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Hemoglobin: Soup to Nuts

Hemoglobin: Soup to Nuts. "A discovery is like falling in love and reaching the top of a mountain after a hard climb all in one, an ecstasy induced not by drugs but the revelation of a face of nature that no one has seen before" -Max Perutz. The Issue.

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Hemoglobin: Soup to Nuts

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  1. Hemoglobin: Soup to Nuts "A discovery is like falling in love and reaching the top of a mountain after a hard climb all in one, an ecstasy induced not by drugs but the revelation of a face of nature that no one has seen before" -Max Perutz

  2. The Issue • How to use one data set to answer multiple questions in multiple classes • Introduce the data set and a simple problem in General Biology (Introductory Cell Biology and Genetics) • Expand the depth and sophistication of questions (but use the same data set!) for more advanced courses (Genetics, Microbiology, Molecular Biology, Biochemistry, Evolution….)

  3. The Answer • Hemoglobin! • DNA and protein sequences are available for the various globin proteins (alpha, beta, embryonic, fetal, adult, disease-causing mutants, plant leghemoglobin) • Crystal structures are available for various globin proteins • Initial time spent setting up data set will pay off in multiple classes AND prevent the Las Vegas syndrome many students exhibit

  4. The Las Vegas Syndrome • “What happens in Vegas stays in Vegas.” • Students seem reluctant to bring knowledge from one class to another class • Using a single molecule for various types of analysis in several classes may help cure the dreaded L.V. Syndrome

  5. Hemoglobin for Introductory Cell Biology and Genetics • Hemoglobins are the oxygen-carrying proteins in red blood cells. They are tetrameric (4-chain) proteins containing two copies each of two different polypeptide chains, which is called the structure. In addition each polypeptide chain contains a heme group, which is a ring-shaped organic molecule in which iron is embedded and to which oxygen is bound.

  6. In humans there are in fact two groups of closely related genes encoding the alpha chain family on Chromosome 16 and the beta chain family on Chromosome 11. Different alpha and beta chain family members are expressed at different times during normal human development. There are embryonic alpha and beta forms that are expressed only during the first 6 to 8 weeks of gestation, after which there is a shift to expression of the adult form of the alpha chain and fetal forms of the beta chain. At about the time of birth adult forms of the beta chains also appear, and these "adult" forms of both chains are normally expressed throughout the remainder of an individual's life. The embryonic and fetal forms of hemoglobin bind oxygen more strongly than the adult form, ensuring that the fetus obtains adequate oxygen in the womb.

  7. Heme group Globin subunit Oxygen (red)

  8. Introduction to workbench • Use ClustalW to align an alpha sequence and a beta sequence • Explain rooted and unrooted tree function

  9. The exercise • Download file of normal embryonic, fetal and adult hemoglobin amino acid sequences • Perform an alignment using ClustalW • Determine which sequences are alpha-like and which sequences are beta-like

  10. >Human_alpha chain MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNA VAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSK YR >Human beta chain MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN ALAHKYH >Human epsilon chain MVHFTAEEKAAVTSLWSKMNVEEAGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGNPKVKAHGKKVLT SFGDAIKNMDNLKPAFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFGKEFTPEVQAAWQKLVSAVAI ALAHKYH >Human epsilon globin MVHFTAEEKAAVTSLWSKMNVEEAGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGNPKVKAHGKKVLT SFGDAIKNMDNLKPAFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFGKEFTPEVQAAWQKLVSAVAI ALAHKYH >Human zeta globin MSLTKTERTIIVSMWAKISTQADTIGTETLERLFLSHPQTKTYFPHFDLHPGSAQLRAHGSKVVAAVGDA VKSIDDIGGALSKLSELHAYILRVDPVNFKLLSHCLLVTLAARFPADFTAEAHAAWDKFLSVVSSVLTEK YR >Human delta globin MVHLTPEEKTAVNALWGKVNVDAVGGEALGRLLVVYPWTQRFFESFGDLSSPDAVMGNPKVKAHGKKVLG AFSDGLAHLDNLKGTFSQLSELHCDKLHVDPENFRLLGNVLVCVLARNFGKEFTPQMQAAYQKVVAGVAN ALAHKYH >HUMAN gamma-A MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPKVKAHGKKVLT SLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFGKEFTPEVQASWQKMVTAVAS ALSSRY >Human gamma globin MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPKVKAHGKKVLT SLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFGKEFTPEVQASWQKMVTAVAS ALSSRYH

  11. Alignment • Link to Workbench goes here showing alignment and rooted and unrooted trees

  12. Debriefing

  13. Future topics • Genetics, Evolution • Abnormal hemoglobins (thalassemias, sickle cell), selective pressures • Microbiology • Relationship of hemoglobin to leghemoglobin, differences in structure and function • Animal Physiology • Comparison of hemoglobins across taxa, oxygen binding coefficients as a function of sequence • Biochemistry • Oxygen loading, cooperativity

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