Podcast
Questions and Answers
Which characteristic is LEAST useful when classifying an organism as 'living'?
Which characteristic is LEAST useful when classifying an organism as 'living'?
Within the binomial nomenclature system, what is the correct way to represent the scientific name of a species?
Within the binomial nomenclature system, what is the correct way to represent the scientific name of a species?
If two organisms are classified within the same order, what other taxonomic levels must they also share?
If two organisms are classified within the same order, what other taxonomic levels must they also share?
How do eukaryotic cells differ from prokaryotic cells?
How do eukaryotic cells differ from prokaryotic cells?
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Which of the following best exemplifies an emergent property?
Which of the following best exemplifies an emergent property?
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A researcher observes that plants grow taller in sunlight than in shade. After formulating a hypothesis, which of the following represents a valid prediction using the 'if...then' structure?
A researcher observes that plants grow taller in sunlight than in shade. After formulating a hypothesis, which of the following represents a valid prediction using the 'if...then' structure?
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After conducting an experiment, the data contradicts the initial hypothesis. What is the MOST appropriate next step in the scientific method?
After conducting an experiment, the data contradicts the initial hypothesis. What is the MOST appropriate next step in the scientific method?
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Considering the process of horizontal gene transfer, which scenario would MOST significantly alter the evolutionary trajectory of a prokaryotic species?
Considering the process of horizontal gene transfer, which scenario would MOST significantly alter the evolutionary trajectory of a prokaryotic species?
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If a new strain of bacteria is discovered, and it thrives in extremely high temperatures and produces methane as a byproduct, to which domain would it MOST likely be classified?
If a new strain of bacteria is discovered, and it thrives in extremely high temperatures and produces methane as a byproduct, to which domain would it MOST likely be classified?
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How might the presence of a capsule enhance a prokaryote's ability to cause disease in a host organism?
How might the presence of a capsule enhance a prokaryote's ability to cause disease in a host organism?
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Considering the role of prokaryotes in chemical cycling, what would be the MOST likely consequence of a widespread disruption of prokaryotic communities in an ecosystem?
Considering the role of prokaryotes in chemical cycling, what would be the MOST likely consequence of a widespread disruption of prokaryotic communities in an ecosystem?
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Which of the following BEST describes the evolutionary significance of endospores in prokaryotes?
Which of the following BEST describes the evolutionary significance of endospores in prokaryotes?
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Why are mtDNAs preferred over other genes when classifying species with narrow classifications?
Why are mtDNAs preferred over other genes when classifying species with narrow classifications?
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What is the significance of the high percentage of homologous genes between humans and other organisms, such as mice and yeast?
What is the significance of the high percentage of homologous genes between humans and other organisms, such as mice and yeast?
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How does gene duplication contribute to evolutionary change?
How does gene duplication contribute to evolutionary change?
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What is the primary advantage of using molecular clocks over morphological changes to measure evolutionary time?
What is the primary advantage of using molecular clocks over morphological changes to measure evolutionary time?
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What data is required to calibrate a molecular clock?
What data is required to calibrate a molecular clock?
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Which level of classification would rRNA be most appropriate for?
Which level of classification would rRNA be most appropriate for?
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If a gene in two related species shows a significantly different rate of evolution than expected based on a molecular clock, what could be a plausible explanation?
If a gene in two related species shows a significantly different rate of evolution than expected based on a molecular clock, what could be a plausible explanation?
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Considering the evolutionary relationships described, which statement is most accurate?
Considering the evolutionary relationships described, which statement is most accurate?
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How can molecular techniques be utilized to investigate the divergence of duplicated genes?
How can molecular techniques be utilized to investigate the divergence of duplicated genes?
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What is the most likely reason for the observed difference in divergence times between sharks/tuna (420 million years ago) and dolphins/bats (60 million years ago)?
What is the most likely reason for the observed difference in divergence times between sharks/tuna (420 million years ago) and dolphins/bats (60 million years ago)?
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How did Charles Lyell's Principles of Geology influence Darwin's thinking regarding evolution?
How did Charles Lyell's Principles of Geology influence Darwin's thinking regarding evolution?
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Which of the following statements accurately reflects the relationship between natural selection and adaptation?
Which of the following statements accurately reflects the relationship between natural selection and adaptation?
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Why is the fossil record considered an incomplete chronicle of evolution?
Why is the fossil record considered an incomplete chronicle of evolution?
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How does the study of molecular homology support the theory of evolution?
How does the study of molecular homology support the theory of evolution?
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What is the evolutionary significance of vestigial structures, such as the small pelvis and hind-leg bones found in ancient whales?
What is the evolutionary significance of vestigial structures, such as the small pelvis and hind-leg bones found in ancient whales?
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In the context of evolution, what is the primary difference between artificial selection and natural selection?
In the context of evolution, what is the primary difference between artificial selection and natural selection?
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Why is genetic variation essential for natural selection to occur?
Why is genetic variation essential for natural selection to occur?
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What are the primary conditions that must be met for a population to be in Hardy-Weinberg equilibrium?
What are the primary conditions that must be met for a population to be in Hardy-Weinberg equilibrium?
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In the context of population genetics, what does the term 'gene pool' refer to?
In the context of population genetics, what does the term 'gene pool' refer to?
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In a hybrid zone where reinforcement is occurring, what would you expect to observe over time?
In a hybrid zone where reinforcement is occurring, what would you expect to observe over time?
