Peptides. The two amino acids are joined through a dehydration reaction.

Transcription

1 Peptides

2 Peptides The two amino acids are joined through a dehydration reaction.

3 Peptides

4 The Peptide Bond The peptide bond is usually drawn as a single bond, but actually has considerable double bond character which prevents free rotation about the bond:the atoms of the double bond, and those directly attached to it, all lie in the same plane.

5 The Peptide Bond The trans-planar nature of the peptide bond accounts for the very high melting and boiling points and a lack of basicity in the simple amides, and plays an important role in determining three-dimensional structure and function in polypeptides.

6 Drawing and Naming Peptides 1) Different constitutional isomers are possible whenever amino acids react to form peptides. (Ala-Val Val-Ala) 2) All peptides have one free α-amino group (N-terminal or amino-terminal residue), and one free α-carboxyl group (C-terminal or carboxyl-terminal residue). 3) When drawing (or naming) peptides the standard convention is to place the N-terminal residue at the left and the C-terminal residue to the right.

7 Drawing a Peptide R R R R R R

8 Ionization of Peptides 1) As in the case of amino acids, each peptide has an isoelectric p (or pi ) at which it does not migrate in an electric field. 2) The pi value of a peptide containing only neutral amino acid residues or equal numbers of acidic and basic residues or both is in the range of pi values for neutral amino acids (p ). 3) The pi of a peptide containing acidic and basic amino acid residues is a) on the acidic side (lower than ) if there is an excess of acidic residues, and b) on the basic side (higher than ) if there is an excess of basic residues. 4) All amino and carboxyl groups, including those on side groups of acidic and basic amino acid residues, are charged at physiological p.

9 Physical Properties of Peptides 1) Peptides have solubility and electrophoresis properties that are p dependent. 2) Peptide solubility is lowest at its isoelectric point. 3) At a given p, each peptide has a particular electrical charge depending upon its isoelectric point and the number of ionizable groups it contains. 4) Electrophoresis can be used to separate peptides of differing charges 5) Peptides are often distinguished from proteins by the number of amino acid residues. Molecules having fewer than 50 amino acid residues are generally called peptides, regardless of physiological activity.

10 Drawing Peptides

11 2 N C C R N C C R N C C R Ala-Leu-Ser 3 N C C N C C N C C C3 C 2 C 2 C 3 C C 3 3 N C C N C C N C C C C 2 3 C 3 C C 3 C 2

12 Thr-Asp-Phe-Met 2 N C C R N C C R N C C N C C R R 3 N C C N C C N C C N C C C C 2 C 2 C 2 C 3 C C 2 S C 3

13 Lys-Val-Asn-Gly 2 N C C R N C C R N C C N C C R R 3 N C C C 2 C 2 N C C C 3 C C 3 N C C C 2 C N 2 N C C C 2 C 2 N 3

14 Glu-Gln-is-Tyr 2 N C C R N C C R N C C N C C R R 3 N C C N C C N C C N C C C 2 2 C C 2 C 2 2 C C 2 N C 2 N C N

15 Chemical Properties of Peptides 1) ydrolysis to amino acids 2) The amino acid cysteine contains a sulfhydryl group, - S. a)pairs of cysteine residues often link two peptide chains or two parts of one peptide chain through disulfide bridges: b)disulfide bridges in peptides may be represented using the 3 letter amino acid abbreviations. c)disulfide bridges generally survive hydrolysis reactions

16 Examples of Physiologically Active Peptides

17 Aspartame - 2 amino acids An Artificial Sweetener

18 Met enkephalin - 5 amino acids Reduces Pain Sensation

19 Bradykinin - 9 amino acids Powerful Vasodilator-Released by mast cells after injuries and during allergic responses. Similar to histamine in actions

20 xytocin 9 amino acids; 1 disulfide linkage Causes contraction of uterine muscles during labor.

