Biology 1009: Study Guide for Midterm Exam I (Lectures 1-6)

Scientific Method and Foundations of Biology

Scientific Method

The scientific method is a systematic approach used by scientists to explore observations, answer questions, and test hypotheses.

• Observation: Gathering information about phenomena.

• Hypothesis: A testable explanation for an observation.

• Experimentation: Testing the hypothesis through controlled experiments.

• Data Collection: Recording and analyzing results.

• Conclusion: Interpreting data to support or refute the hypothesis.

Emergent properties are characteristics that arise from the arrangement and interaction of parts within a system, such as the properties of life that emerge at the cellular or organismal level.

The Unity and Diversity of Life

• All living organisms share certain unifying characteristics (e.g., cellular organization, genetic code, metabolism).

• Diversity arises from evolutionary processes, leading to a wide variety of forms and functions.

Classification of Organisms: The 3-Domain System

Organisms are classified into three domains based on genetic and cellular differences:

• Domain Bacteria: Prokaryotic, unicellular organisms with peptidoglycan cell walls.

• Domain Archaea: Prokaryotic, unicellular organisms with unique membrane lipids and cell wall components; often found in extreme environments.

• Domain Eukarya: Eukaryotic organisms, including protists, fungi, plants, and animals.

Chemistry of Biology

Matter: Atoms, Molecules, and Compounds

• Atoms: The smallest units of matter, composed of protons, neutrons, and electrons.

• Molecules: Two or more atoms bonded together.

• Compounds: Molecules composed of different elements.

Structure and Composition of Atoms

• Protons: Positively charged particles in the nucleus.

• Neutrons: Neutral particles in the nucleus.

• Electrons: Negatively charged particles orbiting the nucleus.

Functional Groups

Functional groups are specific groups of atoms within molecules that determine the chemical properties of those molecules. Examples include hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), and phosphate (-PO42-).

Chemical Bonds

• Covalent bonds: Atoms share electron pairs.

• Hydrogen bonds: Weak attractions between a hydrogen atom and an electronegative atom (e.g., oxygen or nitrogen).

• Ionic bonds: Transfer of electrons from one atom to another, resulting in charged ions.

• Van der Waals interactions: Weak, transient interactions due to temporary dipoles.

Formation and Breaking of Polymers

• Condensation (Dehydration) Reactions: Monomers are joined by removing a water molecule.

• Hydrolytic Reactions: Polymers are broken down by adding a water molecule.

Types of Biological Molecules

• Lipids: Hydrophobic molecules, including fats, oils, and steroids. Saturated fats have no double bonds; unsaturated fats have one or more double bonds.

• Proteins: Polymers of amino acids; perform structural, enzymatic, and regulatory functions.

• Nucleic acids: DNA and RNA; store and transmit genetic information.

• Polysaccharides: Polymers of sugars; serve as energy storage (e.g., starch, glycogen) or structural components (e.g., cellulose).

Water Molecules: Characteristics and Emergent Properties

• Cohesion: Water molecules stick together via hydrogen bonds.

• Adhesion: Water molecules stick to other substances.

• High specific heat: Water resists temperature changes.

• Solvent properties: Water dissolves many substances due to its polarity.

pH

• pH measures the concentration of hydrogen ions ($[H^+]$) in a solution.

• Formula: $pH = -\log_{10}[H^+]$

• Acidic solutions have pH < 7; basic solutions have pH > 7; neutral is pH = 7.

Chemical Reactions: Substrates and Products

• Substrates: Reactants in a chemical reaction.

• Products: Substances formed as a result of the reaction.

Cells

Prokaryotes (Bacteria and Archaea)

• Nucleoid: Region containing the cell's DNA (not membrane-bound).

• Plasmid: Small, circular DNA molecules.

• Ribosomes: Sites of protein synthesis.

• Pili: Hair-like structures for attachment or DNA transfer.

• Shapes: Cocci (spherical), rods (bacilli), spirals (spirilla).

• Cell Wall: Provides structural support and shape.

Eukaryotes (Plant and Animal Cells)

• Comparison to prokaryotes: Eukaryotes have membrane-bound organelles and a nucleus; prokaryotes do not.

• Similarities: Both have plasma membranes, ribosomes, cytoplasm, and genetic material.

