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  1. 1. CHAPTER 2 Proteins • Protein function • Amino acids • Protein structure • Ligand binding sites
  2. 2. Protein function Learning Objectives – Give examples of the wide range of protein functions – Explain a common principle underlying most functions of proteins – Define the term: ligand
  3. 3. Protein function • Proteins are the first cellular macromolecules to be considered because they are so central to biochemistry. • Other macromolecules, while important in some biochemical processes, are generally synthesised, organised, controlled and regulated, packaged and eventually broken down by proteins.
  4. 4. Mechanical functions • Proteins are a major part of the mechanical system of our bodies. • Tendons made from collagen, a fibrous protein, are the inelastic ropes that allow our muscles, the protein motors, to move our bones. • Bones have some protein content, being made from collagen and a calcium phosphate mineral.
  5. 5. Energy production • Energy to drive the muscle motors is obtained from metabolic reactions catalysed by enzymes, which are proteins.
  6. 6. Oxygen carriage • Oxygen needed for metabolic reactions that generate energy is carried to our muscles and most other tissues by another protein, haemoglobin.
  7. 7. Regulatory signals • Signal proteins, notably the protein hormone insulin, regulate the concentrations of fuel molecules circulating to our muscles in our blood. • Insulin and many other hormones move in our blood between the glands that secret them and their target cells, where they are detected by protein receptors on the membrane.
  8. 8. Protein synthesis • Protein are responsible for many aspects of their own synthesis. • Nucleic acids, which provide the information for protein synthesis, are synthesised, packaged, regulated and repaired by proteins.
  9. 9. Proteins bind other molecules specifically • Protein molecules are able to recognise and bind other molecules very specifically and with great affinity. • This binding of other molecules occurs very rapidly and is often reversible. • The molecule that proteins bind are referred to as ligands. • A ligand is a small molecule or part of a large molecule that can occupy a binding site.
  10. 10. Examples of ligand binding in protein function • Protein involved in forming complex structures assemble by ligand binding. • Collagen molecules recognise and bind to other collagen molecules in a regular parallel array to form a fibre. • This initial assembly is followed by covalent crosslinking to form a more permanent structure and eventually a tendon.
  11. 11. Muscle • There are two principal proteins in muscle, myosin and thin filaments, respectively. • These filaments slide over each other as the muscle contracts or relaxes. • The interaction between the filaments enables the muscle to develop tension and to contract.
  12. 12. Enzymes • These catalytic proteins bind the molecules that participate in the reactions they catalyse, their substrates. • By binding two substrates in an orientation favorable for reaction, the rate of the reaction between them is greatly enhanced.
  13. 13. Carriage of oxygen • The haemoglobin which carries oxygen in our blood is formed from a protein, globin, which specifically binds an iron-containing organic group, haem. • Binding of the ham group to globin modifies the properties of haem so that it binds oxygen reversibly, a reaction not possible for haem on its own.
  14. 14. Nucleic acid function • The nucleic acids, particularly DNA, carry genetic information, information on the structures of our proteins. • Nucleic acid function needs the participation of protein molecules. • Enzymes copy DNA, so that after cell division each daughter cell contains an accurate copy of the DNA of the original cell.
  15. 15. Amino Acids Learning Objectives – Define and explain the following terms: amino acid, amino acid side chain, peptide bond, polypeptide chain, amino acid residue, N-terminal, C-terminal – Draw a general structure for (a) an amino acid and (b) a peptide bond
  16. 16. Amino Acids Proteins are polymers of amino acids. • The general structure of an amino acid: four groups are attached by covalent bonds to a single carbon atom, the alpha carbon. • Two of these groups, an amino group and an acidic carboxyl group, give their name to this class of compound and are also involved in forming the peptide bonds that join the amino acids into long peptide chains. •
  17. 17. Amino Acids The other two groups attached to the alpha carbon are a hydrogen atom, and a variable group, the socalled side chain. • It is the side chain that distinguishes one amino acid from another. • Amino acids are often shown as uncharged molecules. • In solutions with pH near neutrality, as in most physiological situations, the representation with charged amino and carboxyl groups is more accurate. •
  18. 18. Amino Acids • All proteins in animals, plants, bacteria and viruses are synthesised from the same set of 20 amino acids. • The side chains of these 20 amino acids contain a limited range of chemical groups.
