Biology Chapter on Endosymbiosis and Taxonomy

Biology Defined

• Biology is the study of life, encompassing the origin of life, how it changes, and its relationship with the environment.
• It's not just the study of living things, but also the evolutionary processes and their interconnections.

Why is Biology Significant?

• The formation of life is significant because without living organisms, other fields like accounting, arts, and computer science are considered insignificant.
• The study of living things is relevant to all fields, as they shape the physical world around us.

Life as We Know It

• Earth is approximately 4.6 billion years old.
• Life first emerged as a simple, self-replicating molecule about 3.85 billion years ago.
• As life forms evolved, those that adapted to their surroundings prevailed, while those that failed to adapt perished.
• Evolution is a fundamental natural process.

Chemicals Required for Life

• Hydrogen (H) is a component of water molecules.
• Carbon (C) forms complex carbon molecules, fundamental to life.
• Oxygen (O) is also part of water molecules.
• Nitrogen (N) is needed for the formation of amino acids.

The Atoms and Molecules of Ancient Earth

• The chemical evolution hypothesis describes how complex carbon-containing compounds, and eventually life, formed from simpler molecules on ancient Earth.

When Did Chemical Evolution Take Place?

• Radiometric dating is used to determine the age of Earth and the emergence of life.

Radioactive Isotopes

• Each element has a distinct number of protons.
• The number of neutrons can vary, resulting in isotopes like 12C and 13C.
• Radioactive isotopes have unstable nuclei that emit particles of radiation and decay into new daughter isotopes.

Half-Lives

• Half-life is the time it takes for half of the atoms in a radioactive sample to decay.
• The decay follows a predictable exponential curve.

How Old Is the Earth?

• Meteorites and moon samples suggest Earth formed 4.5-4.6 billion years ago.
• Earth's initial molten state prevents direct radiometric dating.

First Evidence of Life?

• The earliest evidence of life comes from 3.85 billion-year-old carbon grains.
• These grains show high levels of 12C relative to heavier carbon isotopes, a pattern characteristic of living organisms.

The Building Blocks of Chemical Evolution

• Most cells consist primarily of hydrogen (H), carbon (C), nitrogen (N), and oxygen (O).

Chemical Evolution

• The theory of chemical evolution proposes that simple molecules present on ancient Earth reacted to form increasingly complex molecules.
• The formation of formaldehyde (H₂CO) and hydrogen cyanide (HCN) is a crucial initial step that required energy input.

The Roles of Temperature and Concentration in Chemical Reactions

• High temperatures and high reactant concentrations lead to more collisions, increasing reaction rates.
• Computer models support that significant amounts of formaldehyde and hydrogen cyanide form under the temperature and concentration conditions present on ancient Earth.

How Did Chemical Energy Change during Chemical Evolution?

• In chemical evolution, energy from sunlight was converted into chemical energy, via the formation of H₂CO and HCN.

The Composition of the Early Atmosphere

• The early atmosphere was primarily volcanic gases-mostly carbon dioxide (CO₂), nitrogen (N₂), and water (H₂O).
• Trace amounts of hydrogen (H₂), ammonia (NH₃), and methane (CH₄) were also present, crucial for chemical reactions leading to organic compounds.

Linking Carbon Atoms Together

• The potential energy in carbon compounds (e.g., CH₂O) enabled the formation of complex organic compounds, some of which are found in organisms today.

Chemical Evolution Hypothesis

• Simple molecules in ancient Earth's atmosphere reacted (via redox reactions) to form more complex molecules in the oceans like formaldehyde (H₂CO) and hydrogen cyanide (HCN).
• With heat, organic compounds containing single-carbon atoms could form more complex molecules such as acetaldehyde, glycine, and ribose.

Early Origin-of-Life Experiments

• In 1953, Stanley Miller tested the possibility that the first stages of chemical evolution occurred on early Earth.
• He combined methane, ammonia, and hydrogen in a closed system with water and applied heat and electrical sparks to simulate energy sources.

The Early Oceans and the Properties of Water

• Life originated in and is based on water because water is a great solvent that dissolved the crucial chemicals needed to sustain life.

How Does Water's Structure Correlate with Its Properties?

• Water's unique properties-small size, bent shape, highly polar covalent bonds, and overall polarity- are vital for life.
• Water expands when it solidifies into ice but is denser in its liquid form.
• Water has an unusually high capacity for absorbing heat, keeping the temperature stable in the environments in which life formed.

