Biology Review: Structures, Systems, and Evolution

Organization of Life

Biological Learning Intentions
- Reviewing how organisms are organized from molecules to whole organisms provides an understanding of how internal structures and biological systems work in unison to sustain life.
Universal Characteristics of Life
- All living organisms display a defined set of fundamental characteristics:
  - Cellular Organization: All living entities are composed of one or more structural units known as cells.
  - Metabolism and Energy Processing: Organisms perform biochemical reactions to acquire, transform, and utilize energy for cellular work.
  - Homeostasis: Organisms maintain stable, regulated internal conditions despite fluctuating external environments.
  - Growth and Development: Organisms undergo structured increases in size, mass, and complexity according to instructions stored in genetic material.
  - Reproduction: Living beings possess the ability to produce new offspring, passing genetic traits down via sexual or asexual processes.
  - Response to Environmental Stimuli: Organisms detect and react to biological, chemical, or physical signals in their external or internal surroundings.
  - Evolutionary Adaptation: Populations undergo genetic changes over successive generations, resulting in traits that enhance survival and reproduction.
Non-Living Classification of Viruses
- Viruses are classified as non-living entities because they lack essential characteristics of life:
  - Acellular Structure: Viruses lack cellular organization, consisting only of a nucleic acid genome (DNA or RNA) wrapped inside a protein shell called a capsid, completely lacking plasma membranes, cytoplasm, and organelles.
  - Lack of Independent Metabolism: Viruses do not carry out metabolic reactions, do not generate ATP, and possess no ribosomes for protein synthesis.
  - Inability to Reproduce Independently: Viruses cannot reproduce without invading a host cell and hijacking its molecular machinery.
  - Absence of Homeostatic Maintenance: Viruses cannot regulate an internal biological environment or perform self-repair.
Ten Levels of Biological Organization
1. Biosphere: The global sum of all ecosystems on Earth, incorporating all regions where life exists.
2. Ecosystem: A biological community interacting with all nonliving physical and chemical elements in a specific area.
3. Community: All populations of different biological species inhabiting and interacting within a shared geographical area.
4. Population: A group of interbreeding individuals belonging to the same biological species living within a designated region.
5. Organism: An individual living entity made up of one or more cells.
6. Organ System: A coordinated group of organs that cooperate to perform major physiological bodily functions.
7. Organ: A specialized structural body unit composed of multiple tissue types working together to perform distinct functions.
8. Tissue: An organized group of specialized cells that share a similar structure and function together.
9. Cell: The fundamental, structural, and functional unit of all living organisms.
10. Organelle and Molecule: Subcellular structures that execute distinct cellular functions, composed of chemical structures made of bonded atoms.
Hierarchical Example using the Amazon Rainforest Biome
- Biosphere: The entire living zone of planet Earth.
- Ecosystem: The Amazon Rainforest, comprising biological organisms alongside nonliving elements like sunlight, rain, soil minerals, and atmosphere.
- Community: All interacting organisms in the rainforest, including jaguars, toucans, orchids, soil fungi, and bacteria.
- Population: All individual Jaguars (Panthera onca) inhabiting the Amazon basin.
- Organism: A single Jaguar (Panthera onca).
- Organ System: The cardiovascular system of the jaguar, responsible for oxygen and nutrient delivery.
- Organ: The jaguar's heart.
- Tissue: Cardiac muscle tissue composing the heart wall.
- Cell: A single cardiomyocyte (cardiac muscle cell).
- Organelle and Molecule: A mitochondrion inside the cardiomyocyte generating ATP, or actin and myosin protein molecules.

