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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22 views

Number in amino acids abreviattion

I'm studying biotechnology and now I'm preparing the endonuclease part. When I`m looking information about BglII endonuclease and how it works. When I look for the structure and working process via ...
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47 views

Why can one set the Gibbs free energy change to 0 when calculating the standard free energy change?

I am trying to understand the following equation: $$\Delta G = \Delta G^{\circ} + RT \ln\left(\frac{[C][D]}{[A][B]}\right)$$ for a reversible reaction with reactants A and B and products C and D. The ...
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How do sequences of amino acids perform and what properties do they have? [closed]

I am learning and have a question regarding sequences of amino-acids and their properties, please. There are quite highly detailed accounts of each step of the process getting from the sequence of dna ...
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128 views

Can the environment of a molecule affect its HOMO LUMO gap?

For example, if a particular molecule is inside a particular protein, can its absorption maxima change with respect to the isolated molecule? Also, within the same protein, can the molecule's HOMO-...
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36 views

In electrophoresis of amino acids and dipeptides, how can I rationalize the observed mobilities?

For part b(i) why is the spot tyrosine? I know tyrosine has an overall -2 charge while phenylalanine has an overall -1 charge. However, phenylalanine has a smaller Mr so shouldn't it travel faster? ...
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70 views

Why aldehyde group is easy to oxidize than hydroxyl groups of glucose

In all the reactions i had Seen I pointed out that aldehyde groups of a compound like glucose are easy to oxidize than the hydroxyl groups. I had also read some similar answers but I was unable to ...
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2answers
71 views

H+ or H3O+ in mitocondrial electronic transport chain [closed]

Just learnt that $\ce{H+}$ (aq) is equal to $\ce{H3O+}$ and now I know why. I'm thinking about cell processes that involve $\ce{H+}$ transport. I wonder if that $\ce{H+}$ is $\ce{H3O+}$ too, like ...
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130 views

Ritalin/Concerta/Methylphenidate is an amphetamine?

FIDE (the governing body of international chess competition) says here: The most relevant banned substances for chess are: • Amphetamines – e.g. Adderall, Ritalin (...) Image: I think either ...
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41 views

Phosphate transfer in hexokinase

In glycolysis, hexokinase transfers a phosphate group from ATP to glucose. This is an example of the coupling of an exergonic reaction with an endergonic reaction, such that the endergonic reaction is ...
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Lipophilicity computational prediction

Is there a web based (or otherwise) computational chemistry tool which is able to calculate lipophilicity of a given compound?
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Does changes in pH affects cyclic form of glucose in water solution?

Glucose in water solution is mainly in cyclic form. Both base and acid can catalize formation of hemiacetal, but in distinct mechanisms. I found information that monosacharides eg. glucose exist ...
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91 views

Why isn't the aniline hydrolysed in Sanger's protein sequencing method?

Recently I was reading about identifying N-terminal amino acid residues using Sanger's reagent (1-fluoro-2,4-dinitrobenzene). The following image showing the reaction is taken fro Wikimedia Commons: ...
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165 views

Are all 'dextrorotatory' sugars in biology actually 'd' or '+' in chirality?

When papers or articles say that all proteinogenic amino acids are 'levorotatory' or 'L', they often make a point of saying that only half of them are truly, optically levorotatory. All of them (...
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129 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 ...
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50 views

Help determining Absorption Coefficient & Concentration from Uv-Vis reading

hope you're doing well. I'm having some trouble determining the absorption coefficient and concentration values of a protein from its UV absorption results. The experiment in question involves an ion ...
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45 views

Why does Phenylalanine to Tyrosine release H2O?

So I was reviewing Tyrosine and Phenylalanine metabolism (according to this video) and maybe I'm missing something but in the first step, 1: Oxygen atom reacts with Phenylalanine to make up Tyrosine, ...
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Will concentration of sodium hydroxide affect the result of chicken feather hydrolyzate if i don't standardized it?

