Biology Chapter 8: The Tree of Life

Topic 8: The Tree of Life

• Life on Earth uses carbon (highly abundant on Earth and in the atmosphere), oxygen, hydrogen, and nitrogen. These elements form the majority of biological molecules, including carbohydrates, proteins, fatty acids, and nucleic acids.
• Human body composition is primarily made up of oxygen (65%), carbon (18.5%), hydrogen (9.5%), nitrogen (3.3%), calcium, phosphorus, potassium, sulphur, sodium, chlorine, and magnesium.
• The universe is 13.8 billion years old. Earth is 4.6 billion years old. The first direct evidence of life is 3.5 billion years old.
• Fossils are preserved remnants or impressions of past organisms. Stromatolites are layered rocks formed by photosynthetic prokaryotes that bind sediment.
• The 7 properties of life are: cellular organization, energy and metabolism, reproduction, heredity and evolution, growth and development, regulation and homeostasis, and response to stimuli. Viruses do not exhibit these properties.
• Learning outcomes include describing the 7 properties of life, justifying the importance of CHNO in organic molecules, explaining how life emerged during protocell formation, and listing advantages of ribonucleic acid molecules, explaining how the fossil record shows evolution, comparing two fossil dating methods, describing the Burgess Shale's contribution to evolutionary understanding, defining mass extinction and adaptive radiation, analyzing taxonomic changes, listing characteristics of the Last Universal Common Ancestor (LUCA), and naming characteristics of each domain.
• The formation of protocells from organic molecules involves the abiotic synthesis of monomers, polymerization into macromolecules, packaging into precursors of cells, and the origin of inheritance.
• Stanley Miller's experiment in 1953 showed artificial and spontaneous synthesis of organic matter under conditions mimicking the early Earth's atmosphere, involving methane, ammonia, hydrogen, and lightning.
• The formation of macromolecules can occur spontaneously without enzymes or ribosomes through precursor molecules, thermal energy, and catalysts (Fe2+, Pb2+, Mg2+, etc.). Clay can catalyze RNA polymerization.
• Protocells are droplets with membranes maintaining internal chemistry different from the environment. Experiments show that protocells can divide, have internal metabolism, increase in size, have selective membranes and perform metabolic reactions (response to stimuli).
• RNA molecules can catalyze reactions and act as self-replicating enzymes (ribozymes). This was proposed to be the "RNA World." Natural selection favored faster self-replicating RNA molecules.
• Geological and fossil records are used to analyze the evolutionary history of organisms.

Topic 8.2: Using Fossil Records

• Fossils reveal species that went extinct, species that still exist today, and organisms with rapid morphological change. Mary Anning was a very important paleontologist.
• Biostratigraphy uses relative dating of sedimentary rocks to determine relative ages.
• Radiometric dating provides absolute ages of magmatic rocks using isotopes.
• Faunal succession is a vertical sequence of fossilized flora and fauna that can be reliably tracked across horizontal distances, identifying biozones within geological strata.

Topic 8.3: Mass Extinctions, Adaptive Radiations, and Key Innovations

• Mass extinctions are substantial changes in the fossil record where large numbers of species become extinct. The cause could be changes in temperature, massive volcanic eruptions, or meteorites.
• Mass extinctions are followed by adaptive radiations—evolutionary change where groups of organisms form new species.
• The Cambrian explosion (~535-525 million years ago) resulted in the rapid diversification of many phyla.
• The Burgess Shale shows a high diversity of fossilized animals. These animals had various lifestyles (benthic, endobenthic, nektonic).
• Key innovations in the fossil record include first cells, increase in atmospheric oxygen, endosymbiosis, sexual reproduction, multicellularity, and colonization of land.

Topic 8.4: Three Domains and Millions of Species

• The number of species or members of a taxonomic level can reach an asymptote (apparent maximum). The number of prokaryotic species is still largely unknown.
• The Last Universal Common Ancestor (LUCA) was likely an organism living near deep-sea vents, anaerobic (not requiring oxygen) but using CO2 and H2.

