Comprehensive Biological Science Notes

History of Science

  • Discipline studying the development and evolution of scientific knowledge and practices.
  • Explores modern and premodern scientific traditions, including non-Western systems.
  • Interdisciplinary: intersects humanities and natural sciences.

Biology

  • Bio: life
  • Logos: study
  • Biology: the study of life

Characteristics of Living Things

  1. Cells: Living things are made of cells.
  2. Reproduction:
    • Sexual: fusion of two gametes.
    • Asexual: no fusion of gametes.
  3. Universal Genetic Code: Based on DNA.
  4. Growth and Development: Increase in size and change in form/function via a life cycle, guided by DNA.
  5. Materials and Energy: Utilize chemical reactions (metabolism).
    • Anabolism: Building up.
    • Catabolism: Breaking down.
  6. Response to Environment: Detect and respond to stimuli (light, sound, temperature, touch).
  7. Homeostasis: Maintain a stable internal environment.
    • Example: Regulating body temperature and pH.
  8. Adaptation Through Evolution: Changes over generations for survival and reproduction, driven by natural selection.
  9. Movement: Exhibit some form of movement.

Scientific Methods

  1. Problem/Question
  2. Observation/Research
  3. Formulate a Hypothesis
  4. Experiment
  5. Collect/Analyze Results
  6. Conclusion
  7. Communicate the Results

Precautionary Measures Inside Lab

  1. Wear Proper Personal Protective Equipment (PPE)
  2. Know the Safety Equipment
  3. Handle Chemicals Safely
  4. Label and Store Materials Properly

Microscope

  • Tool to magnify objects.

Compound Microscope

  • Uses two or more lenses to produce a magnified image.
Basic Principles
  1. Magnification: Ability to make small objects appear larger.
  2. Resolution: Ability to distinguish two objects from each other.
Parts of the Microscope
  1. Magnifying Parts
  2. Mechanical Parts
  3. Illuminating Parts

*Anton Van Leeuwenhoek - father of microscopy
First Microscope Invented by Hans and Zacharias Janssen

Magnifying Parts
  1. Ocular or Eyepiece:
    • Used to look through.
    • Magnifies image (10x or 15x).
  2. Objective Lenses:
    • Primary lenses for magnification (4x, 10x, 40x, 100x).
    • Types:
      • Low Power Objective (LPO)
      • High Power Objective (HPO)
    • 10x: low-power lens for locating specimen.
    • 40x: high-power lens for wet preparations (e.g., hanging drop, ova and cyst examination).
    • 100x: oil-immersion lens (requires oil).
Mechanical Parts
  1. Draw Tube: Holds the ocular.
  2. Body Tube: Connects eyepiece to objective lenses.
  3. Revolving Nosepiece: Rotates to change magnification.
  4. Course Adjustment Knob: Moves the stage up/down for focusing.
  5. Fine Adjustment Knob: Sharpens focus under lower power.
  6. Arm: Supports the tube and connects to the base.
  7. Base: Bottom support of the microscope.
  8. Stage: Platform for the specimen.
  9. Stage Clips: Secure the specimen.
  10. Inclination Joint: Allows tilting.
  11. Pillar: Supports parts above the base.
Illuminating Parts
  1. Mirror: Gathers and directs light.
  2. Diaphragm: Regulates light amount.
  3. Condenser: Focuses light onto the specimen.
  4. Illuminator (Light Source): Electric bulb or mirror for reflecting light.

Cell

  • Basic unit of life.

Types of Cells

  • Unicellular: Single-celled (e.g., Bacteria, Amoeba, Paramecium).
  • Multicellular: Many-celled (e.g., Nerve Cells, Red Blood Cells).

Cell Structures and Organelles

  1. Cell Membrane: Barrier controlling entry/exit.
  2. Cytoplasm: Jelly-like fluid holding organelles.
  3. Nucleus: Control center, stores DNA.
  4. Mitochondria: Powerhouse, produces ATP through cellular respiration.
  5. Ribosomes: Build proteins.
  6. Endoplasmic Reticulum (ER): Network of membranes.
    • Rough ER: With ribosomes, makes and transports proteins.
    • Smooth ER: No ribosomes, makes lipids, detoxifies chemicals.
  7. Golgi Apparatus: Modifies, packages, and ships proteins.
  8. Lysosomes: Break down waste and invaders.
  9. Vacuole: Storage sac (water, food, waste), maintains shape in plant cells.
  10. Chloroplast (Plants Only): Performs photosynthesis.
  11. Cell Wall (Plants Only): Rigid outer layer.

