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

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summer assignment

Summer Assignment

Chapters 25, 26, 27, and 28

chapter 25 the history of life on earth
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
25 2 the fossil record documents the history of life
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
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.
photosynthesis and the oxygen revolution
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
the first eukaryotes
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
the origin of multicellularity
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.
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
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
25 6 evolution is not goal oriented
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
chapter 26 overview
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
26 1 phylogenies show evolutionary relationships
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
hierarchical classification
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
linking classification and phylogeny
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
linking phylogeny and classification cont
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)
linking phylogeny and classification cont1
Linking Phylogeny and Classification (cont.)
  • Branch points – dichotomies which represent the relationships in a phylogenetic tree (point where the lineage diverges)
  • Sister Taxa
26 2 phylogenies are inferred from morphological and molecular data
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
sorting homology from analogy
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
sorting homology from analogy1
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.
evaluating molecular homologies
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
26 3 shared characters are used to construct phylogenetic trees
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
  • 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
cladistics continued
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
phylogentic trees with proportional branch lengths
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
maximum parsimony and maximum likelihood
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
phylogenetic trees as hypotheses
Phylogenetic Trees as Hypotheses
  • Scientists make hypotheses based on phylogenetic trees as to who is related to whom and how
26 5 molecular clocks help track evolutionary time
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
26 6 new information continues to revise our understanding of the tree of life
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
a simple tree of all life
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.
is the tree of life really a ring
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
chapter 27 bacteria and archaea
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
other cell surface structures
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.
  • Flagella- Long structures less numerous than cilia
    • Help the cell to perform taxis- movement towards or away from a stimulus.
internal and genomic organization
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.
reproduction and adaptation
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
27 2 rapid reproduction mutation and genetic recombination promote genetic diversity in prokaryotes
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.
genetic recombination transformation and transduction
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
genetic recombination conjugation and plasmids
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
genetic recombination conjugation and plasmids1
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
genetic recombination conjugation and plasmids2
Genetic Recombination- Conjugation and Plasmids
  • R Plasmids carry genes that code for enzymes that specifically destroy or otherwise hinder the effectiveness of certain antibiotics
the role of oxygen in metabolism
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
nitrogen metabolism
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
metabolic cooperation
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
  • 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
  • Proteobacteria
    • Alpha, Beta, Gamma, Delta, Epsilon
  • Chlamydias
  • Spirochetes
  • Cyanobacteria
  • Gram-Positive Bacteria
27 5 prokaryotes play crucial roles in the biosphere
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
27 6 prokaryotes have both harmful and beneficial impacts on humans
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
  • The use of organisms to remove pollutants from soil, air, or water
    • Used in sewage and other waste
chapter 28 protists
Chapter 28 - Protists
  • 28.1 – Most eukaryotes are single-celled organisms
    • Protists exhibit more structural and functional diversity than any other eukaryotic group
      • Example: mixotrophs – combine photosynthetic and heterotropic nutrition
    • Five Supergroups of Eukaryotes
      • Figure 28.2
28 2 excavates include protists with modified mitochondria and protists with unique flagella
28.2: Excavates include protists with modified mitochondria and protists with unique flagella
  • Diplomonads
    • Mitosomes – modified mitochondria
    • Two equal sized nuclei and multiple flagella
  • Parabasalids
  • Euglenozoans
    • Kinetoplastids
      • One large mitochondria, contains kinoplasts
      • Many different environments
    • Euglenids
      • Mixotrophs with one or two flagella on one end
28 3 chromalveolate may have originated by secondary endosymbiosis
28.3: Chromalveolate may have originated by secondary endosymbiosis
  • Secondary endosymbiosis
    • Entering a symbiotic relationship and eventually becoming one organism
28 4 rhizarians are a diverse group of protists defined by dna similarities
28.4: Rhizarians are a diverse group of protists defined by DNA similarities
  • Amoebas
    • Formerly defined as protists that move and feed by pseudopodia
      • Pseudopodia – extensions that may bulge from anywhere on the cell surface
  • Forams
    • Named for their porous shells, called tests
28 5 red algae and green algae are the closest relatives of land plants
28.5: Red algae and green algae are the closest relatives of land plants
  • Red algae, green algae, and land plants make up Archaeplastida
    • Red algae
      • Rhodophytes
      • Reddish pigments caused by phycoerythrin, which masks chlorophyll
      • Species in more shallow water have less phycoerythrin
      • Greenish red in shallow water  Bright red in moderate depths  Almost black in deep water
      • Mostly multicellular
      • Alternation of generations common
green algae
Green Algae
  • Ultra-structure and pigment composition similar to the chloroplasts on land plants
    • Chlorophytes and charophytes
    • Larger size and complexity evolved in chlorophytes by three different mechanisms
      • Formation of colonies of individual cells – e.g. Volvox
      • Formation of true multicellular bodies of cell division and differentiation
      • Repeated division of nuceli with no cytoplasmic division
28 6 unikonts include protists that are closely related to fungi and animals
28.6: Unikonts include protists that are closely related to fungi and animals
  • Unikonta – recently proposed, extremely diverse supergroup of eukaryotes
    • Includes animals, fungi, and some protists
    • Divided into amoebozoans and opisthokonts
    • Support for relationship between amoebozoans and opisthokonts is supported by myosin proteins and studies based on hundreds of genes
  • Controversy : The root of the eukaryotic tree (refer to Figure 28.23)
  • Slime molds
      • Produce fruiting bodies that aid in spore disposal (once thought to be fungi)
    • Plasmodial Slime Molds – Figure 28.24
      • Brightly colored
      • Form a plasmodium
      • Not multicellular
      • Cytoplasmic streaming
  • Cellular Slime Molds – Figure 28.25
    • Individual cells will come together when food is depleted
    • Resembles plasmodialslime mold, but separated by plasma membranes
  • Gymnamoebas
    • Found in soil, freshwater, marine environments
    • Most heterotrophs
    • Some feed on detritus
  • Entamoebas
    • Parasitic
    • Infect both vertebrae and invertebrae
    • E. histolytica – only pathogenic one in humans
28 7 protists play key roles in ecological relationships
28.7: Protists play key roles in ecological relationships
  • Symbiotic Protists
    • Some form symbiotic relationships with other species
    • Examples:
      • photosynthetic dinoflagellates provide nourishment for coral polyps
      • Termites cannot break wood down without wood-digesting termites that live inside them
photosyntetic protists
  • Some are producers
    • Organisms that use light or inorganic chemicals
    • Form the base of the ecological food web
  • Factors that affect the producers will affect everyone else in the food chain