AP Biology Big Idea 1: Part D Natural Processes and the Origin of Living Systems: Hypothesis and evidence of these origins: 4.1, 25.1, 25.3 Scientific evidence from many disciplines: 26.6

Concept 4.1: Organic chemistry is the study of carbon compounds Organic chemistry is the study of compounds that contain carbon Organic compounds range from simple molecules to colossal ones Most organic compounds contain hydrogen atoms in addition to carbon atoms Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Vitalism, the idea that organic compounds arise only in organisms, was disproved when chemists synthesized these compounds Mechanism is the view that all natural phenomena are governed by physical and chemical laws

Sample for chemical analysis Fig. 4-2 EXPERIMENT “Atmosphere” CH4 Water vapor Electrode NH3 H2 Condenser Cooled water containing organic molecules Cold water Figure 4.2 Can organic molecules form under conditions believed to simulate those on the early Earth? H2O “sea” Sample for chemical analysis

Concept 26.6: New information continues to revise our understanding of the tree of life Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics

From Two Kingdoms to Three Domains Early taxonomists classified all species as either plants or animals Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia More recently, the three-domain system has been adopted: Bacteria, Archaea, and Eukarya The three-domain system is supported by data from many sequenced genomes Animation: Classification Schemes

EUKARYA BACTERIA ARCHAEA Fig. 26-21 Land plants Dinoflagellates Green algae Forams Ciliates Diatoms Red algae Amoebas Cellular slime molds Euglena Trypanosomes Animals Leishmania Fungi Sulfolobus Green nonsulfur bacteria Thermophiles (Mitochondrion) Figure 26.21 The three domains of life Spirochetes Halophiles Chlamydia COMMON ANCESTOR OF ALL LIFE Green sulfur bacteria BACTERIA Methanobacterium Cyanobacteria ARCHAEA (Plastids, including chloroplasts)

BACTERIA Green nonsulfur bacteria (Mitochondrion) Spirochetes Fig. 26-21a Green nonsulfur bacteria (Mitochondrion) Spirochetes Chlamydia COMMON ANCESTOR OF ALL LIFE Green sulfur bacteria Figure 26.21 The three domains of life BACTERIA Cyanobacteria (Plastids, including chloroplasts)

ARCHAEA Sulfolobus Thermophiles Halophiles Methanobacterium Fig. 26-21b Sulfolobus Thermophiles Halophiles Figure 26.21 The three domains of life Methanobacterium ARCHAEA

EUKARYA Dinoflagellates Land plants Forams Ciliates Red algae Amoebas Fig. 26-21c EUKARYA Land plants Dinoflagellates Green algae Forams Ciliates Diatoms Red algae Amoebas Cellular slime molds Euglena Trypanosomes Animals Leishmania Figure 26.21 The three domains of life Fungi

A Simple Tree of All Life The tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria The tree of life is based largely on rRNA genes, as these have evolved slowly

There have been substantial interchanges of genes between organisms in different domains Horizontal gene transfer is the movement of genes from one genome to another Horizontal gene transfer complicates efforts to build a tree of life

Bacteria Eukarya Archaea 4 3 2 1 Billions of years ago Fig. 26-22 Figure 26.22 The role of horizontal gene transfer in the history of life 4 3 2 1 Billions of years ago

Is the Tree of Life Really a Ring? Some researchers suggest that eukaryotes arose as an endosymbiosis between a bacterium and archaean If so, early evolutionary relationships might be better depicted by a ring of life instead of a tree of life

Fig. 26-23 Eukarya Bacteria Archaea Figure 26.23 A ring of life

Node Taxon A Taxon B Sister taxa Taxon C Taxon D Taxon E Most recent Fig. 26-UN2 Node Taxon A Taxon B Sister taxa Taxon C Taxon D Taxon E Most recent common ancestor Polytomy Taxon F

Monophyletic group A A A B B B C C C D D D E E E F F F G G G Fig. 26-UN3 Monophyletic group A A A B B B C C C D D D E E E F F F G G G Paraphyletic group Polyphyletic group

Fig. 26-UN4 Salamander Lizard Goat Human

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You should now be able to: Explain the justification for taxonomy based on a PhyloCode Explain the importance of distinguishing between homology and analogy Distinguish between the following terms: monophyletic, paraphyletic, and polyphyletic groups; shared ancestral and shared derived characters; orthologous and paralogous genes Define horizontal gene transfer and explain how it complicates phylogenetic trees Explain molecular clocks and discuss their limitations