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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solid phase oligonucleotide synthesis [duplicate]

I am going produce oligonucleotides in batches of 25 n moles. The DNA synthesizer columns are supplied with 0.05 μ moles of the 3' nucleotide already linked to the glass-beaded solid phase. In each ...
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solid phase nucleotide [closed]

For a designer-gene assembly project you need to produce oligonucleotides in batches of 25 n moles. The DNA synthesizer columns are supplied with 0.05 μ moles of the 3' nucleotide already linked to ...
3
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1answer
79 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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What happens if I add too much potassium iodide in titration of vitamin C? [closed]

For titration we used: Oxalic acid solution (30ml), Potassium iodide solution (5ml), Acetic acid solution (2ml), Starch indicator solution (a few drops) and orange juice (10ml). We titrated the ...
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8 views

Production of Succinic Acid from Cruge Glycerol using Fermentation

So I am writing a short paper on how one can produce Succinic acid from glycerol. I have to find a microorganism which can do that. I have found the following microorganism, which are traditionally ...
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1answer
40 views

Why can DAP be used to elute a protein in affinity chromatography?

A little background: as part of my bioinformatics degree I have to take Protein Chemistry course, but I miss chemistry basics (have CS background), so that's why I'm asking the following question. We ...
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0answers
23 views

How to remove putrescine odour [duplicate]

Does anyone know how to remove the odour remaining from a decomposed corpse which has fallen onto a wooden floor? Aparently the two main chemicals are putrescine (tetramethylenediamine) and cadaverine ...
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31 views

Synthesis of tripeptide using Merrifield peptide synthesis procedure - Inclusion of asparagine

I am supposed to synthesize tripeptide, $\mathrm{Ala-Asn-Phe}$, using Merrifield peptide synthesis procedure. Accordingly, I have done followings: Attached protected $\mathrm{Phe}$ as the first ...
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1answer
45 views

What do X-ray diffraction and NMR tell about the Proteins? [closed]

I have gone through a simple idea that proteins have different conformations; it is a dynamic system. Moreover, whenever we do ensemble experiments, so we get an average picture. There are some ...
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1answer
30 views

How does a vitamin differ from a mineral [closed]

At the molecular level, I would like to know fundamentally how does a vitamin differs from a mineral. I understand both have, to say, Fe (Iron), then what exactly makes it a mineral Iron or a vitamin ...
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1answer
79 views

why Ammonia is proton acceptor

I understand that this is an elementary question, but I tried to find answers which I could not get. I am trying to understand why Nitrogen in Ammonia is a proton acceptor. Now as I can see from the ...
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1answer
178 views

What does “parallel in-register” mean for a protein structure in a fibril?

I read a paper by Ross and Poirier [1, p. S12] which has the following lines (see section Commonalities of amyloid structure) that describe the structure of protein in a fibril: The most ...
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1answer
27 views

Is it possible to calculate the 'overall' redox potential of a system?

For a solution where many redox reactions occur (e.g. cytosol, soil solution), can we consider anything as 'overall' redox potential of a system? Is there a formula to quantify it in relation to the ...
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1answer
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Can there be a compound which stops the pesticide from entering into the fruit or vegetable? [closed]

Can there be a compound which stops the pesticide from entering into the fruit or vegetable? For example, a solution which is sprayed before pesticides and somehow blocks pesticides from entering into ...
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1answer
133 views

Reduce Decomposition Of Glycerin

Background: Glycerin, when heated with a metal coil, decomposes below its boiling point to acrolein, which in turn appears to decompose to formaldehyde and acetaldehyde. (see previous post) Question: ...
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3answers
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Why does radiocarbon dating only work in nonliving creatures? [duplicate]

I understand how carbon dating works, though I do not understand why it doesn't happen while a creature is living. Because while we are alive we still have carbon 14 in us, so shouldn't it work?
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How to convert pepsin into powder form?

