CT-STEM

Computational Biology: Dna Sequencing And Inherited Traits

Computational Biology: Dna Sequencing And Inherited Traits

Subject: Biology
Time: 2-3 class periods (45 minutes each)
Level: Grade 11-12, regular or AP biology

Overview

The students learn about computational biology careers and use professional computational biology tools to carry out DNA sequencing experiments.

Prerequisites

Students need to be familiar with the basics of DNA: they should know that DNA consists of 4 bases, A, T, C, and G, and that the arrangement of these bases codes for genes. Some understanding of algorithms would be helpful but is not required.

Background

Gene sequencing is all over the news these days. It wasn’t too long ago that scientist sequenced the human genome for the first time. Now, there are many genomes that have been sequenced, and people are both excited and terrified by the scientific advances that this might bring. Many news reports on this subject are somewhat misleading, however, in that they imply that by knowing the gene sequence, we know everything about the organism. However, a genome sequence is just a collection of letters. Suppose you have a gene sequence like ATTACGGGCGCAGCT. What could you say about the organism from which it came? In truth, biologists can’t say any more from that sequence than you can.

In the real world, a sequenced genome isn’t the end or the beginning of the end or even the end of the beginning. We need powerful computational techniques to assemble a genome, find the genes, and determine the functions of those genes.

One way to interpret a genetic sequence is to compare sequences. If we have, for example, a sequence of human DNA and we want to know its function, we might see if there is a similar sequence in an organism we have studied more thoroughly, such as yeast. If the two sequences are similar enough, then it is likely that they have similar function.

Comparing sequences is difficult, however, because DNA mutates. The comparison is done using an important computational biology program, the Basic Local Alignment Search Tool, or BLAST.

Compatible With


mac

windows

laptops

chrome books

phones

tablets

What's Next?

Standards

Computational Thinking in STEM
  • Computational Problem Solving Practices
    • Developing Modular Computational Solutions
  • Data Practices
    • Analyzing Data
    • Visualizing Data
  • Systems Thinking Practices
    • Understanding the Relationships within a System

Comments, Feedback, and Quesitons

Computational Biology: Dna Sequencing And Inherited Traits

Teacher Notes

In this lesson, you help your students work with BLAST, notice the similarities and differences between gene sequences, use BLAST to identify a mystery animal, work with their peers to determine the similarities and differences in genetic sequences between animals in a given Class, and then conduct their own research project using the data and CT tools available. This is done in five phases.

 

Phase I. Intro

Start by showing the Computer Science and Medicine promotional video from CS Education Week: http://www.youtube.com/watch?v=88A3ZqJSJs8

Phase II. Getting familiar with BLAST (through Sickle Cell Anemia)

Students are introduced to BLAST and one of its potential uses (determining the similarity between genes in different species). This is done in the context of scientists trying to find a cure for sickle cell anemia.

Before the Activity/Setup

  1. Post on the board gk12northwestern.wikispaces.com/Computational+Biology+with+BLAST

- Provides the links to the relevant websites and files needed for this activity.

With the Students

  1. Go through the slides in preSickleCellWorksheet.ppt (intro material).

  2. The students work individually or in small groups to complete the Sickle Cell handout.

  3. The Extra Credit (question #5) could be used for homework, or as an extension for students who complete the activity faster than others.

  4. Go through the slides in PostSickleCellWorksheet.ppt (career highlight)

Special note for Phase II. If short on time, Part I can be done as a class or as homework the night before.

 

Phase III.  Mystery Animal

Students use genetic sequences and BLAST to identify their mystery species. Then, with their ‘scientific collaborators’, they generate a hypothesis about the relatedness of the species within their group.

Before the Activity/Setup

  1. Post on the board gk12northwestern.wikispaces.com/Mystery+Animal+DNA+Sequences

- Provides the relevant files and link needed for this activity.

With the Students

The students work individually or in small groups to complete the Mystery Animal handout.

For Part I, you will need to assign each student a number between 1 and 30. Ideally everyone has their own number, but fine to repeat if you have more than 30 students.

For Part II

  1. Assign each ‘Class’ (e.g., Mammalia) to an area of the room. Place the page containing pictures of that ‘Class’ on a table in that area. Have the students find the ‘Class’ that contains their mystery animal and sit in that area.

  2. Remind the students that every student in the group must write down their hypothesis. It’s OK if they’re the same hypotheses, but they should all record it on their worksheet.

 

Phase IV. Using Phylogenetic Trees to Evaluate Evolutionary Relationships

Students create a phylogenetic tree for their group’s species to evaluate their evolutionary relationships.

Before the Activity/Setup

  1. Post on the board gk12northwestern.wikispaces.com/Correctly+Labelled+DNA+Sequences

- Provides the relevant files and link needed for this activity.

With the Students

  1. Show slides from PrePhylogeneticWorksheet.ppt (intro material).

  2. The students work individually or in small groups to complete the Phylogenetic Trees handout.

  3. Once the students complete the worksheet, have them draw their phylogenetic tree on the blackboard.

  4. Ask students to share with the class how their prediction(s) compare to what they see in their phylogenetic tree.

  5. Show slides from PostPhylogeneticWorksheet.ppt (career highlight).

Summarize previous phases: students have learned how to compare DNA sequences to one another by performing multiple sequence alignments, and they have used those alignments to construct phylogenetic trees to infer the evolutionary relatedness among the organisms in their group. They have also used these analyses to answer their research question, and to confirm or reject their hypothesis. They also learned the importance of scientific collaboration, by pooling or sharing their DNA data with other group members.

                                

Pre-class Preparation

The teacher should be familiar with and able to use the BLAST program available on the NIH website. If the teacher is able to run through the unit before giving it to the students, this should be sufficient.

 

Materials and Tools

Technology including software and files

Suggested resources or equipment needed

Supplementary documents or handouts

 

Assessment

The student handouts and the final presentation are used to assess student understanding.

Additional Information

These materials are adapted from curricular materials from the eCSite and from the Bio-ITEST program by the Northwest Association for Biomedical Research.

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