Understanding Amino Acids: The Building Blocks of Proteins

1. MOLECULES

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

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

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

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

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

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

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

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

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

11. R group hydrophobic C O O C O O C H H N C H H N 3 3 CH CH 3 2 e.g. Alanine, Ala, A OH Tyrosine, Tyr, Y

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

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

14. A protein with two disulfide bonds -S-S-

15. C  of Cys DISULFIDE BOND CH C  of cysteine 2 S CH H 2 S H S 2H S CH 2 CH 2 of cysteine C  of cysteine C 

16. COO +H3N- Special amino acids Proline. This amino acid produces a “kink” in a polypeptide H Proline, Pro, P C CH HN 2 CH H C 2 2 • Pro is an imino acid (not, strictly speaking, • an amino acid

17. O - + C-O H N 3 O - + H N C-O 3 Forming a peptide bond between 2 amino acids  O  - C +H3N C C-O  +  R R 2 1 H20  O  C C C N   H R R 2 1

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

19. Polypeptide structure • Primary • Secondary • Tertiary • Quaternary

20. 1. Primary structure • Amino acid sequence • Disulfide crosslinking within the polypeptide

21. 1. Primary structure: portion of -chain of human hemoglobin N-terminus Glu Lys Val His Leu Thr Pro Glu 3 1 2 5 7 6 4 8 bla bla bla bla bla bla bla bla Tyr Arg bla bla 140 141 C-terminus aa substitution; Val instead of Glu at position 6 is found in the disease sickle cell anemia

22. 2. Secondary stucture of a protein • The folding of portions (domains) of the protein to form: • -helices • -pleated sheets

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

24. Secondary structure: -pleated sheet R R R Edge view R R R R Polypeptide chains     H-bond

25. 3. Tertiary structure of protein • Overall folding of: •  helices • -pleated sheets and • the regions between them

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