Lec 2 level 3-nu(structure of protein)
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Proteins have four levels of structural organization: primary, secondary, tertiary, and quaternary. The primary structure refers to the linear sequence of amino acids in the polypeptide chain. Secondary structure involves local folding patterns like alpha helices and beta sheets. Tertiary structure describes the overall 3D shape of a single polypeptide chain. Quaternary structure is the 3D structure formed by the assembly of multiple polypeptide subunits. The structures at each level are stabilized by interactions between the R groups of amino acids in the chain.
Lec 2 level 3-nu(structure of protein)
- 1. Nursing - 2 Structure of Protein 1
- 2. Protein Proteins are formed of amino acid residues linked together by peptide bonds. Structure of proteins Protein have different levels of structural organization; primary, secondary, tertiary and quaternary structure. These structures required for its specific biological function or activity. 2
- 3. This refers to the number and sequence of amino acids in the polypeptide chain. Each polypeptide chain has a unique amino acid sequence decided by the genes. The following example may be taken to have a clear idea of the term "sequence". Gly – Ala – Val or Gly – Val – Ala. Both the tripeptides shown above contain the same amino acids; but their sequence is altered. When the sequence is changed, the polypeptide is also different. The primary structure is maintained by the covalent bonds of the peptide linkages. 3
- 4. Importance of the understanding of primary structure: Many genetic diseases result in protein with abnormal amino acid sequences, which cause improper folding and loss or impairment of normal function. It help in diagnose or study the disease. 4
- 5. In protein, amino acids are joined covalently by peptide bonds, which are amide linkages between the α-carboxyl group of one amino acid and the α-amino group of another. Peptide bonds are not broken by conditions that denature proteins, such as heating or high concentrations of urea. Prolonged exposure to a strong acid or base at elevated temperatures is required to hydrolyze these bonds non-enzymatically. 5
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- 8. A fewamino acids together will make an oligopeptide. Combination of 10 to 50 amino acids is called a polypeptide. Bigpolypeptide chains containing more than 50 amino acids are called proteins. 8
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- 10. By convention, the free amino end (N- terminal) of the peptide chain is written to the left and the free carboxyl end (C-terminal) to the right. Therefore, all amino acids sequences are read from the N- to C-terminal end of the peptide. Linkage of many amino acids through peptide bonds results in an uncharged chain called a polypeptide. 10
- 11. Each component amino acid in a polypeptide is called a ‘residue’ because it is the portion of the amino acid remaining after the atoms of water are lost in the formation of the peptide bond. When a polypeptide is named, all amino acid residues have their suffixes (-ine, -an, -ic, or –ate) changed to –yl, with the exception of the C- terminal amino acid. For example, a tripeptide composed of an N- terminal valine, a glycine, and a C-terminal leucine is called valylglycylleucine. 11
- 12. The peptide bond has a partial double-bond character, that is shorter than a single bond, and is rigid and planar. This prevent free rotation around the bond between the carbonyl carbon and the nitrogen of the peptide bond. However, the bonds between the α- carbons and the α-amino or α-carboxyl groups can be freely rotated (although they are limited by the size and character of the R-groups). 12
- 13. This allows the polypeptide chain to assume a variety of possible configurations. The polypeptide bond is generally a trans bond (instead of cis), in large part because of steric interference of the R-groups when in the cis position. 13
- 14. Like all amide linkages, the –C=O and –NH groups of the peptide bond are uncharged, and neither accept nor release protons over the pH range of 2-12. Thus, the charged groups present in polypeptides consist solely of the N-terminal (α-amino group, the C-terminal (α-carboxyl) group, and any ionized groups present in the side chains of the constituent amino acids. The –C=O and –NH groups of the peptide bond are polar, and are involved in hydrogen bonds, for example, in α-helices and β-sheet structures. 14
- 15. The first step in determining the primary structure of a polypeptide is to identify and quantitate its constituent amino acids. A purified sample of the polypeptide to be analyzed is first hydrolyzed by strong acid at 110°C for 24 hours. This treatment cleaves the peptide bonds and releases the individual amino acids, which can be separated by cation-exchange chromatography. 15
- 16. In this technique, a mixture of amino acids is applied to a column that contains a resin to which a negatively charged group is tightly attached. The amino acids bind to the column with different affinities, depending on their charges, hydrophobicity, and other characteristics. Each amino acid is sequentially released from the chromatography column by eluting with solutions of increasing ionic strength and pH. 16
- 17. The separated amino acids contained in the elute from the column are quantitated by heating them with ninhydrin (a reagent that forms a purple compound with most amino acids, ammonia, and amines. The amount of each amino acid is determined spectrophotometrically by measuring the amount of light absorbed by the ninhydrin derivative. 17
