Comprehensive University Biology Study Notes

BIOLOGY AND MAJOR FIELDS OF SPECIALIZATION

• Biology is the study of living things and is a branch of science providing a way of understanding nature. Biologists deal with the living part of nature and the non-living elements that affect living organisms.

• Striving to explain, integrate, and describe the natural world of living things is the primary goal of biologists. While the literal meaning of biology is the study of life, life itself is difficult to define solely through the scientific lens.

• Questions involving the meaning of life or why there is life lie beyond the scope of biology and are left to philosophers and theologians. Biologists focus on matters relating to how life works.

• For biologists, life is defined by a set of characteristics that distinguish living organisms from non-living objects (including dead organisms). These characteristics include being highly organized, having a complex structure, being composed of one or more cells, containing a genetic program, acquiring and using energy, carrying out chemical reactions, growing in size, maintaining a constant internal environment, producing similar offspring, and responding to environmental changes.

• The science of biology is broad, covering every aspect of living things. To study it effectively, it is divided into branches:

  • Ecology: Deals with environmental relations.
  • Embryology: Focuses on development.
  • Physiology: Studies functions.
  • Morphology: Studies form and structure (Anatomy for internal gross structure).
  • Palaeontology: Study of fossils.
  • Histology: Study of tissues.
  • Evolution: Focuses on ancestral history.
  • Genetics: Study of heredity.
  • Zoogeography: Distribution of animals in nature.
  • Molecular Biology: Structure of organisms, cells, and organelles at the molecular level.
  • Environmental Biology: The study of organisms in relation to their environment, specifically organic and inorganic interactions and human activities.
  • Microbiology: Study of microorganisms like Bacteria, Viruses, Protozoa, and microscopic algae and fungi.
  • Freshwater Biology: Deals with organisms in freshwater bodies like rivers and lakes, including chemical and physical parameters.
  • Marine Biology: Study of life in seas and oceans.
  • Parasitology: Deals with parasites, their structure, transmission, life histories, and host-parasite relationships.
  • Human Biology: Study of man, including anatomy, function, evolution, and genetics.
  • Social Biology: Study of social behavior and communal life of humans.
  • Biotechnology: Use of living organisms and processes in manufacturing and service industries.

LEVELS OF BIOLOGICAL ORGANIZATION

• Life maintains itself through hundreds of chemical reactions. Out of $92$ naturally occurring elements, only $16$ are commonly used to form living organisms; these are called bioelements.

• In the human body, six bioelements account for $99\%$ of the total mass: Oxygen ($65\%$), Carbon ($18\%$), Hydrogen ($10\%$), Nitrogen ($3\%$), Calcium ($2\%$), and Phosphorus ($1\%$). The remaining $1\%$ is composed of Potassium ($0.35\%$), Sulfur ($0.25\%$), Chlorine ($0.15\%$), Sodium ($0.15\%$), Magnesium ($0.05\%$), Iron ($0.004\%$), and trace amounts of Copper, Manganese, Zinc, and Iodine.

• Biological organization proceeds through several levels of increasing complexity:

  • Subatomic and Atomic Level: Matter is formed of atoms and subatomic particles such as protons, electrons, and neutrons.
  • Molecular Level: Atoms combine through ionic or covalent bonding into molecules. Micromolecules have low molecular weights (e.g., $CO_{2}$, $H_{2}O$), while macromolecules have high molecular weights (e.g., starch, proteins). Organic molecules contain both carbon and hydrogen; inorganic molecules do not.
  • Organelles and Cell Level: Molecules arrange to form organelles, which are specialized structures within a cell that compare to organs of the body. Prokaryotes have limited organelles, while Eukaryotes are rich in membranous organelles.
  • Tissue Level: Groups of similar cells organized into sheets or bundles performing similar functions (e.g., muscle tissue for contraction, xylem tissue for water conduction).
  • Organ and System Level: Different tissues with related functions assemble into organs (e.g., the stomach for food digestion). Organs are part of organ systems. In animals, these are highly complex; in plants, levels are less definite, including roots, stems, and leaves.
  • Individual (Whole Organism): Assembled organ systems form an individual. In animals, coordination is through the nervous and endocrine systems; in plants, regulation is hormonal.
  • Population: A group of organisms of the same species in the same place at the same time (e.g., rats in a rice field). Attributes include gene frequency, gene flow, and population density.
  • Community: Populations of different species living in the same habitat. Interactions include predation, parasitism, mutualism, and competition.
  • Ecosystem: A community together with its non-living surroundings.
  • Biosphere: Part of the Earth inhabited by living organisms.

