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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63 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 from Wikimedia Commons: ...
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During denaturation of protien why does the 1degree structure remain intact while 2degree and 3 degree structures are destroyed? [closed]

I court the words written in NCERT cbse: "During denaturation 2 degree and 3 degree structures are destroyed but 1 degree structure remains intact. The coagulation of egg white on boiling is a ...
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Do both. alpha and beta glucose, react with Hydroxylamine to produce the same oxime [closed]

When glucose is reacted with Hydroxylamine, the following reaction takes place: The glucose in the reaction is an $D(+)-(\alpha)$ glucose. What if we took beta glucose instead. Will the product be ...
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Ritalin/Concerta/Methylphenidate is an amphetamine?

FIDE says here: The most relevant banned substances for chess are: • Amphetamines – e.g. Adderall, Ritalin (...) Image: I think either Ritalin should be in a separate category called ...
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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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Whats equivalent conductivity and equivalent weight of electrolyte [closed]

I found this but kinda doesn't help : Equivalent conductivity is the specific conductance of an aqueous solution containing one equivalent weight of electrolyte dissolved in the solution.
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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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Will my experimental setup for dielectric breakdown of membrane to form nanopore work? [migrated]

I am attempting to form a nanopore in a silicon nitride membrane using controlled dielectric breakdown. However, I want to do it with a budget < $500. I fear that the equipment I want to use will ...
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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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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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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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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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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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47 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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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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68 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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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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44 views

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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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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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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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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1answer
46 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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1answer
36 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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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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90 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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1answer
38 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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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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1answer
59 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
52 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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2answers
77 views

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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49 views

Why are glyosidic linkage of glucose and fructose rings often occurring at the 1' and 4' prime positions?

Here are some example combinations from my textbook: In all of these combined products, the reactive centres seem to be the carbon at first position/ fourth position from the oxygen in priority. Is ...
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1answer
30 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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80 views

Why don't ant bites kill us?

So, methanol is supposed to be toxic even in minute quantities because it is oxidised in our body to methanal and then methanoic acid. This can cause blindness and even death. Interestingly, ants ...
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55 views

Why does CO2 have a greater affinity for hemoglobin than oxygen?

I know about CO but I am wondering if CO2 has similar mechanism? do you guys have any scientific reference These species help form interactions between amino-acid residues at the interfaces of the ...
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1answer
70 views

Deactivate lectins in beans by baking

Having dried uncooked beans, I read that the lectins can be deactivated by boiling and soaking for a while. What I could not find any information on is if dry baking beans would eventually deactivate ...
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How Bread is made with yeast, sugar and luke warm milk? [closed]

Materials and Apparatus: wheat flour sugar dry yeast glass bowl covering plate milk Procedure: Lukewarm milk is taken in the glass bowl and sugar is added to it. Then, yeast is added to the same. ...
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1answer
68 views

What is a non-organic analog of a metabolic pathway?

The wikipedia page on the Belousov-Zhabotinsky reaction states the following: The discovery of the phenomenon is credited to Boris Belousov. In 1951, while trying to find the non-organic analog to ...
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65 views

How is it decided that a particular chemical or compound is useful for a very specific purpose? [closed]

In textbooks, I often find extremely specific uses of chemicals. Is chemistry research mostly focused towards finding specific use cases? For example, I know that boric acid kills snails. How do ...
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3answers
289 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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1answer
47 views

Using samples in titrations

I've never done an experiment before. So, the methodology provided in this pdf is quite confusing. Link to the pdf: https://www.canterbury.ac.nz/media/documents/science-outreach/vitaminc_iodine.pdf So,...
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1answer
36 views

How do I expand a selection in Jmol to include entire residues?

I know how to select by distance in Jmol: select within(5, ATP) This selects atoms that are within 5 Angstroms of ATP residues. How do I expand the selection to include the entire residues of the ...
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1answer
147 views

What is the pI of lysine tripeptide?

What the the $\mathrm{pI}$ of a tripeptide of lysine? $$ \begin{array}{l|ccc} \hline \text{Group} & \ce{Lys{-}α{-}NH3+} & \ce{Lys{-}ε{-}NH3+} & \ce{Lys{-}α{-}COOH} \\ \hline \mathrm{p}K_\...
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Textbook on Food Additives? [closed]

My Question. Is there a comprehensive textbook on (synthetic) food additives? Many textbooks on nutrition omits any discussion of food additives, so I was hoping there is a book devoted to the subject....

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