Module 5 Instructor Resources =============================== .. rubric:: Instructor Resources for Module 5: Translation: The need for an Open Reading Frame :class: header1 Cover Page ------------------------------- Submission Details ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | 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 Overview ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | 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 | None | | this lesson: | | +-----------------------------------+-----------------------------------+ | Type(s) of student learning | Short answer formative questions | | assessments: | | +-----------------------------------+-----------------------------------+ | Websites and online databases | GEP UCSC Genome Browser | | used: | (http://gander.wustl.edu) | +-----------------------------------+-----------------------------------+ | Resources in addition to the | YouTube videos | | lesson instructions | | +-----------------------------------+-----------------------------------+ Learning Topics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Topics in scientific fields: | - Genetics | | | | | | - Genomics | | | | | | - Molecular Biology | +-----------------------------------+-----------------------------------+ | Topics in mathematics or | - None | | statistics: | | +-----------------------------------+-----------------------------------+ | Topics in bioinformatics or | - GEP UCSC Genome Browser | | data science: | (http://gander.wustl.edu) | +-----------------------------------+-----------------------------------+ Student Prerequisites ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Recommended prior course work: | - High school level biology | +-----------------------------------+-----------------------------------+ | Recommended computer skills: | Basic: Familiarity with web | | | browsers, word processing | +-----------------------------------+-----------------------------------+ Instructor Prerequisites ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | 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) | +-----------------------------------+-----------------------------------+ Implementation Recommendations ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Instructional time required: | 1 class period or less | +-----------------------------------+-----------------------------------+ | Students work as individuals or | Either individual or team work is | | teams? | possible | +-----------------------------------+-----------------------------------+ | Number of students in a class: | More than 50 students (assume no | | | TAs and one computer for each | | | student) | +-----------------------------------+-----------------------------------+ Accessibility ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Available languages: | English | +-----------------------------------+-----------------------------------+ | Additional materials for students | None | | with disabilities: | | +-----------------------------------+-----------------------------------+ .. meta:: :keywords: Amino Acids, Associated Protein Synthesis Factors, Codon, Genome Browser, Messenger RNA, Ribosomes, tRNAs Lesson Plan ------------------------------- Title ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Translation: The need for an Open Reading Frame Objectives ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 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 (:ref:`Investigation 1`). - Identify how to assemble exons to maintain the open reading frame (ORF) for a given gene (:ref:`Investigation 2`). - Define the phases of the splice donor and acceptor sites and how they impact the maintenance of the ORF (:ref:`Investigation 2`). - Identify start and stop codons of an assembled ORF (:ref:`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 (:ref:`Investigation 2`). Pre-requisites ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - :ref:`module1/module1_exercise:Module 1` - :ref:`module2/module2_exercise:Module 2` - :ref:`module3/module3_exercise:Module 3` - :ref:`module4/module4_exercise: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 Order ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Warm Up/Review of Pre-requisites - Investigation 1 - Investigation 2 - Exit Homework ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - None Class Instruction ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 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. Associated Videos ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - `Splicing and Phase video `_