THE LIVING WORLD IN SPACE AND TIME

• The distribution of organisms in space is studied through biomes. A biome is a large regional community determined primarily by climate. Major plant types determine other inhabitants of a biome.

• Organisms are placed in time sequences using fossils and geological time charts. Older organisms are generally in deeper sediment layers. Rock age is determined through radioactive isotope concentrations; older layers contain fewer specific radioactive isotopes.

• Phyletic Lineage: There are nearly $2,500,000$ known species ($53.1\%$ insects, $17.6\%$ vascular plants, $19.9\%$ other animals, and $9.4\%$ fungi/algae/protozoa). Estimates for total species range from $5$ to $30$ million. Life evolved through phyletic lineages—unbroken series of species in ancestor-to-descendant sequences.

BIOLOGICAL METHOD

• Biological science is based on experimental inquiry starting with observations using the five senses. Observations can be qualitative or quantitative (which are more accurate due to measurable numbers).

• A hypothesis is a tentative explanation of observations. It can be formulated via:

  • Deductive Reasoning: Moving from general to specific (e.g., "If all birds have wings, and sparrows are birds, then sparrows have wings").
  • Inductive Reasoning: Moving from specific to general (e.g., "If sparrows, eagles, and parrots have wings and are birds, then all birds have wings").

• Other ways to form hypotheses include intuition, religious/philosophical ideas, and comparison.

• A theory is a series of hypotheses supported by many tests and is predictive. A productive theory suggests new hypotheses. If a theory survives constant skeptical testing and remains irrefutable, it becomes a scientific law (e.g., Hardy-Weinberg law, Mendel’s laws).

BIOLOGY AND HUMAN WELFARE

• Biology aids in food production through selective breeding and genetic engineering. Transgenic plants contain foreign DNA and can be propagated by cloning or tissue culture.

• Biological control uses living organisms to destroy pests instead of toxic pesticides (e.g., a wasp parasitizing an aphid on walnut trees). Integrated disease management uses all relevant methods to control disastrous diseases.

• Hydroponic culture technique involves growing plants in aerated water with mineral salts to test nutrient requirements. Pasteurization, developed by Louis Pasteur, preserves milk and milk products.

• Disease control measures include:

  1. Preventive Measures: Information on causative agents (e.g., HIV for AIDS, transmitted via contact or blood transfusion).
  2. Vaccination/Immunization: Developed by Edward Jenner in $1796$ using cowpox (Latin vacca = cow). Smallpox is claimed to be eliminated globally through this.
  3. Drug Treatment/Gene Therapy: Antibiotics for bacteria; radiotherapy and chemotherapy for cancer. Gene therapy involves inserting normal genes into hosts via bone marrow cells.

• Cloning: Producing genetically identical copies. In $1997$, a sheep was cloned in Scotland by replacing a zygote nucleus with one from a mature individual's cell. Embryo division is another cloning method.

• Environment: Industrialization leads to pollution (lead from vehicles, chromium from tanneries). Bioremediation uses organisms to remove pollutants (e.g., algae absorbing heavy metals).

BIOLOGICAL MOLECULES

• Biochemistry: Study of chemical components and processes in living organisms. Metabolism is the sum of all chemical reactions: Anabolism (building complex molecules, requires energy) and Catabolism (breakdown of molecules, releases energy).

• Bacterial cells are $70\%$ water, $15\%$ protein, and $3\%$ carbohydrates. Mammalian cells are $17\%$ water (total body percentage is higher), $18\%$ protein, and $4\%$ carbohydrates.

• Carbon: Basic element of organic compounds. It is tetravalent, meaning it forms four covalent bonds in a stable tetrahedral configuration. It can form rings, branched chains, and unbranched chains.

• Water: Most abundant compound in organisms ($65\%$ to $89\%$). Bone cells have $20\%$ water, while brain cells have $85\%$. Properties include:

  • Solvent: Excellent for polar substances.
  • Heat Capacity: Specific heat is $1.0$ (calories to raise $1\,g$ of water by $1\,^{\circ}\text{C}$).
  • Heat of Vaporization: $574\,kcal/kg$. Provides cooling; evaporating $2\,ml$ from a liter lowers temperature by $1\,^{\circ}\text{C}$.
  • Ionization: Yields $H^{+}$ and $OH^{-}$ ions. Concentration of each is $10^{-7}\,mole/litre$ at $25\,^{\circ}\text{C}$.

