Endosymbiosis, Phylogeny, and Cell Theory in Biology

Endosymbiotic Theory

Explains the origin of organelles in eukaryotic cells, where mitochondria originate from aerobic bacteria and chloroplasts from photosynthetic cyanobacteria.

Phylogenetics

Study of evolutionary relationships between organisms based on genetic data (often DNA/RNA sequences).

LUCA

Last Universal Common Ancestor; the node where all lineages converge on the phylogenetic tree.

LECA

Last Eukaryotic Common Ancestor; the node where archaeal and eukaryotic lineages diverge from their shared ancestry.

rRNA

Ribosomal RNA used as a conserved genetic marker across all domains, as every cell contains ribosomes made of rRNA and protein.

Three domains of life

Bacteria, Archaea, and Eukarya; the top taxonomic level.

Prokaryotic

Organisms lacking a membrane-bound nucleus, including Bacteria and Archaea.

Eukaryotic

Organisms with eukaryotic cells that contain a nucleus and organelles.

Cellular Life

Refers to the existence of organisms as either unicellular or multicellular.

Unicellularity

The state of being composed of a single cell, typical of Bacteria and Archaea.

Multicellularity

The state of being composed of multiple cells, which arises within the Eukarya domain.

Linnaean Classification

Hierarchical classification system from broad to specific: Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species.

Kingdoms by domain

Bacteria domain: kingdom Bacteria; Archaea domain: kingdom Archaea; Eukarya domain: kingdoms Plantae, Animalia, Fungi, Protista.

Memory mnemonic

King Henry Died Monday Drinking Chocolate Milk, used to remember the order of Linnaean classification.

Deep split in phylogenetic tree

The separation between Bacteria and the common ancestor of Archaea and Eukarya.

Topology of the tree

Suggests Archaea and Eukarya are more closely related to each other than either is to Bacteria.

Ancient Archaean host

Engulfed bacterial lineages, giving rise to mitochondria in the lineage leading to Eukarya.

Photosynthetic cyanobacterium

Led to chloroplasts in plants and algae through an ancient engulfment event.

Genetic data

Information used in modern phylogenetics to infer evolutionary relationships.

Ribosomal RNA sequences

Genomic sequences compared to provide evidence for endosymbiosis and deep relationships.

Eukarya diversity

Reflects substantial diversity within eukaryotic cells, with four kingdoms.

Yeast as an example

Demonstrates that being unicellular is not limited to prokaryotes.

Bacteria and Archaea kingdoms

Each has one kingdom within their domain.

Diversity in Bacteria and Archaea

Includes metabolisms such as oil degradation, rock cycling, photosynthesis, etc.

Properties of Cellular Life

A cell must meet all of the following basic properties to be considered cellular life.

Genetic Program

Has DNA or RNA that encodes the organism's blueprint.

Reproduction

Organisms reproduce and pass on genetic material to offspring (e.g., binary fission in bacteria, mitosis in eukaryotes).

Energy Acquisition and Utilization

Acquire energy, convert it to ATP, and use it for growth and function.

Metabolism

Carry out chemical reactions and metabolic processes.

Mechanical Properties and Movement

Exhibit movement or mechanical activity that requires energy.

Response to Stimuli

Detect and respond to environmental cues.

Self-Regulation

Regulate internal processes (e.g., turning off enzymes not needed during DNA replication, maintaining homeostasis).

Evolution

Populations evolve via genetic changes over time.

Viruses

Meet some criteria (genetic material and the ability to evolve) but lack cellular metabolism and self-reproduction independent of a host cell, so they are acellular.

Prions

Misfolded proteins that can cause disease; they do not have a genetic program and do not evolve via genetic inheritance, so they are not cellular life.

Cell Theory

Composed of three traditional points: 1) All organisms are composed of one or more cells. 2) The cell is the basic unit of life. 3) Cells arise from preexisting cells.

Robert Hooke

Coined the term 'cell' after observing cork under a microscope in the 1600s.

Anton van Leeuwenhoek

Improved lenses and tools, described microscopic life (animacules) in pond water.

Schlieden and Schwann

Formulated the initial cell theory concepts: all organisms are composed of one or more cells; the cell is the basic unit of life.

