Module 5 Instructor Resources¶

Instructor Resources for Module 5: Translation: The need for an Open Reading Frame

Cover Page¶

Submitter:	Anne Rosenwald (rosenwaa@georgetown.edu)
Submission timestamp:	2019/12/16 3:54:56 PM CST
Authors:	Carina Howell, Lock Haven University Leocadia Paliulis, Bucknell University
Corresponding author:	Anne Rosenwald (rosenwaa@georgetown.edu)

Lesson abstract:	Translation of messenger RNA is required for synthesis of proteins. Students will learn to determine the codons for specific amino acids and identify reading frames by looking at the base position track in the genome browser, to assemble exons to maintain the open reading frame (ORF) for a given gene, define the phases of the splice donor and acceptor sites and describe how they impact the maintenance of the ORF, and identify start and stop codons of an assembled ORF.
Lesson keywords:	Amino Acids Associated Protein Synthesis Factors Codon Genome Browser Messenger RNA Ribosomes tRNAs
Organism(s) that are the focus of this lesson:	None
Type(s) of student learning assessments:	Short answer formative questions
Websites and online databases used:	GEP UCSC Genome Browser (http://gander.wustl.edu)
Resources in addition to the lesson instructions	YouTube videos

Topics in scientific fields:	Genetics Genomics Molecular Biology
Topics in mathematics or statistics:	None
Topics in bioinformatics or data science:	GEP UCSC Genome Browser (http://gander.wustl.edu)

Recommended prior course work:	High school level biology
Recommended computer skills:	Basic: Familiarity with web browsers, word processing

Recommended computer skills:	Basic: Familiarity with web browsers, word processing
Instructional requirements:	Basic Computer Lab (Access to laptops/desktops, no large memory or CPU requirements)

Instructional time required:	1 class period or less
Students work as individuals or teams?	Either individual or team work is possible
Number of students in a class:	More than 50 students (assume no TAs and one computer for each student)

Available languages:	English
Additional materials for students with disabilities:	None

Determine the codons for specific amino acids and identify reading frames by looking at the Base Position track in the genome browser.
Assemble exons to maintain the open reading frame (ORF) for a given gene.
Define the phases of the splice donor and acceptor sites and describe how they impact the maintenance of the ORF.
Identify start and stop codons of an assembled ORF.
Use start and stop codons to identify open reading frames by looking at the Base Position track in the genome browser (Investigation 1).
Identify how to assemble exons to maintain the open reading frame (ORF) for a given gene (Investigation 2).
Define the phases of the splice donor and acceptor sites and how they impact the maintenance of the ORF (Investigation 2).
Identify start and stop codons of an assembled ORF (Investigation 2).
Use the coordinates of the start and stop codons and splice sites to generate a model of the coding region of a gene isoform (Investigation 2).

Module 1
Module 2
Module 3
Module 4
Overview of the ribosome, tRNAs, and associated proteins involved in translation (Initiation Factors, Elongation Factors and Release Factors)
Overview of the DNA codon table

Review the process of translation: Overview of the ribosome, tRNAs, and associated proteins involved in translation (Initiation Factors, Elongation Factors and Release Factors)
Review the DNA codon table
Work through the activities using the Genome Browser, with pauses to discuss the answers to the questions.
Conclude with emphasis on main points:
- mRNAs are translated into amino acids using triplet codons
- Identification of ORFs
- The ORF must be maintained across splice sites to generate a working mRNA
- The assembled ORF begins with a start codon and ends with a stop codon.