Exercises For Week Three

The exercise this week explores the dynamics of two molecular components that form the telomerase ribonucleoprotein.
Human telomerase is responsible for the addition of (TTAGGG)n telomeric repeats at the ends of human chromosomes, a feat it accomplishes through the joint action of a reverse transcriptase (Telomerase Reverse Transcriptase, or TERT) and an associated RNA component (Telomerase RNA Component, or TERC).

The following accession numbers lead to the starting point:

Human TERC: NR_001566.1
Human TERT: AF015950.1

What I would like you to explore is the evolution of the two components of telomerase by comparing the patterns of divergence in 10 or more species. To do so, you must first find, download and align the TERC and TERT homologs in the same 10 (or more) species, and compare the patterns of differentiation you derive from these alignments. AT LEAST TWO OF YOUR SEQUENCES SHOULD NOT BE MAMMALIAN.

As you do so, I also want you to keep a couple of functional considerations in mind:

1) TERC is a functional (template) RNA- it will never be translated. That means that some of the constraints about gaps, etc… that so concerned us when we were aligning the HIV sequences in lab may not apply here. Remember, too, that the sequence of telomeric repeats is conserved within species, but differs across species.
2) TERT is known to have two clear functional domains- one responsible for attachment to the RNA (RNA binding domain), another for the reverse transcriptase activity.

Given that Swami appears to still be down, you may want to do this either in the Biology Workbench, or at NCBI. This is a chance for you to take advantage of some of the many tools available at NCBI—I direct your attention specifically to the choices along the right margin of the screen. I, for example, might be tempted by a link called “Run Blast”, or one entitled “Homologs of the TERT Gene”. But that's just me.

Here are the questions that I need you to address in your report. Each of them has multiple correct answers, but please explain your reasoning.

1) Should this analysis (for TERT) be done at the DNA or the protein level? Why?
2) How are you selecting the parameters for your multiple alignment? Are you making different choices for the two components? Why, or why not?
3) Which of the two components of telomerase is evolving more quickly? How do you know (I need a quantitative answer here).
4) Can you – from the alignments— recognize the functional domains in TERT? In TERC? Where are they (give locations in relation to position numbers in the two reference sequences listed above). How did you figure this out?
5) (extra credit) Are either of these components evolving in clock-like fashion? How did you go about addressing this question?
6) (extra credit) Do paralogs of TERT exist in the human genome? Can paralogs of TERC be found in the human genome?