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16 th August 2013. carbohydrates , lipids , proteins and nucleic acids. Molecules of life . Packets of instantly available energy. Energy stores. Structural material. Metabolic workers. Libraries of hereditary information. Cell to cell signals. Slides by : J Sen. - PowerPoint PPT Presentation

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16th August 2013carbohydrates, lipids, proteins and nucleic acidsMolecules of life Packets of instantly available energyEnergy storesStructural materialMetabolic workersLibraries of hereditary informationCell to cell signalsSlides by : J Sen

Proteins are communication devices to conduct biological processes3How are Proteins made?DNA

RNA

Protein

Cellular processesTranscriptionTranslationProteinsEnzymes that carry out chemical reactions are largely proteins.

Most drugs bind to proteins to repair a faulty bio-machine to restore order in the system (organism).

Most drugs bind to proteins to repair a faulty bio-machine to restore order in the system (organism). HIV drugs that bind to a target protein exploits shape complementarityViruses infect by manipulating their proteins

Isolated Viral Capsid proteinFully formed stable virus particle

Proteins play crucial roles in all biological processesTrypsin, Chmytrypsin enzymes

Hemoglobin, Myoglobin transports oxygenTransferrin transports ironFerritin stores iron

Myosin, Actin muscle contraction

Collagen strength of skin and bone

Rhodopsin light-sensitive proteinAcetylcholine receptor responsible for transmitting nerve impluses

Antibodies recognize foreign substancesRepressor and growth factor proetins

Slides by : SankarBiopolymersBuilding Blocks

ProteinsAmino acidsNucleic acidsNucleotidesCarbohydratesSugarsLipidsFatty acids

ProteinsEnzymes carry out these reactions.

Proteins are polymers of amino acidsProteins talk to each other due to shape-complementarity.

The shape is important for its function.Proteins are made up of 20 amino acids

NH2 H C COOHR

R varies in size, shape, charge, hydrogen-bonding capacity and chemical reactivity.

Slides by : Sankar a very small tool kit!!

Only L-amino acids are constituents of proteinsSlides by : Sankar

Nonpolar and hydrophobicAcidicBasicSlides by : Sankar20 amino acids are linked into proteins by peptide bond

Slides by : SankarPeptide bond has partial double-bonded character and its rotation is restricted.

Slides by : SankarPolypeptide backbone is a repetition of basic unit common to all amino acids

Slides by : Sankar

YGGFL is a different polypeptide than LFGGYSlide by : J. Sen17AAlaalanineCCyscysteineDAspaspartic acidEGluglutamic acidFPhephenylalanineGGlyglycineHHishistidineIIleisoleucineKLyslysineLLeuleucineMMetmethionineNAsnasparaginePProprolineQGlnglutamineRArgarginineSSerserineTThrthreonineVValvalineWTrptryptophanYTyrtyrosineLarge proteins - sequence lengths are long.

One letter code is easier to work with than the three-letter codes for amino acids.Slide by : SankarLong polymers : from 20 amino acids

Fold into compact structuresPrimary structureADDFGFIPRELALKRMKGSTPNYProteins

Protein Structure: Four Basic LevelsPrimary Structure

Secondary Structure

Tertiary Structure

Quaternary StructureSlides by : Sankar

Slides by : SankarSETVPPAPAASAAPEKPLAGKKAKKPAKAAAASKKKPAGPSVSELIVQAASSSKERGGVSLAALKKALAAAGYDVEKNNSRIKLGIKSLVSKGTLVQTKGTGASGSFKLNKKASSVETKPGASKVATKTKATGASKKLKKATGASKKSVKTPKKAKKPAATRKSSKNPKKPKTVKPKKVAKSPAKAKAVKPKAAKARVTKPKTAKPKKAAPKKK Histone (human)MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPARhodopsin (human)An educated guess of the proteins function from the primary sequence

How does a proteins three dimensional structure emerge?The primary structure of the protein gives rise to the proteins shape in the following ways:

It allows hydrogen bonds to form between the C=O and N-H groups of different amino acids along the length of the polypeptide chain.

It puts R groups into positions that allow them to interact. Through their interactions the chain is forced to bend and twist.

Slide by : J. Sen

The anatomy of the peptide backboneThese atoms are on the same plane.The peptide bond is essentially plannarSlide by : J. Sen24Second level of protein structureHydrogen bonds form at short intervals along the new polypeptide chain and they give rise to a coiled or extended pattern known as the secondary structure of the protein.

Think of the polypeptide chain as a set of rigid playing cards joined by links that can swivel a bit. Each card is a peptide group. Atoms on either side of it can rotate slightly around their covalent bonds and form bonds with neighboring atoms.Slide by : J. SenAlpha helix ( helix)

Features:It is a rod like structure.

Backbone is inside while side chains are on the outside.

Hydrogen bonding between CO and NH groups of the main chain stabilizes the structure.

CO group of residue R hydrogen bonds with the NH group of residue R+4.

Rise per residue is 1.5 and rotation per residue is 100 degrees, therefore, residues per turn is 3.6.

Most -helices observed naturally are right-handed helices.

Slide by : J. SenPauling and Corey predicted the structure of -helix 6 years before it was actually experimentally observed for the structure of Myoglobin.

The elucidation of the structure of -helix is a landmark in Biochemistry because it was demonstrated that the conformation of a polypeptide chain can be predicted if the properties of its constituents are rigorously and precisely known.

For this work Pauling got the Nobel prize in Chemistry in 1954.The helical content of a protein may vary anywhere between 0% to 100%. 75% of AAs in Ferritin, an iron storage protein is in alpha-helices.-helices are usually less than 45 long. However, two or more -helices can entwine to form a very stable structure, which can have a length of 1000 or more. Such -helical coiled coils are found in many structural proteins e.g. myosin, tropomyosin in muscle, Fibrin in blood, Keratin in hair etc.

-helical coiled coilSlide by : J. SenBeta sheet ( sheet)Where residues per turn is 2 (n=2) it is a -pleated sheet structure. There are two kinds of -pleated sheet structures either the chains (strands) are such that in two successive chains they have same directionality for N>C or they are parallel chains (parallel -sheet) or they are in opposite/ anti-parallel orientation (anti-parallel -sheet).

Features:Distance between two successive amino acids is 3.5.

The side chains are at 180 to each other.

Adjacent -strands are linked by hydrogen bonds.

In antiparallel -sheets the hydrogen bonds between the CO and NH of adjacent strands form between groups that are diametrically opposite to each other.

In parallel -sheets hydrogen bonds between CO group of one amino acids forms with the NH group of two amino acids downstream in the other strand.

-strands are depicted by arrows schematically.

Slide by : J. Sen-sheet is an important structural element in many proteins e.g. fatty-acid binding proteins, important for lipid metabolism, are almost exclusively built of -sheets.

Many -strands (4-10 or more) may come together in a protein. These -strands may be all parallel to each other or anti-parallel or mixed.

A and B are ball and stick and ribbon model of the same polypeptide, respectively. -strands may have twists. Side view of the schematic in B demonstrates the twists.

A protein rich in -sheets, This is a fatty acid binding protein but not necessary that all fatty acid binding proteins are like this. Slide by : J. Sen