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 Chlormephos highly toxic despite requiring metabolic activation?

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/kg. For ...
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Right conductivity of protein sample for Protein A purification of human IgG?

A sample from a cell culture has some IgG and this is to be purified using protein A chromatography. Based on the chromatography handbook from GE-Healthcare/Cytiva, the protein sample should have &...
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25 views

How do structural differences between neostigmine and TL-599 contribute to differences in toxicity?

Stevens and Beutel studied the activity of several carbamate anticholinesterases. Among other things, they found that the (4-trimethylammonio)phenyl dimethylcarbamate iodide (The para-analog of ...
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161 views

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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54 views

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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1answer
155 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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78 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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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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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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42 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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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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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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64 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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48 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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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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464 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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487 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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359 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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357 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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47 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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95 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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339 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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264 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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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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173 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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381 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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84 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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270 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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73 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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1answer
70 views

Why aldehyde group is easy to oxidize than hydroxyl groups of glucose

In all the reactions i had Seen I pointed out that aldehyde groups of a compound like glucose are easy to oxidize than the hydroxyl groups. I had also read some similar answers but I was unable to ...
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16 views

What are the initial experiments to hypothesize or decide the method of protein degradation?

For a protein of interest, How to determine it’s degrading method— protease or proteasome? Is it possible through bioinformatics? What are the initial experiments to hypothesize or decide the method ...
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119 views

What is an enzymatic reaction for which a detailed tertiary structure showing all ligands is available on the PDB?

This is a follow-up to my earlier question here How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center? about the lactate synthase. I am using the lactate ...
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27 views

How can G3P oxidize into 1,3-BPG without energy expenditure?

In glycolysis, one of the important steps is when Glyceraldehyde-3-phosphate is oxidized to 1,3- Bisphosphoglycerate, while reducing $NAD^+$ to NADH and $H^+$. I'm a bit perplexed by this step since ...
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28 views

General cleaning solution for clinical chemistry applications

I want to reuse some plastic and glass items that I am using to do colorimetric concentration analysis of serum and urine. There are some enzymatic assays, mineral assays and so on. I have been trying ...
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28 views

What do natural hybrids of peptides and nucleic acids look like?

Until recently I thought that there was a clean distinction between polypeptides and oligonucleotides, but apparently there are recent studies of therapeutic compounds that could be described as "...
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49 views

Why are glyosidic linkage of glucose and fructose rings often occurring at the 1' and 4' prime positions?

Here are some example combinations from my textbook: In all of these combined products, the reactive centres seem to be the carbon at first position/ fourth position from the oxygen in priority. Is ...
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84 views

Why don't ant bites kill us?

So, methanol is supposed to be toxic even in minute quantities because it is oxidised in our body to methanal and then methanoic acid. This can cause blindness and even death. Interestingly, ants ...
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22 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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24 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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18 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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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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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? ...