I have pepsin powder which is now hydrated due to humidity. I want to convert it back to the powder form. How to do it? I don't have access to a freeze-dryer . I prefer any cheap procedure other than ...
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1answer
41 views

Calculating the Ionic strength of sodium acetylsalicylate

With the addition of aqueous NaOH to an aspirin solutions in water the reaction will yield products of sodium acetylsalicylate and water. I would like to measure the amount of sodium apsirin formed ...
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1answer
42 views

Photosynthesis-Equation [closed]

Everyone knows the simplified photosynthesis-equation from school: $\ce{6CO2 + 6H2O -> C6H12O6 + 6O2}$ Most people assume that the carbondioxide is being split into carbon and oxygen during ...
12
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1answer
297 views

2017 Nobel Prize; What does Cryo-electron microscopy data actually look like?

It was just announced that the 2017 Nobel Prize for Chemistry has been awarded to Jacques Dubochet, Joachim Frank and Richard Henderson "for developing cryo-electron microscopy for the high-...
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0answers
13 views

Copper sulphate use as mould deterrent in evaporative humidifier [closed]

Is it okay to use copper sulphate in an evaporative humidifier to prevent mould growth?
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2answers
924 views

acid alpha glucosidase vs glycogen phosphorylase

What’s the difference between acid alpha glucosidase and glycogen phosphorylase? Both break down the same bonds in glycogen so I thought for a long time that they are exact same enzyme until I ...
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0answers
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Osazone crystal

How does maltose form its osazone crystal? If osazone is to be formed, then there must be aldehyde form for phenylhydrazine to react, but maltose is formed after hemiacetal formation. How do we ...
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1answer
305 views

Peptide at pH=1

In the following peptide: I want to know the net charge of the peptide at pH=1. According to me the as the solution is acidic so every nitrogen will get protonated. Hence the number of charge = ...
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2answers
37 views

Do magnetic fields generated from ion flow through a membrane channel have any physiological relevance?

Membrane pores and transporters see millions of ions flow through them per second. This creates a current and therefore a magnetic field. Do cells have any use for these fields (like maybe drawing ...
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1answer
79 views

Comparing Polarity of Amino Acids

I know that there are polar uncharged amino acids (serine, threonine, asparagine, glutamine, cysteine) and polar charged amino acids (the basic and acidic amino acids). Does the charge on the acidic ...
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1answer
861 views

Calculating charge of amino acids (am I doing it right?)

Please consider this picture of a peptide chain: I've done some examining on the different amino acids and concluded that the chain is as follows: Lys-Leu-Gly-Ser-Citrullin (variant of arginine). I ...
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pKa values for amino acid

To calculate the pI value, we take the average of the pKa values from the 2 groups that result in a net charge of 0. For that to happen, the pKa values should be at the midpoint of titration where ...
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1answer
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How do I calculate the isoelectric point of amino acids with more than two pKa's?

For most amino acids, the $\mathrm{pI}$ is simply the mean of the amino and carboxyl $\mathrm pK_\mathrm a$'s. However, for tyrosine and cysteine, which have more than one $\mathrm pK_\mathrm a$ value,...
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1answer
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Chemichal difference between liquid sucralose and powder sucralose [closed]

In my country (Brazil), sucralose comes in this two forms, liquid and powder. Looking on the nutritional table, liquid sucralose have no significant amount of carbohydrates or kcal; On the powder ...
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1answer
2k views

Reaction of glucose with 2,4-dinitrophenylhydrazine (DNPH)

In its open-chain form, glucose possesses an aldehyde group; however, glucose does not test positive with 2,4-dinitrophenylhydrazine (which typically forms a yellow/orange/red precipitate with ...
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0answers
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Other metabolic reactions aside, what causes beta oxidation to stop?

