Visually comparing bacteria and mammal genomes

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Background Information

Objective:  To have the user visually identify differences between mammalian and bacterial genomes

Difficulty:  Easy

Estimated Time:  under 10 minutes

New Programs Used: OrganismView (video demonstration) & GenomeView (video demonstration)

Lesson

Introduction

     Bacteria and mammals are obviously very different organisms on the outside and inside, but both utilize DNA in very similar fashions. For example they both have sections of DNA that are transcribed into mRNA, which then codes for and is translated into proteins. Nevertheless, when comparing the locations of coding regions on DNA an obvious difference emerges.


Part 1 - Find and observe a mammalian genome

  1. Open OrganismView (quick link) and search for one of the following mammals: Dog, Human, Pig, Horse, or any other mammal you can find in the results field

           - Note: many of the results will be for viruses associated with the animal you searched for.  To be sure you selected a mammal and not a virus look in the "Organism Information" box for "Mammalia"


     2.  Make sure the mammal you searched for is highlighted then click Launch genome viewer near the bottom left side of the page
Horse genome.jpg

           - Note: This will open GenomeView in a new window that displays the mammal's genome.  You can navigate the genome by using your mouse to zoom out and sliding to the right.  The green and grey boxes with arrowheads represent genes. Though there are many graphics to represent other things (i.e. Genomic features) in genomes: example graphics.


     3.  Quickly observe the gene locations, note the space they take up in the genome, their proximity to other genes, and their structure (e.g. introns and exons)


Part 2 - Find and observe a bacterial genome

     1.  Open OrganismView (quick link) and search for Escherichia coli (commonly known as E. coli) and select the first result

     2.  Click Launch genome viewer and observe the organism's gene
Wiki-mammals-Ecoli.jpg

     3.  Quickly observe the gene locations, note the space they take up in the genome, their proximity to other genes, and their structure (e.g. introns and exons)


Part 3 - Identify differences between mammals and bacteria

     1.  List two obvious differences between the genome

     2.  Propose some hypothesizes that explain these differences


Part 4 - Additional concepts

  • What is an operon?
  • Do mammal and/or bacterial genomes have operons?
  • What is the function of operons?

Conclusion

     You should have noticed that the bacteria's genome is significantly smaller than the mammal's genome, and that the genes in the bacteria are much closer together.  Another difference is in the structure of mammal and bacterial genes. Mammal genes often haven introns while bacterial genes never have introns. The mammal's genome is much larger than the bacteria's for MANY reasons.  One reason is that mammal's have many more genes and another reason is that a lot of mammals' genomes don't code for protein. For example, ~83% of the E. coli genome codes for protein, while only ~1.1% of the human genome codes for protein. One suggestion as to why genes in bacteria are located so closely is that bacteria need to rapidly reproduce and a smaller genome makes cell division faster.  In short, bacteria want to minimize the amount of their genome that codes for nothing or whose code is unnecessary.


Biology you should learn from this

The Operon:  An operon is a segment of DNA that codes for many genes.  The special thing about operons is that the genes within them are either all expressed together or none are expressed, as if there is only one on/off switch for all the genes.  Having genes regulated (turned on / off) together allows the bacteria to easily control genes that work together.

     Why would this be useful for bacteria?  -  Well, if a bacteria wants to convert lactose, a difficult molecule to digest, to glucose, a simple sugar, it needs a few different proteins to do this.  Additionally, the bacteria does not want to waste energy on making these proteins when no lactose is present.  An operon can be used as an on/off switch for all of these genes so that all of the genes are made in the presence of lactose and none are made in its absence.  The operon saves 'DNA space' by only requiring one switch for several genes.

See Also

Previous Lecture:  Required Background Information

Next Lecture:  Computationally Comparing Different Genomes

All Lectures:  Tutorial for High School Students

More on operons:  Lac operon