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Which of the following scenarios would be LEAST likely to lead to allopatric speciation?
Which of the following scenarios would be LEAST likely to lead to allopatric speciation?
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What is the primary distinction between prezygotic and postzygotic reproductive barriers?
What is the primary distinction between prezygotic and postzygotic reproductive barriers?
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Which of the following is an example of sympatric speciation?
Which of the following is an example of sympatric speciation?
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What is the most likely outcome for a hybrid zone if reproductive isolation between two species is weak and environmental conditions are similar?
What is the most likely outcome for a hybrid zone if reproductive isolation between two species is weak and environmental conditions are similar?
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Which of the following statements best describes punctuated equilibria?
Which of the following statements best describes punctuated equilibria?
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Which of the following conditions on early Earth is thought to have contributed to the abiotic synthesis of organic molecules?
Which of the following conditions on early Earth is thought to have contributed to the abiotic synthesis of organic molecules?
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During adaptive radiation, what is the relationship between environmental opportunities and the diversification of species?
During adaptive radiation, what is the relationship between environmental opportunities and the diversification of species?
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What is the significance of stromatolites in understanding the early history of life?
What is the significance of stromatolites in understanding the early history of life?
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Which of the following is an example of sexual selection leading to speciation?
Which of the following is an example of sexual selection leading to speciation?
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Flashcards
Biology
Biology
The scientific study of life, focusing on its structure, function, growth, and evolution.
Characteristics of Life
Characteristics of Life
Life is characterized by cells, energy use, response to environment, and reproduction.
Nomenclature
Nomenclature
The naming of organisms using a two-part scientific name format, including genus and specific epithet.
Taxonomy
Taxonomy
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Domains of Life
Domains of Life
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Scientific Method
Scientific Method
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Emergent Properties
Emergent Properties
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Geographic Proximity
Geographic Proximity
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Descent with Modification
Descent with Modification
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Natural Selection
Natural Selection
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Fossils
Fossils
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Transitional Forms
Transitional Forms
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Homology
Homology
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Gene Pool
Gene Pool
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Hardy-Weinberg Equilibrium
Hardy-Weinberg Equilibrium
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Mutation
Mutation
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Reproductive Barriers
Reproductive Barriers
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Prezygotic Barriers
Prezygotic Barriers
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Postzygotic Barriers
Postzygotic Barriers
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Allopatric Speciation
Allopatric Speciation
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Sympatric Speciation
Sympatric Speciation
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Polyploidy
Polyploidy
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Hybrid Zones
Hybrid Zones
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Reinforcement in Hybrid Zones
Reinforcement in Hybrid Zones
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Punctuated Equilibria
Punctuated Equilibria
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Stromatolites
Stromatolites
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Body Lice
Body Lice
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Horizontal Gene Transfer
Horizontal Gene Transfer
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Prokaryotic Cells
Prokaryotic Cells
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Microbiota
Microbiota
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Biofilms
Biofilms
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rRNA
rRNA
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Fungi and Animals
Fungi and Animals
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mtDNA
mtDNA
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Homologous Genes
Homologous Genes
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Gene Duplication
Gene Duplication
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Molecular Clocks
Molecular Clocks
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Shark and Tuna Divergence
Shark and Tuna Divergence
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Dolphin and Bat Divergence
Dolphin and Bat Divergence
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Nucleotide Differences
Nucleotide Differences
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Evolutionary Branch Points
Evolutionary Branch Points
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Study Notes
Course Information
- Course name: BIOL1010
- Course title: Biology: Biological Diversity and Interactions
- Instructor: Dr. Elizabeth Hughes
- Location: 330 Allen Building
- Day and time: Tuesday, Thursday 1:00 – 2:15
- Textbook chapter: 1.1 – 1.10 (for Introduction to Biology)
Introduction to Biology
- Biology: Scientific study of life
- Key characteristics of life:
- Composed of cells
- Regulation of internal environment
- Intake and use of energy
- Response to the environment
- Reproduction, growth, and development
- Energy processing (metabolism)
- Evolutionary adaptation
- Organisms can be unicellular or multicellular
- Nomenclature: The naming of organisms (scientific names)
- Binomial system: Genus and species epithet (e.g., Homo sapiens)
- 1.8 million species named so far
- Estimated 10-100 million species exist
Taxonomy
- Classify species based on evolutionary history and relationships
- Hierarchical classification:
- Domain
- Kingdom
- Phylum
- Class
- Order
- Family
- Genus
- Species
- Example:
- Domain: Eukarya
- Kingdom: Animalia
- Phylum: Chordata
- Class: Mammalia
- Order: Carnivora
- Family: Ailuridae
- Genus: Ailurus
- Species: fulgens (red panda)
Domains of Life
- Prokaryotes:
- Domain Bacteria
- Domain Archaea
- Small simple cells
- Eukaryotes:
- Domain Eukarya
- Includes: protists, fungi, plants, and animals
- Large complex cells
Hierarchy of Organization
- Emergent properties: Novel properties arise at each higher level
- Biosphere → Ecosystem → Community → Population → Organism → Organs and Organ Systems → Tissues → Cells → Organelles → Molecules → Atoms
What is Science?
- Science: An approach to understanding the natural world
- Search for information and explanations for natural phenomena
- Data: Recorded observations (qualitative and quantitative)
The Scientific Method
- Observation
- Question
- Hypothesis (proposed explanation)
- Prediction ("if...then" comments)
- Experiment (controlled conditions)
- Conclusion (was the hypothesis supported or rejected?)
