SCIENCE

MODULE 1: INTRODUCTION TO BIOLOGY

1. What is Biology?

• Definition: Biology is the study of life.

• Etymology: Derived from the Greek words "Bio" (meaning life) and "logos" (meaning study).

• Origin of Life: It is believed that organisms spontaneously formed in the oceans during the first quarter of the 4.5-billion-year-old planet Earth (approximately 3.8 billion years ago).

2. Importance and Uses of Biology

• Understanding Life & Interactions: Helps understand every aspect of living organisms, their environment, and their dynamic interrelationships (coexisting, interacting, and interbreeding).

• Body & Behavior: Explains the functions/reactions of the human body, as well as individual similarities, differences, and behaviors in various situations.

• Environmental Survival: Explains how animals survive, respond, and interact in their environments.

• Population Demands: Helps respond to the demands of an increasing human population.

• Preservation: Provides biological processes to preserve endangered species and their environments.

• Core Impact Areas:

  • Explains changes in human bodies.

  • Shapes different careers.

  • Provides answers to large-scale problems.

  • Teaches concepts on basic living.

  • Helps answer fundamental questions about life.

  • Paves the way for scientific investigations.

3. Branches and Fields of Biology

A. Three Major Traditional Divisions

1. Zoology: The study of animals.

2. Botany: The study of plants.

3. Microbiology: The study of microorganisms.

B. Traditional Fields

• Taxonomy: Naming and classifying organisms.

• Cytology: Structures and functions of cells.

• Genetics: Heredity and genetic variation.

• Ecology: Relationships of organisms in their environment.

• Physiology: Parts and functions of living organisms.

C. Modern Fields

• Embryology: Formation and development of organisms.

• Morphology: Forms and structures of organisms.

• Evolution: Origin and differentiation of organisms.

• Biochemistry: Biochemical compositions of living things.

• Immunology: The immune system.

• Molecular Biology: Molecules that make up cells of living organisms.

• Genomics: Entire genetic material of an organism.

• Proteomics: Different proteins found in a living organism.

• Bioinformatics: Analyzing biological data using computer programs.

• Pharmacogenomics: How genes affect a person’s response to drugs.

• Synthetic Biology: Design of biological parts, devices, and systems.

• Systems Biology: Biological systems, behavior, and interactions of biological entities.

4. Biology as a Science (Two Main Approaches)

• Discovery-based Science: Relies mainly on verifiable observations, measurements, and learning by observing. It frequently leads to questions answered by hypothesis-based science.

• Hypothesis-based Science: Provides answers by means of experimentation and investigation using the Scientific Method.

The Scientific Method Steps

1. Observation: Noting details to clearly identify and define a problem.

2. Gather Data: Collecting initial information.

3. Hypothesis: A tentative, testable explanation, prediction, or intelligent guess regarding a problem.

4. Experimentation: Conducting controlled attempts to test a hypothesis. Includes recording data to justify or verify the hypothesis.

5. Analyze Data: Evaluating experimental findings.

6. Conclusion: Formulating a generalization that accepts, rejects, or modifies the initial hypothesis.

Scientific Method Example

• Problem: "How does the amount of daily sunlight exposure affect the growth height and fruit yield of tomato plants?"

• Observation: Tomato plants shaded by a large oak tree are shorter and have fewer tomatoes than plants getting direct sunlight all day.

• Hypothesis: If tomato plants are given 8 hours of direct sunlight daily, they will grow taller and produce more fruit than plants given 3 hours, because they require light for photosynthesis.

• Experimentation:

  • Independent Variable: Amount of daily sunlight (3 hours vs. 8 hours).

  • Dependent Variable: Plant height (cm) and number of tomatoes harvested.

  • Controlled Variables: Soil type, daily water (200 mL), tomato variety, pot size.

  • Procedure: Grow 10 identical seedlings (5 sunny, 5 shaded) for 6 weeks; measure height weekly and count total fruit.

• Conclusion: Hypothesis supported. Plants with 8 hours of sun averaged 45 cm in height and 12 tomatoes; plants with 3 hours of sun reached only 25 cm and 3 tomatoes.

5. Two Dimensions of Life’s Hierarchy

• Vertical Dimension: Hierarchical levels of biological organization spanning from the microscopic scale up to the entire global biosphere.

• Horizontal Dimension: Shows the diversity and richness of life by naming and classifying different organisms into Three Domains split into Six Kingdoms.