  19. 19. Amino Acids • Aspartic acid and glutamic acid carry acid carboxyl groups on their side chains. Asp (D) Glu (E)
  20. 20. Amino Acids • Asparagine and glutamine are closely related to aspartic acid and glutamic acid, respectively; the side chain carboxyl groups are modified into uncharged hydrophilic amide groups. Asn (N) Gln (Q)
  21. 21. Amino Acids • Arginine, lysine and histidine carry basic functional groups. • Arginine and lysine side chains usually bind protons under physiological conditions and are positively charged. • The imidazole group of histidine can exist in a positively charged form (protonated). Arg (R) Lys (K) His (H)
  22. 22. Amino Acids • Valine, leucine and isoleucine have branched aliphatic hydrocarbon side chains, which are very hydrophobic. Val (V) Leu (L) Ile (I)
  23. 23. Amino Acids • Alanine has a methyl group as its side chain. • Glycine has a second hydrogen atom attached do its alpha carbon and can be considered to have no side chain. Ala (A) Gly (G)
  24. 24. Amino Acids • Cysteine and methionine are sulphur-containing amino acids. • Cysteine has a thiol or sulphydryl group on tis side chain. • Methionine has a methylated sulphur in its side chain. Cys (C) Met (M)
  25. 25. Amino Acids • Phenylalanine, tyrosine and tryptophan all have aromatic side chains. • Phenylalanine is very hydrophobic. • Tyrosine less so since its ring carries a phenolic hydroxyl group. • Trypophan, the largest amino acid, Phe (F) Tyr (Y) Trp (W)
  26. 26. Amino Acids • Proline is the only amino acid to have a secondary amino group, not a primary amino group like all the others. • The side chain of proline loops around to make a bond with the amino nitrogen atom, which, therefore, has two covalent bonds to carbon. • Sticktly speaking proline is an imino acid. Pro (P)
  27. 27. L-Amino acids • All of the amino acids except glycine are optically active, or chiral, having four different groups attached to the alpha carbon. • Proteins are composed of amino acids of the socalled L series. • Amino acids of the D series are very rarely found and never in proteins.
  28. 28. The peptide bond • • • Proteins are composed of amino acids joined by peptide bonds. Peptide bond formation involves the elimination of the elements of water between the alpha carboxyl group of one amino acid and the alpha amino group of another. The dipeptide that is produced has terminal amino and carboxyl groups which can participate in further peptide bonds to extend the chain.
  29. 29. The peptide bond • Side chain carboxyl and amino groups, on those amino acids that posses them, are never involved, so polypeptide chains are linear and never branched. • Polypeptide chain will still have an alpha amino group at one end, known as the N-terminal end, and an alpha carboxyl group at the other, the Cterminal end.
  30. 30. The peptide bond • Polypeptide chains typically contain between 50 and 5, 000 amino acid units. • The group of atoms belonging to each amino acid once it is combined in a peptide chain is known as an amino acid residue. • Many functional proteins contain more than one polypeptide chain.
  31. 31. N-terminal and C-terminal ends • Naming starts from the N-terminal end • Sequence is written as: Ala-Glu-Gly-Lys • Sometimes the oneletter code is used: AEGK (A) (E) (G ) (K)
  32. 32. Protein purification and characterisation Learning Objectives – Give examples of purified proteins that are used therapeutically – Describe the principles of protein electrophoresis – Give examples of the use of protein electrophoresis in clinical investigations
  33. 33. Protein purification and characterisation • Purification is also necessary for proteins used for therapeutic purpose, such as insulin used to treat diabetics and clotting factor VII used to treat haemophiliacs. • The methods depend on differences between the properties of protein molecules, such as: • ligand binding ability • size • solubility • stability • electric charge
  34. 34. Protein purification and characterisation • A single process can rarely achieve purification of a protein from a complex mixture. • Usually it is necessary to combine several purification techniques, each of which removes some of the unwanted components of the mixture while retaining the protein to be purified. • The ratio of the amount of the target protein to the amount of total protein is known as the specific activity.
  35. 35. Electrophoresis: separation of proteins by charge • • • Protein molecules carry electric charge because of their ionised amino acid side chains. The charge depend on the amino acid composition of the protein and also on pH. The charge on each molecule is generally positive at low pH values and falls as the pH increase, reaching zero at a defined pH for each protein, its isoelectric point (pI).