Cellular Structures and Taxonomy

Binomial Nomenclature and Scientific Naming
- Every biological species is assigned a distinct two-part scientific name:
  - Genus Name: Represents the taxonomic genus to which the organism belongs; it is always capitalized and italicized (or underlined).
  - Specific Epithet: Identifies the specific species within the genus; it is always written in lowercase and italicized (or underlined).
  - Example: Panthera onca (Jaguar) or Homo sapiens (Human).
The Three Domains and Six Kingdoms of Life
- Domain Bacteria:
  - Prokaryotic single-celled organisms lacking a defined membrane-bound nucleus.
  - Cell walls contain peptidoglycan.
  - Kingdom Eubacteria: Diverse, true bacteria including autotrophs and heterotrophs.
- Domain Archaea:
  - Prokaryotic single-celled organisms displaying distinct membrane biochemistry (ether-linked lipids with branched chains).
  - Cell walls lack peptidoglycan.
  - Kingdom Archaebacteria: Biochemical extremophiles and mesophiles capable of surviving unique biochemical conditions.
- Domain Eukarya:
  - Eukaryotic organisms possessing membrane-bound nuclei and compartmentalized organelles.
  - Kingdom Protista: Unicellular or simple multicellular eukaryotes that do not fit into plants, animals, or fungi (e.g., protozoa, algae).
  - Kingdom Fungi: Unicellular (yeasts) or multicellular (molds, mushrooms) heterotrophic organisms with chitin-based cell walls that absorb nutrients via extracellular digestion.
  - Kingdom Plantae: Multicellular autotrophic organisms with cell walls containing cellulose that execute photosynthesis using chlorophyll.
  - Kingdom Animalia: Multicellular heterotrophic organisms lacking cell walls that ingest food and digest it internally.
Cell Types: Eukaryotic vs. Prokaryotic Cells
- Definition of Eukaryotic Cells: Cells defined by the presence of a true, membrane-bound nucleus containing linear DNA, along with specialized membrane-bound internal organelles.
- Shared Characteristics between Eukaryotic and Prokaryotic Cells:
  - Enclosed by a plasma membrane composed of a phospholipid bilayer.
  - Contain semi-fluid cytosol / cytoplasm.
  - Utilize DNA as genetic material.
  - Contain ribosomes for protein synthesis.
  - Perform basic metabolic pathways (such as glycolysis).
- Key Differences:
  - Prokaryotic Cells: Lack a nucleus (DNA is localized in an non-enclosed nucleoid region); lack membrane-bound organelles; typically small ( $0.1\,\mu\text{m} - 5.0\,\mu\text{m}$ ); contain circular DNA; possess 70S ribosomes.
  - Eukaryotic Cells: Possess a membrane-enclosed nucleus; contain membrane-bound organelles (e.g., mitochondria, endoplasmic reticulum); typically larger ( $10\,\mu\text{m} - 100\,\mu\text{m}$ ); contain linear DNA bound to histone proteins; possess 80S ribosomes.
Common Eukaryotic Organelles and Functions
- Nucleus: Houses linear genomic DNA, directs protein synthesis via mRNA transcription, and contains the nucleolus for ribosome assembly.
- Ribosomes: Ribonucleoprotein structures responsible for protein translation.
- Rough Endoplasmic Reticulum (RER): Ribosome-studded membrane network involved in synthesizing, folding, and modifying proteins destined for membranes or secretion.
- Smooth Endoplasmic Reticulum (SER): Synthesizes lipids, metabolizes carbohydrates, detoxifies toxins and drugs, and stores calcium ions.
- Golgi Apparatus: Flattened membrane sacs that modify, package, sort, and route proteins and lipids received from the endoplasmic reticulum.
- Mitochondria: Double-membrane organelles that carry out cellular respiration to synthesize cellular energy (ATP).
- Peroxisomes: Metabolic vesicles that oxidize molecules, breaking down fatty acids and converting toxic hydrogen peroxide ( $H_2O_2$ ) into water and oxygen.
- Cytoskeleton: Network of microfilaments, intermediate filaments, and microtubules maintaining cell shape, enabling organelle movement, and facilitating cell division.
Plant Cells versus Animal Cells
- Plant Cell Structures (Absent in Animal Cells):
  - Cell Wall: Rigid structural wall outside the plasma membrane composed of cellulose, preventing osmotic lysis and offering support.
  - Chloroplasts: Double-membrane organelles containing thylakoids and stroma; site of photosynthesis.
  - Large Central Vacuole: Prominent membrane-bound sac maintaining cell turgor pressure and storing water, ions, and waste.
  - Plasmodesmata: Cytoplasmic channels through cell walls facilitating transport and communication between adjacent plant cells.
- Animal Cell Structures (Absent or Rare in Plant Cells):
  - Lysosomes: Hydrolytic enzyme-filled vesicles performing intracellular digestion and autophagy.
  - Centrosomes with Centrioles: Organelles organizing microtubule assembly during nuclear division.
  - Cilia and Flagella: Microtubule projections enabling motility or surface liquid movement.

Energy Transfer in Biological Systems

Energy Transfers in Plant and Animal Cells
- Two Major Energy Conversions in Plant Cells:
  1. Photosynthesis: Converts light energy into chemical energy stored in the bonds of glucose: $6CO_2 + 6H_2O + \text{light energy} \rightarrow C_6H_{12}O_6 + 6O_2$
  2. Cellular Respiration: Breaks down glucose in the presence of oxygen to release chemical energy stored as ATP: $C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \text{ATP}$
- Energy Reaction Present in Animal Cells:
  - Animal cells exclusively perform Cellular Respiration (they do not perform photosynthesis).
Energy Transfer Through Ecosystem Trophic Levels
- Energy flows unidirectionally through food chains and webs across trophic levels:
  - Primary Producers (Autotrophs): Capture light energy or inorganic chemical energy to synthesize organic molecules.
  - Primary Consumers (Herbivores): Ingest primary producers to obtain energy.
  - Secondary Consumers (Carnivores/Omnivores): Ingest primary consumers.
  - Tertiary Consumers: Ingest secondary consumers.
  - Decomposers / Detritivores: Break down dead organic material and metabolic waste, releasing inorganic nutrients back into the abiotic environment.
Energy Loss in Living Systems
- Energy transferred between biological trophic levels is inefficient.
- Energy that is "lost" during metabolic activities and cellular respiration is dissipated as heat energy (thermal energy).
- Approximately $10\%$ of energy is converted to biomass at the next trophic level, with $90\%$ lost as heat or expended on life operations.