Rudolf Virchow

Added the crucial third point to cell theory: cells arise from preexisting cells (not spontaneous generation).

Louis Pasteur

Conducted experiments that argued against spontaneous generation and supported the cell theory.

Pasteur's Swan-Neck Flask Experiment 1

Broth boiled to sterilize; neck broken and open to air. Microbes from the air contaminate broth; broth becomes populated with cells.

Pasteur's Swan-Neck Flask Experiment 2

Swan-neck flask allows air exposure but traps dust and microbes in the bend. Broth remains sterile despite exposure to air.

Conclusion from Pasteur's Experiments

Cells must come from preexisting cells; spontaneous generation is not supported under the conditions tested.

Spontaneous Generation Debate

Required multiple lines of evidence, including microbial evidence trapped in the neck of flasks, to overturn the spontaneous generation hypothesis.

Theories in Science

Not 'proved' in an absolute sense; they are supported by a large body of empirical evidence and can be revised with new findings.

Biosphere

Earth as the global sum of all ecosystems.

Ecosystems

All living organisms plus the abiotic components (air, minerals, climate, etc.) in a given area.

Communities

All living populations within an ecosystem.

Populations

A group of individuals of the same species in a given area.

Organisms

A single individual; composed of organs and organ systems.

Organs and Organ Systems

Examples include the cardiovascular system and digestive system.

Tissues

Groups of similar cells and their extracellular matrix.

Cells

Basic units of life; the focus of much of this course.

Organelles

Structures within cells such as mitochondria, chloroplasts, and nucleus.

Molecules and Atoms

The molecular constituents and atoms forming cellular structures.

Surface Area to Volume Ratio

Governs how efficiently a cell can exchange materials with its environment; small cells maximize surface area relative to volume.

Hooke and Leeuwenhoek

Credited with the discovery of cells; Hooke observed cork and coined the term 'cell', while Leeuwenhoek described living cells in pond water.

Cell Theory Developments

Formalized in the 19th century by Schleiden, Schwann, and later Virchow, with critical evidence provided by Pasteur against spontaneous generation.

Darwin and Wallace

Proposed the theory of evolution by natural selection, based on observations from the Galápagos.

Descent with Modification

Core idea that all species past and present are related by descent from a common ancestor.

Natural Selection Conditions

Three critical conditions: Variation, Heritability, and Differential fitness.

Variation

Individuals within a population vary in heritable traits.

Heritability

Traits are encoded in the genome and can be passed from parent to offspring.

Differential Fitness

Variants that increase survival and reproductive success become more common over generations.

Evolution Implications

Evolution operates at the population level, not the individual level; trait frequencies change over time.

Antibiotic Resistance

An example of natural selection in action, demonstrating rapid adaptations.

Species interbreeding

Species must be the same species to interbreed when discussing genetic inheritance and evolutionary change in a population.

Three-domain system

The deep relationship between Archaea and Eukarya.

rRNA-based phylogenetic analysis

Its role in constructing the phylogenetic tree.

Linnaean hierarchy

The six kingdoms, plus the distinction between cellular and acellular life (viruses vs prions).

Seven properties of cellular life

The eight criteria listed in lecture that define cellular life and how viruses/prions fit or do not fit.

Pasteur's experiments

The historical context of the cell theory.

Darwin and Wallace's theory of evolution

By natural selection and its three conditions.

Biological hierarchy

From biosphere down to molecules, including the significance of surface area to volume in cellular organization.

Unicellular yeast

Belongs to the domain Eukarya and the Kingdom Fungi.

Tree topology supported by rRNA sequencing

Archaea and Eukarya are more closely related than either is to Bacteria; LECA within Archaea and Eukarya lineage.

Criteria for evolution by natural selection

Variation, Heritability, Differential fitness.

Critical piece of Pasteur's experiment

Isolation and identification of microbes from the neck of the swan-neck flask, demonstrating microbes come from air, not spontaneously from broth.

Cell

Basic unit of life; must meet a defined set of criteria to be considered cellular life.

Endosymbiosis

Evolutionary process linking prokaryotic lineages into eukaryotic organelles.

SA/V

Surface area-to-volume ratio, a key factor in cellular design and metabolism.