  36. 36. Ion-exchange chromatography: separation of proteins by charge • • • Proteins can be separated on the basis of their charge by ion-exchange chromatography. The chromatography material is a porous hydrophilic material, cellulose is often used, modified chemically to carry charged groups. Ion exchangers are available with either fixed positive or fixed negative charges.
  37. 37. Ion-exchange chromatography: separation of proteins by charge • When a mixture of proteins flows into the chromatographic column, protein molecules opposite in charge to the charge on the column are bound to the column. • Other proteins can be washed through.
  38. 38. Ion-exchange chromatography: separation of proteins by charge • Changing the pH or increasing the ionic strength of the eluting buffer changes the charge on some of the bound proteins and they will elute. • If the pH is gradually changed, a series of different proteins will emerge from the column depending on their isoelectric points.
  39. 39. Electrophoresis: separation of proteins by charge • The techniques of electrophoresis and isoelectric focusing also exploit the differences in charge between different proteins.
  40. 40. Electrophoresis: separation of proteins by charge • • • Electrophoresis is the movement of charged molecules in an electric field. Electrophoresis of protein is usually carried out in buffer solutions supported by a hydrophobic gel that is porous enough to allow protein molecules to penetrate. The rate at which proteins move through the gel depends on both their charge and their size.
  41. 41. Electrophoresis: separation of proteins by charge • Identical molecules will all move at the same rate so that a sample of purified protein will move as a single band. • This makes electrophoresis a valuable tool for establishing how many molecular species of protein a given protein preparation contains.
  42. 42. Electrophoresis: separation of proteins by charge • Isoelectric focusing is a variant of electrophoresis carried out on a gel that has been set up to contain a gradient of pH. • A protein molecule introduced to the gel will move in the electric field to a region where the pH matches its isoelectric point.
  43. 43. Electrophoresis: separation of proteins by charge • Electrophoresis is a powerful method for detecting the presence of isoenzymes, different molecular forms that have the same catalytic activity. • The identification of isoenzymes in plasma is an important diagnostic procedure.
  44. 44. Protein strtucture Learning Objectives – Define the following terms: amino acid composition, amino acid sequence – Explain the four different levels at which protein structure can be described – Describe the general features of the alpha helix and beta sheet as elements of secondary structure – Describe the role of disulphide bonds in some protein structure – Define the following terms: denaturation, protein subunits, domains
  45. 45. Amino acid composition • A count of the number of times each amino acid occurs in a given protein is known as the amino acid composition of the protein. • The protein molecule is first broken down into its constituent amino acids by cleavage of the peptide bonds.
  46. 46. Proteins have varying levels of structure • Proteins often lose their activity if heated; incubation for a few minutes at 60℃ to 70℃ is sufficient to inactivate many. • Exposure to cold dilute acids or bases inactivates the majority of proteins, and high concentrations of urea or solvents such as ethanol also inactivate them. • None of these treatments, which are said to denature the protein, would be expected to cleave peptide bonds or any other covalent bonds involved in protein structure.
  47. 47. Proteins have varying levels of structure • Some higher level of structure, destroyed by denaturation, must be necessary for protein function. • The structure of proteins can be considered at varying levels of complexity: • primary: amino acid sequence established by covalent peptide bonds • secondary: folding of the chains stabilised by hydrogen bonding between residues that are relatively close together • tertiary: longer range folding stabilised by interactions between side chains; various bonds including • quaternary: aggregates of more than one polypeptide chain, folded together and held by various types of bond.
  48. 48. Primary structure: amino acid sequence • There appears to be no restriction on the order in which amino acids can be joined in a protein; so, with 20 possibilities at every position in the sequence, there is clearly an enormous number of possible proteins. • The primary structure of a protein, the sequence in which amino acids are joined in a protein, makes that protein distinctive and leads to its further levels of structure, or shape, beyond sequence.
  49. 49. Primary structure: amino acid sequence • Small changes in sequence can lead to large changes in properties and functions. • Some inherited diseases are known to be caused by a change involving only one amino acid residue, a change that alters or destroys the function of the protein involved.
  50. 50. Primary structure: amino acid sequence • Information stored in a nucleic acid base sequence directs the machinery of protein synthesis in a cell to make the proteins appropriate for that cell. • Protein amino acid sequences can also be deduced from the base sequences of the nucleic acids that direct their synthesis. • Proteins carrying out similar functions and proteins having the same function in different species almost always have closely related primary structures.
