Bio 110 Exam 3 Study Guide PDF

**PART I: Genetics** 1. **Why is sexual reproduction advantageous, and why is it disadvantageous?** - **Advantages:** Sexual reproduction introduces genetic diversity, which is essential for adaptation to changing environments and survival. The recombination of genes dur...

**PART I: Genetics** 1. **Why is sexual reproduction advantageous, and why is it disadvantageous?** - **Advantages:** Sexual reproduction introduces genetic diversity, which is essential for adaptation to changing environments and survival. The recombination of genes during meiosis creates unique offspring, potentially with advantageous traits. - **Disadvantages:** Sexual reproduction is energetically costly, requires finding a mate, and results in slower population growth compared to asexual reproduction. It also has the potential to pass on genetic mutations or harmful alleles. 2. **Do all sexually reproducing organisms have XY chromosomes? Explain in depth.** - No, not all sexually reproducing organisms have XY sex-determination systems. While mammals use the XY system, other organisms use different mechanisms. For example, birds use a ZW system (where females are ZW and males ZZ), and some reptiles\' sex is determined by environmental factors, such as temperature during development. In some fish and amphibians, sex determination can be even more fluid, demonstrating that sex determination has evolved multiple times in different lineages. 3. **How do scientists think the Y chromosome evolved?** - Scientists believe the Y chromosome evolved from an ordinary autosome. Over time, the Y chromosome gradually lost many of its genes and developed unique sequences that distinguished it from the X chromosome. This process of degeneration led to the Y chromosome being much smaller and containing fewer genes than the X chromosome. 4. **Do the X and Y chromosomes cross over during meiosis?** - No, the X and Y chromosomes do not typically undergo crossover during meiosis because they are largely non-homologous, except for small regions at the tips called pseudoautosomal regions (PARs). Crossing over is limited to these PARs to allow the chromosomes to segregate correctly during meiosis. 5. **Probability of offspring having white fur in a Bb x bb mouse cross:** - White fur requires the genotype \"bb.\" In this cross, the genotypes of offspring would be Bb and bb in a 1:1 ratio. Therefore, there is a 50% probability of the offspring having white fur. 6. **Probability of offspring having white fur and black eyes in a BbCc x bbcc cross:** - A BbCc mouse crossed with a bbcc mouse produces: - White fur (bb) has a 50% chance. - Black eyes (C) also has a 50% chance. - Therefore, the probability of having white fur and black eyes is 50% \* 50% = 25%. 7. **Analyzing pedigrees A-D to determine inheritance patterns:** - Each pedigree can be analyzed for patterns of dominant, recessive, autosomal, or sex-linked inheritance by identifying patterns of affected individuals. For example, an autosomal recessive disorder would typically appear in offspring when both parents are carriers but not affected. 8. **Genotypes of Marie's parents if Marie is Type O and her sister is Type AB:** - Marie (Type O) has genotype ii, and her sister (Type AB) has genotype IAIB. Since both maternal grandparents are Type A, Marie\'s parents' genotypes must be IAi and IBi. The pedigree would show these genotype possibilities in each family member. 9. **Determining gene pairs likely to be linked:** - Gene pairs with lower recombination frequencies are closer together and more likely to be linked. Therefore, C and D, with an RF of 2.5%, are most likely to be linked. **PART II: DNA Replication and Transcription** 1. **How nucleotides bond to form double-stranded DNA:** - Nucleotides bond through hydrogen bonds between complementary nitrogenous bases (A-T and G-C). Adenine pairs with thymine through two hydrogen bonds, while guanine pairs with cytosine through three hydrogen bonds. 2. **Source of energy for forming phosphodiester bonds:** - The energy for forming phosphodiester bonds comes from the hydrolysis of nucleotide triphosphates, specifically the release of pyrophosphate. 3. **Labeling and identifying parts of a nucleotide:** - In a nucleotide, label the phosphate group, deoxyribose sugar, and nitrogenous base. A single nucleotide includes a sugar-phosphate backbone and a nitrogenous base. 4. **Why DNA replication is called semi-conservative:** - DNA replication is semi-conservative because each new DNA molecule consists of one old (parental) strand and one newly synthesized strand. Each parental strand serves as a template for a new complementary strand. 5. **Bonds affected by tautomeric shifts:** - Tautomeric shifts can lead to incorrect hydrogen bonding, which may cause mispairing during DNA replication, potentially leading to point mutations. 