27 votes
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Why is the cyanide ion toxic?

Cyanide is a pretty good ligand for coordination compounds. The electron pair on carbon (which, incidentally, also carries the Lewis structure’s formal charge) is located in the HOMO — much like as in ...
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19 votes

Why do the physical properties of an egg shell change when the egg shell is exposed to vinegar for a week?

It doesn't make calcium carbonate rubbery, it removes the calcium carbonate. Egg shells are not purely calcium carbonate they are more like a composite with a continuous matrix of calcium carbonate ...
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18 votes

Why do unboiled eggs last longer than boiled eggs?

An eggshell is a complex structure. From Wikipedia: Boiling the egg removes the waxy cuticle from the outside of the egg, dissolves a small but not insignificant amount of calcium carbonate from the ...
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10 votes
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What is the difference between crystal structures of proteins, organic and inorganic materials?

Imagine an infantry unit of soldiers marching in file. Each of them may be quite irregular, but together they form a repeating pattern. And that's exactly what happens with protein molecules in a ...
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10 votes
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What happens when you mix milk and coke?

The phosphoric acid causes denaturation of milk proteins which precipitate out of the solution (milk is an emulsion, to be exact). The flock that is formed also adsorbs dye molecules (caramel) which ...
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10 votes
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What is the nature of the Fe–O2 binding in oxymyoglobin and oxyhemoglobin?

TL;DR: It is not really "one or the other" - it is more of "somewhere in between", like a resonance hybrid. If I had to choose, I'd personally lean towards Weiss's $\ce{Fe(III)-O2-}$ model. However, ...
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10 votes

How to use Google’s Alpha-fold to predict the structure of a two-protein complex?

Are you asking how to take code developed to find the MFE (minimum free energy) structure of a single protein, and modify it to instead determine the structure of a two-protein complex? Or are you ...
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  • 11.6k
9 votes

Does quantum mechanics play a role in protein folding?

There's several aspects to your question. Does quantum mechanics play a role in protein folding? Yes. The origin of the van der Waals interaction is ultimately a quantum mechanical one. (At least ...
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  • 4,746
9 votes

Why are there no hydrogen atoms in the crystal structure of a biomolecule?

Typically crystal structures are determined by X-ray diffraction off of electrons within a bond and around the nuclei of each atom. Since H only has 1 electron, and its often involved in a polar type ...
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  • 601
9 votes
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What makes heat resistant proteins heat resistant?

Szilágyi and Závodszky published an article in the journal Structure which analyses a number of different structural parameters of proteins of moderately thermophilic ($45~\mathrm{^\circ C} < \...
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9 votes
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What does "parallel in-register" mean for a protein structure in a fibril?

There is a clear explanation and figure showing this in the following reference: Anton Gorkovskiy, Kent R. Thurber, Robert Tycko, Reed B. Wickner, PNAS 2014, 111 (43) E4615-E4622. A parallel beta ...
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9 votes
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How does X-Ray Crystallography determine the components (as opposed to the structure) of a molecule?

That is because the solution to the structure isn't done just via the plate. The signal you see on the plate is what is called "structure factors" of the experiment. They are associated with ...
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8 votes
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Protein Data Bank: Asymmetric Unit/Biological Assembly

Most of the structures in the Protein Databank are determined with X-ray crystallography. Like inorganic compounds and small organic molecules, under the right conditions proteins can form crystals - ...
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8 votes

What is the difference between crystal structures of proteins, organic and inorganic materials?

Ivan basically gave a nice and clear example of what is going in. I’m going to offer a more in-depth explanation. If you were to consider possible crystal structures of just one type of atom, you can ...
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8 votes

What happens when you mix milk and coke?

This is a bit more complicated than it seems. Milk contains about 3% protein. Most proteins are not soluble -- otherwise our bodies would dissolve when it rained! The most common type that are soluble ...
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8 votes
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Can =NH2+ in Arginine's side chain form hydrogen bonding at physiological pH?

Yes, the arginine side chain is an excellent hydrogen bond donor. Charged N-H groups are even better hydrogen bond donors than the corresponding neutral N-H groups. Here is an article that gives ...
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8 votes
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Peptide bond formation involving side chains of charged amino acids

Equilibrium in aqueous solution In aqueous solution (such as our digestive tract), the equilibrium of the reaction as written is on the side of the reactants. Digestive enzymes catalyze the ...
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8 votes

What is the difference between structure assignment and structure prediction?

Structure assignment is relating e.g., a measured absorbance frequency (like a triplet in $\pu{^1H NMR}$), or a structural feature (like $\Phi$ and $\Psi$ in a Ramachandran plot) to a structure ...
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7 votes
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Is the structure of a crystalized protein the native one?

I'll use quotes from B. Rupp, Biomolecular Crystallography (p. 7-8) to answer. Generally the structure is similar... Comparison of many nuclear magnetic resonance (NMR) solution structure ...
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7 votes
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Why aren't chaperones considered catalysts?

I don’t think you are wrong. Actually molecular chaperones have been named enzymes in some texts. The molecular chaperones comprise several unrelated classes of proteins that have rather different ...
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7 votes

How would I make a basic protein folding algorithm?

It is far, far more difficult that a naive approach suggests The reason why simulating protein folding is extremely hard is the combinatorial complexity of the options you have to explore to get the &...
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7 votes
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SARS-CoV - relative size of the spike protein

Although this is a homework question, I also think OP deserves a help as orthocresol suggested. I'm not going to go into details but leave it at orthocresol's suggestion of this being a Western Blot ...
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7 votes

Is the 3D spacing arrangement of atoms in chemical bond always unique?

From a given number of atoms, you can usually construct multiple molecules (isomers), so we shall just concentrate on the case where the bond connectivity is the same. The terms you are looking for ...
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6 votes

Does quantum mechanics play a role in protein folding?

Protein folding takes a very long time (relatively speaking) when thinking of quantum mechanical effect. First note that, in principle, for the time being, quantum mechanics is considered to be ...
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6 votes
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Why does capping after each coupling in Solid phase peptide synthesis improve the results?

if you cap then you “block” all of the peptides that you are synthesizing.(?) No, you don’t, the order of steps is important. First you try to couple your new amino acid to the solid phase. You will ...
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6 votes
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Why does no antitoxin for botulinum type H exist yet?

The premise of this question is based upon outdated information. According to Study: Novel botulinum toxin less dangerous than thought Researchers from the Centers for Disease Control and ...
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6 votes
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Why does this protein seem to have multiple chains?

Some parts a the protein are a bit more flexible, also in the protein crystal. These parts don't give clear electron density after x-ray diffraction, and are removed from the resulting model structure....
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  • 353
6 votes
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Why is the E2 protein important for protein degradation?

Pretty hard question, "why", as we've not been watching for the millions of years it took to build that system... I think the better way to look at it is to name the advantages this system has and ...
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  • 86
6 votes
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Is chitin actually protein?

Chitin and protein are completely unrelated. The only common thing is that they are polymers. Chitin is a polymer of amino sugars while protein is a polymer of amino acids. Both monomers are very ...
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6 votes
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What dictates cathode vs anode nomenclature use?

Who was responsible for this naming system and how can we change it? Michael Faraday was responsible for the terms anode and cathode more than hundred years ago. All the confusion regarding the ...
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