Exam 1 Review - Lecture notes 1-6 PDF

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Exam 1 Review CHAPTER 23 Science Scientific Method

Taxonomy

Production of knowledge!!! Technique used worldwide to produce knowledge. QuestionBackground research-Hypothesis-experiment to test hypothesesanalyze results then accept or reject hypothesis. Field of biology concerned with classifying organisms and viruses; accepted pattern is Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species (do kings play chess on fine green sand)

Consider: Each taxa, as the hierarchical order descends, has a smaller number of species. So Order, Family, and Genus would have fewer species than Class. Systematics The reconstruction and study of evolutionary relationships (phylogenies) Phylogeny *** READING The evolutionary history of an organism, including which species are TREE closely related and in what order related species evolved; often represented in the form or an evolutionary tree that are constructed based on morphological analysis, DNA sequences, and geographical information

Domains

Consider: Phylogenetically based taxonomy helps us learn about traits in organisms using information in related species. These traits can also include physiology, development, and behavior. Eukarya, Archaea (small, single celled, cell wall, no nucleus, can live in extreme conditions) , Bacteria (greatest # niches) Kingdoms of Plantae, Fungi, Animalia and Protista are all in the Eukarya Domain *** What are the main characters (synapomorphy) that differentiates these kingdoms? Consider: The traits that all 3 domains have in common are hypothesized to be the result of all 3 domains evolving from a common prokaryotic ancestor. Those traits are that all species use the same genetic code (very few exceptions), plasma membranes, and glycolysis.

Protista Fungi Convergent evolution

Consider : Above are the two suggested hypothesis on how these groups are related. polyphyletic paraphyletic group or organisms that do not fit within Animalia, Plantae, or Fungi *** analysis Taxa with a cell wall, external digestion, and lacking photosynthesis capability The independent development of similar structures in organisms that

Derived character ***

cladistics

are not directly related; often found in organisms living in similar environments A characteristic used in taxonomic analysis representing a departure from the primitive (ancestor) form; in cladistics, characteristics between the branch points of a cladogram that are shared by all organisms above the branch point and are not present in any below it Understand the difference between derived and ancestral characteristics. a taxonomic technique used for creating hierarchies or organisms that represent true phylogenetic relationship and descent. This technique has multiple uses including the HIV court case.

ancestral characteristics characteristics that have arisen in organisms as a result of *** common evolutionary descent character state In cladistics, one of two or more distinguishable forms of a character, such as the presence or absence of teeth in amniote vertebrates polarize in cladistics, to determine whether character states are ancestral or derived Cladogram a graphical representation of possible evolutionary relationships, *** based on polarization of characters, in which taxa are placed at the tips, not at the branch points, of the phylogenetic tree and shared, derived characteristics common to taxa above the branch point are placed at the branch point.

clade Synapomorphy ***

plesiomorphy Symplesiomorphy ***

Homoplasy ***

Consider: Steps to construct a cladogram would be - 1. gather data on characters to be used, 2. establish the character states (teeth), 3. polarize the characters (ancestral or derived) 4. select an outgroup (closely related to but not a member) 5. apply principle of parsimony (hypothesis that requires the fewest assumptions) ***QUESTION 48*** a group containing all descendants of a common ancestor in systematics, a derived character that is shared by clade members; best mechanism to analyze the evolutionary sequence in the development of a complex character (I remember this by saying the derived (new) characters are synapy...synapomorphy) in cladistics, another term for an ancestral character state in cladistics, another term for a shared ancestral/primitive or outgroup character state (I remember this by saying the primitive trait is the most symplesiomorphy) in cladistics, a shared character state that has not been inherited from a common ancestor exhibiting that state; may result from convergent evolution or evolutionary reversal. The wings of

principle of parsimony *** READ TREE Monophyletic ***

birds and of bats, which are convergent principle state that scientists should favor the hypothesis that requires the fewest assumptions; simplest phylogenetic tree should be chosen in phylogenetic classification, a group that includes the most recent common ancestor of the group and all its descendants. A clade is a monophyletic group.

