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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Calcium dynamics and its relationship with nitric oxide [closed]

I know that in synaptic transmission nitric oxide release leads to a reduction of calcium inflow. But how does this phenomenon happen quantitatively (for example: I suppose that when the nitric oxide ...
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1answer
153 views

How is “dietary cholesterol” processed in a human body? [closed]

Person eats an egg that is high in animal cholesterol ("dietary cholesterol"). What do chemical reactions play a role in breaking down it in stomach?
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1answer
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Do serotonin drugs contain serotonin or a precursor to it, e.g. tryptophan?

With serotonin drugs, is it actually serotonin in the drug, or is it tryptophan which converts into serotonin through the biochemical conversion process after the drug is consumed? Serotonin can be ...
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68 views

How do scientists figure out the chemical structure of a given compound? [duplicate]

Please bear with me a bit while trying to explain my question as best as I can. I am a 4th year medical student so my command on chemistry is not too good, but I find it fascinating and intriguing, it ...
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1answer
57 views

If 360 rotation is possible, How Molecule exist with particular Configuration

I Have confusion, If we talk about Ethane Molecule, we can get different conformations. For ethane, the eclipsed and staggered are freely inter-convertible and in between these two extreme ...
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0answers
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Why there are just two Ramachandran angles in protein structure for two peptide bonds?

I really want to understand why there are just two ramachandran angles to understand the structure of the protein and why not three or many ? Can someone suggest some reference and explain this ?
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1answer
182 views

How do the pKa and pH indicate to the proper environment of protonation?

I have been reading an abstract of a paper for a couple of minutes (reference below) but I cannot understand a piece of it. The abstract: The ionization state and $\mathrm pK_\mathrm a$ of the ...
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1answer
167 views

Why does a protein crystallize with a specific salt but not with another?

So I am conducting an experiment and I do not understand this super fundamental part. I know salting out works via solubility, and I know crystallization works via ordered structures. But could ...
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2answers
216 views

Is it possible for Cytosine and Hypoxantine to make three hydrogen bonds?

I think the O from Hypoxanthine can bond with one of the Hs in NH2 from Cytosine and the H that is connected to N in Hypoxanthine with the N in Cytosine but is it possible also for the H connected to ...
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1answer
5k views

Monosaccharides configurations (alpha beta, D L) identification

I am really finding it difficult to identify the correct configuration(s) of a given monosaccharide, in fact my friends and I have been trying to solve this, much to our annoyance. In one of our ...
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74 views

Cationic Detergent with no odor [closed]

I am looking for a cationic detergent for a project. Unfortunately most ( or all?) cationic detergents are quaternary ammonium that smell like rotten fish or even worse The product I am working on ...
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1answer
469 views

Osmium tetroxide reaction with cell membrane

Background: $\ce{OsO4}$ is a widely used staining agent used in transmission electron microscopy (TEM) to provide contrast to the image. In the staining of the plasma membrane, osmium(VIII) oxide ...
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1answer
208 views

Could muscarine be an antidote to atropine poisoning?

According to Wikipedia, "Muscarine poisoning is characterized by miosis, blurred vision, increased salivation, excessive sweating, lacrimation, bronchial secretions, bronchoconstriction, ...
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Calcium concentration in NMDARs e Nitric Oxide Synthase

My question is related to calcium $\ce{Ca^{2+}}$ concentration in NMDA receptors and nitric oxide synthase. I've found a very simple model that describes how the time change of calcium can be related ...
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1answer
667 views

What is the difference in the effect of DTT (Dithiotreitol) and SDS (sodium dodecyl sulfate) for PAGE?

In class, we have studied that when running a polyacrylamide gel with our protein sample to separate the proteins by molecular size, we can use several techniques, among which we have denaturing PAGE ...
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2answers
80 views

What is the correct nomenclature for Glucuronyl C5-epimerase?

I see people writing "Glucuronyl C5-epimerase", "Glucuronyl C-5-epimerase", "Glucuronyl-C-5-epimerase" and "Glucuronyl C5 epimerase", which one is correct? Is there a naming convention?
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4answers
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Why is fermentation of cellulose to produce biofuel and nutrients so difficult?

