This bioinformatics course was developed by Dr. Sandra Porter over a ten year period as a semester-long course in the biotechnology program at Austin Community College with a shorter (5 week) version in the biotechnology program at Shoreline Community College. During this course, students learn background knowledge and practice in locating, using, and analyzing molecular information and using their analyses to predict the effects of mutations on a protein's structure and function.
Overview: By the end of the course, we want to be able to give a student a cDNA sequence with a mutation and have them identify the gene of origin, identify and characterize the mutation, identify the affected codon, where it is located in a gene, and the type of mutation (tmissense, nonsense, frameshift), use databases to find information about the mutation, locate the mutation in a molecular structure model, identify chemical bonds that would have been formed by the original amino acid, and predict how the mutation would change the ability to form those bonds. This is the final assignment in the course.
Course-in-a-Box access: To view other materials, log in to your InnovATEBIO account. If you are a biotech faculty member at a college or high school, join InnovATEBIO to get an account. Note - it may take a few days to verify your faculty position and set up the account.
Canvas users: Download and import An Introduction to Bioinformatics from Canvas Commons.
Textbooks: All texts are available in Apple Books.
Additional resources:
Hardware and Software:
1. A computer with a web browser (Chrome or Safari) is essential. Most of the activities can be done with an iPad, but some are easier with a touchpad.
2. Google docs or Microsoft Word
3. Each student should have access to an iPad throughout the course.
4. iCn3D or Molecule World - low cost, user-friendly, molecular modeling software, this runs on the iPad. Volume discounts are available through Apple.
5. Skitch - Skitch is an iPad app that allows you to add arrows and text to images. Skitch is free on the iPad.
Course Development: The order of topics and the need for different activities were identified through a process of backward design. Every year, I looked at the areas where students had problems and revised parts of the course to address those problems.
After taking this course, students should be able to do the following:
1. Locate public databases around the world that contain interesting biological data and conduct a search.
2. Use simple and advanced search tools to construct database queries at the NCBI.
3. Use database fields and indices to count the number of items within a particular database that match a description, for example, the number of exons in the gene database.
4. Use keyboard commands to quickly search web pages.
5. Distinguish between amino acids and nucleotides in a molecular structure.
6. Determine the net charge for an amino acid or nucleotide using molecular modeling software.
7. Determine whether an amino acid or nucleotide is hydrophobic or hydrophilic using molecular modeling software.
8. Use molecular modeling software to identify the following types of chemical bonds or interactions: covalent, disulfide, hydrogen, hydrophobic, ionic, metal.
9. Compare molecular models to identify differences and make predictions about the impact of the different structures on function.
10. Use sequence analysis software such as BLAST and sequence homology to discover ways to repurpose existing drugs to treat a new disease.
11. Use multiple alignment software to align sequences and create a phylogenetic tree to visualize relationships and identify amino acids that are important for protein function.
12. Interpret and use the information a genetic map to understand the size of a gene, the location of control elements, and the location and number of exons and introns.
13. Use a DNA sequence and sequence analysis software, such as BLAST, to determine whether a mutation in a DNA sequence substitutes a new amino acid for the previous residue, creates a frame shift, or inserts a stop codon.
14. Use information about a mutation to model the change in a protein structure in molecular modeling software. For example, if a mutation causes a frameshift, a student should be able to hide the amino acids that would be lost.
15. Predict the effect of a mutation based on the change in a protein’s molecular structure. For example, if a protein normally forms an ionic bond with another protein, and the mutation replaces a charged amino acid with a hydrophobic amino acid, a student should be able to explain why those two proteins no longer interact.
The schedule shown below is from the Austin BITC2350 Bioinformatics Spring 2019 syllabus. There are four main parts (Databases, Molecular Structure, Molecular Sequences, Genetic Variation) and 12 learning guides. Each learning Guide contains the assignments for a one week or two week period.
