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Biochemistry And Molecular Biology
An undergraduate bioinformatics curriculum that teaches eukaryotic gene structureLearning ObjectivesModule 1
- Demonstrate basic skills in using the UCSC Genome Browser to navigate to a genomic region and to control the display settings for different evidence tracks.
- Explain the relationships among DNA, pre-mRNA, mRNA, and protein.
- Describe how a primary transcript (pre-mRNA) can be synthesized using a DNA molecule as the template.
- Explain the importance of the 5' and 3' regions of the gene for initiation and termination of transcription by RNA polymerase II.
- Identify the beginning and the end of a transcript using the capabilities of the genome browser.
- Explain how the primary transcript generated by RNA polymerase II is processed to become a mature mRNA, using the sequence signals identified in Module 2.
- Use the genome browser to analyze the relationships among:
- 5' capping
- 3' polyadenylation
- Identify splice donor and acceptor sites that are best supported by RNA-Seq data and TopHat splice junction predictions.
- Utilize the canonical splice donor and splice acceptor sequences to identify intron-exon boundaries.
- Determine the codons for specific amino acids and identify reading frames by examining 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 the start and stop codons of an assembled ORF.
- Demonstrate how alternative splicing of a gene can lead to different mRNAs.
- Show how alternative splicing can lead to the production of different polypeptides and result in drastic changes in phenotype.
Lights, Camera, Acting Transport! Using role-play to teach membrane transportLearning ObjectivesAt the end of this activity, students should be able to:
- Compare and contrast the mechanisms of simple diffusion, facilitated diffusion, and active transport (both primary and secondary).
- Identify, and provide a rationale for, the mechanism(s) by which various substances cross the plasma membrane.
- Describe the steps involved in the transport of ions by the Na+/K+ pump, and explain the importance of electrogenic pumps to the generation and maintenance of membrane potentials.
- Explain the function of electrochemical gradients as potential energy sources specifically used in secondary active transport.
- Relate each molecule or ion transported by the Na+/glucose cotransporter (SGLT1) to its own concentration or electrochemical gradient, and describe which molecules travel with and against these gradients.
Taking the Hassle out of HasselbalchLearning ObjectivesStudents will be able to:
- Characterize an aqueous environment as acidic or basic.
- Explain that pKa is a measure of how easy it is to remove a proton from a molecule.
- Predict ionization state of a molecule at a particular pH based on its pKa (qualitative use of the Henderson-Hasselbalch equation).
- Calculate the ratio of protonated/unprotonated forms of ionizable groups depending on chemical characteristics and /or environment pH (quantitative use of the Henderson-Hasselbalch equation).
- Apply this knowledge in a medical context.
A Close-Up Look at PCRLearning ObjectivesAt the end of this lesson students will be able to...
- Describe the role of a primer in PCR
- Predict sequence and length of PCR product based on primer sequences
- Recognize that primers are incorporated into the final PCR products and explain why
- Identify covalent and hydrogen bonds formed and broken during PCR
- Predict the structure of PCR products after each cycle of the reaction
- Explain why amplification proceeds exponentially