Functions of the Cell

  1. Structure and Support: Forms tissues and organs.
  2. Growth and Development: Cell growth is essential for development, repair, and regeneration of tissues and organs. - Mitosis ( body cells)
    • Mitosis (body cells).
    • Meiosis (reproductive cells).
  3. Reproduction:
    • Sexual: gametes (sperm and egg) fuse to form a zygote.
  4. Energy Production: Converts nutrients to ATP.
  5. Transport of Substances: Membrane controls movement in/out of the cell.

Difference Between Plant Cells and Animal Cells (Simplified)

  1. Structure:
    • Plant Cells: cell wall, plastids, plasmodesmata, chloroplast; rectangular shape.
    • Animal Cells: centrioles; round or irregular.
  2. Specialization:
    • Plant Cells: photosynthesis and structural support.
    • Animal Cells: movement, sensation, behavior.
  3. Water Storage:
    • Plant Cells: large central vacuole.
    • Animal Cells: smaller multiple vacuoles.
  4. Cell Wall:
    • Plant Cells: Cell wall provides rigidity.
    • Animal Cells: Plasma membrane provides structural support.
  5. Energy Production
    • Plant cells undergoes photosynthesis to create food for the plant
    • Animal Cells consumes other organisms for food and energy.
  6. Obtaining Energy
    • Plant cells mostly uses photosynthesis to obtain energy
    • Animal cells uses cellular respiration by the mitochondria to obtain energy.
  7. Waste Removal
    • Plant cells undergo transpiration to release waste gases.
    • Animal Cells undergoes exocytosis
  8. Storing carbohydrates.
    • Plant cells stores excess carbohydrates as a starch.
    • Animal cells stores excess carbohydrates as a glycogen

Epithelial Tissues

Epithelium Characteristics

  • Consists almost entirely of cells
  • Covers body surfaces and forms glands
  • Has free and basal surface
  • Specialized cell contacts
  • A vascular
  • Undergoes mitosis

Functions of the Epithelial

  • Protecting underlying structures
  • Acting as barriers
  • Permitting the passage of substances
  • Secreting substances
  • Absorbing substances

Based on Layers

  • Simple epithelium: Single cell layer (used for absorption, secretion, filtration)
  • Stratified epithelium: Multiple layers (used for protection).
  • Pseudostratified epithelium: Appears layered due to varying cell heights, but is actually a single layer.

Based on Shape

  • Squamous: Flat and thin cells.
  • Cuboidal: Cube-shaped cells.
  • Columnar: Tall, column-like cells.

Examples:

  • Simple squamous epithelium: Found in alveoli (lungs), allows gas exchange
  • Stratified squamous epithelium: Found in the skin, mouth, protects against abrasion.
  • Simple columnar epithelium: Found in the digestive tract, aids in absorption and secretion.
  • Transitional epithelium: Found in the urinary bladder, stretches to accommodate fluid.

Cellular Respiration

  • Process by which cells convert glucose and oxygen into energy (ATP).
  • Occurs in plants and animals, mainly in mitochondria.

Main Equation

  • Step 1: Glycolysis
    • Glucose (6-carbon) broken down into two pyruvate (3-carbon) molecules.
    • ATP produced: 2 ATP
    • Other products: 2 NADH
    • Oxygen required? No (Anaerobic)

Raw Materials (Cellular Respiration)

  1. Glucose: Simple sugar for energy.
  2. Oxygen: Required to break down glucose.

End Products

  1. Carbon Dioxide: Waste gas.
  2. Water: Formed during electron transport chain.
  3. ATP (Adenosine Tri-Phosphate): Usable energy.

