Bioinformatics for Biology and Biotech

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.

1.  Exploring Biological Databases
2.  Exploring Molecular Structures
3.  Exploring Molecular Sequences

Additional resources:

1. Blasting through the Kingdom of Life
2. You can play with DNA
3. Molecule World Structure Collections
4. Digital World Biology's YouTube channel
5. Amino acid and macromolecule playing cards
    

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.  

• For students to predict the consequences of mutations, they have to be able to identify and distinguish between missense, nonsense, and frameshift mutations.
• To understand the effects of these mutations, they have to understand translation and reading frames.
• To understand the kinds of bonds that amino acids form and be able to model molecular interactions, they have to know the names and chemical properties of amino acids, be able to use a simple molecular modeling program, and be able to identify the main types of chemical bonds and interactions found in biological structures (covalent bonds, disulfide bonds, metal bonds, ionic interactions, hydrophobic interactions, and hydrogen bonds).  
• To identify a sequence and pick the correct database, they have to understand different types of BLAST algorithms and how they work.
• To locate information at the NCBI, they have to know how to use the NCBI databases.

Learning objectives:

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.

Schedule:

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.