Hey all, back with another brakedown. If you guys are not familiar with this, basically when I read a chapter and review the lecture for the chapter, I get the main ideas but sometimes I have little questions about some parts. I can go to my teacher's office hours but the things I am confused on aren't that major and its just me being picky with the chapter. Please you do not have to answer everything below, I know it can be long but most of that stuff is just me rambling. Anyways here it goes
Q1) About protein structure in general: https://imgur.com/UQydEeH
It says secondary structure results from H bonding, my question is, is the primary structure just 1 amino acid sequence or it can be multiple amino acids? For secondary structure the H bonding its not talking about how amino acids are connected via peptide bond or is it? I ask cos I thought H bonding is involved in the backbone of the protein just to keep alpha helix structure.
Question about mechanism here for polypeptide bond formation, let me know if I misunderstood this part, basically amine group of one amino acid attacks carbonyl of another and kicks off 1 bond for the electrons to go on oxygen > the oxygen electrons move back to form the double bond again and kick off the OH > OH attacks H of nitrogen and we lose water and form peptide bond.
But in the picture it doesn't show when nitrogen attacks carbonyl, doesn't show what happens after.
Q3) About peptide group bond angle:https://imgur.com/OeVZkhK
I understood peptide bonds limit conformation cos of their bond angle and so the R groups are alternating because of this. But I didn't understand how they limit conformation? Or I just need to know they limit conformation cos of their bond angle
Do I need to worry about the phi and psi here? Not sure what I want to learn here other than if they are specified then we get backbone path that is known.
Q4) psi and phi is used here: https://imgur.com/E29iYrO
Also not sure whats going on here, I know this is about bond angle How can they tell from the diagram that proline is most restricticed and glycine is least restricted? I understand proline strcuture is cyclic so its very steric hindered and glycine is only H r group so that's less hindered, but should I worry about this?
Not sure what the blue/green and the C,alpha,alphaL, arrows means...
Q5) beta sheet and alpha helix: https://imgur.com/CSjEGFv
So looking at pictures I can't tell too much difference between alpha helix and beta sheet. I know they both have H bonding but I'm not sure whats the key difference between them? The only thing I can spot is that the alpha helix is kinda like DNA while the beta sheet is parallel or anti to each other but thas it
Q6) About quaternary structure: https://imgur.com/o7hD25Y
This one is kinda simple but my question is just about entropy. I understood that entropy gets lower cos of arrangement but not sure how it gets higher when hydrophobic groups are "burying"
I understand hydrophillic heads are outside and they are in high entropy cos of H constantly braking and formin. But not sure how hydrophobic heads being buried causes high entropy