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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What is name of this formulas? [closed]

i have a question what is name of this thing (it should be something with proteins) Thanks for all answers
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Theoretically, given an ample supply of energy, can I convert Carbon Dioxide and Water into C6H12O6 and Oxygen in a Chamber? [closed]

Long story short, I have an insane volume of Carbon Dioxide and I have a bunch of experiments in mind. One of my questions is, would it be theoretically possible to release a high volume of Carbon ...
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To which extent is protein folding conserving subprotein structures?

I am actually a pure mathematician, who stumbled over this paper «Protein-Folding Analysis Using Features Obtained by Persistent Homology» by Ichinomiya et al. (Biophys. J. 118, 2020, 2926-2937; link),...
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Nanocomposite hydrogel for wet adehsion in biomedical applications

my name‘s Tristan and I‘m a bachelor‘s student in Germany. I‘m trying to synthesize an injectable nanocomposite hydrogel for wound closure and wound healing applications. The problem is that, next to ...
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27 views

Gluconeogenesis

So I've been doing research on the production of lactic acid, however, I found that lactate will first reform into pyruvate and then go through gluconeogenesis reforming D-glucose. From what I ...
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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-...
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1answer
138 views

Calculate Michaelis-Menten constant of enzyme catalyzed reaction

I have: $$\begin{array}{c|c} \dfrac{v }{ [S]}/\pu{s^{-1}} & v \cdot 10^2/\pu{mol dm^-3 s^-1} \\ \hline 0.257\ & 5.15\\ 0.895 & 4.48\\ 2.00\ & 3.35\\ 3.59\ & 1.8\\ 4.82\ & 0....
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1answer
36 views

In solid-phase peptide synthesis, why are the formation of aspartimides a problem but not “glutamides”?

I'm studying solid-phase peptide synthesis (SPPS) at the moment, and a common problem is the formation of aspartimides, which disrupt the synthetic process. I understand how they form and why are they ...
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Why does glucose test positive for aldehydes having lost aldehydic nature to gain aromaticity?

It has been proved that glucose 99% of the times is in its cyclic structure (source - khan academy) and that the oxygen atom is busy bridging the 1st and 5th carbon. Then why does it even show ...
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36 views

How does the membrane potential change so drastically during an action potential?

I understand that the Nernst potentials $$V = \frac{k_\mathrm{B}T}{e} \ln\left(\frac{c_\mathrm{out}}{c_\mathrm{in}}\right)$$ for all ions inside and outside a cell barely change when an action ...
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1answer
80 views

Reason for protonation of amino group in amino acids at near neutral pH

What happens to the amino group when amino acid is added to a near neutral solution? How does it come about gaining an extra proton? I understand what happen to the carboxyl group, since it is a ...
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36 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 ...
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How to find the reaction rate in an enzyme reaction?

First time posting questions here, so let me know if I need to edit anything. I need to decide $dC/dt$ and $dP/dt$ when the reaction is like this, where I only know we must have 2 substrates $S$ to ...
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2answers
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Determine vmax and enzyme concentration (Michaelis–Menten)

I am given that the enzyme concentration is $\pu{15 nM}$ and the following data: $$ \begin{array}{rl} \hline S/\pu{mM} & V/\pu{mM s^{-1}} \\ \hline 1 & 0.202 \\ 2 & 0.368 \\ 5 & 0....
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1answer
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Trying to understand phrase in paper: preventing nonspecific binding of AuNP antibody conjugates using a blocking solution

I am working through a paper, Lateral flow immunochromatographic assay on a single piece of paper. I'm having trouble understanding one of the points! Under the Device fabrication question, it says: ...
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1answer
551 views

SARS-CoV - relative size of the spike protein

I am taking an online course in image analysis and have been asked to use the attached image to determine the size of the SARS-S protein of the SARS-CoV relative to the total of its proteins. However, ...
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1answer
35 views

Carbon 11 radiolabeled inhaled Beta-2 agonist or corticosteroids, is it possible?

