1. Amino Acids & Protein

2. Amino Acids What are amino acids? Structure Classification Understand pK Peptides and Peptide bond Examples of related compounds

3. Introduction

4. What are amino acids? Building Blocks

5. Amino acids Building blocks of proteins Building blocks of proteins 20 are present in mammalian proteins ( standard aa) 20 are present in mammalian proteins ( standard aa) Have amphoteric property Have amphoteric property

6. Amino acid: Basic unit of protein COO - NH 3 + C R H An amino acid Amino group Carboxylic acid group Groups attached to α- carbon a carboxyl group an amino group a side chain

7. Proline imino acid imino acid –Has a secondary amino group Amino acids have primary amino group except?????

8. Asymmetrical Carbon Atom ?= optical properties

9. Amino acid: Basic unit of protein COO - NH 3 + C R H An amino acid Amino group Carboxylic acid group Groups attached to α- carbon a carboxyl group an amino group a side chain

10. Stereoisomers, Enantiomers,Optical Isomers

11. L-amino acids – natural amino acids found in protein L-amino acids – natural amino acids found in protein D-amino acids are found in antibiotics (like Gramicidin-S, Actinomycin-D and Valinomycin) and in plant and bacterial cell walls D-amino acids are found in antibiotics (like Gramicidin-S, Actinomycin-D and Valinomycin) and in plant and bacterial cell walls Glycine an exception- no optical activity Glycine an exception- no optical activity

12. Rotate plane polarized light to Rotate plane polarized light to give levorotatory & dextrorotatory forms give levorotatory & dextrorotatory forms

13. Classification of amino acids Neutral, acidic and basic Neutral, acidic and basic Essential or non essential Essential or non essential Glucogenic, ketogenic, or both Glucogenic, ketogenic, or both According to the side chain properties According to the side chain properties

15. Classification of Amino Acids according to properties of their side chain

16. Classification on the basis of side chain Non-polar Non-polar –Side chain does not bind or give off protons –Promote hydrophobic interaction –In aqueous solution- clustered in the interior –Helps giving a 3-D shape

17. Non-Polar Uncharged Amino Acids

18. Classification on the basis of side chain (cont.) Polar Polar –uncharged –Acids –Bases Hydrophilic Hydrophilic

19. Polar Charged Amino Acids Negatively charged Positively charged

20. Polar uncharged amino acids Have zero net charge at neutral pH

22. Sickle Cell Disease It is a pathology that results from the It is a pathology that results from the substitution of polar glutamate by the non- polar valine in the B subunit of hemoglobin

23. Acidic & Basic Properties of Amino Acids

24. Page 65 Acidic carboxylic group Basic amino group General structural formula for α-amino acids

25. Page 65

26. It is the ability of an acid to donate a proton (dissociate) It is the ability of an acid to donate a proton (dissociate) Also known as pKa or acid dissociation constant Also known as pKa or acid dissociation constant It is the pH at which 50% of the acid is dissociated. It is the pH at which 50% of the acid is dissociated. pK Value

27. The pK values of α-carboxylic group is in the range of 2.2 The pK values of an-amino group is in the range of 9.4

28. Remember The smaller the pK the stronger the acid, the larger the pK the weaker the acid The smaller the pK the stronger the acid, the larger the pK the weaker the acid The maximum buffering capacity occurs at a pH= pKa (a range ± 1) The maximum buffering capacity occurs at a pH= pKa (a range ± 1)

29. Buffer: is a solution that resists change in pH following the addition of an acid or a base Buffer: is a solution that resists change in pH following the addition of an acid or a base It can be created by mixing a weak acid (HA) with its conjugate base (A - ) It can be created by mixing a weak acid (HA) with its conjugate base (A - )

30. Titration curve of glycine Page 70

31. An amino acid can act as both an acid and a base (has amphoteric property) An amino acid can act as both an acid and a base (has amphoteric property)

