Skip to main content

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.

Filter by
Sorted by
Tagged with
6 votes
2 answers
145 views

What does ‘D’ in GADP (glyceraldehyde 3-phosphate) stand for?

Wikipedia says glyceraldehyde-3-phosphate can be abbreviated as G3P, GA3P, GADP, GAP, TP, GALP or PGAL, and many resources seem to use GADP as its abbreviation. I have no idea where ‘D’ came from. ...
chrononaute's user avatar
11 votes
2 answers
3k views

Is nitroglycerin synthesis within human digestive system from eating soap possible?

Could you make nitroglycerin by eating large quantities of pure glycerine soap? A quick google search told me flatus are 59% nitrogen, but I couldn't find anyone else with my exact question (which ...
Ivory427e's user avatar
  • 135
5 votes
1 answer
306 views

why is alpha-linolenic acid "alpha"?

I'm learning about how fatty acid names are formed. In the process, I noticed a molecule called alpha-linolenic acid. There's a similar molecule called linoleic acid. Both have 18 carbons, but alpha-...
chrononaute's user avatar
6 votes
1 answer
80 views

Why does tert-butyl alcohol smell like camphor?

Industrial alcohol sold in Taiwan often have a pronounced smell that resembles camphor. When I checked the ingredients at the back, it included tert-butyl alcohol $\ce{(CH_3)_3COH}$, which Wikipedia ...
Jonathan Huang's user avatar
5 votes
3 answers
190 views

How is it known that proteins are polymers of amino acids?

I read the following here. In 1902, Emil Fischer and Frank Hofmeister independently proposed that proteins are formed from many amino acids, whereby bonds are formed between the amino group of one ...
powerful_bob's user avatar
0 votes
0 answers
36 views

Protein quaternary structure in ViewLite

I want to represent the octameric structure of a metalloprotein in the ViwerLite program. I loaded the PDB file related to the protein, but the progranul only displays a monomeric structure (a single ...
Mike's user avatar
  • 41
5 votes
1 answer
187 views

More potent caffeine analogs (in silico study)

Is it possible to do a Structure Activity Relationship for caffeine given that its structure is similar to that of adenosine? Maybe more potent analogues can be made using caffeine as lead compound? ...
C418's user avatar
  • 51
3 votes
0 answers
28 views

Assessing stability of protein used for interaction experiments after changing buffer from tris to HEPES

I have a protein with a theoretical $\mathrm{pI}~9.0$ currently stored in $\pu{25 mM}$ tris and $\pu{250 mM}$ $\ce{NaCl}$ $(\mathrm{pH}~8)$ at $\pu{−80 °C}.$ I need to do experiments in HEPES at $\...
TheChemist's user avatar
0 votes
0 answers
21 views

What is the best alternative to dialysis?

What is the best alternative to dialysis? I want to "design" at a purely theoretical level an industrial installation for the purification of a recombinant protein and dialysis is not ...
Mike's user avatar
  • 41
0 votes
0 answers
37 views

What is the industrial alternative to dialysis?

I want to separate a recombinant protein from imidazole. Both of them are in a solution of pH 8. I was thinking of using ion exchange chromatography with cationite: the imidazole being positively ...
MathEnthusiast's user avatar
0 votes
0 answers
22 views

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
  • 11
2 votes
0 answers
22 views

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
  • 1,264
1 vote
0 answers
19 views

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
0 answers
43 views

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
  • 127
0 votes
1 answer
155 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
  • 19
0 votes
1 answer
79 views

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
0 votes
0 answers
18 views

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
  • 9
1 vote
3 answers
363 views

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
  • 53
0 votes
0 answers
20 views

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
71 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
869 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
  • 131
0 votes
2 answers
69 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
  • 1
0 votes
0 answers
21 views

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
100 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
  • 803
0 votes
0 answers
245 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
0 votes
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
  • 199
2 votes
1 answer
825 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
2k 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
105 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
  • 41
3 votes
0 answers
195 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
542 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
101 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
  • 1,264
3 votes
0 answers
76 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
104 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
174 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
  • 1,264
1 vote
0 answers
68 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
  • 1,264
5 votes
1 answer
89 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
259 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
302 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
450 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
288 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
322 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
134 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
81 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
2 votes
2 answers
142 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
2 3 4 5
22