16 votes
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Why/how is blood red? (colours of hemoglobin)

The $\ce{Fe}$-porphyrin complex is a vastly conjugated $\pi$-system, in which the oxidation state of the $\ce{Fe}$ plays a central role. The wavelength of light absorbed by hemoglobin exactly ...
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14 votes

Confusion about direction of dipole arrow in alpha-helices and other molecules

I (accidentally) stumbled upon the following statement in Atkins' "Elements of Physical Chemistry" (p378): We represent dipole moments by an arrow with a length proportional to $\pmb{\mu}$ and ...
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10 votes
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What could these letters "S" in red circles mean in a biochemical diagram?

It almost certainly refers to the amino acid (residue) serine. The numbers (300, 333, 351) refer to the residue numbers. The COOH at the end signifies the C-terminus of the protein (subunit). The ...
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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

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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8 votes

Confusion about direction of dipole arrow in alpha-helices and other molecules

Let's take a simple case of a positive charge $q_+$ and a negative charge $q_-$ with $q_+ + q_- = 0$ placed along the $x$-axis at $x_+$ and $x_-$, respectively. The dipole at the $x=0$ is $$\mu=q_+x_+ ...
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7 votes
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How to determine the dimensions of a bixin molecule?

There is a paper on bolaamphiphiles (1) where it is stated that measured surface area corresponding to the area of a bixin molecule lying on the water surface with most methyl groups pointing outside ...
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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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  • 361
7 votes
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Kolmogorov backward equations in active biological systems

UPDATED: I wrote a first answer assuming that $t>0$ which got close to what's in the paper, but not quite the same. Thanks go to Karsten Theis for pointing out that $t<0$ in these "backward ...
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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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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)....
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4 votes

Does quantum mechanics play a role in protein folding?

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 ...
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  • 12.6k
4 votes

What is the chemical formula for snake venom?

There are several kinds of snake venom, and as far as I know they are all complex enzymes: it means that they are complex macromolecules, made by amminoacids (these, "small molecules") bound with ...
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4 votes
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Why do chiral biological molecules only exist as one enantiomer? Does it have any advantage?

Are all the biochemicals that our body uses enantiomerically pure or are racemic mixtures too? Many molecules exist in both forms in nature. One fun example are the enantiomeric terpenoids R-(–)-...
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4 votes
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Is a beta pleated parallel sheet always formed from more than one peptide?

While it is true that some antiparallel beta sheets have neighboring strands that are adjacent in primary sequence, other cases do exist. As for parallel beta sheets, the polypeptide chain between ...
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4 votes

Are crystallographic omit maps only used with molecular replacement?

Experimental phasing and molecular replacement provide initial phases used to start model building. Later on (refinement, validation) phases are calculated from the model. If the phases are what ...
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4 votes
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Are crystallographic omit maps only used with molecular replacement?

[OP] ...if we don't have the phases (say for a part of a model), it just wouldn't get built even if we have the amplitudes for that part, right? Or is it that in this case (of omitting a part), there ...
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4 votes
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Which textbook is this image on protein tertiary structure from?

The illustration is likely taken from a later edition of Baum's Introduction to organic and biological chemistry. The first edition [1, p. 292] presents nearly identical illustration under a different ...
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4 votes
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Does migraine medicine Topiramate work by supplanting Pyridoxal phosphate in enzymes?

Background Topiramate (TPM) is an anticonvulsive and antimigraine drug that helps prevent or reduce the frequency of epileptic seizures and that is used as a prophylaxis of migraine. (Shank and ...
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  • 1,349
3 votes
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Biomolecular energy functions and entropy

I am sure that a more definitive answer could be provided by someone more familiar with the field, but here are a couple of observations. First, I think it is a bit of an exaggeration to say that ...
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3 votes

Why energy of some intermediates of glycolysis increases?

Step 1: Phosphorylation activates glucose for the following reactions in the pathway. However, the formation of such a phosphoester is thermodynamically unfavourable and requires energy input to ...
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3 votes

What are some of the more easily manipulated residues on an enzyme?

I'm assuming the OP concerns chemical means of modifying residues. Multiple protein residues other than Lysine may be labeled with an adduct. Here are some examples: Histidine residues may be labeled ...
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  • 1,349
3 votes

Does quantum mechanics play a role in protein folding?

Yes it is true that protein folding takes a long time compared to bond vibrations (few femtosecond) or rotations of a amino acid (picoseconds to nanoseconds) and for small proteins can take of the ...
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3 votes

Is it possible to identify the source of a protein hydrolysate

DNA is not a protein, as @MARamezani states. See http://www.answers.com/Q/Is_DNA_a_protein. There is a prevalence (or lack) of some amino acids in certain sources. For example, maize ("corn" in ...
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3 votes

What is Cβ (C-beta) deviation?

Just browsing through this "Unanswered Question" now (in late 2014). I hope it's not too late? In protein structure validation, Ramachandran outliers are a strong, but not absolute, indicator that ...
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  • 537
3 votes

How to dock aggregated structures comprised of "elementary" protein units like LEGO pieces?

Try DNA origami instead While protein assemblies are well known, rationally using proteins to assemble larger supramolecular structures is still a difficult problem: Predicting protein folding is ...
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3 votes

How do cells form a solid structure?

So how are the cells are arranged to form a solid structure a solid body? Plant cells have cell walls, are filled with liquid, and have strong cell-cell adhesion. This gives a fairly rigid structure ...
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3 votes

What ratio of bicarb to sugarcane juice with a pH level of 4.5-5.5 to neutralize pH level?

You need to know which acids are present in the sample, or determine the required amount experimentally. Without any knowledge of the pKa values of the acid or acids present, there could be very ...
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3 votes
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Distance requirement for hydrogen bonding to occur

You will probably find all this information in biochemistry textbook. To give you an idea in proteins, typically; alpha helices H..O distance is 2.06 Angstrom, and N..O, 2.99. In beta sheets (parallel)...
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3 votes

Are crystallographic omit maps only used with molecular replacement?

The following doesn't fit into a comments box. From the perspective of small molecule crystallography (say, ShelX), once you solved your model completely or completely enough to engage refining, you ...
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