[yourdeath01]

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.

Q2) https://imgur.com/Vxagrh7
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 and https://imgur.com/fKr3XAp
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 and https://imgur.com/W0Xzo9Y
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

[Babcock_Hall]

1) Primary structure is just the sequence of amino acid residues.  There might be slight differences in definitions from one book to another, but one way to define secondary structure is that refers to a stretch of polypeptide that has a regular pattern of hydrogen bonding and all of the residues have similar values of phi and psi.

2) That is not how peptide bonds are formed in vivo.  It nicely illustrates that this is a dehydration reaction, but I would not take it to mean more than that.

4) That is a Ramachandran diagram, and different regions are allowed, forbidden, or allowed with a relaxed assumptions.  This video may help explain what phi and psi are:  https://www.youtube.com/watch?v=Kewhg5spUjs

5) Are the phi and psi angles in a beta-sheet similar to or different from the phi and psi angles in an alpha helix.  How would you describe the hydrogen bonding in each?

6) What do you know about the hydrophobic effect?

Your textbook should help with some of these questions.

[Babcock_Hall]

Not sure what the blue/green and the C,alpha,alphaL, arrows means...

What is different about the two sets of arrows?