AMINO ACID AND PROTEIN CHEMISTRY
Maria Milagros Untalan-Magat, MD,MEM, FPPS,FPAPP
OBJECTIVES:OBJECTIVES:
•General functions of proteinsGeneral functions of proteins
•Structural composition of amino acidsStructural composition of amino acids
•Chemical propertiesChemical properties
•Hierarchy of protein organizationHierarchy of protein organization
Protein Structure and Function
Objective:Objective:
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• Polymers of amino acidsPolymers of amino acids– 20 amino acids20 amino acids– ““Alphabet” of protein Alphabet” of protein
structurestructure– Basic structural unitsBasic structural units
““Proteios”Proteios”
Proteins
Diversity in functionsDiversity in functions– Enzymatic catalysisEnzymatic catalysis– Transport and storageTransport and storage– Coordinated motion and Coordinated motion and
mechanical supportmechanical support– Immune protectionImmune protection– Generation and transmission Generation and transmission
of nerve impulsesof nerve impulses– Control of growthControl of growth
Proteins
Amino Acids: Amino Acids: StructureStructure
CNH3+ H
COO-
R
C NH3+H
COO-
R
L - configuration D - configuration
Amino Acids: Amino Acids: PropertiesProperties
• Tetrahedral carbonTetrahedral carbon– Asymmetric centerAsymmetric center– Chiral centerChiral center– StereocenterStereocenter
CNH3+ H
COO-
R • Side ChainSide Chain– FunctionFunction– ConformationConformation– Electrical Electrical
chargecharge
Amino Acids: Amino Acids: Functional Functional GroupsGroups
• ACIDICACIDIC
CNH3+ H
COO-
R
• CarboxylCarboxyl
• BASICBASIC• AmineAmine
• ImidazoleImidazole
• GuanidinoGuanidino
• NEUTRAL• AmidesAmides
• HydroxylHydroxyl
NH2COOHOH
• ACIDICACIDIC
CNH3+ H
COO-
R
• CarboxylCarboxyl
• BASICBASIC• AmineAmine
• ImidazoleImidazole
• GuanidinoGuanidino
• NEUTRAL• AmidesAmides
• HydroxylHydroxyl
Amino Acids: Amino Acids: Functional Functional GroupsGroups
Amino Acids: Functional GroupsGroup Characteristic Amino Acids
Negatively charged
Additional carboxyl group
Glutamic acid and Aspartic acid
Positively charged
Guanidino groupImmidazolee - B Group
ArginineHistidineLysine
Polar uncharged
OH containingAmide groupThiol group
Serine and threonineAsparagine and glutamineCysteine
Nonpolar aliphatic
No side chainImino groupHydrophobic alkyl groupThioether sulfur atom
GlycineProlineAlanine, valine, leucine, isoleucineMethionine
Aromatic Bulky aromatic side chains
Phenylalanine, tyrosine, tryptophan
Amino Acids: Classification
Amino Acids: Classification
Amino Acids: Classification
Amino Acids: Classification
Amino Acids: Classification
TitrationTitration Quantitative measure of Quantitative measure of
pKapKa Electric chargeElectric charge Buffering capacityBuffering capacity
CH3N+ R
COO
H
pH = 2pH = 7pH = 11NaOH
ZwitterionZwitterion Dipolar ionsDipolar ions
H
H2OH2N
Amino Acids: Ionic State
CNH3+ R
COOH
H
CNH3+ R
COO-
H
CNH2 R
COO-
H
pH = 2 pH = 7 pH = 11
H+
Zwitterion Dipolar ions
NaOH
H+
NaOH
Electric charge = +1
Electric charge = 0
Electric charge = -1
pI = pK1 + pK2
2
Amino Acids: Ionic State
0.5 1.0 1.5
1
2
3
4
5
6
7
8
