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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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37 views

Why does bond breaking in ATP release energy? [duplicate]

We always come across that formation of bonds releases energy, and bond breaking requires energy, but in the case where ATP converts into ADP or AMP (bond breaking), energy is released. Why? Further, ...
1
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1answer
22 views

Acid value of linseed oil

For this we weigh $\pu{1.015 g}$ of linseed oil which is dissolved in alcohol. 3 drops of phenolphthalein (pH indicator) are added and a solution of potassium hydroxide of concentration $C = \pu{9.5e-...
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1answer
21 views

Are enzymes required for reaction coupling? [closed]

In order to couple energetically unfavorable reactions to energetically favorable reactions is an enzyme required?
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0answers
15 views

Does coupling an endergonic reaction to an exgeronic reaction require an enzyme? [closed]

If the reaction A+B->E is composed of the intermediate reactions A+B->C (ΔG=-20) and C+D->E (ΔG=10). In order for A+B->E to spontaneously proceed is an enzyme necessary to couple the intermediate ...
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0answers
21 views

How many natural products are there in existence? [closed]

Hi I'm doing a project on natural products and I'm wondering if somewhere there is at least an estimated number of how many exist? If this exists somewhere can you please provide a reference. ...
0
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1answer
105 views

What do the dots mean in HN.CO.CH3 connected to the second carbon of N- Acetylglucosamine? And what do the N and acetyl indicate?

What do the dots mean in HN.CO.CH3 connected to the second carbon of N- Acetylglucosamine? And what do the N and acetyl indicate?
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0answers
23 views

How to export .pdb files from PyRx virtual screening? [closed]

I have done a virtual screening with PyRx and I want to visualize the interaction in PyMOL. How can I export PDB files of my macromolecule and my ligand while interacting (binding pose)?
1
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1answer
13 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 ...
0
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1answer
21 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 ...
0
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1answer
27 views

Are enzymes with superior catalytic properties more sensitive to temperature changes?

I am wondering whether enzymes with superior catalytic properties are more or less temperature sensitive than average enzymes. I know that enzymes lower the activation energy, Ea. So the more ...
0
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0answers
22 views

Phenomenon of plant cell pattern in condensed herbal coconut oil

This image is of a bottle with herbal coconut oil left overnight by a window in cold weather(approx 19 degree celsius) ,it partially condensed and granules look like a bunch of plant cells .It is ...
0
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0answers
43 views

Why does fructose forms its osazone faster than glucose in the reaction of monosaccharides with phenylhydrazin?

In the reaction of monosaccharides with phenylhydrazine, fructose reacts and forms an osazone within 2 minutes while glucose takes longer time about 5-6 minutes(although both sugars form the same ...
3
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0answers
63 views

When the present state of knowledge concerning central noradrenergic transmission was established?

Some time ago I began to search for descriptions of the mechanisms responsible for the regulation of noradrenergic transmission in the central nervous system of man and to my great surprise the most ...
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0answers
11 views

Lipophilicity computational prediction

Is there a web based (or otherwise) computational chemistry tool which is able to calculate lipophilicity of a given compound?
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0answers
9 views

Gaussian Network Model eigenvalues correspondence to mode frequencies [duplicate]

I am in the process of setting up a coarse-grained Gaussian Network Model (Cα-atoms being representative of each residue) for normal mode analysis of proteins and would like to obtain the wavenumber/...
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2answers
31 views

What's the use of adding 73 mM H2O2 to a supertanant? [closed]

Enzyme assays Determination of catalase specific activity The CAT (EC 1.11.1.6) enzyme activity was measured according to Gallego et al.38 Plant samples were grinded in $\pu{0.1M}\ \ce{...
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0answers
38 views

Enzyme with multiple active sites

I have an enzyme (human HMGCoA reductase) which has four active sites. The experiments had been carried out before from which IC50 values of several molecules were calculated. Now I'm about to carry ...
1
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0answers
30 views

Mobility of Cations in the Environment

I have recently performed an experiment in which I tested the affects of phytotoxic cations on the rate of germination of the common navy bean. I did this out of curiosity, as I have recently been ...
8
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2answers
2k views

Why is arsenic toxic to humans?

I don't understand why arsenic is toxic and why it does damage to humans. Could it be that it is so similar to phosphorous? If so, would that make antimony toxic as well?
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0answers
34 views

What is the purpose of tetrazole in oligonucleotide synthesis?

The ATDBio book on nucleic acids describes tetrazole as an activator required to couple nucleotides. The diisopropylamino group of the nucleoside phosphoramidite is protonated by the activator, ...
0
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1answer
27 views

What does it mean to equilibrate a column in size exclusion chromatography and why is a buffer used?

I'm reading a procedure on size exclusion chromatography and it says that the first step is to equilibrate the column with buffer. What does this mean?
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0answers
12 views

Why absorption changes in schiff-base formation? Coenzyme PLP

Pyrodoxal-5-phosphate (PLP) in enzymes form schiff-base to lysine residue. This can be detected by the change in the absorption from 390 nm to 420 nm (free PLP to stiff-base bound PLP). I remember ...
0
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0answers
10 views

Does oxidation of fatty acids through the process of ketosis versus direct beta oxidation change ATP production?

When insulin levels are low, the liver begins to oxidize fat. The liver oxidizes fat by an incomplete process that yields ketone bodies. The incomplete oxidation of fatty acids by the liver yields ...
1
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1answer
28 views

What citrate is a common anticoagulant?

When I underwent plateletpheresis, something that the staff called "citrate" was added to my blood as an anticoagulant. Everything I can find about this product online refers to it as just "citrate". ...
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2answers
40 views

Are the stereoisomers of nucleosides actually anomers?

