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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Why is tin (II) fluoride more effective in turning apatite into fluorapatite?

In more powerful toothpastes, like Crest Pro-Health, stannous fluoride is used in place of sodium fluoride. According to Wikipedia: Stannous fluoride converts the calcium mineral apatite into ...
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1answer
2k views

What is the formula for migration rate of DNA in agarose gel electrophoresis?

Let's consider a typical agarose gel electrophoresis experiment. An appropriate quantity (not so much that it is overloaded, but not so little that it cannot be visualized) of linear DNA pieces with ...
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A question about potential difference across a membrane

Membrane potential of living cells arising from the difference of concentration of ions on both sides of the membrane, but why didn't someone use selective polymers as AEM (Anion Exchange Membrane) ...
2
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1answer
54 views

Periodate oxidation of sugars

When Methyl D-glucopyranoside is treated with $\ce{HIO4}$, what is the amount of $\ce{HIO4}$ (in moles) consumed per mole of the sugar? I have studied that $\ce{HIO4}$ oxidises only those vicinal ...
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Does ADP + P => ATP produce water?

ADP + P has one oxygen and two hydrogen more atoms than ATP. Are these atoms released as water in the reaction ADP + P => ATP? To balance the equation, would ADP + P => ATP + H2O be more correct?
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How is presupposition of the order of reaction justified in Michaelis-Menten model?

from what I have understood, to derive Michaelis-Menten equation, we first suppose that $\ce{E + S <=>[k_1][k_{-1}] ES->[k_2]E + P }$ and make the 'steady-state assumption', that $k_1[E][S]=...
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11 views

Collagen digestion

As far as I know, pepsin is used very often in collagen solutions extraction. Since it only cleaves the telopeptides and leaves the triple helix chains of the collagen intact. I was wondering if there ...
4
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1answer
25 views

What is a secondary shell in an enzyme?

I've searched the internet for a definition of what the different shells in enzymes/proteins are and haven't found a good answer. This Nature article, which is about an enzyme that catalyzes Kemp ...
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1answer
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What is “dithreitol”?

The article by Hu et al. [1] mentions a compound "dithreitol" in the Saliva Proteome Analysis section (emphasis mine): For the "shotgun" approach, saliva samples (1 mL) were pre-fractionated with ...
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1answer
35 views

Cadmium Selenide, Cadmium Sulfide, Cinnabar and Lead Oxide toxicity

I have a question about the toxicity of the pigments Cadmium Selenide (Cadmium Red), Cadmium Sulfide (Cadmium Yellow), Mercury Sulfide (Cinnabar or Vermillion) and Lead Oxide (Lead White). Not long ...
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2answers
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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
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Disinfectant production [closed]

One of my friends says that he made a disinfectant. These are the materials: 83% methanol isopropyl alcohol propylene glycol and the others are: citral, geraniol, linalool, dlimonene, l alpha ...
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Why does the regulation occur in the irreversible reactions steps of chemical pathways?

During my study of biochemical pathways such as glycolysis and the TCA cycle, I noticed a trend in regulation. Regulation of the pathways seems to occur often in the irreversible reactions of the ...
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Differences in efficacy of oxime reactivators in organophosphate poisoning

Compounds containing an oxime functional group, such as 2-PAM and obidoxime, are used in the treatment of poisoning with organophosphorus compounds. These oximes reactivate the enzyme ...
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1answer
72 views

CO2 kills humans. Does it also kill organisms? [closed]

CO2 kills humans. Does it also kill organisms? Does it also kill viruses?
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1answer
22 views

How does one refer to the amino acids in a peptide?

Once a part of a peptide an amino acid is no longer an amino acid, so how do we refer to the part of the peptide that was once amino acid x?
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1answer
25 views

Esterification of Glycine

I came upon the following statement in a true/false question: Glycine can be esterified by an alcohol in the presence of inorganic acid Is this statement correct? Glycine contains the basic $\ce{-...
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1answer
69 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 ...
6
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1answer
127 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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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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1answer
2k views

Why does capping after each coupling in Solid phase peptide synthesis improve the results?

Why does capping after coupling improve results during solid phase peptide synthesis (SPPS)? The Case: I have conducted a lab experiment where we coupled three Fmoc-protected amino acids, and did a ...
4
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1answer
2k views

Spectrophotometric assay by pNPP

Here is a series of related questions that I want to ask. Background The activity of acid phosphatase is measured by an enzymatic reaction that converts para-nitrophenyl phosphate (pNPP) to para-...
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0answers
24 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 ...
6
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1answer
46 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
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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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
55 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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1answer
44 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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0answers
48 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
31 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
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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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1answer
12k views

How is chlorophyll made in plants?

I've been studying photosynthesis and something made me think about how chlorophyll itself is made in plants.How exactly is it formed ?
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1answer
28 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
525 views

Is lithium L-threonate a potential brain medicine?

Lithium ions have known neuroprotective qualities. That would explain its therapeutic benefit in some mental disorders. It is also well known that lithium carbonate must be taken in toxic doses to get ...
2
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1answer
90 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
41 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
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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 ...
1
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1answer
19 views

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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0answers
9 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 ...
0
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1answer
23 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.
2
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1answer
101 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 ...
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1answer
37 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 ...
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1answer
38 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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0answers
13 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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0answers
142 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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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
41 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
18 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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