Essays for Final Genetics (PDF)

Essays Understanding the experiments of Griffith. How were they performed and what were the results Griffith's Transformation Experiment Setup Bacteria Studied: Diplococcus pneumoniae o IIIS (Smooth strain): Virulent → Causes death in mice. o IIR (Rough strain): A...

Essays Understanding the experiments of Griffith. How were they performed and what were the results Griffith's Transformation Experiment Setup Bacteria Studied: Diplococcus pneumoniae o IIIS (Smooth strain): Virulent → Causes death in mice. o IIR (Rough strain): Avirulent → Does not cause death in mice. Critical Steps of the Experiment: 1. Inject live IIIS → Mouse died. o The bacteria was deadly. 2. Inject live IIR → Mouse lived. o Harmless bacteria didn’t cause disease. 3. Inject heat-killed IIIS → Mouse lived. o Heat destroyed the deadly bacteria, so it wasn’t harmful. 4. Inject heat-killed IIIS + live IIR → Mouse died! o Deadly IIIS bacteria were recovered from the dead mouse. o Somehow, the harmless IIR became deadly when mixed with heat- killed IIIS. The Results: The harmless IIR bacteria were "transformed" into deadly IIIS bacteria. Conclusion Griffith proposed a "transforming principle" was responsible for changing the IIR bacteria into the virulent IIIS form. This experiment laid the foundation for discovering that DNA is the genetic material. Understanding the experiments of Avery, MacLeod and McCarty. How would the results have been different if RNA was the genetic material and not DNA? What Did They Do? Question: Is the genetic material DNA, RNA, or protein? Test: o Used bacteria: § S strain (smooth): Deadly. § R strain (rough): Harmless.  o Mixed dead S strain DNA with live R strain → R strain became deadly (transformation). Key Steps: 1. Took S strain molecules: DNA, RNA, proteins. 2. Used enzymes to destroy one molecule at a time: o Protease: Destroys proteins. o RNase: Destroys RNA. o DNase: Destroys DNA. 3. Checked if R strain transformed (became deadly). What They Found: Destroy proteins → Transformation happened. Destroy RNA → Transformation happened. Destroy DNA → No transformation! Conclusion: DNA is the genetic material. Understanding the Hershey-Chase experiments. How were they performed and what were the results. How would the results have been different if RNA was the genetic material and not DNA? Hershey-Chase Experiment Purpose To figure out if DNA or protein is the genetic material. Short Version of Experiment T2 phage--> 50% DNA and 50% protein P32--> radioactive phosphorus Labeled DNA blue S35 radioactive sulfur Label protein green We assume the phage will inject its genetic material into the unlabeled cells to cause an infection Conclusion: DNA is the genetic material of the phage How They Did It 1. Used T2 phages 50% DNA and 50% protein. 2. Two Labels: o DNA labeled with ³²P (phosphorus). o Proteins labeled with ³⁵S (sulfur). 3. Steps:  o Labeled phages infected bacteria. o Blender shook off the phage "shells." o Centrifuge separated bacteria (pellet) from shells (supernatant). Results ³²P (DNA): Found in the bacteria (pellet). ³⁵S (Protein): Found in the phage shells (supernatant). Conclusion: DNA entered the bacteria → DNA is the genetic material. If RNA Were the Genetic Material ³²P (RNA): Would still be found in the bacteria (pellet). ³⁵S (Protein): Would stay in the phage shells (supernatant). Result: RNA would be identified as the genetic material instead of DNA. Describe the experiments that showed that Hfr strains could be used to determine the relative order of genes on the prokaryotic chromosomes Hfr Mapping Experiments Purpose To find the order of genes on bacterial chromosomes using Hfr strains. How It Worked 1. What Is an Hfr Strain? o An F+ cell with an F plasmid integrated into its chromosome. o During conjugation, the chromosome transfers into an F⁻ cell. 2. Setup: o Mix Hfr strain with F⁻ strain. o Allow conjugation to start. o Stop conjugation at specific times (e.g., 10, 15, 20 min) using a blender to break the mating bridge (sex pilus). 