Chem 27 - Exam 1 Review Wednesday Feb. 22, 2006 Science Center Hall D
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Transcript of Chem 27 - Exam 1 Review Wednesday Feb. 22, 2006 Science Center Hall D
Chem 27 - Exam 1 Review
Wednesday Feb. 22, 2006Science Center Hall D
K.C. O’Brien
Carol Fang
Walter Kowtoniuk
Outline of Topics
• 1) Conformational Analysis of amino acids• 2) Protein Folding
• 3) Edman Degradation(-like) chemistry• 4) Cyanogen bromide(-like) chemistry
• 5) Peptide Coupling/Synthesis• 6) Biosynthesis of Proteins
Conformational Analysis
K.C. O’Brien
Amino Acid Structure
-ONH3
+
O
RH
•Amino acids are chiral molecules
•Stereochemistry at -carbon always as shown (R group coming out)
•All natural amino acids have S configuration, except cysteine
•pKa’s: NH3+ is about 9
COO- is about 2.2
•Hydrophobic, polar and charged side chains
Staggered vs. Eclipsed Conformation
HH
H
H
H H
H
HH
H
HH
+3.0 kcal/mol
staggeredeclipsed
• Hyperconjugation C-HC-H• Newman projections help visualize interactions
Gauche interactions
CH3
H H
CH3
HH
+0.9 kcal/mol
anti gauche
H
H CH3
CH3
HH
Cyclohexane Chair Conformations
H
H3C
H
H3C
CH3
H
H
CH3
• Ring flip changes groups from axial to equatorial• Lower energy conformation has large groups equatorial• A values are used to quantify the energy difference
between the axial and equatorial positions
Syn-pentane Interaction
• Syn-pentane > 3.7 kcal /mol
• 1,3-diaxial groups generate a syn pentane interaction H
H
H
H
H
H
H's cause steric strain
A1,3 Strain
H RR"R'
12
3
HHH
H
HHH
H
• H is in the same plane as double bond
• If R=R’=R”=Me, A1,3=3.5 kcal/mol
• Minimize A1,3 in amide bonds
Template Projection of Amino Acids
NH
H
O
NH
H
O
NH R1
H
R2
O
R1 R3
NH H
H
HR1 O
R2
• Amino acid template projection is based on cyclohexane chair structure• Add up gauche and syn-pentane interactions to find the lowest energy conformation• R1>R2>R3 is a good place to start, but consider other conformations• Make sure you don’t invert the stereochemistry of the amino acid or its side chain!!!!
Protein Folding: Hydrogen Bonds
O H N
R
RR
R
:
• 1-4 kcal/mol• Directionality is
important• N-H-----O=C• Stabilize -helices,
-sheets and turns
Protein Folding: -helix
• stabilized by hydrogen bonding• 3.6 amino acids per turn
Protein Folding: -sheet
• NH’s of one strand H-bond to C=O of next strand• R groups alternate on opposite sides of the plane
Protein Folding: -turn
• C=O and N-H are 10 atoms apart
• Changes the direction of the main chain
Protein Folding: Electrostatic Interactions
O
O-R
N
NR
H
NH2H• Between oppositely
charged amino acids• Most important in
the interior of the protein
• Neutralizes charges
Protein Folding:
Hydrophobic Interactions:
• Hydrophobic amino acids pack into the interior of the protein
• Folding increases the disorder of the solvent
• Positive H is overcome by positive S
Disulfide Bonds:
• Dihedral angle 90o
• ns donates into *S-R
• Two Cys oxidized to form a disulfide bond
Edman Degradation
Carol Fang
N
S
NH
Ph
O
H2N
H
R1 N
S
NH
Ph
R1
O
+ NH2
O
R2
Nucleophilic Amine (primary and secondary)
E and Nu are 5 atoms apartRotatable bond
Thiazolinone DerivativeKinetic product New N-terminal
S
C
N
Ph
H2N
HN
R1
O R2
O
N
HN
R1
O R2
O
N
S
Ph
A H
H
H
B
N
HN
R1
O R2
O
NH
S
Ph
H
1
2
34
5NN
H
S
Ph
H
1
23
4
HN
R1
5O
H A
NNH
S
Ph
H
1
23
4
HN
R1
5O
H
N
S
NH
Ph
O
HN
H
H
H A
R1 N
S
NH
Ph
O
H2N
H
R1
B B
Enol Formation
Potential racemization
PTH, to be detected by HPLCThermodynamic Product
Pre-note
N
S
NH
Ph
R1
O H+
N
S
NH
Ph
R1
OH
N
S
NH
Ph
R1
OH
H+
N
S
NH
Ph
R1
O
+
N
S
NH
Ph
R1
O
H2O
N
S
NH
Ph
R1
O
OH
HB
H A
NH
NO
SR1
Ph
Frame of Reaction
H2N
HN
R1
O R2
O
H3N
R2
O
NH
NO
S
R1
Ph
+
When racemization is taken care of
Brain teasers:
a) a peptide is not reactive to Edman Degradation
b) After a round of Edman degradation, only one fragment is obtained c) After a round of Edman degradation, two PTH products are obtained
d) Bicyclic PTH product from Edman Degradation
c) Special case: Lysine
No nucleophilic amine Cyclic peptide D05
Breaking the peptide bond does not break the molecule
Presence of Nu amine; Cyclic D10, D12
2 Nu amines at both ends / 1 PTH end and 1 Nu amine endD10, D12
A ring before Edman degradationD02, D04
A more protonated amine D09
Cyanogen Bromide Cleavage
NH
HN
O
S
Me
Br C N
NH
HN
O
S
MeC
N
Br
NH
O
NH
S
MeCN
- MeSCNO
HNNH
H2O
O
ONH
NH
H A
HHBH
O
ONH2
NH
HBH
O
NH
O
+ H2N
1
34
5
2
12
34
5
-Br
Nucleophilic SNu and E 5 atoms apartRotatable bond
Met (C) N cleaved
Brain teasers:
1) A peptide gives only one fragment after CNBr cleavage a) A cyclic peptide
b) C-terminal Methionine
2) It is known that a peptide has n Met. It gives n pieces of fragments
3) How about (n+1) fragments?
