Proteins

1. Proteins Dr Una Fairbrother

2. Dipeptides • Two amino acids are combined as in the diagram, to form a dipeptide. • Water is the other product

3. Peptides • Peptides are normally written with the terminal amino group (N-terminal) to the left and the carboxyl group (C-terminal) to the right.

4. Polypeptides • Continued formation of peptide bonds extends the molecule to many amino acids linked by peptide bonds. • Polymers of amino acids called POLYPEPTIDES • Individual units of the polypeptide are called amino acid RESIDUES • Can estimate the no. of amino acid residues in a polypeptide or protein by its molecular weight (Mr). • Assume the mean Mr of an amino acid residue is 110 dalton

5. Protein Structure or Hierarchy • Protein structure is considered at different levels. • Primary • Secondary • Tertiary • Quaternary

6. Primary structure • Describes the unique sequence of amino acids which make up the polypeptide(s). • i.e a bead necklace where each different coloured bead represents an amino acid. • The beads can be arranged in any order or have any frequency

7. Secondary structure • is content of regular or repeating structures i.e. a helix and b pleated sheets. • For the a helix consider the bead necklace twisted into a coil. • The nature and structure of the a helix was elucidated by Linus Pauling and Robert Corey using X-ray diffraction analysis and some simple chemical rules. • polypeptide chain follows a coiled path

8. X ray diffraction • a-keratin - wool • b- keratin - silk a b

9. a helix • Thermodyamically favoured structure - the preferred and thus most stable structure of a polypeptide in the absence of interactions • Stabilised by H-bonding between the carbonyl oxygen and amino hydrogen of the peptide linkages. • Each linkage is H-bonded to 2 other linkages • one three units ahead and one three units behind. • The H-bonds are approximately parallel to the long axis of the helix.

10. Alpha helix • Each turn has 3.6 amino acid residues • Each turn extends 5.4Å along the long axis • Hydrogen bonds • are between every fourth amino acid residue • lie parallel to the long axis • occur between carbonyl oxygens and amino hydrogens within different peptide linkages

11. Helices and other structures • If a protein contains long stretches of a helix it will be semi-rigid and fibrous. • E.g a keratin found in hair and horn • Silk or b-Keratin,excreted by the caterpillar of the silk moth. • A polypeptide of glycine, alanine, and smaller amounts of other amino acids called fibroin • b-Keratin molecules do not form a helix • they lie on top of each other to give ridged sheets of linked amino acids, with glycine appearing on only one side of the sheets. • The sheets then stack one on top of the other. This planar structure is felt when you touch the smooth surface of silk.

12. b pleated sheets • Polypeptide extended, not coiled • polypeptide regions may come to lie alongside each other. • These regions stabilised by H-bonds between the polypeptide regions. • Here, H-bonds are roughly at right-angles to the long axis of the polypeptide chain in contrast to the a helix.

13. b pleated sheet types

14. Globular proteins • Contain only short regions of a helix • No systematic structures. • single chains, • two or more chains which interact in the usual ways • portions of the chains with: helical structures, pleated structures, or completely random structures. • Relatively spherical in shape • Common globular proteins include • egg albumin, hemoglobin, myoglobin, insulin, serum globulins in blood, and many enzymes.

15. Globular proteins and Proline (a) • (a)Regions can be lined up • as parallel (N C to N C) or • antiparallel (N C to C N) • Proline forces the chain to kink and does not allow the a helix to continue • it is a helix breaker residue. • often found in globular proteins at the end of regular sequences where the polypeptide chain bends back on itself. • (b) proline in green and glycine in yellow. • the side chain of proline forms a ring attached to the amino N atom (in blue). • The N atom has no hydrogen so can't act as an H bond donor. • This "breaks the chain" of H-bonds in helix (b)

16. Tertiary Structure • Describes the superfolding of the polypeptide. • The resultant structure contains regular regions of secondary structure • It is stabilised by a range of different interactions or bonds.

17. Bonds in tertiary structure • Hydrogen bonding • is between side chains of the amino acid residues (compare with H-bonding in secondary structure which is between peptide linkages) • Ionic bonds • between oppositely charged side chains (eg positively charged lysine residues and negatively charged glutamic acid residues). • Hydrophobic interactions • between the hydrocarbon side chains in phenylalanine, leucine, isoleucine and valine. • Disulphide bridges • between cysteine residues, these are covalent and more difficult to break.

18. Hexokinase • An example of a protein showing -helices, -structure and connecting loops • Hexokinase phosphorylates glucose

19. Bonds and denaturing agents

20. Quaternary structure • (a) the association of individual polypeptide subunits into a multi-subunit or multimeric protein. • Polypeptides with surface regions of hydrophobic amino acids will tend to associate in order to bring those patches together and reduce interactions with water. (b) Hexokinase, domain 1 and 2

21. What stabilises quaternary structure? • Hydrophobic bonding • Ionic bonding • Hydrogen bonding • unlike tertiary structure there is no covalent bonding such as would be obtained with -S-S- bridges

22. Summary