I understand that when protein is in primary/secondary structure there is more organization of water molecules, hence it has low entropy and when you fold it, the entropy of protein increases but the entropy of water (which becomes more positive) overcomes the entropy of folded protein. I know that proteins like hydrophobic parts inside and hydrophilic outside and that's what's confusing me. If hydrophilic residues are outside, wouldn't that interact with water and make water more organized?
Kaplan physics book had a practice question that asked whether or not the entropy change is positive/negative/zero when you mix oil and water and allow them to separate into layers. The answer was 0
Wouldnβt there be a slight decrease in entropy from water molecules trying to form an ordered solvation layer at the interface with the oil? Or is this negligible
Buried salt bridges can be effectively used by a pair of endoβfunctionalized macrocyclic hosts for the selective recognition of functional carboxylic acids in water, where solvent screening on polar noncovalent interactions is high.
Abstract
Buried salt bridges widely exist in protein structures but are rarely used in synthetic systems for molecular recognition in water. By mimicking the binding pocket of bioreceptors, we designed and synthesized a pair of endoβfunctionalized macrocyclic hosts with secondary ammonium groups in a hydrophobic cavity. We found that these macrocycles are able to selectively recognize carboxylic acids in water through salt bridges and the hydrophobic effect. Moreover, it was demonstrated that these macrocyclic receptors can be used in circularβdichroismβbased optical chirality sensing of chiral carboxylic acids and fluorescent sensing of phenylpyruvic acidβa biomarker for phenylketonuria. This research showcases that buried salt bridges can be effectively used by endoβfunctionalized macrocyclic hosts for molecular recognition in water, where solvent screening on polar noncovalent interactions is high.
https://ift.tt/2IZN2mh
Journal of the American Chemical SocietyDOI: 10.1021/jacs.0c03425
Avanashiappan Nandakumar, Yoshihiro Ito, and Motoki Ueda
https://ift.tt/37uOwNO
Was mentioned here under the header dissolution strategy: weakening hydrophobic interactions
Urea is highly polar but why does it disrupt hydrophobic interactions? Wouldn't urea hydrogen bond with other water molecules, leaving cellulose -OH groups alone?
Thanks for any response!
Would it change how these interact with water enough that it would cause a noticeable difference compared to a standard boat? Would a hydrophobic hull move over water faster? Would a propeller work better worse? What about a paddle? Would it change the friction between the surface and the water?
is it basically like the protein conformation becomes stable because there is a thermodynamically favorable shielding of hydrophobic residues inside the protein but also there are repelling forces between the protein side chains inside the protein. this attraction and repulsion forces known as the hydrophobic effect are balanced and stabilizes a protein conformation? I really don't get this concept and can't find much info on it.
Do the hydropobic parts of a protein go in the center because the non-polar groups have favorable interactions with each other, or do they go in the center because this process would require less water to surround the protein in the solvation (aka hydration) layer, leading to a increase in entropy (favorable)?
Or is it both of those things?
Thanks!
And, besides expense, is there any reason not to?
Hello out there.
I have to clarify that I'am a biologists and not a chemist or physicist and I'm trying to understand a new paper that published in PNAS (http://dx.doi.org/10.1073/pnas.1612480114) about hydrophobic effect.
Probably some of you already read it and saw that researchers have used IR spectroscopy to determine the stretching of the Hydrogen bonds near the hydrophobic solute.
Although i got the main idea behind the experiment i didn't understand some basic things. For example why did they use heavy water (HDO) instead of pure water.
Also if I understood, they calculated the absorbance peaks of heavy water when it is on ice and clathrates form, in order to compare it later with the absorbance peak of the liquid heavy water molecules near the hydrophobic solute. After the comparison they saw a red-shift between the absorbance peak of heavy water molecules near the solute and the heavy water molecules that away from it. Am I right ?
I would appreciate if anyone who read it and has the appropriate knowledge (of a chemist or physicist ) tried to explain the process in more accurately way in order to understand it more deeply.
Thanks.
Hello r/askscience, Studying for my biochem exam and this has been bugging me all semester. Why does the hydrophobic effect exist? More specifically, what are the physical and chemical reasons that hydrophobic substances are soluble in hydrophobic solutes and not in hydrophilic ones, and vice versa? I've taken orgo and gen chem, but have never really asked why this occurs.
It seems like the other non-covalent forces we learn about in gen chem (pi-stacking, dipolar, h-bonding, electrostatic, van der Waals) are mostly attractive in nature compared to hydrophobic forces and moreover, it seems like each of these can be attributed to functional groups or distinct arrangements of atoms. So my question is do we consider hydrophobic forces and their effects to be repulsive hydrogen-bonding forces? Often we consider lipids to be water fearing, but does that mean their non-covalent van der Waals forces dictate their opposition to mingling with water? I'm going to stop now, but I hope someone might be able to shed some light on the matter. Thanks!
Decreased friction? INCREASED FRICTION?
I have no idea.
The lecturers at my uni aren't too great at explaining this
Journal of the American Chemical SocietyDOI: 10.1021/jacs.0c01290
https://ift.tt/38NYSqu