Water is Denser as a Liquid than as a Solid

• Hydrogen bonds in ice create an open crystal structure with more space between water molecules.
• Fewer hydrogen bonds in liquid water allow molecules to pack more closely together, making liquid water denser than ice.

Early Earth Environment

• Water's temperature-buffering capacity protected critical molecules like HCN and H₂CO from destructive energy sources on early Earth.

What Was Water's Role in Chemical Evolution?

• Chemical evolution occurred in the early oceans because water's high specific heat helped to preserve simple organic molecules.

Protein Structure and Function

• The four steps of chemical evolution require energy input.
  1. Creation of small molecules with reduced carbon
  2. Prebiotic soup formation of amino acids, sugars, and nitrogenous bases.
  3. Linkage of organic subunits to make larger organic molecules.
  4. Evolution of a self-replicating molecule.

Amino Acids and Polymerization

• More recent experiments show that amino acids and other organic molecules form easily under early Earth-like conditions.
• All organisms have proteins built from 20 different amino acids.

The Cell Theory

• Robert Hooke and Anton van Leeuwenhoek were the first to observe cells in the late 1660s.

Where Do Cells Come From?

• The cell theory states all organisms are made of cells and all cells come from pre-existing cells.
• Louis Pasteur disproved the theory of spontaneous generation, confirming the cellular origin of life.

Organelles Divide a Large Cell into Compartments

• Eukaryotes solved the size problem by dividing their cell volume into compartments that allowed for multiple functions.

Organelle Examples

• Mitochondria are power generators.
• Chloroplasts are sites of photosynthesis.
• Golgi apparatus packages products.
• Ribosomes synthesize proteins.
• Nucleus houses DNA.
• Endoplasmic reticulum synthesizes and metabolizes.
• Vacuoles store water in plants.

The Endosymbiosis Theory

• Early eukaryotes were probably single-celled organisms with a cytoskeleton and nucleus but no cell wall.
• Symbiosis occurs when individuals of two different species live in physical contact and endosymbiosis occurs when an organism of one species lives inside an organism of another species.
• The theory posits that mitochondria and chloroplasts originated from symbiotic bacteria.

Do the Data Support the Endosymbiosis Theory?

• Mitochondria and chloroplasts are similar in size to bacteria.
• Both organelles replicate by fission and have their own ribosomes for protein synthesis.
• Both organelles have double membranes.
• Mitochondrial and chloroplast DNA resemble bacterial DNA more than eukaryotic DNA.

The Tree of Life

• The cell theory and the theory of evolution suggest that all species descended from a single common ancestor.
• This phylogenetic tree is called 'The Tree Of Life'.

Linnaean Taxonomy

• Linnaeus created a system for classifying organisms using binomial nomenclature (genus and species).
• His system is hierarchical and nested.
• The taxonomic levels are domain, kingdom, phylum, class, order, family, genus, and species, progressing from broadest to most specific grouping.

A New Level

• The classification system now incorporates a new level called "Domain".
• The three domains include Bacteria, Archaea, and Eukarya, the broad categories of life.

How Many Kingdoms Are There?

• Linnaeus grouped organisms into two kingdoms: plants and animals.
• A more recent five-kingdom system is based on phylogeny and distinguishes prokaryotes and eukaryotes.

Characters of Commonality

• Prokaryotic organisms lack a true nucleus and membrane-bound organelles.
• Eukaryotic organisms contain a true nucleus and membrane-bound organelles.
• Unicellular organisms are made of a single cell.
• Multicellular organisms are made of multiple cells.
• Autotrophic organisms produce their own food.
• Heterotrophic organisms obtain food from other sources.
• Saprophytic organisms obtain nutrients from decaying matter.

Using Molecules to Understand the Tree of Life

• Carl Woese and colleagues used small subunit rRNA (a molecule common to all organisms) to study evolutionary relationships among groups of organisms.
• The human genome has 3.1 billion nucleotides.

The rRNA Tree

• The Tree of Life model demonstrates three main groups: Eukaryotes and the Bacteria and Archaea prokaryotes.
• Domains (Bacteria, Archaea, Eukarya), include several kingdoms.

Other Evidence for Relatedness Among Groups

• Vertebrates have similar developmental patterns (embryonic development).
• Vertebrates share homologous biochemical traits and often have similar morphology.

The Tree of Life - On a 1-Year Time Scale

• This depiction shows the events in the history of life across a one-year period.