Scientific Theory
- Broad in scope and supported by a large body of evidence
- Example: The Theory of Evolution
Controlled Experiments
- Independent variable: The factor manipulated by researchers
- Dependent variable: Measure used to judge experiment outcome (affected by independent variable)
- Control group: Compared with experimental group
- Example using mice living on beaches vs. inland
Clinical Studies or Trials
- Tests done on humans
- Placebo: A treatment that does not contain the medication being tested
- Double-blind trial: Neither the subjects nor the scientists know who is in which group
Observational Studies
- Retrospective study: Uses interviews, medical records, and death certificates to look back at factors that may have led to a specific outcome.
- Prospective study: Data systematically collected from an established group (cohort) over a period of time.
The Process of Science
- Exploration and discovery: Observe, ask questions, and research existing literature
- Formation and testing of hypotheses: Collect and interpret data
- Feedback from the scientific community: Peer-reviewed publications, replication of findings, and consensus building
- Societal benefits and outcomes: Solving problems and developing new technologies
Science and Technology
- Science: Gain of knowledge to explain natural phenomena
- Scientists make discoveries
- Technology: Application of scientific knowledge
- Engineers make inventions
- Drawbacks of technology include climate change, toxic wastes, and deforestation.
Evolution as the Core Theme of Biology
- Diversity of life: Differences between species
- Unity of life: Similarities between species
- Evolution: The process of change that has transformed life on Earth and continues today
Darwin's Theory of Evolution
- History of life documented by fossils and other evidence.
- Natural Selection is the mechanism
- Descent with modification: Present-day species are descendants of ancient ancestors.
Darwin's Observations and Inferences
- Individual variation: Individuals within a population vary in their traits.
- Overproduction of offspring: Species have more offspring than the environment can support leading to competition.
- Unequal reproductive success: Individuals with advantageous inherited traits are more likely to survive and reproduce.
- Accumulation of favourable traits over time: Due to unequal reproductive success, the frequency of favourable traits increases within a population over time.
Natural Selection
- Many small changes lead to major alterations of species and new species evolution.
- Evidence from fossil record, experiments, observations of natural selection, and DNA comparisons.
The Tree of Life
- Each species on a branch of the tree of life
- Extends back in time to ancestral species (shows evolutionary relationships)
Artificial Selection
- Humans impact evolution with selective breeding of plants and animals.
- Choose which organisms reproduce to promote certain traits.
- Advancements in biotechnology, ex. genetic engineering of crops (drought tolerance, improved growth & increased nutrition).
Unintentional Evolution
- Habitat loss and climate change cause species loss.
- Antibiotic use causes antibiotic-resistant bacteria evolution.
- Pesticide use causes pesticide-resistant insects evolution.
Topic 2: Evolution
- Textbook chapter 13.1–13.16
Science in the Age of Charles Darwin
- Aristotle: Species are fixed and unchanging.
- Judeo-Christian culture: Each form of life was independently created in its present-day form, and the Earth is 6000 years old.
- Western world concept: All living species came into being relatively recently and are unchanging in form.
Charles Darwin
- Five-year voyage on the HMS Beagle surveying the South American coastline.
- Collected fossils and living plants and animals.
- Observations on geographic proximity and similarities among organisms.
- Inquiry on factors that make an organism well-suited to its environment.
Observations of Geographic Proximity
- Geographic proximity is a better predictor of relationships among organisms than similarity of environment.
- Galapagos Islands: Animals found nowhere else resemble South American species; different varieties of giant tortoises on different islands and the differences among marine iguanas.
Geological Changes
- Charles Lyell's Principles of Geology: Earths sculpted by gradual geologic processes.
- Darwin: An earthquake raised the Chilean coastline confirming the idea that the Earth is still changing.
- Implication for the idea that organisms are also capable of change.
Descent with Modification
- Present-day species are descendants of ancient ancestors that they still resemble in some ways.
- Differences accumulate over time through natural selection.
- Natural selection: Individuals with certain traits are more likely to survive and reproduce than those without those traits.
- Adaptations: Modifications that allow species to fit their specific ways of life in their environments.
Darwin's Writings
- On the origin of species by means of natural selection.
- Observations + experiments in biology, geology, and paleontology.
- Definition of evolution: Genetic changes in a population from generation to generation
Fossils
- Imprints or remains of organisms that lived in the past.
- Organic substances decay, hard parts remain (bones, teeth, shells)
- Casts: Empty molds filled with minerals.
- Imprints: footprints, burrows, coprolites
- Entire organisms: Encased in a medium that prevents decomposition (permafrost, bogs).
- Provide evidence of an organism's behavior.
Fossils (strata + paleontologist)
- Strata; layers of rock (younger strata on top of older strata)
- Paleontologist; scientist who studies fossils
- Fossil record; chronicle of evolution over millions of years of geologic time.
Transitional Forms
- Fossils linking different groups of organisms
- Examples:
- Whales evolved from land-dwelling mammals
- Amphibians evolved from fish
- Birds evolved from dinosaurs
- Mammals evolved from reptilian ancestors
Homology
- Homology: Similarity resulting from common ancestry
- Characteristics are altered by natural selection as descendants face different environmental conditions.
- Homologous structures: Variations on an anatomical structure that has been adapted to different functions.
