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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Glycix (a bioplastic) question

I have made a glycix (a bioplastic) but cannot find information anywhere on how glycix can break down into HCl and acetic acid. Can anyone help me with this?
Heleen Bekaert's user avatar
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Why can't the fructose monomer in sucrose be α-fructose?

In all academic sources, sucrose is identified as α−glucose (1-->2) β−fructose. However, I cannot find any explanation anywhere as to why the fructose monomer has to be in the β configuration. ...
MD P's user avatar
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In what form does the hydrogen ion exist in different solvents and biological environments? [closed]

Hydrogen ion $\ce{H+}$ exists as $\ce{H3O+}$ in water/aqueous interfaces, which is often noted with the following notation: $$\ce{HA(aq) + H2O(l) <=> H3O+(aq) + A-(aq)}$$ In what form do ...
bonCodigo's user avatar
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Would methylenedioxy-methylhexanamine induce seretonin release? [closed]

DMAA (Dimethylamylamine, methylhexanamine, forthane, geranamine) is a norepinephrine/dopamine releasing agent and sympathomimetic. Could methylenedioxy-DMAA or a similar chemical have serotonergic ...
Tom's user avatar
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2 votes
0 answers
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Reason for differences in AChE aging/reactivation kinetics between neutral and charged organophosphorus inhibitors

According to the referenced papers, acetylcholinesterase that has been inhibited by an organophosphate possessing thiocholine as its leaving group is more susceptible to reactivation by oxime ...
user73910's user avatar
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-2 votes
0 answers
195 views

Why does burning a plant sometimes make it bioactive?

If you get a handful of ground marijuana and smell it, nothing will happen to you. Yet when you burn it and inhale the product, it enters your system. Why is it that burning a plant will make it ...
imrobert's user avatar
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Which position do retro aldol reactions occur in (comparing glucose and fructose)?

Regarding glycolysis, my text states: What is the biochemical rationale for the isomerization of glucose 6-phosphate to fructose 6-phosphate and its subsequent phosphorylation to form fructose 1,6-...
user143539's user avatar
4 votes
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How are oxidation states of bioinorganic molybdenum/tungsten complexes determined?

Here a screenshot from our lecture on bioinorganic molybdenum complexes, dealing with the catalytic cycle of xanthine oxidase: It is said that the only biologically relevant oxidation states of Mo ...
Mäßige's user avatar
0 votes
1 answer
105 views

solubility of glutamic acid in water

As we have learned in school, generally speaking polar molecules can dissolve in solutions with other polar molecules. However in the case of glutamic acid, it appears that it is unable to dissolve in ...
Chem's user avatar
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1 answer
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Isoelectric Point

How do we derive the formula of isoelectric point? pI=(pKa1 + pKa2)/2 I read that isoelectric point is defined as the pH at which degree of protonation in amino group is same as degree of ...
Priyanshu Kumar's user avatar
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Dot blotting immunoassay for visualizing the amyloid formation at different time points

We purchased the primary antibody approximately two months ago, and it has been stored in the freezer since then. Currently, we are attempting to assess its functionality through dot blotting. In our ...
Ash's user avatar
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1 vote
3 answers
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Aqueous state on CO2 and O2 in the Photosynthesis Chemical Equation

While reading through a book I came across the equation for photosynthesis: $$ \ce{6CO2(aq) + 12H2O(l) -> C6H12O6(aq) + 6O2(aq) + 6H2O(l)}\tag{1} $$ in the presence of sunlight + chlorophyll. For ...
entropy's user avatar
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0 answers
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Model EC50/Kd values using ordinary differential equations

It is my first attempt at using ordinary differential equations to model Kd for antibody binding and help will be much appreciated. To provide some context, I possess binding curve data for the EC50 ...
hypermiler3's user avatar
2 votes
1 answer
63 views

What can I do if a peptide won't go in solution in a biological assay?

I have working on the realisation of on assay, that is intended to examine the activity of a protein. The assay works in a way, in which the product of the target enzyme is transfered by a support ...
raptorlane's user avatar
2 votes
2 answers
820 views

Why does the measured CO2, TVOC and CH2O increase rapidly when I cook/bake?

I have a device at home that measures $\ce{CO2}$, TVOC (total volatile organic compounds), and $\ce{CH2O}$ (formaldehyde) levels, and I conducted similar observations in my friends' house. I noticed a ...
Suslik's user avatar
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2 answers
62 views

Why does a small decrease in [ATP] cause a large increase in [AMP]

I was wondering how the reaction catalysed by adenylate kinase and its equilibrium of approximately 1 leads to [AMP] changing greatly with a small change in [ATP]. The below information was provided ...
JouMyu's user avatar
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Bioplastic from starch

I am doing research in bioplastic from starch. I have tried many quantities and concentrations of starch, vinegar and glycerol at different temperatures. But I am unable to get a certain result of the ...
Maneeha. Ajmal's user avatar
-4 votes
2 answers
78 views

Does emulsify mean to combine or break down?

