Introduction to Living Organisms – Study Notes (Biology 2E Chapter 1)
The Hierarchy of Life
Biology has many different levels of organization, from the smallest units to the largest ecosystems:
Atomic
Molecular
Macromolecules
Organelle
Cellular
Tissue
Organ
Organismal
Population
Community
Ecosystem
Biosphere
Concept: larger to smaller and smaller to larger perspectives depending on context; the hierarchy helps in selecting a research focus.
Career note: if you plan a career in life sciences, you may develop a preference for which organizational levels you work with.
What does it mean to say that something is alive? The Three Domains of Life
Opening question: What does it mean for an entity to be alive?
The Three Domains of Life (taxonomy framework): Bacteria, Archaea, Eukarya.
Implication: life is organized into large, evolutionarily related groups; the domain classification reflects differences in cellular structure, metabolism, and genetics.
Five Fundamental Characteristics of Life
All living organisms share five fundamental characteristics:
1) Energy
All organisms acquire and use energy.
Why do organisms need energy? To power metabolism, growth, movement, and maintenance of order.
If an organism cannot acquire or use energy, life processes fail and the organism dies.
2) Cells
All organisms are made up of membrane-bound cells.
Sizes and examples discussed include a bacterial cell; consideration of actual sizes and how to determine them from figures; relative sizes between cell types.
3) Replication
All organisms are capable of reproduction.
Modes: sexual reproduction; asexual reproduction (e.g., mitosis-based growth); bacterial fission.
Examples shown include sea urchin, Daphnia, Komodo dragon, spider plant runners; meiosis forms egg or sperm cells.
4) Evolution
Populations continually evolve through natural selection in response to changing environmental conditions.
Mechanisms:
Heritable traits are passed on (e.g., snail shell pattern).
Variants arise due to random mutations in the genetic code leading to different trait expressions.
Certain variants are more optimal under specific environmental conditions.
More individuals with the optimal trait survive and have offspring.
Over long periods, most individuals in the population carry the optimal trait.
The process explains adaptation and diversity across generations.
5) Information
Organisms use hereditary information encoded in genes (DNA/RNA sequences) and respond to environmental information via receptors and sensors.
Example: plant responses to light involve auxin-mediated gene expression and growth changes.
Auxin example (summary): directional light causes auxin to migrate toward the shaded side, stimulating cell growth and elongation, bending the plant toward the light.
Cells and Size
Core statement: All organisms are made up of membrane-bound cells.
Key questions raised:
What are the actual sizes of these cells?
How can you determine this from figures?
What are the relative sizes of these cells compared to each other?
Visual scale and examples:
Bacterial cell is given as a reference example of a small cellular organism.
The slide emphasizes comparing sizes across different cell types.
Observing organisms and their components:
Viruses are smaller than most cells; bacteria are smaller than many plant/animal cells.
Scale from 0.1 nm to 1 m to place atoms, molecules, organelles, cells, and larger organisms on a single continuum:
Scale progression examples include: atom → amino acid → protein → chloroplast → plant/animal cells → mouse → rose → frog egg → virus → most bacteria → human egg → ant → ostrich egg → human eye.
Observation methods:
Electron microscope for nanoscale structures (e.g., virus particles, proteins).
Light microscope for cellular-scale observation.
Representative size markers (conceptual):
0.1\ ext{nm} \le \text{size} \le 1\ \text{m} across the spectrum from atoms to meters.
Typical scale labels include: 0.1\ \text{nm},\ 1\ \text{nm},\ 10\ \text{nm},\ 100\ \text{nm},\ 1\ \mu\text{m},\ 10\ \mu\text{m},\ 100\ \mu\text{m},\ 1\ \text{mm},\ 1\text{ cm},\ 0.1\ \text{m},\ 1\ \text{m},\ 10\ \text{m},\ 100\ \text{m},\ 1\ \text{km}
Platforms shown:
Electron microscope vs light microscope as tools for exploring structures at different scales.
Viruses: Structure and Common Features
What are viruses? Do viruses have cells?
Viruses are acellular particles; they do not have cells.
Three things ALL viruses have in common:
A genome made of either RNA or DNA (not both in the same virion) — genetic material is essential for replication.
A protein coat called a capsid that encases the genome.
Some viruses have a membranous envelope derived from host cell membranes; others are non-enveloped.