The formula for glucose is $\ce{C6H12O6}$ and that of cellulose is very similar $\ce{C6H10O5}$. Glucose can be readily fermented by yeast and other micro-organisms to produce carbon dioxide and ...
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0answers
173 views

What is an example of an endergonic reaction? [duplicate]

I am doing a project where I must find both an endergonic and exergonic reaction. The latter seems to be abundant, but the endergonic reactions seem to be purely biological. I have to present the ...
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1answer
327 views

What is the correct way to notate conformation preferences of polysaccharides?

In some webpages (1 or 2) are found the way to notate the conformational preferences of monosaccharides such as furanose and pyranose. But, it lacks to give a brief description on how to do it with ...
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1answer
326 views

2017 Nobel Prize; What does Cryo-electron microscopy data actually look like?

It was just announced that the 2017 Nobel Prize for Chemistry has been awarded to Jacques Dubochet, Joachim Frank and Richard Henderson "for developing cryo-electron microscopy for the high-...
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66 views

Do any efforts to construct artificial biochemistries exist and what compounds are they based on? [closed]

I'm a researcher interested in the fields of origins of Life, astrobiology and theoretical biology in general but I must admit I think my knowledge of chemistry outside biochemistry is a little bit ...
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0answers
59 views

Formating chemical equations for proteins binding in multiple configurations

I am working on problems involving protein-protein binding, particularly ones in which two proteins may bind in two or more configurations, and where some of the resultant structures may also bind ...
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1answer
77 views

How do the toxicities of arsenate and arsenite compare?

So I was browsing the detoxification metabolistic mechanisms for E. coli, and came across an arsenic detoxification mechanism that converted arsenate to arsenite using a glutaredoxin. So my question ...
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2answers
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Food which does not produce urea [closed]

My professor of bioengineering said that all foods produce urea. Do foods exist which does not produce urea? Thank you very much.
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1answer
186 views

To understand logic and relation of biochemical cycles [closed]

I recenty learned the Kreb cycle, in that I saw many chemical are same. I want to know if there is logic/threrom/technique in which I can write a chemical cycle to get a product i.e I want basic ...
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1answer
1k views

Why are different colors, according to sugar concentration observed in Benedict's test?

Colors range from green yellow orange to red. How does the sugar concentration and Cu2O concentration cause this? I know Cu2O is red. Why is there a green or yellow color instead of just red or some ...
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0answers
748 views

How to measure the amount of lactose in milk/dairy using high school lab equipment?

I am currently a high school student doing their Biology IB IA. For those who don't know, an IA is, in simple terms, an experiment that you design and execute yourself. My topic is "The effect of ...
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1answer
256 views

Derivation of an equality in Michaelis–Menten kinetics

Enzymatic action may be described as follows: $$\ce{Enzyme + Substrate <=>[k_1] ES complex ->[k_\mathrm{2}] Enzyme + Product}$$ The initial rate of enzyme-catalyzed reactions can be ...
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1answer
180 views

Why does adding a charged group to an organic molecule decrease its stability?

As I understand it, during glycolysis, glucose is converted into fructose 1,6-bisphosphate which greatly destabilizes the molecule. This is so it can be divided into pyruvates more easily. Now I don'...
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3answers
3k views

How does the smell of a compound come about, and is it possible to define a smell?

Colour - and eyesight in general - arises because objects reflect/transmit certain wavelengths of colour, which is detected by our eyes. On the other hand, what gives rise to smell? Is there a branch ...
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261 views

Why do many organic halogen compounds smell or taste sweet?

Is it just coincidence that many organic halogen compounds (especially chlorinated ones) tend to either taste or smell sweet? Examples include dichloromethane, vinyl chloride, chloroform, and ...
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1answer
410 views

Why do α-amino acids have a C-H bond at the α-carbon?

I've just started studying biochemistry and I read that a general $\alpha$-amino acid looks like (ignore the ionisation for now): My question is: why isn't the general $\alpha$-amino acid formula ...
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2answers
478 views

How is ATP generated by cellular respiration?

I learned in a high school level Biology class that the chemical equation for cellular respiration is $$\ce{6O2 + C6H12O6 -> 6CO2 + 6H2O + ATP}$$ When I looked up the chemical formula for ATP I ...
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1answer
228 views

How can a Hydrogen make such a difference?

