Transcript 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
• 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….)
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
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
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.
• 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.
Globin
subunit
Oxygen
(red)
Heme
group
Introduction to workbench
• Use ClustalW to align an alpha sequence
and a beta sequence
• Explain rooted and unrooted tree function
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
>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
Alignment
• Link to Workbench goes here showing
alignment and rooted and unrooted trees
Debriefing
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
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