• Differences: Plant cells have cell walls, chloroplasts, and central vacuoles; animal cells have lysosomes and centrioles.

Organelles: Structure and Functions

• Nucleus: Contains genetic material (DNA); site of transcription.

• Endoplasmic Reticulum (ER):

  • Rough ER: Studded with ribosomes; synthesizes proteins.

  • Smooth ER: Lacks ribosomes; synthesizes lipids and detoxifies chemicals.

• Golgi Apparatus: Modifies, sorts, and packages proteins and lipids for secretion or delivery to other organelles.

• Plasma Membrane: Selectively permeable barrier; regulates entry and exit of substances.

• Mitochondria: Site of cellular respiration and ATP production.

• Chloroplast: Site of photosynthesis (in plants and algae).

• Nuclear Envelope: Double membrane surrounding the nucleus.

• Cytoskeleton: Network of protein filaments for cell shape, movement, and transport.

• Lysosomes: Contain digestive enzymes for breaking down macromolecules (mainly in animal cells).

• Central Vacuole: Large storage organelle in plant cells; maintains turgor pressure.

• Cell Wall: Rigid structure outside the plasma membrane (plants, fungi, some protists).

Membranes

Components of the Membrane: Models for Membranes

• Phospholipid bilayer: Double layer of phospholipids with hydrophilic heads and hydrophobic tails.

• Proteins: Integral and peripheral proteins serve as channels, receptors, enzymes, etc.

• Cholesterol: Modulates membrane fluidity and stability (in animal cells).

• Cytoskeleton: Provides structural support and anchors membrane proteins.

• Extracellular matrix: Network of proteins and carbohydrates outside the cell; provides support and signaling.

Functions of the Different Components

• Phospholipids: Form the basic structure and barrier of the membrane.

• Proteins: Facilitate transport, signal transduction, cell recognition, and enzymatic activity.

• Cholesterol: Maintains appropriate membrane fluidity.

Fluidity of the Membrane

• Membrane fluidity is influenced by temperature, fatty acid composition (saturated vs. unsaturated), and cholesterol content.

• Fluidity is essential for membrane function, including movement of proteins and lipids, and cell signaling.

Transport Across the Membrane

Permeability of the Lipid Bilayer

• The lipid bilayer is permeable to nonpolar (hydrophobic) molecules (e.g., O2, CO2).

• The lipid bilayer is not permeable to ions and polar (hydrophilic) molecules (e.g., Na+, glucose).

Ways Molecules Cross the Membrane

• Passive Transport: Movement of substances down their concentration gradient without energy input.

• Active Transport: Movement of substances against their concentration gradient, requiring energy (usually ATP).

• Diffusion: Net movement of molecules from high to low concentration.

• Osmosis: Diffusion of water across a selectively permeable membrane.

Tonicity and Water Balance of Cells

• Hypotonic solution: Lower solute concentration outside the cell; water enters the cell, which may swell or burst.

• Isotonic solution: Equal solute concentration; no net water movement.

• Hypertonic solution: Higher solute concentration outside the cell; water leaves the cell, which may shrink.

Bulk Transport

• Endocytosis: Uptake of large particles or fluids by engulfing them in vesicles.

• Exocytosis: Release of substances from the cell by fusion of vesicles with the plasma membrane.

Types of Proteins Involved in Transport

• Channel proteins: Form hydrophilic channels for specific molecules or ions to pass through.

• Carrier proteins: Bind to specific molecules and change shape to shuttle them across the membrane.

Summary Table: Comparison of Prokaryotic and Eukaryotic Cells

Feature	Prokaryotic Cells	Eukaryotic Cells
Nucleus	No (nucleoid region)	Yes (membrane-bound)
Organelles	Few (no membrane-bound organelles)	Many (membrane-bound)
Cell Wall	Yes (most)	Yes (plants, fungi); No (animals)
Size	Small (1-10 μm)	Larger (10-100 μm)
Examples	Bacteria, Archaea	Plants, Animals, Fungi, Protists

Example: Escherichia coli is a prokaryotic bacterium, while a human skin cell is a eukaryotic cell.

Additional info: Some details, such as the specific functions of organelles and the chemical nature of functional groups, have been expanded for academic completeness.