General Biology: Foundations, Evolution, and Phylogeny Study Notes

Organism Characteristics

Defining Features of Living Organisms

• Cells: All living things are composed of cells, which regulate the passage of materials between their interior and exterior environments.

• Replication: Organisms reproduce either asexually (genetic copy of self) or sexually (genetic variety through different combinations of alleles from parents).

• Information: Cells use genetic information stored in genes to make molecules that determine traits.

• Energy: Organisms acquire and use energy. Autotrophs (e.g., plants) produce their own energy via photosynthesis; heterotrophs consume other organisms.

• Evolution: Populations of organisms evolve over time, leading to changes in allele frequencies and traits.

Evolutionary Change

• Evolution is a change in the heritable traits of a population over generations.

• Occurs via mutation (producing new alleles) and natural selection (adaptive alleles become more common).

• Adaptive alleles increase survival and reproduction, leading to evolutionary change.

Examples of Infectious Agents

• Chronic Wasting Disease in Deer: Neurological disease causing brain tissue breakdown.

• Creutzfeldt-Jakob Disease in Humans: Fatal neurological disease with brain shrinkage and deterioration.

• Prions: Infectious proteins causing these diseases. They misfold, reproduce by altering normal proteins, and lack hereditary information.

Theories in Biology

Major Biological Theories

• Cell Theory: All cells arise from preexisting cells through growth and division.

• Chromosome Theory of Inheritance: Genetic information is encoded in genes located on chromosomes.

• Darwin and Wallace's Theory of Evolution: All species are connected by common ancestry; species characteristics can change over generations.

DNA Structure and Function

DNA and Genetic Information

• DNA is a double-stranded helix (Watson & Crick, 1953; Franklin's data).

• Bases: A (adenine), T (thymine), C (cytosine), G (guanine).

• Base pairing: A pairs with T, C pairs with G.

• Base pairing allows DNA copying and preserves genetic information.

• DNA codes for RNA, which codes for proteins.

Organism Nutritional Needs

• Organisms require chemical energy (e.g., ATP) and molecules for building blocks.

Natural Selection and Evolution

Natural Selection

• Occurs when individuals in a population vary in heritable traits that affect survival and reproduction.

• Natural selection acts on individuals, but evolutionary change occurs in populations.

• Can lead to speciation (formation of new species).

Classification and Diversity of Life

Three Domains of Life

• Bacteria: Prokaryotic, unicellular.

• Archaea: Prokaryotic, unicellular.

• Eukarya: Eukaryotic, membrane-bound nucleus, often multicellular.

Prokaryotes vs. Eukaryotes

• Prokaryotes: No nucleus, can be heterotrophic or autotrophic (e.g., cyanobacteria), use anaerobic respiration.

• Eukaryotes: Multicellular, have a nucleus.

Naming Organisms

• Genus: First part of the scientific name, groups closely related species.

• Species: Second part, identifies the specific organism. Written as Genus species.

Key Vocabulary

• Allele: Alternative form of a gene.

• Gene: DNA segment coding for a heritable trait.

• Population: All individuals of a species in a geographic area.

• Genetic Diversity: Variation in genes within a population.

• Phylogeny: Evolutionary relationships among species.

• Fitness: Ability to produce viable offspring.

• Adaptation: Heritable trait increasing fitness in a particular environment.

Phylogeny and Systematics

Key Terms

• Phylogeny: Branching evolutionary history of species or groups.

• Systematics: Discipline of classifying and characterizing relationships among organisms.

• Data Matrix: Table showing character states of taxa.

• Outgroup: Taxon outside the group being studied, used for comparison.

• Ancestral Trait: Trait from an ancestor.

• Derived Trait: Modified form of ancestral trait.

• Synapomorphy: Shared derived trait in a group.

• Monophyletic Group: Includes ancestor and all descendants.

• Homoplasy: Similarity due to convergent evolution, not common ancestry.

• Convergent Evolution: Independent evolution of similar traits in unrelated groups.

Creating and Analyzing Data Matrices

• Data matrices help compare character states among taxa.

• Outgroups help determine direction of character change.

• More species and characters increase possible phylogenetic trees.

Hennig's Method

• Assumes derived character states evolve only once (homology).

• Assumes no reversals in character states.

Research Methods in Phylogenetics

• Parsimony: Prefers the simplest explanation (fewest changes).

• Evolutionary Distance: Quantifies average frequency of character changes.

• Maximum Likelihood/Bayesian Analysis: Uses probability to find best tree.

Branch Lengths in Phylogenetic Trees

• Show genetic differences and evolutionary time between nodes.

Information from Phylogenetic Trees

• Show evolutionary relationships and structural evidence.

• Taxa with similar physical traits or fewer DNA sequence differences are more closely related.

Fossils and the Fossil Record

Fossilization and Biases

• Paleontologists study fossils to reconstruct past life.

• Fossil record: All discovered and archived fossils.

• Fossilization is more likely for organisms with hard parts and those buried quickly.

• Temporal bias: Recent fossils are more common than ancient ones.

Types of Fossil Evidence

• Ancient pollen, fossilized bodies, trace fossils (tracks, burrows), and molecular evidence (DNA).

• Fossils provide information on appearance, behavior, and environment.

Major Events in the History of Life

Oxygen Revolution and Cambrian Explosion

• Oxygen produced by cyanobacteria led to oxygen-rich atmosphere (~2 billion years ago).

• Cambrian Explosion (~541 million years ago): Rapid diversification of animal life.

Phanerozoic Eon

• Paleozoic Era: Diversification of animals, plants, fungi; ends with Permian extinction.

• Mesozoic Era: Age of reptiles; ends with Cretaceous extinction.

• Cenozoic Era: Age of mammals; current era.

• Anthropocene: Human impact on Earth.

Adaptive Radiation

• Rapid production of many descendant species with diverse forms.

• Triggered by new resources or evolutionary innovations.

Origin of Eukaryotes and Endosymbiosis

Key Features of Eukaryotes

• All have mitochondria or genes for mitochondria, and a nucleus with endomembrane system.

• Eukaryotic flagellum: Made of microtubules and dynein motor protein.

• Bacterial/archaeal flagellum: Made of flagellin protein, rotates for movement.

Endosymbiosis Theory

• Mitochondria originated when a bacterial cell was engulfed by another cell (~2 billion years ago).

• Endosymbiosis: One species lives inside another; mitochondria and chloroplasts are examples.

• Evidence: Mitochondria and chloroplasts have their own DNA, double membranes, and replicate independently.

Nuclear Envelope

• Formed from infoldings of the plasma membrane.

Table: Comparison of Prokaryotes and Eukaryotes

Feature	Prokaryotes	Eukaryotes
Nucleus	Absent	Present
Cell Type	Unicellular	Often multicellular
Organelles	Few, no membrane-bound organelles	Many, including mitochondria and chloroplasts
Examples	Bacteria, Archaea	Plants, Animals, Fungi, Protists

Key Equations and Concepts

• Hardy-Weinberg Equation: Describes allele and genotype frequencies in a population not evolving. $p^2 + 2pq + q^2 = 1$

• ATP Production (Cellular Respiration): $\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} + \text{ATP}$

Summary

• Life is defined by cellular structure, replication, information processing, energy use, and evolution.

• Evolutionary relationships are reconstructed using phylogenetic trees and fossil evidence.

• Major evolutionary events include the origin of eukaryotes, oxygenation of the atmosphere, and adaptive radiations.

• Endosymbiosis explains the origin of mitochondria and chloroplasts in eukaryotes.