AMINO ACIDS AND PROTEINS. HLeeYu Jsuico Junsay Department of Chemistry School of Science and Engineering Ateneo de Manila University

Transcription

1 AMINO ACIDS AND PROTEINS HLeeYu Jsuico Junsay Department of Chemistry School of Science and Engineering Ateneo de Manila University 1

2 Proteins serves as the cell s machinery as well as an organism s other structural features. 2

3 Proteins serves as the cell s machinery as well as an organism s other structural features. 1. Enzymes DNA Polymerase Catalase CK2 Kinase 2. Storage and Transport Hemoglobin Serum albumin Ion channels Ovalbumin Casein 3

4 Proteins serves as the cell s machinery as well as an organism s other structural features. 3. Structure and Movement Collagen Keratin Silk Fibroin 4 Actin Myosin 4

5 Proteins serves as the cell s machinery as well as an organism s other structural features. 4. RegulaEon 5. ProtecEon Insulin Lac repressor Immunoglobulin Thrombin and Fibrinogen Venom Proteins Ricin 5

6 Proteins serves as the cell s machinery as well as an organism s other structural features. 6. Signalling 6

7 Proteins are made up of amino acids. R group or side chain α amino group Carboxyl group α carbon 7

8 The side chain (R group) can have varying groups. 8

9 The side chain (R group) can have varying groups. 9

10 AA with AliphaEc side chains 10

11 AA with AliphaEc side chains 11

12 AA with AliphaEc side chains 12

13 AA with AromaEc side chains 13

14 AA with AromaEc side chains are UV acuve. 14

15 AA with Polar side chains. 15

16 AA with Polar side chains. 16

17 AA with Basic side chains. 17

18 AA with Acidic side chains and their corresponding Amides. 18

19 Amino acids have specific stereochemistry. 19

20 At physiological ph, acidic (and basic) groups are either protonated or deprotonated. Amino acids have IONIC groups. ZwiLerions are ions with a posiuve and negauve charge on the same molecule. 20

21 Amino acids are polyprouc acids. 21

22 Amino acids are polyprouc acids. 22

23 Amino acids are polyprouc acids. 23

24 Amino acids are polyprouc acids. 24

25 Amino acids are polyprouc acids. Net charge: +1 Net charge: 0 Net charge: 1 25

26 The isoelectric point of an amino acid is when it has zero [0] net charge. Recall: this is the equivalence point from the species before (net charge +1) and the zwiaerionic species (net charge 0) ph = pka 1 + pka 2 2 = pk 1 + pk R 2 26

27 Amino acids are polyprouc acids. 27

28 Amino acids are polyprouc acids. 28

29 Amino acids are polyprouc acids. 29

30 Two or more amino acids may be joined together to form pepedes. + H 2 O 30

31 Two or more amino acids may be joined together to form pepedes. 31

32 The pepude bond is essenually an amide bond. RECALL: Amide bonds can be cleaved by acid, bases or enzymes (peedase) 32

33 The pepude bond is planar. 33

34 Two or more amino acids may be joined together to form pepedes. N Terminal End C Terminal End 34

35 Two or more amino acids may be joined together to form pepedes. = 35

36 Two or more amino acids may be joined together to form pepedes. = 36

37 Two or more amino acids may be joined together to form pepedes. 37

38 Naming of pepudes Use of prefixes: di, tri, tetra, penta, hexa, hepta, octa, nona, deca AA = polypepudes More than 100 AA = proteins 38

39 There are short pepude sequences that are biologically important 39

40 There are short pepude sequences that are biologically important 40

41 PROTEIN STRUCTURE 41

42 Proteins have several levels of structure 1. Primary Structure sequence or order of the monomers (in this case, AA) 2. Secondary Structure Localized regions of the primary sequence folded into a regular, repeaung structural element 3. TerEary Structure InteracUng secondary structures to form more intricate 3D shapes 4. Quaternary Structure associauon of one or more chains to form a complex 42

43 Proteins have several levels of structure 43

44 The primary structure is the sequence or order of AA from N terminus to the C terminus. Eg. Insulin (AAA40590) MAPWMHLLTVLALLALWGPNSVQAYSSQHLCG SNLVEALYMTCGRSGFYRPHDRRELEDLQVEQ AELGLEAGGLQPSALEMILQKRGIVDQCCNNI CTFNQLQNYCNVP The info needed for further folding is contained in the 1 o structure. 44

45 Regular local structure based on the hydrogen bonding paaern of the polypepude backbone gives the protein s secondary structure. WHY will there be localized folding and twiseng? Are all conformaeons possible? 45

46 Not all conformauon is possible because of the protein s planar backbone Two degrees of freedom per residue for the pep1de chain Angle about the C(alpha) N bond is denoted phi Angle about the C(alpha) C bond is denoted psi The enure path of the pepude backbone is known if all phi and psi angles are specified Some values of phi and psi are more likely than others. 46

