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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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
37 views

Ramachandran Plot for Phi and Psi angles of peptides

Why do we consider the normal and extreme limits for Ramachandran plots to be less than the Van Der Waal distances between two atoms?
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Which is a better substrate for glycolysis? A monosaccharide like glucose or polysaccharides? [closed]

Since polysaccharides also contain glucose, can they replace glucose as the principal substrate for glycolysis?
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1answer
115 views

Which textbook is this image on protein tertiary structure from?

I am trying to find the original textbook image that is the inspiration for many schematic figures showing tertiary interactions (hydrogen bonding, ionic interactions, hydrophobic interactions, ...
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1answer
33 views

A question about ligand binding

I have done part a and part b but I keep getting a negative concentration for part c. For part a I got $\pu{2 \mu M}$ For part b I got $\pu{5.051 \mu M}$ For part c, I get $2=3.2 + \text{[bound ...
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1answer
31 views

Why is the glycosidic bond between sugars always between the anomeric carbon?

Why can't the hydroxyl group of another carbon condense with another OH of the second sugar (like 2,4 glycosidic bond) Thanks
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2answers
40 views

Does mixing two different foaming soap make it ineffective?

To save soap during this pandemic, I mixed foaming soap of two different brands and then the solution became cloudy (both originally transparent) . It seems foaming okay. But does this make the soap ...
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1answer
22 views

Weak acids compared to strong ones in pH > 7 solution

In the book of Molecular Cell Biology (Big Alberts) by Alberts, at page 46, it is stated that Acids—especially weak acids—will give up their protons more readily if the concentration of > H3O+ in ...
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1answer
40 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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1answer
39 views

Why does hydrolysis of ADP to AMP yields the same amount of energy as ATP to ADP, if ADP is more stable?

I learned about the resonance stability of ADP and the fact, that ATP is less stable due to intramolecular instability. I was surprised to see that the energy net of conversion of ADP to AMP is the ...
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43 views

Transformed chemical potential of formation: something weird in Alberty 2003

I am trying to wrap my head around transformed chemical potentials, as described in Thermodynamics of biochemical reactions (R. Alberty, 2003), however, two equations seem to be contradictory in this ...
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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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Non-water based binder for powder

I am looking for a product that can bind dry powdered charcoal and a dry super absorbent polymer together until it comes into contact with water. Additionally the end-product should be biodegradable (...
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71 views

Which amino acids can be totally synthesized? [closed]

I can't find information regarding which amino acids (say the proteinogenic ones or in general) can be totally synthesized. Is there a reference?
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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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1answer
36 views

How to calculate membrane potentials?

I have recently been reading about membrane potentials in the cell and how they are derived. The textbook (Guyton and Hall Textbook of Medical Physiology, 13th Ed) gave this equation: $$EMF=\pm\frac{...
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2answers
47 views

How does work from other sources affect Gibbs free energy of the system?

In most physical chemistry textbooks, Gibbs free energy is given like this: $$\Delta_\mathrm rG = \Delta_\mathrm rG^\circ + RT\ln Q\tag{1}$$ and Gibbs free energy is part of this three-way ...
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33 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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24 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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1answer
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Why is heroin a more potent drug than morphine, despite having a similar structure?

The structures of heroin and morphine are quite similar, with heroin being formed by acetylation of morphine: Why is heroin so much more potent than morphine, when their structures are so similar? ...
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50 views

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 ...
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0answers
29 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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1answer
41 views

Hydrogen bonding in sugar acids

I recently learnt that the reason for low solubility of mucic acid as compared to glucaric acid was more hydrogen bonding in the crystal state of mucic acid as compared to glucaric acid. I would ...
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2answers
192 views

Oxidation of hydroxyl groups of glucose

In all oxidation reactions of glucose, it seems that the aldehyde group alone gets oxidised and none of the hydroxyl groups. In one reaction with nitric acid, the aldehyde group and the terminal ...
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1answer
61 views

Comparing the solubility of glucaric acid and mucic acid

Why is glucaric acid soluble in water but not mucic acid? The chemical formulae seem to be the same so why is it that one is more soluble than the other?
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1answer
53 views

Acidity of thiamine - how comes hydroxide anion with pK about 15 ionizes thiamine with pK about 18?

Textbooks say removing proton from thiamine's C atom will produce a resonance stabilized carbanion which is hence bioactive. That's OK, but how comes that 1) we abstract the acidic proton with the OH ...
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1answer
36 views

What is an alternate way of preparing a sodium hydrogen phosphate/sodium dihydrogen phosphate buffer through titrating an acid with a strong base?

So my friend and I are stumped. This is in the context of achieving the sodium hydrogen phosphate/sodium dihydrogen phosphate buffer by titrating the acid with a strong base. My friend says the answer ...
2
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1answer
62 views

How to predict amine donor in biochemical reactions (whether glutamine or aspartate)?

