lecture 15 - protein structure: peptide bonds

Question 1

what are the general themes for protein structure? (5)

Answer 1

(1) protein fold is dictated by primary structure (the amino acid sequences)
(2) protein structures are dynamic (exist generally in only few conformations)
(3) protein fold is stabilized by large number of weak non-covalent interations (electrostatic, Hbond, hyrdophobic)
(4) function depends on fold
(5) most proteins undergo confirmational changes during their function - can be small, can be significant

Question 2

where does a peptide bond occur?

Answer 2

• between the C-term and the N-term of two amino acids (between OH and NH2 grp
• bond fromation releases a water molecule

Question 3

what is the configuration of a peptide bond?

Answer 3

planar

Question 4

what bonding capacity do peptide bonds have?

Answer 4

H bond

Question 5

is there free rotation around a peptide bond? why or why not?

Answer 5

• no free rotation about C-N peptide bond
• N has partial double bond character
• provides restriction on conformational freedom

Question 6

is there conformational freedom around the rest of the peptide?

Answer 6

• lots of conformational freedom (implied by phi and psi) but
• R groups can restrict conformational space (phi and psi cannot adopt all possible angles due to steric hindrance)

Question 7

what do Ramachandran Diagrams illustrate?

Answer 7

• accessible conformational space for polypeptide backbone

- has 4 boxes, if one filled, cannot access that conformational space

Question 8

what does phi represent?

Answer 8

roation about alpha C-N

circle with line thingy

Question 9

what does psi represent?

Answer 9

rotation about alpha C-C

poseiden thingy

Question 10

despite conformational restriction, what is still possible?

Answer 10

tremendous diversity of 3D structures

Question 11

what are 2 exceptions to the constrictions around peptide bonds?

Answer 11

(1) Gly - lack of R group provides much more phi/psi space

(2) Pro - ring of R group (connection to N of backbone) limits phi greatly, but not psi

Question 12

1, 3 quadrants of the Ramachandran plot implies what will form?

Answer 12

alpha helix, left hand helix

Question 13

2nd quadrant of the Ramachandran plot implies will what will form?

Answer 13

beta sheet

Question 14

quadrant of a Ramachandran plot 4 implies?

Answer 14

steric hindrace