Foundations of Life, Viruses, and Evolution: Study Notes

What is Life?

Properties of Life

Living organisms share a set of fundamental characteristics that distinguish them from non-living matter. These properties are used to classify entities as living or non-living.

• Order: Living things exhibit complex but ordered organization, from molecules to entire organisms.

• Reproduction: The ability to produce new individuals, either sexually or asexually.

• Growth and Development: Organisms grow and develop according to specific instructions coded in their DNA.

• Energy Processing: Living things acquire and use energy for metabolic processes.

• Response to Environment: Organisms respond to environmental stimuli.

• Regulation (Homeostasis): Maintenance of internal stability despite external changes.

• Evolutionary Adaptation: Populations evolve over generations through adaptations that enhance survival and reproduction.

Cell Theory

The cell theory is a foundational concept in biology, stating that:

• All living things are composed of one or more cells.

• The cell is the basic unit of structure and function in living organisms.

• All cells arise from pre-existing cells.

This theory highlights the importance of cells as the fundamental building blocks of life.

Biological Organization and Hierarchy

Biological systems are organized in a hierarchy from smallest to largest:

• Cells → Tissues → Organs → Organisms → Populations → Communities → Ecosystems

Cells interact with both biotic (living) and abiotic (non-living) factors in their environment.

Types of Cellular Organization

• Unicellular: Organisms made of a single cell (e.g., Escherichia coli).

• Colonial: Groups of identical cells living together, often with limited specialization (e.g., Volvox).

• Multicellular: Organisms composed of many specialized cells (e.g., humans, plants).

Reproduction: Sexual vs. Asexual

• Sexual Reproduction: Involves two parents and the combination of genetic material, increasing genetic diversity (e.g., mammals, flowering plants).

• Asexual Reproduction: Involves a single parent and produces genetically identical offspring (e.g., bacteria by binary fission, hydra by budding).

Benefits: Sexual reproduction increases variation; asexual reproduction is faster and requires less energy.

Energy and Carbon Sources

• Photoautotrophs: Use light as an energy source and CO2 as a carbon source (e.g., plants, cyanobacteria).

• Chemoheterotrophs: Obtain energy and carbon from organic compounds (e.g., animals, fungi).

• Mixotrophs: Can use both autotrophic and heterotrophic modes of nutrition (e.g., Euglena).

Metabolism

Metabolism is the sum of all chemical reactions in an organism. It includes:

• Anabolism: Building up complex molecules (requires energy).

• Catabolism: Breaking down molecules to release energy.

Homeostasis and Feedback Loops

Homeostasis is the maintenance of a stable internal environment. It is regulated by feedback loops:

• Negative Feedback: Reduces the effect of a stimulus (e.g., body temperature regulation).

• Positive Feedback: Amplifies a response (e.g., blood clotting, childbirth contractions).

Responses in Plants and Animals

• Movement: Animals move using muscles; plants may move via growth (phototropism).

• Communication: Animals use nervous and endocrine systems; plants use chemical signals.

• Defense: Animals have immune responses; plants produce defensive chemicals.

• Reproduction: Animals may have complex behaviors; plants use pollination and seed dispersal.

Central Dogma of Molecular Biology

The central dogma describes the flow of genetic information:

• DNA → RNA → Protein

Genes are transcribed into messenger RNA, which is then translated into proteins.

Organismal Hierarchy (Smallest to Largest)

• Atom → Molecule → Organelle → Cell → Tissue → Organ → Organ System → Organism → Population → Community → Ecosystem → Biosphere

Evolution and Adaptation

• Evolution: Change in the genetic composition of a population over generations.

• Adaptation: A heritable trait that increases an organism's fitness in a particular environment.

• The central dogma links genetic changes (mutations) to new proteins, which can lead to adaptations.

Types of Adaptations

• Morphological: Physical features (e.g., beak shape in birds).

• Behavioral: Actions or behaviors (e.g., migration patterns).

• Physiological: Internal processes (e.g., ability to produce antifreeze proteins).

Acclimation vs. Adaptation

• Acclimation: Short-term physiological adjustment to a new environment (not heritable).

