5. Protein structure and function and amino.pptx

proteins and the amino acids

1. Protein Structure and Function A guide by: Thomas Marangwana [email protected] [phone] University of Zimbabwe Department of Biochemistry and Biotechnology, Room 146

2. P r o t eins Proteins are the most abundant organic molecules of the living system. They constitute about 50% of the cellular dry weight. They constitute the fundamental basis of structure and function of life. In 1839, Dutch chemist G.J. Mulder was first to describe about proteins. The term protein is derived from a Greek word proteios, meaning first place. The proteins are nitrogenous macromolecules that are composed of many amino acids.

3. Peptide formation Carboxyl group of one amino acid (with side chain R1) forms a covalent peptide bond with α - amino group of another amino acid (with side chain R2) by removal of a water molecule. The result is : Dipeptide. The dipeptide can then form a second peptide bond with a third amino acid (with side chain R3) to give tripeptide. Repetition of this process generates a polypeptide or protein of specific aminoacid sequence.

4. Peptide formation

5. Structure of proteins Proteins have different levels of organisation Primary Structure Secondary Structure Tertiary Structure Quaternary Structure

6. Structure of proteins

7. Forces that determine the structure Primary structure: determined by covalent bonds Secondary structure: determined by weak forces

8. Protein structures

9. 1. Primary Structure The primary structure of protein refers to the sequence of amino acids present in the polypeptide chain, it contains all the information necessary to make a protein . Amino acids are covalently linked by peptide bonds or covalent bonds . Each component amino acid in a polypeptide is called a "residue” or “moiety ”.

10. 1. Primary Structure By convention the primary structure of protein starts from the amino terminal (N) end and ends in the carboxyl terminal (C) end.

11. 2. Secondary structure It is a local, regularly occurring structure in proteins and is mainly formed through hydrogen bonds between backbone atoms . Pauling & Corey studied the secondary structures and proposed 2 conformations i.e ., α helix β sheets

12. 2. Secondary structure

13. α -Helices The a-helix is a rod like structure. It is one peptide chain which is coiled so that adjacent residues are 1.5A apart . There are H-bonds between the N-H and the C=O groups of the backbone. These link the peptide bonds between every fourth amino acids . The side chains all extend outwards from the helix .

14. α -Helices Although the helix itself is quite a rigid structure, it can be curved or kinked, which lends some flexibility to the protein structure . Two or more polypeptides can entwine to form very long, very stable, structures called α -helical coiled coils . These are often found in keratin (hair), myosin (muscle), epidermin (skin), and fibrin (blood clots).

15. α -Helices Right handed spiral structure . Side chain extend outwards . Stabilized by H bonding that are arranged such that the peptide Carbonyl oxygen (nth residue) bonds with amide hydrogen (n+4 th residue ).

16. α -Helices Amino acids per turn – 3.6 Pitch is 5.4 A ° Alpha helical segments, are found in many globular proteins like myoglobin Length ~12 residues and ~3 helical turns. phi = -60 degrees, psi = -45 degrees

17. α -Helices

18. β -Sheets A polypeptide in a β -sheet is called a β -strand, and is almost fully extended (not coiled) so there is 3.5A between adjacent residues. Formed when 2 or more polypeptides line up side by side. The β -strands in a sheet can either run in the same (parallel) or different (anti-parallel) direction. They are stabilized by hydrogen bond between NH and carbonyl groups of adjacent chains.

19. β -Sheets

20. β -Sheets β sheets come in two varieties . Antiparallel β sheet – neighboring hydrogen bonded polypeptide chains run in opposite direction . Parallel β sheet - hydrogen bonded chains extend in the same direction.

21. β -Sheets

22. Protein folding The peptide bond allows for rotation around it and therefore the protein can fold and orient the R groups in favorable positions . Weak non-covalent interactions will hold the protein in its functional shape – these are weak and will take many to hold the shape . Protein folding occurs in the cytosol.

23. Protein folding

24. Protein folding patterns 2 regular folding patterns have been identified – formed between the bonds of the peptide backbone. α -helix – protein turns like a spiral – fibrous proteins (hair, nails, horns). β -sheet – protein folds back on itself as in a ribbon – globular protein.

