BIOL 2153 EXAM 4 (FINAL NEW INFO)

Organelle Inheritance

  1. Mitochondria & Chloroplasts

    • Own genomes: Mitochondria (mtDNA) and chloroplasts (cpDNA) have their own genetic material.

    • Maternal inheritance: Both are inherited maternally, meaning only the mother contributes mitochondria or chloroplasts to offspring. This pattern can be recognized in pedigrees.

  2. Endosymbiont Theory

    • Mitochondria and chloroplasts evolved from bacteria that fused with nucleated cells.

    • Evidence for endosymbiosis:

      • Own DNA (mtDNA/cpDNA).

      • Lack of nucleosomes (similar to bacteria).

      • Mitochondria use N-formyl methionine (fMET) in translation, like bacteria.

      • Inhibitors of bacterial translation block mitochondria and chloroplasts, but not eukaryotic translation.

      • rRNA gene sequence comparisons show mitochondrial genomes are related to nonsulfur bacteria, and chloroplast genomes to cyanobacteria.

  3. Forensic Use of mtDNA

    • High copy number: mtDNA exists in many copies per cell, aiding extraction from degraded or small samples.

    • Maternally inherited: Provides an exact match between child and maternal grandmother, useful for tracing distant maternal lineages.

  4. Mitochondria and Chloroplasts Inside Cells

    • Gene transfer to the nuclear genome: Organelle genes have been incorporated into the nuclear genome, making organelles reliant on nuclear-encoded proteins.

    • Redundancy and loss of function: Some organelle genes are now nonfunctional due to evolutionary gene transfers.

  5. Homoplasmic vs Heteroplasmic

    • Homoplasmic: All organelles in the cell have the same genome.

    • Heteroplasmic: Cell contains a mix of normal and mutant organelles, which can lead to different genetic outcomes in progeny.

  6. Why Mitochondria are Maternal

    • Sperm contribute little cytoplasm: Sperm contribute very little to the cytoplasm, so mitochondria are inherited from the egg.

  7. Nervous System and Mitochondrial Dysfunction

    • High energy tissues like the nervous system are more affected by mitochondrial dysfunction because they have higher energy demands.

  8. Nuclear Transfer to Treat Mitochondrial Disease

    • Steps: Remove nucleus from egg with mutant mitochondria, remove nucleus from donor egg with healthy mitochondria, transfer donor nucleus to mutant egg, and fertilize in vitro.

Transgenic Organisms

  1. Transgenes and Transgenic Organisms

    • Transgenes: Foreign genes inserted into an organism using recombinant DNA technology.

    • Transgenic Organisms: Organisms containing transgenes that can be inherited by progeny.

  2. Methods for Introducing Transgenes

    • Chemical treatment (for single-celled organisms).

    • Microinjection (for multicellular organisms).

  3. P-element Transformation

    • Used in Drosophila. Involves a helper plasmid containing the transposase gene, which aids in the insertion of the transgene.

  4. Uses of Transgenic Organisms

    • Clarify gene functions.

    • Produce human proteins (e.g., insulin).

    • Model diseases (e.g., gain-of-function mutations in human diseases).

  5. Organismal Cloning Process

    • Steps: Remove nucleus from egg cell, transfer nucleus from somatic cell of the organism to be cloned, and stimulate cell division to create an embryo, then implant into a surrogate mother.

    • Difference: Mitochondria are still maternally inherited, so the clone isn’t completely genetically identical.

  6. Human Gene Therapy

    • In vivo: Gene therapy delivered directly to the body (e.g., via injection).

    • Ex vivo: Cells are removed, treated with the gene therapy, and reintroduced (e.g., bone marrow cells).

    • Vectors:

      • Retroviruses: Integrate into the genome but can cause mutations.

      • AAV vectors: Don’t integrate into the genome; degrade over time.

  7. Gene Editing (CRISPR)

    • CRISPR allows targeted genome modifications by creating double-strand breaks, followed by repair via NHEJ (leading to insertions/deletions) or homologous recombination (point mutations).

    • CRISPRi: Uses dead Cas9 to inhibit gene expression.

    • Base Editing: Directly makes point mutations without creating double-strand breaks.

RNAi (RNA Interference)

  1. Mechanism of RNAi:

    • Dicer cleaves double-stranded RNA (dsRNA) into small pieces.

    • RISC complex uses guide RNA to bind complementary mRNA, leading to its degradation.

  2. RNAi Components:

    • Dicer: Cleaves dsRNA into small fragments.

    • RISC: Contains guide RNA that directs it to the target mRNA for cleavage.

    • Guide RNA: Determines the target sequence.

  3. RNAi Advantages and Disadvantages:

    • Advantages: Can specifically silence genes.

    • Disadvantages: Off-target effects, variable efficiency.

CRISPR-Cas9

  1. Bacterial Immune System:

    • CRISPR stores viral DNA sequences (spacers) to recognize and cut the same virus upon re-infection using Cas enzymes.

  2. Genome Editing in Other Organisms:

    • Cas9 creates double-strand breaks, which are repaired by NHEJ (causing INDELs) or homologous recombination (for precise edits).

  3. Key Components:

    • Guide RNA: Directs Cas9 to the target DNA sequence.

    • PAM Sequence: A short DNA sequence required for Cas9 binding.

  4. CRISPR Applications:

    • Targeted Mutagenesis: Making precise edits like insertions, deletions, or point mutations.

    • CRISPRi: Inhibits gene expression without altering the DNA.

    • Base Editing: Makes direct point mutations without causing double-strand breaks.

Cancer Genetics

  1. Regulation of Cell Cycle:

    • Growth factor receptors, kinase cascades, and transcription factors control the progression of the cell cycle.

  2. Cancer Cells' Evading Mechanisms:

    • Autocrine signaling: Cancer cells produce their own signals for division.

    • Loss of contact inhibition: Cells continue dividing despite overcrowding.

    • Avoidance of apoptosis: Cancer cells evade programmed cell death.

  3. Oncogenes vs. Tumor Suppressors:

    • Oncogenes: Dominant gain-of-function mutations lead to cancer.

    • Tumor Suppressors: Recessive loss-of-function mutations contribute to cancer.

  4. Telomeres and Cancer:

    • Telomerase activation in cancer cells prevents telomere shortening, allowing for indefinite cell division.

Population Genetics

  1. Hardy-Weinberg Equilibrium (HWE)

    • Assumptions: No mutation, random mating, no selection, no migration, and an infinitely large population.

    • HWE Equation: p² + 2pq + q² = 1 (where p and q are allele frequencies).

  2. Genetic Drift:

    • Bottlenecks and founder effects reduce genetic variation in small populations, influencing allele frequencies.

  3. Natural Selection:

    • Alleles that confer higher fitness become more common in a population over time.

  4. Linkage Disequilibrium (LD):

    • The non-random association of alleles at two loci can be used in GWAS to identify genes associated with complex traits.

Heritability and Trait Mapping

  1. Heritability:

    • Proportion of phenotypic variance explained by genetic variance.

    • Estimated using the formula Heritability=VgVpHeritability=Vp​Vg​​.

  2. QTL Mapping:

    • Identifying genes that contribute to complex traits by measuring phenotypic values and correlating them with genetic markers.

  3. Genome-Wide Association Studies (GWAS):

    • GWAS identify genes associated with traits by looking at genetic variation across many individuals.

    • Recent variation due to population growth is not universally spread, leading to variation in allele frequency across populations.