Week |
Date |
Learning guide and assignments |
Due |
---|---|---|---|
1
|
Jan 22nd
|
Part I Databases: Simple database searches 1. Complete the orientation survey 2. Discussion 1: Introductions: Introduce yourself and tell us what you'd like to learn about bioinformatics. 3. Get software and textbooks. 4. Take the syllabus quiz Assignment: A1. Orientation - start working on this & do reading Learning guide 1: Orientation & databases |
D1, survey, syllabus quiz due Tuesday, Jan 29 A1 orientation assignment due Tues, Jan 29th |
2 |
Jan 28th |
Part I Databases: More complicated searches, using query builder, and boolean terms Discussions: D2 Post information about a database from the NAR annual database issue - see the Exploring Biological Databases iBook for instructions Assignment: A2. Databases Learning Guide 2: Databases |
D2, A2 databases due Feb. 5th |
3 |
Feb 4th
|
Part II Molecular Structures: Proteins, nucleic acids, amino acids, and nucleotides Discussions: 1. D3 Major & minor grooves 2. D4 Nucleotides and amino acids 3. D5 Amino acids & charge 4. D6 Amino acids & hydrophobicity Assignment: A3 Amino acids and nucleotides Learning Guide 3: Molecular structures: proteins, nucleic acids and their building blocks |
D3, D4, D5, D6 due Feb. 12th A3 due Feb 12th
|
4 |
Feb 11th |
Part II Molecular Structures: Identifying chemical bonds, levels of protein structure Discussions: 1. D7 covalent bonds 2. D8 disulfide bonds 3. D9 metal bonds Assignment: A4 Chemical bonds in biological polymers and levels of protein structure Learning Guide 4: Chemical bonds |
D7, D8, D9 due Feb. 19th
|
5 |
Feb 18th |
Part II Molecular Structures: Investigating levels of protein structure, levels of protein structure Discussions: 1. D10 ionic interactions 2. D11 hydrophobic interactions 3. D12 hydrogen bonds Assignment: A4 Chemical bonds in biological polymers and levels of protein structure Learning Guide 4: Chemical bonds |
D10, D11, D12 due Feb. 26th A4 due Feb 26th |
6 |
Feb 25th |
Part II Molecular Structures: Comparing drug sensitive (normal) and drug resistant (mutant) structures Discussions: Discussion: D13 Influenza and drug resistance Assignment: A5 Influenza and chemical bonds Learning Guide 5: Comparing molecular structures and reviewing bonds |
D13, A5 due Mar 5th
|
7 |
Mar 4th |
Part III Molecular Sequences: Experimenting with blastn - the effect of word size and algorithm Assignment 6: Blasting the flu Learning Guide 6: nucleotide blast, and word size |
A6 due Mar 12th
|
8 |
Mar 11th |
Part III Molecular Sequences: Drug discovery and alignments Assignment: A7 Drug discovery & Zika virus Learning Guide 7: Molecular Sequences, protein blast & drug discovery |
A7 due Mar 26th |
Spring Break | |||
9 |
Mar 25th |
Part III Molecular Sequences: Multiple alignments, simple phylogenetic trees, why are some residues conserved through evolution? Discussion: D14 Molecular Murder Mystery Assignment: A8 Multiple alignments, phylogenetic trees, and sequence conservation Learning Guide 8: Multiple alignments and evolution |
A8 due Apr 2nd D14 due Apr 2nd |
10 |
Apr 1st |
Part III Molecular Sequences: Understanding gene maps - the relationship between sequence and structure Assignment: A9 Gene structure and using genetic maps Learning Guide 9: Molecular Sequences and genetic maps |
A9 due April 9th |
11 |
Apr 8th |
Part III Molecular Sequences: Using primer BLAST to pick PCR primers Assignment: Assignment 10 Using blast to pick PCR primers Learning Guide 10: BLAST and PCR, primer blast, blastn, reading maps |
A10 due Apr 16th
|
12 |
Apr 15th |
Part IV Genetic Variation: Identifying and understanding small mutations Discussions: D15 Stop codon mutations D16 Frameshift mutations Assignment: A11 Mutations - Identifying variants Identify and map mutations Learning Guide 11: Mutations and translation |
D15, D16, A11 pt. 1 due Apr 23rd
|
13 |
Apr 22nd |
Part IV Genetic Variation: Identifying and understanding the impact of mutations on protein structure Discussion: D17 Frameshift models Assignment: A11 part 2 Modeling frameshift variants Model the impact of a frameshift mutation on protein structure and predict the effect on activity Learning Guide 11: Mutations and translation |
D17, A11 pt. 2 Due Apr 30th
|
14 |
Apr 29th |
Part IV Genetic Variation: Final project - investigating the effect of a clinically relevant mutation Assignment: A12 Genetic variants and disease Read about and describe a genetic disease, create and post a model showing variation Learning Guide 12: Missense variants and variants of unknown significance |
|
15 |
May 6th |
Part IV Genetic Variation: Final project - investigating the effect of a clinically relevant mutation Assignment: A12 Genetic variants and disease Learning Guide 12: Missense variants and variants of unknown significance Finish up |
A12 due May 13th |
16 | Finish up |