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Chem 239Amino Acids, Peptides, and Proteins
Representations:Classification20 common amino acidsFisher projections and D-L notation
Chemical Properties of Amino Acids:Acid-base behaviorSynthesis
Reactions of Amino Acids:Laboratory chemistry Biochemical reactions
Peptides:Nature of peptidesAnalysis: Composition, end-group, sequenceSynthesis: protection, bond-formationSynthesis: Solution vs solid-phase
Proteins:Secondary structuresTertiary and quarternary structuresCoenzymes
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ClassificationAmino Acids
ContainContain——NHNH22
and and ——COCO22
HH
Actually Actually ——NH NH 3+3+
and and ——COCO22
––
Classified as Classified as αα, , ββ, , γγ, , etcetc. amino acids . amino acids according the carbon that bears the according the carbon that bears the nitrogen.nitrogen.
++HH33 NNCHCH22 CHCH22 CHCH22 COCO22
––
CC CC
OO
OO––
HH
HH
HH33 NN++
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Naming Amino Acids
NHNH33
++
COCO22––
11--Aminocyclopropanecarboxylic acid:Aminocyclopropanecarboxylic acid:an an --amino acid that is anamino acid that is an intermediate in the biosynthesisintermediate in the biosynthesis of ethyleneof ethylene
++HH33 NNCHCH22 CHCH22 COCO22
––33--Aminopropanoic acid:Aminopropanoic acid:a a --amino acid that is one ofamino acid that is one of the structural units present inthe structural units present in coenzyme Acoenzyme A
++HH33 NNCHCH22 CHCH22 CHCH22 COCO22
–– 44--Aminobutanoic acidAminobutanoic acid::a a --amino acid involved amino acid involved in the transmission of in the transmission of nerve impulsesnerve impulses
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The 20 Key Amino AcidsThe 20 Key Amino Acids
•
More than 700 amino acids in nature.
•
20 amino acids are the building blocks of proteins. All are α-amino acids.
•
Differ in the group attached to the α
carbon.
CC CC
OO
OO––
RRR
HH
HH33 NN++
Vary in:Vary in:
Size and shapeSize and shape
Electronic characteristicsElectronic characteristics
nonpolar side chains
polar but nonionized side chains
acidic side chains
basic side chains
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The only achiral aaThe only achiral aa
Disrupts local protein structureDisrupts local protein structure
CC CC
OO
OO––
HH
HH
HH33 NN++
GlycineGlycine
(Gly or G)(Gly or G)
Small achiral side chainSmall achiral side chain
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Nonpolar side chainNonpolar side chain
CC CC
OO
OO––
CHCH33
HH
HH33 NN++
AlanineAlanine (Ala or A)(Ala or A)
CC CC
OO
OO––
CH(CHCH(CH33 ))22
HH
HH33 NN++
ValineValine (Val or V)(Val or V)
CC CC
OO
OO––
CHCH22 CH(CHCH(CH33 ))22
HH
HH33 NN++
LeucineLeucine (Leu or L)(Leu or L)
CC CC
OO
OO––
CHCH33 CHCHCHCH22 CHCH33
HH
HH33 NN++
IsoleucineIsoleucine (Ile or I)(Ile or I)
Alkyl groups as side chainsAlkyl groups as side chains
Nonpolar and hydrophobic Nonpolar and hydrophobic
Often found in core of soluble proteinsOften found in core of soluble proteins
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Nonpolar side chainNonpolar side chain
CC CC
OO
OO––
CHCH33 SCHSCH22 CHCH22
HH
HH33 NN++
MethionineMethionine (Met or M)(Met or M)
ProlineProline
CC CC
OO
OO––
CHCH22
HH
HH22 NN++
HH22 CCCC HH22
(Pro or P)(Pro or P)
Only secondary amineOnly secondary amine
Disrupts local protein structuresDisrupts local protein structures
AUG coded AUG coded
““startstart””
amino acidamino acid
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Nonpolar side chainNonpolar side chain
