Genetics Notes (1) PDF

**10/3/24 -- Gene Regulation** LAC Operon Regulation - Discovery: Jacob and Monod, 1961 Lactose Present - Operon active; transcription occurs - Lactose binds to repressor, causing a conformational change - Repressor/lactose complex cannot bind to operator - RNA polymerase binds to p...

**10/3/24 -- Gene Regulation** LAC Operon Regulation - Discovery: Jacob and Monod, 1961 Lactose Present - Operon active; transcription occurs - Lactose binds to repressor, causing a conformational change - Repressor/lactose complex cannot bind to operator - RNA polymerase binds to promoter, initiating transcription Lactose Absent - Three enzymes regulated as a single unit: - LacZ: β-galactosidase - LacY: Galactose permease - LacA: Thiogalactoside transacetylase - Regulatory regions precede genes - Repressor protein binds to operator, blocking RNA polymerase - Transcription prevented; no mRNA produced The Lac Operon in E. coli - Comprises lacZ, lacY, lacA, and promoter region (Plac) - Without lactose, transcription of Z-Y-A genes is turned off by repressor Inducible and Repressible Control - Parts of gene regulation pathway Gene Regulation in Eukaryotes - Differential Gene Expression: Different cell types (e.g., muscle, pancreas, blood) - Importance: - Determines which genes are expressed - All cells have a complete copy of genes (\~37 trillion cells) - Different genes turned on/off produce various proteins - Many genes regulated during fetal development - Multiple mechanisms including operon-type feedback Mechanisms of Gene Regulation in Eukaryotes - DNA Packing: Prevents transcription access - Eukaryotic transcription involves enhancers, silencers, and proteins - Alternative RNA Splicing: Leads to multiple mRNAs - MicroRNAs & RNA Interference: Regulation beyond transcription - Translation Regulation: Controls events post-transcription Eukaryotic Transcription Complexes - Multiple proteins and regulatory factors involved - Enhancers - DNA sequence that transcription factors bind - Transcription Factors - Bind enhancer - Helps RNA polymerase bind to the promoter - Promoter - DNA sequence that RNA polymerase binds to initiate transcription - RNA Polymerase - Enzyme that transcribes gene into RNA - Transcription Factors (TF): - 10% of human genome functions as TFs - Promote/block RNA polymerase - Critical for gene expression timing - Most important: homeodomain proteins - Coded for by HOX genes Homeobox (HOX) Genes - Regulate body plan along "head-tail" axis in flies - Essential for proper development in organisms (e.g., Drosophila) Gene Control and Body Segmentation - Embryos - William Bateson - Animal structure: repeating segments - Animals developed with segments in the wrong places - Blueprint was disrupted - Fruit flies - Give embryos radiation/poison - Flies had segments in the wrong place - DNA causes embryo to divide into segments - Ed Lewis - Each segment directed by certain genes - Antennapedia - Expressed in the thorax normally - Fruit fries can use the same gene for a mouse's eye to make its own; same gene HOX Genes and Development - Expressed in specific body regions - Discovered with different colored dyes - Example: HOX gene Ubx affects wing development in flies - Needs to be expressed with precise timing - If turned off, fly develops a second pair of wings rather than halteres Conservation of HOX Genes - Common set of HOX genes across species from flies to humans - Controls body regions consistently - Same HOX gene in flies controls posterior portion of humans Linkage to Evolution - HOX genes play a role in the evolution of body plans, especially during the Cambrian explosion Epigenetics - Study of heritable changes in gene expression without DNA sequence alteration - Changes phenotype without altering genotype Epigenetics Video - "Above genetics" - Methyl groups - Binds to gene - "don't express this gene" - Carbon and hydrogen - Geone does work, epigenome tells it what to do - Environmental factors can change epigenomes - Bad diet = methyl groups binding to wrong places - Most epigenetic tags don't get passed on, but some do - Mainly bad ones Epigenomic Control of Gene Expression - Agents include: - Methyl groups: Activate/repress genes - Acetyl groups: Modify histone packaging - Small RNA molecules: Regulate gene expression - Turn genes on/off in DNA/histones - Changes can lead to: - Cancer - Developmental disorders - Abnormal gene activity - Metabolic problems RNA Interference (RNAi) - RNA molecules suppress gene expression by destroying mRNA or blocking translation - Discovered by Craig Mello