Chapters 25, 26, 27, and 28 Summer Assignment
Feb 24, 2016
Chapters 25, 26, 27, and 28
Summer Assignment
25.1-Conditions on early Earth made the origin of life possible
The Origins of LifeThe abiotic synthesis of small organic molecules The joining of these small molecules into
macromoleculesThe packaging of these molecules into “protobionts”
Collections of abiotically produced molecules surrounded by a membrane-like structure
The origin of self-replicating moleculesSome RNA, called rybozymes, can also carry out a
number of enzyme-like catalytic functions
Chapter 25- The History of Life on Earth
RocksFossils are dated with radiometric
dating, based on the decay of radioactive isotopesExpressed by the “half-life, the time required
for 50% of the parent isotope to decay.Figure 25.5
25.2- The fossil record documents the history of life
The First Single-Celled OrganismsStromalites- 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.
25.3- Key events in life’s history include the origins of single-celled and multicelled organisms and the colonization of land
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
Photosynthesis and the Oxygen Revolution
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 First Eukaryotes
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 emergedColonization of land occurred roughly 500
million years ago.
The Origin of Multicellularity
Continental DriftFigure 25.13Mass ExtinctionsFigure 25.14Adaptive RadiationsAdaptive 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
25.4- The rise and fall of dominant groups reflect continental drift, mass extinctions, and adaptive radiations
Evolutionary Effects of Developmental GenesHeterochrony- an evolutionary change in
the rate or timing of developmental eventsPaedomorphosis- when reproductive
organs develop relatively faster than non-reproductive organs
Homeotic genes- determine such basic features as where limbs or flower parts are arrangedSmall changes can have great effects
25.5- Major Changes in body form can result from changes in the sequences and regulation of developmental genes
Sometimes new stuff works well, and it is kept, and sometimes it is negative and is selected against
25.6- Evolution is not goal oriented
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
Chapter 26 Overview
Binomial Nomenclature Most common names do not accurately reflect
the type of organism something is – e.g., silverfish, jellyfish, crayfish
Format: Genus speciesExample: Tiger – Panthera tigris
26.1: Phylogenies show evolutionary relationships
Taxonomic system named after Carolus Linnaeus (Linnaean system)
Increasingly specific categories to classify an organismDomain Kingdom Phylum Class Order
Family Genus SpeciesE.g. – Domain: Eukarya Kingdom: Animalia
Phylum: Chordata Class: Mammalia Order: Carnivora Family: Felidae Genus: Panthera Species: Panthera tigris
Hierarchical Classification
Phylogenetic tree – branching diagram in which the evolutionary history of a group of organisms can be representedSometimes 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 Classification and Phylogeny
PhyloCode – example of evolutionary-relationship approach to classificationOnly names groups that include a common
ancestor and all of its descendentsWould 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 (cont.)
Branch points – dichotomies which represent the relationships in a phylogenetic tree (point where the lineage diverges)
Sister Taxa
Linking Phylogeny and Classification (cont.)
Morphological and Molecular HomologiesHomologies – similarities due to shared
ancestry Organisms that share similar morphologies
(body structures)or similar DNA sequences usually have a closer relationshipSome cases: morphological difference great and
molecular difference smallE.g., Hawaiian silversword plant
26.2: Phylogenies are inferred from morphological and molecular data
Analogy – convergent evolutionCan 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 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.
Sorting Homology from Analogy
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 analogyResemblance at many points may be homology,
while coincidental matches at a few points could be analogy
Evaluating Molecular Homologies
Reconstructing phylogeniesStep 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
26.3: Shared characters are used to construct phylogenetic trees
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 descendantsRanks within larger ranks, similar to taxonomic
ranksA taxon is equivalent to a clade only if it is
monophyletic
Cladistics
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
Cladistics (continued)
Some tree diagrams have branch lengths proportional to amount of evolutionary change or to the times at which particular events occurred
Phylogentic Trees with Proportional Branch Lengths
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 changesMaximum 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
Maximum Parsimony and Maximum Likelihood
Scientists make hypotheses based on phylogenetic trees as to who is related to whom and how
Phylogenetic Trees as Hypotheses
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
26.5: Molecular clocks help track evolutionary time
From Two Kingdoms to Three DomainsBased on morphological evidence, scientists
tried to classify all living organisms into five main kingdoms.