Topic 9: Bacteria and Archaea

• Prokaryotes (pro- before; karyon- nucleus) are a paraphyletic group that includes the common ancestor and some descendants. There are 750,000 species of prokaryotes. Archaea are not bacteria.
• Prokaryote size is 0.5-5µm
• Key prokaryote structures are the plasma membrane, cytoplasm, nucleoid (circular chromosome), fimbriae, capsule, and the absence of organelles.
• Bacteria lack histones and have a protective cell wall made of peptidoglycan (different in archaea—pseudomurein). Flagella are for locomotion; taxis is directed movement towards/away from a stimulus.
• Bacteria are classified into Gram-positive and Gram-negative based on cell wall structure.
• Prokaryotes are diverse in nutrition.
• Prokaryotes reproduce through binary fission (simple doubling and division).
• Prokaryotes can adapt rapidly and have evolved mechanisms that contribute to antibiotic resistance. Processes include mutations, horizontal gene transfer (conjugation, transduction, transformation) that result in recombination events.
• Prokaryotes are important for the ecosystem. They do decomposition (recycling).
• Growth curve phases (lag, log, stationary, death).

Topic 10: Eukaryotes

• Eukaryotes (eu- true; karyon- nucleus) are a monophyletic group that contains the common ancestor and all descendants.
• Key eukaryotic structures are plasma membrane, cytoplasm (cytosol, organelles, inclusions), nucleus.
• Eukaryotes evolved from prokaryotes through serial endosymbiosis (prokaryotic cells engulfed by an ancestral archaeal cell).
• Eukaryotes have mitochondria and chloroplasts (organelles with circular DNA, own transcription/translation proteins) which increases metabolic diversity.
• Eukaryotes have a cytoskeleton (microtubules, microfilaments, intermediate filaments) giving structure, function and support for motility.
• Eukaryotes have peroxisomes for oxidizing and lysosomes for digesting macromolecules.
• Photosynthetic eukaryotes have chloroplasts, including the different types of plastids: chloroplasts for photosynthesis, chromoplasts for fruit/flower pigmentation, and amyloplasts for starch storage.
• Many eukaryotes show structural variation in organelles, cell walls (cellulose, chitin), and may not have flagella or pseudopodia (extensions used for movement).
• Sexual reproduction involves meiosis (reduction of chromosome number from diploid to haploid gametes), fertilization (fusion of gametes) and development of a diploid zygote.
• Life cycles as seen in fungi, protists, plants, and animals differ.
• Protists, fungi, plants, and animals share a common ancestor but have diversified features. Important examples of protists include Plasmodium (malaria), dinoflagellates (“red tides”), and myxomycetes (slime molds). Fungi can be heterotrophic and decomposers. Lichen is a symbiotic relationship between algae and fungi.
• Choanoflagellates are related to animals through having single posterior flagellum and chitin, the same material in certain animal's exoskeletons.

Topic 11: The Evolution of Plants

• Plants (embryophytes) evolved 470 million years ago. Plants are eukaryotes with multicellularity, photoautotrophy (synthesize their own food), cell walls (cellulose), chloroplasts (containing chlorophyll, beta-carotenes, xantophylls).
• Key innovations in plants include the protection of the embryo, vascularization, heterospory, seeds, flowers and fruits.
• Nonvascular plants (bryophytes) lack vascular tissue to transport water and nutrients. They often have a haplodiplontic life cycle.
• Vascular plants (tracheophytes) have specialized tissue for water transport (xylem) and sugar transport (phloem) and lignin-strengthened cell walls, allowing them to grow large. They often have a heterosporous reproductive method.
• Seed plants (spermatophytes) produce seeds that provide nourishment and protection for the embryo, allowing them to survive for extended periods until optimal conditions for germination arise. They often have reduced gametophytes.
• Flower plants (angiosperms) and their seeds are enclosed in protective structures, fruits and flowers. This co-evolved with animal pollinators. Double fertilization (two sperm cells), forming a zygote and a nutritive tissue (endosperm) is a distinguishing characteristic.

Topic 12: The Evolution of Animals I

• Animals, in general, are eukaryotic, multicellular, heterotrophic, mobile organisms that lack cell walls, but are capable of undergoing both sexual and asexual reproduction.
• Asexual reproduction includes budding, regeneration, and parthenogenesis.
• Body plans can have radial symmetry or bilateral symmetry. Bilateral animals show greater specialization of tissues.
• The origin of animals may have come from the common ancestor of animals and choanoflagellates. Some animals have "stolen" plastids from algae.
• Key processes in animal embryogenesis include cleavage of the zygote into blastula, gastrulation forming endoderm, mesoderm, ectoderm tissues, formation of the coelom, and eventually development of organs and tissues.
• The appearance of a notochord in the embryo was an important adaptation for evolution in animals.

Explore the foundational concepts of life on Earth and the elements that constitute biological molecules. This quiz covers the age of the universe, fossil evidence, and the properties that define living organisms. Understand the significance of each element in the human body and life forms across the planet.