• Adaptation: Long-term genetic change in a population (heritable).

Fitness and Adaptations

• Fitness: The ability of an organism to survive and reproduce in its environment.

• Individuals with beneficial adaptations are more fit and more likely to pass on their genes.

Emergent Properties

Emergent properties are new characteristics that arise at each level of biological organization, not present at the preceding level (e.g., consciousness in brains, life in cells).

Viruses

Are Viruses Cells?

• Viruses are not considered cells. They lack cellular structure and do not carry out metabolism independently.

• Viruses consist of genetic material (DNA or RNA) enclosed in a protein coat; some have lipid envelopes.

• Prokaryotic cells (e.g., bacteria) and eukaryotic cells (e.g., animal, plant cells) have complex structures and can reproduce independently.

Properties of Life in Viruses

• Viruses exhibit some properties of life (e.g., reproduction, evolution) only when inside a host cell.

• They do not metabolize or maintain homeostasis independently.

Types of Viruses

• DNA Viruses: Use DNA as genetic material (e.g., herpesvirus).

• RNA Viruses: Use RNA as genetic material (e.g., influenza, HIV).

• Lytic Cycle: Virus replicates rapidly, destroying the host cell.

• Lysogenic Cycle: Viral DNA integrates into host genome and can remain dormant before activating.

Vaccination and Viral Evolution

• Some viruses (e.g., measles) are genetically stable, so one vaccine provides long-term protection.

• Others (e.g., influenza) mutate rapidly, requiring annual vaccines.

Pattern and Process of Evolution

Modern Phylogeny vs. Historical Classification

• Historical: Aristotle and Linnaeus classified organisms based on observable traits.

• Modern Phylogeny: Uses molecular (DNA, protein) and morphological data to infer evolutionary relationships.

Pattern vs. Process of Evolution

• Pattern: The observable outcomes of evolution (e.g., diversity of life, phylogenetic trees).

• Process: The mechanisms that drive evolution (e.g., natural selection, gene flow).

Evolutionary Mechanisms

• Natural Selection: Differential survival and reproduction of individuals due to differences in phenotype.

• Gene Flow: Movement of genes between populations.

• Genetic Drift: Random changes in allele frequencies, especially in small populations.

• Mutations: Changes in DNA sequence, introducing new genetic variation.

Phylogeny and the Tree of Life

Binomial Nomenclature

• Scientific names use a two-part format: Genus species (e.g., Homo sapiens).

• Genus is capitalized; species is lowercase; both are italicized.

Linnaeus’ Hierarchy and Modern Phylogeny

• Linnaeus’ system: Kingdom, Phylum, Class, Order, Family, Genus, Species.

• Modern phylogeny incorporates genetic and morphological data to refine relationships.

Types of Phylogenetic Trees

• Rooted Tree: Shows a common ancestor.

• Unrooted Tree: Shows relationships without a common ancestor.

• Cladogram: Branching diagram showing relationships based on shared characteristics.

• Phylogram: Branch lengths represent evolutionary change.

• Dendrogram: General term for tree diagrams.

Building Parsimonious Trees

• Use shared, derived characteristics (synapomorphies) to build the simplest tree (fewest evolutionary changes).

Phylogenetic Tree Terminology

Term	Definition
Node	Common ancestor
Branch	Lineage
Sister Group	Closest relatives on the tree
Clade	Group including ancestor and all descendants (monophyletic)
Outgroup	Taxon outside the group of interest
Ingroup	Group of interest
Monophyletic	Includes ancestor and all descendants
Paraphyletic	Includes ancestor and some, but not all, descendants
Polyphyletic	Does not include the most recent common ancestor

Extinct vs. Extant Taxa

• Extinct: No longer living.

• Extant: Still living today.

Interpreting Phylogenetic Trees

• Analyze branching patterns to infer relationships and shared characteristics.

• Divergent evolution: Two species evolve from a common ancestor.

• Convergent evolution: Unrelated species evolve similar traits independently.

Phylogenies as Hypotheses

• Phylogenetic trees are graphical hypotheses about evolutionary relationships, subject to revision as new data emerge.