Biology 1414 Lab Practical #1 Review (Lab #1-4)

BIO 1414 (LAB #1-4) LAB PRACTICAL #1 REVIEW LAB 1: MOLECULAR PHYLOGENY LAB 2: EVOLUTION LAB 3: MICROBIOLOGY LAB 4: PLANT-ANIMAL INTERACTION **Please wear appropriate lab attire and bring a scientific calculator with you on your test day!** LAB 1: MOLECULAR PHYLOGENY ❏Learn the process and utility of DNA barcoding -Barcodes distinguish between different species with one group because they show the variation and difference in each DNA sequence -During the process of DNA barcoding, discrete gene loci are chosen as barcode regions, then unique DNA primer sets are determined that used to amplify these same regions across a range of species by the polymerase chain reaction (PCR), the result will be sequenced and compared -Several barcoding primers: ●GMOs: The primers amplify a 190 base pair fragment of the EPSPS gene ●Fungi: The primers amplify a 560 base pair fragment that is an internal transcribed spacer that surrounds the 5.8S ribosomal RNA gene ●Plants: The primers amplify a 600 base pair fragment of the chloroplast gene rbcL ●Animals: The primers amplify a 700 base pair fragment of the mitochondrial cytochrome c oxidase subunit 1 gene ●Prokaryotes: The primers amplify a 1500 base pair fragment that is within the 16S rDNA, that encodes for the 16S ribosomal RNA ❏Steps to PCR -Denaturation – 94-98°C, separates the template DNA into single strands -Annealing – 55-70°C, allows primers to bind to the template with their specific complementary sequences -Extension – 65-72°C, allows the DNA polymerase to build complementary DNA extending from each primer 3'OH ❏Analysis of barcoding PCR products -The size of the fragments produced from the PCR reaction will be determined by comparing their migration to the migration of a marker, which is also run on the gel and has fragments of a known size -When plotting the log graph for analysis, treat it like a normal graph ●Include graph title, x-axis, and y-axis with units and a legend for when there are multiple lines/bars -X-axis should be the distance traveled (cm) and y-axis should be the size of the DNA fragment/marker (bp) -The distance of a fragment of DNA moves into the gel is inversely proportional to the size of the fragment in bp ●Which means a smaller sized fragment would more likely to travel farther ❏Learn the pros and cons of how to detect genetically modified foods -Arguments in favor of GMOs: ●Agricultural: Increased yield, and the ability to feed an ever-growing population ●Environmental: Reduced use of pesticides, herbicides, and fuel ●Nutritional: Improved quality of food ●Disease prevention: Foods that work like edible vaccines -Arguments against GMOs: ●Exposure to possible allergens and toxins ●Harm to the environment if not contained ●Antibiotic resistance ●The spread of introduced genes to non-target plants by outcrossing and pollen drift ❏Learn how to draw phylogeny trees -Phylogeny trees are drawn to understand the lineage of various species and how various functions evolved -Trees can be rooted or unrooted, the tips of the tree represent groups of descendent taxa and the nodes on the tree represent the common ancestors of those descendants -Two descendants that split from the same node are called sister groups, meaning they are closely related to each other ●The orientation of species within a sister group does not impact their lineage (see picture) -An outgroup is a taxon outside of interest -Step 1: Carefully observe the amino acid sequences and anatomy -Step 2: Rank the traits from the simplest to the most complex, certain traits will be shared by two or more taxa ●Parsimony decides between different tree topologies by identifying the tree that involves the shortest evolutionary pathway (the one with the