Molecular Homology
- Molecular biology: Study of the molecular basis of genes and gene expression
- Homologous genes: Genes with closely matched sequences-inherited from a relatively recent common ancestor.
Darwin's Boldest Hypothesis
- All life-forms are related.
- Same genetic language (DNA, RNA)
- Genetic code
- Many homologous genes
- Similarities seen early in development that are less evident in mature organisms.
Homology (Vestigial structures + Pseudogenes)
- Vestigial structures: Remnants of features that served important functions in an organism's ancestors
- Small pelvis/hind leg bones in ancient whales
- Eye remnants in blind cave fish
- Pseudogenes: Genes that have lost their function but still have homologous genes in other related species.
- Example: GLO enzyme for making vitamin C.
Evolutionary Trees and Homology
- Each branch point represents a common ancestor of the lineages
- Extends back in time to ancestral species
Artificial Selection
- Darwin used artificial selection to study natural selection.
- Selective breeding of domesticated plants and animals to promote desirable traits.
Natural Selection
- Variation among individuals
- Heritability: Transmission of a trait from parent to offspring
- Production of more individuals than the limited resources can support leads to a struggle for existence.
- Over time, many adaptations will accumulate.
- Natural selection is adaptive evolution
Examples of Natural Selection
- Change in beak size of Galapagos finches
- Pesticide resistance in insects
- Antibiotic resistance in bacteria
Notes on Natural Selection
- Individuals do not evolve, populations evolve.
- Only heritable traits can be amplified or diminished.
- Evolution does not lead to perfectly adapted organisms
- Natural selection is an editing process; not a creative mechanism
- Natural selection is contingent on time and place
Genetic Variation
- Mutation produces new alleles.
- Can be beneficial or detrimental.
- Benefits are most obvious when the environment is changing in ways that mutations previously deemed disadvantageous are now favorable.
- Example; DDT resistance in houseflies.
- A mutation reduces growth rate; but once DDT was introduced this mutation was advantageous, meaning that natural selection increased the frequency of this mutation.
- Chromosomal mutations, prokaryotes, sexual reproduction
Populations
- Population: A group of individuals of the same species living in the same area and capable of interbreeding.
- Members of a population are more closely related to each other than members of other populations.
Gene Pool
- Gene pool: All copies of every type of allele at every locus in all members of the population.
- Microevolution: Changes in allele frequency in a generation
Hardy-Weinberg Equation
- Determines whether a population is evolving.
- Hardy-Weinberg equilibrium: Allele frequencies in the gene pool remain constant (assuming that no evolution occurs).
Conditions for the Hardy-Weinberg Equilibrium
- Very large population
- No gene flow between populations
- No mutations
- Random mating
- No natural selection
Hardy-Weinberg Equation in Public Health
- Example: Calculating the number of carriers of a recessive disease (e.g., phenylketonuria).
Genetic Drift
- Genetic drift: Chance events cause allele frequencies to unpredictably fluctuate from one generation to the next in small populations.
- Bottleneck effect: Catastrophes reduce population size and the surviving population is unlikely to have the same genetic makeup as the original population.
- Founder Effect: When a few individuals colonize an island or other new habitat, there is a reduced chance that the genetic makeup of the colonists represent the gene pool of the larger population.
Gene Flow
- A population may gain or lose alleles when fertile individuals move into or out of a population or when gametes are transferred between populations.
- Reduces differences between populations.
Relative Fitness
- Relative fitness: contribution an individual makes to the gene pool (relative to other individuals).
- Fittest individuals produce the most viable, fertile offspring.
- Survival of the fittest.
- Direct/Indirect competition
Natural Selection (directional, stabilizing, disruptive)
- Directional selection: Acts against individuals at one phenotypic extreme.
- Stabilizing selection: Favours intermediate phenotypes.
- Disruptive selection: Favours individuals at both ends of a phenotypic range
Sexual Selection
- Sexual selection: Individuals with certain traits are more likely to obtain mates.
- Sexual dimorphism: Differences in appearance between males and females of a species (ex: size, colouration, adornments).
- Intrasexual and intersexual selection.
Topic 3: Speciation
- Textbook chapter 14.1–14.11
- Speciation: The process by which one species splits into two or more species.
- Explains diversity and unity of life.
- New species share many characteristics because they are descended from a common ancestor.
Species
- How can we define a species?
- Similarity between two species
- Diversity within a species
The Biological Species Concept
- Species: A group of populations whose members have the potential to interbreed in nature and produce fertile offspring.
- United by being reproductively compatible
- Drawbacks: distinct species capable of interbreeding may produce hybrids; no way to know if ancient organisms were able to interbreed; cannot use to classify asexually reproducing organisms.
Other Definitions of Species
- Morphological species concept: Classification based on physical traits (shape, size, and other morphological features).
- Ecological species concept: Identifies species based on ecological niches and unique adaptations.
- Phylogenetic species concept: Smallest group of individuals that share a common ancestor that form one branch on the tree of life (morphology, DNA sequences, biochemical pathways).
Reproductive Barriers
- Biological features of organisms that prevent individuals of different species from interbreeding successfully.
- Prezygotic barriers: Prevent mating or fertilization (Habitat, temporal, behavioral, and mechanical isolation).
- Postzygotic barriers: Operate after hybrid zygotes have formed (Reduced hybrid viability, reduced hybrid fertility, hybrid breakdown).
Allopatric Speciation
- A population is divided into geographically isolated subpopulations.