The title of the paper: Isolation and characterization of keratin from chicken feathers https://doi.org/10.1063/5.0002792 Here is the method: Keratin was isolated by dissolving 5g of chicken feather ...
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Why doesn’t the amount of ligand needed to reach a fraction-bound value of 0.5 increase as the starting protein concentration increases?

In a Kd binding curve of fraction-bound on the y-axis and ligand concentration on the x-axis, it’s known that the Kd is equal to the ligand concentration [L] needed for [PL]/[Ptotal] =0.5. However, I’...
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71 views

Do the phosphoester and glycosidic bonds of dNTPs increase thermal stability?

A while ago, I provided an answer to a question on Biology.SE concerning the half-life of dNTPs under PCR conditions. At the beginning of my answer, I give a qualification: Caveat: ignoring the ...
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530 views

Why does hydrolysis of ADP to AMP yields the same amount of energy as ATP to ADP, if ADP is more stable?

I learned about the resonance stability of ADP and the fact, that ATP is less stable due to intramolecular instability. I was surprised to see that the energy net of conversion of ADP to AMP is the ...
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What are the initial experiments to hypothesize or decide the method of protein degradation?

For a protein of interest, How to determine it’s degrading method— protease or proteasome? Is it possible through bioinformatics? What are the initial experiments to hypothesize or decide the method ...
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155 views

Do enzymes that digest D-glucose react with L-glucose?

D-glucose most common in nature and L-glucose is synthesized in the lab. I know that humans can't use L-glucose in their aerobic pathways because it doesn't match the active site of the enzyme ...but ...
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193 views

How can semicarbazide occur during meat processing other than from nitrofuran treatment/feeds?

Since nitrofurans are banned e.g. in the EU from use in food-producing animals, but not entirely as medications for humans, there have been some stories/reports of possible diversion of human-intended ...
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668 views

Why is the 1,6 linkage in Amylopectin an alpha link and not a beta link? [closed]

The alpha link as I have understood it means that the $\ce{OH}$ molecules which make up the glycosidic bond lie on the same side of(above/ below) the plane and for beta, one lies above the plane and ...
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38 views

How much salt in a cup of water would it take to neither hydrate nor dehydrate the average person? [closed]

I don't know a lot about chemistry, and this question came up during lunch with my friend. I was interested in this question so I thought I could ask here. Sorry if I didn't use the right tags.
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Biocompatible positively charged functional groups on the pH range 5–9

In drugs and biomolecules, there are quite a few groups that are negatively charged around neutral pH (pH 5 to 9): carboxylates, sulfates, sulfonates, phosphates, phosphonates, tetrazoles, certain ...
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Isomerization of tertiary carbocations in cholesterol synthesis

The following reaction mechanism happens in cholesterol synthesis inside human body. I am unable to understand why on earth the hydride shift happens here. I mean its already a tertiary carbocation, ...
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70 views

What do sequence numbers in PDB files actually mean and why don't they match the sequence?

I am studying the 3D structure of the LDH from x-ray crystallographic imaging I was pointed to from Is there any stereospecific enzyme in PDB that catalyzes an anabolic reaction and has an entry ...
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119 views

What is an enzymatic reaction for which a detailed tertiary structure showing all ligands is available on the PDB?

This is a follow-up to my earlier question here How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center? about the lactate synthase. I am using the lactate ...
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218 views

Why are MD simulations necessary for obtaining Boltzmann populations?

Given that MD simulations converge to the Boltzmann distribution $\rho \sim \exp(-\beta \epsilon)$ after sufficiently long times, and all the macroscopic quantities can be computed from the Boltzmann ...
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How can energy be gained from oxidative deamination?

In (most cases of) degradation of amino acids, the process start with the amino group being transferred to $\alpha$-ketoglutarare, replacing its keto group. This turns $\alpha$-ketoglutarare into ...
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Hypothetical Alternative for Nitrogen [closed]

Recently I was surfing the internet and I found thisWikipedia article. It states that The element silicon has been much discussed as a hypothetical alternative to carbon. Silicon is in the same group ...
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why is energy not required for the first step in the TCA?