In biochemical reactions amine $(\ce{-NH2})$ transfer is done in multiple pathways (e.g. urea cycle, purine biosynthesis etc.). In many of the situations glutamine donates amine group (e.g. xanthosine ...
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28 views

Function of sodium amalgam and CO2 in formation of aldohexose

There is this following conversion in my book: $$\gamma-\text{Lactone}\ce{->[Na/Hg +CO2]}\text{Aldohexose}$$ I'm not sure how this reaction takes place. I searched for mechanisms and couldn't ...
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1answer
217 views

Why are Tyrosine and Tryptophan considered hydrophobic?

Since Tyrosine and Tryptophan are amino acids, their polarity is determined on their side chains or R groups. If their R groups are polar, the amino acid is polar. Both Tyrosine and Tryptophan are ...
2
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1answer
92 views

Why is the overall change in entropy of Photosynthesis positive? [closed]

Net Reaction: $$\ce{6CO2(g) +6H2O(l) -> 6O2(g) + C6H12O6(aq)}$$ The net reaction shows that 12 moles become 7 moles; 6 of gas,and 1 complex molecule. This implies a decrease in entropy over the net ...
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1answer
55 views

Why is PLGA so expensive in comparison to PLA?

A Google search has lead me to believe that PLGA goes for anywhere between 8 USD and 100 USD per gram. Meanwhile, for PLA (3d printer grade), prices float around 50-100 USD per kilogram. I understand ...
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37 views

Synthesis question: Using reductive amination to form pyrrolidine

What molecule results from treating 4-oxopentanal with $\ce{NH4Cl}$ and $\ce{NaCNBH3}$? Why? Is this a good, high yield reaction? I believe that pyrrolidine is formed because amination will convert ...
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34 views

What specific toxins are formed during deep frying? And how (chemically) do they attack the body cells? [closed]

From what I understand, deep frying causes the oxidation of lipids into advanced lipid oxidation products. When these are consumed and metabolized by the body, they release ROS or free radicals which ...
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1answer
59 views

What is the mechanism of AChE inhibition by Onchidal?

A naturally-occuring neurotoxin, called Onchidal, produced by a species of sea slug acts as an irreversible inhibitor of acetylcholinesterase. The structure of Onchidal is presented below: How and ...
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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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1answer
452 views

How can I properly calculate the isoelectric point (pI) of amino acids?

The following amino acid is called lysine. I was asked to calculate its isoelectric point, with the given $\mathrm pK_\mathrm a$ values. I've searched a lot, and the most helpful post that I found ...
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1answer
154 views

Why is the 1,6 linkage in Amylopentin an alpha link and not a Beta link? [closed]

The alpha link as I have understood it means that the $\ce{OH}$ molecules which make up the glycosidic bond lie on the same side of(above/ below) the plane and for beta, one lies above the plane and ...
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4answers
1k views

How were urolithins discovered and named?

Urolithin is a product of the degradation of ellagic acid by gut flora and has significant biological activity. (Wikipedia) I am curious as to how it was discovered but cannot find the story. Although ...
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1answer
77 views

What is the main contributor of the color of honey? [closed]

I was told that the color of honey contains so much chemistry and that was interesting to me and after doing a couple of research I found that the color of honey depends on the presence of plant ...
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1answer
91 views

Why is methyl parathion less toxic than ethyl parathion?

According to the PubChem pages on ethyl parathion and methyl parathion (pages 11 and 12 of the toxicity section, respectively), methyl parathion is significantly less toxic than ethyl parathion. The ...
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0answers
25 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 ...
3
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1answer
52 views

Can aged acetylcholinesterase be reactivated?

it is a well-known fact that certain phosphorus compounds can inhibit the enzyme acetylcholinesterase, and that the treatment of poisoning with such compounds is administration of atropine and some ...
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1answer
44 views

How does sodium rosinate enhances lathering property? [closed]

Why don't we use sodium carbonate or sodium stearate? What does sodium rosinate contain that the other two don't?
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1answer
40 views

Multiday lab courses in classic chemistry [closed]

This time of the year I usually get some extra income I can use on interesting courses. Usually rescue or sport courses. However, I also have a master degree in chemistry, and would like to spend some ...
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0answers
99 views

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-...
5
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1answer
104 views

Who was C.H. Kao?

I am editing a Wikipedia article about the Chen-Kao reaction that is used to identify ephedrine, but I am unable to find biographical info on C. H. Kao: K.K. Chen and C.H. Kao - Ephedrine and ...
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1answer
56 views

Finding the sensitivity of zero-order ultra sensitivity and its parameter dependence

I am provided a one-dimensional reaction system showing zero-order ultra sensitivity. $$\ce{X_1 ->[f_1] X_2}, \quad \quad \quad \ce{X_2 ->[f_2] X_1}$$ The reaction rate function is the reduced ...
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0answers
31 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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0answers
24 views

Dispersity of synthetic DNA [closed]

Recently I was reading an article about DNA nanostructures and I was wondering-- I know that DNA in living systems is monodisperse, but when we make DNA synthetically, is it truly monodisperse or ...

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