Chapter 6: 3D Structure of Proteins Flashcards
What was the first protein to be sequenced and who sequenced it?
Insulin and Sanger
is protein structure generally still planar and trans?
yes.
Peptide bond (amide bond) still causes the chain to be planar (because it still can’t rotate) and trans configuration is still thermodynamically/sterically favorable. (so it’s more often found in nature)
what does a Ramachandran plot show you?
The thermodynamic favorability of all possible psi and phi angles for a given alpha carbon in a protein
what does the ‘L’ space on a Ramachandran plot show you?
the configuration where most L amino acids appear
what does a little ‘alpha’ symbolize on a Ramachandran plot?
The configuration from which alpha helices arise
what does a little up and down arrow symbolize on a Ramachandran?
The configuration from which beta sheets arise
where is the ‘L’ space on a Ramachandran plot?
On the left hand side of the plot
where is the ‘D’ space on a Ramachandran plot?
On the right hand side of the plot
which axis shows you the phi angle on a Ramachandran plot?
x axis
which axis shows you the psi angle on a Ramachandran plot?
y axis
why does the Ramchandran plot have so many configuration possibilities for glycine?
because glycine (being achiral) is neither L nor D and has no hindering side chain
in 1951, What did Linus Pauling and Robert Corey both simultaneously propose about proteins’ secondary structure?
- the structure is sterically allowed & favorable (according to Ramachandran plot)
- the structure maximized H bonds between the protein backbone’s amide and carbonyl groups
which amine and carbonyls (in a protein chain) participate in hydrogen bonding when the protein is in its 2o structure?
all of them!
how many residues does it take for a protein chain to turn over on itself IN A HAIRPIN TURN?
exactly 4 amino acids
what does the term ‘pitch’ describe in reference to a protein with alpha helix structure?
the distance the helix rises per turn
= 5.4 Angstroms
Do L amino acids have right handed alpha helix or left handed alpha helix?
right
in an alpha helix, which amino acid is the ‘i’ acid hydrogen bonded to?
i + 4
in an alpha helix, which way to the side chains point (in/towards the core or out/away from the core)
out
in an alpha helix, what are the 2 reasons (r/t size and H bonding) why the side chains point out/away from the core?
- this minimizes steric hinderance
2. maximizes hydrogen bonding between the amine and carbonyls in the back bone
which amino acids are more likely to result in an alpha helix structure: large or small amino acids?
small ones; because they have less steric hinderance
which two amino acids rarely result in alpha helices, even though they are small?
glycine and proline (of course); they typically form hair pin turns instead
why don’t glycine and proline typically form alpha helices?
They have too many thermodynamically favorable bond angle combos to be constricted to the helix shape
why does proline especially not form alpha helices all that often?
The ring won’t conform to the needed angles.
It will cause a kink in the protein if it tries
which structure is drawn as a helical wheel when viewed from a bird’s eye view: alpha helix or beta sheet?
alpha helix