H3N
NH
HN
NH
NH2
O
OS
NN
O
O
O H
H
HN
O
OH
NHO
O
OH
NH2
How this reacts with CNBr? (2004 Exam 1)
Why S / C=O combo can be so different in these two
reactions?
S
O
S
O
Edman Degradation CNBr Cleavage
C=S bond, S is Nucleophilic3 C-S bond, S has an extra Covalent bond; adjacent C is ready for SN2
Peptide Syntheses
Walter Kowtoniuk
Amide Bond Synthesis
- Synthesis of an amide bond using the corresponding carboxylic acid and amine.
- Use DCC to both activate the acid and serve as a dehydrating agent
HN C
R
O
O
H
N
C
N
R2
NH2
HN C
R
NH
O
R2
NH
CNH
O
Amide Bond Synthesis
HN C
R
O
O
H
N
C
N
HA
B-
HN C
R
O
O
N
C
N
H
HN C
R
O
O
NC
N
H
HA
HN C
R
O
O
NC
N
H
H
R2
NH2
HN C
R
O
O
NH
CNH
R2N
HH
B-
HN C
R
O
O
NC
N
H
H
R2
H2N
Amide Bond Synthesis
HN C
R
O
O
NH
CNH
R2N
HH
B-
HN C
R
O
R2NH
Protecting GroupsWhy do we need them?
Protecting Groups
Lecture Notes pg33
Protecting Groups
• t-Boc Synthesis
• t-Boc Deprotection
H3C
H3C
H3C
OH
O
Cl
Cl
H3CH3C
CH3
O
O
ClR
NH3C
H3C
CH3
O
O
H HH2N
R
B-
RNHH3C
H3C
CH3
O
O
RNHH3C
H3C
CH3
O
OTFA
H+
RNHH3C
H3C
CH3
O
OH
RNHCH3
H2C
CH3
O
OH
H+
RH2N
CO2
(gas)
HE1
CH3H2C
CH3
Protecting Groups
• Cbz follows the same mechanism as shown for t-Boc
Cl Cl
O OH
OCl
O
ONH
O
R
or
OO
O
R
ONH
O
R TFA
H2C
NH2R
CO2 H3CEt3Si-H
Protecting Groups
• Ts synthesis
• Ts Deprotection
H2NC
OH
O
HNNH2
NH CH3S
O
Cl
O
H2NC
OH
O
HNN
NH2
CH3
S
O
OH
B-
H2NC
OH
O
HNN
NH2
CH3
S
O
O
H2NC
OH
O
HNN
NH2
CH3
S
O
OH
F
HFF-
H2NC
OH
O
HNNH
NH2CH3S
O
O
F
Protecting Groups
• DNP synthesis
• DNP deprotection
H2N
OHO
HNN
NO2
NO2
HS H2N
OHO
HNN
NO2
NO2S
H2N
OHO
HNN
H
B-
H2N
OHO
HNN Cl
O2N NO2
H2N
OHO
HNN
NO2
NO2Cl
H2N
OHO
HNN
NO2
NO2
C to N Directionalitywhy not N to C?
NH
O
R2
N
O O
R1
HN
NH
Cy
Cy
B-
H
NH
O
R2
N
O
R1
H
B-
NH
O
R2
N
O
R1NH
O
R2
N
O
R1
H
HA
Solid Phase Peptide Synthesis
Solid Phase Peptide Synthesis
Peptide Fragment Coupling
• Thioester
• True coupling
O
NH
O
RO
NH
O
RSH
O
NH
O
RSH2N
SHO
HN
O
R
N
O
NH
O
R
HH
H+
O
NH
O
RHN
HS
O
NH
O
RS
O
HN
O
R
NHH
SH
H
B-
O
NH
O
R
SO
HN
O
RN
H H
H+
B-
O
NH
O
RO
NH
O
RS
Br
B-
H
O
NH
O
RS
O
NH
O
RS
O
NH
O
R
Determining Yield
• Synthesizing a 100mer requires 99rxns, thus n=99
• If we factor in the initial coupling to the solid phase, the 100mer requires 100rxns, thus n=100
• For convergent synthesis we are concerned with the longest linear sequence of steps. In this case the yield of each individual reaction is multiplied
Translation
Biological Carbonyl Activation
Biological Carbonyl Activation
Biological Carbonyl Activation
Ribosome
Role of A2486