PhenylalaninePhenylalanineCC CC
OO
OO––
CHCH22
HH
HH33 NN++
(Phe or F)(Phe or F)
CC CC
OO
OO––
CHCH22
HH
HH33 NN++
HH
TryptophanTryptophan
(Trp or W)(Trp or W)NN
Contribute to AContribute to A280280
nmnm
(along with Try and Phe)(along with Try and Phe)
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Polar (nonPolar (non--ionizable) side chainionizable) side chain
CC CC
OO
OO––
CHCH22 OHOH
HH
HH33 NN++
SerineSerine
(Ser or S)(Ser or S)
CC CC
OO
OO––
CHCH33 CHOHCHOH
HH
HH33 NN++
ThreonineThreonine
(Thr or T)(Thr or T)
Can form hydrogen bondsCan form hydrogen bonds
Can be phosphorylatedCan be phosphorylated
Can be glycosylatedCan be glycosylated
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Polar (nonPolar (non--ionizable) side chainionizable) side chain
Can form disulfidesCan form disulfides
CC CC
OO
OO––
CHCH22 SHSH
HH
HH33 NN++
CysteineCysteine
(Cys or C)(Cys or C)
CC
CC
OO
OO––
CHCH22 SS --HH
HH33 NN++
CC
CC
OO
OO––
HH
HH33 NN++
SCHSCH22
CystineCystine
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Polar (nonPolar (non--ionizable) side chainionizable) side chain
TyrosineTyrosine
CC CC
OO
OO––
CHCH22
HH
HH33 NN++
OHOH
(Tyr or Y)(Tyr or Y)
AsparagineAsparagine
CC CC
OO
OO––
HH
HH33 NN++
HH22 NCCHNCCH22
OO
(Asn or N)(Asn or N)
GlutamineGlutamine
CC CC
OO
OO––
HH
HH33 NN++
HH22 NCCHNCCH22 CHCH22
OO(Gln or Q)(Gln or Q)
All can Form H-bonds
Can be phosporylated
Can be glycosylated
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Ionizable (acidic) side chainsIonizable (acidic) side chains
CC CC
OO
OO––
HH
HH33 NN++
OCCHOCCH22
OO
––
Aspartic AcidAspartic Acid
(Asp or D)(Asp or D)
CC CC
OO
OO––
HH
HH33 NN++
OCCHOCCH22 CHCH22
OO
––Glutamic AcidGlutamic Acid
(Glu or E)(Glu or E)
All can form H-bondsAll can form ionic bonds with (+) charged residues
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Ionizable (Basic) side chainsIonizable (Basic) side chains
CC CC
OO
OO––
CHCH22 CHCH22 CHCH22 CHCH22 NHNH33
HH
HH33 NN++
LysineLysine
++
(Lys or K)(Lys or K)
CC CC
OO
OO––
CHCH22 CHCH22 CHCH22 NHCNHNHCNH22
HH
HH33 NN++
ArginineArginine
++NHNH22
(Arg or R)(Arg or R)
HistidineHistidine
CC CC
OO
OO––
HH
HH33 NN++
CHCH22
(His or H)(His or H)
NN NHNH
All can form H-bondsAll can form ionic bonds with (-) charged residues
Some acetylated and methylated
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Varying polarity of side chainsVarying polarity of side chains
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Configurations of α-Amino Acids
HH33 NN++
HH
RR
COCO22––
All common All common amino acids amino acids
(except glycine) (except glycine) have at least one have at least one
chiral centerchiral center
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Properties of GlycineProperties of Glycine
High melting point:
When heated to 233°C,
it decomposes before it melts
Solubility:
Soluble in water;
Not soluble in nonpolar solvent
OO
OHOHHH22 NCHNCH22 CC••••
••••
••••
•••• ••••
––••••
OO
OOHH33 NNCHCH22 CC ••••
••••
•••• ••••++
more consistent more consistent with thiswith this
than thisthan this
a a zwitterionzwitterion or or dipolar iondipolar ion
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AcidAcid--Base Properties Base Properties of Glycineof Glycine
––••••
OO
OOHH33 NCHNCH22 CC ••••
••••
•••• ••••++
––••••
OO
OOHH22 NCHNCH22 CC ••••
••••
•••• ••••
••••
OO
OHOHHH33 NCHNCH22 CC++
••••
••••
•••• ••••
ppKKaa = 2.34= 2.34
ppKKaa = 9.60= 9.60
The The pI pI of of glycine is 5.97.glycine is 5.97.
