Amino Acids - Building Blocks of Protein

Amino Acids: Building Blocks of Protein Definition • Proteins are linear heteropolymers of L-a-amino acids. • These are organic acids with an amino group at the a-position, or the 2-position. C–C–C–C–C–Functional e d g b a Group (COO–) 6 5 4 3 2 1 • The amino group is basic and the carboxylate group is acidic (of course). The R-groups are different. 2 1 Amino Acids: Building Blocks of Protein Definition • Proteins are linear heteropolymers of L-a-amino acids. • These are organic acids with an amino group at the a-position, or the 2-position. C–C–C–C–C–Functional e d g b a Group (COO–) 6 5 4 3 2 1 • The amino group is basic and the carboxylate group is acidic (of course). The R-groups are different. 2 1 The 4 S’s: Size Amino Acids: Building Blocks of Protein 3 Å diameter 8 Å diameter CH 2 The 4 S’s: Shape Amino Acids: Building Blocks of Protein Here we have to discuss stereochemistry: particularly what is meant by the “L” configuration Recall: Clockwise is R The “L” configuration means levorotary, or rotates polarized light Counterclockwise is S counter-clockwise, or left handed What is the relationship between R/S and D/L? In R/S, this is what? R=D S=L ③ H ① ② The 4 S’s: Shape Amino Acids: Building Blocks of Protein Clockwise is R Counterclockwise is S R=D S=L Fisher Projection (S) 1. Carbon chain vertical with functional group at top 2. At each carbon the vertical bonds to carbons are behind, projecting away from the viewer 3. At each carbon the horizontal bonds are projecting towards the viewer 4. If the functional group (not H) is to the left it’s L (R) 5. If the functional group (not H) is to the right it’s D The 4 S’s: Stability Amino Acids: Building Blocks of Protein All amino acids are stable to acid, base, and heat Exceptions are: 1. Trp (oxidation) 2. Cys (oxidation) 3. Asn (deamination) 4. Gln (deamination) àN-formyl-kynurenine àDisulfides (R’-S–S-R”) àHydrolysis of amide: Asp àHydrolysis of amide: Glu The 4 S’s: Solubility Amino Acids: Building Blocks of Protein • As zwitterions, most amino acids are soluble to some degree. But, depending on the R group they are less soluble or more soluble • The general grouping puts 10 as less soluble: A, V, L, I, P, W, Y, F, M, C • and 10 as more soluble: G, S, T, N, Q, D, E, H, K, R Amino Acids Have Three Common Properties • Groups Attached to the α Carbon. The α carbon always has four substituents and is tetrahedral. – an acidic carboxyl group connected to the α carbon – a basic amino group (1° or 2°) connected to the α carbon – an α hydrogen connected to the α carbon – A fourth substituent called an “R group.” • All Amino Acids are chiral with the L configuration (except glycine where the R-group is a hydrogen). Zwitterion • Acid/Base properties: Net Charge = +1 What is the predominant form at physiological pH (7.4)? H+ Net Charge = 0 H+ a pKa = ~2.3 pKa = ~9.6 Net Charge = –1 Amino Acids Have Three Common Properties • Groups Attached to the α Carbon. The α carbon always has four substituents and is tetrahedral. – an acidic carboxyl group connected to the α carbon – a basic amino group (1° or 2°) connected to the α carbon – an α hydrogen connected to the α carbon – A fourth substituent called an “R group.” • All Amino Acids are chiral with the L configuration (except glycine where the R-group is a hydrogen). Zwitterion • Acid/Base properties: Net Charge = +1 H+ Net Charge = 0 H+ Net Charge = –1 a What is the predominant form at physiological pH (7.4)? pKa = ~2.3 pKa = ~9.6 Amino Acids: Classification Essential • The 20 amino acids found in proteins can be placed in five families based on the physical and chemical properties of their R groups: Table: Name ✓ • Hydrophobic, aliphatic (6) • Hydrophobic, aromatic (3) • Special (hydrophobic/hydrophilic)(2) • Hydrophilic, polar (4) • Hydrophilic, charged (5) Must KNOW % 3-letter 1-letter Year abundance discovered in proteins NOTES Structure mnemonic device Hydrophobic, aliphatic Amino Acids: Classification Pro % Name 3-letter 1-letter Glycine Gly Alanine Ala Valine ✓ Val Leucine✓ Leu Isoleucine✓Ile Proline Pro G A V L I P Hydrophobic, aliphatic Year abundance discovered in proteins 1820 1888 1856 1819 1904 1901 7 8 7 10 6 5 NOTES Structure mnemonic device Smallest, not chiral H Foundational for ~10 other AA Methyl isopropyl V-shaped Most abundant, dominant Ala + Val Two chiral centers (L & D) Val + Me 5-membered ring; Only imino acid (2° amine); special bonds in proteins; is modified by hydroxyl same #C’s as Val Amino Acids: Classification Gavlip family Pro % Name 3-letter 1-letter Glycine Gly Alanine Ala Valine ✓ Val Leucine✓ Leu Isoleucine✓Ile Proline Pro G A V L I P Year abundance discovered in proteins 1820 1888 1856 1819 1904 1901 7 8 7 10 6 5 NOTES Structure mnemonic device Smallest, not chiral H Foundational for ~10 other