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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 ...

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Finding ph for maximum activity

Active site residues of an enzyme are one His, one Asp and one Glu. The approximate pKa values for the ionisable groups of the above three amino acids, when they are free in solutions, are: Amino-...
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22 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, ...
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29 views

How to convert thyroxine into phenylalanine and hydroquinone?

Hey. I wanna know how to convert thyroxine into phenylalanine and hydroquinone. I don't care about hydroquinone, I just want the phenylalanine. There are just 2 things to do, breaking the ether bond ...
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35 views

Mixing Aspirin, Lidocaine, and Water [closed]

So here's the story of how I came to this question. For a long time I've used acetylsalicylic acid(Aspirin) tablets, ground down in a pestle and mortar. Then mixed with just enough water to make a ...
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11 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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8 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 ...
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12 views

How Glycogen phosphorylase stops at 4th residue from branch point? [closed]

Question is same as it is in head title. I am asking for Biochemical mechanism of stopping this enzyme at that specific point.Is it still unknown for science? thanks in advance.
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11 views

Calculate specific catalytic activity

I am hoping that someone can help me to calculate the specific catalytic activity of an enzymatic reaction. The reaction is the hydrolysis of p-nitrophenylphosphate to p-nitrophenol via ...
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5 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 ...
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1answer
21 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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0answers
20 views

why does 8-oxoguanine undergo Hoogsteen base pairing

8-oxoguanine, an oxidized form of purine base guanine, is reported to form 2 hydrogen bonds with adenine(Hoogsteen base pairing)- (Source: https://en.wikipedia.org/wiki/8-Oxoguanine). However, the ...
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1answer
26 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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15 views

What's causing this artifact in FCS data?

This is a fluorescence autocorrelation curve from a fluorescence correlation spectroscopy experiment. I am very inexperienced with FCS and the setup I used has never been used for FCS specifically (we ...
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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
31 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. ...
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9 views

Charge of nucleosides at 7.3 p

I am looking for electric charge values of adenine ($\ce{C5H5N5}$), cytosine ($\ce{C4H5N3O}$), thymine ($\ce{C5H6N2O2}$), guanine ($\ce{C5H5N5O}$) and uracil ($\ce{C4H4N2O2}$) at $\mathrm{pH} = 7.3$ ...
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0answers
24 views

Bishydroxy ethyl terephthalate precipitation in Minimal media

Please how can I avoid precipitation of Bishydroxy ethyl Terephthalate solution while trying to make a culture media with it as a sole carbon source in an M9 minimal growth medium. Is there any media ...
2
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0answers
29 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 ...
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0answers
8 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 ...
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0answers
10 views

If a reagent in a metabolic reaction has a gas and an aqueous form, which one to use when computing Gibbs energy of reaction?

In many cases, the chemical reactions catalyzed by cells involve chemical species having a gas form and an aqueous form (eg: CO2, O2, CH4). The Gibbs energy differential of a chemical reaction greatly ...
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2answers
59 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 ...
2
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1answer
21 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?
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2answers
86 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
24 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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1answer
135 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
24 views

How biosensor mediator enzyme work?

I actually new in this discipline. I read how biosensor-enzymes worked from journal : 1.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697141/ 2.https://www.sciencedirect.com/science/article/pii/...
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0answers
53 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
119 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 ...
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0answers
27 views

Is bentonite self-healing?

I want to make a shallow pond (3 - 4 ft. max depth) lined with bentonite for both my ducks and willow tree. However, the willow's roots need to be able to penetrate the pond liner and thus the liner ...
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1answer
47 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
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1answer
113 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 ...
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0answers
44 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 ...
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0answers
17 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 ...
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1answer
22 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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67 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 +...
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1answer
224 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
38 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 ...
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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 ...
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0answers
22 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 ...
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1answer
67 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.
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2answers
132 views

why does ring flip of L-fructose occur?

when drawing the chair conformation for beta-L-fructose, I got the structure above (in the picture). The answer said that the conformation above had a ring flip. Why does a ring flip occur and how can ...
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1answer
47 views

Book about biochemistry for physicist [closed]

I want to understand the basics of biochemistry, from a physicist point of view. I am looking for a textbook that discusses things like the covalent bond and the oxidation number, starting from first ...
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0answers
45 views

Why does blood turn reddish brown?

Why does blood take on such a colour after a couple of hours? Is this the iron in my blood being oxidised to iron (III) oxide or is this something else? I have checked this article, and no I do not ...
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1answer
70 views

Why does the structure of haemoglobin change when the ferrous ion changes to ferric ion?

It is said that $\ce{Fe^2+}$ can bind oxygen while $\ce{Fe^3+}$ cannot. Why is that so? $\ce{Fe^3+}$ has an extra electron, it could bind more easily to the oxygen. And how and why does the structure ...
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0answers
19 views

Enols and enolates in biosynthetic pathways

I'm having a little trouble unterstanding the way organisms carry out aldol and claisen type reactions. I'm familiar with the laboratory procedures to which I understand there is a correlation. ...
3
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1answer
43 views

Extracting metallic magnesium from cholorphyll

My understanding is that when chlorophyll is exposed to an increased concentration of hydrogen ions (or rather the pH is lowered), the magnesium is displaced by a hydrogen ion and chlorophyll is ...
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1answer
90 views

Modification to improve antibacterial activity

I have difficulties with part b). For C, it's clear to make a bulky dimethoxybenzene group in order to block the C=O group from reacting with b-lactamase. However, in A, how does the structure of ...