An anomer is an epimer at an (hemi)-acetal carbon like $\ce{R2C(OR')2}$. Why is the 1'-position of a nucleoside referred to as the anomeric center despite the lack of acetal functional groups?
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0answers
22 views

What would be the weight loss equation be for Ketosis? [closed]

This is the formula for how the body uses fat: $$\ce{C55H104O6 + 78O2 -> 55CO2 + 52H2O + energy}$$ From this video: What would be the equivalent formula for Ketosis?From my research ketones can ...
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1answer
35 views

Which is more soluble in water ammonia or Sodium dodecyl sulfate

I've tried looking this up and can't seem to find the solubility of SDS if any one knows the answer I would really appreciate it. Which is more soluble in water ammonia or Sodium dodecyl sulfate. ...
2
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0answers
33 views

What do cannabinioids have in common structurally?

I'm looking at the wikipedia page for cannabinioids, and trying to find structural similarities between them. For plant based ones it's hard enough, the only similarity I could find seemed to be 6 ...
0
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0answers
10 views

What is the life span of MLV (multilamella lipid vesicle) dry film?

This suits better as a biochemistry question. Use this method to to produce multilamellar lipid vesicles. Usual life span of extruded, suspended lipid vesicles are less than 36 hours. There's a ...
1
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2answers
66 views

How does the human body deal with free radicals it creates itself?

I know that free radicals are created all over your body all the time as a byproduct of its chemical processes, (or maybe I do not and that is false). However I am confused about the distinction ...
3
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1answer
33 views

Can Molisch test be used to separate monosaccharides from polysaccharides?

Do the results of Molisch test on monosaccharides have any differences with when it's done to disaccharides or polysaccharides?
0
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2answers
105 views

Why are some ions mutagenic and others are not?

It is my understanding that when ionic species (such as $\ce{He^2+}$, or alpha particles) enter the human body, they tend to react with biomolecules, causing damage by (for example) mutating DNA. If ...
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1answer
25 views

What is a protein interface account? [closed]

I'm not a specialist but I'd like to get into meaning of what is written in some articles. In the sentences: "The large numbers of salt bridges and hydrogen bonds in the protein interface account ...
2
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2answers
199 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 ...
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0answers
68 views

redox signaling molecules and electrolysis

There is a product whose presentation screams of snake oil, allegedly consisting of nothing but electrically treated salt water. The product is claimed to be chock full of "redox signaling molecules" ...
4
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1answer
166 views

Is chitin actually protein?

Recently insects are featured as a protein rich source for human nutrition. That humans can really digest chitin through chitinase enzym has been only recently confirmed. But, does the chitin shell ...
0
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1answer
52 views

DNA dye: Are there any natural dye for DNA (instead of artificial ones)?

In order to make easy and low-cost experiments, we are searching for natural dyes (or easy to make) that can color DNA, instead of for instance Ethidium Bromide that is hard to find and is expensive. ...
2
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0answers
26 views

How to determine charge of compounds in solution with many amphoteric functional groups?

I am curating a metabolic model that has compounds such as NADH/NADPH/Etc. that have multiple ionize-able hydrogens. Normally with amino acids there are only a few hydrogen with varying pKas that ...
4
votes
1answer
118 views

Can we predict with any reliability whether a chemical is carcinogenic in people?

I know that some chemical compounds have been known to be carcinogenic in humans. But can we make a reliable prediction of how likely a substance is to be carcinogenic based on the chemical and ...
0
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0answers
56 views

Parallel reactions with for and reverse reaction

I am working on protein folding-unfolding kinetics and recently we have encountered a problem with fitting the data because we are lacking the analytical equation describing our model. We have a ...
0
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0answers
18 views

Peptide linkage

When Glycine reacts with Alanine,what are the products formed? My textbook shows that glycine's $\ce{COOH} $ group reacts with alanine's $\ce{NH_2}$ group to give Glycylalanine. Can it happen the ...
0
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1answer
23 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 ...
6
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0answers
70 views

Does this cycle of reactions appear in nature?

Does anyone know a real-world example of a cycle exactly like this: or in other words, this: $$\begin{array}{ccc} \ce{A + C1 -> C2}\\ \ce{X + C2 -> C3}\\ \ce{C3 -> B + C4}\\ \ce{C4 -> Y +...
1
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1answer
388 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 ...
3
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0answers
46 views

Calculating amino acid mol/mol ratios

I am trying to understand how the authors calculated the TRP/LNAA (mol/mol) ratios in Table 1 in this paper. For example, when I calculate the TRP/LNAA (mol/mol) ratio for HPROT, I get 0.14 instead ...
20
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5answers
2k views

Why do some chemical reactions require many steps?

I posted the following question in Physics SE and was advised to transfer it to Chemistry SE. I studied physics in college ten years ago and I recently started to learn biochemistry. I enjoy finding ...
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0answers
40 views

origin of use of differential equations for modeling chemical reactions? [closed]

what are some of the original examples of uses of differential equations for modeling and analyzing chemical reactions, particularly those relevant to biochemistry, involving proteins and enzymes? ...
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0answers
41 views

Methionine/Cysteine under redox control [closed]

Methionine and cysteine are the principal sulfur-containing amino acids, and oxidation of cysteine and methionine residues had been well studied. How come NOT all proteins carry Methionine and/or ...
0
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0answers
23 views

Possible reversible inhibition of a cysteine protease (similar mech to serine protease)

I'm trying to work out how this molecule might inhibit cysteine protease. The protease enzyme uses a cysteine residue to nucleophilically attack the carbonyl of an amide bond, and an adjacent ...
0
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1answer
79 views

What is an uninegative ligand

I can't find a simple definition via google. All I get are research papers, that I don't understand.