1. Proteins Dr Una Fairbrother

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

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

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

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

7. Secondary structure  is content of regular or repeating structures i.e.  helix and  pleated sheets.  For the  helix consider the bead necklace twisted into a coil.  The nature and structure of the  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   keratin - wool u b- keratin - silk ab

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

10. Alpha helix u Each turn has 3.6 amino acid residues  Each turn extends 5.4Å along the long axis u Hydrogen bonds u are between every fourth amino acid residue u lie parallel to the long axis  occur between carbonyl oxygens and amino hydrogens within different peptide linkages 10Å = 1nm

11. Helices and other structures u If a protein contains long stretches of  helix it will be semi-rigid and fibrous. u E.g  keratin found in hair and horn  Silk or  -Keratin,excreted by the caterpillar of the silk moth. u A polypeptide of glycine, alanine, and smaller amounts of other amino acids called fibroin   -Keratin molecules do not form a helix u 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. u The sheets then stack one on top of the other. This planar structure is felt when you touch the smooth surface of silk.

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

13.  pleated sheet types

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

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

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

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

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

19. Bonds and denaturing agents

20. Quaternary structure u (a) the association of individual polypeptide subunits into a multi- subunit or multimeric protein. u 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? u Hydrophobic bonding u Ionic bonding u Hydrogen bonding u unlike tertiary structure there is no covalent bonding such as would be obtained with -S-S- bridges

22. Summary