2
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0answers
242 views

determination of glucose syrup in sugar product

I work with a sugar product that contains saccharose (approx. 70 %), glucose syrup (approx. 15 %), glycerine (approx. 3 %) and some other ingedrients, e.g. water. Glucose syrup consists of 5 % glucose ...
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82 views

Formation of a pH gradient using carrier ampholites

In a technique called isoelectric focusing, the crucial part is the formation of a pH gradient using carrier ampholytes. What is the exact principle by which the gradient is formed? How do the ...
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0answers
49 views

Difference between “isoaspartyl” and “isoaspartate” in antibody deamidation

I'm translating a text where antibody deamidation is mentioned. One sentence goes like this: We used reversed-phase HPLC to analyze the aspartyl forms of the monoclonal antibody. (Russian original ...
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0answers
62 views

What chemicals would need to be added to human urea to make it a nutritional substance?

I've been thinking about food supplies, waste management and sustainable living, particularly in highly isolated areas like a Mars colony or a space station, or also in a non-technically advanced ...
2
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0answers
61 views

Is it possible to observe ATP energy transport in table experiment?

Is it possible to take AMP or ADP, then phosphorylate it convert to ATP to charge with energy, then transport to other place an then observe energy freeing? In table / home / school experiment?
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303 views

Mechanism: explanation of final step in synthesis of the thyroid hormones (T4, T3)

In the following mechanism for the synthesis of T3 (triiodothyronine) on thyroglobulin, what are the factors causing the last step to occur? Does it have something to do with the electron density of ...