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CC CC
OO
OO––
HH
HH
HH33 NN++
GlycineGlycineppKKa1a1 = = 2.342.34 ppKKa2a2 == 9.609.60 ppI I == 5.975.97
Aspartic acidAspartic acid
ppKKa1a1 = = 1.881.88 ppKKa2a2 == 3.653.65 ppKKa3a3 == 9.609.60 ppI I == 2.772.77
HH33 NN CC CC
OO
OO––
HH++
OCCHOCCH22
OO
––
LysineLysine ppKKa1a1 = = 2.182.18 ppKKa2a2 == 8.958.95 ppKKa3a3 == 10.5310.53 ppI I == 9.749.74HH33 NN CC CC
OO
OO––
HH++
CHCH22 CHCH22 CHCH22 CHCH22 NHNH33
++
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Synthesis of Amino AcidsSynthesis of Amino Acids
From -Halo Carboxylic Acids
CHCH33 CHCOHCHCOH
BrBr
OO
2NH2NH33++
HH22 OO
CHCH33 CHCOCHCO
NHNH33
OO
++
––
(65(65--70%)70%)
++ NHNH44 BrBr
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Strecker Synthesis
NHNH44 ClCl
NaNaCNCN
CHCH33 CHCH
OO
CHCH33 CHCHCC
NHNH22
NN
CHCH33 CHCHCCOO
NHNH33
OO
++
–– (52(52--60%)60%)
1. H1. H22 O, HCl, heatO, HCl, heat
2. HO2. HO––
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Using Diethyl Acetamidomalonate
1. NaOCH1. NaOCH22 CHCH33
2. 2. CC66 HH55 CHCH22 ClCl
OO OO
CHCH33 CHCH22 OCCCOCHOCCCOCH22 CHCH33
HHCHCH33 CCNHNH
OO
OO OO
CHCH33 CHCH22 OCCCOCHOCCCOCH22 CHCH33
CHCH22 CC66 HH55CHCH33 CCNHNH
OO
(90%)(90%)
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HBr, HHBr, H22 O, heatO, heat
OO OO
HOCCCOHHOCCCOH
CHCH22 CC66 HH55HH33 NN++
OO OO
CHCH33 CHCH22 OCCCOCHOCCCOCH22 CHCH33
CHCH22 CC66 HH55CHCH33 CCNHNH
OO
OO
HCCOHHCCOH
CHCH22 CC66 HH55HH33 NN++(65%)(65%)
––COCO22
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Reactions of Amino AcidsReactions of Amino Acids
Acylation of Amino GroupAcylation of Amino Group
OO
HH33 NNCHCH22 COCO––++++ CHCH33 COCCHCOCCH33
OO OO
CHCH33 CCNHNHCHCH22 COHCOH
OO OO
(89(89--92%)92%)
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Fisher Esterification of Carboxyl GroupFisher Esterification of Carboxyl Group
++ CHCH33 CHCH22 OHOH
HClHCl
OO
HH33 NNCHCOCHCO––++
CHCH33
(90(90--95%)95%)
OO
HH33 NNCHCOCHCHCOCH22 CHCH33
++
CHCH33
––ClCl
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Amino acids are detected by the formation of a purple color on treatment with ninhydrin.