  51. 51. Secondary structure • The folding of the chain of amino acid residues through hydrogen bonding between residues that are close together in the chain is known as the secondary structure of the protein. • Folding patterns such as the alpha helix, the beta sheet and the triple helix are examples of secondary structure.
  52. 52. The alpha helix • In the alpha helix, the backbone of the polypeptide chain is folded into a helix. • There are 3.6 residues per turn and the pitch of the helix is 0.54 nm, so each residue adds 0.15 nm to the length of the helix.
  53. 53. The alpha helix • For each residue, the amino hydrogen forms a bond to the carbonyl oxygen fourth earlier in the chain and the carbonyl oxygen forms a bond to a later amino hydrogen. • Folded in this way, the hydrogen-bonding capacity of the backbone peptide bonds can be completely satisfied within the helix and a stable structure results.
  54. 54. The alpha helix • The alpha helix is the predominant secondary structure of unstretched keratin, the fibrous protein of curl hair, skin and nails. • The alpha helix does not involve the amino acid side chains; these project from the helix.
  55. 55. Beta sheets • In the beta sheets, polypeptide chains are almost fully extended and run side by side so that hydrogen bonds can be formed between adjacent chains in the sheet. • Peptide chains in a beta sheet may be parallel or antiparallel.
  56. 56. Beta sheets
  57. 57. Beta sheets • Stretched keratin can assume the beta sheet structure. • Many globular proteins, for example immunoglobulins, contain sections of beta sheet or even barrel-like structures formed from a curved sheet.
  58. 58. The triple helix and collagen • The triple helix is found principally in collagen, the protein that makes the strong low-elasticity fibres of connective tissue. • Three polypeptide chains that are almost fully extended are wound around each other to form a ropelike structure.
  59. 59. The triple helix and collagen • Much of the stability of the structure results from hydrogen bonds between the backbones of the three chains. • The individual chains in the helix are in almost fully extended configurations so fibres composed of collagen molecules combine high strength with low elasticity.
  60. 60. Tertiary structure • Many globular proteins have compact tertiary structures; the long polypeptide chains within them must be folded or wound up like a ball of string. • Many globular proteins can form crystals. • X-ray diffraction studies of protein crystals have led to the determination of the threedimensional structure of a wide variety of protein molecules.
  61. 61. Tertiary structure • These structures show how the polypeptide chain winds back and forth through the molecule, sometimes in the form of an alpha helix, sometimes forming beta sheets, sometimes in turns and less regular structure. • Tertiary structures are often stabilised by covalent disulphide bonds. • The structures formed by folded polypeptides depend on hydrogen bonds and hydrophobic interactions, so they can be fragile and easily disrupted by changes in temperature or pH.
  62. 62. Disulphide bonds • Many proteins, especially those that function outside cells, have their folded structures reinforced by disulphide bonds. • These bonds can also hold subunits together. • Disulphide bonds are strong covalent bonds. oxidize
  63. 63. Disulphide bonds 2 Cysteine Cystine —SH + HS— = —S—S— + 2H • Disulphide bonds are formed when the side chains of two cysteine residues that are close together in the folded structure react together, losing the hydrogen atoms of their sulphydryl groups in an oxidation reaction.
  64. 64. Disulphide bonds • Disulphide bonds are particularly important in keratin, the fibrous structural protein of hair, skin and nails, where parallel alpha helices are crosslinked by disulphide bonds. • Keratin is chemically very resistant because its structure can maintain its integrity even after breakage of some peptide or disulphide bonds.
  65. 65. Formation of tertiary structure • The tertiary structure that a protein forms is dependent upon its amino acid sequence. • Tertiary structure largely results from the properties of the amino acid side chains. • Hydrophoic side chains such as those of Phe, Val, Leu and Ile are always found on the inside of the structure, while charged groups such as Arg, Lys, His, Asn and Gln are always on the surface of the molecule.
  66. 66. Formation of tertiary structure • There is no empty space within the molecule. • The hydrophobic side chains that form much of the core are close-packed, out of contact with the water that surrounds the protein molecules. • Except on the surface of the molecule, groups capable of forming hydrogen bonds are virtually all in a position to form hydrogen bonds.