6. **Possible results of DNA replication errors:** - Errors in DNA replication can lead to mutations, such as point mutations, insertions, deletions, or frameshift mutations, which can disrupt gene function and potentially cause diseases. 7. **Role of single-stranded binding proteins (SSBs):** - SSBs prevent reannealing of the DNA strands and protect them from nuclease digestion during replication. 8. **Role of helicase and primase enzymes:** - Helicase unwinds the DNA double helix, creating a replication fork, while primase synthesizes RNA primers needed to initiate DNA synthesis. 9. **Transcription of DNA to mRNA, and effects of mutations:** - The mRNA transcribed from the DNA segment 5'-TAAAATGGCATAATGCTGA-3' would be complementary and follow base-pairing rules. Point mutations or deletions would alter the mRNA sequence, potentially affecting the resulting amino acid sequence and protein function. 10. **Direction nucleotides are added by DNA polymerase:** - DNA polymerase adds nucleotides to the 3' end of the growing DNA strand, moving in a 5' to 3' direction. 11. **End where RNA polymerase adds nucleotides in mRNA synthesis:** - RNA polymerase adds nucleotides to the 3' end of the mRNA strand during transcription. 12. **Template strand in DNA transcription:** - The template strand is the strand that RNA polymerase reads to synthesize complementary mRNA. The other strand is the coding strand. 13. **Purpose of DNA replication:** - The purpose of DNA replication is to ensure that each new cell has an identical copy of the genome for proper functioning and growth. 14. **Purpose of transcription and translation:** - Transcription produces mRNA from a DNA template, and translation synthesizes proteins based on the mRNA sequence. 15. **Defining parts of a replication bubble:** - Leading strand: synthesized continuously in the direction of the replication fork. - Lagging strand: synthesized in short segments called Okazaki fragments, opposite to the fork. - Origin of replication: starting point for DNA replication. - RNA primer: short RNA sequence that initiates DNA synthesis. - Topoisomerase: relieves strain caused by unwinding DNA. - DNA polymerase: enzyme that adds nucleotides to form DNA. - Ligase: enzyme that joins Okazaki fragments on the lagging strand. 16. **Source of variation in Canary Island lizards:** - **Answer:** (B) Random changes in the DNA created new traits. 17. **Central Dogma and gene expression:** - The Central Dogma states that genetic information flows from DNA to RNA to proteins. DNA is transcribed into mRNA, which is then translated into proteins that perform cellular functions. 18. **Comparison of mRNA and tRNA:** - mRNA carries the genetic code from DNA to the ribosome, while tRNA brings specific amino acids to the ribosome to build the protein based on the mRNA code. **PART III: Regulation of Gene Expression** 1. **Organisms with the lac operon:** - The lac operon is present in prokaryotes, particularly bacteria like *E. coli*. 2. **Default state of the lac operon:** - The default state of the lac operon is \"off\" because, without lactose, a repressor binds to the operator, blocking transcription of lactose-metabolizing genes. ### PART IV. Regulation of Gene Expression #### 1. **In what type of organism is the lac operon present?** The lac operon is present in prokaryotic organisms, specifically in bacteria like *Escherichia coli (E. coli)*. This operon is a key example of gene regulation in prokaryotes, allowing them to efficiently manage resources in response to environmental changes, such as the presence or absence of lactose. #### 2. **What is the default state of the lac operon and why?** The default state of the lac operon is \"off.\" This is because, in the absence of lactose, a repressor protein binds to the operator region of the operon, preventing transcription of the downstream lactose-utilization genes. This regulation allows bacteria to conserve energy by not producing enzymes for lactose metabolism when lactose is not available. #### 3. **Explain the lac operon using the following terms: Lactose, Regulatory Genes, Operator, Repressor, Promoter, RNA Polymerase, Lactose-utilization Genes, Transcription Factor, Glucose.** The lac operon is a set of genes in *E. coli* involved in lactose metabolism. Regulatory genes code for a repressor protein that binds to the operator in the operon, blocking RNA polymerase from transcribing lactose-utilization genes. When lactose is present, it binds to the repressor, inactivating it, so RNA polymerase can bind to the promoter and transcribe the operon. When glucose is present, transcription is suppressed because the cell prefers glucose as an energy source. Transcription factors modulate this process by assisting or hindering RNA polymerase attachment. #### 4. **Explain 7 ways that gene expression can be regulated.