Summer Assignment

1. Summer Assignment Chapters 25, 26, 27, and 28

2. Chapter 25- The History of Life on Earth • 25.1-Conditions on early Earth made the origin of life possible • The Origins of Life • The abiotic synthesis of small organic molecules • The joining of these small molecules into macromolecules • The packaging of these molecules into “protobionts” • Collections of abiotically produced molecules surrounded by a membrane-like structure • The origin of self-replicating molecules • Some RNA, called rybozymes, can also carry out a number of enzyme-like catalytic functions

3. 25.2- The fossil record documents the history of life • Rocks • Fossils are dated with radiometric dating, based on the decay of radioactive isotopes • Expressed by the “half-life, the time required for 50% of the parent isotope to decay. • Figure 25.5

4. 25.3- Key events in life’s history include the origins of single-celled and multicelled organisms and the colonization of land The First Single-Celled Organisms • Stromalites- layered rocks that form when certain prokaryotes bind thin films of sediment together. • Show that single-celled organisms probably originated as early as 3.9 billion years ago.

5. Photosynthesis and the Oxygen Revolution • O2 dissolved in the water precipitated with dissolved iron as iron oxide, forming red layers of rock • Once the water became saturated, the oxygen began to gas out

6. The First Eukaryotes • Endosymbiosis- mitochondria and plastids were formally small prokaryotes that began living within larger cells. • Serial endosymbiosis- mitochondria evolved before plastids through a sequence of endosymbiotic events • Figure 25.9

7. The Origin of Multicellularity • Cambrian explosion- time in the early Cambrian period during which many phyla of living animals appeared • Predators over 1 m in length emerged that had claws and other features for capturing prey • New defensive adaptations also emerged • Colonization of land occurred roughly 500 million years ago.

8. 25.4- The rise and fall of dominant groups reflect continental drift, mass extinctions, and adaptive radiations Continental Drift • Figure 25.13 Mass Extinctions • Figure 25.14 Adaptive Radiations • Adaptive Radiations- periods of evolutionary change in which groups of organisms form many new species whose adaptations allow them to fill different ecological roles, or niches, in their communities

9. 25.5- Major Changes in body form can result from changes in the sequences and regulation of developmental genes Evolutionary Effects of Developmental Genes • Heterochrony- an evolutionary change in the rate or timing of developmental events • Paedomorphosis- when reproductive organs develop relatively faster than non-reproductive organs • Homeotic genes- determine such basic features as where limbs or flower parts are arranged • Small changes can have great effects

10. 25.6- Evolution is not goal oriented • Sometimes new stuff works well, and it is kept, and sometimes it is negative and is selected against

11. Chapter 26 Overview • Phylogeny – the evolutionary history of a species of a group of species. • Systematics – a discipline focused on classifying organisms and determining their evolutionary relationships • Systematists use data such as fossils, molecules, genes, etc., in order to infer how organisms are related evolutionarily

12. 26.1: Phylogenies show evolutionary relationships • Binomial Nomenclature • Most common names do not accurately reflect the type of organism something is – e.g., silverfish, jellyfish, crayfish • Format: Genus species • Example: Tiger – Pantheratigris

13. Hierarchical Classification • Taxonomic system named after Carolus Linnaeus (Linnaean system) • Increasingly specific categories to classify an organism • Domain  Kingdom  Phylum  Class  Order  Family  Genus  Species • E.g. – Domain: Eukarya  Kingdom: Animalia  Phylum: Chordata  Class: Mammalia  Order: Carnivora  Family: Felidae  Genus: Panthera  Species: Pantheratigris

14. Linking Classification and Phylogeny • Phylogenetic tree – branching diagram in which the evolutionary history of a group of organisms can be represented • Sometimes matches the hierarchical classifications (groups within more inclusive groups) • Some groups classified by similarities within organisms • Some systematists propose that classification be based entirely on evolutionary relationships

15. Linking Phylogeny and Classification (cont.) • PhyloCode – example of evolutionary-relationship approach to classification • Only names groups that include a common ancestor and all of its descendents • Would change the way taxa are defined and recognized, but not the names • No ranks (family, order, etc.) • Some groups would become part of others of the same rank (e.g. Aves part of Reptilia)

16. Linking Phylogeny and Classification (cont.) • Branch points – dichotomies which represent the relationships in a phylogenetic tree (point where the lineage diverges) • Sister Taxa