9
10
11
12
Equivalents OH-
pH
pK2 = 9.7
pK1 = 2.3
pI = 6.0pK1
+ pK22
Titration Curve: Alanine
CNH3+
RCOOH
COOH
H
pK = 2.2
pK = 4.3
pK = 9.9
H20
NaOH
+1
0
-2
CNH3+
RCOOH
COO-
H
CNH3+
RCOO-
COO-
HCNH2
RCOO-
COO-
H
-1
NaOH
H20
H20
NaOH
Titration : Glutamic acid
CNH3+ R
COOH
H
CNH3+ R
COO-
H
CNH2 R
COO-
H
pH = 2 pH = 7 pH = 11
H+
Zwitterion Dipolar ions
NaOH
H+
NaOH
Electric charge = +1
Electric charge = 0
Electric charge = -1
pI = pK1 + pK2
2
Titration : Glutamic acid
0.5 1.0 1.5
1
2
3
4
5
6
7
8
9
10
11
12
Equivalents OH-
pH
pK2 = 9.9
pK1 = 2.2
pI = 3.25pK1
+ pKR2
pKR = 4.3
Titration curve: Glutamic acid
AMINO ACID pK1 pK2 pKR
ALANINE 2.35 9.87ARGININE 1.82 8.99 12.48
ASPARAGINE 2.1 8.84ASPARTIC ACID 1.99 9.90 3.90
CYSTEINE 1.92 10.78 8.33GLUTAMIC ACID 2.10 9.47 4.07
GLUTAMINE 2.17 9.13GLYCINE 2.35 9.78
HISTIDINE 1.80 9.33 6.04ISOLEUCINE 2.32 9.76
LEUCINE 2.33 9.74LYSINE 2.16 9.18 10.79
METHIONINE 2.13 9.28PHENYLALANINE 2.16 9.18
PROLINE 1.95 10.65SERINE 2.19 9.21 ~13
THREONINE 2.09 9.10 ~13TRYPTOPHAN 2.43 9.44
TYROSINE 2.20 9.11 10.13VALINE 2.29 9.74
Proteins:
Structural Organization
+OH HH2CH2N
H
C
R1 O
CN
H
COOH
R2
CH2N
H
C
O
CN
H
COOH
H
R1 R2
H2O+
Peptide bond formation
Covalent bond : – amino and – carboxyl groups Elimination of H2O
Partial double bond character - C, H, N, and O are co-planar Trans form is favored
Peptides: Characteristics
DNA - dependent Sequence of peptide-bonded amino acids Directionality – NH3 and COOH
Disulfide bonds
PRIMARY STRUCTURE
CH2N
H
C
OR1
CN
H
COO
H
R2
CN
H
COO
H
R3
CN
H
COOH
H
R4
Peptides: Structural Organization
Arrangement in space Motifs of hydrogen bonding
SECONDARY STRUCTURE
CH2N
H
C
OR1
CN
H
COO
H
R2
CN
H
COO
H
R3
CN
H
COO-
H
R4
Peptides: Structural Organization
Alpha helixAlpha helix
2o Sequence Beta PleatsBeta Pleats
Hydrogen bonds
Peptides: Structural Organization
3 – dimensional arrangement of atoms3 – dimensional arrangement of atoms Over-all folding of polypeptide chainOver-all folding of polypeptide chain Highest order for monomeric proteinHighest order for monomeric protein
TERTIARY STRUCTURE
Peptides: Structural Organization
Manner of interaction between subunits of multimeric proteins
Domains
QUATERNARY STRUCTURE
Types Assembly of two proteins that have two different
structures Multiple copies of the same protein
Peptides: Structural Organization
Heirarchy of Protein Structure
•Amino acids are built around an asymmetric - carbon.
•Amino acids are grouped based on similarities of side chain characteristics.•The primary structure of proteins is dictated by genetic information.
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1.1. Differentiate proteins, peptides & Differentiate proteins, peptides & amino acidsamino acids
2. Explain D, L system of configuration2. Explain D, L system of configuration
3. Define stereoisomerism; enantiomers3. Define stereoisomerism; enantiomers4. Define chirality4. Define chirality
5. Define polarity5. Define polarity
6. Describe zwitter ion6. Describe zwitter ion
7. Define R group : relevance7. Define R group : relevance8. Define pKa, pH, pI8. Define pKa, pH, pI