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1. 1 Peptides. Proteins and peptides are polymers made up of amino acid units (residues) that are linked together through the formation of amide bonds (peptide bonds) from the amino group of one residue and the carboxylate of a second residue By convention, peptide sequences are written left to right from the N-terminus to the C-terminus backbone lecture one Prof Faten Abou-elella

2. Double bond character of peptide bond The bond that connects a carbonyl carbon to the α-nitrogen is partial double bonds ( 60 % double bond )so it cannot rotate, Consequently, the O, C, N, and H atoms of a peptide bond are coplanar . The imposed semirigidity of the peptide bond has important consequences for the manner in which peptides and proteins fold to generate higher orders of structure. lecture one Prof Faten Abou-elella 2

3. Planarity of Peptide Bonds Planar molecule means that all of its atoms lie in the same plane. Peptide bonds have a second resonance form, as demonstrated below. This means that the peptide bond (the C=O and N-H) all residue in a single plane. Thus, there is no rotation around the peptide bond. lecture one Prof Faten Abou-elella 3

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5. Cis and trans configuration Trans peptide bonds are more stable than cis peptide bonds, because there is no interfering between the side chain groups as in cis configuration and they are low energy. lecture one Prof Faten Abou-elella 5

6. Phi φ and psi ψ angels φ ( phi) = The angel of rotation around the single bond between nitrogen and α carbon ψ ( psi) = The angel of rotation around the single bond between carbonyl and α carbon ω ( omega) = The angel of rotation around the single bond between carbonyl and nitrogen lecture one Prof Faten Abou-elella 6

7. Physiological active peptide Peptides are short chains of  amino acid linked by  peptide bonds . The   peptide bonds are formed when the carboxyl group of one amino acid reacts with the amino group of another. The shortest peptides are  dipeptides, consisting of 2 amino acids joined by a single peptide bond, followed by  tripeptides, tetrapeptides , etc. lecture one Prof Faten Abou-elella 7

8. Peptides vs proteins Peptides are distinguished from proteins on the basis of size, Peptides contain approximately 50 or fewer amino acids.   Polypeptide  is a long, continuous, and unbranched peptide chain   Proteins consist of one or more polypeptides arranged in a biologically functional  lecture one Prof Faten Abou-elella 8

9. Short peptides Biosynthesis Dipeptides, tripeptides and tetrapeptides are produced from polypeptides by the action of the hydrolase enzyme dipeptidyl peptidase The short peptides are mainly ribosomal peptides, usually with hormonal activity. lecture one Prof Faten Abou-elella 9

10. Short peptides Peptides are released by posttranslational proteolytic cleavage of precursor proteins. lecture one Prof Faten Abou-elella 10

11. Function of peptides Natural Antioxidant Hormonal peptides Antimicrobial peptides Neuropeptides Enzyme regulators or inhibitors peptides lecture one Prof Faten Abou-elella 11

12. Natural antioxidant Glutathione  ( GSH ) .  It is a tripeptide with a  gamma peptide linkage between the carboxyl group of the  glutamate  side chain and the amine group of  cysteine , and the carboxyl group of cysteine is attached by normal peptide linkage to a  glycine. Glutathione is a natural antioxidant. lecture one Prof Faten Abou-elella 12

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14. Glutathione function 2 GSH + ROOH → GSSG + ROH + H 2 O   IS capable of preventing the cellular damage caused by reactive oxygen species such as free radicals, peroxides, lipid peroxides GSSG Reduced glutathione oxidized glutathione lecture one Prof Faten Abou-elella 14

15. Hormonal peptides Gastrin  is a peptide hormone that stimulates secretion of gastric acid ( HCl ) by the  G cells of the stomach secreted into the bloodstream. Gastrin in various forms, primarily the following three: gastrin-34 ("big gastrin") gastrin-17 ("little gastrin") gastrin-14  (" minigastrin ") The presence of gastrin stimulates the stomach to secrete hydrochloric acid ( HCl )/gastric acid lecture one Prof Faten Abou-elella 15

16. Neuropeptides Enkephalin is a  penta -peptide and it is a small neurotransmitters in brain and responisble for inhibition of pain fibre Two forms of enkephalin have been found, one containing  leucine  (" leu "), and the other containing methionine ("met"). Met- enkephalin is Tyr- Gly - Gly - Phe - Met . Leu-enkephalin has Tyr- Gly - Gly-Phe- Leu . lecture one Prof Faten Abou-elella 16

17. Enkephalin lecture one Prof Faten Abou-elella 17

18. Antimicrobial peptides Nisin  is a polycyclic antibacterial peptide produced by the bacterium  Lactococcus lactis that is used as a food preservative. It has 34 amino acid residues, including the uncommon amino acids lanthionine (Lan), methyllanthionine  ( MeLan ),  didehydroalanine  ( Dha ), and  didehydroaminobutyric acid ( Dhb ). lecture one Prof Faten Abou-elella 18

19. lecture 3 Prof Faten Abou-elella 19 Levels of Protein Structure Primary structure Secondary structure Tertiary structure Quaternary structure

20. lecture 3 Prof Faten Abou-elella 20 Primary Structure is a poly peptide chain When an amino acid sequence of a peptide, polypeptide, or protein is displayed, the amino-terminal end is placed on the left, the carboxyl-terminal end on the right. The sequence is read left to right, beginning with the amino-terminal end. Primary Structure

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22. lecture 3 Prof Faten Abou-elella 22 22 Primary Structure of Insulin Insulin was the first protein to have its primary structure determined. has a primary structure of two polypeptide chains linked by disulfide bonds. has a chain A with 21 amino acids and a chain B with 30 amino acids.

