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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What is the name of this chemical C15H35COOC3H7? [closed]

My friend needs help with his homework and I don't know what is the name of this C15H35COOC3H7. Does it even exist?
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What is the increase in intracellular concentration? [closed]

bearing in mind intracellular conc of Na⁺ is 15mM and extracellular is 140mM, I can’t seem to be able to work out the answer without finding out the volume (which we don’t have)
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The role of carbon dioxide in temperature regulation? [closed]

Common concept 1) is that human body cells turns sugar into energy via combustion, using oxygen and releasing heat, carbon dioxide and water. Common concept 2) is that both oxygen and carbon dioxide ...
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What are the compounds that this article refers to?

The linked article studies the effects of a set of organophosphorus compounds on the bioelectrical activity in the digestive system. The OP compounds studied are referred to in the abstract as IMFF, ...
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How does coenzyme A produce proton from pyruvate ions?

Coenzyme A (CoA) is a complex molecule consisting of mercaptamine, β-alanine, pantoic acid, diphosphate, pentose, phosphate and adenine moieties: Which part of it actually plays role in the formation ...
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-2 votes
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Difference between Protoporphyrin and Porphyrin?

I understand that Porphyrin is defined as 4 pyrole rings linked by methenyl bridges. When this porphyrin ring is associated with a Ferrous ion (Fe 2+) we get the Heme molecule. However my book ...
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1 answer
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How does CO2 'dissolve' in water (or blood)?

I'm trying to understand CO2 dissolved in blood, carbonic acid and the bicarbonate ion. I think of 'dissolving' as in NaCl dissociating into Na+ and Cl- ions sloshing around in water. CO2 isn't ...
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Why does a big protein move during gel electrophoresis but to a lesses extent through a size exclusion column?

A big protein going through gel electrophoresis will be forced through the gel, it will drift a small way and will show on the top of the gel, while in size exclusion, the big protein is not forced to ...
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How significant is the effect of pi stacking on substituent bond dissociation in an enzyme?

Let there be a system of phenylalanine in a T-shaped pi-stacking configuration with a tyrosine. Both are part of a longer peptide (~40 amino acid separation in the chain). In this system, an oxonium-&...
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How does Calanolide A react with NaOH solution? [closed]

Calanolide A is an anti-HIV drug I assume the ester group, phenolic hydroxyl group and carboxyl group formed by hydrolysis in the molecule can react with NaOH. Is that correct? How many moles of NaOH ...
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Is LCP working well in real experiments? or is it more of an oversimplified principle?

I have a question for people who have applied Le Chatelier's principle (LCP) to their experiment or have knowledge about people who have done that to increase the yield. Essentially, I am curious &...
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1 answer
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How does creatine increase DHT levels?

I'm interested in learning how creatine increases DHT levels in the context of 5α-reductase inhibitors (5ARIs). A study (doi: 10.1016/j.urology.2013.02.045) found that 5ARI-induced DHT deficiency ...
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Why is the cyclic form of glucose more stable than the linear form?

I am aware of this question What makes the cyclic structure of glucose more stable than the open chain structure? This is meant as a sort of follow-up question and if possible I would prefer if any ...
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3 votes
1 answer
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Chelation of iron: is it removed or just contained?

I have a question that came up in my research (neurobiology), maybe someone can help me out! I read that neuromelanin, which is found in certain brain structures, can chelate iron and protect cells ...
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How does protein denaturation speed change with temperature? [closed]

So this is something that I had been wondering since middle school. We "roughly" know that protein denaturation occurs above a temperature of 72 degrees Celsius, and is the reason why it is ...
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1 answer
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How is it possible for Enzymes to get absorbed undigested [closed]

We as medical practitioners frequently prescribe enzymatic preparations like Trypsin-Chymotrypsin, which actually are proteins. Often I wonder how come a protein gets absorbed undigested, through our ...
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2 votes
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DNA staining agent with good absorbance at 532 nm

I need to stain some double-stranded DNA with an intercalating fluorescent dye. For imaging, I am using a microscope setup equiped with a 532 nm green laser. What is the staining agent of choice to ...
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2 answers
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why is benzene ring ubiquitous in almost all the organic compounds [closed]

Could you please give me a reasonable cause why benzene ring is found in every organic compound in food, pharmaceuticals, dyes . In addition, benzene is a known canceriogen, why shouldn't it be toxic ...
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3 votes
1 answer
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Are there any examples of chemiluminescent reaction catalyzed by Group 1/2 metals?

While researching chemiluminescent reaction that normally require enzymes but are replaced with metallic catalysts, as mentioned in this research paper: Direct and Indirect Chemiluminescence: ...
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1 vote
1 answer
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How does a freeze-thaw cycle separate a mixture?

Imagine that I defrost a tube of serum (only the yellow stuff, with blood cells removed) standing still and upright in ambient air. I have seen that as it defrosts the sample separates into different ...
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2 votes
1 answer
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Best description of forces/ mechanisms that stabilize the interaction between a hydrophobic protein binding pocket and a hydrophobic ligand

This is a more theoretical or definition question that is related to the terms "hydrophobic effect", "hydrophilic interaction", and "van der Waals' forces" (and others I ...
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1 vote
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Can you use Michaelis–Menten kinetics to model the ATP production rate for glycolysis and OXPHOS with glucose as a substrate?

I am an applied mathematician researching cell metabolism, but I have little experience in biochemistry. Currently, my PI and I are considering using Michaelis–Menten kinetics to study how varying ...
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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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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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4 votes
1 answer
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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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1 vote
2 answers
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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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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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0 votes
1 answer
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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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2 votes
1 answer
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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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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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1 answer
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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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1 vote
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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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4 votes
1 answer
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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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1 answer
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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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4 votes
1 answer
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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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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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2 votes
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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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5 votes
1 answer
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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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6 votes
1 answer
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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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1 answer
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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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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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1 vote
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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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1 vote
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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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1 answer
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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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1 vote
1 answer
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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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