12
CHEM 461 – Fundamentals of Biochemistry Sample Midterm Exam Solu?ons Instructor: Yunus Emre Türkmen Bilkent University Department of Chemistry
CHEM461–Fundamentalsof
BiochemistrySampleMidtermExam
Solu?ons
Instructor:YunusEmreTürkmen
BilkentUniversityDepartmentofChemistry
Solu?on:
• Tyrosine:phenol,HBDandweakHBA• Tryptophan:indole,HBD• Methionine:thioether,weakHBA• Lysine:ammonium,protonatedform:HBD• Arginine:guanidinium,protonatedform:HBD• His?dine:imidazole,HBAandHBD
• Asparagineandglutamine:amide,HBAandHBD• Serineandthreonine:alcohol,HBAandHBD• Cysteine:thiol,weakHBAandHBD• Aspartateandglutamate:carboxylate,deprotonatedform:HBA
Solu?on:Phenylalanine(Phe),tyrosine(Tyr),tryptophan(Trp)andhisCdine(His)arecapableofparCcipaCnginπ-πinteracCons.
Strengthofπ-πinteracConswiththeelectron-deficienthexafluorobenzene:Trp>Tyr>Phe>His
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Solu?on:Lysine(Lys)andarginine(Arg)canparCcipateascaConcomponentsincaCon-πinteracCons.HisCdineisparCallyprotonatedatphysiologicalpH(pH=7.4),andcanparCcipatetosomeextentincaCon-πinteracCons.
Solu?on:Prolineistheonlyaminoacidhavingasecondaryaminegroupinitsstructure,andtherefore,itistheidealcandidateforuseasanorganocatalystintheabovetransformaCon.
Solu?on:Glycineisthesmallestaminoacid,andduetothisreason,itispresentRepeatedlyintheinteriorregionofcollagen.
C+H3NCO2H
HCH2CH2CO2H
fully protonated formof glutamate
C+H3NCO2-
HCH2CH2CO2H
C+H3NCO2-
HCH2CH2CO2-
CH2NCO2-
HCH2CH2CO2-
H3A+ H2A HA- A2-
pK1 = 2.19 pK2 = 4.25 pK3 = 9.67
pI = (2.19+4.25)/2 = 3.22
Solu?on:
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Solu?on:
C+H3NCO2H
HCH2SH
fully protonated formof cysteine
C+H3NCO2-
HCH2SH
C+H3NCO2-
HCH2S-
CH2NCO2-
HCH2S-
H3A+ H2A HA- A2-
pK1 = 1.96 pK2 = 8.18 pK3 = 10.28
pI = (1.96+8.18)/2 = 5.07
Solu?on:
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Solu?on:
C+H3NH
CCH2CH2CH2
O HN C
H
CH2C
CH
NHC+H2NNH2
CH3H3C
O HN C
HCO2H
H2C
N
NH
H
fully protonated formof Arg-Leu-His
H4A3+
H4A3+ H3A2+ H2A+ A-pK1 = 1.82 pK2 = 6.00 pK2 = 9.04
HApK2 = 12.48
pI = (9.04+12.48)/2 = 10.76
C+H3NH
CCH2CO2H
O HN C
H
CH2C
CH2
O HN C
HCO2H
CH2
fully protonated formof Asp-Lys-Asn
H4A2+
H4A2+ H3A+ H2A A2-pK1 = 2.02 pK2 = 3.65 pK2 = 9.60
HA-pK2 = 10.53
pI = (3.65+9.60)/2 = 6.63
CH2CH2NH3+
O NH2
Interiorregionoftheionchannel:ThehydrophilicregionofAmB–theregionenclosedbythegreenrectangle–willfacetheinteriorregionoftheionchanneltocreateapolar,hydrophilicenvironment.TheinteracConsofthepolarfuncConalgroupswiththeionscanbedescribedasion-dipoleandion-ion(ionpair)interacCons.Morespecifically,alcoholgroupscancoordinatetoNa+andK+caCons,andcanmakeH-bondstoCl-anions.EstergroupcancoordinatetoNa+andK+caCons.Thecarboxylate(CO2-)groupwillhaveanion-pairwithNa+andK+,whiletheammonium(NH3+)willhaveanion-pairwithCl-.Exteriorregionoftheionchannel:ThehydrophobicpolyeneregionofAmB–theregionenclosedbytheredcircle–willfacetheexterioroftheionchannelsothatitwillhaveafavorableinteracConwiththehydrophobiclipidbilayerviaVanderWaalsinterac?ons.
Solu?on:
Solu?on: Interac?onstrengths:C>D>B>E>A
NN
ONH
N
O
CH3H3C
O
H3C O
O
O NH
O
HN
ONH
OHO
O
Enopeptin B
2
1
3
1: Proline2: Alanine3: N-Methylalanine
NN
ONH
N
O
CH3H3C
O
H3C O
O
O NH
O
HN
ONH
OHO
O
P1
P2
P3 P4
P5
an amide bond, but notbetween two amino acids
non-peptide bond between proline carbonyl and serine -OH.
NN
ON
N
O
CH3H3C
O
H3C O
O
O NH
OH
HN
OHNH
OHO
O
Enopeptin B4
56
4: Proline5: Serine6: Phenylalanine
