BIBC 100 – Structural Biochemistry TA: Lydiesther Martinez

Dr. Mauricio Montal Lymartin@ucsd.edu

Spring ’11 Section: Mon 7pm
WEEK 1
AMINO ACIDS
o Amino acids can be categorized into four major groups
o Polar :
 Although____ and ____ have a nitrogen with a lone pair, it
will not easily accept H+ due to resonance with adjacent
carbonyl.
o Hydrophobic :
o (+) Charged :
 Some textbooks may consider Histidine non-charged because N in rings
has___________. However, it is much more sensitive to ___________than Asn or Gln.
o (–) Charged :
o The amino terminal can act as a___________, accepting a proton, and the
carboxy terminus can act as an___________, giving up a proton. This is
important in peptide bond formation

PEPTIDE BOND
o Peptide bond is a ___________bond formed between two AAs
o Obtained by way of a ___________reaction
o Why is the bond rigid?
o

ROTATION and RAMACHANDRAN PLOT

o Alpha carbon bonded with the carboxy carbon  ___________
o Alpha carbon bonded with the N’ terminus  ___________
o Rotation limiting factor is due to steric hindrance from R groups
o ___________AA will have less available rotations
o The R.Plot – was named after a scientist who came up with a graph that
plots available rotations (degress) for one AA.
o Which alpha plot is the most common?

PROTEIN STRUCTURE
Central Dogma: ___________ ___________ ___________
o Primary: AA sequence via ___________bond (rigid & planar) with free rotation about psi/phi bonds
o Secondary: fold so all hydrophilic groups can H bond to adjacent groups, motifs.
o Alpha helix: wrap around imaginary axis with R groups sticking out (Right handed)
 Glycine too flexible so not stable in alpha helices,
 Proline introduces ___________also making them unfavorable.
o Beta sheet: zig-zag structure with H bonds between project segments not necessarily adjacent in
primary structure (___________molecular H bonds), R groups point ___________ and
___________out of sheet plane
o Tertiary: 3D arrangement in space, can be shown with ribbon, mesh, surface contour, etc
o Disulfide Bonds – cysteine S—S (+ reducing agent = break into –SH HS--)
o Quaternary: 3D structure of multi-subunit proteins

WATER
BIBC 100 – Structural Biochemistry TA: Lydiesther Martinez
Dr. Mauricio Montal Lymartin@ucsd.edu
Spring ’11 Section: Mon 7pm
o Why is water so important? ___________. Hydrophilic molecules can dissolve easily in water where
H2O-- H2O interactions replaced by H2O--solute interactions
o Hydrophobic effect: association of ___________groups with each other, driven by H2O molecules
seeking most ___________favorable state
o An increase in entropy for water is energetically favorable because it will drive ___________. Protein
will fold so that hydrophobic molecules are on the inside.

Sample Problems
1. Glycine is a highly conserved amino acid in the evolution of proteins; why?

2. Why does G have a different Ramachandran plot than all other amino acids?

3. What is the structure and purpose of a disulfide bridge?

4. Name the three AA’s with OH groups?

5. For one AA, the N in the backbone cannot hydrogen bond with the double bonded oxygen in the carboxylic
acid group of another AA. What AA is this and why can’t it hydrogen bond?

6. What process takes place in bond deformation?

7. Which 3 AA aromatic?

8. What is the basic unit of AA?

9. Draw Tyrosine attached to Glycine and mark

o Phi/Psi angles
o Peptide bond
o C-terminus and N terminus
o Hydrogen bond donor
o Hydrogen bond acceptor