Paraphyletic ***

in phylogenetic classification, a group that includes the most recent common ancestor of the group, but not all its descendants Polyphyletic *** in phylogenetic classification, a group that does not include the most recent common ancestor of all members of the group the concept that defines species as groups of populations that have biological species concept (BSC) the potential to interbreed and that are reproductively isolated from other groups phylogenetic species the concept that defines species on the basis of their phylogenetic concept (PSC) relationships reproductive isolation not being able to mate outside one's group outgroup An outgroup is an organism that is considered not to be part of the group in question, but is closely related to the group. The evolutionary conclusion from this is that the outgroup branched from the parent group before the other two groups branched from each other. horizontal gene transfer transfer of genes between different species, both prokaryotic or eukaryotic ● ●

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Ingroup: the "study group" Sister group: the group that is genealogically most closely related to the ingroup, and included for comparative purposes; we can conclude that species D is more closely related to species E than it is to species A. Outgroup: a more distantly related group (not part of the clade: ancestor and all descendants that share a derived character state called synapomorphy)

Here is something you may find helpful: What's the difference between a phylogeny, an evolutionary tree, a phylogenetic tree, and a cladogram? For general purposes, not much. This site, along with many biologists, use these terms interchangeably — all of them essentially mean a tree structure that represents the evolutionary relationships within a group of organisms. The context in which the term is used will tell you more details about the representation (e.g., whether the tree's branch lengths represent nothing at all, genetic differences, or time; whether the phylogeny represents a reconstructed hypothesis about the history or the organisms or an actual record of that history; etc.) However, some biologists do use these words in more specific ways. To some biologists, use of the term "cladogram" emphasizes that the diagram represents a hypothesis about the actual evolutionary history of a group, while "phylogenies" represent true evolutionary history. To other biologists, "cladogram" suggests that the lengths of the branches in the diagram are arbitrary, while in a "phylogeny," the branch lengths indicate the amount of character change. The words "phylogram" and

"dendrogram" are also sometimes used to mean the same sort of thing with slight variations. These vocabulary differences are subtle and are not consistently used within the biological community. For our purposes here, the important things to remember are that organisms are related and that we can represent those relationships (and our hypotheses about them) with tree structures. Some Example Questions 1. The evolutionary history of a species or group of species is most accurately referred to as: A) systematics. B) ontogeny. C) taxonomy. D) bioinformatics. E) phylogeny. 2. Which one of the following do all three domains of life have in common? A) the same genetic code B) plasma membranes C) glycolysis D) (A) and (C) E) (A), (B) and (C) 3. In a cladistic approach to phylogeny, a trait shared with a distant common ancestor is referred to as a(n): A) symplesiomorphy. B) ingroup. C) synapomorphy. D) outgroup. E) shared derived character. 4. The principle of parsimony suggests that: A) neutral mutations occur at a fairly constant rate over time. B) the most accurate phylogenetic tree is the one with the most tips. C) species grouped into larger taxa for a cladogram should be from a single clade for the results to be reliable. D) the preferred hypothesis is the one that is the simplest. E) None of the above accurately describes the principle of parsimony. 5. A __________ taxon consists of members of several evolutionary lines and does not include the most recent common ancestor of the included lineages. A) parsimonious B) paraphyletic C) monophyletic D) chronophyletic E) polyphyletic

6. Many researchers who study the kingdom Protista argue that all of these organisms should not be placed in the same kingdom, because these organisms could not have evolved from a common ancestor. In other words, they argue that the kingdom Protista is _____. A. polyphyletic B. paraphyletic C. monophyletic D. heterophyletic E. none of the above 7. The science of describing, naming, and classifying extant and extinct organisms is A. evolution. B. phylogeny. C. taxonomy. D. nomenclature. E. biology. 8. Which of the following would be homologous structures? A. the wing of a bird and the wing of a bee B. the wing of a bee and the wing of a bat C. the wing of a bat and the arm of a human D. All of these answers are correct. 9. A paraphyletic group contains ***QUESTION 22*** A. a common ancestor but not all of its descendants. B. groups of species with different common ancestors. C. a common ancestor and all of its descendants. D. a common ancestor and all of its descendants but not the most recent common ancestor. E. every species ever derived from a common ancestor 10.Choose the true statement about the morphological data in the chart shown below. The "1" in the box means the trait is present and the "0" indicates that the trait is absent.