and Andrew Fire (Nobel Prize, 2006) RNAi Video Introduction to RNA and Its Importance - RNA\'s Role: RNA (Ribonucleic Acid) is crucial for translating DNA (Deoxyribonucleic Acid) recipes into living organisms. - Building Life: RNA converts the chemical codes of DNA into proteins, essential for forming cells and tissues. - Historical Perspective: RNA has been integral to life for over three billion years. Accidental Discovery of RNA Interference (RNAi) - Origin: RNA interference (RNAi) was discovered accidentally by geneticist Rich Jorgensen in 1986 while attempting to create a more vibrant purple petunia. - Unexpected Results: Instead of producing purple flowers, the petunias turned white due to the unexpected interaction of added genes with existing ones. Mechanism of RNA Interference - Cell Defense Against Viruses: Cells have evolved a defense mechanism to counteract viral invaders that attempt to replicate within them. - Cops of the Cell: A defensive component (referred to as \"the cop\") identifies and destroys suspicious RNA shapes associated with viruses. - Mirror Image Mechanism: The defense system targets RNA with a specific structural anomaly (mirror image), eliminating harmful messages. Practical Applications of RNA Interference - Therapeutic Potential: RNAi can potentially treat various diseases by turning off malfunctioning genes. - Case Study - Marty Russell: A patient with macular degeneration received RNAi therapy that improved her vision by reducing the number of problematic blood vessels in her eyes. - Broader Implications: RNAi has shown promise in treating conditions like Huntington\'s disease, breast cancer, and HIV, with the potential to revolutionize disease treatment. Understanding Gene Function - Gene Manipulation: RNAi enables researchers to deactivate specific genes to determine their functions, facilitating a deeper understanding of genetics. - Gene Function Analysis: By turning off genes systematically, scientists can observe resulting changes in traits, leading to insights about gene roles in health and disease. Conclusion - Significance of RNA: RNA, while modest, is fundamental to understanding and manipulating biological systems. - Future Potential: RNAi represents a breakthrough in genetics, offering tools to decode and harness the potential of every living organism. Role of MicroRNAs (miRNA) - Major in regulating gene expression - siRNA: Silence specific genes - binds to specific regions of mRNA with the same sequence of base pairs - miRNA: Silence multiple genes - binds with only part of the sequence **9/30/24 -- Genes, Cell Division, and Regulation** - Transcription - RNA polymerase - Unzips strand - Binds to promoter region - Adds complementary bas pairs to template strand (RNA) - Unbinds at terminator region - Template strand (antisense) - Complementary to mRNA strand - T U - Post-transcription - Exons - Important sequences; coding regions - Introns - "genetic gibberish;" non-coding regions - mRNA - GTP cap at 5' end prevents degredation - Poly-Adenine tail at 3' end nuclear export signal - Introns removed via spliceosomes - Mutations: damage and repair - **Mismatch repair** - **DNA polymerase: cuts out and replaces** - **Other proteins check and do the same** - **Base excision repair** - **Nucleotide excision repair** - **UV light nucleotides fused together** - **Many bases cut out and replaced** - **Homologous recombination** - **Non-homologous end joining** - Cell Division - Karyotype: normal number of chromosomes in the nucleus of eukaryotic cells - 23 pairs of chromosomes - 22 pairs of autosomal - 1 pair of sex chromosomes - 23 haploid - Sperm/egg cells - 46 diploid - Mitosis - Somatic cells - Full diploid complement of chromosomes is passed on - Diploid cells 2 homologous sets of chromosomes - Haploid cells 1 set of chromosomes - Stages - Interphase - G~1~ - Grows - G~0~ - Rest phase - S - DNA replication - G~2~ - Grows - Organelles replicate - Prophase - Chromosomes visible - Centrioles move to opposite poles of cell - Metaphase - Chromosomes line up in the center - Spindle fibers attach to centromeres - Anaphase - Sister chromatids separated - Telophase - Chromosomes gather at opposite ends of cells - Lose rod shape - 2 nuclear membranes begin to form around chromosomes - Cytokinesis - Cell membrane pinches, divides in half - 2 new cells identical to original cell - Plant cells: cell plate - Animal cells: cleavage furrow - Meiosis - Occurs in sex organs - 1 set of chromosomes - Fertilization union of germ cells (sperm/egg) - Zygote diploid chromosome number - One from