StudyGuide4Final_LabsterSimulationQuestions_Lab7-Lab13_11242023

1. What do you suspect causes the double muscling condition? - The weather - Their DNA - The diet - It is random 2. We now need to collect DNA from the animals to deduce what gene is the cause of double muscling. From where can we get the relevant DNA? - From their blood - From the grass that they eat - From the water that they drink - From the farmer 3. DNA can be extracted from blood because it is present in .... - The red blood cells - Plasma - The white blood cells - Serum 4. How can a genome scan limit the candidate region? - The DNA markers will light up the candidate region - By identifying a DNA marker with known position that co-segregates with double muscling - A mutated DNA marker will cause double muscling - By arranging metaphase chromosomes in a karyotype and scan for chromosomal defects 5. How would identification of the candidate region help you to identify the gene? - It would directly identify the gene - It would tell you whether it is a missense or nonsense mutation - It would limit the genomic region to search for the candidate gene - It would provide you with a list of genes expressed in skeletal muscles 6. PCR on STR marker A in a heterozygous cow (100/150) results in following product(s). - Equal amounts of 100bp and 150bp fragments - Only 150bp fragments - Mainly 150bp fragments - No product 7. The DNA is ... charged. - Positively - Negatively - DNA has no charge - Highly 8. When the PCR only generates one band, such as for STR A marker on both animals, the animals are ... for the marker. - Heterozygous - Recessive - Homozygous - Dominant 9. When the PCR generates two bands, such as for animal III-3's STR B marker, the animal is ... for the marker. - Heterozygous - Homozygous - Recessive - Dominant 10. How will you proceed with the investigation of the three candidate genes? - Run PCR on those genes - Perform restriction analysis on those genes - Sequence the DNA of those genes - Perform microarray of those genes

11. How can we easily identify this 11bp deletion in the DNA? - Perform microarray - Perform gene cloning - Perform PCR and gel electrophoresis - Perform a test cross 12. A master mix contains a mixture of all the reagents needed for a PCR. What are the reagents? - DNA, primers and nucleotides - RNA, nucleotides and polymerase - DNA, RNA and nucleotides - Primers, nucleotides and polymerase 13. The primers are positioned at the ... of the PCR product. - Ends - Middle - Right side - Left side 14. The PCR products get a certain length due to .... - Restriction enzymes - The placement of the primers - The DNA breaking off - The heat in the PCR machine 15. The DNA polymerase extends the primers into a new DNA strand by .... - Adding nucleotides to the 3' end of the primers - Adding more primers to the strand - Adding nucleotides to the 5' end of the primers - Adding nucleotides to the 3' and 5' end of the primers 16. The mutation we are looking for is present in all of the body's cells, including the blood. Which type of DNA are we going to use to check for this mutation? - Complementary DNA - Genomic DNA - Mitochondrial DNA - Noncoding DNA 17. Which blood component contains the highest concentration of genomic DNA? - Red blood cells - Plasma - White blood cells - Platelets 18. What is a microsatellite? - Repeating sequences of two to six base pairs of DNA - A non-coding gene - A gene that is known to jump around the genome - Short genes that have been fused together 19. What is NOT the purpose of the loading buffer? - To add color to the sample so that you can view approximately how far the sample has progressed - To make the sample heavy so that it sinks to the bottom of the well - To provide visual track of the DNA - To fasten the electrophoresis experiment 20. How many copies of DNA are required to see bands on the electrophoresis gel? - Millions of copies - None - 1000 copies - 10 copies