  67. 67. Denaturation destroys secondary and tertiary structure • Primary structure depends on covalent bonds. • Secondary and tertiary structures are stabilised by a very large number of weak bonds, principally hydrogen bonds, by hydrophobic forces and by the electrostatic forces between charged groups. • If too much disruption of the weak stabilising bonds occurs, such as denaturation, partners in a broken bond may move too far apart for the bond to be formed again; as a result, the whole structure falls apart.
  68. 68. Primary structure is responsible for specific folding • • • • • Bovine pancreatic ribonuclease (RNAase) is a protein with 124 amino acid residues in its single polypeptide chain. The structure of ribonucleas is reinforced by disulphide bonds. Addition of mercaptoethanol and urea, disulphide bonds are broken and hydrogen bonds are disrupted, respectively. This combined treatment completely inactivated the enzyme. The activity could be restored by removal all of them.
  69. 69. Denaturation destroys secondary and tertiary structure • Anfinsen concluded that the polypeptide chain must have refolded as directed by its primary sequence and that, once refolded, the original disulphide bonds must have formed again. Christian B. Anfinsen in 1969
  70. 70. Domains • Long polypeptides may contain several folding domains. • These domains are tethered to each other by short flexible polypeptide sequences.
  71. 71. Domains • The heavy H chains of immunoglobulin G each contain four domains while the light L chains each contain two domains.
  72. 72. Quaternary structure and subunits • Many proteins contain more than one polypeptide chain. • Usually the individual chains fold into subunits that specifically bind to other subunits to make up the complete protein. • Multiple subunit proteins are important because they create the possibility of interaction between subunits; the state of one subunit can influence the functioning of another.
  73. 73. Quaternary structure and subunits • Many proteins contain more than one polypeptide chain. • Usually the individual chains fold into subunits that specifically bind to other subunits to make up the complete protein. • Multiple subunit proteins are important because they create the possibility of interaction between subunits; the state of one subunit can influence the functioning of another.
  74. 74. Quaternary structure and subunits • • • Each molecule of haemoglobin contains four polypeptide chains, each of which is folded to form a subunit that contains a bound haem group. In the case of the four haemoglobin subunits, there are two alpha (α) chains and two beta (β) chains. Alpha and beta chains have related amino acid sequences and have similar tertiary structures.
  75. 75. Quaternary structure and subunits • The subunits making up a protein are usually held together by specific but non-covalent forces such as hydrogen bonds, hydrophobic forces and electrostatic attractions. • These numerous but weak forces are sometimes reinforced by strong covalent disulphide bonds between the subunits.
  76. 76. Quaternary structure and subunits • Immunoglobulin G, a plasma protein that protects the body by recognising antigens, contains four polypeptides chains: two heavy H chains and two light L chains joined by disulphide bonds.
  77. 77. Ligand binding sites Learning Objectives – Explain how folding of polypeptide chains creates specific binding sites for ligands – Give examples of the importance of ligand binding in biochemistry.
  78. 78. Ligand binding sites • Proteins achieve specific binding of their ligands by means of forces similar to those they use to those they use to achieve specific folding. • Achievement of a specific tertiary structure does not involve all the side chains in the amino acid sequence. • Other amino acid side chains, can be brought together in space in a specific three-dimensional conformation to form a binding site.
  79. 79. Ligand binding sites • The binding site of protein has a structure complementary to the structure of the bound ligand. • If the ligand has the potential to form hydrogen bonds, the binding site will have hydrogen bond donor and acceptor groups situated to form bonds with the ligand. • If the ligand has a hydrophobic region, hydrophobic side chains in the binding site make close contacts with it. • A group of opposite charge in the binding site matches a charge group on the ligand. • Specificity and affinity of binding are achieved by numerous weak interactions.
  80. 80. Ligand binding sites • Protein function, and hence all of life, depends on the ability of proteins to recognise and bind tightly to their specific ligands even though the ligand molecules may only be present in very small amounts in complex mixtures of similar molecules. • Since ligand binding by proteins depends on mumerous weak interactions, it is reversible and rapid.
  81. 81. Ligand binding sites • Ligands do not have to form the ligandprotein complex in one step; they can collide with and occupy part of the binding site and then trigger changes in protein conformation that create other parts of the binding site and hence increase the affinity of binding. • Ligand binding is important in enzyme function, the subject of the next chapter.