Scientific Inquiry and the Nature of Science

Descriptive and Hypothesis-Based Inquiry

Scientific inquiry involves systematic investigation to understand natural phenomena. Two main approaches are used:

• Descriptive Inquiry: Involves collecting evidence and using inductive reasoning to form generalizations.

• Hypothesis-Based Inquiry (Scientific Method): Involves forming hypotheses, making predictions, and testing them through experimentation and deductive reasoning.

Scientific Method Steps:

• Ask a non-trivial question

• Formulate hypotheses (true/false)

• Make predictions

• Test predictions with experiments or observations

Darwin's Premises for the Theory of Evolution

• Organisms are products of common descent

• New species are generated by gradual change

• Change occurs due to differences in reproductive success among individuals

Classification of Life: Domains and Taxonomy

Three Domains of Life

Life is classified into three domains based on cellular and genetic characteristics:

Taxonomy: Based on Linnaeus' binomial nomenclature system.

Levels of Biological Organization

Hierarchy of Organization

Biological systems are organized in a hierarchy from the largest to smallest:

• Biosphere

• Ecosystems

• Communities

• Populations

• Organisms

• Organs and organ systems

• Tissues

• Cells

• Organelles

• Molecules

• Atoms

Emergent Properties

• Properties that arise at each level of organization that are not present at the previous level.

• Example: Photosynthesis is an emergent property of chloroplasts.

Basic Chemistry for Biology

Atoms and Elements

Atoms are the basic units of matter, composed of protons, neutrons, and electrons.

• Element: A substance that cannot be broken down by chemical reactions.

• Isotopes: Atoms of the same element with different numbers of neutrons.

Major and Trace Elements

• Major Elements: P, Na, K, Ca, Mg, S, Cl

• Trace Elements: Fe, Zn, Cu, I, B, Cr, Co, F, Mn, Mo, Se, Si, V

• Example: Iodine deficiency causes goiter.

Molecules and Compounds

• Molecule: Two or more atoms held together by covalent bonds.

• Compound: Substance composed of two or more different elements.

Chemical Bonds

• Covalent Bonds: Atoms share electrons.

• Ionic Bonds: Atoms transfer electrons, forming charged ions.

• Hydrogen Bonds: Weak attraction between a hydrogen atom and an electronegative atom.

• Van der Waals Interactions: Weak attractions due to asymmetrical electron distribution.

pH and Buffers

• pH: Measures hydrogen ion concentration in solution.

• Acids increase ; bases decrease $[H^+]$.

• Buffer: Maintains pH stability by absorbing or releasing or ions.

Dissociation of Acids and Bases

Chemical Composition of Organisms

Organic Molecules

• Carbohydrates: sugars

• Nucleic Acids: DNA and RNA

• Proteins: perform cellular functions

• Lipids: variety of functions

• Carbon is the central element in organic molecules, often combined with O, N, H, P, S.

Variation in Carbon Skeletons

• Isomers: Molecules with the same formula but different structures.

• Enantiomers: Mirror-image isomers (e.g., L-Dopa vs. D-Dopa).

Monomers and Polymers

Macromolecules: Structure and Function

Polymers

• Polysaccharides (carbohydrates)

• Proteins (polypeptides)

• Nucleic Acids (polynucleotides)

• Lipids

Functions of Carbohydrates

• Cellular respiration: ATP production

• Energy storage: Polymers of glucose

• Structural: Cell wall

Proteins: Structure and Function

• Enzymes

• Transport

• Structural components

• Contractile molecules

• Hormones

• Defensive

• Storage

• Signal (receptors)

• Gene regulation

Protein Structure

• Primary: Linear chain of amino acids

• Secondary: Stabilized by hydrogen bonding

• Tertiary: 3D shape stabilized by side chain interactions

• Quaternary: Association of two or more polypeptides

Important: Protein function depends on its 3D structure, which is sensitive to pH and temperature.

Nucleic Acids (DNA & RNA)

• Store, replicate, and transmit genetic information

• DNA is anti-parallel and complementary

• Three types of RNA

Functions of Lipids

• Energy storage

• Cell membrane structure

• Hormones

Cell Structure and Function

Cell Theory

• All organisms are composed of cells

• Cells are the structural and functional unit of life

• All cells come from pre-existing cells

Domains and Cell Types

• Domain Bacteria: Cyanobacteria, 1-5 μm diameter

• Domain Archaea: Methanogens, extreme halophiles, 1-5 μm diameter

• Domain Eukarya: Protists, fungi, animals, plants, 10-100 μm diameter

Prokaryotic Cell Structure

• Cell wall

• Plasma membrane

• Ribosome

• Cytoplasm

• Flagella

• Nucleoid

• Plasmid

Genetic Recombination in Prokaryotes

• Transduction

• Bacterial conjugation

• Transformation

Major Nutritional Modes

Prokaryotes and Oxygen

• Obligate aerobes: Require oxygen

• Facultative anaerobes: Can use oxygen or live anaerobically

• Obligate anaerobes: Poisoned by oxygen

Prokaryote Impacts

• Symbiotic relationships

• Disease recyclers

• Bioremediation

• Nitrogen fixation

Eukaryotic Cell Structure

Animal Cell

• Cytoplasm/cytosol

• Endoplasmic reticulum

• Golgi apparatus

• Lysosome

• Mitochondrion

• Nucleus

• Plasma membrane

• Ribosomes

Plant Cell

• Cell wall

• Central vacuole

• Chloroplast

• Cytoplasm/cytosol

• Endoplasmic reticulum

• Mitochondrion

• Nucleus

• Plasma membrane

• Ribosomes

Chloroplast Structure

• Circular DNA

• Granum

• Inner/outer membrane

• Stroma

• Thylakoid

Endomembrane System

• Nuclear envelope

• Endoplasmic reticulum

• Golgi apparatus

• Lysosomes

• Vacuoles

Viruses

Structure and Function

• Infectious particles with a viral genome in a protein shell (capsid)

• Obligate intracellular parasites

• Specific host range

Virus Transmission

• Respiratory secretions

• Damaged skin

• Mother to child

• Fecal-oral

• Blood exchange

• Sexual contact

• Animal/insect vectors

Protection Against Viral Pathogens

• Natural protection: immune system

• Vaccination

• Anti-viral drugs

Virus vs. Cell

• Virus: Nucleic acid in protein capsid, DNA or RNA, few enzymes, no metabolism

• Cell: Organic molecules, DNA and RNA, many enzymes, diverse functions, highly metabolic

Membranes and Transport Processes

Plasma Membrane

• Defines cell boundary

• Regulates movement of material

• Site of chemical reactions

• Facilitates communication

• Provides unique identity

Components of Plasma Membrane

• Lipids: phospholipids, cholesterol

• Proteins

Additional info:

• Some content inferred and expanded for clarity and completeness.

• Tables and lists reconstructed for study purposes.