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Structure of Proteins Structure of Proteins

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Relationship btw structure and function : 

Relationship btw structure and function Different proteins can be formed from 20 a.a in diff sequences determined by the genetic code Native conformation of a protein( unique 3D structure) is determined by the sequence Binding sites are formed after folding, dictating function of the protein

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Changes in protein structure Conformational changes in proteins that affect solubility and degradability E.g. Amyloidosis- Ig chains form an insoluble protein aggregate called amyloid in organs and tissues Prion diseases result from misfolding and aggregation of normal cellular protein SCA, point mutation in Hb affects the 4° structure and its solubility, not ability to bind oxygen Clinical consequences

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Proteins rock! Roles that proteins play: Catalytic Structural Regulatory Cell differentiation Cell communication Muscle contraction Transport Storage

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Primary structure - linear sequence of amino acids - peptide bonds Secondary structure - local folding( Regular arrangements of amino acids) - H-bonding within the backbone Tertiary structure - over all folding and 3D conformation - mainly R group interactions within one chain Quaternary structure - multi-chain interactions - mainly R group interactions among polypeptide chains Description of Protein Structure? Levels of Structure

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Primary structure gives the kind, number and sequence of amino acids in the linear polypeptide chain. basis for abnormality in genetic diseases starts with the N-terminus and ends with the C-terminus amino acids ends are joined together by peptide bonds in a polypeptide chain Primary structure

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Peptide Bond Formation

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Characteristics of the peptide bond -partial double bond (shorter, rigid and planar) -trans configuration -polar and involved in hydrogen bonding

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Secondary structures locally folded structure/regular arrangements in regions of the polypeptide mainly formed through hydrogen bonds between backbone atoms Types: stable secondary structures (interior and surface) alpha helices beta-sheets unstable secondary structures (surface) bends, random coils, loops, turns

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right -handed helix H-bonding almost parallel to main axis of helix (weak bonds) allows extensibility PRO and GLY disrupt alpha helices ?-helix

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?-bends Reverse the direction of a polypeptide chain, helping it form a compact, globular shape Often found on the surface of protein molecules Generally composed of four amino acids with proline and glycine as common components

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SUPER Secondary structures combinations of secondary structures also called motifs

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Tertiary structure describes the packing of alpha-helices, beta-sheets and random coils with respect to each other on the level of one whole polypeptide chain due to R group or side chain interactions or between R groups at a distance and backbone associated with domains

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Tertiary structure Side chain interactions (R groups) which stabilize the tertiary structure H-bonds – O or N bound H atoms of Ser, Thr with COO- or carbonyl grp.? solubility Disulfide bonds – Cysteine ?Cystine e.g. in Igs secreted by cells Ionic Bonds – btw acidic n basic side chains (salt bridges) Hydrophobic interactions – non-polar side chains on the interior and vice-versa

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Quaternary structure only exists if there is more than one polypeptide chain present in a complex protein describes the spatial organization of the chains associated with subunits assembled usually via electrostatic, H-bonding or hydrophobic interactions

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Chaperones (“heat shock” proteins) Specialized group of proteins assists protein folding prevent protein aggregation and misfolding by limiting the number of unproductive folding pathways

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Why do proteins fold? To achieve a stable 3D Conformation Flexible Able to function in the correct site of the cell Capable of being degraded by cellular enzymes

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Protein Denaturation Unfolding and disorganization of the protein’s secondary, tertiary and quaternary structures. Peptide bonds are not hydrolyzed. (Primary structure) Denaturing agents: heat, organic solvents, mechanical mixing, strong acids or bases, detergents and heavy metal ions lead and mercury Ideally, protein denaturation is reversible. Folded Protein Unfolded Protein

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Protein Misfolding Diseases When we boil or fry an egg, the proteins in the white unfold. But when the egg cools, the proteins do not return to their original shapes. Instead, they form a solid, insoluble (but tasty) mass. This is misfolding !

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When Proteins Go Unwell Mutation in the DNA so that the amino acid sequence differs from normal. Lack of an enzyme or chaperone needed to fold a protein. Correctly folded protein becoming misfolded by accumulated damage due to oxidation or other chemical reaction. Interaction with other misfolded proteins.

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a group of protein misfolding diseases characterized by the accumulation of insoluble fibrillar protein that leads to cell death and tissue degeneration Amyloidosis

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?-antitrypsin emphysema Ig light chain myeloma Apolipoprotein hereditary aortic disorder Cystatin C cerebral hemorrhage Procalcitonin thyroid medullary cancer Amylin diabetes type 2 Bri-L familial British dementia keratoepithelin dystrophy of the cornea ?-2-microglobulin dialysis related amyloidosis A? peptide Alzheimer Disease ?-synuclein Parkinsonism Huntingtin Huntington Disease Amyloidoses

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Mad cow and other mad species are infectious diseases transmitted by prions known as TSE- CJD, Scrapie and BSE transmitted by inoculation, cannibalism, genetic inheritance PrP PrPSc FIBRILS Infectious Non-infectious

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Character may be manifested in the great moments, but it is made in the small ones. – Phillip Brooks

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