25. Protein folding patterns

26. 3. Tertiary structure The tertiary structure defines the specific overall 3-D shape of the protein, how the peptide chain folds so that sidechains are packed and organized. Tertiary structure is stabilized by various types of interactions between the side-chains of the peptide chain. These interactions are: Disulfide bonds Hydrophobic interactions Hydrogen bonds Ionic interactions Vander Waals force

27. 3. Tertiary structure

28. 1. Disulphide Bonds If two cysteine side chains are close to one another and the local environment is conducive to oxidation, then they can form a disulphide bond/bridge. The residues can either be in the same peptide chain (forming a loop) or in different chains. They mainly occur in secreted proteins and in the parts of membrane proteins which face the outside. NB, disuphide bridges only form after the protein has folded into its tertiary structure.

29. 1. Disulphide Bonds

30. 2. Hydrophobic Interactions Close attraction of non-polar R groups through dispersion forces. They are non attractive interactions, but results from the inability of water to form hydrogen bonds with certain side chains. Very weak but collective interactions over large area stabilize structure. Repel polar and charged molecules/particles.

31. 2. Hydrophobic Interactions

32. 3. Hydrogen Bonds When unfolded, all polar/hydrophillic sidechains can interact via H-bonds with water. When the protein folds, they must H-bond to each other and exclude much of the water. All groups capable of forming a hydrogen bond MUST, hence H-bonding in the backbone (C=O to N-H) by way of helices and sheets is an efficient way of ensuring stability

33. 3. Hydrogen Bonds The capacity of proteins to form hydrogen bonds is an important determinant of protein stability . Hydrogen bonds can be between backbone groups, as in helices and sheets; between side chains, such as serine or threonine O-H groups and carbonyl carbons of side chains (-C=O); and between backbone groups and side chain groups.

34. 3. Hydrogen Bonds

35. 4. Ion Pairs When amino acid side chains of opposite charge are in close proximity, they can form an ion pair (also called a salt bridge). Since charge is affected by pH, so is the formation and the breakage of these ion pairs. Ions on R groups form salt bridges through ionic bonds. NH3 +and COO- areas of the protein attract and form ionic bonds.

36. 4. Ion Pairs

37. Non-Covalent Bonds Hydrophobic interactions, hydrogen bonds and salt bridges are all non-covalent interactions. These are all relatively weak interactions but the large number in a protein combine to give the overall stability of the structure. If these interactions are maintained the protein keeps its tertiary ("native") structure. However once the bonds maintaining the structure begin to be disrupted the tertiary structure is destroyed and the protein is said to be "denatured

38. I n t e r actions

39. Globular proteins Globular proteins fold up into compact, spherical shapes. Their functions include biosynthesis, transport and metabolism, eg, myoglobin is a globular protein that stores oxygen in the muscles. Myoglobin is a single peptide chain that is mostly α -helix – The O2 binding pocket is formed by a heme group and specific amino acid side-chains that are brought into position by the tertiary structure

40. Globular proteins

41. Fibrous proteins Fibrous proteins consist of long fibers and are mainly structural proteins, eg α -keratins are fibrous proteins that make hair, fur, nails and skin. hair is made of twined fibrils, which are braids of three α – helices (similar to the triple helix structure of collagen) the α -helices are held together by disulfide bonds. β -keratins are fibrous proteins found in feathers and scales that are made up mostly of β -pleated sheets

42. Fibrous proteins

43. Subunits and Quaternary Structure Proteins containing more than one polypeptide chain exhibit an additional level of structural organisation . In this case, each polypeptide chain is a "subunit". Quaternary (4D) structure describes the way the subunits are arranged together and the nature of their contacts . Subunits associate by non-covalent interactions similar to those involved in tertiary structure. .

44. Subunits and Quaternary Structure There are two kinds of quaternary structures: both are multisubunit proteins . Homodimer : association between identical polypeptide chains . Heterodimer : interactions between subunits of very different structures.

45. Subunits and Quaternary Structure

46. Subunits and Quaternary Structure Quaternary structure adds stability by decreasing the surface/volume ratio of smaller subunit Simplifies the construction of large complexes – viral capsids and proteosomes

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