AP Biology Unit 7 Study Notes

Chapter 25: History of Life on Earth

• Protocells: Protocells are primitive entities that exhibit some characteristics of life, such as a lipid bilayer structure and metabolic activities. Understanding these early models is key to deciphering the conditions and processes that could have led to the first true living cells.

• Age of Earth: The Earth is approximately 4.5 billion years old. This extensive time frame allows for many significant evolutionary events to occur, underpinning the complexity of life we see today.

• Hydrothermal Vents: Hydrothermal vents are unique ecosystems found on the ocean floor, where heated water rich in minerals rises. These environments may provide essential conditions for the origin of life, as they can offer the right combination of chemicals and energy sources for early biological systems.

• Significance of Meteorites: Meteorites can serve as historical records of the early solar system's chemistry and are thought to carry essential organic compounds, such as amino acids, which might have contributed to the development of early life. Additionally, meteorites may contain microorganisms that bear implications for the evolution of life on Earth and potentially elsewhere in the universe.

• RNA as Genetic Material: RNA, which can act as both genetic material and a catalyst for biological reactions, is proposed to have been the first form of genetic material on Earth. Its ability to self-replicate and store information positions it as a crucial molecule in early biogenesis.

• Ribozymes: Ribozymes are RNA molecules that have catalyzed biochemical reactions, providing support for the idea that RNA played a central role in early life forms. This property suggests that RNA could have facilitated early evolutionary processes even prior to the advent of proteins and DNA.

• Importance of Fossils: Fossils provide valuable evidence of past life forms and ecological dynamics, enabling scientists to reconstruct evolutionary changes and the history of life on Earth, including patterns of extinction and diversification.

• Bias in Fossil Records: Understanding the biases in fossil records is crucial for interpreting evolutionary history.

  • Niche Bias: Certain environments, like riverbeds or lake beds, are more conducive to fossilization, while others may never yield fossils.

  • Time Bias: Consequently, more recent fossils typically outnumber those from earlier ages, skewing our understanding of evolutionary lineages.

  • Natural events such as floods or landslides can exacerbate these biases by dispersing remains, complicating paleontological interpretations.

• Radiometric Dating: This scientific method employs the decay of radioactive isotopes, such as carbon-14 and uranium-lead, to accurately determine the age of fossilized remains. Understanding half-lives is fundamental to interpreting the chronology of biological evolution.

• Geologic Records: Geologic strata provide comprehensive layers documenting Earth's history, including climatic changes, significant events like mass extinctions, and the development of life.

• Stromatolites: Stromatolites, often formed by cyanobacteria, are among the oldest evidence of life on Earth. Their layered structures offer insights into early biological activity and the role of microorganisms in Earth's biosphere development.

• Oxygen Revolution: The Oxygen Revolution marks a pivotal transformation in Earth's atmosphere driven by photosynthetic organisms, drastically changing the planet’s conditions, resulting in mass extinction for anaerobic species and paving the way for the evolution of aerobic life forms.

• Endosymbiosis: This theory proposes that eukaryotic cells arose through a process where free-living bacteria, such as ancestral mitochondria and chloroplasts, were engulfed by early eukaryotic cells, establishing symbiotic relationships that led to more complex cellular structures.

• Evidence of Mitochondria as Bacteria: Modern mitochondria and chloroplasts share significant similarities with bacteria, such as their own circular DNA and double membranes, providing compelling evidence for their prokaryotic ancestry and evolutionary significance.

• Cambrian Explosion: Occurring around 540 million years ago, the Cambrian Explosion denotes a dramatic and rapid increase in the diversity of life forms, leading to the emergence of most major animal phyla and reshaping marine ecosystems.

• Speciation Rate after Extinction Events: Following mass extinction events, the subsequent reduction in competition among surviving species facilitates rapid speciation, allowing for the exploitation of newly available ecological niches.

• Pangaea: The supercontinent Pangaea, which existed approximately 335 million years ago, significantly influenced patterns of evolution and extinction as geographic barriers shifted climates and habitats, contributing to the diversity and distribution of life forms.

• Causes of Mass Extinctions: Mass extinctions can result from critical events such as volcanic eruptions, climatic shifts, meteor impacts, and human-induced changes in the environment, leading to significant biodiversity loss.

• Heterochrony: Heterochrony encapsulates the concept of evolutionary change in the timing or rate of development, affecting the shape and form of organisms over generations.

• Paedomorphosis: This phenomenon occurs when juvenile characteristics are retained into adulthood, resulting in significant changes in an organism's morphology and life history.

• Nature of Evolution: Evolution is not a linear or goal-oriented process but is guided by natural selection, which acts on existing variations within a population. This process leads to adaptations tailored to current environments rather than towards an envisioned 'ideal' form.

Chapter 26: Phylogeny and the Tree of Life

• Phylogeny: Phylogeny examines the evolutionary relationships and lineage distinctions among biological entities, commonly visualized as a branching tree structure that reflects historical connections.

• Systematics: This scientific discipline not only classifies organisms based on shared characteristics but also focuses on understanding their evolutionary history and relationships through both comparative morphology and molecular data.

