1. Mir Ishruna Muniyat

4. 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 ）

5.  Secondary structure is the regular arrangement of amino acid residues in a segment of a polypeptide chain, in which each residue is spatially related to its neighbors in the same Way.  The most common secondary structures are the α-helix, the beta-conformation, and beta-turns.

7.  Figure: Hydrogen-Bonding Scheme For an a helix. In the a helix, the CO group of residue n forms a hydrogen bond with the NH group of residue n+ 4.

9. A.A ribbon depiction with the a-carbon atoms and side chains (green) shown B.A side view of a ball-and-stick version depicts the hydrogen bonds (dashed lines) between NH and CO groups C. An end view shows the coiled backbone as the inside of the helix and the side chains (green) projecting outward D. A space-filling view

10.  The ß-Conformation Organizes Polypeptide Chains into Sheets  In the conformation, the backbone of the polypeptide chain is extended into a zigzag rather than helical structure.  The zigzag polypeptide chains can be arranged side by side to form a structure resembling a series of pleats.  In this arrangement, called a sheet, hydrogen bonds are formed between adjacent segments of polypeptide chain.

11.  Holds proteins in a parallel arrangement with hydrogen bonds.  Has R groups that extend above and below the sheet  In a ß-sheet, hydrogen bonds are formed between H- of NH- of one chain and carbonyl oxygen of adjacent chain (or segment).  These secondary structures can be of two types-  Antiparallel ( when the adjacent polypeptide chains run in opposite direction )  Parallel (a djacent polypeptide chains running in the same direction)  The tendency of a peptide for forming ß-sheet also depends on its sequence.

12.  Characteristics of the Beta-pleated sheet include- 1. – Each peptide bond is planar and has the trans conformation 2.- The C=O and N-H groups of peptide bonds from adjacent chains point toward each other and are in the same plane so that hydrogen bonding is possible between them 3.- All R- groups on any one chain alternate, first above, then below the plane of the sheet, etc.

13. Figure: An Antiparallel b Sheet. Adjacent b strands run in opposite directions. Hydrogen bonds between NH and CO groups connect each amino acid to a single amino acid on an adjacent strand, stabilizing the structure.

14. Figure:A Parallel b Sheet. Adjacent b strands run in the same direction. Hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand.

19.  The b-turn is the simplest secondary structure and turn, connecting two helices and/or sheets.  The turn ultimately reverses the direction of the chain.  The turn is composed of four amino acid residues, where the CO of the 1st amino acid residue hydrogen bonds with the NH group of n+3 residues from it.  They are known as well as  reverse turns,  hairpin bends or  Omega-loops;  Beta-turn loops allow for protein compaction, since the hydrophobic amino acids tend to be in the interior of the protein, while the hydrophilic residues interact with the aqueous environment.

20. Figure: Structure of a Reverse Turn. The CO group of residue i of the polypeptide chain is hydrogen bonded to the NH group of residue i + 3 to stabilize the turn.

21.  They occur often in 5 amino acid residues or less.  They lie on the protein surface because they are hydrophilic.  Two types of b-turns are defined as Type I or Type II.  In Type I b-turns the CO group of n+1 residue points away from the side chains of residues n+2 and n+3.  In Type II b-turns the CO group of n+1 residue points in the same direction of side chain n+2 where the n+2 residue is always glycine.

23. Type I turns occur more than twice as frequently as Type II. Type II ß-turns always have Gly as the third residue. Note the hydrogen bond between the peptide groups of the first and fourth residues of the bends. (Individual amino acid residues are framed by large blue circles.)

24.  Observe in the following figure how alpha-helix structures and Beta- conformations (beta strands represented by arrows) are linked through bents and beta turns that make this protein compact

25.  Different amino acids favor different kind of secondary structures:  while alanine, glutamate, and leucine have a propensity for being in α helices,  valine and isoleucine apparently favor β strands, and  glycine, asparagine, and proline tend to be present in beta-turns.

26.  The folding pattern of the secondary structure into a three-dimensional conformation  The tertiary structure of proteins is usually defined as the spatial conformation of the protein stabilized through several interactions between the R side chains of distant amino acids residues.  Distant means that they can be very apart in the sequence, but because of the molecule folding, their lateral chains can interact through their functional groups.  These interactions stabilize the spatial conformation of the protein.

27.  The main interactions that maintain the spatial conformation of the proteins are:  Hydrophobic interactions  Hydrogen bonds between the R side chain of distant amino acids  Ionic interactions  Disulfide bridges

29.  The structure that results of the assembly of several polypeptide to make an unique functional protein.  Stabilized through several noncovalent interactions between the R side chain of amino acids from different peptide chains.  The non covalent interactions that maintain this structure are the same non covalent interactions that maintain the tertiary structure:  Hydrogen bonds,  Ionic interactions,  Hydrophobic attractions and  Van der Waals Forces.

30.  Some examples for clarifying the concept:  Myoglobin is formed by a single peptide chain and a hem group. Since Myoglobin is formed by just one peptide chain, it does not show quaternary structure.  Insulin, for example, is formed by two peptide chains, but since these two chains are linked by disulfide linkage, insulin does not qualify as a protein with quaternary structure.  Hemoglobin is formed by four peptide chains (and four Hem groups) that are forming a unique functional protein.  These peptide chains are associated through non covalent bonds between their lateral chains: Hemoglobin is the typical example of a protein with quaternary structure.

31. Quaternary Structure