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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1answer
72 views

How does gefitinib affect the EGFR(ecptor) and why is there relapse

Gefitinib has been shown to be an effective tyrosine kinase inhibitor in a fraction (~$10$%) of non-small cell lung cancer patients. These patients are characterized as having a mutation (usually a ...
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1answer
57 views

Can someone explain the article below? [closed]

This is the article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5611670/ I'm not a Chemist, so I can't understand the article very well. The conclusion states that the molecules tested should not ...
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2answers
228 views

AChE Aging time of organophosphorus compounds containing hydroxyl groups

Organophosphorus compounds are known to inhibit the enzyme acetylcholinesterase (AChE). This occurs when the OPC phosphorylates the serine-203 residue of the enzyme. If the enzyme is not reactivated ...
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0answers
25 views

When and how do mineral chelates separate in the body?

If one consumes an amino acid chelate such as iron bisglycinate, it is generally absorbed intact as far as I am aware. At some point, presumably the iron could be used for say hemoglobin synthesis and ...
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0answers
28 views

To get clear plasma out of a minute particle (such as fibrin), is it necessary to vortex sample before centrifugation? [closed]

I'm going to analyse plasma samples that contain a lot of fibrin. It is necessary to centrifuge the samples to be able to pipette the plasma. After the samples are centrifuged I can't vortex them ...
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1answer
61 views

How can subtilisin still function without its catalytic triad?

I read chapter 9 in the book Biochemistry (5th edition), by Berg, Tymoczko, and Stryer (provided in the NCBI site here). It describes the mechanism of action of the chymotrypsin enzyme. The catalysis ...
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0answers
15 views

Fed-Batch Titer Calculation

If the titer concentration is provided in g/L. Let us consider the following problem. Problem Lets say that titer concentration is X g/L, and using the titer concentration, the amount of water is ...
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1answer
38 views

Chemical Reaction for making Acetic Acid from Glycerol inside Fermenter

I have been trying to find a chemical reaction for the formation of acetic acid from glycerol. I have been searching different literature, but apparently the reaction can not be found. I was hoping ...
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1answer
51 views

Options to keep someone awake against their will? [closed]

I already asked this on Worldbuilding Stack, but they told me to ask here. It is for a RPG campaign. Are there any options that an evil person could use to keep someone awake against their will? Like ...
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1answer
59 views

How to derive the steady-state solution for simple two-step reaction with differential equations? [closed]

Consider this simple two step reaction, a variant of a Michaelis-Menten type of problem, where $\ce{A}$ and $\ce{B}$ reversibly bind to make $\ce{AB}$, and $\ce{AB}$ and $\ce{C}$ reversibly bind to ...
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0answers
54 views

Data-processing pipeline for protein x-ray crystallography: uncertain of terminology and order of procedures [closed]

Background: I am trying to get an overview of the data-processing pipeline for solving protein structures by x-ray crystallography, and in a very simple way understand what mathematical procedures are ...
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1answer
42 views

Nucleophilicity Of Amino Acid Side Chains [closed]

Out of the side chains of aspartic acid, methionine, threonine, and tyrosine, which is the least nucleophilic?
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1answer
272 views

Why can't C-C double bonds rotate? [duplicate]

The alkyl chains of saturated fat molecules can readily rotate about their carbon-carbon single bonds, giving them flexibility and viscosity. What is different about the carbon-carbon double bonds of ...
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0answers
43 views

Why is Cadmium so carcinogenic compared to other heavy metals?

This free article as well as this article do a good job highlighting the carcinogenic effects of Cadmium and the mechanisms by which they occur. However, my question is why is Cadmium so carcinogenic ...
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0answers
15 views

The Limitation of Solid Phase Peptide Synthesis In Case of Polyglycine

I was wondering if I could use your experience and all the precautions you would like to recommend for a long peptide synthesis via SPPS. I've already got a low loading resin so this way I'll minimize ...
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0answers
10 views

In vivo, does it take energy to move double bonds from cis to trans long chain unsaturated fatty acids

In vitro, long chain fatty acids may yield more energy when bonds break, but in vivo, I understood that energy is burned before unsaturated fatty acids can be oxidized because the side groups with ...
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2answers
155 views

Why are drugs mixed with their sodium salts?

I have come across quite a few drugs that are of the form $\ce{HA + NaA}$, where $\ce{A}$ is your target organic compound. A few examples of this are: Carmicide which is a mixture of Sodium Citrate ...
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1answer
25 views

Using the electrical potential created by the electron transport chain to power electrical systems

My friend and I were discussing the extremely low energy density of modern batteries and read that food has a much higher energy density. Thus, we were considering the possibility of using biological ...
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1answer
50 views

Human gastric lipase

Does anyone know if the human gastic lipase has a quaternary structure? If not, why not? I can not seem to find this information anywhere.
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1answer
44 views

Is the solution isotonic, hypertonic, or hypotonic?