This was decreased to two kingdomsEventually went to three domains: Bacteria,
Eukarya, and Archaea
26.6:New information continues to revise our understanding of the tree of 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.
A Simple Tree of All Life
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
Is the Tree of Life Really a Ring?
27.1- Structural and functional adaptations contribute to prokaryotic successCell Surface Structures- Gram StainingMost 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
peptidoglycanAlso contain an outer layer with lipopolysaccharidesMore dangerous infectors, their outer layer protects them from
the body’s defenses and antibiotics
Chapter 27 – Bacteria and Archaea
Capsule- Sticky layer of polysaccharide or proteinEnables prokaryotes to adhere to thingsSome also protect against dehydration, and
some shield from the immune systemFimbriae- hair-like protein appendages
also known as attachment piliShorter and more numerous than sex pili,
appendages that pull two cells together prior to DNA transfer from one cell to the other.
Other Cell Surface Structures
Flagella- Long structures less numerous than ciliaHelp the cell to perform taxis- movement
towards or away from a stimulus.
Motility
Nucleoid- a region of cytoplasm that appears lighter than the surrounding cytoplasmContains the circular prokaryotic chromosome In addition to the single chromosome,
prokaryotic cells may also have plasmids- much smaller rings of separately replicating DNA.
Internal and Genomic Organization
Prokaryotes are smallThey reproduce by binary fissionThey have short generation times
Populations can consist of trillions of individualsIn harsh conditions, they develop endospores
Like prokaryote horcruxes Original cell produces a copy of its chromosome
and surrounds it with a tough wallWater is removed, and metabolism haltsAfter conditions improve, they can rehydrate and
resume metabolism
Reproduction and Adaptation
Rapid Reproduction and MutationProkaryotes reproduce asexually, through
binary fissionThey 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.
27.2- Rapid reproduction, mutation, and genetic recombination promote genetic diversity in prokaryotes
Transformation- a prokaryote takes up foreign DNA from its surroundingsHarmless strains of bacteria can be transformed
into pathogenic strains Foreign allele is incorporated into the cell’s
chromosomeCell is now a recombinant, pathogenic bacteria
Transduction- bacteriophages carry bacterial genes from one host cell to anotherOccur when lytic viruses accidentally take the
bacterial genes instead of their replicated viral genes, then inject them into the next bacterial host
Genetic Recombination- Transformation and Transduction
Conjugation- when genetic material is transferred between two bacterial cells that are temporarily joinedConjugation is one-way: Donor uses sex pili to
attach to recipient Temporary “mating bridge” forms between two
cells
Genetic Recombination- Conjugation and Plasmids
Depends on the F-factor- the genes required to form sex pili and donate DNAIn plasmid form it’s called the F plasmidIf 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 Plasmids
R Plasmids carry genes that code for enzymes that specifically destroy or otherwise hinder the effectiveness of certain antibiotics
Genetic Recombination- Conjugation and Plasmids
Table 27.1
27.3- Diverse nutritional and metabolic adaptations have evolved in prokaryotes
Obligate aerobes use O2 for cellular respiration
Obligate anaerobes are poisoned by O2FermentationAnaerobic respiration
Nitrite or sulfate accept electrons instead of O2
Facultative anaerobes use O2 but can go without
The Role of Oxygen in Metabolism
Nitrogen fixation- When cyanobacteria and some methanogens convert atmospheric nitrogen to ammonia.Then incorporate “fixed” bacteria into amino
acids and other organic molecules
Nitrogen Metabolism
Cyanobacterium Anabaena 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
Metabolic Cooperation
Table 27.2
27.4 Molecular systematics is illuminating prokaryotic phylogeny
