Strings and Files
Class
AP Computer Science
Teacher
Mark Rorabaugh
Unit
Strings and Files
Lesson
Bioinformatics
The Cartoon Guide to Genetics, Larry Gonick, Harper Collins Publishers, 2005
DNA Tutorial Website: www.dnatutorial.com/ReplicationofDNA.shtml
Ensembl Genome Project: www.ensembl.org/index.html
Materials
DNA Online Quiz: www.rcs.rome.ga.us/hargett/biology/dna/qzDNA.htm
DNA/RNA Protein Synthesis Quiz:
www.cst.cmich.edu/users/benja1dw/bio101/tools/quiz/dnarna.htm
Goals & Essential Questions
PA Academic Standards for Science and Technology
3.2 Inquiry and Design:
3.2D Identify, apply, analyze and use the technological design processes to solve
problems.
3.3 Biological sciences:
3.3C Describe and explain gene inheritance and expression at the molecular level.
3.6 Technology education:
3.6B Apply knowledge of information technologies of encoding, transmitting, receiving,
storing, retrieving and decoding.
Established
Goals/Standards 3.7 Technology devices:
3.7C Apply and evaluate basic computer operations and concepts.
3.7D Utilize and evaluate computer software to solve specific problems.
3.8 Science, Technology and Human Endeavors:
3.8A Analyze, synthesize and evaluate the interactions and constraints of science and
technology on society.
3.8B Analyze and apply the use of ingenuity and technological resources to solve
specific societal needs and improve the quality of life.
3.8C Evaluate the consequences and impacts of scientific and technological solutions.
Essential
Questions
How do I write a Java computer program that can be used to transcribe a DNA Codon
into mRNA, and then translate the mRNA sequence into the correct amino acid?
Know
BIOLOGY
Codon
DNA
DNA Sequencing
Genetic Code
Genome
mRNA
Mutation
Nucleotide
Protein Synthesis
Ribosome
RNA
Start Code
Stop Code
Termination Sequence
Transcription
Translation
SNP
COMPUTER SCIENCE
String Class
File Streams
Loops
Arrays
ArrayLists
Decision Structures
Graphical Use Interface
(GUI) Environment
Methods
Classes
Objects
Understand








Reading a DNA Sequence
Transcribing a DNA sequence
into mRNA sequence
Translating a mRNA sequence
into a protein sequence
Recognizing a Start Code and
Stop Code in the mRNA
Sequence
Reading of a Codon Chart or
Table
Recognizing invalid or
unreadable mRNA sequences.
The FASTA Format for
representing nucleotide
sequences in the Ensembl
database.
Recognizing effects of a
mutation in the DNA
sequence.
Do






Translate a small sample DNA
Sequence into a Protein
Sequence by hand.
Write a Java program to
translate a sample DNA
Sequence from the keyboard
into a Protein sequence for
display.
Write a Java program to
translate a sample DNA
Sequence from a text file into
a Protein sequence for either
display or to a text file.
Download a DNA sequence
for a given chromosome from
the Enbembl Genome Project
Website.
Write a Java program to find
the effects of a SNP in the
genetic code.
Locate the staring positions of
a given DNA sequence
supplied by the user.
Planned Learning Activities & Assessments
Day 1: Review the basic terminology and basic concepts of The Genetic Code. Using the basic
resources provided, study the process of transcribing a DNA sequence to mRNA, then translating
mRNA sequence to a protein sequence. Students will have access to the materials described above.
Formative Assessment: DNA Online Quiz.
Assignment: More research on DNA Basics
Day 2: Formative Assessment: DNA / RNA/ Protein Quiz. Use this quiz to determine the readiness of
the class for this project. Give the students some simple DNA sequences to translate into a protein
sequence. Students will learn the major tests for validating the code:
1.
2.
3.
4.
Letters must be A, C, G, or T only.
The length of the code must be a multiple of three.
The coding must begin with a start codon (ATG).
The code must end with a stop codon (TAG, TAA, or TAG).
Teacher will observe the students as they work on these problems.
Programming Project #1: Given a Program Template, complete the code that will allow the user
to enter a simple DNA sequence from the keyboard. Test the sequence for validity. If there is an
error, indicate the reason for the error. If the sequence is valid, display the mRNA code, and the
resulting protein sequence.
Day 3: Review the concept of opening, reading, and closing text files.
Programing Project #2: Given a Program Template, complete the code that will allow the user to
select a text file that contains a DNA sequence. Test the sequence for validity. If the sequence is
valid, display the mRNA code, and the resulting protein sequence. This program will use the basic
structure of Programming Project #1. Output must be in a form that allows the user to easily
compare the DNA, mRNA, and Protein sequences.
Day 4: Review the concept of mutations (SNP) in the DNA sequence and the effect of producing
proteins based on this mutation.
Programming Project #3: Given a DNA sequence from a text file, randomly cause a mutation at
a single location in the DNA sequence. Compare this to the original sequence to determine
whether or not there is a change in the protein. Identify the mutation a silent, missense, or
nonsense.
Day 5:
Programming Project #4: Have the use enter a specific DNA sequence, then find the starting
location for all occurrences on this sequence for this given gene or indicate that it does not exist.