• Carbohydrates: Hydrated carbons with general formula $C_{x}(H_{2}O)_{y}$. Classified as:

  • Monosaccharides: Simple sugars (3-7 carbons). Glucose ($C_{6}H_{12}O_{6}$) is the most important hexose. Blood contains $0.08\%$ glucose.
  • Oligosaccharides: Yield 2-10 monosaccharides on hydrolysis. Sucrose (cane sugar) yields glucose and fructose.
  • Polysaccharides: Complex, branched, and tasteless. Starch (plant energy storage), Glycogen (animal starch), and Cellulose (plant cell walls).

• Lipids: Insoluble in water. Acylglycerols (triglycerides) are esters of glycerol and three fatty acids. Saturated fatty acids have no double bonds and are solid at room temperature (fats). Unsaturated fatty acids have double bonds and are liquid (oils).

• Proteins: Polymers of amino acids ($20$ standard types). Linked by peptide bonds ($C-N$ link). Structures: Primary (sequence), Secondary (alpha-helix or beta-pleated sheet), Tertiary (globular shape), Quaternary (aggregation of chains).

• Nucleic Acids: DNA and RNA. Composed of nucleotides (pentose sugar, nitrogenous base, phosphoric acid). Nitrogenous bases are Purines (Adenine, Guanine) and Pyrimidines (Cytosine, Thymine, Uracil).

ENZYMES

• Biologically active proteins that catalyze reactions by lowering activation energy. They are globular and have an active site.

• Cofactors: Non-protein parts essential for function. Activators are inorganic ions; prosthetic groups are covalently bonded; coenzymes are loosely attached vitamins.

• Models of Action:

  • Lock and Key (Fischer): Active site is rigid.
  • Induced Fit (Koshland): Substrate binding induces structural changes in the enzyme.

• Factors Affecting Rate: Enzyme concentration (direct proportionality), Substrate concentration (saturation point), Temperature (optimum is $37\,^{\circ}\text{C}$ for humans), pH (different optima for different enzymes, e.g., Pepsin at $2.00$, Arginase at $9.70$).

• Inhibitors: Irreversible (form covalent bonds) and Reversible. Reversible are either Competitive (structural similarity to substrate) or Non-competitive (bind elsewhere and alter structure).

THE CELL

• Cell Theory Evolution: Robert Hooke discovered cells in $1665$. Robert Brown reported the nucleus in $1831$. Schleiden and Schwann proposed the original Cell Theory. Virchow added that cells arise from pre-existing cells. Pasteur provided proof for Virchow using bacteria. Salient features: Organisms are made of one or more cells, cells arise from pre-existing cells, and the cell is the basic structural/functional unit.

• Tools: Light microscope (resolution $2.0\,nm$) and Electron microscope (resolution $2-4\,\text{Angstrom}$). Cell fractionation separates organelles using density gradient centrifugation.

• Organelles:

  • Plasma Membrane: Lipid bilayer with mosaic proteins. Selectively permeable. Uses active transport ($ATP$ required).
  • Cell Wall: Composed of Cellulose (plants), Peptidoglycan (prokaryotes), or Chitin (fungi).
  • Endoplasmic Reticulum: RER (protein synthesis/ribosomes attached) and SER (lipid metabolism/detoxification).
  • Ribosomes: Ribonucleoprotein particles ($80S$ in eukaryotes with $60S$ and $40S$ subunits; $70S$ in prokaryotes).
  • Golgi Apparatus: Flattened sacs (cisternae) for modifying and packing secretions.
  • Lysosomes: Contain hydrolytic enzymes. Secondary lysosomes include digestive vacuoles and autophagosomes. Mutation leads to storage diseases like Tay-Sach’s (lipid catabolism failure).
  • Mitochondria: Double membrane, cristae (infolds), $F_{1}$ particles. Self-replicating with own DNA and ribosomes. Generates $ATP$.
  • Nucleus: Contains chromatin and nucleolus (rRNA synthesis). Chromosome numbers: humans ($46$), fruit fly ($8$), garden pea ($14$).

VARIETY OF LIFE

• Classification is based on homologies, biochemistry, and genetics. Basic unit is the Species (groups that interbreed freely). Hierarchy: Kingdom > Phylum > Class > Order > Family > Genus > Species.

