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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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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 +...
John Baez's user avatar
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Solve this chemical or biological mystery

I hope this is the best place to pose this unique question. Please forgive me if it's not. I went into a closet to get a prescription medication that was filled about a year ago. The label on the ...
End Antisemitic Hate's user avatar
6 votes
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204 views

Why is the reverse aldol cleavage of fructose 1,6-bisphosphate highly endergonic under standard conditions?

I have another question similar to this one. I just don't have intuition for why reactions are thermodynamically favorable or unfavorable and I'd like to build it. This time I'd like to ask about ...
Katie's user avatar
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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 ...
PB Vanc's user avatar
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Do disulfide bonds determine the 3-dimensional structure of a protein or do they just stabilise the 3D structure?

I noticed that most disulfide bonds occur when two cysteine side chains exist in close proximity to each other. Do those cysteine side chains "look out" for each other during folding, that ...
Doe Pual's user avatar
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Why are S-thiocarbamates less toxic than carbamates?

According to Haley and Rhodes, neostigmine bromide (alternatively known as Prostigmine) has an LD50 in mice of around 0.165 mg/kg by IV injection. Pubchem claims that this is also the LD50 for ...
user73910's user avatar
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Interaction of trifluoroacetates with acetylcholinesterase

There exists a substance called TMTFA, or 3-(N,N,N-Trimethylammonio)-2,2,2-trifluoroacetophenone. It is known for being able to inhibit acetylcholinesterase at femtomolar concentrations. The TMTFA-...
user73910's user avatar
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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. ...
Matt Whitelock's user avatar
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1k 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 ...
andselisk's user avatar
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Phlorizin content in grapes

I work in a winery and we have some problems about a new process involving phlorizin. We know that phlorizin is the major dihydrochalcone found in apples. I have been reading that this compound is ...
ines's user avatar
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What methods could be used to preserve scorpion venom?

As extracting scorpion venom goes, how would one most effectively store and preserve the venom for future research? My thoughts are lyophilization, however I am not sure that would be the best of all ...
Adam Cat's user avatar
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Catalyzation in Carbonic Acid

I understand the basics of carbonic acid + 1 kcal breaking down into water and carbon dioxide. However, my professor wants me to draw an energy map showing the catalyst in human blood reducing the ...
Jeff Holiday's user avatar
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How are oxidation states of bioinorganic molybdenum/tungsten complexes determined?

Here a screenshot from our lecture on bioinorganic molybdenum complexes, dealing with the catalytic cycle of xanthine oxidase: It is said that the only biologically relevant oxidation states of Mo ...
Mäßige's user avatar
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Are there natural enzymes that catalyze different reactions under different conditions?

Are there natural enzymes that catalyze different reactions under different conditions? For example an enzyme undergoes a conformational change under certain pH and starts catalysing a different ...
Euphorbium's user avatar
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133 views

What do we know about the structure of the amylopectin iodine complex?

I am studying a method of finding the ratio between amylose and amylopectin using the difference in color of the amylose-iodine complex(blue) and the amylopectin-iodine complex (red/brown). Through ...
jettosutorimu's user avatar
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135 views

Why can't NAD+ undergo single-electron reduction?

$\ce{FAD}$ can undergo single-electron reduction to form a stable radical, which can then be reduced again to $\ce{FADH2}$. This is supposedly possible due to resonance stability, where the unpaired ...
chematwork's user avatar
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Can bis-quaternary aromatic compounds act directly on acetylcholine receptors?

The book Cholinesterases and Anticholinesterase Agents gives examples of bis-quaternary aromatic compounds that are capable of inhibiting acetylcholinesterase. Page 400 gives examples of some such ...
user73910's user avatar
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Metal coordination in enzymes: What type and number of bonds form between amino acid residues and Fe(II)?

My understanding: Transition (d-block) metals, as found in intracellular proteins, are limited to about 10 elements including amongst others Fe, Ni, and Cu. Due to the reductive environments inside ...
CuriousTree's user avatar
4 votes
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343 views

Synthesis of tripeptide using Merrifield peptide synthesis procedure - Inclusion of asparagine

I am supposed to synthesize tripeptide, $\mathrm{Ala-Asn-Phe}$, using Merrifield peptide synthesis procedure. Accordingly, I have done followings: Attached protected $\mathrm{Phe}$ as the first ...
Geek's user avatar
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Thyroid peroxidase - can atomic iodine serve as iodinating agent?