Examples with sizes (as depicted in the slides):
Tobacco mosaic virus: 18 \times 250\ \text{nm}
Adenoviruses: 70-90\ \text{nm} \text{ (diameter)}
Influenza viruses: 80-200\ \text{nm} \text{ (diameter)}
Bacteriophage T4: 80 \times 225\ \text{nm}
Notes:
Viruses vary widely in morphology (rod-like, icosahedral, tailed, etc.) but share the three core features above.
They require host cells to replicate, since they lack the full cellular machinery of life.
How Biologists Observe Organisms, Cells, Organelles, and Molecules
The scale of observation spans from atoms to whole organisms.
Two main microscope types:
Electron microscope (high resolution, for nanoscale objects such as viruses and macromolecules).
Light microscope (suitable for cells and many organelles).
Relative positions along the size spectrum:
From atoms and small biomolecules up to cells and organisms, all can be placed on a common scale with labeled examples.
Practical takeaway:
Understanding size informs which visualization method to use and what kind of data (structure, organization) can be observed.
Replication (Reproduction) in Living Systems
Central idea: All organisms reproduce to pass on genetic information.
Modes of reproduction:
Asexual reproduction: typically via mitosis in eukaryotes or binary fission in prokaryotes.
Sexual reproduction: involves meiosis to form eggs and sperm, followed by fertilization.
Examples mentioned:
Sea urchin (sexual reproduction)
Daphnia (able to reproduce sexually or asexually)
Komodo dragon (can reproduce via parthenogenesis in some cases)
Spider plant sprouting runners (asexual reproduction via vegetative propagation)
Key terms:
Mitosis: cell division producing two genetically identical daughter cells (used in asexual growth).
Meiosis: cell division producing haploid gametes (egg/sperm).
Evolution
Core idea: Populations evolve through natural selection in response to changing environments.
Conditions for evolution via natural selection:
Heritable traits are passed on to offspring (genotypes expressed as phenotypes).
Variation exists in traits due to mutations in the genetic code, leading to different expressions of traits (e.g., shell patterns).
Some trait variants are more fit in a given environment, leading to differential survival and reproductive success.
Over many generations, the frequency of advantageous traits increases in the population, changing the population.
Darwin’s Finches (Galápagos) as a classic example:
Ancestral finch species arrived from the mainland with medium beak size and shape.
Islands have different vegetation and food sources (cacti, low brush, grasses, seeds, insects).
Individuals with beak sizes/shapes best suited to available food survive and reproduce more, spreading those traits.
Over time, island-specific finch populations diverged, resulting in multiple distinct species on different islands.
Current understanding: 13 distinct species across the Galápagos islands.
Resource: HHMI BioInteractive video titled “Galapagos Finch Evolution.”
Summary of natural selection and evolution (reframed):
Environmental conditions drive differential survival and reproduction based on genetic diversity.
NS acts on individuals; evolutionary change occurs in populations over generations.
Therefore, adaptation and diversification are population-level processes, not individual changes.
Information and Plant Responses to Stimuli
Information in biology is twofold:
Hereditary information encoded in genes (genetic information).
Environmental information processed by receptors and sensors, leading to responses to stimuli.
Example: Plant response to directional light via auxin:
Light from one direction causes auxin to accumulate on the shaded side of the plant tip.
Auxin stimulates gene expression that increases rate of cell replication and cell elongation on the shaded side.
Result: bending toward the light source (phototropism).
The auxin gradient is central to directional growth and shape changes.
Examples of Plant Responses to Stimuli
Helio- and phototropism:
Young sunflowers move to face the sun during the day, tracking the sun across the sky.
They typically move from east to west and then back to east in the morning, governed by internal circadian rhythms and hormone signaling.
Mechanistic note: internal clocks coordinate growth responses with environmental cues to optimize light capture.
Three Central, Unifying Ideas in Biology
1) Cell Theory
The cell is the fundamental structural unit of life.
All cells arise from pre-existing cells (no spontaneous generation in modern biology).
2) Theory of Evolution
All species are related by common ancestry.
Species change over time in response to natural selection and other evolutionary forces.
3) Chromosome Theory of Inheritance
Cells store hereditary information on chromosomes.
Chromosomes contain regions of DNA called genes that encode information for specific traits.
Inherited traits are passed on to offspring during reproduction.