In chemistry, emulsification is defined as the "an additive which helps two liquids mix" (Source: Wikipedia), "a mixture of two or more liquids that are normally immiscible owing to ...
suse's user avatar
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200 views

Why does glucose react with hydroxyl amine and HCN but doesn't give Schiff's test or react with NaHSO3?

I can't understand this because if there isn't a free CHO group then it also shouldn't react with NH2OH and HCN. On the same note can anyone also explain why pentaacetate of glucose not react with ...
Tanush Gupta's user avatar
2 votes
2 answers
234 views

Tollen's Test - Clean Up

In school, we had an experiment to find out the biomolecules contained by the different food-stuffs. After doing Tollen's test which turned out to be positive, our teacher instructed us to clean the ...
Harikrishnan M's user avatar
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0 answers
45 views

Reason for large barrier of hydrogenation of ATP

Why does hydrogenation of ATP have high barrier (mostly doesn't happen spontaneous in typical biological conditions) compared to hydrogenation of OH- (does happen spontaneously). Both contain Oxygen ...
Bohan Xu's user avatar
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2 votes
1 answer
521 views

How do I interpret the results of this DNA gel electrophoresis performed with potentially mislabeled samples?

Here is the cropped image I am working with: It doesn't really matter for my question, but this was performed with 0.8% agarose gel in 1xTBE buffer using ethidium bromide and a TriDye 1kb DNA ladder, ...
Sidereus's user avatar
0 votes
0 answers
50 views

Dissolution of CO2 over time in a high pH solution

I asked this question in the biology stack-exchange but thought it might be more appropriate here. I am running a batch experiment using penicillin bottles where I have bacteria growing for 21 days in ...
Franco Grosso's user avatar
1 vote
1 answer
58 views

Explain estimating intercellular fluxes

Formula that I am using to calculate intercellular fluxes: $$ J = \frac{4D}{\pi d} \big([C]_1 - [C]_2\big), $$ where the flux through a hole is $d$ of a solute with a diffusion coefficient $D$ that is ...
user137376's user avatar
-1 votes
2 answers
1k views

Are Starch, Amylose and, Amylopectin reducing sugars?

Amylose and Amylopectin; As per the information I've learnt, Amylose is considered a reducing sugar but Amylopectin is not because Amylose has a free "reducing end" which Amylopectin lacks, ...
pointlessHumility01's user avatar
4 votes
1 answer
97 views

Hückel's rule for FAD (isoalloxazine) electronic structure

Isoalloxazine is called aromatic in literature. It's a part of FAD cofactor. In some PDB structures it has flat geometry (3DK9) in some cases it has not (3GYJ). I've applied Hückel's $4n+2$ rule for $\...
Holin's user avatar
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3 votes
0 answers
170 views

Why is folic acid very slightly soluble in water while it's a B vitamin?

The solubility of folic acid is just 1.6 mg/L (25 °C). Why is it so insoluble in water while it is one of B vitamins which are called water-soluble vitamins beside Vitamin C?
Walter Heisenberg White's user avatar
-3 votes
1 answer
297 views

Why have my recent boiled eggs contain water within the membrane?

My wife recently boiled eggs from the grocery. Every single one of the eggs has contained water with in the membrane where the hollow portion of the egg is normally. I have only seen this if maybe the ...
Fred Shalackey's user avatar
3 votes
1 answer
99 views

Effect of presence of competitive inhibitor on observed reaction constant

Suppose there is a solution of enzyme, its substrate, a competitive inhibitor, and a suicide inhibitor. The reaction rate constant for the reaction of the suicide inhibitor with the enzyme is known. ...
user73910's user avatar
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3 votes
0 answers
75 views

Two questions regarding the fourth step of glycolysis

I am studying the 10 steps of glycolysis, and is currently on step 4. In this step, a molecule of fructose-1,6-biphosphate is cleaved into dihydroacetone phosphate (DHAP) and glyceraldehyde 3-...
Cam's user avatar
  • 49
-2 votes
1 answer
98 views

Sodium Citrate / Sodium Phosphate Buffer Calculations

I'm trying to work through the calculations of a specific paper (linked here / below) but, my numbers are way off and I can't get them to match for the life of me. I need to make the same buffer but ...
user136195's user avatar
3 votes
1 answer
172 views

Effect of competitive inhibitor on substrate inhibition

In an enzyme that undergoes substrate inhibition, how would the presence of a competitive inhibitor affect said substrate inhibition? Would the substrate concentration at which substrate inhibition ...
user73910's user avatar
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1 vote
0 answers
67 views

How do aqueous nanoparticle suspensions behave?

I have found many pictures of nanoparticle suspensions on the web, but I can find no indication of how these suspensions behave, e.g. do the nanoparticles remain in suspension indefinitely, or do they ...
Shaun Ross's user avatar
2 votes
0 answers
39 views

How are enzyme inhibition constants assayed for "multi-inhibitors"?

Suppose there is a suicide inhibitor of an enzyme that reacts with the enzyme to form an inactive enzyme and another product. This "Another product", however, is capable of acting as a ...
user73910's user avatar
  • 1,254
5 votes
1 answer
86 views

Biocompatible, high refractive index medium for 780 nm?