17. 26.2: Phylogenies are inferred from morphological and molecular data • Morphological and Molecular Homologies • Homologies – similarities due to shared ancestry • Organisms that share similar morphologies (body structures)or similar DNA sequences usually have a closer relationship • Some cases: morphological difference great and molecular difference small • E.g., Hawaiian silversword plant

18. Sorting Homology from Analogy • Analogy – convergent evolution • Can be a potential “red herring” if scientists try and construct a phylogeny based on this instead of on homology • Convergent evolution – similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages

19. Sorting Homology from Analogy • Homoplasies – another way of describing analogous structures that arose independently (from the Greek for “to mold in the same way”) • The more points of similarity two organisms have, the higher likelihood that they evolved from a common ancestor.

20. Evaluating Molecular Homologies • The more closely related two species are, the fewer differences in sequences there are. • Differences caused by insertions, deletions, etc. • Figure 26.8 • Distinguishing between homology and analogy • Resemblance at many points may be homology, while coincidental matches at a few points could be analogy

21. 26.3: Shared characters are used to construct phylogenetic trees • Reconstructing phylogenies • Step 1: distinguish homologous features from analogous features (only the former reflects evolutionary history) • Step 2: biologists must choose a method of inferring phylogeny from these homologous characters

22. Cladistics • An approach to systematics in which common ancestry is the primary criteria used to classify organisms • Clades – group into which species are places which includes an ancestral species and all of its descendants • Ranks within larger ranks, similar to taxonomic ranks • A taxon is equivalent to a clade only if it is monophyletic

23. Cladistics (continued) • Monophyletic – consists of an ancestral species and all of its descendants • Paraphyletic – consists of an ancestral species and some, but not all, of its descendants • Polyphyletic - includes taxa with different ancestors

24. Phylogentic Trees with Proportional Branch Lengths • Some tree diagrams have branch lengths proportional to amount of evolutionary change or to the times at which particular events occurred

25. Maximum Parsimony and Maximum Likelihood • Maximum parsimony – principle that states that we should first investigate the simplest explanation that is consistent with the facts (“Occam’s razor”) • The most parsimonious tree requires the fewest base changes • Maximum likelihood – principle that states that given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events. • Figure 26.15

26. Phylogenetic Trees as Hypotheses • Scientists make hypotheses based on phylogenetic trees as to who is related to whom and how

27. 26.5: Molecular clocks help track evolutionary time • Molecular clocks • A “yardstick” for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates

28. 26.6:New information continues to revise our understanding of the tree of life • From Two Kingdoms to Three Domains • Based on morphological evidence, scientists tried to classify all living organisms into five main kingdoms. • This was decreased to two kingdoms • Eventually went to three domains: Bacteria, Eukarya, and Archaea

29. A Simple Tree of All Life • Figure 26.21 • Archaea and eukaryotes are more closely related to each other than either are to bacteria • Horizontal gene transfer – a process in which genes are transferred from one genome to another though mechanisms such as exchange of transposable elements and plasmids, viral infections, or fusion of organisms.

30. Is the Tree of Life Really a Ring? • Horizontal gene transfers were so common that the early history of life should be represented as a tangled web instead of the simple branched tree. • Hypothesis: eukaryotes were from an endosymbiotic relationship between bacteria and archaea – something that cannot be represented in a tree of life, but a ring

31. Chapter 27 – Bacteria and Archaea 27.1- Structural and functional adaptations contribute to prokaryotic success • Cell Surface Structures- Gram Staining • Most bacterial cell walls contain peptidoglycan, a network of modified-sugar polymers cross-linked by short polypeptides. • Gram staining can classify many bacteria into Gram-positive or Gram-negative bacteria • Gram-positive bacteria have simpler walls with more peptidoglycan • Gram-negative bacteria have more complex walls with less peptidoglycan • Also contain an outer layer with lipopolysaccharides • More dangerous infectors, their outer layer protects them from the body’s defenses and antibiotics

32. Other Cell Surface Structures • Capsule- Sticky layer of polysaccharide or protein • Enables prokaryotes to adhere to things • Some also protect against dehydration, and some shield from the immune system • Fimbriae- hair-like protein appendages also known as attachment pili • Shorter and more numerous than sexpili, appendages that pull two cells together prior to DNA transfer from one cell to the other.

33. Motility • Flagella- Long structures less numerous than cilia • Help the cell to perform taxis- movement towards or away from a stimulus.

