Final Exam Study Guide PDF

From Exam 2 =========== During replication, why is the lagging strand made in segments? What is between these segments that needs to be removed and replaced before they're joined? What is the common telomere repeat sequence? What is the purpose for telomeres folding up into g-quadruplexes? Why ca...

From Exam 2 =========== During replication, why is the lagging strand made in segments? What is between these segments that needs to be removed and replaced before they're joined? What is the common telomere repeat sequence? What is the purpose for telomeres folding up into g-quadruplexes? Why can't a eukaryotic RNA polymerase begin translating any promoter region that is available like prokaryotes can? What is required for a eukaryotic RNA polymerase to be able to bind to a promoter and begin transcription? Some molecules can be bound to a histone tail to cause them to close tightly together, others cause the histones to spread out. What molecules cause those different changes? What characteristics of the molecules cause those changes? What are the differences between miRNA and siRNA in terms of 1) their origin 2) degree to which they match their sequence matches target RNA and 3) the action taken by their RISC complex once they sequence match? If a cell had the ability to very finely regulate TRANSLATION of an mRNA, what cis-regulatory elements would you expect the mRNA to contain? Be specific with number and type. How can simple transposable elements enable evolution of new gene functions? Why can't retrotransposons do that? Lecture 13 - DNA damage and repair ================================== Generally, why are single strand issues easier to repair than double strand issues? What issue can be caused by DNA polymerase slipping backward? When repairing a single strand issue, what are the two kinds of nucleases (enzymes that cut nucleotide strands) are used and how are they different? What can haploid organisms do to try to repair a double strand break? Why is this type of damage repair unlikely to save the prokaryote cell? Lecture 14 - Molecular technologies =================================== Restriction enzymes are able to cut DNA in specific places? How do they find the right place to cut? What are the "sticky ends" that result from the cut and how are those ends useful? What does it mean to clone a gene? What is the source of vectors used in cloning a gene? What is PCR used for? What is the ideal makeup for the primers used, in terms of sequence and length? CRISPR-Cas systems can be used to study activity of a gene in three unique ways, what are those ways? How are each of those accomplished, what would a researcher change to get those different methods? If you wanted to find out what DNA a protein of interest interacts with, how would you use ChiP-Seq to do that? Lecture 15 - Biotechnology ========================== Living organisms can help to remove toxic substances, what types of substances can microorganisms help with and what types of substances can plants help with? How do vaccines work to teach your immune system how to recognize viruses? How can genetic modification aid in pharmaceutical production? There are two different organism types that can be used. What is the potency of stem cells? Why are embryonic stem cells more useful in medicine than adult stem cells? What is it that stem cells are able to be used for that other medicines can't yet do? Traditional farming in the US can negatively impact the health of surrounding ecosystems, how could genetic modification of crops reduce those harms? There are other benefits to genetic modification in improving our crops that breeding is impossible or too slow to effectively meet humanities needs, what are some of these? Genetic modification of plants is much easier than genetic modification of animals, what are some reasons for this? Lecture 16 - Genomic analysis and bioinformatics ================================================ Microsatellites are useful in localizing where in the genome the gene coding for a trait or disease is located. How are they useful in this? What do microsatellites look like and what aspect of them makes them useful in comparing individuals? How do we amplify only the microsatellite we want and not other related microsatellites? What is the purpose of chromosome walking? What information do you need in order to begin walking from one gene of interest to another gene of interest? There are two distinct pieces of information that are found in very different ways. De novo genome sequencing is when you don't know any of the sequence of a genome, or very little information. How can you begin this sort of sequencing? What is required of your sequenced segments that enables piecing them together? What are some benefits of completely sequencing the human genome? Illumina sequencing is a form of sequencing by synthesis and parallel sequencing. What do each of those mean? How is sequencing by synthesis similar to sanger sequencing? How can metagenomic studies of all DNA found in a sample aid our understanding of various impacts on ecosystems? What is functional genomics? How does this differ from normal genomics? What is being collected from cells to study functional genomics? Lecture 17 - Population genetics ================================ What is the difference between a population and a local population? What is a population's gene pool? Which individuals contribute to the gene pool of the next generation? What is the most general definition of genetic diversity in a population? Is genetic diversity also seen as phenotype diversity? Why? What are common things that separate local populations from being considered one population? When we are talking about frequencies in a population there are three different aspects we could be considering, what are those? What are the most common types of polymorphisms that we look at in a population? Adhering to all the constraints required to be in Hardy-Weinberg is unlikely, so why do we bother calculating whether a gene is at Hardy-Weinberg equilibrium? Alleles can be at any frequency and still be in equilibrium, what frequencies do matter here? Natural selection as a cause of evolution requires that what be true for a trait? There are several factors but they all focus on one thing, what is that? If you are interested in genomic regions that might be important for a species' success you could do Genome Wide Selection Scan. If doing a full genome sequencing for several individuals isn't something you can do, what might you be able to use instead? If a region is heavily selected for, what would you expect to find in the sequences between individuals? Why are alleles of unrelated genes able to hitchhike and go to fixation due to the success of a nearby allele that is advantageous? In other words, why doesn't just the advantageous allele go to fixation? What are the patterns of selection and what is a real-world scenario that you would see each pattern for? You don't need to remember the specific names but should be comfortable with their causes and outcomes. If an animal has an extremely exaggerated feature what would be a likely selective pressure that brought this feature about? What would be an advantage for many local populations having frequent migration between them? What could be a disadvantage of frequent migration for these local populations?