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)

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

Free amino acids are zwitterions

Mirror images

Handedness of amino acids

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!

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®)

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

+ 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)

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

• 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

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

pKR = 10.5 pKR = 12.5 pKR = 6.0

Resonance stabilized N lone pair in double bond, therefore pKa is lower.

pK1 = 1.82

H

pKR = 6.0 pK2 = 9.17

2

Histidine titration

+2 +1 0 -1

pKR = 3.7 pKR = 4.3