Course covers prokaryote structure, growth, central dogma mechanisms, and molecular diversity. Course will explore bacterial and archaeal differences and similarities, applying knowledge through peer-reviewed material, discussions, presentations, and questions. Areas needing further research will also be examined.
Additional Requirements for Graduate Students: Graduate students will be required to write a 12-15 page term paper.
Athena Title
Prokaryotic Biology
Prerequisite
MIBO 3500 or MIBO 3500E or MIBO 3500H
Semester Course Offered
Offered fall and spring
Grading System
A - F (Traditional)
Student Learning Outcomes
By the end of Unit I, students will be able to identify prokaryotic structures and compare how prokaryotic cells generally grow, divide, and communicate: both intracellularly and with each other. Methods to assess would include a combination of assessments of oral presentations, group and individual exams, homework, and term papers.
By the end of Unit II, students should describe molecular systems that drive replication, transcription, and translation; diagram how these systems are regulated and the phenotypic outcome of a given signaling condition.
By the end of Unit III, students examine the phylogenetic and taxonomic classification of bacteria and archaea, and students should be able to recall some of the distinct characteristics of specific prokaryotic organisms highlighted in this section and match them accordingly.
Students will begin to effectively interpret published data and assess how the outcomes of experiments support or disprove stated hypotheses. Furthermore, some basic knowledge of scientific techniques used will be examined.
Topical Outline
Unit I: Bacterial Structure and Growth
By the end of Unit I, students will be able to identify prokaryotic structures and compare how prokaryotic cells generally grow, divide, and communicate: both intracellularly and with each other. Methods to assess would include a combination of assessments of oral presentations, group and individual exams, homework, and term papers
Students will learn the ultrastructural differences between Gram-negative, Gram-positive, and archaea at the molecular level.
• Membrane structure and function
• Peptidoglycan synthesis
• Flagellar biosynthesis
• Nutrient acquisition pathways (transport)
Dissect typical and atypical cell division pathways and understand bacterial community structure.
• MinCDE/FtsZ functions
• Cell wall remodeling
• Bacillus sporulation pathways, Caulobacter asymmetric division
• Biofilm structure and formation pathways
Students will know different mechanisms of bacterial cell:cell communication and signaling pathways.
• Molecular dissection of chemotaxis (signaling via methylation and phosphorylation)
• Two component regulators (PhoPQ, EnvZ/OmpR, integrated pathways)
• DNA uptake systems/conjugation
• Toxin-antitoxin systems
Unit II: Central Dogma at the molecular level
By the end of Unit II, students should describe molecular systems that drive replication, transcription, and translation; diagram how these systems are regulated and the phenotypic outcome of a given signaling condition.
Students will understand the processes which initiate, drive, and terminate genomic replication.
• DnaA function, DNA polymerase complex formation and subunit activities
• Ter-dependent termination of replication
Students will understand the processes which initiate, drive, regulate, and terminate transcription.
• RNAP subunit makeup, individual activities, functions of sigma factor
• Rho-dependent and -independent transcriptional termination
• Transcription is regulated by a number of transcriptional regulators (LacI, AraC, TrpR), transcriptional pausing (NusA, NusG, RNA stem-loop functions), and small RNA molecules
• Riboswitches
Students will understand the processes which initiate, drive, regulate, and terminate translation.
• General ribosome structure, function, and biochemical activity
• Translational regulation via attenuation, stringent response, and small RNAs
Students will be able to understand the post-translational fates of some proteins in the cell.
• Protein folding pathways, degradation pathways, and chaperone activity (GroEL/ES, DnaJ/K/GrpE, ClpXP, tmRNA)
• Protein secretion (SecYEG, Tat, numbered secretion system highlights (1-7))
Students will be able to dissect the lifecycle and lytic/lysogenic decision-making process of bacteriophage λ by using all of the information given above.
Unit III: Bacterial diversity
By the end of this unit, students examine the phylogenetic and taxonomic classification of bacteria and archaea, and students should be able to recall some of the distinct characteristics of specific prokaryotic organisms highlighted in this section and match them accordingly.
Various representative bacteria and archaea are highlighted throughout this section and identified via its appropriate phylogenetic group. Specific molecular, biochemical, and physiological attributes of a particular organism is highlighted. Molecular biology and physiology of archaea are directly compared/contrasted to “typical” bacterial pathways.
Overarching topic: Primary literature
Students will begin to effectively interpret published data and assess how the outcomes of experiments support or disprove stated hypotheses. Furthermore, some basic knowledge of scientific techniques used will be examined.
In a typical semester, three papers are read by students on their own. In the classroom, the paper is presented by the instructor “journal club” style, and salient points of the work are highlighted.