The Three Domains of Life

1. Domain Archaea

2. Domain Bacteria

3. Domain Eukarya

The Six Kingdoms of Life

1. Kingdom Archaea

2. Kingdom Eubacteria

3. Kingdom Protista

4. Kingdom Fungi

5. Kingdom Plantae

6. Kingdom Animalia

MODULE 2: LEVELS OF BIOLOGICAL ORGANIZATION

Life is structured in levels increasing in size and complexity:

$\text{Cell} \rightarrow \text{Tissue} \rightarrow \text{Organ} \rightarrow \text{Organ System} \rightarrow \text{Organism} \rightarrow \text{Population} \rightarrow \text{Community} \rightarrow \text{Ecosystem} \rightarrow \text{Biosphere}$

Microscopic & Organismal Levels

• Cell: The basic, microscopic unit of life (e.g., animal cell, plant cell).

• Tissue: A group of similar cells working together (e.g., muscle tissue, leaf tissue layers).

• Organ: A structure composed of tissues performing specific functions (e.g., a bone, a heart, a leaf).

• Organ System: A group of organs working together to perform complex functions (e.g., skeletal system, cardiovascular system, root/shoot systems).

• Organism: An individual living entity (e.g., a dog, a zebra, a tree, a frog).

Ecological Levels

• Population: A group of individuals belonging to the same species living in a specific area (e.g., a pack of dogs).

• Community: All the different interacting populations of various species living together in an area (e.g., dogs, birds, and grass interacting).

• Ecosystem: A community of living organisms interacting with their non-living physical environment (e.g., animals, plants, soil, water, and weather).

• Biosphere: The global ecological system integrating all living beings and their relationships; the living sphere of the entire world.

MODULE 3: THE CELL - HISTORY, THEORY, AND CLASSIFICATIONS

1. History of Cell Discovery

• Hans and Zacharias Jansen: Invented the microscope, marking the starting point of cell history.

• Robert Hooke ("The English Father of Microscopy"): Modified the microscope and discovered cells by examining a thin slice of cork. He noted that the cork structure resembled small rooms.

• Anton van Leeuwenhoek: A microscope maker who was the first to observe live microorganisms under a microscope.

  • Discovered "Animalcules" (known today as protozoa) in pond water and rainwater.

  • First to discover bacteria, protozoa, nematodes, rotifers, and many other microscopic organisms.

2. The Cell Theory

Developed by later scientists who expanded on early cell discoveries:

• Theodore Schwann (Zoologist): Discovered that animal tissues are composed of cells.

• Matthias Schleiden (Botanist): Concluded that all plant tissues are composed of cells.

• Rudolf Virchow: Studied the growth and development of cells and concluded that all cells arise from preexisting cells.

The Three Core Tenets of Cell Theory

1. All living organisms are composed of one or more cells.

2. Cells are the basic unit of structure and function of all organisms.

3. All cells arise only from preexisting cells.

3. Classifications of Living Organisms

Living things are classified based on cell structure complexity and cell quantity.

A. Prokaryotic vs. Eukaryotic Cells

• Prokaryotic Cells:

  • Simpler and smaller cells.

  • Lack membrane-bound organelles.

  • DNA is found in an unbound Nucleoid Region.

  • Generally single-celled organisms.

  • Examples: Bacteria, Blue-green Algae, and Archaeans.

• Eukaryotic Cells:

  • Larger, more complex cells.

  • Contain membrane-bound organelles and a true, distinct nucleus.

  • Can be single-celled or multicellular organisms.

  • Examples: Found in plants, animals, fungi, protozoa, and other complex organisms.

B. Unicellular vs. Multicellular Organisms

• Unicellular Organisms:

  • Consist of a single, independent cell.

  • Can be both prokaryotic or eukaryotic.

  • The single cell manages all vital life tasks, including feeding, waste removal, and reproduction.

  • Examples: E. coli bacteria, Amoeba, Paramecium, Chlamydomonas, and Yeast.

• Multicellular Organisms:

  • Composed of multiple cells.

  • All are exclusively eukaryotic.

  • Cells are highly specialized to form specific tissues, organs, and organ systems.

  • Examples: Humans, birds, dogs, insects, octopuses, petromyzons (lampreys), trees, and flowering plants.

MODULE 4: CELL STRUCTURES AND FUNCTIONS

Cells are the building blocks of life and vary in size, shape, and complexity. Below are the structures (organelles) and their functions:

1. Cell Membrane (Plasma Membrane)

• A double-layered membrane that encloses the cell.

• It is the outermost covering of animal cells.

• Functions: Serves as a selectively permeable barrier that regulates the entrance and exit of substances; provides protection; enables cell-to-cell recognition; acts as a filtration barrier.

2. Cytoplasm

• The largest part of the cell where most life processes occur.

• A semifluid matrix where organelles and cellular inclusions are suspended.

3. Nucleus

• The most visible, roughly spherical organelle, generally located at the center of eukaryotic cells.