I find biochemistry challenging since the basics aren't very well explained, such as why some reactions require energy while others do not. One of the constants I've been able to find is that energy (...
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60 views

What happens when you dilute a surfactant solution at the critical micelle concentration?

Say if instance I have a 100 ml solution with micelles formed using some surfactant. Now if I pour that 100 ml solution into 500 ml of water, will those micelles break up into free surfactant again? ...
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54 views

Is there any stereospecific enzyme in PDB that catalyzes an anabolic reaction and has an entry showing both reactant ligands?

I am desperately searching for an anabolic enzymatic reaction, ideally with a metal ion involved in the reaction complex, and for which -- unlike in the case of the lactose synthase -- we have ...
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27 views

How can G3P oxidize into 1,3-BPG without energy expenditure?

In glycolysis, one of the important steps is when Glyceraldehyde-3-phosphate is oxidized to 1,3- Bisphosphoglycerate, while reducing $NAD^+$ to NADH and $H^+$. I'm a bit perplexed by this step since ...
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47 views

How can all amino acids point outwards from an alpha helix, if peptides are mostly trans?

My textbook in biochemistry ("Biochemistry" - Berg,Tymoczom Gatto, Stryer) tells me that: "Almost all peptide bonds in proteins are trans" (p. 40) At the same time, it states the ...
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3answers
206 views

what is the difference between how taste and smell are detected?

Taste and smell are both chemical processes ... parts of the food dissolved in saliva come into contact with the taste receptors.[1] These are located on top of the taste receptor cells that ...
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37 views

Molybdenum assay (phosphorus vs inorganic phosphate)?

Recently, I have been getting blood tests done for phosphorus. I see some laboratories report phosphorus and others report inorganic phosphate. The normal range for phosphorus seems to be about 0.1 ...
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What's the effect of temperature on buffering capacity?

I did some research online but I still couldn't get any conclusion. Some said that the buffering capacity decreases when temperature increases because of the increase in ionisation of the weak acid ...
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111 views

Why is Nylon-2,6 biodegradable but Nylon-6,6 isn't?

Both have similar functional groups so what causes Nylon 2,6 to be biodegradable while Nylon 6,6 is not?
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General cleaning solution for clinical chemistry applications

I want to reuse some plastic and glass items that I am using to do colorimetric concentration analysis of serum and urine. There are some enzymatic assays, mineral assays and so on. I have been trying ...
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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 ...
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42 views

How to troubleshoot absorbance analysis when readings fluctuate

I am trying to measure creatinine in fluids by using an enzymatic (creatinine) test. I try to determine the concentration by the difference in absorbance before and after 5 minutes after a reagent is ...
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28 views

What do natural hybrids of peptides and nucleic acids look like?

Until recently I thought that there was a clean distinction between polypeptides and oligonucleotides, but apparently there are recent studies of therapeutic compounds that could be described as "...
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What are "molar equivalent amounts" in a description of an immune cross-reaction assay?

From "Folate Receptor Alpha Autoantibodies in Autism Spectrum Disorders: Diagnosis, Treatment and Prevention" (2021): Figure 2. (A) Folate receptor concentrations in milk. (B) Immune cross-...
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64 views

What is the maximum length of peptide which considered to be hard for synthesis by the current technology?

I am a molecular biologist and work with recombinant proteins. I am wondering what the cut point, in terms of length, is at which I should produce the peptide using heterologous expression rather than ...
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1answer
59 views

How to identify 'water' mistakes in protein crystal structures: Are B-factors and occupancy good indicators?

When solving the structure of a protein from diffraction data (x-ray crystallography), it can sometimes be difficult know what should be modelled into small spheres of electron density that are not ...
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294 views

What is the difference between structure assignment and structure prediction?

I am absolutely new to structural bioinformatics (only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using machine learning. ...
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Is it false that the absorbance of two concentrations is the sum of the absorbances of the concentrations?

I am in the lab and trying to perform the molybdenum blue test for phosphorus using a photometer. It appears common speak in colorimetric lab sheets that Absorbance of a mix of two concentrations is ...

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