21 Insulin 51 amino acids ; 3 disulfide linkages Regulator of carbohydrate metabolism and absorption

22 Insulin 51 amino acids ; 3 disulfide linkages Regulator of carbohydrate metabolism and absorption

23 Insulin Maturation

24 Insulin Gene Mutations

25 Protein Structure and Function

26 Protein Structure Classification of Proteins Based on Components Simple proteins - Proteins containing only polypeptides Conjugated proteins - Proteins containing nonpolypeptide molecules or ions 1) Apoprotein - The polypeptide part of a conjugated protein 2) prosthetic group - The nonpolypeptide part of a conjugated protein

27 Protein Structure Classification of Conjugated Proteins 1) Glycoproteins 2) emoproteins 3) Lipoproteins 4) Metalloproteins 5) Nucleoproteins 6) Phosphoproteins

28 Three-Dimensional Structure of Proteins The conformations of the individual bonds in all the amino acid residues within the protein produces a unique 3-D shape, which in turn produces a unique physiological function. The overall folding of a protein is described at four levels: 1º 2º 3º 4º

29 Levels of Protein Structure Primary structure is the amino acid sequence of a polypeptide. Secondary structure is the conformation in a local region of a polypeptide molecule. The conformation usually involves a regular coiling or layering of the protein chain. Tertiary structure exists when the polypeptide has different secondary structures in different local regions. Tertiary structure describes the threedimensional relation among the different secondary structures in different regions. Quaternary structure exists only in proteins in which two or more polypeptide molecules aggregate together. It describes the threedimensional relationship between the different polypeptides.

30 Determinants of Protein Conformation The most stable conformation of a protein is determined by:. 1) The bonds in the linear chain a) No free rotation about the peptide bond b) Limited rotations about the bonds of the alpha carbon 2) ydrogen-bonding between peptide amide bonds from different residues 3) Interactions of side chains with each other & with water a) The tendency of non-polar side chains to avoid water b) The attraction of non-polar side chains for each other 1º 2º 3º ydrophobic effect c) ydrogen bonding between polar side chains & water d) Ionic attractions between charged side chains e) Disulfide bonds between side chains

31 Secondary Protein Structure - The α-elix The polypeptide chain is arranged like a coiled spring with a hydrogen bond between each peptide group s C= oxygen and the hydrogen of the N- group of the fourth residue farther down the chain.

32 Secondary Protein Structure - The β-pleated Sheet Peptide chains are extended and run sideby-side each other in either a parallel or an antiparallel arrangement. Neighboring chains are held together by hydrogen bonds between an N- on one chain and a C= on a neighboring chain. Side chains extend alternately above and below the plain of the sheet.

33 Secondary Protein Structure - The β-pleated Sheet

34 Levels of Protein Structure

35 Levels of Protein Structure Representation of a Simple Protein

36 Protein Structure Structural Classification of Proteins Fibrous Proteins Silks, Keratins, Collagens 1) Elongated, water insoluble 2) Structural and contractile functions 3) No tertiary structure, but generally possess a single conformational pattern throughout most of the chain (secondary structure) 4) Most have a quaternary structure involving the aggregation of polypeptide chains Globular Proteins Enzymes, Antibodies, ormones 1) Remain soluble in water in order to carry out their metabolic functions 2) Spherical, Globular 3) Remain water soluble by folding up so as to segregate hydrophobic side chains in the interior of the molecule and hydrophilic side chains on the exterior of the molecule

37 Fibrous Proteins α-keratins The structural component of hair, horn, hoofs, nails, skin, and wool. These materials have a hierarchical structure. Coiling at higher and higher levels is a mechanism for enhancing physical strength.

38 Fibrous Proteins α-keratins The packing within the α-keratins is stabilized by disulfide bridges and secondary forces between different polypeptide molecules. Disulfide bridges are more important than secondary forces in imparting insolubility, strength, and resistance to stretching. Interchain disulfide bonds are often called cross-links. The degree of hardness of an α-keratin depends upon its degree of cross-linking. igh cysteine content results in increased hardness (hair, horn, nail) compared to low cysteine content (skin, callus).

39 Fibrous Proteins Permanent air Waving Permanent waving of hair is accomplished by breaking and reforming cysteine cross-links within the hair fiber:

40 Fibrous Proteins β-keratins β-keratins and Silk Fibroins The β-keratins make up the proteins in bird feathers, reptile scales, and silk fibroin. β-keratins are almost completely composed of β- pleated sheets.