• Functions: Controls all cell activities and serves as the storage site for hereditary factors (DNA).

4. Chromatin

• Made up of DNA and proteins.

• Functions: Forms distinct chromosomes during cell division.

• Note: Humans have 46 chromosomes total (22 pairs of autosomes and 1 pair of sex chromosomes).

5. Endoplasmic Reticulum (ER)

• A network of intercommunicating channels composed of membrane-enclosed sacs and tubules.

• Functions: Serves as an intracellular highway to transport molecules from one part of the cell to another.

• Two Types of ER:

  • Rough Endoplasmic Reticulum (RER): Appears rough due to the presence of ribosomes attached to its surface. Cells rich in RER produce large amounts of proteins to be inserted into or exported outside the membrane.

  • Smooth Endoplasmic Reticulum (SER): Tubular and nongranular due to the absence of ribosomes. It plays a major role in the manufacture and metabolism of lipids and assists in transporting large molecules inside the cell.

6. Golgi Apparatus

• A structure made of a stack of flattened sacs located close to the ER, surrounded by numerous fluid-filled vesicles.

• Functions: Responsible for processing, packaging, and sorting secretory materials for use within or outside the cell.

7. Vesicles

• Small fluid-filled structures that carry substances in and out of the cell.

• Functions: Facilitate the transport of food particles and materials needed by the cell.

8. Vacuoles

• Membrane-bound spaces used for the storage of water, food, enzymes, and other waste or essential materials.

9. Mitochondrion

• Known as the "Powerhouse of the cell".

• Functions: Contains enzymes that assist in the chemical oxidation of food molecules to produce energy in the form of Adenosine Triphosphate (ATP).

10. Ribosomes

• Composed of two organic compounds: proteins and RNA.

• Functions: Synthesis of proteins.

11. Lysosomes

• Small, spherical, membrane-bound organelles containing around 40 different types of digestive enzymes.

• Functions: Helps regulate and execute intracellular digestion and clean-up activities.

12. Centrosome and Centrioles

• Made up of a pair of centrioles.

• Functions: Assists in cell division by forming the Mitotic Spindle, which helps move chromosomes.

13. Cytoskeleton

• An internal framework that provides motility, resiliency, and structural strength for the cell against external forces.

• Composed of fibers, including:

  • Microtubules: Long, slender protein tubes made of linear polymers of tubulin. They maintain cell shape, form the cores of cilia and flagella (e.g., in sperm cells), and form spindle fibers during division.

  • Microfilaments: Help the cell maintain structure and shape, offering resilience against forces that alter its shape.

14. Plant-Specific Organelles

• Cell Wall: Located outside the cell membrane in plants; provides rigid shape and protection.

• Plastids / Chloroplasts: Double-membrane organelles found in plant cells. Chloroplasts contain green chlorophyll pigments and serve as the site of photosynthesis (food manufacturing).

• Peroxisomes: Structures containing enzymes that detoxify harmful substances and break down fatty acids.

• Crystalline Inclusions: Plants also contain specialized crystals like Raphide Crystals and Druse Crystals within their cells.

Organelle Presence/Absence Matrix

The differences between plant and animal cells include:

Special Prokaryotic Structures

Prokaryotes contain unique structural components distinct from eukaryotes:

• Nucleoid: The region where the cell’s circular DNA is located (unenclosed by a membrane).

• Cell wall: Formed of peptidoglycan in bacteria to provide shape and protection.

• Flagella: Tail-like structures used for movement (simpler structure than eukaryotic flagella).

• Pili: Hair-like surface structures used for attachment (adhesion) and genetic exchange.

• Plasmids: Small, circular DNA molecules that replicate independently of the primary chromosomal DNA.

MODULE 5: THE COMPOUND LIGHT MICROSCOPE

Cells vary from 0.001 mm to 0.1 mm in size, making light microscopes necessary to observe them up close by providing a magnified image.

1. Anatomy of a Microscope

The compound light microscope features 3 primary categories of parts:

A. Mechanical Parts

• Body Tube: A hollow tube that holds the eyepiece.

• Revolving Nosepiece: Holds and switches the objective lenses.

• Arm: Connects the base and the body tube together; used for carrying.

• Stage: The flat platform where slides or specimens are placed for examination.

• Stage Clips: Metal clips that hold the slide firmly in place on the stage.

• Base: Gives structural support to the whole microscope and serves as the attachment point for illuminators.

• Inclination Joint: A joint used for tilting the microscope back for comfortable viewing.

• Coarse Adjustment Knob: Rapidly moves the objective lens closer to or farther from the specimen to facilitate initial focusing.

• Fine Adjustment Knob: Slowly moves the lens to fine-tune focus and achieve optimal clarity and detail.

