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 structureThe origin of self-replicating molecules

Some 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

Figure 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 O2

FermentationAnaerobic 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 surface

ForamsNamed 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