- 18. Many polypeptides have a primary structure composed of more than 100 amino acids. Such molecules can not be sequenced directly from end to end. However, these large molecules can be cleaved at specific sites, and the resulting fragments sequenced. By using more than one cleaving agent (enzyme and/or chemicals) on separate samples of the purified polypeptide, overlapping fragments can be generated that permit the proper ordering of the sequenced fragments, thus providing a complete amino acid sequence of the large polypeptide. 18
- 19. Enzymes that hydrolyze peptide bonds are termed peptidases (proteases). Examples: Exopeptidases cut at the ends of proteins, and are divided into aminopeptidases and carboxypeptidases. Carboxypeptidases are used in determining the C- terminal amino acid. Endopeptidases cleave within a protein. 19
- 20. Coiling, folding or bending of the polypeptide chain leading to specific structure kept by interactions of amino acids close to each other in the sequence of polypeptide chain. There are two main regular forms of secondary structure; α-helix and β-pleated sheets . 20
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- 24. α- Helix β- Pleated 1. It is rod like structure, coiled 1. It is Sheet like structure, polypeptide chain arranged in composed of two or more spiral structure peptide chain 2. All the peptide bond 2. All the peptide bond components participate in components participate in hydrogen bonding hydrogen bonding 3. All hydrogen bonding are 3. Interchain between separate intrachain polypeptide chain and intrachain in Eg. It is abundant in hemoglobin a single polypeptide chain folding and myoglobin back on its self. 4. The spiral of α-helix prevents 4. The chain are almost fully the chain form being fully extended extended and relatively flat. They may be parallel or anti parallel. 24
- 25. 3. Tertiary structure of proteins: It denotes three-dimensional structure of the whole protein Occurs when certain attraction occurs between α- helix and β-pleated sheets to gives the overall shape of the protein molecules. It is maintained by hydrophobic bonds, electrostatic bonds and Van der Waals force. It is the three dimensional structure of each polypeptide chain. There are two main forms of tertiary structure: fibrous and globular types. 25
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- 27. Domains are the fundamental functional and three- dimensional structural units of polypeptides. Polypeptide chains that are greater than 200 amino acids in length generally consist of two or more domains. Folding of the peptide chain within a domain usually occurs independently of folding in other domains. Therefore, each domain has the characteristics of a small, compact globular protein that is structurally independent of the other domains in the polypeptide chain. 27
- 28. The following four types of interactions cooperate in stabilizing the tertiary structures of globular proteins: 1. Disulfide bonds. 2. Hydrophobic interactions. 3. Hydrogen bonds. 4. Ionic interactions. 28
- 29. Protein folding, which occurs within the cell in seconds to minutes. As a peptide folds, its amino acid side chains are attracted and repulsed according to their chemical properties. For example, positively and negatively charged side chains attract each other, similarly charged side chains repel each other. 29
- 30. In addition, interactions involving hydrogen bonds, hydrophobic interactions, and disulfide bonds all exert an influence on the folding process. This process of trial and error tests many, but not all, possible configurations, seeking a compromise in which attractions outweigh repulsions. This results in a correctly folded protein with a low-energy state. 30
- 31. Definition: It is loss of native structure (natural conformation) of protein by many physical or chemical agents leading to unfolding in the secondary, tertiary and quaternary structure of proteins. due to rupture of the non-covalent bonds (hydrogen bonds, hydrophobic bonds and electrostatic bonds and may be disulphide, but not peptide bonds), with loss of biological activity. 31
- 32. Denaturing agents: Heat Organic solvent Strong acid or base Detergent Ions of heavy metals such as lead and mercury 32
- 33. 4. Quaternary structure of proteins: Certain polypeptides will aggregate to form one functional protein. Proteins possess quaternary structure if they consist of 2 or more polypeptide chains (monomer or subunit). 33
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- 35. Primary structure Is determined by the sequence of amino acids Secondary structure Occurs when amino acids are linked by hydrogen bonds Tertiary structure Is formed when alpha helices and beta sheets are held together by weak interactions Quaternary structure Consists of more than one polypeptide chain 35
- 36. Protein folding is a complex, trial-and-error process that can sometimes result in improperly folded molecules. These misfolded proteins are usually tagged and degraded within the cell. However, this quality control system is not perfect, and intracellular or extracellular aggregates of misfolded proteins can accumulate, particularly as individual age. Deposits of these misfolded proteins are associated with a number of diseases 36
- 37. Causes: 1. Spontaneously. 2. By mutation in a particular gene, which then produces an altered protein. 3. After abnormal proteolytic cleavage in some apparently normal protein on a unique conformational state that leads to the formation of long, fibrillar protein assemblies consisting of β- pleated sheets. 37
- 38. Accumulation of these insoluble, spontaneously aggregating proteins, called amyloids Amyloids has been implicated in many degenerative diseases- particularly in the age- related neurodegenerative disorder, Alzheimer disease. The dominant component of the amyloid plaque that accumulates in Alzheimer disease is amyloid β (Aβ), a peptide containing 40-42 amino acid residues. The aggregation of this peptide in a β-pleated sheet configuration, is neurotoxic, and is the central pathogenic event leading to the cognitive impairment characteristic of the disease. 38