- Splinter populations evolve their own evolutionary course.
- Gene flow is blocked.
- Some populations are more easily divided than others (isolation).
Geographic Isolation and Speciation
- Speciation occurs when reproductive barriers are established (different food sources, pollinators, and predators).
- Natural selection must act on pre-existing variations.
Example of Evolution of Reproductive Barriers
- Initial sample, mating experiments between different populations of fruit flies.
- Results: The experiment showed that reproductive barriers evolved in laboratory populations of fruit flies due to geographical isolation to different food sources.
Sympatric Speciation
- A new species arises within the same geographic area as its parent species.
- Polyploidy, habitat differentiation, and sexual selection may cause speciation.
- Polyploidy is particularly common in plants- a new species through the multiplication of chromosomes.
- Animals are more likely to undergo habitat differentiation or sexual selection.
Polyploidy
- Cells have more than two complete sets of chromosomes.
- Example of rapid speciation producing a viable fertile hybrid from two species (A and B).
Sexual Selection (in relation to speciation)
- Individuals with certain traits are more likely to obtain mates in a specific environment.
- Divergent females prefer different mates based on traits like colouration.
- Example; African cichlids develop different coloration preference in relationship to the water column's light availability.
Adaptive Radiations
- Periods of evolutionary change in which many new species evolve from a common ancestor.
- Mass extinctions.
- Evolutionary innovation that allows a group of organisms to exploit an unused resource.
- Ex. Colonization of land (proliferation of plants and resulting exploitation by pollinators and herbivores).
- Eventual re-colonization of the original island and the coexistence with the original ancestral species.
Hybrid Zones
- Regions where members of different species meet and interbreed, producing some hybrid offspring.
- Outcomes:
- Reinforcement
- Fusion
- Stability
Outcomes of Hybrid Zones (Reinforcement, Fusion, Stability)
- Reinforcement: Hybrid offspring are less fit than members of both parent species; reproductive barriers strengthen where they overlap. Example; pied flycatchers and collared flycatchers.
- Fusion: Speciation process reverses due to weak reproductive barriers. Example; African cichlids.
- Stability: Hybrids continue to be produced and allow for some gene flow between populations. Each species maintains its own integrity. Example; an island with two finch species that occasionally interbreed.
Punctuated Equilibria
- Long periods of little apparent morphological change, interrupted by relatively brief periods of sudden change.
- Many fossils appear suddenly in rock layers and persist unchanged through many strata before disappearing.
- Other fossils diverge gradually.
- Speed of speciation: 4000 years - 40 million years.
- Average: 6.5 million years
Evolutionary History
- Textbook sections 15.1–15.9
- Conditions on early Earth • 4.6 bya: Earth formation; immense heat; molten mass sorted into layers by density • 4 bya: Bombardment slowed; atmosphere thick with water vapor and compounds released by volcanic eruptions (N2,N2O,CO2,CH4,NH3,H2,H2S); Earth cools, water vapor condenses into oceans; intense lightning, volcanic activity, and UV radiation.
Earliest Evidence for Life
- Fossils 3.5 billion years old (Stromatolites)
- Made by ancient photosynthetic prokaryotes
- Prokaryotes bound thin films of sediment together
- Still formed today in shallow bays (ex: Shark Bay, Australia)
- Life likely arose approximately 3.9 bya
How Did Life Arise?
- Louis Pasteur: Life arises only by the reproduction of pre-existing life.
- Abiotic synthesis of small organic molecules- The joining of these small molecules into polymers/packaging molecules into “protocells”/origin of self-replicating molecules
Abiotic Synthesis of Organic Molecules
- Oparin and Haldane: Conditions on early Earth could have spontaneously generated organic molecules.
- Reducing atmosphere, energy from lightning, and intense UV radiation.
- Stanley Miller (1953): Tested this hypothesis, and identified several organic molecules.
- Additional hypotheses: Life may have begun in submerged volcanoes or deep sea hydrothermal vents/Meteorites were the source of Earth's first organic molecules.
Abiotic Synthesis of Polymers
- Present-day: Enzymes catalyze the joining of monomers.
- Experiment: Drip dilute solutions of monomers on hot sand, clay, or rock, heat vaporizes water, concentrating monomers, and allows for the formation of monomers in chains. Simulation of waves splashing monomers onto lava or hot rocks then into the sea
Formation of Protocells
- Small membrane-enclosed vesicles form when lipids are mixed with water.
- Clay is common in early earth = faster rate of vesicle formation from lipid + water
- Organic molecules concentrated on clay surface and vesicles grew and divided = reproduction.
- Vesicles can absorb clay particles
Self-Replicating RNA
- Short RNA molecules assemble spontaneously from nucleotide monomers.
- New RNA molecules are complementary to the starting molecule and can assemble.
- Ribozymes; RNA molecules that act as catalysts.
- RNA world: Hypothetical period where RNA served as both rudimentary genes and catalytic molecules.
- 2013: Researcher constructed a protocell enclosing self-replicating RNA
Conclusions
- 2013: Researcher constructed a protocell enclosing self-replicating RNA
- Natural selection would have shaped the properties of these protocells and early “genes.”
- Mutations would result in new variation.
- DNA replaced RNA as the repository of genetic information (More stable molecule).
Macroevolution
- Evolutionary change above the species level.
- Origin of new groups of organisms through speciation and mass extinctions.