3. Data Collection: o Plate the F⁻ bacteria on selective media to determine which genes transferred at each time point. Results Genes closer to the origin of transfer are transferred first. Genes farther away transfer later. Example At 10 min: Gene A transferred. At 15 min: Genes A and B transferred. At 20 min: Genes A, B, and C transferred. Conclusion The time it takes for a gene to transfer shows its position on the chromosome. Key Takeaway Hfr strains transfer genes in a specific order. Scientists mapped bacterial chromosomes by timing gene transfer Understand how the fluctuation test was performed. What were the two hypothesis that were being tested? What were the results that were obtained and how would the results have been different if the other hypothesis was correct? Fluctuation Test: Mutations Two Models of Mutation 1. Adaptive Mutation Model: o Mutations happen after stress (e.g., exposure to a virus). 2. Spontaneous Mutation Model: o Mutations happen randomly before stress. Luria & Delbrück’s Fluctuation Test Objective: Test if mutations are adaptive or spontaneous. Steps: 1. Grew 10 identical cultures of E. coli. 2. Exposed all cultures to T1 phage 3. Counted the survivors in each culture, varied in each culture. Results: Survivor numbers varied a lot between cultures. Conclusion: Mutations are spontaneous and happen before stress, not triggered by it. Describe the Linderberg –Zinder experiment and the nature of transduction Lederberg-Zinder Experiment What They Wanted to Know Can bacteria exchange DNA without direct contact? Setup 1. Used two bacterial strains: o LA-2 and LA-22 (both auxotroph’s → need extra nutrients to grow). 2. Used a U-tube:  o Filter in the middle: Allowed media to pass but blocked bacteria. o Bacteria couldn’t touch each other. 3. Tested for DNA exchange: o Checked if bacteria could grow (prototrophs) when placed on minimal media. Results 1. LA-22 Side: Some bacteria grew (DNA exchange happened). 2. LA-2 Side: No growth (no DNA received). Conclusion DNA exchange happened without physical contact. A phage (virus) carried DNA from LA-2 to LA-22. Key Takeaway Bacteria can exchange DNA through transduction using viruses, even when they can’t touch each other! Understand the evidence that Watson and Crick used in order to describe the double helical nature of DNA. Be able to describe Watson and Crick’s model for the DNA double helix. Watson and Crick: Evidence for the DNA Double Helix Evidence Used to Build the Model: 1. Chargaff’s Rules: o A = T, C = G → Suggested base pairing. 2. Rosalind Franklin’s X-ray Diffraction: o DNA is a helix with repeating patterns. o Width: 2 nm → A purine pairs with a pyrimidine. 3. Chemical Bond Knowledge: o Covalent bonds hold the sugar-phosphate backbone. o Hydrogen bonds link base pairs. Watson and Crick’s DNA Model: 1. Structure: Double helix. 2. Backbone: o Sugar-phosphate backbone on the outside. 3. Base Pairing: o A pairs with T (2 hydrogen bonds). o C pairs with G (3 hydrogen bonds). 4. Antiparallel Strands: o One strand runs 5' to 3', the other runs 3' to 5'. 5. Dimensions: o Width: 2 nm.  o 1 turn = 10 base pairs (34 nm). Key Takeaway: Watson and Crick used Chargaff’s rules, Franklin’s X-ray, and bond knowledge to create the first accurate DNA model, explaining DNA’s information storage and replication. Be able to describe the experiment that first showed that bacteria can exchange DNA First Experiment Showing Bacteria Can Exchange DNA Who Did It? Lederberg and Tatum (1946) Setup 1. Two Bacterial Strains (Auxotroph’s): o Strain A and Strain B: they’re complimentary o Neither strain could grow on minimal media (media without added nutrients). 2. Steps: o Grew Strain A and Strain B separately → Neither grew on minimal media. o Mixed Strain A + Strain B together in the same culture. o Plated the mixed culture on minimal media. Results Bacteria grew on minimal media when the two strains were mixed. These were prototrophs → They had the ability to make all nutrients. Conclusion Bacteria can exchange DNA to share traits. This process was later called conjugation, where one bacterium transfers DNA to another. Conjugation requires the formation of a sex pillius. Key Takeaway Mixing different bacterial strains can result in DNA exchange, enabling them to grow in conditions they couldn’t survive in alone! Be able to describe the complete life cycle of a bacteriophage Life Cycle of a Bacteriophage What is a Bacteriophage?  