SCIE3005 Science II: Earth and Life Sciences Part I Study Guide

Objectives and Core Characteristics of Life

Learning Objectives: - Explain the basic characteristics of living things. - Identify the various levels of organization of living things. - Assess the importance of taxonomic classification. - Describe the characteristics of microorganisms, plants, and animals. - Explain why viruses and viral particles are not classified as living things.
Core Characteristics of Life: - All organisms must possess certain traits to be considered alive: - Composed of cells. - Grow and develop. - Regulate metabolic processes. - Respond to stimuli. - Reproduce. - Adapt to the environment.
GRIMNER Mnemonic for Life Processes: - G – Growth. - R – Reproduction. - I – Irritability (response to stimuli). - M – Movement. - N – Nutrition. - E – Excretion. - R – Respiration.

Cellular and Biological Organization

Cellular Basis of Life: - Every living organism is composed of one or more cells. - New cells are formed exclusively by the division of previously existing cells. - Unicellular life-forms: Consist of a single cell. - Multicellular organisms: Depend on the coordinated functions of cells organized into tissues, organs, and organ systems.
Internal Cell Structures: - Plasma membrane: Protects the cell and regulates the passage of materials between the cell and its environment. - DNA: Specialized molecules containing genetic instructions for transmitting genetic information. - Organelles: Internal structures specialized to perform specific functions.
Cell Types: - Prokaryotic cells: Exclusive to Bacteria and Archaea; structurally simple without a nucleus or membrane-bound organelles. - Eukaryotic cells: Contain a variety of organelles enclosed by membranes, including a nucleus that houses DNA.
Biological Growth and Development: - Biological growth: Defined as an increase in the size of individual cells, the number of cells, or both. - Development: Encompasses all changes that occur during an organism’s life.
Metabolism and Homeostasis: - Metabolism: Includes all chemical activities in an organism, such as nutrition-related reactions, growth and repair, and energy conversion. - Homeostatic mechanisms: Carefully regulate metabolic processes to maintain a balanced internal environment.
Responding to Stimuli: - Stimuli: Physical or chemical changes in the internal or external environment that cause movement/reaction. - Animals possess highly specialized cells to respond to specifics like light. - Plants respond to light, gravity, water, and touch.
Reproduction: - Asexual: Variation occurs only through mutations. - Sexual: Involves the fusion of egg and sperm.
Adaptation: - Inherited characteristics that enhance survival in a specific environment. - Types: Structural, physiological, biochemical, behavioral, or a combination.

Hierarchical Levels of Organization

Biological Levels: - Atoms and molecules form cells. - Cells associate to form tissues. - Tissues organize into functional structures called organs. - Organs function as organ systems (especially in animals). - Organ systems work together as a complex, multicellular organism.
Ecological Levels: - Population: All members of one species living in the same geographic area at the same time. - Community: Populations of various organisms interacting in a particular area. - Ecosystem: A community together with its nonliving environment.

Principles of Taxonomy and Systematics

Key Definitions: - Systematics: The study of the diversity of organisms and their evolutionary relationships. - Taxonomy: A subspecialty of systematics; the science of naming and classifying organisms. - Taxa (singular: Taxon): A group of organisms at a particular level in a classification system.
The Linnaean Binomial System: - Developed by Carolus Linnaeus in the $18^{th}$ century. - Each species has a two-part name (Scientific Name): - Genus: The first part, always capitalized. - Specific epithet: The second part, refers to a particular species within the genus, not capitalized. - The entire name is written in italics. - Examples: Canis familiaris (domestic dog), Canis lupus (timber wolf).
Species Concept: - A group of organisms with similar structure, function, and behavior capable of breeding with one another; shares a common gene pool and ancestry.
The Taxonomic Hierarchy: - Related genera are grouped into Families. - Families into Orders. - Orders into Classes. - Classes into Phyla (singular: Phylum). - Phyla into Kingdoms. - Kingdoms into Domains. - Inverse Relationship: As you move from species to domain, the number of organisms and diversity increases.

