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 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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139 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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1answer
413 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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1answer
58 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
90 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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1answer
53 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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0answers
35 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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2answers
182 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
50 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
135 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
28 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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2answers
1k 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
181 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
773 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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2answers
118 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
30 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
147 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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1answer
28 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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85 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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2answers
937 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
82 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
3k 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
60 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
48 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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1answer
138 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
440 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
104 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
96 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
177 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
23 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. ...
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1answer
105 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
102 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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1answer
471 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
27 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
50 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
2k 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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57 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
958 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
207 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
478 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
894 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 ...
2
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1answer
72 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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0answers
146 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
51 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
136 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 $\...
2
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1answer
494 views

Chemical tests given by glucose (biomolecule)

We know that glucose gives Tollen's test because it's a reducing sugar, and having a hemiacetal group, on hydrolysis can be converted into an aldehyde group, giving the positive test. But, when we ...
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2answers
50 views

Why does the isoelectric range decrease as an Alanine chain grows longer?

The pK1 and 2 values for alanine are 2.3 and 9.7. In the dipeptide Ala-Ala, they are 3.1 and 8.3 and in tri-peptide Ala-Ala-Ala, they are 3.3 and 8.0. Why does this trend in pKa values exist? Why does ...
3
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1answer
61 views

Simplest way to convert glucose into water and carbon dioxide other than burning?

What is the simplest pathway from glucose to $\ce{H2O}$ and $\ce{CO2}$, such that all reactions happen in aqueous solution with pH between 5 and 8, temperature is in range between 0 and 35 °C, no (...
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0answers
31 views

Fatty Acid synthesis - enzymes that vertebrates cannot make

In the fatty acid elongation and desaturation reactions, how are enzymes that insert double bonds after the 9th carbon different from those that insert at the 9th or before? Vertebrates (at least ...
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2answers
1k views

What does pO2 of blood mean and why do we use it?

I understand the basic Dalton's law of partial pressures in gases. Also, Henry's law of diffusion, says, the concentration of gas dissolved in a fluid is proportional to the partial pressure above it. ...