A virus that infects bacteria. Steps of the Life Cycle 1. Phage is adsorbed into the bacterial host cell 2. Phage uses contractile sheath to open the host cell to inject DNA. Then the DNA is degraded 3. Phage DNA is replicated; phage protein components are synthesized 4. Mature phages are assembled 5. Host cell is lysed; phages are released (doesn’t always kill the host cell) Key Takeaway A bacteriophage infects a bacterium, hijacks its machinery to make more phages, and then bursts the bacterium to release new viruses! Understand how gene duplication functions to allow for the formation of new genes Gene Duplication and the Formation of New Genes What Is Gene Duplication? Definition: An extra copy of part of a chromosome is made. Why It Matters: 1. Essential Genes: § Duplications ensure survival (e.g., rRNA in Drosophila). 2. Phenotypic Changes: § Example: Bar-eyed flies (Drosophila): § 1 copy = normal eyes. § 2 copies = Bar-eyed. § 3 copies = Double Bar-eyed. 3. New Genes: § Duplicated genes can mutate and take on new functions, increasing genetic diversity. How Gene Duplication Creates New Genes: 1. Duplication: A gene is copied. 2. Two Paths: o Copy 1 keeps the original job (Function A). o Copy 2 mutates and evolves into a new gene (Function B). Example: Original Gene A: Breaks down sugar. After Duplication: o Copy 1: Keeps breaking down sugar. o Copy 2: Mutates → Breaks down a new sugar. Why It’s Important: Adds new abilities to the organism. Helps organisms adapt to new environments. Drives evolution and increases genetic diversity. Understand how compounds are tested to determine if they are in fact carcinogens How Compounds Are Tested to Determine if They Are Carcinogens The Ames Test Purpose: Detect if a compound is a mutagen (mutagens can be carcinogens). Steps: 1. Prepare Bacteria: o Use 4 strains of Salmonella: § 3 prone to frameshift mutations. § 1 prone to point mutations. 2. Set Up Plates: o Mix bacteria with liver enzymes (simulate metabolism). o Plate bacteria on 2 minimal media. 3. Test Compound: o Mix the potential mutagen with liver enzymes. o Soak the mixture on filter paper. 4. Expose Bacteria: o Place the filter paper on the test plate. o Incubate to allow bacterial growth and assess. 5. Compare to Control: o Control Plate: Without the compound. o Test Plate: With the compound. Results: Mutagen: More bacterial growth on the test plate vs. control. Non-Mutagen: Same or less growth on the test plate vs. control. Key Takeaway: The Ames Test checks if a substance causes mutations, which indicates its potential to be a carcinogen. Be able to describe the first two levels of chromosome packing and the key pieces of evidence that supported these two models First Two Levels of Chromosome Packing Level 1: Nucleosome Formation What Happens: o DNA wraps around histones, forming a "beads-on-a-string" structure. o Each "bead" is a nucleosome (~147 base pairs of DNA around 8 histones). Evidence: 1. Electron Microscopy: Showed "beads-on-a-string" under a microscope. 2. Micrococcal Nuclease: Cutting DNA produced 147 bp fragments, proving repeating units. Level 2: 30-nm Fiber Formation What Happens: o Nucleosomes stack into a thicker 30-nm fiber for compact storage. o Histone H1 helps with folding. Evidence: 1. X-Ray Diffraction: Showed a regular, tightly packed structure. 2. Biochemical Experiments: Removing H1 disrupted the 30-nm fiber. Quick Summary: 1. Level 1: Nucleosomes = "beads-on-a-string." 2. Level 2: Nucleosomes fold = 30-nm fiber (compact). Be able to describe the process of DNA Proofreading during DNA replication Understand how DNA proofreading by DNA polymerase works DNA Proofreading by DNA Polymerase: Purpose: Ensures DNA polymerase makes an error only once in every 10⁷ bases during replication. Steps in Proofreading: 1. Base Addition: o DNA polymerase adds a new base to the growing DNA strand. 