Exploring hemoglobin with bioinformatics

These research activities are focused on using bioinformatics tools to understand the properties of hemoglobin and the effects of mutations in two of the hemoglobin genes (HBA and HBB).

Lesson I.  How does hemoglobin carry oxygen?

1.  Download oxyhemoglobin and deoxyhemoglobin from Digital World Biology's hemoglobin collection and open them in Molecule World (both the iPad and iPhone versions work for this).

2.  Open the sequence viewer in both structures and touch the label to highlight the heme groups (HEM).  (In the iPhone version, touch the eye and turn off the protein to highlight the heme groups.) 

3.  Open the color key and use it to help answer the following questions:

  • What does oxygen look in Molecule World?
  • How many heme groups are in hemoglobin?
  • In the oxyhemoglobin, how many heme groups are bound to oxygen?
  • In the deoxyhemoglobin, how many heme groups are bound to oxygen?
  • What atom does oxygen bind to in the heme group?
  • Alternate between the two structures, how does the structure of hemoglobin change when it binds oxygen?

 

Lesson II.  Which gene contains the sickle cell mutation?

To answer this question, you will use NCBI BLAST to compare a nucleotide sequence from a variant of the hemoglobin gene, associated with a common form of sickle cell anemia,  with the nucleotide sequences of HBA and HBB.  The HBA and HBB genes encode the two protein chains found in hemoglobin.    *Note:  the nucleotide sequences we're using are the DNA equivalents of the mRNAs, since this is the way scientists work with gene sequences.

1.  Go to the NCBI nucleotide BLAST page.  

2.  Check the "Align two or more sequences" box to compare sequences as shown in the image below.

3.  Copy the nucleotide sequence below and paste it in the top field (Query Sequence).  This sequence (HBS_variant) codes for the mutant sickle cell protein.

>HbS_variant
ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGT
GGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGC
AGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATG
CTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGC
TCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGAT
CCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCA
CCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCA
CTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACT
GGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC

 

4.  Copy all three sequences below and paste them in the bottom (Subject) field.   The first sequence is a positive control.

>HbS_variant
ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGT
GGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGC
AGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATG
CTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGC
TCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGAT
CCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCA
CCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCA
CTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACT
GGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC

>Homo_sapiens_HBB_mRNA 
ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGA 
GGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGC 
AGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATG 
CTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGC 
TCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGAT 
CCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCA 
CCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCA 
CTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACT 
GGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC

>Homo_sapiens_hemoglobin_HBA1_mRNA 
CATAAACCCTGGCGCGCTCGCGGCCCGGCACTCTTCTGGTCCCCACAGACTCAGAGAGAACCCACCATGG 
TGCTGTCTCCTGCCGACAAGACCAACGTCAAGGCCGCCTGGGGTAAGGTCGGCGCGCACGCTGGCGAGTA 
TGGTGCGGAGGCCCTGGAGAGGATGTTCCTGTCCTTCCCCACCACCAAGACCTACTTCCCGCACTTCGAC 
CTGAGCCACGGCTCTGCCCAGGTTAAGGGCCACGGCAAGAAGGTGGCCGACGCGCTGACCAACGCCGTGG 
CGCACGTGGACGACATGCCCAACGCGCTGTCCGCCCTGAGCGACCTGCACGCGCACAAGCTTCGGGTGGA 
CCCGGTCAACTTCAAGCTCCTAAGCCACTGCCTGCTGGTGACCCTGGCCGCCCACCTCCCCGCCGAGTTC 
ACCCCTGCGGTGCACGCCTCCCTGGACAAGTTCCTGGCTTCTGTGAGCACCGTGCTGACCTCCAAATACC 
GTTAAGCTGGAGCCTCGGTGGCCATGCTTCTTGCCCCTTGGGCCTCCCCCCAGCCCCTCCTCCCCTTCCT 
GCACCCGTACCCCCGTGGTCTTTGAATAAAGTCTGAGTGGGCGGCAAAAAAAAAAAAAAAAAAAAAA

 

5.  Click BLAST.

6.  Change the formatting options in the results to show the differences more clearly.  

To do this, click the Formatting options link at the top of the page, choose Pairwise with dots for identities, and click Reformat.

 

7.  Use your results to answer the question(s) below:

  • Which gene contains the Hemoglobin S sickle cell mutation?
  • What data tell you that you've identified the correct gene?

 

Lesson III.  How does the Hemoglobin S sickle cell mutation change the protein sequence?

To answer this question, you will compare protein sequences.

1.  Go to the NCBI protein BLAST page.  

2.  Check the "Align two or more sequences" box to compare sequences as shown in the image below.

3.  Copy the protein sequence of the normal protein chain and paste it in the top (query) field.  This is the chain that would be affected by the sickle cell mutation. 

>Human_Deoxyhemoglobin
VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGA
FSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANA
LAHKYH

 

4.  Copy all the sequences below and paste them in the bottom box.  

>Human_Deoxyhemoglobin
VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGA
FSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANA
LAHKYH

>Deoxyhemoglobin_S_Chain_A
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAV
AHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKY
R

>Deoxyhemoglobin_S_Chain_B
VHLTPVEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGA
FSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANA
LAHKYH

 

5.  Click BLAST.

6.  Change the formatting options in the results to show the differences more clearly.  

To do this, click the Formatting options link at the top of the page, choose "Pairwise with dots for identities," and click Reformat.

7.  Use your results to answer the question(s) below:

  • Which letter changes as a result of the Hemoglobin S sickle cell mutation?
  • Which protein chain contains the mutation?
  • Write down the two letters on each side of the mutation to give a five letter sequence.  *Each letter represents an amino acid.  

 

Lesson IV.  Where is the Hemoglobin S sickle cell mutation located in the hemoglobin protein?

1.  Open either oxyhemoglobin or deoxyhemoglobin in Molecule World.  (For this activity, you will need the iPad version).

2.  Change the coloring style to Molecule, so that you can tell the chains apart.

3.  Open the selection menu and type in the five letter sequence you found in part III.  

4.  Touch "Search" to highlight this sequence in the hemoglobin protein.

5.  Notice which chains contain this sequence and where this sequence is located in the protein.  

6.  Open the sequence viewer and touch the amino acids that are not the mutant residue to deselect them.  

7.  Change the coloring style to residue and use the color key to get the three letter code for the mutant residue.

8.  Touch the mutant residue and look at the number above the sequence viewer to see where it's located in the protein.

  • What is the three letter code for the mutant residue Hemoglobin S mutation and what is it's position in the protein chain?

 

Lesson V.  How does the Hemoglobin S sickle cell mutation affect the structure of the hemoglobin protein?

1.  Download Hemoglobin S from Digital World Biology's hemoglobin collection and open it in Molecule World.

2.  Compare the structure of hemoglobin S with the structure of either deoxyhemoglobin or oxyhemoglobin.  

3.  Highlight the mutant residue that you identified in part IV. 

  • How are the structures different?
  • Where is the mutant amino acid located?

 

 
    Resource files: 

    Privacy     |     Using Molecule World Images    |    Contact

    2017 Digital World Biology®  ©Digital World Biology LLC. All rights reserved.