Archaea share certain traits with bacteria and others with eukaryotes
Some are extremophilesExtreme halophiles- highly saline
environmentsExtreme thermophiles- thrive in very hot
environmentsMethanogens- Use CO2 to oxidize H2
Archaea
ProteobacteriaAlpha, Beta, Gamma, Delta, Epsilon
ChlamydiasSpirochetesCyanobacteriaGram-Positive Bacteria
Bacteria
Chemical recyclingDecomposers
Ecological InteractionsSymbiosis- larger is host, smaller is symbiont
Mutualism: +/+Commensalism: +/0Parasitism: +/-
ParasitePathogens
27.5- Prokaryotes play crucial roles in the biosphere
Pathogenic BacteriaExotoxins: proteins secreted by certain
bacteria and other organismsEndotoxins: lipopolysaccharide components
of the outer membrane of gram-negative bacteria- released when they die and their cell walls break down
27.6- Prokaryotes have both harmful and beneficial impacts on humans
The use of organisms to remove pollutants from soil, air, or waterUsed in sewage and other waste
Bioremediation
28.1 – Most eukaryotes are single-celled organismsProtists exhibit more structural and
functional diversity than any other eukaryotic groupExample: mixotrophs – combine
photosynthetic and heterotropic nutritionFive Supergroups of Eukaryotes
Figure 28.2
Chapter 28 - Protists
DiplomonadsMitosomes – modified mitochondriaTwo equal sized nuclei and multiple flagella
ParabasalidsEuglenozoans
KinetoplastidsOne large mitochondria, contains kinoplastsMany different environments
EuglenidsMixotrophs with one or two flagella on one end
28.2: Excavates include protists with modified mitochondria and protists with unique flagella
Secondary endosymbiosis Entering a symbiotic relationship and
eventually becoming one organism
28.3: Chromalveolate may have originated by secondary endosymbiosis
AmoebasFormerly defined as protists that move and
feed by pseudopodia Pseudopodia – extensions that may bulge from
anywhere on the cell surfaceForams
Named for their porous shells, called tests
28.4: Rhizarians are a diverse group of protists defined by DNA similarities
Red algae, green algae, and land plants make up Archaeplastida Red algae
RhodophytesReddish pigments caused by phycoerythrin,
which masks chlorophyllSpecies in more shallow water have less
phycoerythrinGreenish red in shallow water Bright red
in moderate depths Almost black in deep water
Mostly multicellularAlternation of generations common
28.5: Red algae and green algae are the closest relatives of land plants
Ultra-structure and pigment composition similar to the chloroplasts on land plantsChlorophytes and charophytesLarger size and complexity evolved in
chlorophytes by three different mechanismsFormation of colonies of individual cells – e.g.
VolvoxFormation of true multicellular bodies of cell
division and differentiationRepeated division of nuceli with no cytoplasmic
division
Green Algae
Unikonta – recently proposed, extremely diverse supergroup of eukaryotesIncludes animals, fungi, and some protistsDivided 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)
28.6: Unikonts include protists that are closely related to fungi and animals
Slime moldsProduce fruiting bodies that aid in spore disposal
(once thought to be fungi)Plasmodial Slime Molds – Figure 28.24
Brightly coloredForm a plasmodium Not multicellularCytoplasmic streaming
Ameobozoans
Cellular Slime Molds – Figure 28.25Individual cells will come together when
food is depletedResembles plasmodial slime mold, but
separated by plasma membranes
Amoebozoans
GymnamoebasFound in soil, freshwater, marine environments Most heterotrophsSome feed on detritus
EntamoebasParasiticInfect both vertebrae and invertebraeE. histolytica – only pathogenic one in humans
Amoebozoans
Symbiotic ProtistsSome form symbiotic relationships with other
speciesExamples:
photosynthetic dinoflagellates provide nourishment for coral polyps
Termites cannot break wood down without wood-digesting termites that live inside them
28.7: Protists play key roles in ecological relationships
Some are producersOrganisms 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
Photosyntetic Protists