- 4 eons of geologic time; Hadean, Archaean, Proterozoic, and Phanerozoic
- Origin of prokaryotes, oxygenation of the atmosphere, origin of single-celled eukaryotes, origin of multicellular eukaryotes, colonization of land, and the Cambrian explosion.
Major Events of Macroevolution
- Origin of Prokaryotes (3.9bya) - Origin of Single-celled eukaryotes - Origin of Multicellular eukaryotes - Colonization of land
- Major life changes during these eons, ex:
- Prokaryotic photosynthesis saturated the seas with oxygen
- Mass extinction of prokaryotes due to oxygenation
- Origin of cellular respiration
- Various events marking boundaries between geologic time eons
Radiometric Dating
- Calculate the age of rocks and fossils
- Radiometric dating: Based on the decay of radioactive isotopes (Half-life); The time required for 50% of the isotope in a sample to decay
- Example; C-14 dating (Useful for relatively young fossils, ex: Up to about 75,000 years old) /Potassium-40 dating (Used to date volcanic rock hundreds of millions of years old; half-life = 1.3 billion years).
- Date rocks above and below the fossil.
Diversity of Life - Prokaryotes
- Textbook chapter 16.1-16.11
Prokaryotic Cells
- No membrane-bound nucleus
- No membrane-bound organelles
- Much smaller than eukaryotes
- Found anywhere there is life
- Biomass of prokaryotes is 10X that of eukaryotes
- Metagenomics: Isolation and sequencing of DNA in environmental samples
- Microbiome; collection of genomes of all species in the environment
- Domains bacteria and archaea
Microbiota
- Community of microorganisms that live in and on our bodies
- Carry out various positive functions for our health
- Example; intestinal microbiota supply us with vitamins and aid in nutrient extraction from foods
- Microbiota guards against pathogenic intruders
- Pathogens; disease-causing agents
Prokaryotes in the Environment
- Decompose dead organisms and organic waste material
- Return vital chemicals to the environment(chemical cycling)
- Example; They make nitrogen available to plants and other organisms
Cell Shape
- Important for identifying bacteria
- Cocci (coccus); spherical - Streptococci, staphylococci.
- Bacilli (bacillus); rod-shaped
- Spirilla; short, rigid spirals
- Spirochete; longer more flexible spirals
Cell Wall
- Function, physical protection, protection from osmotic lysis
- Made from peptidoglycan in bacteria, different substance in archaea.
- Gram Stain: distinguish between Gram-positive and Gram-negative cells
- Gram-positive cells: thick cell wall- stains purple
- Gram-negative cells: thin cell wall sandwiched between cell membrane and outer membrane- stains pink
Capsule
- Sticky layer of polysaccharides and sometimes proteins
- Allows adherence to surfaces and other individuals in a colony
- Shields pathogenic prokaryotes from attacks by their host’s immune system
- Example: capsule of Streptococcus allows it to attach to respiratory tract cells
Prokaryotic DNA
- Chromosome; 1/1000 the size of eukaryotic genome, one long circular chromosome (All genes needed for survival under typical conditions)
- Plasmid; Small circular DNA molecules replicate independently of the chromosome carry genes that enhance survival (can be transferred)
Endospores
- Formed under harsh or unfavorable conditions
- A cell encloses a copy of its DNA inside a thick protective coat
- Endospore dehydrates to stop its metabolic activity
- When conditions improve, the endospore rehydrates and resumes growth
- Survive all kinds of conditions and persist in a dormant state for decades
- Very difficult to destroy
Nutritional Diversity
- Sources of energy
- Phototrophs; energy from sunlight
- Chemotrophs; energy stored in chemicals (organic; sugars, inorganic; H2S,S,Fe-compounds, NH3).
- Sources of Carbon
- Autotrophs; acquire carbon from inorganic sources
- Heterotrophs; obtain carbon from organic compounds.
Modes of Nutrition
- Photoautotrophs, photoheterotrophs, chemoautotrophs, chemoheterotrophs
Biofilms
- Highly organized colonies attached to surfaces (rock, soil, organic material, living tissue, metal, plastic, stagnant water)
- Formation- Prokaryotes secrete signaling molecules to attract cells into a cluster/Cells produce a substance that glues cells together/Members of the community coordinate division of labour, defense against invaders, and other activities/Channels allow import of nutrients and export of wastes
- Common in disease-causing bacteria (ex: ear infections, urinary tract infections, and pneumonia)
- Form on implanted devices (catheters, replacement joints, and pacemakers),
- Antibiotics often do not penetrate beyond the outer layer of cells
- Form in the environment (clog and corrode pipes, coat hulls of ships, and can even survive chlorination).
Bioremediation
- The use of organisms to remove pollutants (soil, air, or water).
- Prokaryotes are capable of degrading pollutants. (oil, solvents, pesticides)
- Workers use methods to speed up the activity of microbes (ex; spray chemical dispersants on oil spills to break it into smaller droplets that microbes can attack).
Wastewater Treatment
- Sewage passed through screens and shredders
- Solid material (sludge) settles out from liquid waste
- Sludge is added to a culture of anaerobic prokaryotes and microbes decompose the organic matter
- Liquid wastes are sprayed onto rocks covered in biofilm bacteria (which remove organic material)
- Outflow is sterilized and released into rivers or oceans
Prokaryotic Evolution
- First major split in history of life was the divergence of bacteria from other organisms.
- Later divergence separated archaea and eukarya.
