26

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 $\ce{CO}$, whose molecular orbitals can be found in this answer by Martin (replace oxygen with nitrogen to arrive at $\ce{CN-}$) — making it a good Lewis base ...


23

It seems that NickT was looking for an experimental solution. My post deals, however, with a computational solution. How would I quantify how significant the interaction is? Determining the interaction energy between two defined monomers such as your aromatic triazole and amide is a rather straightforward process. This process is referred to as the ...


20

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 and a smaller continuous matrix of protien. When you put the egg in vinegar, you etch away this calcium carbonate matrix leaving the formerly less noticeable ...


18

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 shell, damages the protein matrix that holds calcium carbonate crystals in place in the shell, and can disrupt or destroy the two shell membranes. All of ...


10

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 crystal. When we say that a protein is irregular, we mean it on a different level. Indeed, one molecule of our protein is irregular if we are talking about the ...


9

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 is why the solution become clear. There is nothing coke-specific about it. Any acid would denature milk just like that. And nearly any huge organic molecule ...


9

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 the induced dipole portions: how the electrons move with respect to each other and an external electrical field is driven by quantum mechanics.) Also, while part ...


9

Szilágyi and Závodszky published an article in the journal Structure which analyses a number of different structural parameters of proteins of moderately thermophilic ($45~\mathrm{^\circ C} < \vartheta_\mathrm{opt} < 80~\mathrm{^\circ C}$) and hyperthermophilic ($\vartheta_\mathrm{opt} \approx 100~\mathrm{^\circ C}$) organisms compared to homologous ...


9

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, there will always be people who disagree, and there is still no general consensus amongst the scientific community. There is an excellent - and recent - ...


9

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 sheet is one where the direction from N- to C-termini on adjacent strands run in a parallel direction (rather than antiparallel). In-register means that each ...


8

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 bond (hence doesn't spend much time by the H nucleus when bonded) it is notoriously hard to "see" with X-rays. In order to have X-rays diffract accurately off ...


8

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 boil the possible structures down to a set of similar structures, the Bravais lattices. Only 14 of these exist with different constraints: i.e. the C-centred ...


7

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 functions. Most molecular chaperones are ATPases (enzymes that catalyze ATP hydrolysis), which bind to unfolded polypeptides and apply the free energy of ...


6

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 universally valid at all size and time scales. So, in general, it does not really matter how big a system is or how long a process takes: every system is a quantum ...


6

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 ensembles with crystallographic structure has shown that the core structure of protein molecules remains unchanged compared with the solution state during ...


6

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 are the albumins, which rely on their tertiary structure for solubility. Hence anything that disrupts the tertiary structure -- denatures it -- can expose ...


6

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 - ordered, repeating patterns of protein molecules, filling a 3D space. That is, you can take a basic building block and rotate and translate this building block ...


6

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 hypothesize on it's selection. BTW in biology a good answer to why is always because. I would guess though that given the function of ligases, it has been ...


6

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 examples of arginine side chains in hydrogen bonds. It showcases bidendate hydrogen bonds (i.e. two hydrogen bonds from the arginine side chain) with carboxylates ...


5

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 Prevention (CDC) and the University of Wisconsin (UW), writing in the Journal of Infectious Diseases (JID), said it turns out that the novel toxin can be blocked by ...


5

The paper "Trichloroacetic acid-induced protein precipitation involves the reversible association of a stable partially structured intermediate" (Rajalingam et al. 2009 Protein Science 18(5), 980–993.) may be relevant. In the introduction, they mention the conventional explanation is that "TCA forces protein to precipitate by sequestering the protein-bound ...


5

No, acidic conditions (i.e. low pH) shouldn't be enough by itself to break a disulfide bond. The main reaction that breaks a S–S bond is cleavage by reduction. This is in a way similar to peroxides, which are stable even at very low pH (see e.g. mixtures of sulfuric acid and hydrogen peroxide).


5

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. Often the N- and C-terminal ends are removed, this is something you'll find in many .pdb structures, but sometimes also loops are removed, resulting in two ...


5

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 different and are not converted one to the other. In fact, chitin, like cellulose, is not fragmented by animals, so it is not absorbed. Moreover, chitin is a ...


5

According to the Oxford dictionary, a machine is: An apparatus using mechanical power and having several parts, each with a definite function and together performing a particular task. Based on that definition, I think some proteins and enzymes could definitely be considered machines. A good example for that, in my opinion, would be ATP Synthase and all ...


5

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 nomenclature will vanish if you do not associate electrostatic signs with these two terms. One should identify the electrode labels with the redox processes rather ...


4

I was curious to see what kind of research had been done on this topic, and didn't expect to find much, but I was quite wrong. So, I'll summarize some articles that I found and give the references at the bottom. Why would we ever consider quantum mechanics in protein folding? First, an introduction to why someone would even try to come up with a quantum ...


4

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 end up with uncoupled ends with free amino groups and coupled ends with a protected amino group. Then you cap, e.g. with phenoxyacetic acid anhydride. This will ...


4

The buffer capacity of a weak acid-conjugate base buffer is defined as the number of moles of strong acid needed to change the $\ce{pH}$ by 1 unit. $$\beta = \frac{\mathrm{d}[A]}{\mathrm{dpH}} $$ and the acid is present as $$[A]= \frac{K_\mathrm{w}}{[\ce{H+}]}-[\ce{H+}] +\frac{C_\mathrm{B}K_\mathrm{a}}{[\ce{H+}]+K_\mathrm{a}}$$ where $K_\mathrm{w}$ is the ...


4

You are correct that the hydrophobic interactions are stabilized at higher temperatures. However, I believe the addition of heat mainly disrupts protein structure by breaking hydrogen bonds through increased thermal motion. Once the secondary structure starts to go, any tertiary interactions will get scrambled, likely resulting in the separation of ...


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