- Adding nucleotides to the 3' and to the 5' end of the primers 31. Why are induced pluripotent stem cells (iPS) used instead of embryonic stem cells (ES)? - iPS are better to avoid immunological reactions - High efficiency in establishing the cell line - iPS have more ethical concerns that have to be considered - Cheaper to implement 32. How do we obtain a protein sample from cells? - Freeze the cells - Lyse the cells. - Grow the cells - Thaw the cells 33. As we discussed before, the RAD52 gene can be isolated from the yeast cells. What should we do first so we can isolate the gene we need? - Perform DNA extraction - Perform DNA sequencing - Separate the DNA using gel electrophoresis - Use a restriction enzyme 34. There is a plasmid containing eGFP on your workbench. How can we cut the eGFP gene from the plasmid? - Perform DNA sequencing on the whole plasmid - Isolate the DNA using phenol-chloroform extraction - Insert the plasmid into bacteria so they secrete the gene - Perform restriction enzyme digestion 35. How can you confirm that we have successfully extracted the DNA from the yeast? - Analyze it using gel electrophoresis and an analytical scale - Analyze it using gel electrophoresis and the NanoDrop - Weigh it using an analytical scale - Analyze it using the UV transilluminator 36. Which of the following techniques are we going to use in order to insert exogenous DNA into the yeast cells? - Transformation - Conjugation - Transduction - All of the options 37. It is common that only some of the yeast cells will successfully take up the plasmid. How do we determine which yeast colonies contain the pTRE-RAD52-eGFP plasmid? - It cannot be determined - Through antibiotic selection - By sequencing each colony - Through gel electrophoresis 38. How can the RAD52-eGFP gene construct help us to study the DNA repair mechanism? - We can observe the eGFP - Analyze the RAD52 gene with sequencing - Transformed yeast will grow better in UV light - We know the DNA sequence of eGFP 39. There are many advantages of using the Next Generation Sequencing (NGS) technique as compared to the Sanger sequencing. Which one of these is an advantage of NGS? - We can sequence only very long DNA strands - We can sequence many DNA molecules in parallel - We can use fluorescence-labeled bases - It takes a longer time to sequence DNA with other techniques 40. What are the possible applications of NGS? - Perform SNP profiling

- Perform gene expression profiling - Detecting genetic aberration - All of these options 41. What is the first step that you need to do to prepare the bone sample for DNA sequencing? - Perform fragmentation - Extract the DNA - Ligate the adapters - Perform A-overhang 42. Why do we skip the fragmentation part when we are sequencing ancient DNA like this sample? - Because the fragmentation costs a lot of money - Because we need to process the DNA immediately - Because the DNA is already partially degraded - Because the DNA contains G - A base substitution 43. We only run PCR amplification for 10-12 cycles which is much lower than the usual 30 cycles. What is the reason for this? - The PCR reagents are too expensive - Minimizing error introduced in replication due to lower sample quality - The ancient DNA cannot withstand repeated high temperatures - We have plenty of DNA to begin with 44. Now that we have performed the PCR amplification and accumulated enough DNA, what is the next step? - Sequencing - Adapter ligation - Generating clusters - Data analysis 45. What is the name of the process that is currently shown in the animation, where the DNA molecules bend and bind each end to an adapter on the flow cell? - Bridge PCR - Emulsion PCR - Microdroplet PCR - Pyro PCR 46. According to Hardy-Weinberg theory, what would it mean if the distribution of allelic frequencies within a population shifted over time? - Random mating is the norm within the population - External evolutionary pressure is acting on the population - The population is in evolutionary equilibrium with its environment - A genetic mutation has not taken place and introduced new alleles 47. The incremental changes we've considered in the canid colony are the building blocks of evolution. Speciation can occur in many different ways. What is the difference between genetic drift and natural selection? - Tricky. They are the same thing - Genetic drift means the best-adapted organisms survive. Natural selection is used by breeders to produce better-adapted groups or organisms - Genetic drift influences evolution through random chance. Evolution by natural selection results in better environmentally adapted populations - Genetic drift relies on constant new mutations whereas mutations do not influence natural selection 48. Which forces are involved in the process of evolution? - Mutation, selection, genetic drift, gene flow - Fertility, genetic drift, gene flow, mutation - Gene flow, infectious diseases, fertility, natural disasters - Genetic drift, natural disasters, mutation, infectious diseases 49. Both fish and dolphins inhabit similar environments and have analogous structures and shapes. However, dolphins are placental mammals and possess vastly different DNA sequences and nervous systems than fish do. What is that example of?

56. The diagram above shows a eukaryote cell where the central dogma of molecular biology is represented. This dogma shows the flow of genetic information. What are the correct terms to fill boxes A, B, C, and D? You can click the VIEW IMAGE button to get more information about the image. - Transcription, ribosome, pre-mRNA, mRNA - Translation, mRNA, pre-mRNA, mitochondria - Transcription, pre-mRNA, mRNA, ribosome - Translation, pre-mRNA, mRNA, Golgi apparatus 57. Which colony should we pick for the expression analysis? You can access the transformation results by clicking ' VIEW IMAGE ' button. - A - B - C - D 58. Why should we pick a single colony? - To ensure all cultured yeast cells are identical - To ensure all cells grown are genetic clones of a single original cell - To avoid large genetic variance in the expanded culture - All answers are correct