I am trying to find a medium for optics experiments on living cells. I have been using yeast cells, saccharomyces cerevisiae and saccharomyces boulardii, and need a medium with refractive index (RI) ...
Isabela Sousa's user avatar
4 votes
1 answer
256 views

How to pronounce Aʹα-helix?

The LOV protein structure contains a Jα- and an Aʹα-helix. Would “A prime alpha helix” be the correct pronunciation for Aʹα-helix? I'm speaking soon in front of the scientists in the field that I ...
Andrea Flores-Ibarra's user avatar
0 votes
1 answer
233 views

Operating a chemostat at the optimum dilution rate [closed]

I am wondering what precautions should one take to operate a chemostat at the optimal dilution rate. This is a question on one of the exercise sheets from a class I took two semesters ago and that I ...
TheZone's user avatar
  • 119
2 votes
1 answer
41 views

Removing 9-Aminoacridine from tissue?

There's this compound 9-Aminoacridine, that I need removed from the tissue slides it was applied to. Thing is everytime I use ethanol, Acetone, water, methanol, all the usual solvents; our pathologist ...
Sciguyyy's user avatar
3 votes
1 answer
412 views

How much water is needed or released in the process of burning 1000 kcalories from fat reserves?

Recently, I have started working on my weight and, having a curious mind, I looked deeper into this whole exercise/metabolism/energy production thing. And I became curious how much water is needed to ...
Renat's user avatar
  • 141
4 votes
1 answer
267 views

What are the best conditions for EDC coupling of 2 small molecules?

I want to couple 2 small molecules, one is a DNA oligo with an amine group and the other one a small molecule with with a carboxyl group. I found protocols for EDC (1-Ethyl-3-(3-dimethylaminopropyl)...
Brenlla's user avatar
  • 191
3 votes
1 answer
234 views

Why does Alcohol-Dehydrogenase prefer ethanol over methanol?

So I've had this experiment at university, where we tried using (yeast) ADH on different alcohols and measuring which one gets turned over the fastest. We also learned that ADH prefers shorter ...
m0n74g3's user avatar
  • 33
-2 votes
1 answer
127 views

Are the anomeric hydroxy groups of α-maltose and β-maltose, axial or equatorial, respectively?

This Q&A is a continuation from the following Q&A; What do we get when we joint two α- glucoses via an α1,4 bond? More straightforwardly, the question may focus on whether the bond represented ...
Blue Various's user avatar
3 votes
1 answer
128 views

What do we get when we joint two α- glucoses via an α1,4 bond?

What do we get when we joint two α- glucoses via an α1,4 bond? Is it alpha maltose or beta maltose? In other words, if we cleave amylopectin with amylase (α-amylase or β-amylase), which form of ...
Blue Various's user avatar
3 votes
0 answers
75 views

Ethylene Glycol in Wall Primer [closed]

No scientific background here! Due to a chemical sensitivity, and general concern for healthier indoor air quality in a home I am renovating, I opted to choose "greener" alternatives in ...
Violetta Sur's user avatar
0 votes
0 answers
43 views

post-treatment of silicon surface after silanisation

I recently attempted to make a silicon oxide surface hydrophobic using trimethoxyoctylsilane and methanol as a solvent in ambient air conditions. I left the silicon in the solution for 24 hours, but ...
Sonia S's user avatar
2 votes
2 answers
137 views

Does the word "restraint" have any special meaning in the case of protein or biochemistry?

The following screenshot is taken from the book The Encyclopedia of Physical Science & Technology, volume: Biochemistry, Edition: 3rd, Page-197. The text says: FIGURE 3 Schematic representation ...
user avatar
1 vote
2 answers
225 views

How does industry separate glucose from fructose using liquid chromatography when producing high-fructose corn syrup?

Can someone explain how the separation of glucose and fructose is achieved using liquid chromatography in the industrial production of high-fructose corn syrup? I've seen references to ion-exchange ...
vossman77's user avatar
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0 votes
0 answers
66 views

The overall Gibbs free energy in Gluconeogenesis

Gluconeogenesis is an exergonic process but I wonder what is the overall Gibbs free energy in step 3 and step 10? I know there’s about $\pu{2\times ( -31.4 ) kJ/mol}$ for 2 pyruvates convert to 2 ...
Gordon Chao's user avatar
3 votes
0 answers
154 views

Why is this a non-reducing end?

I was told that C is a non-reducing end. To my understanding, only anomeric carbon involved in glycosidic bond cannot be in the linear form, and in other words, is a non-reducing end. But C is an ...
user307640's user avatar
-1 votes
1 answer
61 views

What are the direct reaction products of the urease reaction (H. pylori) in vivo? How do I know this? [closed]

In the literature, several options can be found: Benini et al. 1999: urea + H2O --> carbamate (H2NCOO-) + NH3 [+ apparently one proton somewhere] Mazzei et al. 2020 (review): urea + H2O --> ...
Thranduil's user avatar

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