Blg1502 Study Summary Notes 2022

BLG1502 STUDY SUMMARY NOTES 2022. BLG1502 - Animal And Plant Diversity Phylogeny and Systematics Textbook pages: 519 – 538 PHYLOGENY : THE EVOLUTIONARY HISTORY OF A SPECIES OR GROUP OF SPECIES SYSTEMATICS : A DISCIPLINE FOCUSED ON CLASSIFYING ORGANISMS AND DETERMINING THEIR EVOLUTIONARY RELATIONSHIPS . TAXONOMY : THE SCIENTIFIC DISCIPLINE OF HOW ORGANISMS ARE NAMED AND CLASSIFIED . HOMOLOGIES : PHENOTYPIC AND GENETIC SIMILARITIES DUE TO SHARED ANCESTRY . ANALOGY : THE SIMILARITY FUNCTION AND SUPERFICIAL RESEMBLANCE OF STRUCTURES THAT HAVE DIFFERENT ORIGINS . SIMILAR STRUCTURES IN COMPLETELY UNRELATED SPECIES DEVELOPED INDEPENDENTLY AS ADAPTATIONS TO A COMMON FUNCTION DUE TO SIMILAR ENVIRONMENTAL PRESSURES AND NATURAL SELECTION . CLADISTICS : AN APPROACH TO SYSTEMATICS IN WHICH COMMON ANCESTRY IS THE PRIMARY CRITERION USED TO CLASSIFY ORGANISMS . MONOPHYLETIC : A GROUP OF ORGANISMS CONSISTING OF A COMMON ANCESTRAL SPECIES AND ALL OF ITS DESCENDANTS . PARAPHYLETIC : A GROUP OF ORGANISMS CONSISTING OF A COMMON ANCESTRAL SPECIES AND SOME , BUT NOT ALL , OF ITS DESCENDANTS . POLYPHYLETIC : A GROUP OF ORGANISMS CONSISTING OF DISTANTLY RELATED SPECIES BUT DOES NOT INCLUDE THEIR MOST RECENT COMMON ANCESTOR . ORTHOLOGOUS GENES: HOMOLOGOUS GENES FOUND IN DIFFERENT GENE POOLS AFTER A SPECIATION EVENT . PARALOGOUS GENES: RESULT FROM GENE DUPLICATION AND ARE FOUND IN MORE THAN ONE COPY IN THE SAME GENOME . THESE GENES DIVERGE (MUTATE ) FROM ONE ANOTHER WITHIN A SPECIES . THIS GIVES RISE TO A NEW GENE THAT HOLDS A NEW FUNCTION , ALTHOUGH THIS FUNCTION MAY BE RELATED TO THAT OF THE ANCESTRAL GENE . A KEY STEP TO RECONSTRUCTING PHYLOGENIES IS TO DISTINGUISH HOMOLOGOUS FEATURES FROM ANALOGOUS ONES Describe the binomial nomenclature system. Binomial nomenclature is the nomenclature (terminology) that biologists use when naming and referring to organisms, to avoid ambiguity. The organism’s Latin scientific name is used and consists of two parts (a binomial). The first part is the name of the genus (plural – genera) to which the organism belongs and is always capitalized. The second part of the name is the specific epithet, which is unique for each species within the genus, and is not capitalized. The entire binomial is written in italics. Example – Homo sapiens Explain the hierarchical system of classification. Hierarchical classification is the grouping of species into a hierarchy of increasingly inclusive categories. Species that appear to be closely related are grouped into the same genus. Related genera are grouped into the same family. Families are grouped into orders, orders into classes, classes into phyla (singular – phylum), phyla into kingdoms and kingdoms into domains. A taxon (plural – taxa) is the named taxonomic unit at any level of the hierarchy. Example – Homo is the taxon at the genus level in the case of humans. 2 Taxa broader than the genus are not italicized, only capitalized List the different hierarchical classification groupings. Listed from broadest to narrowest: Domain Kingdom Phylum Class Order Family Genus Species Discuss cladistic analysis on which systematics is based. The basis of cladistic analysis is data on traits of the organisms that we are interested in. A clade is a group of species that includes an ancestral species and all its descendants. Each clade can be nested within larger clades. A valid clade is monophyletic. A shared ancestral (primitive) character is found in both the clade being analysed, as well as older (ancestral) clades. A shared derived character is unique to a clade and is useful in establishing a phylogeny. Outgroup comparison is used to differentiate shared ancestral characters from shared derived characters by. An outgroup is a species or group of species that is closely related to the species that we are studying but known to be less closely related than any members of the study group are to one another. A cladogram presents the chronological sequence of branching during the evolutionary history of a set of organisms. NOTE: A cladogram is NOT a phylogenetic tree but may merely act as the base for one. S - The study-notes marketplace 3 In a phylogram, the length of a branch reflects the number of genetic changes that have taken place in a particular DNA or RNA sequence in a lineage. Discuss the principle of parsimony and maximum likelihood. Principle of Parsimony: First investigate the simplest explanation that is consistent with the facts. Maximum Likelihood: Identifies the tree most likely to have produced a given set of DNA data, based on certain probability rules about how