each parent - Stages - Interphase - Duplicates chromosomes - 92 chromatids - 46 chromosomes - Meiosis 1 - Prophase - Chromosomes match up with homologous pairs - Crossing over recombinant chromosomes - Metaphase - Chromosomes in pairs middle - Anaphase - Chromosomes pulled apart (not chromatids) - Telophase - Nucleus membranes form around chromosomes on both ends - Cytokinesis - Splits cytoplasm - 2 non-identical diploid cells - Meiosis 2 - Prophase - Metaphase - Chromosomes in center no pairs - Anaphase - Chromatids pulled apart - Telophase - Cytokinesis - 4 non-identical haploid cells - Cancer - Interphase checkpoints are broken - Grows out of control divides rapidly - Chemotherapy examples - Prevents cell from copying/dividing - Prevents cells from splitting - Can damage normal cells - Hair loss - Gene Regulation - Regulation - Deciding which genes are "on" or "off" - Proteins that increase/decrease transcription - Operons - RNA polymerase - Operator region where repressor can bind - Repressors: prevents RNA polymerase from binding - Lac operon example - Gene codes for repressor creation - If lactose is absent, repressor binds - If lactose is present, lactose binds to repressor; can't bind to operator - Prokaryotic transcriptional regulation - Ability to change metabolic activities due to environment - Capability to induce/repress entire enzyme pathways - Examples - Lac operon (inducible control) - Discovered by Jacob and Monod in 1961 - Trp operon (repressible control) **9/26/24 -- DNA Structure and Function** - DNA - Deoxyribose Nucleic Acid - Instructs amino acids - Building blocks of life - \~20 different amino acids - Put together to make proteins - Inside the nucleus - Carries information in genes - Codons to code for amino acids - Copy itself for cell division - Generate genetic variation - RNA - Copies of DNA (transcription) - Travels to Ribosome - Translates RNA - Codons code for amino acids - History & Groundbreaking Discoveries 1952-1953 - Watson and Crick - Double helix published structure - Won Nobel Prize with Maurice Wilkins - Rosalind Franklin - Photo 51: clearest image of DNA - Used X-ray diffraction - Nucleotides - Building blocks of DNA - Phosphate group, sugar, nitrogenous base - Purines - Adenine and guanine - Pyrimidines - Cytosine and thymine - DNA Structure - Complementary, antiparallel - Sugar phosphate backbone - Purine bonds with pyrimidines - AT - GC - Hydrogen bonds - DNA Replication - 5' 3' direction - 5' has free phosphate - 3' has free hydroxyl group - Helicase enzyme - Binds to start codon - Unwinds strands - Single-strand binding proteins - Keeps leading strand/lagging strand separated - Primase - Adds RNA primer - DNA polymerase - Adds free hydroxyl group at 3' end to lengthen chain - Adds complementary nucleotides - Okazaki fragments - On lagging strand - Polymerase pairs in fragments - Ligase - Seals gaps and connects fragments into a continuous strand - Replaces RNA primer with DNA - Packaging DNA - Histones - Proteins - DNA wraps around these proteins - 1^st^ step - "beads on string" - Nucleosome - More tightly wound - Chromatine - Tightly wound nucleosomes - Fiber - Chromatine loops are formed - Chromosomes - Only form when cells are divided - Supercoils of chromatines - Translation - mRNA carries transcribed RNA to ribosomes - Thymine uracil - tRNA has anticodons that code for mRNA codons - tRNA brings amino acids - Central Dogma - DNA (transcription) RNA (translation) protein - Defined by Francis Crick - One way flow of information from DNA to mRNA to proteins - Genetic Code - Information encoded in specific nucleotide base sequences of DNA - Sequences translated into their corresponding amino acids - Amino acids form proteins in ribosomes - George Gamow - Proposed 3-base codes - Genes and Genetic Variation - Genes - Physical and functional units of heredity - Specific locations on DNA chromosomes - Made of codons - Encodes info used to generate phenotypes - Only 1.5% of the bases in human DNA code for proteins - Mutations - Change in nucleotide sequences due to replication errors or mutagens - Substitutions - Replacement of one nucleotide with another - Impact only if amino acid change alters protein function - Sickle cell anemia - Single substitution - Hemoglobin - A substituted for T - Molecules group into long bundles that form larger structures that stretch and distort the cell - Deletions and insertions - Alters reading frame of mRNA - Nucleotides grouped into different codons - Shifts sequence by one letter - Can lead to significant amino acid sequence changes