41 Fibrous Proteins - Collagen The most abundant protein in vertebrates is collagen. Collagen is a stress-bearing component of connective tissues such as bone, cartilage, cornea, ligament, teeth, tendons, and the fibrous matrices of skin and blood vessels. Collagen contains much more glycine and proline and much less cysteine than does α-keratin. Much of the proline present is converted into hydroxyproline. A single collagen molecule forms a lefthanded helical structure, much more elongated than an α-helix. Three left-handed collagen helices twist around each other to form a righthanded superhelix called a triple-helix or tropocollagen. Tropocollagen is further organized into fibrils and higher-level structures.

42 Fibrous Proteins - Collagen diameter 1.5 nm nm 0.5-3μm

43 Fibrous Proteins - Collagen

44 Globular Proteins Globular proteins do not aggregate into macroscopic structures but remain soluble in order to carry out their metabolic functions: catalysis, transport, regulation, and protection. Globular proteins remain soluble by folding up in such a way as to segregate their hydrophobic amino acid side chains in the interior of the molecule, and their hydrophilic amino acid side chains on the exterior of the molecule, in contact with water.

45 Globular Proteins Myoglobin and emoglobin emoglobin in red blood cells binds oxygen in the lungs, transports it through the blood stream, and releases it in the tissues. Myoglobin has a higher affinity for oxygen than does hemoglobin and is found in muscle tissue. Myoglobin serves as a storage reserve for oxygen within the muscle.

46 Globular Proteins - Myoglobin Myoglobin consists of a single polypeptide chain containing 153 amino acid residues, organized into 8 α-helical regions that surround a prosthetic group called a heme group.

47 eme Group The iron atom on the heme group is the site of attachment of the 2 molecule.

48 In 1971, Professor of Biochemistry F. R. Gurd assembled a model of myoglobin. The model was constructed of precisely bent wire segments to represent the amino acids, each fragment fastened to its neighbors using links that were screwed together. Wires were stretched throughout the structure to ensure that the various parts were held in proper alignment. A separate "space-filling" model is visible in the background. Prof. Gurd required three weeks and an entire 20 X 30 foot room to assemble the model. Today, a comparable three-dimensional model of myoglobin can be displayed in a matter of seconds. (Univ of Indiana)

49 Levels of Protein Structure

50 Globular Proteins - emoglobin 4 polypeptide chains 2 α-chains (141 residues each) 2 β-chains (146 residues each) Each α and β chain folded in a manner similar to that of myoglobin contains a heme group capable of carrying oxygen

51 EMGLBIN A GLBULAR PRTEIN WIT QUATERNARY STRUCTURE The surfaces of the α and β chains contain some hydrophobic residues which cause all 4 chains to aggregate into a tetramer. A space at the center of the tetrameric structure can bind a molecule of 2,3-bisphosphoglycerate (BPG) which regulates the affinity of the hemoglobin molecule for oxygen.

52 Globular Proteins - Denaturation Denaturation - the loss of native conformation due to a change in environmental conditions. The non-functioning protein is called a denatured protein. Denaturation results from the disruptions of the weak secondary forces holding a protein in its native conformation. (Disulfide bridges confer considerable resistance to denaturation because they are much stronger than the weak secondary forces.)

53 Globular Proteins - Denaturation A variety of denaturing conditions or agents lead to protein denaturation: 1) Increased temperature (or microwave radiation) 2) Ultraviolet and ionizing radiation 3) Mechanical energy 4) Changes in p 5) rganic chemicals 6) eavy metal salts 7) xidizing and reducing agents

54 The sickle cell mutation causes hemoglobin molecules to clump t o g e t h e r i n a n a b n o r m a l manner. The valine in position 6 adheres to a notch on the o p p o s i t e s i d e o f a n o t h e r molecule of b, causing long chains to form.

55 In sickle cell anemia, the normal hemoglobin molecule mutates by exchanging the 6th amino acid on the beta chain from glutamic acid to valine. Normal b has the genotype SS. Sickle cell anemia occurs when an individual inherits two recessive alleles (ss). Sickle cell trait exists when one inherits the heterozygous condition (Ss). The malaria parasite (Plasmodium falciparum) does not survive in these individuals; they may have a slight anemia, but they survive better than either normal individuals (SS- who often die of malaria), or those who die of sickle cell disease (ss).

56 Sickle Cell Anemia

57 Sickle Cell Anemia Comparison of the distribution of malaria (left) and sickle-cell anaemia (right) in Africa