OHOH
OO
OO
OHOH++
OO
HH33 NNCHCOCHCO––++
RR
OOOO
OO
NN
OO
––
OO
RCHRCH ++ COCO22 ++ HH22 OO ++
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Biochemical Reactions of Amino AcidsBiochemical Reactions of Amino Acids
Transamination Transamination viavia
LL--Glutamic AcidGlutamic Acid
HOHO22 CCHCCH22 CHCH22 CHCOCHCO22––
NHNH33++
++ CHCH33 CCOCCO22 HH
OO
enzymesenzymes
HOHO22 CCHCCH22 CHCH22 CCOCCO22 HH
OO
++ CHCH33 CHCOCHCO22––
NHNH33++
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Biosynthesis of LBiosynthesis of L--TyrosineTyrosine
CHCH22 CHCOCHCO22––
NHNH33++
OO22 , enzyme, enzyme
CHCH22 CHCOCHCO22––
NHNH33++
HHOO
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DecarboxylationDecarboxylation
CHCH22 CHCHCOCO22––
NHNH33++
––COCO22 , enzymes, enzymes
CHCH22 CHCH2 2 NHNH22
NN
NN HH
NN
NN HH
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PeptidesPeptides
CHCH33
OO
CC++
HH
CC OO––
HH33 NN
OO
CC
HH
HH
CCHH33 NN++
OO––
CHCH33
OO
CCHH33 NN++
HH
CC
OO
CCNN
HH
HH
CC OO––
HH
Two α-amino acids are joined by a peptide bond in alanylglycine.
It is a dipeptide.
AlanylglycineAlanylglycine
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CHCH33
OO
CCHH33 NN++
HH
CC
OO
CCNN
HH
HH
CC OO––
HH
HH
OO
CCHH33 NN++
HH
CC
OO
CCNN
HH
CHCH33
CC OO––
HH
AlanylAlanylglycineglycineAlaAla——GlyGly
AAGG
GlycylGlycylalaninealanineGlyGly——AlaAla
GGAA
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CHCH33
OO
CCHH33 NN++
HH
CC
OO
CCNN
HH
HH
CC OO––
HH
The peptide bond is characterized by a planar geometry.
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Introduction to Peptide Structure DeterminationIntroduction to Peptide Structure Determination
Amino Acid Analysis
Acid-hydrolysis of the peptide (6 M HCl, 24 hr)
Separated by ion-exchange chromatography
Detected using ninhydrin.
Automated method; requires only 10-5
to 10-7 g of peptide.
End Group Analysis
Several chemical methods have been developed for identifying the N-terminus
FFOO22 NN
NONO22
NNHCHHCH22 CC NNHCHCOHCHCO
CHCH33
NNHCHCHCHC
CHCH22 CC66 HH55
HH22 NNCHCCHC
OO OOOOOO
CH(CHCH(CH33 ))22
––
++
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Introduction to Peptide Structure DeterminationIntroduction to Peptide Structure Determination
Edman Degradation
1. Method for determining N-terminal amino acid.
2.
Can be done sequentially one residue at a time on the same sample. Usually one can determine the first 20 or so amino acids from the N-terminus by this method.
3. 10-10 g of sample is sufficient.
4. Has been automated.
The key reagent in the Edman degradation is phenyl isothiocyanate.
NN CC SS
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Introduction to Peptide Structure DeterminationIntroduction to Peptide Structure Determination
peptidepeptideHH33 NNCHCCHC
OO
RR
++NNHHCC66 HH55 NN CC SS ++
CC66 HH55 NNHCHCNHNHCHCCHC
OO
RR
NNHH
SS
peptidepeptide
HClHCl
HH33 NN++
++CC66 HH55 NNHH CC
SSCC
NN CHCH
RR
OO
peptidepeptide
++ HH33 NN++
peptidepeptideCCCC
NN
HNHN CHCH
RR
OOSS
CC66 HH55
phenylthiohydantoin (PTH)phenylthiohydantoin (PTH)derivative.derivative.
phenyl isothiocyanate
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Introduction to Peptide Structure DeterminationIntroduction to Peptide Structure Determination
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Introduction to Peptide Structure DeterminationIntroduction to Peptide Structure Determination