Background Positron emission tomography (PET) is a highly sensitive imaging modality that can provide in vivo quantitative information of biological processes at a biochemical level. PET relies upon ...
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3answers
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When an aqueous extract of a substance is said to be administered at a certain quantity, is the quoted mass analogous to one as original substance?

I'm trying to read studies about the possible toxicity of the leaves of some plant often said to possess positive medicinal properties. In the studies, performed on rats, it is usually said that an ...
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4answers
640 views

Ramachandran plot Phi(ϕ) Psi(ψ) dihedral angle Convention for Zero, Positive and Negative value- old and new

Update: possible duplicate: What is the precise definition of Ramachandran angles?. Question modified. G.N. Ramachandran et al, in their own work (PMC) (DOI), did not used phi(ϕ) and psi(ψ) as we use ...
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25 views

Electrolysis in Electrophoresis of proteins and DNA

Can electrolysis happen in an electrophoresis assay (such as SDS-PAGE)? To perform electrophoresis, the substances must be dissolved in an aquatic buffer with a previously determined ionic strength. ...
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1answer
1k views

How to I neutralize the smell of (VERY) spoiled milk [closed]

Let's say I have a cup full of milk that had been at room temperature for months (apparently my son was running an experiment...). The smell started seeping out of the makeshift lid, and it's horrible....
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64 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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1answer
73 views

Carbon atoms types in amino-acids [closed]

I'm looking for a table or another kind of schema where I can find which type of carbon atoms (sp3, sp2 etc.) are present in each amino-acid. In my biochemistry books these informations are not ...
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1answer
27 views

Do phosphoryl thiocholines, their uncharged analogs, and other organophosphates, interact differently with Acetylcholinesterase?

As asked in the title, would the various salts -such as hydrochloride or methyl iodide- of V-Agents interact any differently with acetylcholinesterase compared to the neutral compound? For instance, ...
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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 ...
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26 views

What is meant by the term 'biosynthetic origin'?

I keep seeing the term biosynthetic origin used in medicinal related papers. Does it just refer to the biological precursors to the molecule? So, for example, the biosynthetic origin of Paclitaxel is ...
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1answer
134 views

Why is the formation of a peptide bond not spontaneous?

Why is the formation of a peptide bond from a carboxylic acid and amine not spontaneous? I'm not looking for the free energy calculation; I have it from several sources. I'm just asking for an ...
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1answer
2k views

Why do green bell peppers become bitter when cooked?

Why do green bell peppers taste sweet raw, but become bitter when cooked (steamed)? What chemical process is responsible for this? (I don't believe the temperatures are high enough for the Maillard ...
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0answers
30 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 ...
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2answers
54 views

How to run electrochemical tests on Microorganism (bacteria in a medium)?

I am trying to run some electrochemical tests(e.g.CV (Cyclic Voltammetry) & EIS (electrical impedance spectroscopy)) using half cell configuration on micro-organisms (e.g.bacteria). The bacteria ...
4
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1answer
48 views

Why is the hydrolysis of ATP to AMP more energetic than the hydrolysis of ATP to ADP?

I am confused as to why the hydrolysis of ATP to AMP and pyrophosphate is more energetic than hydrolysis to ADP and inorganic phosphate, especially since pyrophosphates are more unstable than ...
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17 views

How carbon nanotube sensors works?

How carbon nanotube sensors works? Is the protein (or chemical compound used as part of the sensor) placed inside the tube or where is it placed? and how is the technology used to place the protein ...
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35 views

Michaelis–Menten kinetics applied to a solution with two enzymes

Two enzymes are added to a solution containing a tow concentration of a substrate that they can both use. Which statement is correct? A. Both enzymes will use equal amounts of the substrate. B. ...
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1answer
103 views

How do enzymes affect a reaction's equilibrium?