B. Illuminating Parts

• Mirror: Reflects light from surroundings up through the stage into the specimen.

• Condenser: Concentrates and focuses the light beams from the mirror/light source onto the specimen.

• Iris Diaphragm: Regulates the specific amount of light that reaches the specimen.

• Aperture: The opening that determines the ability to gather light and resolve fine specimen details.

C. Magnifying Parts

• Eyepiece (Ocular Lens): The lens through which an observer looks directly to view the specimen.

• Objective Lenses: The primary lenses that magnify the specimen. They include:

  • Scanning Objective Lens: $4\times$ magnification

  • Low Power Objective Lens: $10\times$ magnification

  • High Power Objective Lens: $4\times$ magnification

  • Oil-Immersion Objective Lens: $100\times$ magnification

2. Step-by-Step: How to Use a Microscope

1. Turn the light microscope on (or position the mirror to reflect ambient light up towards the eyepiece) and verify that the iris diaphragm/aperture is wide open.

2. Turn the revolving nosepiece until the lowest power objective lens points directly down.

3. Securely place your specimen slide onto the stage using the stage clips.

4. Look through the eyepiece and slowly rotate the coarse adjustment wheel to bring the specimen into general focus.

5. Slowly rotate the fine adjustment wheel until the specimen image reaches maximum clarity and detail.

6. Examine and explore the specimen, keeping it still or manually sliding it slowly with your thumbs.

7. Once centered and clear under low power, switch to medium or high-power objective lenses. Only use the fine adjustment wheel to bring the image back into focus under higher powers.

MODULE 6: NOTABLE BIOLOGISTS AND CONTRIBUTIONS

Historical International Biologists

• Louis Pasteur: Developed vaccines against anthrax, cholera, and rabies. He invented Pasteurization, a heating process that kills harmful microorganisms to safely ferment milk, beer, cheese, etc.

• Gregor Mendel ("The Father of Genetics"): Conducted experiments on pea plants that led to tracking and understanding the transmission of genes across generations (Mendelian Genetics).

• Charles Darwin ("The Father of Evolution"): Authored The Origin of Species by Means of Natural Selection. He studied living organisms at the Galapagos Islands (South America) to organize his findings into evolutionary theories.

• Carolus Linnaeus ("The Father of Taxonomy"): Invented the formal system used to name and classify living organisms. He introduced binomial nomenclature, which identifies every organism using two Latin or Latinized words.

• James Watson & Francis Crick: Elucidated the three-dimensional double-helix structure of DNA.

• Frederick Sanger & Walter Gilbert: Developed advanced DNA sequencing methods, leading to rapid gene mapping and discovery.

• Georges J.F. Köhler & César Milstein: Developed the laboratory process to mass-produce monoclonal antibodies, drastically transforming modern therapeutic and diagnostic medicine.

• Kary Mullis: Developed the Polymerase Chain Reaction (PCR) technique, a method used to produce millions of copies of specific DNA sequences for molecular research and genetic disease diagnosis.

Renowned Filipino Biologists

• Benjamin Cabrera: Extensively studied the biology and epidemiology (incidence, distribution, and control) of filarial parasites to establish treatment, diagnosis, and prevention protocols.

• William Padolina: A phytochemist and biotechnologist who advanced local research by isolating organic, natural chemicals from native plants.

• Clara Lim-Sylianco: Researched environmental mutagens, antimutagens, and bioorganic mechanisms. Her work extensively defined how mutagens (like UV light, X-rays, or chemical compounds) cause heritable mutations in cellular DNA, and her texts are widely used to teach biochemistry in local colleges.

• Quintin Kintanar: Evaluated molecular mechanisms regulating lipoprotein biosynthesis (the proteins that package and transport cholesterol and triglycerides through the bloodstream).

• Magdalena Cantoria: Conducted detailed research into the morphology, physiology, and biochemistry of local medicinal herbs, particularly mint and plants containing volatile oils and alkaloids.

• Paulo Campos ("The Father of Nuclear Medicine in the Philippines"): Constructed the nation’s very first radioisotope laboratory, making it possible to conduct basal metabolism testing and radioactive iodine therapies locally.

• Alfredo Santos ("The Father of Natural Products Research in the Philippines"): Devoted his career to isolating and studying therapeutic chemicals found within diverse medicinal plants native to the Philippines.

• Julian Banzon: Investigated agro-cultural wastes to extract alternative chemicals and green fuels. He pioneered methods capitalizing on the energy potential of local renewable products like coconut and sugarcane.

• Lourdes Cruz: Mapped out toxic peptides found in the venom of marine fish-hunting Conus snails. She turned these toxins into precise biochemical probes used to analyze human brain activity.