3D structure of proteins

Question 1

what are the four levels of protein structure?

Answer 1

primary, secondary, tertiary, quaternary

Question 2

what is the secondary structure?

Answer 2

stable arrangement of AA residues (helises and strands)

Question 3

what is the tertiary structure?

Answer 3

3D fold of single polypeptide chain

Question 4

what is the quaternary structure?

Answer 4

3D spatial arrangement of 2 or more polypeptide subunits

Question 5

what can the peptide chain rotate around?

Answer 5

phi and psi bonds

Question 6

what is the phi torsion angle? (a is alpha carbon)

Answer 6

N-Ca

Question 7

what is the psi torsion angle? (a is alpha carbon)

Answer 7

Ca-C

Question 8

what is the omega torsion angle?

Answer 8

C-N (peptide bond)

Question 9

what is unique about each AA residue in a peptide?

Answer 9

set of torsion angles

Question 10

what are the four principle elements of secondary structure found in proteins?

Answer 10

helices, sheets, turns, random coils

Question 11

what is the most simple and elegant arrangement of a peptide chain?

Answer 11

right handed (N to C) spiral conformation known as the ‘alpha helix’

Question 12

what is the helix stabilized by?

Answer 12

hydrogen bonds between main chain atoms

Question 13

what is true about helical radius and the number of residues per turn?

Answer 13

helical radius increases with the number of residues per turn

Question 14

what forms zig-zags in a more extended conformation?

Answer 14

beta sheet

Question 15

what do beta turns involve?

Answer 15

4 amino acid residues in a 180 degree turn connecting segments of antiparallel beta sheets

Question 16

what amino acid is involved in type 1 beta turns?

Answer 16

proline

Question 17

what amino acid is involved in type 2 beta turns?

Answer 17

glycine

Question 18

what do gamma turns involve?

Answer 18

3 amino acid residues in a 180 degree turn and proline is always the second residue

Question 19

what is true about the H-bonds in beta sheets?

Answer 19

in-line between antiparallel strands but angled in parallel strands SO overall bonding between parallel strands is weaker

Question 20

why can there not be knots in our proteins?

Answer 20

they would not be able to be broken down

Question 21

what is the difference between a beta sheet and an alpha helix in regards to hydrogen bonds?

Answer 21

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

Question 22

how do beta strands and alpha helices differ in regards to peptide bond direction?

Answer 22

beta strand: points in opposite directions
alpha helix: all point in the same direction

Question 23

what is the distance between adjacent residues along the strand in beta strands?

Answer 23

3.5 Angstroms

Question 24

what is the distance between adjacent residues along the strand in alpha helix?

Answer 24

1.5 Angstroms

Question 25

what is true about the polypeptides in B-conformation vs A-helical?

Answer 25

B-conformation is far more extended

Question 26

what is the frequency of occurence of an amino acid residue in secondary structure for alpha helix?

Answer 26

Kristin Has Marvelous LACE Q-tips

Question 27

what is the frequency of occurence of an amino acid residue in secondary structure for beta sheet?

Answer 27

IVY For The Win

Question 28

what is the frequency of occurence of an amino acid residue in secondary structure for reverse turns?

Answer 28

SPDNG (SPeeDiNG without vowels)

Question 29

what do you need to know about the Ramachandran Plot? (go look at one rn)

Answer 29

the areas/regions