Amino%20Acids,%20Peptides%20and%20Proteins

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Amino Acids, Peptides and Proteins
Chapter 3 Part 1
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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 pHs.
• To know the general pKas of amino acids their
  carboxyls, aminos, the R-group weak acids.

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Proteins Enzymes, Binding Proteins, Structural
Proteins all made from Amino Acids
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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
• Capacity to polymerize
• Useful acid-base properties
• Varied physical properties
• Varied chemical functionality

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Amino acids share many features, differing only
at the R substituent
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L and D forms
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Carbon Numbering System
A
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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)

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Invented the One Letter Amino Acid Code.
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Spectrophotometry
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UV light Absorption by Proteins due to 2 Amino
Acids
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Cysteine can form Disulfide Bonds
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Uncommon Amino Acids
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Amino acids in Proteins Can be Reversibly Modified
A
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Non Protein Amino Acids
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Toxic Amino Acids
A search for compounds producing Yunnan Sudden
Unexplained Deaths found related to eating a
mushroom.
Halford, B. CE News Feb 13, 2012
Trogia venenata Zhu L
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Which Form Occurs in Water ?
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Glycine Acid/Base Titration
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Compare Amino Acids to Simple Carboxylic Acids
and Amines
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Glutamate has 3 pKas
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Histidine has 3 pKas
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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?

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Peptide Bond Formation
Where does this occur?
Where does
this occur?
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Structure of a Simple Peptide
Ser-Gly-Tyr-Ala-Leu or SGYAL
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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 one-
  letter code can be used
• SGYAL

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AEGK
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Aspartame
A
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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)

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Proteins are

• Polypeptides (covalently linked ?-amino acids)
  possibly
• cofactors
• functional non-amino acid component
• metal ions or organic molecules
• coenzymes
• organic cofactors
• NAD in lactate dehydrogenase
• prosthetic groups
• covalently attached cofactors
• heme in myoglobin
• other modifications

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Sample Written Exercise - Choose One

1. You have a solution of tyrosine. You decided to
   modify Y by methylation of the carboxyl, explain
   how this would change the acid-base titration of
   this molecule.
2. You have a solution of tyrosine. You decided to
   modify Y by methylation of the alcohol, explain
   how this would change the acid-base titration of
   this molecule.
3. You have an 28 amino acid long peptide that
   contains three cysteines. Explain why when
   examining the structure of this peptide the same
   two cysteines were involved in a disulfide bond,
   but not the other one.

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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 pHs.
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.