McMurry's Organic Chemistry (7th Ed.) states, that Tyrosine is iodinated by mechanism of electrophilic aromatic substitution and the iodinating agent is $\ce{I+}$ or $\ce{HIO}$ formed by thyroid ...
mpribis's user avatar
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Why do heavy metals like mercury and lead have an affinity for sulfur or sulfur compounds?

Many of the heavy metals such as mercury, lead, thallium, cadmium, and arsenic exert toxic effects largely by binding to or otherwise interfering with organic sulfur compounds or groups in the body. ...
amylakin's user avatar
4 votes
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62 views

Is there a model for (quality of) two-component-polymerization (dependent on e.g. concentration)?

Sadly my chemistry background is only from high school (I'm a roboticist), but I try my best to explain the problem: Situation: Lets say I have two water based solutions/suspensions. One contains ...
Mofef's user avatar
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What are the chemical similarities between gallium and barium?

I am analyzing nutrient concentrations in wood, and I have found that in all my samples the distribution of gallium and barium are closely related. As a related phenomenon, the presence of these ...
Darwin PC's user avatar
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632 views

Calculating volume ethanol in an fermented aqueous solution of sucrose, water, and ethanol

I've been working on a biology experiment where I calculate the fermentation yield of yeast under various light induced stress responses inhibiting the translation of various fermentation enzymes. My ...
Mikey G's user avatar
  • 41
4 votes
1 answer
71 views

Is it possible to have an anhydrous solvent for virology, specifically in vitro phage assembly?

Typical protocols for lambda phage in vitro assembly call for you to dump all your viral components and buffer solutions into water. Water is a great solvent, drives extraction of energy from atp, and ...
edmund shelto's user avatar
3 votes
0 answers
32 views

Assessing stability of protein used for interaction experiments after changing buffer from tris to HEPES

I have a protein with a theoretical $\mathrm{pI}~9.0$ currently stored in $\pu{25 mM}$ tris and $\pu{250 mM}$ $\ce{NaCl}$ $(\mathrm{pH}~8)$ at $\pu{−80 °C}.$ I need to do experiments in HEPES at $\...
TheChemist's user avatar
3 votes
0 answers
198 views

Why is folic acid very slightly soluble in water while it's a B vitamin?

The solubility of folic acid is just 1.6 mg/L (25 °C). Why is it so insoluble in water while it is one of B vitamins which are called water-soluble vitamins beside Vitamin C?
Walter Heisenberg White's user avatar
3 votes
0 answers
76 views

Two questions regarding the fourth step of glycolysis

I am studying the 10 steps of glycolysis, and is currently on step 4. In this step, a molecule of fructose-1,6-biphosphate is cleaved into dihydroacetone phosphate (DHAP) and glyceraldehyde 3-...
Cam's user avatar
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Why is this a non-reducing end?

I was told that C is a non-reducing end. To my understanding, only anomeric carbon involved in glycosidic bond cannot be in the linear form, and in other words, is a non-reducing end. But C is an ...
user307640's user avatar
3 votes
0 answers
213 views

Why neglecting Bradford Solution Volume in the assay?

I would like to know why do we not need to take account of Bradford agent solution in dilution calculation? For example, $\pu{2.5 \mu g mL-1}$ BSA will calculate from $\pu{0.4 \mu L}$ of $\pu{1 mg mL-...
Pete Kittinun's user avatar
3 votes
0 answers
140 views

What is the structural formula of a monomer of hydroxypropyl methylcellulose?

I'm studying the properties of the polymer hydroxypropyl methylcellulose (HPMC) with the static scattering technique. I'm trying to interpret the molar mass obtained with a Zimm plot, that is $\pu{(3....
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3 votes
0 answers
33 views

Differences in AChE inhibition kinetics between VX and VR

According to the referenced paper, VR has an AChE inhibition reaction rate constant almost 4 times that of VX. Interestingly, its reaction rate constant for aging of the enzyme is less than that of VX,...
user73910's user avatar
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3 votes
0 answers
76 views

Does ADP + P => ATP produce water?

