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Bio 98 - Lecture 3
Amino acids &
the peptide bond
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The 20 common amino acids
1. Building blocks of all proteins• proteins are linear heteropolymers of AAs• same 20 AA used in all life forms on earth
2. Other uses • neurotransmitters• metabolic energy• precursors to other molecules
3. Essential vs. non-essential• some bacteria are able to synthesize all
20 • humans can synthesize only 11 of the 20, the other 9 are essential in our diet
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Structures and properties of amino acids
1. Structures• memorizing “groups” will help (see next slide)
2. Properties • abbreviations, pKa values, mass, pI (see last
slide)
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H3N-CH-C-O-
CH2
CH2
O C O-
Two examples of amino acids
+
O
H3N-CH-C-O-
CH3
+O
side chains
-amino-carboxyl
-carboxyl
glutamate glutamic acid
Glu, E
alanineAla, A
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Free amino acids are zwitterions
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Mirror images
Handedness of amino acids
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Peptide bond formation
Sneak preview to Bio99:This reaction is catalyzed by the rRNA (ribozyme!) of the large subunit of the ribosome at a rate of about 15 per second!
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peptide bond
Structure of a dipeptide
NH-CH-C-O CH2
H3N-CH-C- CH2 O C O
+O O
CH3
aspartyl-phenylalanine-methyl ester aka aspartame (Nutrasweet®)
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Polypeptides
Useful terms
1. Oligopeptide - a peptide of few amino acids• dipeptide: RF (Arg-Phe)• tripeptide: YES (Tyr-Glu-Ser)• tetrapeptide: HELP (His-Glu-Leu-Pro)
2. Polypeptide – many amino aids, no formal definition with regard to size
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3. Protein (applicable when mol wt > ~10,000 Da)
• cytochrome c (mitochondrial protein) 104 amino acids, mol wt 13,000 Da or 13 kDa• titin (structural protein in muscle) 34,350 amino acids, mol wt 2,993,000 Da or 3 MDa empirical chemical formula C132,983H211,861N36,149O40,883S693
http://en.wikipedia.org/wiki/Titin
As the largest known protein, titin also has the longest IUPAC name. The full chemical name, which starts with methionyl... and ends in ...isoleucine, contains 189,819 letters and is sometimes stated to be the longest word in the English language.
1 mole of titin would weigh 3 metric tons (~1 elephant)!Compare: 1 mole of H2O weighs 18 grams
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3. Protein (continued)
• most proteins have a molecular weight in the range of ~20,000 - ~80,000 Da
Left-to-right convention
+ OH3N-Phe-Gly-Ala-Val-Ser-C-O-amino or
N terminuscarboxyl or C terminus
F-G-A-V-S
Zwitterion at pH 7 (formal charges cancel)
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Molecular weight calculations
Molecular weight• free amino acid vs amino acid residue in
protein Glu Ala-Glu-Phe-Gly
147.18 Da 129.12 Da
• amino acid residue masses are 18 mass units (Da) less than the free amino acid
• each peptide bond eliminates one H2O
• the molecular weight of a peptide/protein = sum of all residue masses + 18 Da
• the molecular weight of a peptide/protein = sum of all free AA masses - (NAA-1) * 18 Da
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• average residue mass of the 20 AAs = 118.9 Da / AA
• for a protein of typical composition, average residue mass is ~110 Da, because some amino acids occur more frequently than others in proteins
• so to estimate the mass of a 150 AA protein150 x 110 Da = 16,500 Da = 16.5 kDa
For our “monster” protein titin (34,340 residues) this would predict 3.7 MDa (about 0.7 MDa too high).
Estimating molecular weight of polypeptides
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OVERVIEW OF
AMINO ACID STRUCTURES
AND FUNCTION
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pKR = 8.2
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Cysteines can form disulfide bonds
insulin
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Insulin processing
insulin
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pKR = 10.0
Absorb UV light - used to determine [protein]
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Positively charged R groups
pKR = 10.5 pKR = 12.5 pKR = 6.0
Resonance stabilized N lone pair in double bond, therefore pKa is lower.
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pK1 = 1.82
H
pKR = 6.0 pK2 = 9.17
2
Histidine titration
+2 +1 0 -1
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pKR = 3.7 pKR = 4.3
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