- Archaea are more closely related to eukaryotes than to bacteria.
Archaea
- Abundant in many habitats, including the oceans
- Thrive in extreme environments (unusual proteins to adapt and survive.)
- Extreme halophiles; live in extreme salty conditions (Dead Sea, evaporating ponds)
- Extreme thermophiles; live in very hot water (deep-ocean vents, or acidic pools).
- Methanganogens; Live in anaerobic mud/swamp/landfills
- and make methane as a waste product.
Groups of Bacteria
- 5 groups based on comparisons of genetic sequences.
- Proteobacteria
- Gram-positive bacteria
- Cyanobacteria
- Chlamydias
- Spirochetes
Proteobacteria
- Gram-negative
- All 4 modes of nutrition are included.
- Chemoheterotrophs
- Photoautotrophs
- Photoheterotrophs
- Chemoautotrophs
- Can live symbiotically with eukaryotic hosts. (symbiosis/endosymbiosis).
Gram-Positive Bacteria
- High amount of diversity
- Actinomycetes (colonies of branched chains of cells found in soil that decompose organic matter.)
- Streptomyces (cultured by pharmaceutical companies for antibiotics).
- Pathogens such as Staphylococcus and Streptococcus, and Bacillus anthracis
Cyanobacteria
- Only group having plant-like oxygen-generating photosynthesis.
- Provide food for organisms in freshwater and marine ecosystems
- Some specialized cells that fix nitrogen
- Many symbiotic relationships (fungi, mosses).
- Endosymbiotic cyanobacteria are the origin of chloroplasts
Chlamydias
- Live inside eukaryotic host cells.
- Example; Chlamydia trachomatis; common cause of blindness in developing countries and non-gonococcal urethritis in the US.
Spirochetes
- Helical bacteria that spiral through their environment by rotating internal filaments.
- Example; Treponema pallidum(syphilis), Borrelia burgdorferi (Lyme disease)
Some Bacteria Cause Disease (Exotoxin)
- Exotoxins: Proteins that bacterial cells secrete into their environment.
- Ex. Staphylococcus aureus (commonly found on skin or nasal passages, causes disease if it enters through a wound. One exotoxin destroys
- white blood cells (e.g., MRSA). Foods can be contaminated with exotoxins that cause vomiting and diarrhea.)
Some Bacteria Cause Disease (Endotoxin)
- Endotoxins: Lipid component of the outer membrane of Gram-negative bacteria.
- Released when the cell dies or is digested by a defensive cell.
- Symptoms: fever, aches, and septic shock (drop in blood pressure).
Bacteria as Biological Weapons
- Due to their disease-causing potential
- Antibiotics can kill the bacteria but not eliminate the toxins already present in the body
- Highest priority threats
- Bacillus anthracis endospores, Clostridium botulinum exotoxin
Koch’s Postulates
- 4 postulates to identify a bacterium's role in a specific disease.
- Find the same bacterium in every case of the disease. Isolate the bacterium and grow it in pure culture. Show that the bacterium causes disease in a healthy subject. Re-isolate the bacterium.
- Example; Barry Marshall hypothesis : Helicobacter pylori causes inflammation of the stomach lining that causes ulcers/ swallowed and developed gastritis before curing it with antibiotics.
Stomach Microbiota
- Most strains of Helicobacter pylori do not cause ulcers—they are instead important members of our microbiota- Low levels of H. pylori continuous outputs hormone ghrelin; leads to overeating; Absence of H. pylori correlated to increased body mass index
Dating Fossils
- Determining the age of rocks and fossils ex: • C-14 (useful for relatively young fossils; up to 75,000 years old). • Potassium-40 (used to date volcanic rocks hundreds of millions of years old).
The Fossil Record
- Sequence in which fossils appear in rock strata.
- Archive of evolutionary history.
- Geologic record of Earth's history.
Hadean, Archaean, and Proterozoic Eons
- Hadean Eon; Earth's origin
- Archaean Eon; First life on earth; Prokaryotes, oxygenation of the atmosphere.
- Proterozoic Eon; First eukaryotes appeared in the fossil record, first unicellular and multicellular eukaryotes.
Phanerozoic Eon
- Divided into three eras (Paleozoic, Mesozoic, and Cenozoic)
- Each era is further divided into periods. Boundaries between eras are marked by mass extinctions, and boundaries between periods are often, but not always marked by lesser extinctions.
Adaptive Radiations (after mass extinction)
- Periods of evolutionary change; many new species evolve from a common ancestor.
- Mass extinctions
- Evolutionary innovation that allow a group of organisms to exploit an unused resource (ex: colonization of land- plants led to adaptive radiation of pollinators and herbivores).
- Evolution of a new group of organisms can cause the adaptive evolution of another new group of organisms.
Genes that Control Development (evo-devo)
- Evo-devo: interface of evolutionary biology and developmental biology.
- Slight genetic changes- magnified into major morphological differences between species.
- Genes that program development control the rate, timing, and spatial pattern of change in an organism's form as it goes from a zygote to an adult.
Changes in Rate and Timing of Developmental Events (Paedomorphosis and Examples)
- Paedomorphosis: The retention of juvenile features in the adult body. Example; Salamanders (aquatic larvae with gills → metamorphosis for lungs- but the axolotl retains gills and larval features as an adult.)
