1. Bio 98 - Lecture 3 Amino acids & the peptide bond

2. 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 diet9 are essential in our diet

3. Structures and properties of amino acids 1.Structures memorizing “groups” will help (see next slide) 2. Properties abbreviations, pK a values, mass, pI (see last slide)

5. H 3 N-CH-C-O - CH 2 O C O - Two examples of amino acids +    O H 3 N-CH-C-O - CH 3 + O side chains  -amino  -carboxyl  -carboxyl glutamate glutamic acid Glu, E alanine Ala, A

6. Free amino acids are zwitterions

7. Mirror images Handedness of amino acids

8. 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!

9. peptide bond Structure of a dipeptide NH-CH-C-O CH 2 H 3 N-CH-C- CH 2 O C O + O O CH 3 aspartyl-phenylalanine-methyl ester aka aspartame (Nutrasweet ® )

10. 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

11. 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 MDa34,350 amino acids empirical chemical formula C 132,983 H 211,861 N 36,149 O 40,883 S 693 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 H 2 O weighs 18 grams

12. 3. Protein (continued) most proteins have a molecular weight in the range of ~20,000 - ~80,000 Da Left-to-right convention + O H 3 N-Phe-Gly-Ala-Val-Ser-C-O - amino or N terminus carboxyl or C terminus F-G-A-V-S Zwitterion at pH 7 (formal charges cancel)

13. 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 H 2 O 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 - (N AA -1) * 18 Da

14. 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). Estimating molecular weight of polypeptides

15. OVERVIEW OF AMINO ACID STRUCTURES AND FUNCTION

17. pK R = 8.2

18. Cysteines can form disulfide bonds insulin

19. Insulin processing insulin

20. pK R = 10.0 Absorb UV light - used to determine [protein]

21. Positively charged R groups pK R = 10.5pK R = 12.5pK R = 6.0 Resonance stabilized N lone pair in double bond, therefore pK a is lower.

22. pK 1 = 1.82 H pK R = 6.0 pK 2 = 9.17 2 Histidine titration +2 +1 0 -1

23. pK R = 3.7 pK R = 4.3