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Online Lectures on Bioinformatics

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Biological preliminaries


Answers

  1. What does Hexokinase do?
    (hint: use Swissprot, Genecards, KEGG)


    Swissprot:
    Choose full text search, which gives the whole family and the comment:

    	 -!- CATALYTIC ACTIVITY: ATP + D-HEXOSE = ADP + D-HEXOSE 6-PHOSPHATE.
    	CC   -!- ENZYME REGULATION: HEXOKINASE IS AN ALLOSTERIC ENZYME INHIBITED
    	CC       BY ITS PRODUCT GLC-6-P.
    	CC   -!- PATHWAY: FIRST STEP OF SEVERAL METABOLIC PATHWAYS.
    	CC   -!- SUBUNIT: MONOMER.
    	CC   -!- SUBCELLULAR LOCATION: BOUND TO THE OUTER MITOCHONDRIAL MEMBRANE.
    	CC       ITS HYDROPHOBIC N-TERMINAL SEQUENCE MAY BE INVOLVED IN MEMBRANE
    	CC       BINDING.
    	CC   -!- IN VERTEBRATES THERE ARE FOUR MAJOR GLUCOSE-PHOSPHORYLATING
    	CC       ISOENZYMES, DESIGNATED HEXOKINASE I, II, III AND IV (GLUCOKINASE).
    	CC   -!- SIMILARITY: THE N- AND C-TERMINAL HALVES OF THIS HEXOKINASE
    	CC       SHOW EXTENSIVE SEQUENCE SIMILARITY TO EACH OTHER. THE CATALYTIC
    	CC       ACTIVITY IS ASSOCIATED WITH THE C-TERMINUS WHILE REGULATORY
    	CC       FUNCTION IS ASSOCIATED WITH THE N-TERMINUS.
    	CC   -!- SIMILARITY: BELONGS TO THE HEXOKINASE FAMILY.
    

    Genecards:
    shows which members exist in man.

    KEGG:
    search by EC (enzyme classification): swissprot lists hexokinase as EC 2.7.1.1
    -> Search and Compute with KEGG
    -> Search enzymes (matching EC numbers) in the metabolic PATHWAY database

    Result of Pathway Search:
    	map00010 Glycolysis / Gluconeogenesis
    	EC 2.7.1.1      Hexokinase
    	map00051 Fructose and mannose metabolism
    	EC 2.7.1.1      Hexokinase
    	map00052 Galactose metabolism
    	EC 2.7.1.1      Hexokinase
    	map00500 Starch and sucrose metabolism
    	EC 2.7.1.1      Hexokinase
    	map00530 Aminosugars metabolism
    	EC 2.7.1.1      Hexokinase
    



  2. Obtain the sequence of all yeast hexokinase proteins.
    (hint: use Swissprot at expasy)


    Swissprot entries with IDs HXKA_YEAST and HXHB_YEAST


  3. Obtain the yeast hexokinase A gene.
    (hint: EMBL entry SCHKA , ACcession number X03482 from EBI)


    EBI:
    -> Services
    -> Nucleotide Sequences
    -> Database Entry Retrieval
    -> Simple Sequence Retrieval


  4. Translate the gene and compare the protein sequence to the swissprot sequences.
    (hint: use ORF Finder at NCBI)


    Copy the DNA-Sequence found at EBI and paste it into the ORF Finder at NCBI.
    Compare the result to the Swissprot entry.


  5. Obtain the genomic DNA of a human hexokinase (AC MMHEXII3 from EBI) and translate it into protein.
    What's the result and why?
    Compare to human protein hexokinase 2.


    EBI: Copy the genomic DNA (Simple Sequence Retrieval: Acc. Number: MMHEXII3). Translate, e.g. by going to

    Swissprot
    -> Proteomics tools (bottom of the page)
    -> List of gene identification software sites
    -> GENESCAN home page

    Paste the sequence into GENESCAN and compare the result to the Swissprot entry of human hexokinase 2 (ID HXK2_HUMAN)

Comments are very welcome.
luz@molgen.mpg.de