Mitosis and Meiosis

Mitosis

  • Parent cell divides to make two identical daughter cells.
  • Unicellular: asexual reproduction
  • Multicellular: growth and repair
Stages
  • Interphase: Cell grows and replicates DNA.
  • Prophase: Chromosomes coil tightly, nucleolus disappears.
  • Metaphase: Chromosomes align in the center, attach to microtubules.
  • Anaphase: Chromatids separate and move to opposite ends.
  • Telophase: Two new nuclei form, and cells begin to split.
  • Cytokinesis: Cytoplasm splits to form two daughter cells.

Meiosis

  • Cell divides twice to produce four daughter cells with half the genetic material (sex cells).
Meiosis 1
  • Prophase 1: Chromosomes condense, nucleolus breaks down. Homologous chromosomes pair and exchange material (chromosomal crossover).
  • Metaphase 1: Chromosomes line up by pair in the center.
  • Anaphase 1: Chromosomes pulled away from each other (still with two sister chromatids).
  • Telophase 1: Chromosomes reach poles, cell divides into two.
Meiosis 2
  • Prophase 2: Nuclear membrane breaks, and spindle network appears.
  • Metaphase 2: Chromosomes line up at the metaphase ii plate at the cells center.
  • Anaphase 2: Sister chromatids split and move to opposite ends.
  • Telophase 2: Nuclei enclose chromosomes, cell divides into two daughter cells.
  • Cytokinesis: splits the parent cell's cytoplasm.
  • MEIOSIS 1 - To reduce the chromosome number by half and
Meiosis 1 - Also known as “Reduction Division”
  • MEIOSIS 2 - “Separation of Sister Chromatids”
    -To separate sister chromatids in each haploid cell to form individual chromosomes.
  • Four genetically unique haploid gametes, each with one set of chromosomes.

Mitosis and Meiosis Comparison

  • Purpose: Mitosis aims for growth, repair and asexual reproduction. While Meiosis is for sexual reproduction.
  • Mitosis has identical to parent cell While Meiosis is different from parent cells.
  • Nondisjunction: Failure of chromosomes to split, leading to abnormal chromosome numbers.

Genetics

  • Trait: Characteristics passed from parent to offspring.
  • Heredity: Passing of traits from parents to offspring
  • Genetics: Study of heredity
  • Punnett Square: Used to help solve genetics problems.
  • Alleles: Two forms of a gene (Dominant & Recessive)
  • Dominant: Stronger gene, represented by capital letter (Rr)
  • Recessive: Gene shows up less often, represented by lowercase letter
  • Genotype: Gene combination (RR, Rr, rr)
  • Phenotype: Physical feature from genotype (red/white)
  • Homozygous: Gene combination of 2 dominant and 2 recessive genes
  • Heterozygous: Gene combination of one dominant and one recessive. Also known as hybrid
Principles of Dominance
  • Law of Dominance: In pure contrasting traits, only one trait appears in the next generation.
  • Law of Segregation: During gamete formation, alleles separate.
  • Dihybrid Cross
Non-Mendelian Genetics
  • Incomplete Dominance: Neither allele is completely dominant, resulting in a mix of traits.
  • Codominance: Two alleles are expressed (multiple alleles) in heterozygous individuals which means that both traits appear side by side
  • Sex-Linked Traits
    XXXX - Genotype for Females
    XYXY - Genotype for Males
  • Polygenic Inheritance: Trait controlled by multiple genes, often on different chromosomes (e.g., hair color, eye color, height, weight).

Evolution

  • Process of change in a living system over time.

Jean Lamarck

  • Lamarck’s Theory of “Acquired Traits”
    -Theory of Use and Disuse If an organ is used , it becomes stronger and better developed. If an organ is not used, it becomes weaker and withers away.
  • An organism acquires traits from its experience (not genes) and those traits are passed down, or inherited by their offspring.
  • Example Situation: Lamarck believed that giraffes stretched their necks to reach food. Their offspring and later generations inherited the resulting long necks.

