Lecture 6 Bioinformatics


Content Focus

  • Part One will emphasize core knowledge gained throughout the semester, with an expected duration of 20-30 minutes.

  • Part Two will require students to engage in analytical tasks pertinent to:

    • Creating standard curves for protein concentration and size, emphasizing critical analytical skills in experimental design.

    • Performing calculations related to cell counting, ensuring students can demonstrate accuracy in their mathematical competencies.

    • Undertaking bioinformatics tasks that center around online protein sequence analysis, which will test students' ability to synthesize information from various digital resources.

Lab Component for Midterm

Students will take part in practical lab activities as part of their midterm preparation:

  • Hands-on experience with pipetters and scales will enhance grading efficiency, providing students with vital skills applicable in laboratory settings.

  • Familiarity with negative pressure pipettes is encouraged, as these tools may present challenges for those without prior experience.

Review of Labs for Midterm

Lab One

Focus on lab safety procedures, requiring students to review safety quizzes and related materials essential for ensuring a secure laboratory environment.

Lab Two

Concentrates on cell culture techniques that include:

  • Understanding aseptic techniques crucial for preventing contamination in cell cultures.

  • Recognizing phenol red as a pH indicator within cell culture environments.

  • Implementing cell freezing protocols using cryoprotectants like DMSO or glycerol to preserve cell viability.

  • Competency in using a hemocytometer for cellular counting, equipping students to calculate cells/mL with precision.

Lab Specifications

Students must be able to differentiate between pipettes, specifically the use of serological pipettes for larger volumes versus micropipettes for smaller, precision volumes. It is crucial to understand the distinction between primary and secondary literature, with students expected to reference credible sources such as PubMed in their work.

Important Laboratory Procedures

  • Cell Line Usage: The A549 cell line, derived from lung epithelial cells, will be predominantly employed in experiments, giving students experience in working with commercially relevant cell types.

  • Staining Techniques:

    • Nucleus staining will be conducted using Hoechst dye to visualize nuclear morphology.

    • Plasma membranes will be stained using Glutamine, ensuring clear visualization of cell boundaries.

    • The cytoskeleton will be visualized utilizing GFP tagging for actin and tubulin, allowing for the exploration of cytoskeletal architecture.

  • Cytoskeleton Components:

    • Understanding the functions of microfilaments (actin), microtubules (tubulin), and intermediate filaments, with recognition of their roles in cellular structures and dynamics.

    • Exploring polymerization processes in constructing cellular structures, providing foundational knowledge essential for advanced biology.

Advanced Topics in Midterm Prep

Students should focus on:

  • The role of microtubules and the microtubule-organizing center (MTOC) in cell division and function, as these structures are key in various cellular processes.

  • The significance of acetylated tubulin in intracellular transport, particularly within neuronal cells, emphasizing its relevance to neurobiology.

  • Post-translational modifications, highlighting the importance of acetylation and serine phosphorylation in regulating protein function.

  • Understanding the mutational impacts on protein function, particularly how specific substitutions can significantly affect overall protein functionality and interaction.

Resources and Study Aids

Preparation Material

  • A review guide has been developed that aligns with lab sessions, allowing students to connect theoretical principles with practical applications. Quizzes from lab sessions offer straightforward initial questions concerning safety protocols.

  • A Quizlet created by a previous Teaching Assistant is available and focuses on content relevant for midterm preparation.

  • Discussions regarding potential additional review sessions are encouraged, with opportunities for open dialogue on scheduling these review sessions with Mariana.

Today's Lab on Bioinformatics

The lab will focus on the National Center for Biotechnology Information (NCBI) and GenBank, showcasing the critical role these databases play in modern biological research.

  • Historical context emphasizes how biological data collection began in the 1980s, evolving into the extensive databases we rely on today.

  • An introduction to bioinformatics will be provided, underlining its relevance specifically to protein analysis, with a keen focus on acetylated tubulin.

  • The lab will cover:

    • Gene testing and registries (GTR) important for understanding genetic mutations.

    • Utilizing databases like String to map protein-protein interactions, enhancing students' comprehension of proteomics.

    • The significance of homologs and paralogs to understand evolutionary relationships within proteins.

Hands-On Activities

The practical segment will encourage students to analyze datasets directly and engage in activities that simulate examination conditions, effectively preparing them for real-world bioinformatics applications.