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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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 ...
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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 ...
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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 ...
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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, ...
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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 ...
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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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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, ...
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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 $\...
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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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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 ...
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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. ...
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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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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 ...
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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 ...
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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 ...
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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 ...
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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) ...
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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 ...
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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 ...
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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 ...
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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 ...
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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)...
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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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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
user124269
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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 ...
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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 ...
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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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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 --> ...
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Methods for immobilization of DNA on gold surfaces?
I've been looking for methods for immobilizing 5'-Thiol modified dsDNA on gold slides. Most of what I've come across suggests using DTT followed by a desalting step or using TCEP. However, I haven't ...
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Why is AChE inhibited by triflates not susceptible to reactivation?
According to a report, certain esters of trifluoromethanesulfonic acid are capable of acting as irreversible inhibitors of acetylcholinesterase. Also, 3-PAM, while capable of reactivating AChE ...
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Stability of different tautomers of vitamin C
Above all four tautomers represent Vitamin C (Ascorbic acid)
So here are some basic rules that I learnt.
1.Usually keto form is more stable due to bond enthalpy considerations
2.Enol form is stable if ...
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Could there be any reaction between piperine and Pink curing salt #2 [closed]
EDIT: I originally (incorrectly) asked this question re: capsaicin; but found that the actual compound of concern in black pepper is "piperine".
This question originates on a forum dedicated ...
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Carbon monoxide question [closed]
When reading lots of articles about carbon monoxide poisoning cases I came across to it being referred as "silent killer" many times. Now, I know that carbon monoxide is a byproduct of an ...
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Glycation of peptides (Maillard reaction) by reductive amination
I would like to link glucose to the primary amines in a peptide containing lysine. Can I just mix glucose and the peptide and add some cyanoborohydride to perform a reductive amination? As long as my ...
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Are there natural enzymes that catalyze different reactions under different conditions?
Are there natural enzymes that catalyze different reactions under different conditions? For example an enzyme undergoes a conformational change under certain pH and starts catalysing a different ...
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Process of Arecoline Extraction
What would be the proper procedure to extract and isolate arecoline, an alkaloid ester, from the seed of the Areca nut, and is it possible to mass produce arecoline using that method?
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What is the charge of amino acid in alkaline conditions?
This problem refers to the protein buffer in a living system.
"If the blood pH becomes alkaline, there is a release of a proton from the
$\ce{NH3+}$ ion, which takes the $\ce{NH2}$ form."
I ...
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Do whey proteins precipitate with heat?
I am currently studying about the biochemistry of yoghurt and when reading about the effect of heat in milk proteins specifically whey, my book says that heat can denature whey proteins.
So after the ...
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Why is collagen fibre autofluorescent?
Why is collagen fibre autofluorescent? Proteins with increased amount of trp, tyr, phe tend to fluoresce but I don't think collagen fibre has increased percentage of any of them. Some say collagen ...
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How does the branched structure of glycogen, increase its ability to be hydrolysed?
"Glycogen branching is essential because it allows for increased water solubility and several sites to break it down; this allows for easy and quick glycogen utilization when it is broken down&...
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Can lipases cleave fatty acids linked with amides instead of the usual esters?
The typical substrate for lipases are esters, such as triglycerides where fatty acids are linked to the glyerol through ester linkages. I'm interested in whether lipases (such as pancreatic lipase) ...
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Are lipid membranes destabilized by aligning so many negatively charged phosphates in close proximity?
From my understanding, lipid membranes in biological systems are made mostly of phospholipids, which have a hydrophobic chain region and hydrophilic head group containing a phosphate. In the membranes,...
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Why do hydrogen bonds between atoms of the polypeptide backbone, form both helix and pleated structures, instead of only one structural type?
Proteins have segments of their polypeptide chain/chains that can be repeatedly coiled or folded into helix and pleated structures, respectively. This is due to hydrogen bonds between partially ...
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Stable thioesters in biological millieu?
It seems that most thioesters are highly reactive in cells and blood due to the high concentration of biological thiols. Are there any derivatives of thioesters that are stabilized at physiological ...
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Why are proteins made up of alpha amino acids and not beta amino acids?
Why are proteins made up of alpha amino acids and not beta amino acids? Or gamma amino acids? My idea on this would be that a world with beta or gamma amino acids would be too complicated? Is that ...
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Can pyruvate get reduced after glycolysis?
During cellular respiration, the first step is glycolysis where the glucose is split into 2 pyruvates, 2 NADH, and 2 ATP. The pyruvate either goes through the citric acid cycle or goes through lactic ...
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