Looking at familiar bodily fluids for a learning session. At first glance they both look the same. Then I noticed the N=C in biliverdin and HN-C in bilirubin. How can a N=C (imine group) and HN-C (...
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1answer
399 views

Glycoside Formation Reaction

Whenever we add $\ce{H+}$/ Ethanol to glucose in its hemiacetal form, why doesn't pinacone/pinacolone rearrangement take place in place of nucleophillic substitution. The product would lead to ...
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1answer
413 views

Why in solution glucose not convert into galactose or mannose? [closed]

In glucose solution glucose is present in ring form but 1% can be in open chain form. As carbon carbon bond (c-c) roation is possible. Then why does Glucose can't be converted in galactose or mannose ...
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1answer
5k views

Can reaction of gastric acid with swallowed things be dangerously exothermic?

Okay, okay. I know that swallowing a large enough amount of any substance would be considered dangerous. That isn't the point of this question, however. As you probably know, the stomach has ...
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2answers
15k views

What is the difference between a glycosidic bond and peptide bond [closed]

What is the difference between a glycosidic bond and peptide bond because both of them involve the elimination of water but what exactly is different in between them?
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1answer
1k views

Why is gadolinium specifically used in MRI contrast agents?

Gadolinium(III) chelate complexes are routinely used as contrast agents in magnetic resonance imaging (MRI);1 the usual explanation is that paramagnetic species contain unpaired electrons, which cause ...
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0answers
982 views

Selective sorption of toxins by polymethylsiloxane polyhydrate

Polymethylsiloxane polyhydrate (PMSPH) is used as enterosorbent for a couple of decades (nowadays under the trademark "Enterosgel"), intended for binding in the gastrointestinal tract and excretion of ...
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2answers
1k views

Does deuterated water slow down the overall metabolism of a cell?

Would deuterated water, being heavier, slow down the metabolic rate of the cell and subsequently the aging process? edit: lets say I wanted to observe a cellular event, like the formation of the ...
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1answer
2k views

Proton leak during ATP synthesis

I was told there is a proton leak during ATP production. When going through the mechanisms we went over in class, I was unable to find when this occurs. During what part of ATP production is there a ...
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2answers
1k views

Etymology of “click chemistry”

According to Wikipedia, the term click chemistry was coined by K. Barry Sharpless in 1998. What does the word 'click' mean here? I guess it means "join" here but I'm not sure.
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1answer
2k views

What is the nature of the Fe–O2 binding in oxymyoglobin and oxyhemoglobin?

Deoxymyoglobin ($\ce{Mb}$) is known to have iron in the +2 oxidation state; I believe this was deduced from its magnetic moment, which corresponds to four unpaired electrons in high-spin $\mathrm{d^6}$...
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2answers
998 views

Why are peroxides unstable but disulfide bridges considered stable? Why are esters stable but thiolesters are unstable?

I can not understand why a peroxide $\ce{R-O-O-R}$ is considered reactive and unstable. Going down one row on the periodic table, a disulfide bridge ($\ce{R-S-S-R}$) is apparently super stable and ...
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1answer
699 views

Chemical function of Mg and Conjugated bonds in Chlorophyll [closed]

This question has 3 parts, each related to the title. In biochem, we were shown the chemical structure of chlorophyll. The light-absorbing head has many carbon-rings with alternating single and ...
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1answer
221 views

How does a hydrophobic environment help in bond formation?

The glucose-induced structural changes are significant in two respects. First, the environment around the glucose becomes more nonpolar, which favors reaction between the hydrophilic hydroxyl group of ...
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2answers
851 views

What does 2 vol (w/v) mean?

I came across a protocol saying: Homogenize 50 g powdered plant material (accurately weighed and recorded) in 2 vol (w/v) acidified methanol. What does 2 vol (w/v) mean?
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1answer
459 views

What is the mechanism behind the decomposition of enediol phosphate intermediate to methyl glyoxal?

I can't seem to figure out the mechanism for the decomposition of enediol intermediate (in glycolysis) to methyl glyoxal? How does the phosphate group get replaced by a hydrogen?
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160 views

Simulated Body fluid recipe

I'm working on preparing SBF in my school's lab however a couple of components are missing which are $\ce{NaHCO3}$ (0.350 g) and $\ce{K2HPO4}$ (0.228 g) . Is it possible to replace these components ...

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