Transcript Amino Acids, Peptides and Proteins

Amino Acids, Peptides and Proteins
Chapter 3
Part 1
CHAPTER 3, Part 1
Amino Acids and Peptides
Learning goals:
• To know the structure and naming of all 20 protein
amino acids
• To know the structure and properties of peptides and the
particularly the structure of the peptide bond.
• Ionization behavior of amino acids and peptides at
different pH’s.
• To know the general pKa’s of amino acids: their
carboxyls, aminos, the R-group weak acids.
Proteins: Enzymes, Binding Proteins, Structural
Proteins – all made from Amino Acids
Amino Acids:
Building Blocks of Protein
• Proteins are linear heteropolymers of -amino acids
• Amino acids have properties that are well-suited to carry
out a variety of biological functions
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Capacity to polymerize
Useful acid-base properties
Varied physical properties
Varied chemical functionality
Amino acids share many features,
differing only at the R substituent
L and D forms
Carbon Numbering System
A
Amino Acids: Classification
Common amino acids can be placed in five basic
groups depending on their R substituents:
• Nonpolar, aliphatic (7)
• Aromatic (3)
• Polar, uncharged (5)
• Positively charged (3)
• Negatively charged (2)
Invented the One Letter
Amino Acid Code.
Spectrophotometry
UV light Absorption by Proteins – due to 2 Amino Acids
Cysteine can form Disulfide Bonds
Uncommon Amino Acids
Amino acids in Proteins Can be Reversibly Modified
A
Non Protein Amino Acids
Toxic Amino Acids
A search for compounds producing Yunnan
Sudden Unexplained Deaths found related to
eating a mushroom.
Halford, B. C+E News Feb 13, 2012
Trogia venenata Zhu L
Which Form Occurs in Water ?
Glycine Acid/Base Titration
Compare Amino Acids to Simple Carboxylic Acids
and Amines
Glutamate has 3 pKa’s
Histidine has 3 pKa’s
How to Calculate the pI When the Side Chain
is Ionizable
• Identify species that carries a net zero charge
• Identify pKa value that defines the acid strength of this
zwitterion: (pK2)
• Identify pKa value that defines the base strength of this
zwitterion: (pK1)
• Take the average of these two pKa values
What is the pI of histidine?
Peptide Bond Formation
Where does this occur?
Where does this occur?
Structure of a Simple Peptide
Ser-Gly-Tyr-Ala-Leu or SGYAL
Naming peptides:
start at the N-terminus
• Using full amino acid names
– Serylglycyltyrosylalanylleucine
• Using the three-letter code abbreviation
– Ser-Gly-Tyr-Ala-Leu
• For longer peptides (like proteins) the oneletter code can be used
– SGYAL
AEGK
Aspartame
A
Peptides: A Variety of Functions
• Hormones and pheromones
– insulin (think sugar)
– oxytocin (think childbirth)
– sex-peptide (think fruit fly mating)
• Neuropeptides
– substance P (pain mediator)
• Antibiotics
– polymyxin B (for Gram – bacteria)
– bacitracin (for Gram + bacteria)
• Protection, e.g., toxins
– amanitin (mushrooms)
– conotoxin (cone snails)
– chlorotoxin (scorpions)
Proteins are:
• Polypeptides (covalently linked -amino acids) + possibly:
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cofactors
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coenzymes
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functional non-amino acid component
metal ions or organic molecules
organic cofactors
NAD+ in lactate dehydrogenase
prosthetic groups
 covalently attached cofactors
 heme in myoglobin
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other modifications
Things to Know and Do Before Class
1. Know Structure and chemistry of all 20 amino acids.
2. Approximate pKa of amino acid ionizable groups and their
ionization state at different pH’s.
3. Modifications of amino acids in proteins.
4. Disulfide bonds, make and break them, and diagram
them.
5. The Peptide bond, make and break it, and diagram them.
6. EOC Problems 1, 2, 3a, 4-7: we will have problems to
solve (clicker questions) in class like these. Please
practice these well before class.