• Taxonomic Hierarchy: Organisms are organized in a hierarchical structure that ascends from Domain to Kingdom, Phylum, Class, Order, Family, Genus, and finally Species, reflecting evolutionary connections and lineages.

• Taxon: In the context of systematics, a taxon refers to a named group of organisms that can range from a single species to broader classifications such as families or kingdoms.

• Sister Taxa: These are groups of organisms that emerge from a common ancestor, illustrating the branching points in phylogenetic trees that elucidate evolutionary relationships.

• Rooted Tree: A rooted phylogenetic tree includes a root representing the most recent common ancestor for all taxa of interest, establishing a reference point for tracing lineages.

• Phylogenetic Trees: Scientists construct these trees using various evidence sources, including fossils, morphological characteristics, genetics, and biochemical data, providing insights into the nature of evolutionary processes.

• Homology vs. Analogy: Homologous traits emerge from shared ancestry and reflect evolutionary divergence, while analogous traits arise independently through convergent evolution, demonstrating similar adaptations to similar environmental pressures.

• Clade: A clade represents a group of organisms that share a common ancestor, including all descendants, reflecting significant evolutionary diversity.

• Monophyletic, Paraphyletic, and Polyphyletic: These classifications describe how groups are defined based on common ancestry; monophyletic groups contain all descendants of a common ancestor, paraphyletic groups exclude some, while polyphyletic groups include unrelated organisms that do not share a recent common ancestor.

• Shared Ancestral vs. Shared Derived Characters: Ancestral characters stem from more distantly related ancestors and appear in broader clades, while derived characters are those that appear more recently in a lineage and are unique to smaller clades.

• Outgroup vs. Ingroup: In systematic studies, an outgroup serves as a point of comparison for an ingroup, assisting in the determination of characteristics that are ancestral versus derived.

• Maximum Parsimony vs. Maximum Likelihood: These are two contrasting methodologies for developing phylogenetic trees; maximum parsimony looks for the simplest explanation that minimizes evolutionary changes, while maximum likelihood seeks the tree that is most probable given the data.

• Orthologous vs. Paralogous Genes: Orthologous genes arise from speciation events and reflect evolutionary divergence between species, whereas paralogous genes originate from gene duplication events within the same genome.

• Molecular Clocks: These stable genetic markers utilize mutation rates to estimate divergence times between species, aiding in the construction of evolutionary timelines.

• Horizontal Gene Transfer: This phenomenon is particularly prevalent in bacteria and refers to the transfer of genetic material between organisms through non-reproductive means, significantly contributing to genetic diversity and evolution amongst prokaryotes.

Chapter 27: Bacteria

• Bacterial Habitat: Bacteria are remarkably versatile, colonizing diverse environments from extreme thermal and acidic conditions in hydrothermal vents to the human gut, demonstrating their evolutionary success and adaptability as one of the earliest life forms on Earth.

• Bacteria vs. Archaea: Although both organisms fall under the Prokaryote domain, they are distinguishable through cellular structure, metabolic pathways, and genetic makeup, with Archaea often found in extreme environments such as high salinity or temperature conditions.

• Peptidoglycan: This vital polymer composes the cell wall in most bacteria, providing structural integrity and shape, and is a key feature used to differentiate between Gram-positive and Gram-negative bacteria.

• Gram Staining: This critical laboratory technique categorizes bacteria based on their cell wall composition; Gram-positive bacteria retain the crystal violet stain due to a thick peptidoglycan layer, while Gram-negative bacteria present a thinner layer under an additional outer membrane, which also has implications for antibiotic sensitivity.

• Fimbriae vs. Pili: Fimbriae are short projections that aid bacterial adherence to surfaces and biofilm formation, whereas pili are longer, facilitating bacterial conjugation by enabling genetic material transfer between cells.

• Taxis: This behavioral response showcases a bacterium's ability to move toward beneficial stimuli (like nutrients) or away from harmful environmental factors, indicating their adaptive capabilities.

• Bacterial DNA Structure: Bacterial DNA typically resides in a nucleoid region and exists as a circular chromosome; in addition, bacteria often have plasmids that carry non-essential but advantageous genes, such as those conferring antibiotic resistance.

• Genetic Diversity in Prokaryotes: Prokaryotes can exhibit high genetic diversity through mechanisms such as transformation (uptake of free DNA), transduction (gene transfer via bacteriophages), and conjugation (direct DNA transfer between bacteria through pili), allowing rapid adaptation to changing environments.

• Difference between Conjugation Mechanisms: Classic conjugation primarily involves the transfer of the F plasmid which contains genes for pilus formation, while Hfr conjugation involves the transfer of chromosomal DNA, showcasing the complexity and variability of genetic exchange among bacteria.

• R Plasmids: These are specialized plasmids that harbor genes providing resistance to antibiotics, complicating treatment strategies and contributing to the growing public health challenge of antibiotic-resistant infections.

• Extremophiles: Extremophiles represent a fascinating group of organisms that thrive in extreme environments. Extreme Halophiles exhibit remarkable adaptations to high salinity, while Extreme Thermophiles can exist in environments with high temperatures, providing insights into both evolutionary processes and potential biotechnological applications.