Gene Expression, Regulation, and Research Exam 3.

Introduction to Research Opportunities at SDSU

  • Presentation points outlined to assist students seeking research involvement at SDSU.

  • Resource links provided at the top of the module for students to access.

  • Google Form to be filled out for further information on research opportunities.

  • Workbook resources detailing the application process for research involvement.

Create Scholars Program

  • A cancer research partnership between SDSU and UCSD.

  • Available resources to learn more about the program: recruitment video, information sessions.

  • Information on research areas, eligibility, and program requirements.

  • Encouragement for students to engage in research to apply course concepts in practice.

Lecture Review of mRNA and Translation Process

  • Emphasis on the completion of mRNA signaling readiness for translation into protein.

Codons and Reading Frames

  • Definition of codon: a repeating unit of three nucleotides in mRNA that specifies an amino acid for protein construction.

  • Importance of the reading frame in translation:

    • A shift in the reading frame changes the sequence of codons,

    • Example of frame one: UCU CUA

    • Example of frame two: CUA UAA

    • Example of frame three: UAA UGG

  • Consequences of shifting reading frames:

    • A different protein product results from a shift in the frame.

    • The ribosome's role: scans for start codons (AUG) to determine the reading frame.

    • Initial untranslated region (UTR) is not involved in protein synthesis.

Activity Overview

  • Two-part discussion: 1) RNA processing 2) Translation and reading frame incorporation.

  • Educational interaction through student engagement regarding mRNA and reverse transcription.

Discussion on Reverse Transcription and Differences in cDNA Formation

  • Question posed: Will reverse transcribed cDNA differ from the original DNA?

    • Answer: Exons are retained, introns are excluded during mRNA splicing; thus, cDNA is shorter and lacks overlap with original DNA.

    • Splicing parameters were explored by students.

Current Lecture Focus: Gene Expression and Cellular Identity

  • Gene transcription from DNA to RNA.

  • Protein translation: various controls at every stage of expression.

  • Topics to cover:

    • Chromatin accessibility

    • Roles of transcriptional regulators (activators, repressors)

    • Post-transcriptional regulation (microRNAs, long non-coding RNAs)

    • Post-translational modifications.

Cellular Development and Differentiation Overview

  • Explanation of cellular origin: one cell from paternal (sperm) and maternal (egg) origins undergoes division and specialization.

  • Importance of DNA regulation in differentiation leading to specialized cell functions based on gene usage.

  • Availability of specific genes regulated according to cellular roles and responses.

  • Stem cells discussed as precursors to specialized cells; not elaborated upon until the next unit.

The Central Dogma of Molecular Biology

  • Information flow:

    1. DNA to Transcription (mRNA)

    2. mRNA exits nucleus to Cytosol

    3. Ribosome translates mRNA to Proteins.

Regulatory Controls at Various Stages

  • Transcription Control: Is the gene accessible? Has the poly A tail been added? Are regulatory proteins bound to the mRNA?

  • mRNA Degradation Control: Influence of poly A tail length on stability and translation potential.

  • Translational Control: Ribosome activity ty and its ability to bind mRNA.

  • Post-translational Control: Mechanisms determining if proteins are active or inactive through modifications.

Chromatin Organization and DNA Accessibility

  • Definition of chromosomes as densely packed supercoiled DNA wrapped around histones.

  • Impact of chromatin modifications affecting transcription potential:

    • Proteins changing shape to allow DNA accessibility for RNA polymerase binding.

    • Highlight of the TATA binding protein's role in transcription initiation.

Enhancers and Control Elements in Gene Regulation

  • Enhancers:

    • DNA sequences that can activate transcription from distant sites when bound by activators.

    • Interaction of proteins along loops of DNA affecting RNA polymerase recruitment to the promoter region.

  • Activators enhance gene transcription, while repressors halt the process.

  • Example of feedback inhibition role played by environmental concentrations, such as tryptophan.

Combinatorial Control of Gene Expression

  • Multiple, coordinated activators and repressors impact mRNA production levels.

  • Variability in gene expression tailored for specialized functions across different cellular environments.

  • Illustration of regulatory complexity within cell signaling and gene expressivity.

Transcriptional Regulators' Functions

  • Control mechanisms based on signals governing gene activation:

    • Ability of transcription regulators to turn on/off various genes depending on the cellular demand.

    • The iterative process of regulatory engagement determines cell identity and function.

Levels of Post-Transcriptional and Post-Translational Regulation

Non-coding RNA Roles

  • Types of non-coding RNA:

    • MicroRNAs: short sequences targeting mRNA for degradation, inhibiting protein synthesis.

    • Long non-coding RNAs: act as scaffolds for protein localization, allowing for specific gene expression regulation.

Mechanisms of MicroRNA Activity and Structure

  • Mechanism: microRNA binds to complementary mRNA sequences and triggers degradation.

  • Interaction capabilities between non-coding RNAs and either DNA or mRNA through structural changes.

  • Specific long non-coding RNAs may serve unique functions such as X chromosome inactivation.

Post-Translational Modifications and Their Effects on Protein Activity

  • Post-translational modifications influence the behavior and functionality of proteins:

    • Covalent alterations such as phosphorylation altering protein activity.

    • Addition of ubiquitin tags indicating proteins for degradation.

    • Proteins change quaternary structure through interactions that affect activity.

Understanding the Complexity of Gene Regulation

  • Summary of critical mechanisms enabling nuanced control of protein synthesis and activity throughout cellular processes.

  • Importance of learning the variety of checkpoint processes as key determinants in protein availability and function in maintaining cellular homeostasis.

Activities and Interactive Discussions

  • Engaging activities to identify appropriate microRNA candidates targeting specific mRNAs for study purposes.

  • Importance of directionality in the complementarity of nucleic acid sequences emphasized in hands-on exercises.