01-Proteins_1 - What are proteins Proteins are responsible...

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What are proteins? Proteins are responsible for many biological processes including catalysis (enzyme), communication (receptors, ion channels), and recognition (antibodies)…… Proteins are linear polymers built of chiral monomer units called L- α -amino acids (20 natural).
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Proteins are Polypeptides Composed of L- α -Amino Acids Proteins are linear polymers built of chiral monomer units called L- α -amino acids. H 3 N O CH 3 O N H 3 O CH 3 O mirror plane H 3 N O CH 3 O 180° rotation L - α -amino acid residue amide bond or peptide bond Backbone: black Side chain: magenta N N N N O H H R 1 R 2 O H R 3 O H R 4 O N N N N O H H R 1 R 2 O H R 3 O H R 4 O α
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Ionic Forms of α -Amino Acids and pH pK a ~ 2 for carboxylic acid pK a ~ 9 for ammonium group K a = [ H + ][ A - ] [ HA ] pK a =- log K a H + + A - HA
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Encoded L- α -Amino Acids H 3 N O O Glycine, Gly, G H 3 N O O H 3 N O O H 3 N O O H 3 N O O N H 2 O O H 3 N O O S H 3 N O O Alanine, Ala, A Valine, Val, V Isoleucine, Ile, I Leucine, Leu, L Proline, Pro, P Methionine, Met, M Phenylalanine, Phe, F H 3 N O O O O H 3 N O O O O H 3 N O O NH 3 H 3 N O O HN H 3 N NH H 3 N O O N HN Aspartate, Asp, D Glutamate, Glu, E Lysine, Lys, K Arginine, Arg, R Histidine, His, H H 3 N O O HO H 3 N O O HO H 3 N O O NH 2 O H 3 N O O O NH 2 H 3 N O O HS H 3 N O O HO H 3 N O O HN Serine, Ser, S Threonine, Thr, T Cysteine, Cys, C Asparagine, Asn, N Glutamine, Gln, Q Tyrosine, Tyr, Y Tryptophan, Trp, W Hydrophobic Charged Polar
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The Simplest Amino Acids Glycine: achiral, no asymmetric carbon, backbone conformation most flexible Alanine: chiral, methyl side chain
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Hydrophobic Amino Acids Val, Ile: β -branched side chains, sterically more demanding
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Proline Side chain bond to both C α and N. Conformationally restricted both on backbone and on side chain. Promotes backbone kinks.
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Aromatic Amino Acids Tyr and Trp have UV absorption ε 280 nm Trp: 3400 M -1 ·cm -1 Tyr: 1400 M -1 ·cm -1
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Hydroxyl-Containing Amino Acids Thr is β -branched and has two asymmetric centers. Ser, Thr frequently hydrogen bond to backbone
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Thiol-Containing Amino Acid Cys can form disulfide bonds, important for cross- linking to stabilize proteins (insulin, RNase) Such crosslinks are often observed in extracellular protein but not in intracellular proteins.
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Basic Amino Acids Lys: primary amine side chain with pK a 10.8 Arg: guanidinium side chain with pK a 12.5 His: imidazole side chain with pK a 6.0
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Acidic and Related Amino Acids Asp and Glu have carboxylate side chains with pK a ~4.1 Asn and Gln have carboxyamide side chains
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One and Three Letter Codes Remember both one and three letter codes and the corresponding chemical structures including stereochemistry. These are the alphabets for proteins.
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a of Ionizable Groups in Proteins The pH in different environments and cell compartments are different, therefore the ionization states of functional groups may change. The pK
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01-Proteins_1 - What are proteins Proteins are responsible...

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