** 1. DNA Methylation: Adds methyl groups to DNA, often silencing gene expression. 2. Histone Modification: Alters chromatin structure, affecting transcription. 3. Transcription Factors: Proteins that promote or inhibit transcription initiation. 4. RNA Splicing: Alternative splicing can produce different mRNA variants. 5. mRNA Stability: Determines how long mRNA is available for translation. 6. Translation Control: Regulatory proteins can inhibit or enhance translation. 7. Protein Modification: Post-translational modifications, like phosphorylation, can alter protein activity. #### 5. **How do retinal cells differ from intestinal cells using the same DNA?** Retinal and intestinal cells express different genes, producing proteins specific to each cell's function. This differential gene expression, driven by regulatory mechanisms, leads to cells with distinct structures and functions even though they share the same DNA. #### 6. **What is cell differentiation?** Cell differentiation is the process by which a cell becomes specialized to perform a specific function. This involves the selective expression of genes that define the cell\'s role within an organism. #### 7. **Difference between embryonic and adult stem cells?** Embryonic stem cells are pluripotent, meaning they can differentiate into almost any cell type. Adult stem cells are multipotent, restricted to differentiating into a limited range of cells within their tissue type. #### 8. **What are induced pluripotent stem cells?** Induced pluripotent stem cells (iPSCs) are adult cells genetically reprogrammed to revert to a pluripotent state, allowing them to differentiate into various cell types, much like embryonic stem cells. #### 9. **Explain CRISPR-Cas9 origin, uses, and function.** CRISPR-Cas9 originated as a bacterial immune system against viruses. Scientists adapted it to edit genes precisely by introducing a guide RNA that targets a specific DNA sequence. The Cas9 enzyme then makes a cut, allowing for gene editing for medical, agricultural, and research applications. #### 10. **How can hormones be produced using gene technology?** Gene technology can insert human genes encoding hormones like insulin or human growth hormone into bacteria or yeast, which then produce these hormones. This biotechnology has enabled the mass production of critical hormones for therapeutic use. #### 11. **Emergence of antibiotic resistance and how bacteria acquire resistance.** Bacteria develop antibiotic resistance through mutations and acquiring resistance genes from other bacteria via horizontal gene transfer methods like conjugation, transformation, and transduction. Overuse of antibiotics accelerates this process, as resistant strains survive and proliferate. #### 12. **How prokaryotes transfer genes and its impact on antibiotic resistance.** Bacteria transfer genes through conjugation, transformation, and transduction, spreading antibiotic resistance genes rapidly within bacterial populations. This gene transfer allows bacteria to evolve resistance quickly, posing a challenge for healthcare. #### 13. **Method for identifying antibiotic susceptibility of bacteria.** The disk diffusion method or Kirby-Bauer test is used to determine bacterial susceptibility. Antibiotic-impregnated disks are placed on an agar plate with bacteria, and zones of inhibition around disks indicate susceptibility or resistance based on bacterial growth response. ### PART V. Immunology #### 1. **How vaccines prevent severe infections.** Vaccines introduce a harmless form of a pathogen or its antigens, training the immune system to recognize and remember it. This enables a faster and stronger immune response upon actual exposure, preventing severe infections by preemptively equipping the body with specific defenses. #### 2. **How vaccinating healthy individuals protects immunocompromised individuals.** Vaccinating healthy individuals contributes to herd immunity, reducing pathogen spread in a population. This protects immunocompromised individuals who cannot be vaccinated by lowering their chances of exposure to the disease. #### 3. **How innate immunity protects our bodies from pathogens.** Innate immunity provides immediate, non-specific defense against pathogens. It includes physical barriers like skin, chemical barriers like stomach acid, and cellular responses like phagocytosis and inflammation to prevent or contain infections. #### 4. **How adaptive immunity protects our bodies from pathogens.** Adaptive immunity involves specialized responses to specific pathogens. B cells produce antibodies targeting specific antigens, while T cells identify and destroy infected cells. Memory cells allow faster responses to previously encountered pathogens, conferring long-lasting immunity.