Lecture 3: Amino Acids

• Friday, January 14 th

• Reading assignment: Chapter 3

• Overview
- introduction to protein function
- chemical structure of amino acids; chirality
- types of amino acids: non-polar, polar uncharged, charged
- ionization of amino acids
- peptide bonds
 Protein Terminology

• Proteins are made up of one or more polypeptides

- polymers of amino acids
- linked by peptide bonds
• Polypeptides of fewer than 50 amino acids are called
“peptides”
• Some proteins also contain non-amino acid parts called
“prosthetic groups”
- covalently or noncovalently bound to polypeptide
 Protein Populations

• Number of possible proteins in an organism:

- determined by the number of genes
• E. coli: 6000
• yeast: 12,000
• humans: 25,000
• plants: 25,000
• Number of proteins per cell
- subsets from the total possible
- approximately 5,000 in eukaryotic cells
• Differential gene expression
- expression of a gene results in presence of a polypeptide
 Protein Functions

• Structural proteins
- cell architecture
- physical movements
• Transporters and carriers of small molecules
- passage across membranes
• Enzymes - reaction catalysts
• Protection
- antibodies or toxins
- detoxification
• Signal detection and transmission
• Nitrogen storage
 Amino Acid Structure (i)

• Twenty different amino acids in proteins

- these are the standard amino acids
• General structure
- central α carbon (usually chiral) bound to:
• amino group
• carboxylic acid group
• hydrogen atom
• one of 20 different R groups
• R group chemical properties vary
• Amino and carboxyl groups are ions at pH 7
Amino Acid Structure (ii)
 Amino Acid Chirality

• Four different constituents on α carbon

- enantiomers
• referred to as D and L
- glycine is exception because R group is a second hydrogen
• Almost all amino acids in biomolecules are L
Amino Acid
Chirality
 R-group Properties: Hydrophobic

• Non-polar (hydrophobic)
- neutral at pH 7
- aliphatic
• glycine, alanine, valine, leucine, isoleucine, proline, methionine
- aromatic
• phenylalanine,
tryptophan
R-group Properties: Hydrophobic
R-group Properties: Hydrophobic
R-group Properties: Polar, Uncharged, Hydrophilic

• Neutral at pH 7
- aliphatic
• threonine, serine, asparagine, glutamine, cysteine
- aromatic
• tyrosine
R-group Properties: Polar, Uncharged, Hydrophilic
 R-group Properties: Charged, Hydrophilic

• Negative at pH 7 (acidic)
- aspartate, glutamate
 R-group Properties: Charged, Hydrophilic

• Positive at pH 7 (acidic)
- lysine, arginine, histidine
- histidine is special case
• can be positive
or neutral
 Ionization Of Amino Acids

• Amino acids two or three ionizable groups

- both an acid and a base
• acid: the α carboxyl group; pK = ~2
a

• base: the α amino group; pK = ~9.5

a

• zwitterions at pH 7
• Some R groups also can accept or donate H+
- acids
• Asp, Glu
- bases
• Lys, Arg, His
Ionization Of Amino and Carboxyl Groups
Ionization Of Amino Acids
 Ionic States of Aspartic Acid

high pH, low [H+],

fully dissociated

low pH, high [H+],

fully protonated
pKa for Functional Groups in Proteins
pKa for Functional Groups in Proteins
 Titration Of Amino Acids

• Two or three inflection points

• Isoelectric point (pI)
- pH at which the net charge is 0
 Ionization of Histidine

• pKa of the imidizole nitrogen near physiological pH

• Both protonated and dissociated form can be present in
significant proportions
- they can convert back and forth
- important as a proton acceptor/donor in many catalytic mechanisms
 Non-protein Functions of Amino Acids

• Metabolic intermediates used to produce:

- neurotransmitters:
• GABA, serotonin
- synthesis of nucleic acid bases, heme,
chlorophyll
- nitrogen excretion cycle
• citrulline, ornithine
- hormones
• indole acetic acid
 Essential Amino Acids

• Nine amino acids cannot be synthesized by humans

- must be acquired in the diet