1. Amino Acid and Protein1

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3.  The formation of a peptide bond between glycine and alanine is shown in Figure 5.8. The product is called dipeptide, the reaction can be eliminated a water molecule. Amino Acid and Protein3 EGAK

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5.  The portion of each amino acids remaining in the chain is called an amino acid residue  Chains containing a few amino acid residues are collectively referred to as oligopeptides.  If the chain is very long, it is called a polypeptide. Oligopeptides and polypeptides are formed by polymerization of amino acids via peptide bonds  In writing the sequence of an oligopeptide or polypeptide that the convention is to always write the N-terminal amino acid (the residue has a free α-amino group) to the left, and the C-terminal to the right. (the residue has a free α-carboxyl group) Amino Acid and Protein5

6.  Large peptide chain. Protein polypeptide chain are typically more than 100 amino acid residue. All proteins are polypeptides. This is why understanding the nature of polypeptides and the peptide bond is so important a part of biochemistry.  Small peptide chains are common and often have important biologic roles. For example the hormone glucagon has 29 residues, vasopressin has 9 residue and thyrotropin- releasing hormone has 3 residue Amino Acid and Protein6

7. CONFORMATION OF PROTEINS Every protein in its native state has a unique three- dimentional structure, which referred to as its conformation. The function of a protein arises from its conformation. Protein structures can be classified into four levels of organization : primary, secondary, tertiary, and quartenary. Amino Acid and Protein7

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9.  The primary structure is the covalent “backbone” of the polypeptide formed by the specific sequence. This sequence is coded for by DNA and determines the final three dimensional from adopted by the protein in its native state Amino Acid and Protein9

10.  The secondary structure is the spatial relationships of neighboring amino acid residue. 1. Secondary structure is dictated by primary structure. The secondary structure arises from interactions of neighboring amino acids. Because DNA –coded primary sequence dictated which amino acids are near each other, secondary structure often form as the peptide chain comes off the ribosome. Amino Acid and Protein10

11. 2. Hydrogen bonds, these formation very important characteristic of secondary structure, (H-bond) between the CO- group of one peptide bond and the –NH group of another nearby peptide bond. (a). If the H-bonds form between peptide bonds in the same chain, either helical structure such as the α-helix develop or turn such as β-turns are formed. (b). If the H-bonds form between peptide bonds in different chains, extended structures form, such as the β-pleated sheet. Amino Acid and Protein11

12. 3. The α-helix is rod like structure with the peptide bond coiled tightly inside and the side chain of the residue protruding outward. (a). Characteristics (1.) Each –CO is hydrogen-bonded to the –NH of a peptide bond that is four residues away from it along the same chain 2.) There are 3.6 amino acid residue per turn of the helix, and the helix is right-handed (turn in a clockwise around the axis) (b). Helical structures in proteins were predicted by Linus Pauling from his studies of fibrous proteins. However, the α-helix can also be important in the structure globular proteins, although those chains are much shorter than the chains in fibrous proteins Amino Acid and Protein12

13. Amino Acid and Protein13  -Helix  -Sheet

14.  Tertiary structure refers to the spatial relationships of more distant residues 1. Folding. The secondary ordered polypeptide chains of soluble proteins tend to fold into globular structure with the hydrophobic side chain in the interior of the structure away from the water and the hydrophilic side chains on the outside in contact with water. This folding is due to associations between segments α-helix, extended β-chains, or other secondary structures and represent a state of lowest energy (greatest stability) Amino Acid and Protein14

15. 2. The conformation result from: a.Hydrogen bonding within a chain or between chains b.The flexibility of the chain at points of instability, allowing water to obtain maximum entropy and thus govern the structure to some extent c.The formation of other non covalent bonds between side chain groups, such as salt linkages, or η- electron interaction of aromatic rings d.The sites and numbers of disulfide bridges between Cys residues within the chain Amino Acid and Protein15

16. Amino Acid and Protein16

17. Quartenary structure refers to the spatial relationships between individual polypeptide chains in a multi chain protein; that is, the characteristic noncovalent interaction between the chains that form the native conformation of the protein as well as occasional disulfide bonds between the chains 1. Many proteins larger than 50 kdal have more than one chain and are said to contain multiple subunits, with individual chains known as protomers. 2. Many multisubunit proteins are composed of different kinds of functional subunits. Amino Acid and Protein17

18. Denaturation Denaturation is the organization of the overall molecular shape of a protein. It can occur as an unfolding of uncoiling of helices, or as separation of subunits. Denaturation is usually is accompanied by a major loss in solubility. Several reagents or physical force like heat, UV radiation, shaking, ethanol, heavy metals, and strong acids and bases that cause denaturation. Amino Acid and Protein18

19. Amino Acid and Protein19 denaturation renaturation

20.  The gene-encoded primary structure of polypeptide is the sequence of its amino acids. Primary structure are stabilized by covalent peptide bonds.  Its secondary structure results from folding of polypeptide into hydrogen- bonded motifs can form supersecondary motifs. Secondary structure (higher orders) are stabilized by weak force-multiple hydrogen bond, electrostatic bond (salt bond), and association of hydrophobic R groups.  Tertiary structure concern the relationships between secondary structure domains.  Quartenary structure of proteins with two or more polypeptides (oligometric proteins) is a feature based on the spatial relationships between various types of polypeptide Amino Acid and Protein20