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 favors the active transport in a membrane?

I was reading about active transport in membranes where ATP is used. ATP "reacts" with the protein pump and converts into ADP and also make a conformational change to the pump. Now this ...
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Molecular dynamics simulation of a protein in acidic medium

I want to perform an MD simulation of a protein under acidic solvent conditions. A quick literature search seems to indicate that people are more interested in the protonation of protein side chains (...
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24 views

Reaction rate constants for the inhibition of cholinesterases by various carbamates

Darvesh et al. [1] have conducted a study on the anticholinesterase activity of various carbamates derived from phenothiazine. The authors measured the inhibition rate constants of rivastigmine for ...
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20 views

Halogen vs H-Bond Donor/Acceptor: How do they differ?

I know that in rational design sometimes the researcher might use Cl or F instead of a H-Bond donor/acceptor. What kind of interaction does a halogen provide compared to the H-bond donor/acceptor? ...
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1answer
116 views

Do enzymes that digest D-glucose react with L-glucose?

D-glucose most common in nature and L-glucose is synthesized in the lab. I know that humans can't use L-glucose in their aerobic pathways because it doesn't match the active site of the enzyme ...but ...
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43 views

Solving for Concentration Using pseudo-First Order Kinetics

The following graphs represent a pseudo-first order bi-molecular reversible reaction with the formula $\ce{A + B <=> C}$: The reaction product has an extinction coefficient of $\pu{50000 M-1 cm-...
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233 views

Why is it rational that salt-bridges (in proteins) are described as a combination of H-bond and ionic bond?

This is a fundamental question that came to me as I was trying to draw the electrostatic attraction between Aspartate (D) and lysine (K). I have always considered the charge on nitrogen, in the lysine ...
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27 views

expression of apparent reaction quotient

question When computing the Gibbs energy change of a reaction using Legendre-transformed $\Delta_fG'$ values for a given $\mathrm{pH}$, the formula of the $\Delta_rG'$ of the reaction is: $\Delta_rG' ...
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33 views

What is “protein redox conformation”?

From an article by Frye et al. [1]: Reduced glutathione (GSH) is the major intracellular redox buffer and is essential in free radical scavenging, redox homeostasis, maintenance of protein redox ...
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36 views

Why are carbamates capable of inhibiting acetylcholinesterase?

Certain carbamate compounds, such as the insecticide carbaryl or the Edgewood carbamates such as EA-3990, can inhibit the enzyme acetylcholinesterase. Unlike organophosphorus compounds, however, they ...
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79 views

Differences in efficacy of oxime reactivators in organophosphate poisoning

Compounds containing an oxime functional group, such as 2-PAM and obidoxime, are used in the treatment of poisoning with organophosphorus compounds. These oximes reactivate the enzyme ...
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16 views

Oxidative phosphorylation analogue

Does the salt bridge in galvanic cells resemble the ATP pump in the inner mitochondrial membrane? And if yes than did someone use this pH difference in harvesting this energy?
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28 views

why do cone cells have broad responsivity spectra peaks?

My understanding of vision is that, although the cone cells in our eyes can detect three colors, there is enough overlap in the responsivity spectra (as shown here: https://en.wikipedia.org/wiki/...
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63 views

What's causing this dip in the FCS curve?

This is a fluorescence correlation spectroscopy measurement of light harvesting complexes. What could be causing the dip at 100 microseconds? Edit: The same thing was observed using fluorescence ...
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43 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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34 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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47 views

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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79 views

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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452 views

How can I calculate the percentage of urea in animal feed?

I'am having some doubts in the calculation that concerns the urea percentage in animal feed using the method AOAC $967.07$ How can I calculate the urea percentage using the following data: The ...
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474 views

proteolysis - how to determine the partial or completeness of the cleavage reaction?

Though the question is about biomolecules, we agree the underlying functions, formation, degradation etc come down to chemistry, (then physics and maths). I am posting it here to receive an ...
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338 views

Differentiating random and ordered sequential mechanisms in enzyme kinetics

Can random and ordered sequential mechanisms be descern by Lineweaver-Burk plot? Why or why not? Because for orederd sequential mechanism I got different LB plot depending on which substrate is held ...
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318 views

determination of glucose syrup in sugar product

I work with a sugar product that contains saccharose (approx. 70 %), glucose syrup (approx. 15 %), glycerine (approx. 3 %) and some other ingedrients, e.g. water. Glucose syrup consists of 5 % glucose ...
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46 views

Can we create human muscles artificially?

Can chemical processes create sarcomeres? Not the entire cell with mitochondria, just what basically makes the muscle contract, myosin and actin, in the goal of reproducing our muscles. The source of ...
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91 views

Formation of a pH gradient using carrier ampholites

In a technique called isoelectric focusing, the crucial part is the formation of a pH gradient using carrier ampholytes. What is the exact principle by which the gradient is formed? How do the ...
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53 views

Difference between “isoaspartyl” and “isoaspartate” in antibody deamidation

I'm translating a text where antibody deamidation is mentioned. One sentence goes like this: We used reversed-phase HPLC to analyze the aspartyl forms of the monoclonal antibody. (Russian original ...
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63 views

What chemicals would need to be added to human urea to make it a nutritional substance?

I've been thinking about food supplies, waste management and sustainable living, particularly in highly isolated areas like a Mars colony or a space station, or also in a non-technically advanced ...
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63 views

Is it possible to observe ATP energy transport in table experiment?

