Transcript No Slide Title

Bio 98 - Lecture 3
Amino acids &
the peptide bond
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
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)
Two examples of amino acids
-amino
+ 
-carboxyl
O
H3N-CH-C-O
 CH2
CH2
-carboxyl O C
Oglutamate
glutamic acid
Glu, E
O
+
H3N-CH-C-OCH3
side
chains
alanine
Ala, A
Free amino acids are zwitterions
Handedness of amino acids
Mirror images
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!
Structure of a dipeptide
O
O
+
H3N-CH-C-NH-CH-C-O CH3
CH2
CH2
OC
peptide bond
O
aspartyl-phenylalanine-methyl ester
aka aspartame (Nutrasweet®)
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
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
3. Protein (continued)
• most proteins have a molecular weight in the
range of ~20,000 - ~80,000 Da
Left-to-right convention
F-G-A-V-S
amino or
N terminus
O
+
H3N-Phe-Gly-Ala-Val-Ser-C-O
carboxyl or
C terminus
Zwitterion at pH 7 (formal charges cancel)
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
Estimating molecular weight of polypeptides
• 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 protein
150 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).
OVERVIEW OF
AMINO ACID STRUCTURES
AND FUNCTION
pKR = 8.2
Cysteines can form disulfide bonds
insulin
Insulin processing
insulin
pKR = 10.0
Absorb UV light - used to determine [protein]
Positively charged R groups
Resonance
stabilized N
lone pair in
double bond,
therefore pKa
is lower.
pKR = 10.5
pKR = 12.5
pKR = 6.0
Histidine titration
H
2
pK1 = 1.82
+2
pK2 = 9.17
pKR = 6.0
+1
0
-1
pKR = 3.7
pKR = 4.3