Gene Expression and Inheritance

Genome Definition
- A genome is the complete set of genetic material (DNA sequence) present within a cell or organism.
Physical and Functional Nature of Genes
- Physical Definition: A gene is a specific sequence of nucleotides located at a precise locus on a DNA molecule.
- Functional Definition: A gene is the basic physical unit of heredity that contains instructional information needed to synthesize a functional molecular product (a polypeptide chain or functional RNA molecule).
Mechanism of Gene Expression
- Gene expression is the process by which genetic information encoded in DNA directs the synthesis of functional biochemical products: $\text{DNA} \xrightarrow{\text{Transcription}} \text{mRNA} \xrightarrow{\text{Translation}} \text{Protein}$
- Transcription converts DNA into messenger RNA inside the nucleus, and translation converts mRNA into functional amino acid sequences (proteins) at the ribosome.
Inheritance Across Generations
- Genes are replicated through DNA replication and passed to offspring during reproduction:
  - Asexual Reproduction: Genes are copied and passed via mitotic or binary division, producing genetically identical offspring (clones).
  - Sexual Reproduction: Specialized haploid gametes (sperm and egg) formed through meiosis fuse during fertilization, recombining genetic traits to generate genetically unique diploid offspring.

Ecological Systems and Feedback Regulation

Feedback Regulation Mechanisms
- Feedback regulation is a biological control mechanism where the accumulation of an end-product modifies the biological process that generates it.
- Negative Feedback:
  - A pathway where the end-product inhibits or slows down the initial steps of the process, counteracting changes to restore stability and maintain homeostasis.
  - Example: Blood glucose regulation. High blood glucose triggers insulin release to store glucose; low blood glucose causes insulin levels to drop.
- Positive Feedback:
  - A pathway where the end-product accelerates or amplifies the initial stimulus, driving the system further from its baseline toward a distinct completion point.
  - Example: Blood clotting or child labor. Uterine contractions stimulate oxytocin release, which causes stronger contractions until birth occurs.
Ecological Interactions in Ecosystems
- Biotic-Biotic Interactions (Organism-Organism):
  - Predation: Predators consuming prey species.
  - Competition: Organisms competing for finite resources like light, food, water, or territory.
  - Symbiosis: Mutualism (both species benefit), Commensalism (one species benefits, one is unaffected), and Parasitism (one species benefits at the expense of a host).
- Biotic-Abiotic Interactions (Organism-Environment):
  - Plants absorbing water and nitrates from soil and taking in atmospheric carbon dioxide.
  - Plants releasing oxygen gas during photosynthesis and transpiring water vapor into the atmosphere, altering local microclimates.

Evolutionary Mechanisms and Biological Diversity

Definition of Evolution
- Evolution is defined as the change in the genetic composition and allele frequencies of a biological population over successive generations.
- What changes from generation to generation: Allele frequencies, gene pool composition, and inherited trait distributions within a population over time.
Selection and Evolutionary Fitness
- Selection: The non-random process where specific phenotypes experience differential survival and reproductive success due to environmental pressures.
- Evolutionary Fitness: The measure of an individual's relative reproductive success—specifically, its ability to survive, mate, and produce viable, fertile offspring that contribute genes to the next generation.
Sources of Genetic Variety in Populations
1. Mutation: Random alterations in DNA nucleotide sequences, producing novel genetic alleles.
2. Sexual Reproduction / Genetic Recombination: Independent assortment of chromosomes, crossing over during meiosis, and random fertilization create new combinations of existing alleles.
3. Gene Flow: The transfer of genetic alleles between distinct populations due to the migration of individuals or movement of gametes.
Adaptation Definition
- An adaptation is an inherited structural, physiological, or behavioral trait that increases an organism's likelihood of survival and reproduction in a specific environment.
Natural Selection Definition
- Natural selection is the evolutionary process by which environmental pressures act upon heritable phenotypic variation in a population, causing individuals with advantageous traits to survive and reproduce at higher rates, thereby increasing the frequency of those traits in subsequent generations.
Phylogenetic Trees and the Tree of Life
- A phylogenetic tree (or Tree of Life) is a branching diagram representing hypotheses about the evolutionary relationships, common ancestry, and lineage divergences among biological species over time.
Unity versus Diversity in Evolution
- Unity: Refers to shared biochemical traits, universal genetic codes, and common cellular structures across living organisms, pointing to origin from a shared common ancestor.
- Diversity: Refers to the wide variety of specialized traits, biological body plans, and species resulting from natural selection adapting distinct lineages to different ecological niches.