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49 G. N. Ramachandran was the first to Sasisekharan demonstrate the convenience of plohng phi,psi combinauons from known protein structures The sterically favorable combinauons are the basis for preferred secondary structures 49

50 One favorable conformauon forms a structure called alpha helix. 50

51 Alpha helices are stabilized by Hbonds between the C=O and the N H of the pepude backbone 51

52 Residues (side chains) are poinung outwards. 52

53 Another favorable conformauon forms pleated sheets called beta sheets. β sheets are formed by linking 2 or more strands by H bonding 53

54 Strands can be parallel or ane parallel to each other 54

55 Strands can be parallel or ane parallel to each other 55

56 Side chain is placed on top and at the boaom of the sheet (alternately). 56

57 Turns may also be found as secondary structure (usually proline and glycine). 57

58 Individual elements of secondary structure are ojen combined into stable geometrical arrangements called supersecondary structure or moefs. 58

59 A protein domain is a part of protein sequence and structure that can evolve, funcuon and exist independently of the rest of the protein chain. 59

60 RECALL: primary structure determines secondary structure WHY?! The α helix can be regarded as the default conformauon Amino acids that favor α helices: Glu, Gln, Met, Ala, Leu Amino acids that disrupt α helices: Val, Thr, Ile, Ser, Asx, Pro 60

61 RECALL: primary structure determines secondary structure WHY?! 61

62 RECALL: primary structure determines secondary structure WHY?! Branching at the β carbon, such as in valine, destabilizes the α helix because of steric interacuons Ser, Asp, and Asn tend to disrupt α helices because their side chains compete for H bonding with the main chain amide NH and carbonyl Proline tends to disrupt both α helices and β sheets Glycine readily fits in all structures thus it does not favor α helices in parucular 62

63 SO CAN YOU PREDICT the 2 structure of a given AA sequence? 1.LAKKKKFG 2.GAAGSGAPAGAASYG 3.FFVMATSGPGAFTLFK 4.GEDDEDF 63

64 SO CAN YOU PREDICT the 2 structure of a given AA sequence? PredicUons of secondary structure of proteins adopted by a sequence of six or fewer residues have proved to be 60 to 70% accurate Many protein chemists have tried to predict structure based on sequence BUT secondary structure is influenced by tereary structure. 64

65 The tereary structure is the over all 3D fold of the polypepude chain. Governed by the hydrophobic effect a thermodynamic effect, and stabilized by IMFAs 65

66 The tereary structure is the over all 3D fold of the polypepude chain. Governed by the hydrophobic effect a thermodynamic effect, and stabilized by IMFAs Can be FIBROUS or GLOBULAR 66

67 Fibrous proteins usually perform structural roles (mechanically strong), insoluble and take the form of triple helices. Alpha KeraUn: hair, nails, claws, horns, beaks Beta KeraUn: silk fibers (alternaung Gly Ala Ser) 67

68 COLLAGEN: Nearly one residue out of three is Gly Proline content is unusually high Unusual amino acids found: (4 hydroxyproline, 3 hydroxyproline, 5 hydroxylysine) Special uncommon triple helix! 68

69 Globular proteins are water soluble proteins. An amphiphilic helix in flavodoxin: A nonpolar helix in citrate synthase: A polar helix in calmodulin: 69

70 Globular proteins are water soluble proteins. An amphiphilic helix in flavodoxin: A nonpolar helix in citrate synthase: A polar helix in calmodulin: 70

71 Disulfide bonds are also important in maintaining teruary structure. 71

72 Disulfide bonds are also important in maintaining teruary structure. 72

73 Folding of proteins into its teruary structure is usually spontaneous, but others may require accessory proteins called molecular chaperones. 73

74 Molecular chaperones provide a safe haven for secondary structures and moufs. (to prevent unwanted aggregauon of hydrophobic regions) 74

75 Because proteins interact by means of IMFAs, these may be disrupted using different agents. 75

76 Denatured proteins are biologically inacuve. AcUvity maybe returned, when proper condiuons are met. 76

77 Quaternary structure involves the spaual arrangements of mulu subunits of a protein molecule. May have hetero or homo subunits. Insulin (hetero subunits) ADVANTAGES of 4 o Structures Stability: reducuon of surface to volume rauo GeneUc economy and efficiency Bringing catalyuc sites together CooperaUvity 77

78 Quaternary structure involves the spaual arrangements of mulu subunits of a protein molecule. May have hetero or homo subunits. 78

79 Quaternary structure involves the spaual arrangements of mulu subunits of a protein molecule. May have hetero or homo subunits. 79

80 Proteins have several levels of structure 1. Primary Structure sequence or order of the monomers (in this case, AA) 2. Secondary Structure Localized regions of the primary sequence folded into a regular, repeaung structural element 3. TerEary Structure InteracUng secondary structures to form more intricate 3D shapes 4. Quaternary Structure associauon of one or more chains to form a complex 80

81 Proteins have several levels of structure and it determines the protein s funceon 81