1. 1 10/26/2015 MOLECULES

2. 2 10/26/2015 H 2 N-CH-C-OH O R Monomer E.g. protein Monomer vs polymer amino acid monomer R is a side group

3. 3 10/26/2015 H 2 N-CH-C-OH O The 20 amino acids found in proteins each have different side chains, R R R R R R

4. 4 10/26/2015 Each amino acid has at least one carboxyl group X C O OH At cell pH, the carboxyls dissociate to form carboxylate ions C O OH X +H + C O O X

5. 5 10/26/2015 Proteins are the working language of biology The 20 amino acids found in proteins are the alphabet Let's start with the letter A A Alanine, Ala, A All the common amino acids have 3-letter and 1-letter abbreviations

6. 6 10/26/2015 CH H 3 N R Note asymmetry around the  carbon (all 4 side groups are different) Most amino acids have D- and L- isomers* *But only L-amino acids are present in typical proteins C OO

7. 7 10/26/2015 Glycine, Gly, G is unusual R group is a second H-atom Hence, no asymmetry round CH H 3 N  carbon C OO No L- and D- isomers H

8. 8 10/26/2015 Classes of amino acid R-groups CH H 3 N C OO R group Polar, uncharged CH 2 OH e.g. Serine, Ser, S

9. 9 10/26/2015 Classes of amino acid R-groups CH H 3 N C OO R group* is negatively charged CH 2 e.g. Aspartic acid, Asp, D COO *An additional -COO - group

10. 10 10/26/2015 Classes of amino acid R-groups CH H 3 N C OO R group positively charged (CH 2 ) 4 e.g. Lysine, Lys, K NH 3

11. 11 10/26/2015 CH H 3 N C OO R group hydrophobic CH 3 e.g. Alanine, Ala, A CH H 3 N C OO CH 2 OH Tyrosine, Tyr, Y

12. 12 10/26/2015 Glycine, Gly, G (mentioned before) The "baby" (smallest) of the amino acids No special hydrophilic or hydrophobic character CH H 3 N C OO H "Special" amino acids

13. 13 10/26/2015 CH H 3 N C OO "Special" amino acids CH 2 SH Cysteine, Cys, C Important in forming disulfide (S-S) crosslinks within a protein

14. 14 10/26/2015 -S-S- A protein with two disulfide bonds

15. 15 10/26/2015 CH 2 S H H S 2 C  C  of Cys of cysteine S CH 2 C  of cysteine CH 2 S C  of cysteine 2H DISULFIDE BOND

16. 16 10/26/2015 Special amino acids Proline. This amino acid produces a “kink” in a polypeptide COO H C CH 2 2 H 2 C HN Proline, Pro, P Pro is an imino acid (not, strictly speaking, an amino acid + H 3 N-

17. 17 10/26/2015 Forming a peptide bond between 2 amino acids R 2 C  C-O - O +H3N+H3N  + C   R 1 H 3 N + O C R 1 C  - O H 3 N +  C  R 2 - O N  H H20H20

18. 18 10/26/2015 C   R 1 H 3 N + O C C  R 2 C-O - O N  H A dipeptide. All peptides and proteins have: carboxyl end an amino end C-terminal N-terminal end and a

19. 19 10/26/2015 Polypeptide structure n Primary n Secondary n Tertiary n Quaternary

20. 20 10/26/2015 1. Primary structure n Amino acid sequence n Disulfide crosslinking within the polypeptide

21. 21 10/26/2015 1. Primary structure: portion of  -chain of human hemoglobin Val His Leu Thr ProGlu Glu Lys Tyr Arg bla bla bla bla bla 12 3 4 5 6 7 8 140 141 N-terminus C-terminus aa substitution; Val instead of Glu at position 6 is found in the disease sickle cell anemia

22. 22 10/26/2015 2. Secondary stucture of a protein n The folding of portions (domains) of the protein to form:  -helices  -pleated sheets

23. 23 10/26/2015 Secondary structure:  -helix 3.6 aa's per turn Hydrogen bonding

24. 24 10/26/2015 Secondary structure:  -pleated sheet Edge view    R R R R RR R  Polypeptide chains H-bond

25. 25 10/26/2015 n Overall folding of:  helices  -pleated sheets and – the regions between them 3. Tertiary structure of protein

26. 26 10/26/2015 4. Quaternary structure of protein Ordering of several different polypeptide strands to form a functional protein complex e.g. Hemoglobin    