Historical Development and Current Classification

Timeline of Kingdoms: - Aristotle ( $2,000$ years ago): First classified organisms. - Until 1866: Only two kingdoms (Animalia and Plantae). - 1866: Single-celled organisms moved to Kingdom Protista. - 1938: Prokaryotes moved to Kingdom Monera. - 1959: Fungi moved to their own kingdom. - 1977: Kingdom Monera split into Kingdom Bacteria and Kingdom Archaea.
The Three-Domain Model: - Proposed by Carl Woese based on rRNA studies of prokaryotes. - Domains: Bacteria, Archaea, and Eukarya.
The Six-Kingdom System: - Animalia, Plantae, Fungi, Protista, Archaebacteria, Bacteria.

Classification Examples of Specific Organisms

Human (Homo sapiens): - Domain: Eukarya - Kingdom: Animalia - Phylum: Chordata - Class: Mammalia - Order: Primates - Family: Hominidae - Genus: Homo - Species: Homo sapiens
Cat (Felis catus): - Domain: Eukarya - Kingdom: Animalia - Phylum: Chordata - Class: Mammalia - Order: Carnivora - Family: Felidae - Genus: Felis - Species: Felis catus
White Oak (Quercus alba): - Domain: Eukarya - Kingdom: Plantae - Phylum: Anthophyta - Class: Eudicotyledones - Order: Fagales - Family: Fagaceae - Genus: Quercus - Species: Quercus alba
Eastern Gray Squirrel (Sciurus carolinensis) Hierarchy: - Eukarya -> Animalia -> Chordata -> Subphylum Vertebrata -> Mammalia -> Rodentia -> Sciuridae -> Sciurus -> Sciurus carolinensis.

Viruses and Subviral Agents

Status of Viruses: - Discovered by Martinus Beijerinck ( $1898$ ). - Viewed as nonliving particles because they are not cellular, cannot carry on metabolic activities independently, and cannot reproduce without a host. - Defined as obligate intracellular parasites.
Structure and Size: - General size: $20$ to $300\,nm$ . - Giant viruses: Mimivirus, Megavirus, and Pandoraviruses (up to $1\,μm$ ). - Consist of a nucleic acid core (DNA or RNA, single or double-stranded) surrounded by a protein coat called a capsid. - Genome size: $5,000$ to over $100,000$ bases. - Capsid: Made of subunits called capsomers, determining shape (helical, polyhedral, or complex).
Enveloped Viruses: - HIV is an example; it is surrounded by an outer envelope of plasma membrane derived from the host. - HIV produces proteins that extend out as spikes to interact with host cells.
Viral Classification: - Not in the three domains. - Classified by host range, size, shape, envelope presence, and transmission method. - Systems: ICTV and the Baltimore classification system.
Bacteriophages: - Viruses that infect bacteria. - Structure: Polyhedral head with coiled nucleic acid and a tail for penetration. - Historically used for phage therapy; research is resurfacing in the U.S. as an alternative to antibiotics.
Viral Replication Cycles: - Lytic and Lysogenic cycles.
Subviral Agents: - Satellites: Depend on a helper virus for co-infection (e.g., Hepatitis D requires Hepatitis B). - Viroids: Very short, circular, single-stranded naked RNA ( $250$ to $400$ nucleotides). No protein coat. Infect plants (e.g., potato spindle tuber viroid) by silencing host genes through siRNAs. - Prions: "Proteinaceous infectious particles" discovered by Stanley Prusiner ( $1982$ ). Misfolded proteins (PrP) that induce other proteins to misfold. Cause Transmissible Spongiform Encephalopathies (TSEs) like CJD, Mad Cow disease, and Scrapie.