AA Methyl isopropyl V-shaped Most hydrophobic Ala + Val Two chiral centers (L & D) Val + Me Only imino acid (2° amine); special bonds in proteins; is modified by hydroxyl 5-membered ring; same # as Val; 3C Amino Acids: Classification • The 20 amino acids found in proteins can be placed in five families based on the physical and chemical properties of their R groups: • Hydrophobic, aliphatic (6) • Hydrophobic, aromatic (3) • Special (hydrophobic/hydrophilic)(2) • Hydrophilic, polar (4) • Hydrophilic, charged (5) Hydrophobic, aromatic Gavlip family Amino Acids: Classification Recall: % Name 3-letter Phenylalanine✓Phe Tyrosine Tyr Tryptophan ✓ Trp Year abundance 1-letter discovered in proteins F Y W 1879 1846 1901 4 3 1 NOTES l Extinction coefficient (x10-3) pKa Structure mnemonic device max aromatic Phenyl+Ala Absorb 259 0.7 pKa≈10.1 aromatic, can ionize; p-phenol+Ala UV light 278 1.1 amphipathic aromatic & fluorescent; 279 5.2 Indole+Ala least abundant, largest AA Hydrophobic, aromatic Amino Acids: Classification Recall: PTT family (push-to-talk) Absorb UV light 360 nm Fluorescent Name lmax Extinction coefficient (x10-3) 259 0.7 278 1.1 279 5.2 % 3-letter Phenylalanine✓Phe Tyrosine Tyr Tryptophan ✓ Trp Year abundance 1-letter discovered in proteins F Y W 1879 1846 1901 4 3 1 NOTES pKa Structure mnemonic device aromatic Phenyl+Ala aromatic, can ionize; pKa≈10.1 p-phenol+Ala amphipathic aromatic & fluorescent; Indole+Ala least abundant Amino Acids: Classification • The 20 amino acids found in proteins can be placed in five families based on the physical and chemical properties of their R groups: • Hydrophobic, aliphatic (6) Gavlip family • Hydrophobic, aromatic (3) PTT family • Special (hydrophobic/hydrophilic)(2) • Hydrophilic, polar (4) • Hydrophilic, charged (5) Amino Acids: Classification Special (Sulfur) Hydrophobic /Hydrophilic (Cys) AA Hydropathy index (DG) Ile 4.5 Val 4.2 Leu 3.8 Phe 2.8 Tyr –1.3 Met 1.9 Cys 2.5 • Cysteine can ionize: Cys–SH ⇌ Cys–S– (thiolate anion) + H+ • Cysteine can form disulfide bonds: R1–S–S–R2 ⇌ R1–SH + R2–SH Oxidized Cystine (1810) Reduced Cysteine % Name 3-letter Methionine ✓ Met Cysteine Cys Year abundance 1-letter discovered in proteins M C 1922 1899 2 2 NOTES pKa Structure mnemonic device Most like straight-chain aliphatic Ala+Me/ether can ionize; nucleophile 10.5 Ala+SH (thiol) Amino Acids: Classification Special (Sulfur) Hydrophobic /Hydrophilic (Cys) MC family (master of ceremony) • Cysteine can ionize: Cys–SH ⇌ Cys–S– (thiolate anion) + H+ • Cysteine can form disulfide bonds: R1–S–S–R2 ⇌ R1–SH + R2–SH Oxidized Cystine (1810) Reduced Cysteine % Name 3-letter Methionine ✓ Met Cysteine Cys Year abundance 1-letter discovered in proteins M C 1922 1899 2 2 NOTES pKa Structure mnemonic device Most like straight-chain aliphatic Ala+Me/ether can ionize; nucleophile 10.5 Ala+SH Amino Acids: Classification • The 20 amino acids found in proteins can be placed in five families based on the physical and chemical properties of their R groups: • Hydrophobic, aliphatic (6) Gavlip family • Hydrophobic, aromatic (3) PTT family • Special (hydrophobic/hydrophilic)(2) MC family • Hydrophilic, polar (4) • Hydrophilic, charged (5) Amino Acids: Classification Hydrophilic, polar Gln Name Glutamine Asparagine Serine Threonine ✓ Ser Asn 3-letter Gln Asn Ser Thr Year 1-letter discovered Q N S T 1883 1806 1865 1935 % abundance in proteins 4 4 7 6 Thr NOTES Structure mnemonic device Amide of Glu Glx; gets hydrolyzed to Glu First isolated from asparagus Amide of Asp Asx; gets hydrolyzed to Asp Isolated from Sericin, polar hydroxyl+Ala cousin of Ala Two chiral centers (L & D) Me+Ser Amino Acids: Classification Hydrophilic, polar These amino acids side chains can form hydrogen bonds. Qnst family Gln Amides Ser Asn Alcohols Thr Structure mnemonic device % Name 3-letter Glutamine Asparagine Serine Threonine ✓ Gln Asn Ser Thr Year abundance 1-letter discovered in proteins Q N S T 1883 1806 1865 1935 4 4 7 6 NOTES Glx; gets hydrolyzed to Glu Amide of Glu First isolated from asparagus Asx; gets hydrolyzed to Asp Amide of Asp Isolated from Sericin, polar hydroxyl+Ala cousin of Ala Two chiral centers (L & D) Me+Ser Amino Acids: Classification • The 20 amino acids found in proteins can be placed in five families based on the physical and chemical properties of their R groups: • Hydrophobic, aliphatic (6) Gavlip family • Hydrophobic, aromatic (3) PTT family • Special (hydrophobic/hydrophilic)(2) MC family • Hydrophilic, polar (4) • Hydrophilic, charged (5) Qnst family Hydrophilic, Charged Amino Acids: Classification Asp Lys Negative Name 3-letter 1-letter Aspartate Glutamate Asp Glu D E % Year abundance discovered in proteins 1868 1866 5 7 His Positive NOTES a-amino-succinate; Most acidic a-amino-glutarate pKa Structure mnemonic device 3.7 Ala+carboxyl 4.3 Ala+acetate