2. Pause to Check: o DNA polymerase pauses to verify if the newly added base is correctly paired with its complementary base. Outcomes: Correct Base: o If the base is correct, replication continues. Incorrect Base: o DNA polymerase detects the mismatch and uses its 3' → 5' exonuclease activity to remove the incorrect base. o The incorrect base is replaced with the correct one. Result: This proofreading mechanism reduces replication errors, maintaining DNA sequence fidelity. Describe the Lyon hypothesis and the data that supports the Lyon hypothesis Lyon Hypothesis Key Points 1. What Is It? o Females (XX) randomly inactivate one X chromosome in each cell. o The inactivated X becomes a Barr body. 2. Why It’s Important: o Balances X-linked gene activity between males (XY) and females (XX). Evidence Supporting the Lyon Hypothesis 1. Barr & Bertram (First Evidence): o What they found: A dark spot (Barr body) in female cell nuclei during interphase. o What it means: The Barr body is the inactivated X chromosome. 2. Random Inactivation: o Lyon Hypothesis (1961): § Either the maternal or paternal X is randomly inactivated. § Once inactivated, it stays off in all descendant cells. 3. G6PD Enzyme Study: o What is G6PD? A gene on the X chromosome. o Experiment: § Scientists studied women with one normal and one mutant G6PD gene. § Results: § 50% of cells made the enzyme (normal gene active). § 50% didn’t (mutant gene active). o Why it matters: Proved X-inactivation is random. How It Works:  1. X-Inactivation Center (XIC): o Each X has a special region called XIC. 2. XIST RNA: o The XIC produces XIST RNA, which coats the X chromosome to inactivate it. 3. Self-Inactivation: o The coated X condenses into a Barr body and turns off its genes. Quick Recap: 1. Barr body = inactive X chromosome. 2. Random inactivation: Either X can be inactivated in each cell. 3. G6PD study: Showed 50/50 enzyme activity supports randomness. 4. Mechanism: XIST RNA coats the X chromosome and turns it off. Be able to describe the differences between maternal effect and organelle heredity Maternal Effect vs. Organelle Heredity Maternal Effect 1. What It Is: o Proteins in the mother’s egg influence the offspring’s phenotype. 2. How It Works: o Offspring phenotype depends entirely on the mother’s genotype, not its own. o The mother’s phenotype may not match the offspring’s phenotype. Organelle Heredity 1. What It Is: o Traits determined by mitochondrial or chloroplast DNA. 2. How It Works: o Offspring inherit organellar DNA (from mitochondria or chloroplasts) directly from the mother. o The mother’s genotype and phenotype usually match the offspring. Key Similarities Both involve maternal inheritance: o Traits are passed directly from the mother. o Due to the cytoplasm contributed by the egg during fertilization. Key Differences 1. Source of Traits: o Maternal Effect: Traits depend on proteins or factors in the egg, not DNA. o Organelle Heredity: Traits depend on mitochondrial or chloroplast DNA. 2. Mother’s Phenotype:  o Maternal Effect: The mother’s phenotype may differ from the offspring. o Organelle Heredity: The mother’s phenotype matches the offspring. 3. Location of DNA: o Maternal Effect: Does not rely on DNA directly. o Organelle Heredity: Involves DNA outside the nucleus (mitochondria or chloroplasts). Be able to describe how a monosomy or trisomy arises and give an example of a disease caused by each How Monosomy and Trisomy Arise Key Cause: Non-Disjunction What Happens: o Chromosomes fail to separate properly during meiosis. o Gametes end up with either too many or too few chromosomes. Monosomy Definition: Missing one chromosome (only 1 copy instead of 2). How It Happens: o A gamete missing a chromosome combines with a normal gamete → Zygote ends up with 45 chromosomes instead of 46. Example Disease: Turner Syndrome (45, X): o Cause: Missing one X chromosome. o Symptoms: Short stature, incomplete ovaries, webbed neck, average intelligence. Trisomy Definition: Having an extra chromosome (3 copies instead of 2). How It Happens: o A gamete with an extra chromosome combines with a normal gamete → Zygote ends up with 47 chromosomes. Example Disease: Down Syndrome (Trisomy 21): o Cause: Extra copy of chromosome 21. o Symptoms: Flat face, epicanthic eye folds, short stature, intellectual disabilities, risk of heart defects. Key Takeaway Monosomy: Missing a chromosome (e.g., Turner Syndrome). Trisomy: Extra chromosome (e.g., Down Syndrome). Both arise from non-disjunction during meiosis! Be able to describe the Davis U-tube experiment and what the significance of the results of this experiment were Davis U-Tube Experiment What Was the Question? Does bacterial DNA exchange (conjugation) require direct physical contact? Setup: 1. U-Shaped Tube: o Two compartments separated by a filter: § Liquid and nutrients pass through. § Bacteria are blocked. 