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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 ...
A.K.'s user avatar
  • 12.6k
14 votes

Why does this lysozyme powder not look crystalline?

The typical protein crystal does not withstand mechanical stress equally well than e.g., the ones of table salt, or refined sucrose. Hence the varying shapes of grains. Photos about nice protein ...
Buttonwood's user avatar
11 votes
Accepted

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 ...
vapid's user avatar
  • 2,088
10 votes
Accepted

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} < \...
Jan's user avatar
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10 votes
Accepted

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, ...
orthocresol's user avatar
  • 71.3k
10 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 ...
Karsten's user avatar
  • 40.6k
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 ...
theorist's user avatar
  • 12.2k
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 ...
StevieD's user avatar
  • 631
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 ...
R.M.'s user avatar
  • 4,924
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 ...
PCK's user avatar
  • 1,149
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 ...
urquiza's user avatar
  • 721
9 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 ...
Buttonwood's user avatar
9 votes
Accepted

Why is collagen fibre autofluorescent?

Two proteins, collagen and elastin, are giving autofluorescence and both have a Pyridinoline compound as a cross linker, deoxypyridinoline in collagen and desmosine in elastin: Thus, these two ...
Mathew Mahindaratne's user avatar
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 ...
Securiger's user avatar
  • 586
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 ...
Karsten's user avatar
  • 40.6k
8 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 &...
matt_black's user avatar
  • 36.7k
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 ...
marcin's user avatar
  • 361
7 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 ...
Wildcat's user avatar
  • 19.1k
7 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....
VonBeche's user avatar
  • 373
7 votes
Accepted

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 ...
xavier_fakerat's user avatar
7 votes
Accepted

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 ...
Raoul Kessels's user avatar
7 votes

How would I make a basic protein folding algorithm?

In short: Joining amino acids to build proteins does not just assemble rigid bodies together. Maybe you think it is joining a carboxylic acid and an amine to form an amide and to identify a ...
Buttonwood's user avatar
7 votes
Accepted

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 ...
Mathew Mahindaratne's user avatar
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 ...
FusRoDah's user avatar
  • 772
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 ...
Dan's user avatar
  • 86
6 votes
Accepted

Why is copper(II) sulfate added drop by drop during the Biuret test?

The Biuret Test is a chemical assay that detects the presence of proteins in a sample. The test is not named after any famous scientist, but after an urea dimer called biuret $(\ce{H2NC(O)NHC(O)NH})$. ...
Mathew Mahindaratne's user avatar
6 votes
Accepted

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 ...
AChem's user avatar
  • 40.8k
6 votes
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Adding hydrogens to multiple pdb files using Openbabel GUI software

If you got an installation of openbabel's GUI, you equally have an installation of openbabel for the terminal (e.g., in Linuxes) / command line cmd.exe (in Windows)....
Buttonwood's user avatar
6 votes
Accepted

Generating electron density from protein coordinate (PDB)

For the more recent structures, you can view the density (based on measured diffraction data and the model, so-called 2Fo-Fc density) directly in the protein data bank, e.g. http://www.rcsb.org/3d-...
Karsten's user avatar
  • 40.6k
6 votes

Why don't proteins form branched polymers?

Note that branching is not unheard of, for instance glutathione is an abundant short branched peptide formed by condensation of the carboxylic group on a glutamic acid side chain to the main chain ...
Buck Thorn's user avatar
  • 22k

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