Phylogenies and the History of Life

• The history of life spans roughly 3.85 billion years, and phylogenies and fossil records help to trace lineages.

Using Phylogenies

• Biologists read phylogenetic trees, noting branches, nodes and tips, to determine relationships between groups of organisms.

Populations, Branches, Nodes, and Tips

• Phylogenetic trees represent populations as branches, and nodes signify ancestral splits into separate lineages.
• Branch tips represent extant species or the end of a lineage.

All Phylogenies, Rooted

• The root shows the common ancestor of all species being studied.
• Phylogenies use outgroups (taxa that diverged before the others) to place the root correctly.

How Do Researchers Build Phylogenies?

• Morphological, developmental, biochemical, and genetic characteristics inform phylogenetic estimations.
• Characterizing the similarities and differences are used to create phylogenies.

Phenetic Approach

• A statistical analysis is computed to summarize the overall similarities among populations to construct a tree that groups the most similar populations.

Cladistic Approach

• Researchers using the cladistic approach focus on synapomorphies—shared, derived characteristics—to distinguish a group.
• A computer program identifies the unique traits of each monophyletic group and places them appropriately on the tree.

Parsimony Hypothesis

• The simplest explanation for any evolutionary phenomenon is the most likely one, assuming the fewest evolutionary changes.

Whales Evolution: A Case History

• Morphological data traditionally placed whales outside of artiodactyls based on the pulley-shaped astragalus.

DNA Sequence Data

• Some DNA sequence analysis suggests a close relationship between whales and hippos, potentially contradicting the morphological findings.

How similar is DNA between taxa?

• Percent similarity between DNA of species varies greatly, from 5% similarity (bacteria) to 99% (chimpanzees).

If whales are related to hippos, then two evolutionary changes occurred in the astralagus.

• The diagram illustrates two evolutionary changes in the astragalus if whales are similarly related to hippos.

The Nature of Natural Selection and Adaptation

• Natural selection does not act on individuals but on populations with different observable traits who will result in observable evolutionary changes.
• Adaptation occurs when a population changes; not individuals alone.
• Acclimation is a temporary change that only refers to individual response.

Evolution is not Progressive

• Modern evolutionary theory dispels the idea of a hierarchical "ladder of life," instead positing an evolutionary tree of related species with shared ancestry.

Evolutionary Processes

• Evolution within populations is caused by natural selection, genetic drift, gene flow, and mutation.

Natural Selection and Sexual Selection

• Natural selection favors individuals with certain heritable traits, increasing their reproductive success, which increases the frequency of the alleles responsible for these traits.
• Sexual selection involves competition among males and mate choice by females to increase reproductive success.

Heterozygote Advantage

• Heterozygote advantage is when heterozygous individuals (with different alleles) demonstrate a higher fitness than homozygous individuals (with identical alleles).

Directional Selection

• Directional selection increases the frequency of one particular allele, reducing population genetic diversity.

Stabilizing Selection

• Stabilizing selection maintains intermediate phenotypes within a population.

Disruptive Selection

• Disruptive selection favors extreme phenotypes rather than intermediate ones.

Sexual Selection

• Mate choice plays a crucial role in speciation.

The fundamental asymmetry of sex

• Females generally invest more in their offspring.

Sexual Dimorphism

• Sexual dimorphism refers to differences in physical characteristics between males and females of the same species.

Genetic Drift

• Genetic drift is random fluctuations in allele frequencies in populations.
• Genetic drift is especially prominent in smaller populations, leading to the potential loss or fixation of alleles.

How Do Founder Effects Cause Genetic Drift?

• A founder effect arises when a small group from a larger population colonizes a new area.
• The new population exhibits different allele frequencies than the source population due to chance events.

How Do Population Bottlenecks Cause Genetic Drift?

• Population bottlenecks are reductions in population size due to natural disasters or other events.
• The reduced population has a different genetic makeup than the original population.

Gene Flow

• Gene flow represents the relocation of alleles among populations.
• Individuals migrating between populations introduce new alleles and decrease variations in the populations.

Mutation as an Evolutionary Mechanism

• Mutation creates new alleles and is essential for genetic diversity.

Speciation

• Genetic isolation, caused by reduced gene flow, genetic drift or natural selection can lead to divergence into new species.
• Populations may diverge if they occupy different geographic areas, different habitats within the same area, or if breeding is impossible between them.