ADP + P has one oxygen and two hydrogen more atoms than ATP. Are these atoms released as water in the reaction ADP + P => ATP? To balance the equation, would ADP + P => ATP + H2O be more correct?
Tien's user avatar
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3 votes
0 answers
3k views

Why dried, closed coconuts go through carbonation?

Some dried, closed coconuts go through carbonation: The white meat of the coconut becomes disintegrated and smeary The liquid becomes carbonated with a bit sour-salty tasted coconut water (which ...
user avatar
3 votes
0 answers
123 views

How to control pH in a fermenter based on the acid produced by mircoorganism

I have got a bioreactor with an aqueous medium which produces biomass (yeast; S.cerevisiae) after inoculation. I am observing and collecting data over the whole process via probes/etc. on different ...
Capt.Krusty's user avatar
3 votes
0 answers
82 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 ...
Noir's user avatar
  • 131
3 votes
0 answers
311 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 ...
Jacob's user avatar
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3 votes
0 answers
642 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 ...
user 33690's user avatar
3 votes
0 answers
88 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 ...
Abijah's user avatar
  • 197
3 votes
0 answers
975 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 ...
IBstressed's user avatar
3 votes
0 answers
70 views

What component of the human DNA reacts with 4,5-benzo[a]pyrene oxide and 7,8-benzo[a]pyrene oxide to produce cancerous tumors

I read in an article that we have this enzyme called P450 that converts aromatic compounds into water soluble compounds that can be eliminated. This enzyme converts aromatic compounds into arene ...
Anonymous's user avatar
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3 votes
0 answers
839 views

How do thiol groups act as reducing agents?

In my biochemistry practicals, we used reducing agents such as beta mercaptoethanol: and dithiothreitol (DTT) Both of these have S-H groups, and I am sure that these are involved in the reduction ...
Meep's user avatar
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3 votes
0 answers
497 views

Why does the Michaelis-Menten constant decrease in the presence of non-competitive inhibitor?

Non-competitive inhibitors don't bind to the active sites of enzymes. However, in the presence of non-competitive inhibitors, the Michaelis-Menten constant is found to decrease. Why is this so?
angrycarbocation's user avatar
3 votes
0 answers
71 views

Questions about Genetic algorithm paper of Gilman and Ross

I want to reproduce an (old) biochemistry paper of Gilman and Ross, i.e. " Genetic algorithm selecetion of a regulatory structure that directs flux in a simple metabolic model." ( The following link ...
maxE's user avatar
  • 131
3 votes
0 answers
1k views

Measuring reaction rates when reactants and products both have (different) molar extinctions at the chosen wavelenghth

In my Biochem labs we would always measure the consumption of NADH, and they always noted that it was useful that NAD+ had essentially no absorbance at 340 nm, which allowed us to directly relate ...
Jory's user avatar
  • 235
3 votes
0 answers
625 views

The Health Effects of Alkaline Ionized Water?

I came across alkaline ionized water as my aunts bought a system called Kangen Water from Enagic Inc. The water produced by this system is claimed to contain smaller water clusters (4-6 molecules) ...
Huy Nguyen's user avatar
3 votes
0 answers
71 views

Can one dichlorotriazine molecule form two bonds with cellulose?

In all the reactions I saw online, dichlorotriazine is shown to form only one bond with cellulose (example 1, example 2; paper). But cellulose has many potential sites for bonding. Can ...
Sparkler's user avatar
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3 votes
0 answers
279 views

Why does egg yolk turn white when washed with water?

I recently noticed that whenever I washed the egg yolk stuck on some utensils the water becomes milky white. It has to be the egg yolk that turns white and give off the white color to water right?
therealssj's user avatar
3 votes
0 answers
475 views

Why would ethanol or water give poor yields in a peptide deprotection hydrogenolysis?

A homework question asks: The following reaction was carried out using ethanol or water as solvents, but gave poor yields in both cases. Suggest why this might be the case and how these ...
user5434's user avatar
  • 549
3 votes
0 answers
97 views

Enzyme Assay - pectinase

I am working on Enzyme Assay.I assayed the enzyme in different buffers from $pH\ 1-12.5$ However,the enzyme has good activities starting from $pH\ 1-10.5$ Is that possible to have enzyme activity in ...
Oli's user avatar
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