Domain Prokaryota: Bacteria and Archaea

General Characteristics: - Discovered by Anton van Leeuwenhoek ( $1674$ ). - Approximately $\frac{1}{10}$ the size of eukaryotic cells.
Domain Archaea: - Cell walls lack peptidoglycan; possess unusual lipids and rRNA. - Methanogens: Reduce $CO_2$ to methane using hydrogen gas. - Extremophiles: Thermophiles (heat), Halophiles (salt), pH tolerant, Pressure tolerant. - Nonextreme archaebacteria: Grow in standard environments.
Domain Bacteria: - Most abundant organisms on Earth. - Shapes: - Cocci (Spherical): Singly, diplococci (pairs), streptococci (chains), staphylococci (clumps). - Bacilli (Rod-shaped): Single or chains. - Spirals: Spirochete (flexible), spirillum (rigid), or vibrio (comma-shaped). - Cell Structure: Peptidoglycan cell wall, capsules, fimbriae (attachment), flagellum (movement), nucleoid area (DNA), and plasmids (extra circular DNA).

Kingdoms Fungi, Protista, and Plantae

Kingdom Fungi: - Characteristics: Eukaryotic, heterotrophic (saprophytes/decomposers, symbionts, or parasites), non-motile, cell walls made of chitin. - Body Forms: Unicellular (yeast), filamentous (hyphae), aggregate of hyphae (mycelium), hardened mass (sclerotium). - Phyla: - Zygomycota (Bread Molds: Rhizopus). - Oomycota (Water Molds: Blight, Mildew). - Ascomycota (Sac Fungi: Yeast, Truffles). - Basidiomycota (Club Fungi: Mushrooms, Rusts). - Deuteromycota (Fungi Imperfecti: Penicillium).
Kingdom Protista: - Eukaryotes that are NOT fungi, plants, or animals. Mostly unicellular. Can be autotrophic or heterotrophic.
Kingdom Plantae: - Characteristics: Eukaryotic, non-motile, photosynthetic (chlorophyll in chloroplasts), cell walls made of cellulose, usually contain a large central vacuole. - Diversity: Found on land and water; ranges from microscopic phytoplankton to large trees (Samaan). - Classification: - Nonvascular (Bryophytes): Mosses, Liverworts, Hornworts. - Vascular: - Seedless: Ferns, Club mosses. - Seed-bearing: Gymnosperms (naked seeds on cones) and Angiosperms (covered seeds in flowers/ovaries). - Angiosperms are divided into Monocots and Dicots.

Kingdom Animalia

General Characteristics: - Eukaryotic, motile, consumers (take food from others), lack chlorophyll and cell walls. Highly developed endocrine and nervous systems.
Invertebrates ( $97\%$ /Over $90\%$ of animals): - No backbone. Diverse sizes from microscopic to Giant Squid. - Groups: Porifera (Sponges), Cnidaria (stinging cells), Echinoderms (spiny-skinned/starfish), Mollusks (soft-bodied/snails), Arthropods (exoskeleton/jointed legs), Annelids (segmented worms), Flatworms. - Symmetry: Radial or Bilateral.
Vertebrates (Less than $10\%$ / $3\%$ of animals): - Possess a backbone and a head with sense organs. - Closed circulatory system (red/white cells). - Classes: - Mammals: Fur/hair, warm-blooded, feed young milk. - Birds: Feathers, wings, beaks, eggs, warm-blooded. - Reptiles: Dry scaly skin, eggs on land, cold-blooded. - Amphibians: Moist skin, eggs in water, cold-blooded. - Fish: Scales, gills, cold-blooded.

Questions & Discussion

Breakout Room 1: Describe problems encounterable if living things were not classified (e.g., an uncatalogued library). State at least $4$ advantages of classification. - Key takeaway: Classification allows for easier identification, shows relationships, provides universal nomenclature, and aids in organizing vast biological information.
Breakout Room 2: Discuss advantages and disadvantages of Viruses, Bacteria, and Fungi.
Spread of Disease: - Bacteria/Viruses: Most common agents; spread via air, droplets, or contact. - Fungus: Spreads in warm/damp areas via spores or skin contact. - Protozoa: Spread via contaminated food or vectors (e.g., mosquitoes/malaria). - Helminthes: Parasitic worms from undercooked meat. - Prions: Mutated proteins via infected tissue.
Differences Between Bacteria and Viruses: - Bacteria: Living cells, cell wall, can reproduce outside host, killed by antibiotics. - Viruses: Not cells, nucleic acid in protein coat, obligate parasites, not killed by antibiotics.