34. Internal and Genomic Organization • Nucleoid- a region of cytoplasm that appears lighter than the surrounding cytoplasm • Contains the circular prokaryotic chromosome • In addition to the single chromosome, prokaryotic cells may also have plasmids- much smaller rings of separately replicating DNA.

35. Reproduction and Adaptation • Prokaryotes are small • They reproduce by binary fission • They have short generation times • Populations can consist of trillions of individuals • In harsh conditions, they develop endospores • Like prokaryote horcruxes • Original cell produces a copy of its chromosome and surrounds it with a tough wall • Water is removed, and metabolism halts • After conditions improve, they can rehydrate and resume metabolism

36. 27.2- Rapid reproduction, mutation, and genetic recombination promote genetic diversity in prokaryotes Rapid Reproduction and Mutation • Prokaryotes reproduce asexually, through binary fission • They still have genetic diversity due to insertions, deletions, and base-pair substitutions • Each day in a person’s intestine there are approximately 2,000 bacteria that have a mutation in every given E. coli gene, or 9 million total mutations per day per human.

37. Genetic Recombination- Transformation and Transduction • Transformation- a prokaryote takes up foreign DNA from its surroundings • Harmless strains of bacteria can be transformed into pathogenic strains • Foreign allele is incorporated into the cell’s chromosome • Cell is now a recombinant, pathogenic bacteria • Transduction- bacteriophages carry bacterial genes from one host cell to another • Occur when lytic viruses accidentally take the bacterial genes instead of their replicated viral genes, then inject them into the next bacterial host

38. Genetic Recombination- Conjugation and Plasmids • Conjugation- when genetic material is transferred between two bacterial cells that are temporarily joined • Conjugation is one-way: Donor uses sex pili to attach to recipient • Temporary “mating bridge” forms between two cells

39. Genetic Recombination- Conjugation and Plasmids • Depends on the F-factor- the genes required to form sex pili and donate DNA • In plasmid form it’s called the F plasmid • If F-factor is located in the chromosome, chromosomal genes can be transferred during conjugation. • These cells are designated Hfr cells, for High frequency of recombination

40. Genetic Recombination- Conjugation and Plasmids • R Plasmids carry genes that code for enzymes that specifically destroy or otherwise hinder the effectiveness of certain antibiotics

41. 27.3- Diverse nutritional and metabolic adaptations have evolved in prokaryotes • Table 27.1

42. The Role of Oxygen in Metabolism • Obligate aerobes use O2 for cellular respiration • Obligate anaerobes are poisoned by O2 • Fermentation • Anaerobic respiration • Nitrite or sulfate accept electrons instead of O2 • Facultative anaerobes use O2 but can go without

43. Nitrogen Metabolism • Nitrogen fixation- When cyanobacteria and some methanogens convert atmospheric nitrogen to ammonia. • Then incorporate “fixed” bacteria into amino acids and other organic molecules

44. Metabolic Cooperation • CyanobacteriumAnabaena has genes for both nitrogen fixation and photosynthesis, but can’t carry out both at once. In a colony, most cells perform photosynthesis, while some designated cells called heterocytes perform nitrogen fixation. The cells share the fixed nitrogen and carbohydrates. • Some colonies have surface-coating biofilms, consisting of cells that secrete signaling molecules that recruit nearby cells

45. 27.4 Molecular systematics is illuminating prokaryotic phylogeny • Table 27.2

46. Archaea • Archaea share certain traits with bacteria and others with eukaryotes • Some are extremophiles • Extreme halophiles- highly saline environments • Extreme thermophiles- thrive in very hot environments • Methanogens- Use CO2 to oxidize H2

47. Bacteria • Proteobacteria • Alpha, Beta, Gamma, Delta, Epsilon • Chlamydias • Spirochetes • Cyanobacteria • Gram-Positive Bacteria

48. 27.5- Prokaryotes play crucial roles in the biosphere • Chemical recycling • Decomposers • Ecological Interactions • Symbiosis- larger is host, smaller is symbiont • Mutualism: +/+ • Commensalism: +/0 • Parasitism: +/- • Parasite • Pathogens

49. 27.6- Prokaryotes have both harmful and beneficial impacts on humans Pathogenic Bacteria • Exotoxins: proteins secreted by certain bacteria and other organisms • Endotoxins: lipopolysaccharide components of the outer membrane of gram-negative bacteria- released when they die and their cell walls break down

50. Bioremediation • The use of organisms to remove pollutants from soil, air, or water • Used in sewage and other waste