Charles Darwin (1809 - 1882)

  • A naturalist (studied and preserved biological specimens that he collected)
  • 5 year voyage around the world aboard the HMS Beagle.
  • Theory of evolution by natural selection – Nature will select the organisms that have variations that allow them to better survive (survival of the fittest)
  • Descent by Modification
  • Darwin collected different species that were very similar and hypothesized that they shared a common ancestor
  • Darwin's Famous Work: "On the Origin of Species" (1859) — his groundbreaking book where he introduced and supported his theory with evidence from nature.
Variation in Organisms

Each species has organisms with varying characteristics for example:
– some are taller
– some have bigger feet
– some run faster
– some have better vision
– some smell better

Evidence for Darwin’s Theory
  • Fossil Record
  • Biogeography
  • Comparative Anatomy
  • Embryology
  • Biochemistry

Patterns and Evidences

  • The Geological time scale is a record of the life forms and geological events in Earth’s history.
    Precambrian Time covers 88% of earth’s history.
Paleozoic Era (Ancient Life)
  • Explosion of life in the oceans began during this era.
  • Most of the continents were covered in warm, shallow seas.
  • The Cambrian (beginning) opened with the breakup of the world-continent Rodinia and closed with the formation of Pangaea, as the Earth's continents came together once again.
Mesozoic Era (Middle Life)
  • At the beginning of this era the continents were joined as Pangaea.
  • Pangaea broke up around the middle of this era.
  • Reptiles became the most abundant animals because of their ability to adapt to the drier climate of the Mesozoic Era.
  • Dinosaurs were also very active in this era.
  • First small dinosaurs appeared in the Triassic Period.
  • Larger and more abundant dinosaurs appeared in the Jurassic Period.
  • This era ended with a mass extinction event about 65 million years ago.
  • Many groups of animals, including the dinosaurs disappeared suddenly at this time
Cenozoic Era – Recent Life

-Began about 65 million years ago and continues today.

  • Climate was warm and mild.
  • Marine animals such as whales and dolphins evolved.
  • Mammals began to increase and evolve adaptations that allowed them to live in many different environments – land, air and the sea.
  • Grasses increased and provided a food source for grazing animals
  • Many mountain ranges formed during the Cenozoic Era Alps in Europe and Himalayas in India; Rocky Mountains in the USA

Evidences

  • Fossils: Preserved remains of ancient life (older than 10,000 years), supported by radioisotope dating.
  • Selective Breeding: select & breed individuals with desired characteristics and produced breeds often very different to the wild species
  • Homologous Structure: Share a common origin and embryonic tissue, indicating a shared ancestry
  • Speciation: how a new kind of plant or animal species is created
  • Endemic Species: Only found in one geographical location or known as regional animals/plants
  • Gradual Divergence: Refutes belief that species were created as distinct types incapable of change
  • Adaptation: trait that increases organisms chances of survival
  • Defense Mechanism: Different ways for organisms to defend Themselves.
  • Mimicry: Copying appearance of dangerous species or concealment (Camouflage)
  • Camouflage: Ability to blend into environment.
  • Speciation: 2 populations become Separated

Microorganisms

Types

  • Bacteria, fungi, algae, and protozoans
  • Viruses (reproduce only in host organisms)
Examples
  • Algae: Chlamydomonas, Spirogyra
  • Fungi: Bread Mould, Penicillium, Aspergilles
  • Protozoans: Amoeba, Paramaecium
  • Lactobacilius: produce lactic acid as a by-product of glucose metabolism.
  • Vaccines: are dead or weakened microbes introduced into the body to produce antibodies.
  • Pathogens: disease-causing organisms or agents, also known as infectious agents or germs.
  • Prokaryotes: are the smallest and structurally simplest true-living organisms, and the oldest life forms on Earth.
  • Bacteria: It constitute a major part of the organic matter that feeds countless bottom-dwelling animals.
  • Cyanobacteria: They are important oxygen producers and form symbiotic relationships with plants as chloroplasts
  • Marine Snow: is a continuous shower of mostly organic detritus falling from the upper layers of the water column
  • Symbiotic Bacteria: microorganisms that live in a mutually beneficial relationship with other organisms, where both the bacteria and the host benefit from the interaction.
  • Archaea (Domain Archaea) - are among the simplest, most primitive forms of life
  • Eukaryotes (Domain Eukarya): Possess a nucleus.
  • Kingdom Protista: is the 'trouble-maker' of the classification system
  • Algae: are a diverse group of protists
  • Diatoms: are unicellular, although many species aggregate to form chains
  • Dinoflagellates: are another important group of planktonic, unicellular protists. Two flagella; one wrapped along a groove along the middle of the cell, the other trailing free
  • Zooxanthalae: A group of dinoflagellates live in close association with animals such as coral, sea anenomes, sponges and giant clams.
  • Coccolithophorids: are unicellular protists covered with ornamental plates made of calcium carbonate (CaCo3)
  • Radiolarians: are planktonic marine protists that secrete elaborate shells made of silica and other materials.
  • Ciliates: are protists with many hair-like cilia used in locomotion and feeding
  • Conjugation: a process where genetic material is transferred between two organisms through direct contact or sexual reproduction.