32. Zwitter ions pI = pH at which the molecule is electrically neutral

34. At physiological pH, most amino acids contain both positive and negative charges with a net charge of zero At physiological pH, most amino acids contain both positive and negative charges with a net charge of zero

35. Some biologically produced derivatives of “standard” amino acids and amino acids that are not components of proteins Page 77

36. Gamma amino butyric acid (GABA, a derivative of glutamic acid) and dopamine (from tyrosine) are neurotransmitters Gamma amino butyric acid (GABA, a derivative of glutamic acid) and dopamine (from tyrosine) are neurotransmitters Histamine (Histidine) is the mediator of allergic reactions Histamine (Histidine) is the mediator of allergic reactions Thyroxine (Tyrosine) is an important thyroid hormone Thyroxine (Tyrosine) is an important thyroid hormone

37. Peptides

38. Peptides Amino acids can be polymerized to form chains Amino acids can be polymerized to form chains 2 a.a. - dipeptide 2 a.a. - dipeptide 3a.a. -tripepeptide 3a.a. -tripepeptide 4a.a.-tetrapeptide 4a.a.-tetrapeptide Few (~ 10)- oligo peptide Few (~ 10)- oligo peptide more- polypeptide more- polypeptide

39. Polymers of amino acids R1R1 NH 3 ＋ C CO H R2R2 NH C CO H R3R3 NH CCO H R2R2 NH 3 ＋ C COO ー H ＋ R1R1 NH 3 ＋ C COO ー H ＋ H2OH2O H2OH2O Peptide bond AA F N G G S T S D K A carboxylic acid condenses with an amino group with the release of a water

40. Amino acids are joined together in a chain by peptide bond [CO–NH linkage] Amino acids are joined together in a chain by peptide bond [CO–NH linkage] Known as peptide bond Known as peptide bond Each amino acid in a chain makes two peptide bonds except ??? Each amino acid in a chain makes two peptide bonds except ???

42. Glutathione (abbreviated GSH) is a tripeptide composed of glutamate, cysteine and glycine that has numerous important functions within cells: a reductant ; is conjugated to drugs to make them more water soluble; a cofactor aids in the rearrangement of protein disulfide bonds Glutathione

43. Take Home Message

44. Proteins

45. Protein Structure What are proteins? Four levels of structure (primary, secondary, tertiary, quaternary) Protein folding and stability Protein denaturation Protein misfolding and diseases Structure-function relationship

46. What are proteins? Proteins are polymers of amino acids joined together by peptide bonds Proteins are polymers of amino acids joined together by peptide bonds

47. Proteins play key roles in a living system Three examples of protein functions Three examples of protein functions –Catalysis: Almost all chemical reactions in a living cell are catalyzed by protein enzymes. –Transport: Some proteins transports various substances, such as oxygen, ions, and so on. –Information transfer: For example, hormones. Alcohol dehydrogenase oxidizes alcohols to aldehydes or ketones Haemoglobin carries oxygen Insulin controls the amount of sugar in the blood

48. Close relationship between protein structure and its function enzyme A B A Binding to A Digestion of A! enzyme Matching the shape to A Hormone receptor Antibody Example of enzyme reaction enzyme substrates

49. Hierarchical nature of protein structure Primary structure (Amino acid sequence) ↓ Secondary structure （ α -helix, β -sheet ） ↓ Tertiary structure （ Three-dimensional structure formed by assembly of secondary structures ） ↓ Quaternary structure （ Structure formed by more than one polypeptide chains ）

50. Proteins are linear polymers of amino acids R1R1 NH 3 ＋ C CO H R2R2 NH C CO H R3R3 NH CCO H R2R2 NH 3 ＋ C COO ー H ＋ R1R1 NH 3 ＋ C COO ー H ＋ H2OH2O H2OH2O Peptide bond The amino acid sequence is called as primary structure AA F N G G S T S D K A carboxylic acid condenses with an amino group with the release of a water

51. Primary Structure It is the linear sequence of amino acids It is the linear sequence of amino acids Many genetic diseases result in proteins with abnormal aa sequence, which cause improper folding & abnormal functioning Many genetic diseases result in proteins with abnormal aa sequence, which cause improper folding & abnormal functioning Peptide bond is a covalent bond that is not broken by broken by condition that denature proteins as heating or high concentrations of urea. Peptide bond is a covalent bond that is not broken by broken by condition that denature proteins as heating or high concentrations of urea.