2. Strains Used: o Strain A and B (both auxotrophic) placed on opposite sides. Key Steps: 1. Separate Strains on Minimal Media: o Result: No growth (autotrophs can’t grow alone). 2. Filter in Place (No Contact): o Strains plated → No growth. o Conclusion: No DNA exchange (bacteria couldn’t touch). 3. Filter Removed (Direct Contact): o Strains mixed → Prototrophs grew on minimal media. o Conclusion: DNA exchange happened when bacteria touched. Conclusion: Conjugation requires direct physical contact between bacteria. This contact happens via a sex pilus (DNA bridge). How Is This an Extension? 1. Before Davis: o Combining two autotrophs made prototrophs, proving bacteria can exchange DNA. 2. Davis's Experiment: o Showed how DNA exchange happens: physical contact is necessary. How to Remember: 1. Filter blocks contact = No DNA exchange. 2. Remove filter = DNA exchange, prototroph growth. 3. Contact = DNA bridge (sex pilus). Significance: Proved that physical contact is required for DNA transfer in bacteria. Led to the discovery of the sex pilus for conjugation. Understand when the lac operon is expressed and is not expressed and what the nature is of the regulation on the promoter that leads to the expression of the operon under those conditions: in the absence of sugar and in the presence of lactose and in the presence of lactose and glucose Lac Operon Expression and Regulation (Simplified for Index Card) 1. Absence of Lactose (No Sugar) Expression: OFF. Why: o LacI repressor binds the operator → Blocks RNA polymerase. o No lactose to inactivate the repressor. 2. Presence of Lactose (No Glucose) Expression: ON. Why: o Lactose binds and inactivates LacI → Operator opens. o Low glucose = High cAMP → CAP-cAMP complex forms. o CAP-cAMP helps RNA polymerase bind strongly → High transcription. 3. Presence of Lactose + Glucose Expression: Reduced. Why: o Lactose inactivates LacI → Operator stays open. o High glucose = Low cAMP → No CAP-cAMP complex. o RNA polymerase binds weakly → Low transcription. Key Takeaways: 1. No Lactose: Operon OFF → Repressor blocks RNA polymerase. 2. Lactose Only: Operon ON → Repressor removed; full activation with CAP- cAMP. 3. Lactose + Glucose: Operon Reduced → Repressor removed, but no CAP- cAMP support. Understand how the cis-trans test worked to identify the roles of lacO and lacI in the regulation scheme for the lac operon Cis-Trans Test for LacI and LacO Purpose Determine if LacI (repressor) and LacO (operator) act cis (on nearby DNA) or trans (across DNA molecules). 1. LacI (Repressor) Setup: o Use a lacI⁻ mutant (operon always ON). o Add a plasmid with lacI⁺ (functional repressor). Results: o Both plasmid and chromosomal operons were regulated (OFF when lactose was absent). Conclusion: o LacI is trans-acting → It’s a protein that works across DNA molecules. 2. LacO (Operator) Setup: o Use a lacOᶜ mutant (operon always ON). o Add a plasmid with lacO⁺ (functional operator). Results: o Only the plasmid operon was regulated; the chromosomal operon stayed ON. Conclusion: o LacO is cis-acting → It’s a DNA sequence that works only on its local operon. Key Takeaway 1. LacI: Trans-acting (protein works across DNA). 2. LacO: Cis-acting (DNA sequence affects only its local DNA). Understand when the trp operon is expressed and is not expressed and how the regulation at the promoter leads to the expression of the operon under those conditions Trp Operon Expression 1. No Tryptophan (Trp) Expression: ON. Why: o No tryptophan → Repressor is inactive. o RNA polymerase binds to the promoter → Operon transcribed. o Result: Enzymes are made to synthesize tryptophan. 2. Tryptophan Present (High Trp) Expression: OFF. Why: o Tryptophan acts as a corepressor → Binds to the repressor. o Repressor-corepressor complex binds to the operator → Blocks RNA polymerase. o Result: No enzymes are made. Quick Summary No Trp: Operon ON → Makes tryptophan. Trp Present: Operon OFF → Stops making tryptophan.