23. lecture 3 Prof Faten Abou-elella 23 Secondary Structure of protein 1- Alpha helix 2- beta –sheet 3- Turn and Loop 4- triple helix

24. lecture 3 Prof Faten Abou-elella 24 24 Secondary Structure – Alpha Helix The secondary structure of an alpha helix is a three-dimensional spatial arrangement of amino acids in a polypeptide chain. held by H bonds between the H of –N-H group and the O of C=O of the fourth amino acid down the chain. a corkscrew shape that looks like a coiled “telephone cord”. Copyright © 2005 by Pearson Education, Inc. Publishing as Benjamin Cummings

25. lecture 3 Prof Faten Abou-elella 25 Alpha Helix A complete turn of the helix contains an average of 3.6 aminoacyl residues, (Figure 5–2). Since the peptide bond nitrogen of proline lacks a hydrogen atom, it is incapable of forming a hydrogen bond with a carbonyl oxygen. Consequently, proline can only be stably within the first turn of an α helix. When present elsewhere, proline disrupts the conformation of the helix, producing a bend. Because Glycine possesses such a small R group, it also frequently induces bends within α helices .

26. Alpha Helix , The polar R groups of each aminoacyl residue in an α helix face outward. FIGURE 5–3 View down the axis of a polypeptide α helix. lecture 3 Prof Faten Abou-elella 26

27. : In proteins found in aqueous solutions, side chains tend to cluster in interior of protein  i.e., fill up interior of folded protein  help give 3D shape. In proteins located in membranes, non-polar R-groups are on outside surface, interacting with lipid of the cell membrane. Location of Non-polar amino acids in proteins

28. Many α helices have hydrophobic R groups and hydrophilic R groups projecting from the other side. These amphipathic helices are well adapted to the formation of interfaces between polar and nonpolar regions, Example of amphipathic helices Clusters of amphipathic helices can create channels , or pores, through hydrophobic cell membranes that permit specific polar molecules to pass. lecture 3 Prof Faten Abou-elella 29 Amphipathic helices

29. lecture 3 Prof Faten Abou-elella 30 b - sheet b -pleated sheet secondary structure is exhibited by polypeptide chains held together by hydrogen bonds between chains Types of beta sheet 1- A parallel β sheet, in which the adjacent segments of the polypeptide chain proceed in the same direction amino to carboxyl, 2-An antiparallel sheet, in which they proceed in opposite directions 3-Mixed beta sheet contains parallel and antiparallel sheets 30

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31. lecture 3 Prof Faten Abou-elella 32 32 Mixed beta sheet Anti Parallel part Parallel part

32. lecture 3 Prof Faten Abou-elella 33 Turns and bends Turns and bends refer to short segments of amino acids that join two units of the secondary structure, such as two adjacent strands of an antiparallel β sheet. β turn It is containing 4 amino acids residues and stabilized by hydrogen bond between Carbonyl oxygen of the first and amide hydrogen of fourth residue

33. lecture 3 Prof Faten Abou-elella 34 Note: Glycine and Proline are often part of the β turn Proline is capable of forming cis peptide bond . The presence of a built-in bend in the case of proline allow the polypeptide backbone to fold into a tight U-shaped structure. , while Glycine has a small side chain group that’s capable to generate a unique phi and psi angels permitting a high Felixable β turn . Without turns, a protein would be large, extended, and loosely packed.

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35. Proline The side chain and α -amino group form a ring Thus it contains imino group , rather than amino Its unique geometry contributes to formation of fibrous structure of collagen, and often interrupts α -helices found in globular proteins

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37. lecture 3 Prof Faten Abou-elella 38 Types of beta turn Type1 ( has proline ) Type II ( has glycine)

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39. lecture 3 Prof Faten Abou-elella 40 FIGURE 4-9 Ramachandran plots showing a variety of structures. (a) The values of ϕ and ψ for various allowed secondary structures are overlaid on the plot

40. Loops are regions that contain residues more than the minimum number necessary to connect adjacent regions of secondary structure. It can changes the direction of polypeptide chain about 180ᵒ degree. loop can connect between α helix with β sheets polypeptide. loops serve key biologic roles. 1- For many enzymes , the loops responsible for binding substrates 2- Its aminoacyl residues participate in catalysis many DNA binding proteins such as repressors and transcription factors . 3- Many loops and bends reside on the surface of proteins, such as epitopes , for recognition and binding of antibodies. lecture 3 Prof Faten Abou-elella 41

41. lecture 3 Prof Faten Abou-elella 42 Triple helix Collagen is an example for the triple helix

42. lecture 3 Prof Faten Abou-elella 43 Collagen has evolved to provide strength. It is found in connective tissue such as tendons, cartilage, .The collagen helix is a unique secondary structure, quite distinct from the α helix. It is left-handed and has three amino acid residues per turn ( Fig. 4-12 and Table 4-1).

