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Lecture 4

BIOC12FAll2012 Lecture Week 4 Notes

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Biological Sciences
Rongmin Zhao

2012 Lecture Week 4 Structure of Proteins Chapter 6 Notes 1192012 120200 PM BIOC12Fall2012 Lecture Week 4 Structure of Proteins Chapter 63D Structure of a Protein o Primary Structure the protein amino acid sequence o Secondary Structure the local spatial arrangement of a polypeptides backbone atoms through Hbond interactions without consideration of side chains o Tertiary Structure 3D structure of the entire polypeptide chain o Quaternary structure spatial arrangement of different polypeptide chains in a proteinnot all proteins have a quaternary structure Human Hemoglobin and its 3D structureo Human hemoglobin contains 4 polypeptide chains subunits 2 alpha and 2 beta chainsoo the sequence in part a is a fragment from the BchainDifferent Ways to View 3D structureso Space filling modelEach atom is shown as a solid sphereIt shows the overall shape of the protein and the surface exposed to the aquous solvent Excellent to show surface ligand binding Ballandstick model o Excellent for showing bonding arrangemento Backbone model o Shows general course of the polypeptide chaindifficult to see secondary structureso Only shows the bonded amide bonds backboneo Cartoon ribbon diagram o Concentrates on the backbone of the polypeptide chaino Amino acid side chains are eliminatedeasier to see 3D shapeo Can see into the interior of the proteino Can use diagram to depict the common folds and patterns in proteinso Noncovalent Interactions Stabilize the Higher Levels of Protein StructureSecondary tertiary and quaternary structure of proteins is formed and stabilized by weak forcesHydrogen bonds are formed wherever possibleHydrophobic interactions drive protein folding Ionic interactions occur on the protein surfaceCan der Waals interactions are abundant Electrostatic Interactions in Proteins Electrostatic interactionsionic interactionsoccurs between 2 charged atomsExample between lysine and glutamate in IRAK4 which is an enzyme that phosphorylates other proteins A Proteins Conformation Can be Described as Its Overall 3D Structure BIOC12FAL
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