DNA sequences change over time. Phylogenetic trees are simply hypotheses and the principle of parsimony just helps us create the simplest hypothesis. The Tree of Life The Tree of Life consists of three great domains – Bacteria, Archaea and Eukarya S - The study-notes marketplace Downloaded by: tbosmvenyane | Distribution of this document is illegal S - The study-notes marketplace 4 Learning Unit 2: Prokaryotes and the Origins of Metabolic Diversity Textbook pages: 625 – 644 PHOTOTROPHS : ORGANISMS THAT OBTAIN ENERGY FROM LIGHT . CHEMOTROPHS : ORGANISMS THAT OBTAIN ENERGY FROM CHEMICALS . AUTOTROPHS : ORGANISMS THAT NEED ONLY CO2 OR RELATED COMPOUNDS AS A CARBON SOURCE . HETEROTROPHS : ORGANISMS THAT REQUIRE AT LEAST ONE ORGANIC NUTRIENT TO MAKE OTHER ORGANIC COMPOUNDS . Name the two main branches of prokaryotic evolution. Bacteria and Archaea are the two main branches of prokaryotic evolution. The fact that prokaryotes can survive extreme conditions, which most eukaryotes cannot, accounts for the fact that they are far more abundant on Earth. Although they are extremely small (0.5 – 5 micrometres in diameter) when compared to eukaryotes (10 – 100 micrometres in diameter), prokaryotes are well organized and achieve all of an organism’s life functions within a single cell. Describe the structure, function and reproduction of bacteria. The cell wall maintains cell shape, protects the cell and prevents it from bursting in hypotonic environments. Most bacterial cell walls contain peptidoglycan. There are 2 types of cell walls – gram-positive and gram-negative. Gram-positive: simple, thick cell walls. Gram-negative: thin, more complex cell walls – peptidoglycan layer surrounded by plasma membrane and outer membrane – are more resistant antibiotics and host’s immune defence. In a hypertonic environment, prokaryotes plasmolyze (lose water and shrink away from cell wall). This inhibits reproduction. That’s why salt can be used to preserve food – it prevents food-spoiling prokaryotes from rapidly multiplying. S - The study-notes marketplace Downloaded by: tbosmvenyane | Distribution of this document is illegal S - The study-notes marketplace 5 Reproduction in bacteria is asexual by binary fission. Bacteria to not have gene transfer by sexual reproduction, but genes do transfer. There are three ways for genes to be transferred between cells: • Transformation – cell takes up genes from the surrounding environment. • Conjugation – direct transfer of genes from one prokaryote to another using sex pili. • Transduction – viruses transfer genes from one prokaryote to the next when moving from on prokaryotic host to the next. Describe the structure, composition and function of prokaryotic cell walls. Many prokaryotic cell walls are surrounded by a capsule (well-defined sticky layer of polysaccharide or protein) or slime layer (not so well-defined sticky layer of polysaccharide or protein). This allows prokaryotes to adhere to their substrate or other individuals in a colony. In some cases, this also protects against dehydration and shield pathogenic prokaryotes from their host’s immune system. Describe how prokaryotes can survive extreme conditions. Certain bacteria develop endospores (resistant cells) when they lack water or essential nutrients. The original cell creates a copy of its chromosome and this copy with a multi-layered structure. Water is removed and the endospore’s metabolism halts. The original cell lyses to release the endospore which can rehydrate and resume metabolism when the environment improves. Capsules and slime layers also help prokaryotes survive unfavourable conditions. Distinguish between the staining properties of gram-positive and gram-negative bacteria. Gram-positive: The crystal violet enters the cell wall, where it forms a complex with the iodine in the stain. This complex is too large to pass through the thick cell wall, so it is not removed by the alcohol rinse. Therefor – the darker crystal dye masks the red safranin dye. Gram-negative: The crystal violet-iodine complex can pass through the thin cell wall, so it is removed by the alcohol rinse. Therefor – the safranin dye stains the cell pink or red. Explain how the genetic organisation of the prokaryotic genome differs from that of eukaryotic cells. The genome of a prokaryote usually has much less DNA than the genome of a eukaryote. Prokaryotes generally have circular chromosomes and lack a nucleus (their chromosome is in the nucleoid), whereas eukaryotes have linear chromosomes and a true nucleus. Prokaryotes may have plasmids (smaller rings of independently replicating DNA molecules).