To my understanding beta oxidation is when a fatty acid has its carbons plucked off in groups of 2 (acetyl groups) into acetly-coa which we can dump into the TCA. At what point would this process ...
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1answer
42 views

qualitatively: Why are thioesters more reactive than regular esters? [duplicate]

In ochem students are taught that shorter bonds (like alkynes) have more energy than longer bonds such as alkanes. However in biochem we are taught that thioesters are very energetic bonds and release ...
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2answers
398 views

What dictates cathode vs anode nomenclature use?

what was the justification for the use the cathode and anode terminology in IEF? There is no redox taking place in IEF, just proteins interacting with an electric field
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0answers
34 views

Isoelectric point defintion [closed]

My professor said that in order to have PI, both + and - charge have to exist, and therefore phosphoric acid cannot have a Pi. I am confused because I can't find any definition that states both + and -...
2
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1answer
75 views

Ratio of uncharged to charged side chains [closed]

The $\mathrm{p}K_\mathrm{a}$ of the side chain imidazole group of histidine is $6.0.$ What is the ratio of uncharged to charged side chains at $\mathrm{pH}~7?$ Here's my attempt to the solution: $$7 ...
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0answers
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Selective Esterification of Amino Acid

I am going to prepare tert-butyl protected threonine. I was going for the classic esterification methodology which is acid catalyzed (sulfuric acid) esterification under reflux of tert butyl alcohol + ...
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1answer
101 views

Why does a lowered dielectric constant cause RNA/DNA precipitation in ethanol precipitation?

For ethanol precipitations, as mentioned in https://en.wikipedia.org/wiki/Ethanol_precipitation, given that the attraction of water molecules to charged ions like phosphates is based on Coulombic ...
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0answers
27 views

What is the definition of a “Simple enzyme” exactly? Is it an enzyme that does not require a co-factor?

I'm having a hard time making a distinction between simple and complex enzymes. the definitions I've found so far all say this: Simple enzymes are enzymes that are only made out of protein, and ...
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1answer
25 views

EtG formation outside the liver

Ethyl glucuronide (EtG) is formed by conjugation with glucuronic acid catalyzed by the enzyme UDP-glucuronosyltransferase. My question: Is it possible for EtG to form spontaneously in a urine sample ...
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2answers
1k views

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 ...
4
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3answers
375 views

Choice of solvent during thin layer chromatography

I understand most of the theory behind TLC and that different volatile solvents have different polarities and cause the 'spotted' substances to move at different rates, but what is the point of ...
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2answers
603 views

Mercury vapor release from amalgam fillings [closed]

What would cause vapour release from elemental mercury? Would it be pressure, friction... could one stop the vapour release through cooling the mercury?
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0answers
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How to compute for the ATP molecule that can be produced from an unsaturated Free Fatty Acid?

From studying Beta-oxidation of Free Fatty Acids, I've learned how to compute for the ATP equivalence of Even-Chain and Odd-Chain Free fatty acids. What really bothers me now is how to compute for ...
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1answer
1k views

Making artificial sweat

I'm currently working on a chemistry investigation wherein I need to dilute a compound with artificial sweat. I have looked at various forums, including this, which gave answers, but is very outdated. ...
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1answer
285 views

How do I calculate the ensemble-average net charge of an amino acid at given pH?

I am given an amino acid with an ionizable side chain at a certain pH. How do I determine the net charge of that amino acid when there are mixed protonation states of one or more of the groups at that ...
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1answer
50 views

Is sugar in mead different from “regular sugar”?

My understanding of the process of making mead is that you combine honey, yeast and water in an anaerobic environment. The yeast-bacteria ferments the sugar in the honey and produces ethanol (among ...
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1answer
132 views

Theory behind Experiment: Extraction and Identification of DNA

A few days ago, in my chemistry lab class, I performed an experiment aimed at extracting and identifying DNA. The class is mostly practical oriented, so I thought of asking my theoretical doubts on ...
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1answer
28 views

Can you discriminate a monooxygenase from other enzymatic mechanisms by the requirement of NADPH?

I am working on a project about CYPs 450. It seems that most of them function as monooxygenases but there are other categories as well. Assuming that the question makes sense, is it correct to say ...
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1answer
86 views

What Is the Difference Between Radiation and Radioactivity? [closed]

Does all radiation glow green and mutates people on contact?