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Midterm #1 Review This is a composition of lecture notes and other useful information for the first half of Protein Structure and Function. This covers X-ray crystallography, as well as Soubeyrand's protein structure section and everything leading up to

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University of Ottawa
John Baenziger

BCH 3125 REVIEW I INTRODUCTION TO PROTEINSProteins are a complex molecule with structures that are diverse and have diverse functionsFor a protein with a single polypeptide chain a small protein would be about 5 to 10 kDa a medium protein wouldbe 20 kDa and a large protein on the order of 50 kDaMultisubunit proteins are hugeWhat are the roles of proteinsProteins are the molecule machines that make life possibleif we are to understand life we must understand protein functionand when proteins have mutations this lead sot human diseaseproteins are the targets of most pharmaceutical products if we understand how proteins work and what s not working properly in diseased states we may be ableto design pharmaceuticals that correct the abnormalities associated with human diseaseEnzymes catalyze the millions of chemical reactions that occur in cellsex luciferaseenzyme in fireflies which catalyzes the oxidation of luciferin releasing green lightTransporttransport proteins move molecules from one area of the body to another across membranes etcEx haemoglobin binds oxygen and transports it from lungs to peripheral tissues lipoproteins in blood carry lipids from the liver to tissuesNutrient and storagethe seeds of many plants store nutrients as proteinsovalbumin the major protein of egg whites nutrient proteincasein the major protein of milk nutrient proteinMobilityContractilityproteins allow cells to contract change shape and swimActin and myosin form contractile systems in skeletal musclesStructuralmany proteins serve as supporting filaments to give biological structuresEx fibroin is major component of spider webscollagen forms tendons and cartilage Defenseproteins defend organisms against invasionthe castor bean produces a protein called ricin that is cytotoxic in animalsHumans use antibodies to defend themselves against foreign invaders IgGRegulatorymany proteins regulate cellular activity mutations in proteins that control cell growth can lead to tumour formation The Story of Sickle Cell Anaemia Discovery of SCAAn individual named Walter Clement Noel from West Indiesfirst patient identified with sickle cell anaemiaSept 14 1904 he arrived in New York from Barbados to study at the Chicago College of Dental Surgery3 months later he was admitted to Chicago Presbyterian Hospital suffering from severe respiratory distressDr Ernest E Irons was the intern on dutythe attending physician was Dr James B Herrick blood smear showed the patient was anaemic about half the normal number of RBCs and that many ofthe blood cells adopted an elongated sickle shapethe doctors followed Noel for 25 years with admissions including respiratory problems muscle and joint pain etcwith other physicians it was noticed this was not an isolated case but no diagnosispatients often from tropical countries where malaria persistsat low O RBC of SCA adopt a sickle shapewhich does not pass easily through capillariesSickle cells are 2 usually cleared from blood in the spleen for destruction and recycling thus leading to anaemiathey can also block or impair circulation to peripheral tissue damagecells are also quite fragileat low oxygen levels they can rupture due to the formation of fibres inside the cells Experimental TechniquesIn the 1940s Linus Pauling hypothesized that Hb in SCA patients have a different shapetried new technique called ELECTROPHORESIS from negative end to positive end are separated the proteins HbS has between 2 and 4 fewer negative charges than HbAAnother way is to find the mutation in the proteineasiest to divide and conquer 1950s Vernon Ingram developed technique called PEPTIDE FINGERPRITNING1 purify both normal and HbS haemoglobin2 treat with samples of protease such as trypsin cuts after positive residues or chymotrypsin cuts afteraromatic residues3 separate out the individual peptides and identify the peptides with chemical differences either by HPLCor 2D separation 4 sequence the identified short peptide to identify chemical modifications Ingram showed that HbS has a Glu to Val mutation at position 6 of haemoglobin in the beta subunitCrystal Structure of myoglobin and haemoglobin 1962 Perutz and Kendrew Nobel Prize in Chemistry methods were first applied to myoglobin and then haemoglobin including from HbS crystal structure shows that glutamate is on protein surface while valine causes polymerizationThe Full ShaBANGOxygen changes the conformation of haemoglobinAt low oxygen concentration a pocket arises containingLeu88 and Phe85 on the beta chain of haemoglobinglutamate residue at position 6 is exposed to the solvent and does not interact with adjacent B chain due tohydrophobicity charge prefers to be surrounded by watervaline residue is nonpolar and when pocket is formed it is not solvated in water and enters pocket insteadcausing polymerizationwhen the haemoglobin polymerizes the sickle shape in the cell is formed and able to burststudies show that human disease can be caused by a change in chemistry of a proteinchemical basisDNA codes for amino acid sequences of protein understanding human disease requires elucidation of cellular function at the biochemical levelprotein structure dictates functionnoncovalent interactions are fundamental in protein structure and function and thus play a central role in all ofbiology and disease
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