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Bioinformatics for Biology and Biotech

Bioinformatics course areas

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, idenfity the affected codon, where it is located in a gene, and the type of mutation (missense, 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:  Additional materials and datasets are available to members of high school or college Bio-Link programs, or faculty who belong to Bio-Link.  You must be logged in to view these materials.  If your college or high school has not become a Bio-Link program or you do not have a Bio-Link faculty membership, join Bio-Link today!

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 touch pad.
2.  Google docs or Microsoft Word
3.  Each student should have access to an iPad throughout the course,
4.  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 affects 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.
By the end of the course, we should be able to give a student a sequence of RNA, with a mutation, and have them do the following:
1. Identify the gene.
2. Find and characterize the mutation.
3. Locate the mutation in the gene.
4. Use databases to determine if the mutation is pathogenic and learn about the phenotypic consequences.
5. Characterize the effect of a mutation on a protein structure in terms of changes in chemical bonds.
 

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 DNA barcoding to identify a species based on a DNA sample.
14.  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.
15.  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.
16.  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.
 

Week

 Date

 Learning guide and assignments

 Due

1

 

Jan 22nd

 

Part I Databases:  Simple database searches

Discussion items and survey

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