• Binomial Nomenclature: Two-word names (Generic name starts with capital, specific with small). Example: Homo sapiens. Fungi, plants, animals, protists, and monera form the five kingdoms.

• Viruses: Non-cellular entities with DNA or RNA in a protein coat (capsid). Obligate intracellular parasites. T-phage structure: pyramidal head and tail with six fibers.

  • Lytic Cycle: Virus takes over host and causes it to burst (lysis).
  • Lysogenic Cycle: Viral DNA (prophage) integrates into host chromosome without immediate lysis.
  • Retroviruses: RNA viruses using reverse transcriptase to make DNA (e.g., HIV which targets helper T-lymphocytes).

KINGDOM PROKARYOTAE

• Bacteria Discovery: Leeuwenhoek reported "animalcules." Robert Koch formulated germ theory; его postulates prove a specific microbe causes a disease.

• Morphology: Cocci (spherical), Bacilli (rod-shaped), Spiral (Vibrio, Spirillum, Spirochete). Sizes range from $0.1$ to $600\,nm$.

• Structure: Cell wall contains peptidoglycan (Murein). Gram-positive (Stain purple/thick wall); Gram-negative (Stain pink/thin wall with outer membrane). Pili are for attachment and conjugation.

• Nutrition: Most are heterotrophic (saprophytes or parasites). Autotrophs are photosynthetic (using $H_{2}S$) or chemosynthetic.

• Growth phases: Lag (no growth), Log (rapid division), Stationary (death = division), and Death (decline).

• Cyanobacteria: Largest group of photosynthetic bacteria. Contain phycocyanin (blue) and chlorophyll a. Nostoc has heterocysts for nitrogen fixation.

KINGDOM PROTISTA AND FUNGI

• Protista: Diverse eukaryotic group. Includes Protozoans (Amoeba, Zoolagellates, Ciliates), Algae (Photosynthetic, e.g., Euglenoids, Kelps, Diatoms), and Fungus-like protists (Slime molds, Water molds). Phytophthora infestans caused the Irish potato famine.

• Fungi: Absorptive heterotrophs with chitinous cell walls. Body is a mycelium made of hyphae (septate or coenocytic). Nuclear mitosis occurs. Groups: Zygomycota (Zygospores), Ascomycota (Ascospores), Basidiomycota (Basidiospores), Deuteromycota (Imperfect fungi with unknown sexual phase). Symbiotic relationships: Lichens (algae/fungi) and Mycorrhizae (roots/fungi).

BIOENERGETICS

• Photosynthesis: Light reactions occur on grana; water is photolyzed, oxygen released, $ATP$ and $NADPH$ formed. Calvin cycle (Dark reactions) occurs in stroma, fixing $CO_{2}$ into sugar. Rubisco is the fixing enzyme.

• Respiration: Cellular breakdown of glucose ($C_{6}H_{12}O_{6}$). Glycolysis (cytosol) breaks glucose into pyruvate ($2\,ATP$ net). Krebs cycle (mitochondria matrix) releases $CO_{2}$ and generates $NADH$/$FADH_{2}$. Respiratory chain (ETC) uses oxygen as the final electron acceptor to generate significant $ATP$ via chemiosmosis and oxidative phosphorylation.

NUTRITION AND TRANSPORT

• Plant Nutrition: Minerals (N, P, K, Mg) from soil. Insectivorous plants (Sundew, Pitcher plant) supplement nitrogen. Transport via Xylem (Water/minerals; Cohesion-Tension theory) and Phloem (Sugar; Pressure-Flow theory).

• Animal Transport: Open circulation (Cockroach) vs. Closed circulation (Earthworm/Vertebrates).

• Human Circulation: Heart is a four-chambered double pump. Cardiac cycle: diastole (relaxation), atrial systole, ventricular systole. Pacemaker (S-A node) initiates impulses.

• Blood: Plasma ($55\%$, water/proteins) and Cells ($45\%$, Erythrocytes, Leucocytes, Platelets). Leucocytes are Granulocytes (Neutrophils, etc.) or Agranulocytes (Monocytes, Lymphocytes).

• Lymphatic System: Returns excess tissue fluid to blood, absorbs fats via lacteals, and aids immunity.

• Immunity: Active (vaccines) vs. Passive (antisera). Cell-mediated (T-cells) vs. Humoral (B-cells producing antibodies).