A. All organisms in this chart share all of the derived characteristics. B. Only the gorilla and humans share all of the derived characteristics. C. The lamprey is the only outgroup since it shares none of the derived characteristics. *** D. The salamander and the tiger are outgroups because they only share two of the derived characteristics (jaws and lungs). E. The shark is an outgroup since it only has one of the derived characteristics (jaws).

Origins and Diversity of Life Review ancient earth - age of ~4.5by - early reducing atmosphere including carbon dioxide, water, hydrogen sulfide, methane, no oxygen Ancient earth

oldest microfossils

Miller Urey experiment

properties of life

Bacteria and Archaebacteria Domains

life's diversity

Water on earth

Fossils Glaciation

Cooling allowed for the formation of the earth’s crust. Plate tectonics has modified the land configuration in the globe and has affected evolution. What are some of the evidence that plate tectonic is true?

prokaryotes, emerging ~3.5 bya Consider: Eukaryotic cells were not until ~2.1 bya & multicellular organisms not until ~700 mya included assembling a reducing atmosphere with H2, CH4, NH3, and H2S, placing this atmosphere over liquid water, increasing the temperature of the gases, and providing energy with electrical spark discharges which produced amino acid glycine, hydrogen cyanide, and formaldehyde Consider: If the atmosphere had been an oxidizing one, life may never have arisen because oxygen is corrosive and tends to strip off electrons there by destroying organic compounds...the reducing atmosphere promoted buildup of organic compounds cellular organization, sensitivity, growth, development, reproduction, regulation, homeostasis, and heredity Consider: The diversity of life is the result of mutation, sexual reproduction, multicellularity, horizontal gene transfer, and endosymbiosis contain no eukaryotes Consider: Archea and eukaryotes are more closely related to each other than to bacteria. One characteristic they (archea & Eukarya) share is tRNA methionine. New Archae called Lokiarchaeota that is even closer to Eukarya results from sexual reproduction, endosymbiosis, horizontal gene transfer, and mutation Consider: Eukaryotic cells acquired mitochondria (purple and chloroplasts (from cyanobacteria) through endosymbiosis What are some of the hypothesis for the existence of water on earth? Rare event but important for the reconstruction of evolution. These events strongly affected the evolution of the species and some of the mass extinction. Plants might have created its own glaciation event by consuming the CO2 with the help of big algae

Earths changing systems Oxygen DNA *** radioisotope dating

earliest cells

blooms. How has climate led to increased diversity but has also led to mass extinction. Excreted oxygen allowed for the formation of the ozone layer. What are these 2 so important for life. found in nucleus, mitochondria, chloroplasts Fossils can be dated using a measured amount of a given isotope as well as the amount of isotope (decay product) produced when the isotope decays probably anaerobic, heterotrophic, prokaryotic and arose during Archean Eon

endosymbiosis

prokaryotic cells being engulfed and becoming internal symbionts within an early eukaryotic cell Multicellularity Leads to cell specialization in eukaryotic organisms. Single celled organisms have limitations. Compartmentalization In eukaryotic organisms we see increases subcellular specialization and nuclear membranes allow for additional levels of control in transcription and translation. Sexual reproduction Leads to increased diversity (meiosis, crossing over). Cambrian Explosion rapid increase in major animal groups' diversity; oxygen levels support larger animals First Plants (nonAppeared just over 500MYA: Land plants, Fish algae) and Animals land plants appear in fossil record Ordovician Period which most likely originated from algae fishes Started in the Silurian (450MYA) reptiles appear during Carboniferous Period (300MYA) Dinosaurs existed from the Triassic to the end of the Cretaceous (200MYA to 100MYA) mammals arose from mammal-like reptiles in the Triassic but remained small and insignificant while dinosaurs dominated (60MYA) mass extinctions have occurred about 4 or 5 times in fossil record, due in some cases to catastrophic changes 1. The age of the Earth according to modern estimations is 8 billion years. 4.5 billion years. 3.5 billion years. 1.5 billion years. a few thousand years. 2. The oldest microfossils are of prokaryotes.

