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.
1,076
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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?
0
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20
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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. ...
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0
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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 ...
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0
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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 ...
2
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0
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21
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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 ...
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0
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195
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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 ...
1
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0
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19
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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-...
4
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0
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39
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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 ...
0
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1
answer
105
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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 ...
0
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1
answer
60
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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 ...
0
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0
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16
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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 ...
1
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3
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166
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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 ...
0
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0
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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 ...
2
votes
1
answer
63
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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 ...
2
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2
answers
820
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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 ...
0
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2
answers
62
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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 ...
0
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0
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18
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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 ...
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2
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78
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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 ...
0
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0
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200
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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 ...
2
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2
answers
234
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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 ...
0
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0
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45
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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 ...
2
votes
1
answer
521
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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, ...
0
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0
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50
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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 ...
1
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1
answer
58
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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 ...
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2
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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, ...
4
votes
1
answer
97
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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 $\...
3
votes
0
answers
170
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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?
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1
answer
297
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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 ...
3
votes
1
answer
99
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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. ...
3
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0
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75
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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-...
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1
answer
98
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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 ...
3
votes
1
answer
172
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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 ...
1
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0
answers
67
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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 ...
2
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0
answers
39
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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 ...
5
votes
1
answer
86
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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) ...
4
votes
1
answer
256
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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 ...
0
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1
answer
233
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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 ...
2
votes
1
answer
41
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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 ...
3
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1
answer
412
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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 ...
4
votes
1
answer
267
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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)...
3
votes
1
answer
234
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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 ...
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1
answer
127
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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 ...
3
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1
answer
128
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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 ...
3
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0
answers
75
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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 ...
0
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0
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43
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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 ...
2
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2
answers
137
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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 ...
1
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2
answers
225
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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 ...
0
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0
answers
66
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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 ...
3
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0
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154
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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 ...
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1
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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 --> ...