3D structure of proteins Flashcards
what are the four levels of protein structure?
primary, secondary, tertiary, quaternary
what is the secondary structure?
stable arrangement of AA residues (helises and strands)
what is the tertiary structure?
3D fold of single polypeptide chain
what is the quaternary structure?
3D spatial arrangement of 2 or more polypeptide subunits
what can the peptide chain rotate around?
phi and psi bonds
what is the phi torsion angle? (a is alpha carbon)
N-Ca
what is the psi torsion angle? (a is alpha carbon)
Ca-C
what is the omega torsion angle?
C-N (peptide bond)
what is unique about each AA residue in a peptide?
set of torsion angles
what are the four principle elements of secondary structure found in proteins?
helices, sheets, turns, random coils
what is the most simple and elegant arrangement of a peptide chain?
right handed (N to C) spiral conformation known as the ‘alpha helix’
what is the helix stabilized by?
hydrogen bonds between main chain atoms
what is true about helical radius and the number of residues per turn?
helical radius increases with the number of residues per turn
what forms zig-zags in a more extended conformation?
beta sheet
what do beta turns involve?
4 amino acid residues in a 180 degree turn connecting segments of antiparallel beta sheets
what amino acid is involved in type 1 beta turns?
proline
what amino acid is involved in type 2 beta turns?
glycine
what do gamma turns involve?
3 amino acid residues in a 180 degree turn and proline is always the second residue
what is true about the H-bonds in beta sheets?
in-line between antiparallel strands but angled in parallel strands SO overall bonding between parallel strands is weaker
why can there not be knots in our proteins?
they would not be able to be broken down
what is the difference between a beta sheet and an alpha helix in regards to hydrogen bonds?
beta sheet: two or more polypeptide chains run alongside each other and linked by H-bonds between backbone of one chain segment and the N-H of another chain segment
alpa helix: H-bonds involve the same element of polypeptide chain
how do beta strands and alpha helices differ in regards to peptide bond direction?
beta strand: points in opposite directions
alpha helix: all point in the same direction
what is the distance between adjacent residues along the strand in beta strands?
3.5 Angstroms
what is the distance between adjacent residues along the strand in alpha helix?
1.5 Angstroms
what is true about the polypeptides in B-conformation vs A-helical?
B-conformation is far more extended
what is the frequency of occurence of an amino acid residue in secondary structure for alpha helix?
Kristin Has Marvelous LACE Q-tips
what is the frequency of occurence of an amino acid residue in secondary structure for beta sheet?
IVY For The Win
what is the frequency of occurence of an amino acid residue in secondary structure for reverse turns?
SPDNG (SPeeDiNG without vowels)
what do you need to know about the Ramachandran Plot? (go look at one rn)
the areas/regions
