chemical biology 03 blood - amherst college · 2009. 9. 16. · properties of peptide bond...
TRANSCRIPT
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Chemical Biology 03BLOOD
Biomolecular Structure
III. Amino Acid to Protein
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Chemical Biology 03BLOOD
Biomolecular Structure
III. Amino Acids to Proteins
Lecture 5&6: 9/16/09
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Organic Chemical Groups
PROTEINS
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Biological Macromolecules: Proteins
• The general formula is
• H2N-CHR-COOH– amino ( H2N---- )
– acid ( ----COOH )
– ----CHR--- group varies, and gives its identity to one of 20 amino acids used in proteins
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Proteins are made up of Amino Acids
• About half of the amino acids are "essential" meaning that they cannot be made by metabolic conversion from other molecules and thus need to be eaten
– For the ten essential amino acids:• Threonine, Tryptophan, Valine, Arginine, Histidine, Lysine, Phenylalanine,
Leucine, Isoleucine, Methionine
– Remember this phrase:• These Ten Valuable Amino Acids Have Long Preserved Life In Man
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….20 amino acids that are used to make all Proteins
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Post-translational Amino Acid Modification
• amino acids are used by the ribosome to make proteins
• these amino acids side groups in the protein may be further modified to have sugars, fats, other modifications elsewhere in the cell
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Side Group Functionality
small
• Gly and Ala
nucleophillic
• Ser, Thr, Cys
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Side Group Functionality
hydrophobic
• Val, Leu, Ile, Met, Pro
aromatic
• Tyr, Phe, Trp
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Side Group Functionality
Acidic and Amide
• Asp, Glu, Asn, Gln
Basic
• Arg, Leu, His
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Amino Acids join together using Peptide Bonds
• Peptide bonds link amino acids together through -NH2 on one amino acid and –COOH on another
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Peptide Bond is Planar
* The peptide plane consists of six atoms, C 1, C, O, N, H, C
* H-N-C bond angle is 121o, not 109.5o.
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Resonance in Peptide Bond
The peptide bond is rigid and planar due to the double bond resonance form, which shortens the C-N distance to 0.16 A shorter than a normal C-N bond.
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Properties of Peptide Bond
• Barrier to Rotation about C-N bond is 20 kcal
• Peptide bond is planar with C groups typically trans to the peptide bond (better accommodate R groups)
• C and N are planar (2-D) and not able to rotate
• C groups are tetrahedral (3-D) and able to rotate though some angles are unfavorable due to steric repulsion with other atoms.
• C Naturally occurring amino acids are ALMOST exclusively the L stereoisomer.
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Thinking Ahead: Why do we have twenty different amino acids and not just one or two or one hundred?