54. αα helix is right-handed It has 3.6 amino acid residues per turn Stabilized by hydrogen bonding Between 1st carboxylic group and 4th amino group The side chains point outward and downward from the helix The core of the helix is tightly packed α α helix

55. b Sheets Usually Two or more polypeptide chains make hydrogen bonding with each other Usually Two or more polypeptide chains make hydrogen bonding with each other Also called pleated sheets because they appear as folded structures with edges Also called pleated sheets because they appear as folded structures with edges

58. Antiparallel β sheets Two or more hydrogen-bonded polypeptide chains run in opposite direction Two or more hydrogen-bonded polypeptide chains run in opposite direction Hydrogen bonding is more stable Hydrogen bonding is more stable

59. Parallel β sheets Two or more hydrogen-bonded polypeptide chains run in the same direction Two or more hydrogen-bonded polypeptide chains run in the same direction Hydrogen bonding is less stable (distorted) Hydrogen bonding is less stable (distorted)

61. Other Secondary Structures Turns (reverse turns) Turns (reverse turns) Loops Loops Β bends Β bends Random coils Random coils

62. Fibrous Proteins Provide mechanical support Often assembled into large cables or threads a-Keratins: major components of hair and nails Collagen: major component of tendons, skin, bones and teeth

63. Collagen – a triple helix A fibrous protein A fibrous protein Part of connective tissues: bone, teeth, cartilage, tendon, skin, blood vessels Part of connective tissues: bone, teeth, cartilage, tendon, skin, blood vessels Contains three left-handed coiled chains Contains three left-handed coiled chains Three residues per turn:-Gly-X- Y (X= proline,Y=hydroxyproline or hydroxylysine) Three residues per turn:-Gly-X- Y (X= proline,Y=hydroxyproline or hydroxylysine)

64. Glycine and Proline in collagen Rich in glycine & proline a.a. Rich in glycine & proline a.a. Proline facilitates helical conformation of each α-chain by causing kinks Proline facilitates helical conformation of each α-chain by causing kinks Glycine, the smallest a.a. fits into the restricted spaces where the three chains of the helix come together Glycine, the smallest a.a. fits into the restricted spaces where the three chains of the helix come together

65. Non-standard amino acids in collagen Proline is converted to 4-hydroxyprolyl residue by prolyl hydroxylase enzyme( it stabilizes the triple-helical structure of collagen by maximaizing interchain hydrogen formation). Proline is converted to 4-hydroxyprolyl residue by prolyl hydroxylase enzyme( it stabilizes the triple-helical structure of collagen by maximaizing interchain hydrogen formation). The enzyme requires vitamin C for its function The enzyme requires vitamin C for its function

66. Collagen diseases Scurvy: due to vitamin C deficiency Scurvy: due to vitamin C deficiency

67. Super-secondary structures or motifs β α β motif: a helix connects two β sheets β α β motif: a helix connects two β sheets β hairpin: reverse turns connect antiparallel β sheets β hairpin: reverse turns connect antiparallel β sheets α α motif: two α helices together α α motif: two α helices together β barrels: rolls of β sheets β barrels: rolls of β sheets