Is it possible to take AMP or ADP, then phosphorylate it convert to ATP to charge with energy, then transport to other place an then observe energy freeing? In table / home / school experiment?
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324 views

Mechanism: explanation of final step in synthesis of the thyroid hormones (T4, T3)

In the following mechanism for the synthesis of T3 (triiodothyronine) on thyroglobulin, what are the factors causing the last step to occur? Does it have something to do with the electron density of ...
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261 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?
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57 views

Identify “decoupling sites” in glucose oxydase reaction

Given the following coupled reactions: $$\ce{glucose + O2 + H2O + glucose~oxydase -> gluconic~acid + H2O2}$$ $$\ce{H2O2 + TMB(star) -> TMB}$$ Identify: A potential reagent or ...
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172 views

What is the Chemistry behind “good” and “bad” cholesterol & their relation to Cis/Trans fatty acids?

I have searched Google for this but cannot seem to find an explanation. My question is as follows - what is the Chemistry/Biochemistry behind cis and trans fatty acids resulting in "Bad" LDL and "Good"...
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372 views

Delta G values for Pyruvate--> Alanine vs. Oxaloacetate -> Aspartate ->Asparagine

What are the delta G values for the mammalian (human) biosynthesis of alanine from pyruvate, and for the conversion of oxaloacetate to asparagine? (assuming no particular cellular restriction or other ...
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79 views

Mercury binding agents which cross the blood brain barrier

The two substances I have come across are cilantro and lipoic acid. How effective would either of them be? Are there any other agents known which produce the desired results?
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256 views

Can TBE electrophoresis buffer be stored in a PETE container?

I'm doing a science project on agarose gel electrophoresis and would like to know if it is safe to store Tris/Borate/EDTA buffer solution inside a PETE container since I will be making about 10L of ...
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72 views

Determine max of 2 parameter functions

I have 12 experimental tables with OD(substrate concentration, time), where OD is optical density and one table with $\mu$ (substrate), where $\mu$ is growth speed. OD and $\mu$ are functions. The ...
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11 views

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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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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16 views

pH Dependency of IR Stretching Frequency in CO-binded Heme Protein

If one consumes CO, then CO binds with Heme Protein forming a Fe-CO bond. My question is if there will be any pH dependency on IR Stretching Frequency, i.e. ν(CO) and ν(Fe-CO). And if there is, then ...
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25 views

Why does the emission of dansyl group diminish with time in this experiment?

I don't know how to make sense of this. I what is happening when an enzyme (carboxypeptidase, which contains tryptophan as its only chromophore and uses a Zn(II) ion in its active center) hydrolises a ...
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36 views

In electrophoresis, are positive and negative molecules obviously separated?

I have just studied electrophoresis in biochemistry. The charged particles move to the oppsite charged electrodes whose speed is depended on their particle size. If that so, are negative and positive ...
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37 views

Does HI-6 form a covalent adduct with acetylcholinesterase?

According to sources provided below, the oxime HI-6, or Asoxime Dichloride, as it is also called, besides being a reactivator of acetylcholinesterase that has been inhibited by organophosphorus ...
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36 views

Hydrolysis of phosphoryl-oximes

When acetylcholinesterase that has been inhibited by an organophosphorus compound is reactivated by an oxime, a phosphoryl-oxime is formed, which is then somehow hydrolyzed in the blood. One study ...
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29 views

How is presupposition of the order of reaction justified in Michaelis-Menten model?

from what I have understood, to derive Michaelis-Menten equation, we first suppose that $\ce{E + S <=>[k_1][k_{-1}] ES->[k_2]E + P }$ and make the 'steady-state assumption', that $k_1[E][S]=...
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Collagen digestion

As far as I know, pepsin is used very often in collagen solutions extraction. Since it only cleaves the telopeptides and leaves the triple helix chains of the collagen intact. I was wondering if there ...
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49 views

Why is Cadmium so carcinogenic compared to other heavy metals?

This free article as well as this article do a good job highlighting the carcinogenic effects of Cadmium and the mechanisms by which they occur. However, my question is why is Cadmium so carcinogenic ...
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In vivo, does it take energy to move double bonds from cis to trans long chain unsaturated fatty acids

In vitro, long chain fatty acids may yield more energy when bonds break, but in vivo, I understood that energy is burned before unsaturated fatty acids can be oxidized because the side groups with ...
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25 views

Pyridinium ion in inositol nicotinate

I have read about inositol nicotinate which is used as a medication for deficiency in vitamin B-3. I think that if acetic acid was applied to this medication it would form pyridinium ion and acetate ...
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29 views

How to convert pepsin into powder form?

I have pepsin powder which is now hydrated due to humidity. I want to convert it back to the powder form. How to do it? I don't have access to a freeze-dryer . I prefer any cheap procedure other than ...
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45 views

Selective Esterification of Amino Acid

I am going to prepare tert-butyl protected threonine. I was going for the classic esterification methodology which is acid catalyzed (sulfuric acid) esterification under reflux of tert butyl alcohol + ...
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Protein purification pressure limits confusion, about the X-MPa limit for FPLC?

I have always been a bit confused about column pressure limits. I have to elaborate a bit on the problem to get to my question: In protein purification we use the äkta purification machines (e.g. ...