Marlou Snelleman 2011

1. Proteins and amino acids MarlouSnelleman 2011

2. Overview • Proteins • Primary structure • Secondary structure • Tertiary structure • Quaternary structure • Amino acids • Building blocks of proteins • Properties

3. Proteins • Primary structure • The sequence • Secondary structure • α-helices • β-strands • Turns • Loops • Tertiary structure • Interactions between the secondary structure elements to form the structured protein • Quaternary structure • Dimers or multimers of proteins

4. Primary structure • Proteins are polymers • The monomers (residues) are amino acids • The sequence: • is the order of the amino acids in the protein • starts at the amino (N) terminus and ends at the carboxy (C) terminus • For example: Met-Val-Lys-Leu-Cys-Ala N C

5. Proteins • Primary structure • the sequence • Secondary structure • α-helices • β-strands • Turns • Loops • Tertiary structure • Interactions between the secondary structure elements to form the structured protein • Quaternary structure • Dimers or multimers of proteins

6. Secondary structure • The amino acids form four different secondary structure elements: • α-helices • β-strands • Turns • Loops

7. Secondary structure – α-helix N-terminus C-terminus

8. Secondary structure – β-strand • A β-sheet consists of at least two β-strands interact with each other Anti-parallel Parallel

9. Secondary structure – Turn • Turns connect the secondary structure elements

10. Secondary structure - Loop • A loop is everything that has no defined secondary structure

11. Proteins • Primary structure • the sequence • Secondary structure • α-helices • β-strands • Turns • Loops • Tertiary structure • Interactions between the secondary structure elements to form the structured protein • Quaternary structure • Dimers or multimers of proteins

12. Tertiary structure • The secondary structure elements interact to form the structured protein

13. Proteins • Primary structure • the sequence • Secondary structure • α-helices • β-strands • Turns • Loops • Tertiary structure • Interactions between the secondary structure elements to form the structured protein • Quaternary structure • Dimers or multimers of proteins

14. Quaternary structure • Some proteins can interact with each other to form dimers or multimers

15. Amino acids • The (secondary and tertiary) structure of the protein depends on • the primary structure • and therefore on the sequence • and therefore on the amino acids • When you understand the amino acids, you understand everything!

16. Amino acids – Structure • Every amino acid has the same basic structure: the backbone with • an amino group • an Cα • an carboxyl group α α “Textbook picture” In the cytosol (water)

17. Amino acids – Structure • The Cα is bound to an R group: the side chain • different for each amino acid • the atoms are labeled δ β ζ α ε γ

18. Amino acids – Peptide bond • The amino acids can make polymers via peptide bonds

19. Amino acids – Codes • There are 20 different amino acids

20. Amino acids – Properties • Each side chain has different structural and chemical properties • Hydrophobicity • Electric charge • Size • Sulfur containing • Rigidity • Secondary structure preference • Polar • Alcoholic • Aliphatic • Aromatic • Etc.

21. Amino acids – Properties • Amino acids are not easily put into boxes according to their properties • Every amino acid belongsto several categories • Every amino acid is unique

22. Amino acids – Hydrophobicity • Hydro = water; phobe = fear; phile = love • Some amino acids like to stick into water (hydrophile) • Asp, Glu, His, Lys, Asn, Gln, Arg • Some amino acids like to stick to each other (hydrophobe) • Ala, Cys, Phe, Ile, Leu, Met, Pro, Val, Trp • And some are inbetween • Gly, Ser, Thr, Tyr

23. Amino acids – Hydrophobicity • Hydrophobicity is the most important property • It drives the folding of a protein • The sticky amino acids glue together • The non-sticky amino acids point to the water • The waters must be ‘happy’

24. Amino acids - Hydrophobicity (Not scaled!!!)

25. Amino acids – Electric charge • Some amino acids carry a charge • Positive: Lys, Arg • Negative: Asp, Glu • Positive, neutral and negative: His • Depending on the environment Lys Arg His Glu Asp

26. Amino acids – Size • Small amino acids • Ala, Cys, Gly, Pro, Ser, Thr, Val • Smallest: Gly • Inbetween • Asp, Ile, Leu, Asn • Large amino acids • Glu, Phe, Lys, Gln, Arg, Trp, Tyr • Largest: Trp Gly Trp

27. Amino acids – Sulfur containing • Cys and Met contain sulfur • The sulfur of Cys is very reactive • can make sulfur bridges with other cysteines Cys Met Sulfur bridge

28. Amino acids – Rigidity • Especially rigid • Pro: an imino acid • Especially flexible • Gly: no side chain • Rigid guanidinium group • Arg Pro Arg • Flexible side chain • Lys Gly Lys

29. Amino acids – Secondary structure preference • Most amino acids have a secondary structure preference for • helices • strands • or turns

30. Amino acids – Secondary structure preference • Residues that are good for a helix • Ala, Met, Glu, Leu, Lys (AMELK) • Residues that are good for strands • Val, Ile, Thr, Trp, Tyr, Phe (VITWYF) • Residues that are good for turns • Pro, Ser, Asp, Asn, Gly (PSDNG)

31. It is all about amino acids MVKLCA…