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.

145 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
8
votes
1answer
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 ...
7
votes
0answers
107 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 +...
7
votes
0answers
213 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 ...
5
votes
0answers
99 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-...
5
votes
0answers
273 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. ...
5
votes
0answers
34 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 ...
5
votes
0answers
1k 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 ...
5
votes
0answers
93 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 ...
5
votes
0answers
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 ...
5
votes
0answers
110 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 ...
4
votes
0answers
48 views

Metal coordination in enzymes: What type and number of bonds form between amino acid residues and Fe(II)?

My understanding: Transition (d-block) metals, as found in intracellular proteins, are limited to about 10 elements including amongst others Fe, Ni, and Cu. Due to the reductive environments inside ...
4
votes
0answers
65 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 ...
4
votes
0answers
58 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 ...
4
votes
0answers
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 ...
4
votes
0answers
244 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
votes
0answers
556 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 ...
3
votes
1answer
52 views

Acidity of thiamine - how comes hydroxide anion with pK about 15 ionizes thiamine with pK about 18?

Textbooks say removing proton from thiamine's C atom will produce a resonance stabilized carbanion which is hence bioactive. That's OK, but how comes that 1) we abstract the acidic proton with the OH ...
3
votes
0answers
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?
3
votes
0answers
190 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 ...
3
votes
0answers
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 ...
3
votes
0answers
112 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 ...
3
votes
0answers
63 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 ...
3
votes
0answers
765 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 ...
3
votes
0answers
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 ...
3
votes
0answers
517 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 ...
3
votes
0answers
407 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?
3
votes
0answers
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 ...
3
votes
0answers
641 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 ...
3
votes
0answers
530 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) ...
3
votes
0answers
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
votes
1answer
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 ...
3
votes
0answers
264 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 ...
2
votes
0answers
25 views

Solving for Concentration Using pseudo-First Order Kinetics

The following graphs represent a pseudo-first order bi-molecular reversible reaction with the formula $\ce{A + B <=> C}$: The reaction product has an extinction coefficient of $\pu{50000 M-1 cm-...
2
votes
0answers
31 views

Why is it rational that salt-bridges (in proteins) are described as a combination of H-bond and ionic bond?

This is a fundamental question that came to me as I was trying to draw the electrostatic attraction between Aspartate (D) and lysine (K). I have always considered the charge on nitrogen, in the lysine ...
2
votes
0answers
23 views

expression of apparent reaction quotient

question When computing the Gibbs energy change of a reaction using Legendre-transformed $\Delta_fG'$ values for a given $\mathrm{pH}$, the formula of the $\Delta_rG'$ of the reaction is: $\Delta_rG' ...
2
votes
0answers
29 views

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 ...
2
votes
0answers
31 views

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 ...
2
votes
0answers
74 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 ...
2
votes
0answers
15 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?
2
votes
0answers
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/...
2
votes
0answers
58 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 ...
2
votes
0answers
38 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 ...
2
votes
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
votes
0answers
547 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 ...
2
votes
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 ?
2
votes
0answers
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
votes
0answers
424 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
votes
0answers
440 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
votes
0answers
255 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 ...
2
votes
0answers
84 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 ...