43. lecture 3 Prof Faten Abou-elella 44 The amino acid sequence in collagen is generally a repeating tripeptide unit, Gly–X–Y, where X is often Pro, and Y is often 4-Hyp. Only Gly residues can be accommodated at the very tight junctions between the individual α chains (Fig. 4-12b). The Pro and 4-Hyp residues permit the sharp twisting of the collagen helix. The amino acid sequence and the supertwisted quaternary structure of collagen allow a very close packing of its three polypeptides.

44. lecture 3 Prof Faten Abou-elella 45 Structure of collagen fibrils. Collagen ( M r 300,000) is a rod shaped molecule, about 3,000 Å long and only 15 Å thick. Its three helically intertwined α chains may have different sequences; each chain has about 1,000 amino acid residues. Collagen fibrils are made up of collagen molecules aligned in a staggered fashion and cross-linked for strength.

45. lecture 3 Prof Faten Abou-elella 46 L-Ascorbic acid (vitamin C) and relation with collagen Ascorbate is necessary to good health. Due to its role in the formation of collagen. A collagen is constructed of the repeating tripeptide unit Gly–X–Y, where X and Y are generally Pro or 4-Hydroxye proline .In the absence of vitamin C, cells cannot hydroxylate the Pro at the Y positions. This leads to collagen instability and the connective tissue problems

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47. Tertiary Structure of protein 48 lecture 3 Prof Faten Abou-elella The term “tertiary structure” refers to the entire three-dimensional conformation of a polypeptide. A domain is a section of the protein structure sufficient to perform a particular chemical or physical task such as binding of a substrate or other ligand. .

48. lecture 3 Prof Faten Abou-elella 49 What holds a protein into its tertiary structure 1-Ionic interactions or salt bridges 2-van der Waals dispersion forces 3-Sulphur bridges 4-Hydrogen bonds

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50. lecture 3 Prof Faten Abou-elella 51 Structural and Functional Domains The  tertiary structure  of large proteins is subdivided into globular or fibrous regions called  domains A structural  domain  consists of 100–200 residues in various combinations of α helices, β sheets, turns, . A domain is a section of the protein structure sufficient to perform a particular chemical or physical task . Domains sometimes are defined in functional terms. may be responsible for catalytic activity (e.g., a  kinase   domain ) or binding ability (e.g., a  DNA -binding domain,  membrane -binding domain).

51. Quaternary Structure of protein 52 lecture 3 Prof Faten Abou-elella Hemoglobin

52. lecture 3 Prof Faten Abou-elella 53 Examples of proteins in quaternary structure 1- lactate dehydrogenase is two domains, an N-terminal NAD+-binding domain and a C terminal binding domain for the second substrate 2- Hemoglobin consists of four polypeptide chains as subunits 3- Hydrophobic domains anchor proteins to membranes or enable them to span membranes. 4- collagen

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54. Catalysis – enzymes Structural – keratin Transport – hemoglobin Trans -membrane transport – Na+/K+ ATPases Toxins – rattle snake venom, ricin Contractile function – actin, myosin Hormones – I nsuli n Storage Proteins – seeds and eggs Defensive proteins – antibodies Protein Functions 55 lecture 3 Prof Faten Abou-elella

55. Protein Classification according to the number of chains 56 lecture 3 Prof Faten Abou-elella Monomeric protein is One polypeptide More than one called multimeric protein The multimeric protein can be classified into 1- Homomultimer – all one kind of chain 2-Heteromultimer - two or more different chains (e.g. Hemoglobin is a heterotetramer. It has two alpha chains and two beta chains).

56. Fibrous – polypeptides arranged in long strands or sheets water insoluble (lots of hydrophobic AA’s) strong but flexible Structural (keratin, collagen) Globular polypeptide chains folded into spherical or globular form water soluble contain several types of secondary structure diverse functions (enzymes, regulatory proteins ) Protein Classification according to its shape 57 lecture 3 Prof Faten Abou-elella

57. 58 Denaturation involves The disruption of bonds in the secondary, tertiary and quaternary protein structures. heat and organic compounds that break apart H bonds and disrupt hydrophobic interactions. acids and bases that break H bonds between polar R groups and disrupt ionic bonds. heavy metal ions that react with S-S bonds to form solids. agitation such as whipping that stretches peptide chains until bonds break . Denaturation of protein lecture 4 prof. Faten