Changes in Spatial Patterns (Homeotic Genes and Examples)
- Homeotic genes determine where basic features will develop. Example; Tetrapods vs. snakes. One pattern of expression results in forelimb and rib formation, while a different pattern leads to rib formations without limbs.
New Genes and Changes in Genes and Gene Regulation
- Gene duplications give rise to mutations that result in the evolution of new genes. Example; evolution of vertebrates from invertebrates, changes in homeotic gene regulation allowed evolution of snakes, or three-spined stickleback fish in ocean vs. lakes in western Canada.
Novel Structures
- Process of refinement; complex structures evolve from simple structures with the same basic functions/Example; evolution of eyes (simple ancestral patches of photoreceptor cells/All animals with eyes have the same master genes for eye development), exaptations: structures evolve with function are co-opted for another function (natural selection improves existing structures in the context of current use; example- Evolution of feathers- a lineage of dinosaurs had feathers but could not fly initially/insulation (thermoregulation) and camouflage could have become the initial functions before long forelimbs with feathers evolved flight.)
Evolution is not Goal Directed
- Trends are not goals; ex: Evolution of horses; Hyracotherium- size of a large dog, front feet had 4 toes, and hind feet had 3; Modern horses (Equus)- larger, just one toe. Trend to larger, grazing, one toe. Reality; lineages with variations, however one did survive ex: Evolution through strong selection pressure for fast grazers—they lived in grasslands and had many predators.
Studying Evolutionary Trends
- Speciation
- Extinction
- New species diverge from their ancestral species
- Unequal survival of species & unequal generation of new species- The species that generates the greatest number of new species determines the direction of evolutionary trends.
Taxonomy
- Why do we need a scientific naming method for species?
- Ambiguity of common names
- Same common name may refer to different species in different regions. ex: Bluebells in Scotland, England, and Texas could mean different species. ex: fish often go by a common name that doesn't reflect their actual classification (ex; Jellyfish, Crayfish, and Silverfish).
Phylogeny
- Phylogeny; evolutionary history of a species/group of species.
- Systematics; classifying organisms and determining their evolutionary relationships
- Indicates the patterns of descent from the last common ancestor
- Phylogenetic trees; branching diagrams that reflect hierarchical classification of groups.
Constructing a Phylogenetic Tree
- Important features that result from common ancestry, morphological and molecular data, evidence from the fossil record.
Convergent Evolution
- Convergent evolution: Similar adaptations arise in unrelated organisms due to the need to adapt to similar environments.
- Analogy: Similarity due to convergent evolution. Example; Australian ‘mole’ and American mole—similarities came about as they adapted to a burrowing lifestyle.
Cladistics
- Method for constructing phylogenetic trees
- Cladistics; organisms are grouped by common ancestries.
- Clade; ancestral species and all its evolutionary descendants.
- Monophyletic; inclusive group
- Shared ancestral character; common to members of one clade but originated in a distant ancestor Example; mammals all have backbones
- Shared derived character; common to members of one clade, but not found in its ancestors.
Inferring Phylogeny using Outgroups and Ingroups
- Compares organisms based on the presence or absence of characters
- Outgroup; Species from a lineage that is closely related to a group of species being studied, but not part of the group being studied
- Ingroup; The group of species under investigation.
Parsimony
- The adoption of the simplest explanation—in phylogeny; phylogenetic trees should be constructed to have the smallest number of evolutionary branching points possible
- Example; likely that gestation evolved twice (unlikely that beavers are to kangaroos as closely—as to a platypus).
- Tree construction using computers and complex data.
Molecular Systematics
- Using DNA or other molecules to infer evolutionary relatedness
- Early impact of DNA analysis; determining domain level classifications (Previously there were five kingdoms).
- Example; Fungi are more closely related to animals than to plants.
- Genes that evolve slowly (Ex. rRNA) are used for broad classifications, while genes that evolve quickly (Ex. mtDNA) are used for narrow classification.
Genome Evolution
- Homologous genes can extend over great evolutionary distances ex. rRNA gene.
- Example; 99% of genes in humans and mice are homologous, 50% of human genes are homologous with yeast genes).
- Common feature; demonstrates that all living organisms share many biochemical and developmental pathways
- Gene duplications increase the number of genes, provides opportunities for evolutionary changes
- Molecular techniques trace when and where genes diverged
Molecular Clocks
- Molecular changes provide better time keeping than morphology changes.
- Example; sharks and tuna diverged 420 million years ago; dolphins and bats diverged 60 million years ago.
- Molecular clock; estimates time to accumulate given amount of evolutionary change using a constant rate of some genes (regions of genomes).
- Graph the number of nucleotide differences against the dates of evolutionary branching points known from the fossil record.
Other Examples of Molecular Clocks
- Example; When humans started wearing clothes (linked to the evolution of body lice that lives on human hair/clothing provide new habitats that lead to two different species- Head lice and body lice). Using divergence to estimate when humans started wearing clothes.
Constructing the Tree of Life
- Hypotheses are constantly being revised as new evidence evolves. -Example; lots of questions surrounding Protist classifications and whether or not they should be considered a single kingdom.
Horizontal Gene Transfer
- Genes are transferred from one genome to another through mechanisms such as plasmid exchange and viral infection, or the fusion of organisms
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Test your understanding of key concepts in biology, including the classification of living organisms, binomial nomenclature, and the scientific method. This quiz also covers differences between eukaryotic and prokaryotic cells, emergent properties, and the implications of horizontal gene transfer. Perfect for students studying biology at any level.