The problem is shown below. I don't understand how can the tonicity of a solution be determined if the solution has multiple solutes dissolved in it. Do I take the total sum of the mass of solutes ...
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1answer
38 views

Estimating protein binding and disassociation

I don't have a background in the area of drugs or pharmacokinetics/Pharmacodynamics but I am trying to understand about protein binding. I was going through this paper. If $C_b$ is the ...
2
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1answer
119 views

Carcinogenicity of polynuclear hydrocarbons and benzene rings

(1933) established that polynuclear aromatic hydrocarbons (PAHs) were carcinogenic components of pitch. ... Although less is known about their health effects than about those of PAHs, it is clear that ...
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0answers
15 views

Oxidative phosphorylation analogue

Does the salt bridge in galvanic cells resemble the ATP pump in the inner mitochondrial membrane? And if yes than did someone use this pH difference in harvesting this energy?
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2answers
29 views

Why is it important to remove the used up electrons in oxidative phosphorylation?

I get that oxygen is the terminal electron acceptor in oxidative phosphorylation. But why is it essential to accept these electrons and remove them as $\ce{H2O}?$ Oxygen is essential for cellular ...
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0answers
43 views

Is there a software that can predict the shape of a custom protein, given its amino acid sequence?

I know that the internet is full of enzyme and protein simulators which can show active site and 3D structure (like bioblender), but the problem with these programs is that they use predefined ...
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1answer
19 views

R and T conformations in relation to Activators and Inhibitors; Km of reaction in relation to uncompetitive and non-competitive inhibitor

Do -Activators -Competitive Inhibitors -Non-Competitive Inhibitors -Uncompetitive Inhibitors all change the conformation of the targeted enzyme from T to R (activator), and from R to T (the rest) ...
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1answer
60 views

A question about thiamine [closed]

How does the the nitrogen of thiazole in thiamine acquire a positive charge without being stabilized by another negative charge or by being a salt of an anion?
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0answers
174 views

Why dried, closed coconuts go through carbonation?

Some dried, closed coconuts go through carbonation: The white meat of the coconut becomes disintegrated and smeary The liquid becomes carbonated with a bit sour-salty tasted coconut water (which ...
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0answers
23 views

∆G° and ∆G°' for acid dissociation

For the dissociation of an acid AH, where $\ce{AH <=> A- + H+}$, if $∆G°$ is $\pu{+25 kJmol-1}$ at $\pu{300 K}$, what is $∆G°'$? I know that for $∆G°$, $\ce{[H+]}$ is $\pu{1M}$, whereas for $∆G°'...
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0answers
23 views

Pyridinium ion in inositol nicotinate

I have read about inositol nicotinate which is used as a medication for deficiency in vitamin B-3. I think that if acetic acid was applied to this medication it would form pyridinium ion and acetate ...
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2answers
393 views

How does one tell (or conclude) if a substance is carcinogenic?

It's common to read statements like: Tetrachloroethene ($\ce{CCl2=CCl2}$) was earlier used as a solvent for dry cleaning, but since it contaminated ground water and is a suspected carcinogen, ...
5
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2answers
209 views

Peptide bond formation involving side chains of charged amino acids

Peptide bonds are formed as such: Aspartic acid, glutamic acid and lysine all contain either one extra $\ce{-COOH}$ or $\ce{-NH2}$ group in them. Why does that extra group not participate in peptide ...
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4answers
3k views

What is a word for “atom or molecule”?

What is a word for "atom or molecule"? As in: "The entry of an atom or molecule across a cell membrane into a cell is dependent on its size and solubility." This keeps coming up, and it's really ...
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3answers
161 views

Fitting multiple pKa's

I have three histidine residues that are next to each other in a protein. When I compute the fraction of unprotonated states for each individual histidine as a function of $\mathrm{pH}$ my titration ...
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1answer
61 views

Production of Succinic Acid from Crude 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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0answers
24 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 ...
4
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0answers
60 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
40 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 ...
0
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1answer
53 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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2answers
363 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 ...
4
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1answer
199 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 ...
2
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2answers
48 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
26 views

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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3answers
2k views

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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0answers
28 views

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 ...
1
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1answer
81 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 ...
1
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1answer
61 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 ...
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0answers
23 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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1answer
50 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 ...
0
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1answer
59 views

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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