Lesson 3

Question 1

steps for estimating pI

Answer 1

(1) draw peptide at most protonated form (low pH)
(2) calculate overall charge
(3) calculate change in charge as pH rises - noting pkas of each ionizable group
(4) use 2 pkas surrounding peptide at 0 charge

Question 2

what happens when amino acids react together

Answer 2

• a molecule of water is released
• peptide bond formed between alpha carboxyl group of one amino acid and an alpha amino group of another amino acid

Question 3

properties of peptide bond

Answer 3

• longer than C-N double bond
• shorter than C-N single bond
• 40% partial double bond character

Question 4

where does the partial double bond character come from in a peptide bond

Answer 4

RESONANCE –> bond is amide like - TRANS and PLANAR

Question 5

phi

Answer 5

alpha carbon and nitrogen

Question 6

psi

Answer 6

alpha carbon and carbon

Question 7

true/false: trans conformation is thermodynamically favorable due to the fewer steric clashes occurring

Answer 7

true

Question 8

alpha helix

Answer 8

repeating pattern of weak forces
- very stable combination of phi and psi
- 3.6 residues per turn

Question 9

what stabilizes the alpha helix

Answer 9

H-bonding in a specific pattern (with peptide backbone)

Question 10

what is the H-bonding pattern in an alpha helix

Answer 10

carbonyl oxygen w/ amide hydrogen at positions n and n+4

Question 11

R group relationship to central axis

Answer 11

come out form and perpendicular to

Question 12

is there a central cavity

Answer 12

no - interior is filled completely by atomic radii
- no water allowed in the alpha helix - would disrupt the hydrogen bonding