Amino Acids and Peptides

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Amino Acids and Peptides

• Precursors of Proteins

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Proteins(Amino Acids)
Only 20 naturally-occurring amino acids Only
linear structures
3
Functions of Proteins I

• Catalysts and Metabolic Regulation Enzymes
• Protection
• Serum antifreeze proteins
• Blood coagulation
• Antibodies
• Membrane Transport Nutrients
• Signal Transduction Cell Surface Receptors
• Structural Support Collagen

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Functions of Proteins II

• Coordinated Motion Muscle Contraction
• Genetic Regulation DNA Binding Proteins
• Transport Hemoglobin
• Generation and Transport of Nerve Impulses
• Nutrient Storage
• Seed proteins
• Casein in milk

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Function of proteins largely due to properties of
constituent amino acids
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Standard Amino Acids (20)
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Dipolar Ions(Zwitterions)
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Peptide Bonds
Linear Polymers
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Nomenclature
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Peptides

• Dipeptides
• Tripeptides
• Oligopeptides
• Polypeptides

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Diversity

• Number 20n

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Variations in length and sequence contribute to
the diversity of shapes and biological functions
of proteins
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Nonpolar and HydrophobicAmino Acids I
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Nonpolar and HydrophobicAmino Acids II
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Polar Amino Acids I
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Polar Amino Acids II
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Acidic Amino Acids
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Basic Amino Acids
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Notation for 20 Standard AAs
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Greek Nomenclature
Figure 4-8
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Amino Acids in Peptides
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Nomenclature of Peptides(Primary Structure)

• L-alanyl-L-seryl-L-aspartic acid
• aspartate
• Alanylserylaspartate
• AlaSerAsp
• ASD

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Diversity(Tripeptide 3 x 2 x 1 6
arrrangements)
For 20 amino acids (small peptide) 20! 2.43 x
1018
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Stereochemistry Review

• Optical Activity

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Diagram of a Polarimeter
Figure 4-9
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Rotation of Plane of Polarized Light

• Dextrorotatory
• (rotation to the right) d or
• Levorotatory
• (rotation to the left) l or -
• Empirical

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Optically Active Molecules are Asymmetric(i.e.
not superimposible on their mirror image)
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Chiral (Asymmetric) Carbon

• Four different substituents
• Stereoisomers
• Number of stereoisomers 2n

C? atoms of amino acids (except glycine) are
asymmetric centers!
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Chiral Centers Give Rise to Enantiomers(non-super
imposible mirror images)
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Distinguishing Stereoisomers

• Rotation of plane of polarized light (not related
  to absolute configuration)
• Cahn-Ingold-Prelog Method (R/S)
• Fischer Method (projections)

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Cahn-Ingold-Prelog Method (R/S)(1956)
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Fischer Convention(1891)
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Protein Amino Acids
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Fischer Method/Projections (L/D)
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L-?-Amino Acids
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Chirality and Biochemistry

• Life is Based on Chiral Molecules
• Biosynthetic processes almost invariably produce
  pure stereoisomers e.g. L-amino acids

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Pharmaceutical Industry

• Racemic Mixtures

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Benign
Figure 4-12
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Devastating
Figure 4-13
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Chiral Synthesis

• Goal of Organic Chemistry

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Protein Amino Acid Derivatives
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Some Modified Peptidyl Amino Acids
Figure 4-14
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Biologically Active Amino Acid Derivatives
Figure 4-15
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Disulfide Bond Formation(Cystine)
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Hydroxylation
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Phosphorylation
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Acetylation
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Formylation(amino terminal methionine)
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Other Modifications

• Methylation (methyl group)
• Glycosylation (sugar)

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Non-protein Amino Acids
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Green Fluorescent Protein
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Aequorea victoria
Box 4-3 figure 1
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Box 4-3 figure 2
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Green Fluorescence Protein (GFP)

• GFP cloned in the early 1990s and expressed in E.
  coli.

http//www.conncoll.edu/ccacad/zimmer/GFP-ww/GFP2.
htm
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GFP-like and GFP variants

• GFP-like proteins identified in
  non-bioluminescent organism (i.e. corals)
• Mutants with faster and brighter fluorescence
  have since been identified.

http//www.conncoll.edu/ccacad/zimmer/GFP-ww/GFP2.
htm
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In vivo Imaging
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Cool Green Things!
http//www.conncoll.edu/ccacad/zimmer/GFP-ww/GFP4.
htm