68. β barrels β α β β hairpinα Crosssover connection Reverse turn/loop loop

69. Tertiary Structure It is the 3-D structure of an entire polypeptide chain including side chains It is the 3-D structure of an entire polypeptide chain including side chains It includes the folding of secondary structure (α helix and β sheets) and side chains It includes the folding of secondary structure (α helix and β sheets) and side chains The primary structure of apolypeptide chain determines its tertiary structure The primary structure of apolypeptide chain determines its tertiary structure

70. Globular proteins Globular proteins Usually water soluble, compact, roughly spherical Hydrophobic interior, hydrophilic surface Globular proteins include enzymes, carrier and regulatory proteins

71. Domains Polypeptide chains (>200 amino acids) fold into two or more clusters known as domains Polypeptide chains (>200 amino acids) fold into two or more clusters known as domains Domains are functional units that look like globular proteins Domains are functional units that look like globular proteins Domains are parts of protein subunits Domains are parts of protein subunits

72. Quaternary Structure Many proteins contain two or more polypeptide chains Many proteins contain two or more polypeptide chains Each chain forms a three- dimensional structure called subunit Each chain forms a three- dimensional structure called subunit It is the 3D arrangement of different subunits of a protein It is the 3D arrangement of different subunits of a protein The subunits may be structurally related or totally unrelated. The subunits may be structurally related or totally unrelated.

73. Hemoglobin & Myoglobin Both can bind to oxygen Both can bind to oxygen Both are globular proteins Both are globular proteins Myoglobin is only formed Myoglobin is only formed of one subunit? of one subunit? A multisubunit protein is called oligomer A multisubunit protein is called oligomer Hb is composed of α 2 β 2 subunits (4 subunits) Hb is composed of α 2 β 2 subunits (4 subunits)

74. Forces that stabilize 3ry& 4ry protein structure Hydrophobic effect: Hydrophobic effect: –Nonpolar groups to minimize their contacts with water –Nonpolar side chains are in the interior of a protein Hydrogen bonding Hydrogen bonding –A weak electrostatic bond between one electronegative atom like O or N and a hydrogen atom Electrostatic interactions (ion pairing): Electrostatic interactions (ion pairing): –Between positive and negative charges Disulphide bonds: covalent bonds which prevents proteins from being denatured in the extra cellular enviroment Disulphide bonds: covalent bonds which prevents proteins from being denatured in the extra cellular enviroment

76. Protein Denaturation Denaturation: A process in which a protein looses its native structure Denaturation: A process in which a protein looses its native structure Factors that cause denaturation: Factors that cause denaturation: –Heat: disrupts hydrogen bonding –Change in pH: alters ionization states of aa –Detergents: interfere with hydrophobic interactions –Chaotropic agents: ions or small organic molecules that disrupt hydrophobic interactions

77. Protein Misfolding Every protein must fold to achieve its normal conformation and function Every protein must fold to achieve its normal conformation and function Abnormal folding of proteins leads to a number of diseases in humans Abnormal folding of proteins leads to a number of diseases in humans Alzheimer’s disease: Alzheimer’s disease: –β amyloid protein is a misfolded protein –It forms fibrous deposits or plaques in the brains of Alzheimer’s patients

78. Creutzfeldt-Jacob or Prion disease: Creutzfeldt-Jacob or Prion disease: –Prion protein is present in normal brain tissue –In diseased brains, the same protein is misfolded from a-helix to B-sheets –Therefore it forms insoluble fibrous aggregates that damage brain cells

79. Take Home Message

80. Proteins are key players in our living systems. Proteins are key players in our living systems. Proteins are polymers consisting of 20 kinds of amino acids. Proteins are polymers consisting of 20 kinds of amino acids. Each protein folds into a unique three-dimensional structure defined by its amino acid sequence. Each protein folds into a unique three-dimensional structure defined by its amino acid sequence. Protein structure has a hierarchical nature. Protein structure has a hierarchical nature. Protein structure is closely related to its function. Protein structure is closely related to its function. Protein misfolding leads to diseases Protein misfolding leads to diseases