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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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Choosing a catalyst and solvent for knoevenagel condensations? [on hold]

How would one pick up a suitable catalyst and solution combination for performing a knoevenagel condensation reaction between an aldehyde and a Nitro compound and calculate the amount required? I am ...
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2answers
48 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 ...
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1answer
13 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
75 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
22 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 ...
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1answer
36 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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21 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
17 views

aminoacids and relation between pKa and pH

I just started studying biochemistry and I'm having a hard time finding the relationship between the pKa's of amino and carboxylic groups of aminoacids and pH, and what it can tell about the ...
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38 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" ...
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1answer
76 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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24 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
45 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. ...
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0answers
25 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 ...
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1answer
107 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
39 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
16 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
20 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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0answers
65 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
71 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
37 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
38 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
37 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
21 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
63 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
73 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
45 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
44 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
48 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
40 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
79 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 ...
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0answers
33 views

Coagulation and Bio-Coagulants

In an experiment, I used plantain peels (with a very high starch content and very little cellulose) and grapefruit peels (with a very high cellulose content and no starch) as coagulants (ensuring that ...
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1answer
68 views

Living organisms are not at equilibrium with their surroundings [closed]

Why the living organisms can never be at equilibrium with their surroundings?
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0answers
20 views

Why Fe(III) can't coordinate with O2 in methemoglobin

I know methemoglobin's heme group has a change on its shape, what makes oxygen unable to coordinate, but... What causes that change? Does the electronic structure of $\ce{Fe(III)}$ matter or it's only ...
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0answers
25 views

Why don't aldohexoes (like glucose) form 7 membered rings? [duplicate]

Normally when forming a hemiacetal, the glucose's C5 OH may attack the C1 carbonyl carbon, or the C4 OH may attack to make a glucopyranose (6 membered ring) and a glucofuranose (glucofuranose) ...
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0answers
37 views

How do sulphate esters compare to phosphate esters? [closed]

In particular, the energy released from hydrolysis of the -S-O-S- bonds and how stable are they in aqueous solution compared to phosphate esters?
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2answers
642 views

Why Lysine is abbreviated as 'K'? [duplicate]

It does not has a 'K' in its name. It does not have a potassium in its chemical composition. Would be nice to know why Glutamine is Q too, some of these abbreviation seems simply random.
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36 views

Approaches to cap/modify the terminal 3' OH of DNA polymer

I am looking for a procedure that would cap/protect the 3' hydroxyl of DNA molecules with high efficiency. I have tried to perform a similar step enzymatically using dideoxynucelotide triphosphates ...
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0answers
367 views

What is the difference between transaldolase and transketolase in the pentose phosphate pathway?

What is the difference between transaldolase and transketolase in the pentose phosphate pathway? From what I understand, they both catalyze the transfer of carbon chains from 1 aldose into 1 ketose to ...
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0answers
68 views

Why do nitrogen molecules not act as ligands in haemoglobin?

Nitrogen molecules ($\ce{N2}$) have lone pairs, which, as far as I know, is the property of oxygen molecules ($\ce{O2}$) that allows them to act as ligands bonding to iron in haemoglobin in the blood. ...
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0answers
33 views

Chemistry of Benedict's Reagent

I want to understand what is the exact mechanism by which "enediols" reduce cupric to cuprous of Benedict's reagent. The principle of Benedict's test is that when reducing sugars are heated in ...
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1answer
172 views

What is the charge of the amino acid lysine at pH 2?

What is the charge of the amino acid lysine at $\mathrm{pH}=2$? $\mathrm{p}K_\mathrm{a}$'s are carboxylic: 2.18; amino: 8.95; side chain: 10.79. The side chain of lysine is an amine group, so I ...
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1answer
42 views

Relative fraction of population of different enzyme conformations, knowing the rate constants

Say we have an enzyme that has multiple structural conformations, say A, B, C and D. Additionally, we say that the enzyme must go through all conformations, to get to one end to the other, i.e. $$\...
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131 views

Difference in alpha and beta glycosidic bonds [duplicate]

I have learned that the cellulose has a much rigid and orderly branched structure than the starch. However, the only significant difference between them is the different type of bond formed after ...
3
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0answers
86 views

Does melanostatin peptide whiten the skin in a similar manner as to how melanotan darkens it?

I was reading about peptides and came across an interesting peptide that bodybuilders use to darken their skin. How can peptides change the genetic makeup of someone's skin and darken it? I also ...
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0answers
87 views

Retro-aldol reaction (glucose 1,6-bisphosphate)

I am interested if glucose 1,6-bisphosphate can undergo aldol cleavage (retro-aldol reaction) and result in the formation of a two-carbon and a four-carbon compound. I think 1,6-bisphosphate can not ...
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30 views

Is it possible to test presence of diacetyl (2 3-butanedione) in beer at home?

I am trying to understand if I can perform diacetyl test at home. To get actual number. For example just received test result from lab and it says 200ppb, can I perform this test at home?
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0answers
28 views

Will additional ascorbic acid preserve hemp milk for a longer duration? [closed]

Ascorbic acid is known as a natural preservative and many food manufacturers add it to their food to prolong its shelf life. Hemp milk is a drink that is created by blending 1 part hemp seeds with 2/...
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2answers
62 views

Biomolecules : Enzymes [closed]

My class $12$ board exams are approaching and i'm having a doubt in this question: This is from my class $12$ NCERT exemplar book Activation energy for the acid catalysed hydrolysis of sucrose is $\...