Body Systems

Circulatory System

  • Transports blood, nutrients, oxygen, carbon dioxide, and hormones.
    • Key organs: heart, blood, blood vessels (artery, capillary, veins).
    • Known diseases: Anemia and Hypertension

Respiratory System

  • Gas exchange: brings oxygen in, removes carbon dioxide.
    • Key organs: mouth, nasal cavity/nose, pharynx (throat), larynx (voice box), trachea (windpipe), lungs.
    • Known diseases: Asthma and Tuberculosis

Digestive System

  • Breaks down food into absorbable nutrients.
    • Key organs: Esophagus, stomach, small/large intestine, liver, pancreas.
    • Known diseases: GERD and Chron’s Disease

Skeletal System

  • Framework of the human body.
    • Key organs: Bones, Cartilage, Joints and Ligaments
    • Known diseases: Fracture and Osteoporosis.

Muscular System

  • Movement, posture, circulation, and heat generation.
    • Types: skeletal, smooth, cardiac.

Immune System

  • Defends against germs and pathogens.
    • Key organs: White Blood Cells, Spleen, Lymph Nodes, Skin, Bone Marrow
    • Known diseases: HIV and Sepsis

Excretory System

  • Removes waste products to maintain homeostasis.
    • Key organs: Kidneys, Ureters, Urinary Bladder, Urethra
    • Known diseases: UTI and Kidney Stones

Reproductive System

  • Produces offspring.
    • Male reproductive system (testes, scrotum, penis).
    • Female reproductive system (ovaries, fallopian tube, uterus, cervix, vagina).
    • Known diseases: STD and Infertility

Nervous System

  • Coordinates actions and sensory information via signals.
    • Central nervous system (brain and spinal cord).
    • Peripheral nervous system (nerves).
    • Brain: Controls thoughts, emotions.
    • Spinal Cord: Relays signals between the brain and the rest of the body
    • Nerves: Transmit signals throughout the body.
  • Cerebrum Largest part of the brain Divided into lobes:
    • Frontal lobe: Reasoning, planning, movement, emotions, problem-solving
    • Parietal lobe: Sensory perception (touch, temperature, pain)
    • Temporal lobe: Hearing, memory, language
    • Occipital lobe: Vision
  • Cerebellum - Coordination of movement, balance, posture.
  • Brainstem - Controls vital life functions like heartbeat, breathing, and blood pressure
  • Limbic System - Emotions, memory, motivation

Endocrine System

  • Creates and secretes hormones.
    • Consists of various tissues and glands in different locations in the body
  • PINEAL GLAND
    • A tiny gland in the brain that is under of the back part of the corpus callosum
    • Creates and Releases Melatonin
  • PITUITARY GLAND
    • A small, pea-sized gland located below the hypothalamus at the base of the brain.
    • Responsible for multiple hormonal activity of the body.
  • THYROID GLAND
    • A small, butterfly-shaped gland at the front of the neck.
    • Responsible for releasing hormones that controls your metabolism
  • ADRENAL GLAND
    • Small, triangle-shaped glands typically located on top of each of the kidneys.
    • Releases several hormones that manages different bodily functions such as metabolism, blood pressure and stress response.
  • HYPOTHALAMUS
    • An organ deep inside the brain that is the main link of the endocrine system and the nervous system.
    • Makes two hormones that is stored in the pituitary gland namely: Oxytocin and Vasopressin.
    • Mainly creates and releases the hormones Dopamine and Somatostatin.
  • PANCREAS - Located at the back of the abdomen or belly that is both an organ and gland and is also part of the digestive system.
    -Releases two hormones that are responsible for maintaining blood sugar Insulin and Glucagon