I am not sure to understand something I read in a educational journal (1) Introduction Lets consider the following reversible enzyme-catalysed reversible reaction; $$E + S \leftrightharpoons ES \...
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4answers
2k views

In sourdough bread baking what do the wild yeast and bacteria not eat during dough fermentation and why?

I bake bread using a sourdough starter. The starter is a culture of lactobacillus and some kind of yeast. They apparently eat the sugars or carbohydrates in the dough during fermentation but when I ...
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1answer
101 views

Does anyone know what program was used to make this molecular structure picture? [closed]

I am a quantum chemistry beginer, and this picture color scheme is classic. I wonder how to make such pictures by myself.
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1answer
59 views

How ph affects aesculune fluorescence?

I am facing a ween problem. I am trying to find out, how would look like the graph for fluroscence of aesculine (intensity of fluoroscence on Y axis and pH on X axis). I know, that increasing the pH ...
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1answer
641 views

Can sugars dissolve in liquid ammonia?

Can monosaccharides and disaccharides dissolve in liquid ammonia due to hydrogen bond formation? My rationale is that these sugars may be able to form hydrogen bond with ammonia ($\ce{NH3}$).
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2answers
91 views

Biological activity of the isotopes of the same element

I have a question regarding biological activity of different isotopes of the same elements, notably $\ce{^206Pb}$ and $\ce{^208Pb}$. Lead is known to be toxic, such that it can replace calcium from ...
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0answers
32 views

Differences in AChE inhibition kinetics between paraoxon and methyl paraoxon

According to literature, dimethyl paraoxon has a reaction rate constant for the aging (spontaneous dealkylation) of acetylcholinesterase of $\pu{0.186 h-1}$, a spontaneous reactivation rate constant ...
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0answers
67 views

Haworth structures of sucrose and lactose

The haworth structures of lactose and sucrose is My question is regarding the glyosidic linkage, in lactose it is represented as a zig zag and in sucrose it is a "V". What does that mean. ...
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0answers
23 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,...
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2answers
382 views

Why does denaturation of albumen protein cause pH of solution to increase?

I'm interested in the denaturation of proteins by alcohols, specifically by ethanol. I have devised a simple experiment in which I inject solutions of ethanol (of variable concentrations) into ...
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0answers
14 views

Structure-Activity Relationship of Chlormephos and Parathion

According to the book "The Chemistry of Organophosphorus Pesticides", the insecticide Chlormephos (S-(chloromethyl) O,O-diethyl phosphorodithioate) has an oral LD50 in rats of 7 mg/k. ...
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28 views

Why is there a mirror image effect in the absorbance and fluorescence spectra?

I've read some answers online but I still can't seem to understand the mirror image effect. Why is the highest energy absorption (v" = 0 to v' = 4) the lowest energy fluorescence (v' = 4 to v&...
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0answers
30 views

How can DI water inhibit peroxidase activity?

I'm troubleshooting an IHC staining issue, and according to Thermo-Fischer's website, "Deionized water can sometimes contain peroxidase inhibitors that can significantly impair enzyme activity.&...
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29 views

Which electrons are in HOMO in a peptide bond?

We've recently studied the absorption of UV light by polypeptides, and found that the peptide bonds itself absorhs UV light at around 210nm. I'm confused about what feature causes this to happen.
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1answer
87 views

How do point mutations affect complementary base-pairing and widths of the nucleotide pairs?

Point mutations are divided into two categories: transitions and transversions. Since point mutations only occur during DNA replication (an integral process of both mitosis and meiosis), the mutated ...
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1answer
32 views

Depicting a mechanism of peptide bond formation with protonated and deprotonated amino group

I've noticed that some textbooks and video lectures use an amino acid wherein the amino group has two hydrogens, and others use an amino acid with three hydrogens in the amino group (in the formation ...
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1answer
54 views

Is selenite (hydrous calcium sulfate) dangerous when you grind it up?

I was wondering about the safety of a specific mineral, Selenite. From my research, I have read that selenite is the crystalline form of gypsum, which is hydrous calcium sulfate. I was wondering if I ...

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