eukaryotes. insects. pollen grains. small animals. 3. Life apparently originated on Earth about *** 1 million years ago. 6000 years ago. 4.5 billion years ago. 8 billion years ago. 3.5 billion years ago. 4. The early Earth's reducing atmosphere probably contained all of the following except *** carbon dioxide. water. oxygen. hydrogen sulfide. methane. 5. An experimental test of the hypothesis to explain the origin of the first organic compounds on Earth might include all of the following sequential steps except assembling an atmosphere with H2, CH4, NH3, and H2S. placing this atmosphere over liquid water. inoculating with a few bacteria to get the process started. increasing the temperature of the gases. providing energy with electrical spark discharges. 6. Which of the following was produced in experiments on primitive Earth conditions conducted by Miller-Urey and others? ammonia and water amino acids CO2 and H2O formaldehyde and hydrogen sulfide methane and oxygen 7. All of the following were produced in experiments on primitive Earth conditions conducted by Miller-Urey and others, except for amino acids. organic molecules. prokaryotes. hydrogen cyanide. urea. 8. Which of the following was demonstrated by the Miller-Urey experiment? *** Life began in the oceans. Life can be started experimentally in the laboratory.

Organic molecules important to life could have been formed from a vast array of simple chemicals. Life began on the pre-biotic Earth 3.5 billion years ago. 9. Eukaryotic cells acquired mitochondria and chloroplasts by endosymbiosis. exocytosis. pinocytosis. mutation. natural selection. 10. Two principal organelles of eukaryotes that share features with one another and with bacteria from which they apparently were derived are the flagella and cilia. microfilaments and microtubules. mitochondria and chloroplasts. rough ER and smooth ER. plasma membrane and nuclear membrane.

Microbiome

prokaryote modern classification *** prokaryote facts ***3 exam questions

The full array of microorganisms (the microbiota) that live on and in humans and, more specifically, the collection of microbial genomes that contribute to the broader genetic portrait, or metagenome, of a human. The genomes that constitute the human microbiome represent a remarkably diverse array of microorganisms that includes bacteria, archaea, fungi, and even some protozoans and nonliving viruses. Bacteria are by far the most numerous members of the human microbiome: the bacterial population alone is estimated at between 75 trillion and 200 trillion individual organisms, while the entire human body consists of about 50 trillion to 100 trillion somatic (body) cells. based on sequencing of proteins, DNA and RNA 1) oldest organisms on Earth with fossils ~3.5 billion years old 2) structurally simplest organisms 3) most abundant life forms on earth 4) 90-99% unknown and undescribed. 5) lack a membrane bound nucleus and other organelles or cell inclusions. 6) Lack of cell compartments. 6) Include 2 domains Bacteria and Archaea. Consider: Archaea and Eukarya share nucleic acid

cyanobacteria

prokaryotes differing from eukaryotes bacteria differing from Achaea

prokaryote structure (bacteria) ***

exchange of genetic material via horizontal transfer

similarities so Eukarya split off from Archaea group of bacteria that produced oxygen and changed the Earth's atmosphere from an anoxic one to one rich in oxygen cell size, multicellularity, chromosomes, organelles, reproduction Note: Eukaryotes and Prokaryotes both have ribosomes. 1. cell wall composition 2. plasma membrane make-up 3. DNA replication 4. gene expression 5. Bacteria have peptidoglycan which Archae lack. Consider: Archaea are able to live in the most extreme environments. have cell walls consisting of a network of polysaccharides connected by cross links of polypeptides (peptidoglycan) flagella - used for movement have enzymes used for cellular respiration attached to cell membrane have 3 shapes (due to cell walls): bacillus, coccus, and spirillum can form biofilms occurs through conjugation (depends on presence of conjugative plasmids when genes are transferred through rigid, tubular sex pili), transduction (occurs when viruses (bacteriophage) package host DNA and transfer it upon subsequent infection), transformation (bacterial cells pick up free pieces of DNA from the medium-pieces that were released from dead bacteria), and exchange of R plasmids (plasmids are different from bacterial chromosomes in that plasmids have few genes, bacterial chromosome have many) increases genetic diversity; helps infer phylogeny; common occurrence in bacteria; can produce large genetic change

gram-positive Vs gram- positive bacteria have a thicker peptidoglycan wall with negative small amounts of teichoic an...