Genetics Notes (1) PDF
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Uploaded by GreatMandolin6812
Rensselaer Polytechnic Institute
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These notes provide an overview of gene regulation, focusing on the LAC operon and eukaryotic mechanisms. Topics include differential gene expression, HOX genes, epigenetics, and RNA interference. They also discuss the importance of gene regulation in various biological processes, including development.
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**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