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Marlou Snelleman 2011

Proteins and amino acids. Marlou Snelleman 2011. Overview. Proteins Primary structure Secondary structure Tertiary structure Quaternary structure Amino acids Building blocks of proteins Properties. Proteins. Primary structure The sequence Secondary structure α -helices β -strands

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Marlou Snelleman 2011

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  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…

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