Teacher Notes - Bioinformatics Activity Bank

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Process Coding Sequences of Transcripts
AP Computer Science Object Oriented Version
Teacher Notes
Overview and concepts
Overview
Students will complete a Java OOP program that consists of six classes which represent a Gene, a
Transcript, and Dictionaries. The Dictionary classes can be used for DNA to RNA transcription and RNA to
Protein translation. The Transcript class will contain methods to transcript a DNA coding sequence into an
mRNA sequence and to translate an mRNA sequence into a protein. The Gene class contains Transcript
objects.
Grade level
Grades 9-12
Concepts covered
Computer Science: OOP, constructors, methods, instance data, arrays, Lists, ArrayLists, dictionary
Bioinformatics: genetics, chromosomes, genes, DNA, RNA, mRNA, nucleobases (bases), DNA coding
sequence, transcript, codon, protein, amino acid, enzyme, transcription, translation
Prior knowledge required
Students must be familiar with Object Oriented Programming including constructors, methods, instance
data, inheritance, and abstract classes. They must also have a working knowledge of arrays, Lists, and
ArrayLists.
Activity notes
Time frame
 Teacher introduction to the Lab (Biology and Dictionary Data Structure): 30 minutes
 Student Internet research of DNA-RNA complementary bases used in transcription and codonamino acid relationships used in translation: 30 minutes
 Students work on lab (programming assignment): 200 minutes
 Teacher class discussions as necessary: 10 minutes
Materials
 Process Coding Sequences Assignment.doc - the student assignment.
 Process Coding Sequences Javadocs folder - the Java Documentation for the assignment. index.html
is the top-level page.
 Process Coding Sequences Assignment Student folder - the student starter code (includes a
JCreator project)
 Process Coding Sequences Assignment Teacher folder - the completed project
Teaching Tips / Activity Overview
1. Teacher introduces the Lab which includes
o Discussion of the purpose, goals, and work products of the lab.
o Review of the genetics concepts and definitions involved in DNA coding sequences, mRNA,
proteins, transcription, and translation.
o Introduction to the Dictionary Data Structure.
2. Student use the Internet to research DNA-RNA complementary bases used in transcription, and
codon-amino acid relationships used in translation.
3. Students work on lab (programming assignment). Each student is responsible for completing his
own assignment. Students may consult, but may not copy.
4. Teacher will circulate in the classroom as students work and
o help students as appropriate.
o make sure that students stay engaged.
o ask questions to assess understanding.
o discuss common difficulties with the class as a whole.
Assessment
 Pre-assessment: none
 Summative assessment: Teacher will observe student engagement during the programming.
 Post-assessment: Completed programming assignments will be evaluated for adherence to the
requirements specified in the assignment (90%) and programming style based on Checkstyle results
(10%).
Extensions
 The Dictionary class can be expanded in various ways:
o Methods could be added to make it more general including methods to add entries, remove
entries, and determine if the entries include a specific key.
o Entries could be maintained in sorted order.
 DNA Coding sequences and mRNA could be displayed in groups or three (codons).
 File Input/Output requirements have been minimized in this assignment. Students could write
code to process the chromosome21.txt file directly.
 A GUI (Graphical User Interface) could be added to improve the user interface to the assignment.
Resources
Teachers might benefit from the following websites:
 Introduction to Genetics: http://en.wikipedia.org/wiki/Introduction_to_genetics
 DNA: http://en.wikipedia.org/wiki/DNA
 RNA: http://en.wikipedia.org/wiki/RNA
 Base Pairs: http://en.wikipedia.org/wiki/Base_pair
 Codon to Amino Acid Table: http://www.biogem.org/codon.jpg
 DNA Transcription: http://library.thinkquest.org/C004535/dna_transcription.html
 RNA Translation: http://library.thinkquest.org/C004535/rna_translation.html
Acknowledgments
This lesson and teacher notes were produced by Robert Glen Martin, School for the Talented and Gifted,
Dallas ISD. They were based on a project by Dr. Jing Hu, PhD, Franklin & Marshall College, 2011
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