Unit 1 Study Guide
How to conduct a scientific inquiry (scientific method):
Formulating and testing hypotheses: Scientific inquiry involves formulating explanations for observations (hypotheses) that can be rigorously tested through experimentation.
Controlled experiments: Experiments are designed with a control group (not treated, serving as a baseline for comparison) and a test (experimental) group (receives the treatment).
Independent Variable (IV): This is the 'cause' factor, what is intentionally manipulated by the experimenter.
Dependent Variable (DV): This is the 'effect' factor, what is measured as a response to the manipulation of the independent variable.
Credible experiments are carefully controlled to isolate the effect of the independent variable.
Requirements for observations, experiments, and hypotheses:
Repeatability: Observations and experiments must be repeatable, meaning other researchers should be able to replicate the methods and achieve similar results.
Testability: Hypotheses must be testable, allowing for empirical investigation to either support or refute them.
Definition of a scientific theory:
A theory is an explanation for natural phenomena that has strong support from various consistent observations and experimental results. If hypotheses are repeatedly confirmed and explain observations, they may mature into a theory.
2.1 Properties of Atoms
Atoms, subatomic particles, and ions:
Atom: The smallest unit of matter that retains the properties of an element.
Subatomic particles:
Protons: Positively charged, located in the nucleus.
Neutrons: Neutrally charged, located in the nucleus.
Electrons: Negatively charged, orbit around the nucleus, with negligible mass relative to protons/neutrons.
Ions: Atoms that have either a positive or negative charge due to the loss or gain of electrons.
2.2 Molecules and Chemical Bonds
Covalent, ionic, and hydrogen bonds:
Covalent bonds: Formed by the sharing of electron pairs between atoms.
Nonpolar covalent bonds: Electrons are shared equally; electronegativity difference (\Delta EN \approx 0 \text{ to } 0.4).
Polar covalent bonds: Electrons are shared unevenly; electronegativity difference (\Delta EN \approx 0.4 \text{ to } 1.7). Example: O–H bond in water.
Ionic bonds: Result from the complete transfer of electrons between atoms, leading to the formation of positively charged cations and negatively charged anions. Occur when there is a large electronegativity difference (\Delta EN > \sim 1.7).
Hydrogen bonds: Weaker attractions that occur between a partially positive hydrogen atom (often bonded to O or N) and a negatively charged atom (often O or N). These are crucial for structure and interactions in biomolecules.
2.3 Water
Structure and chemistry of water:
Water (H_2O) is a polar molecule due to its polar covalent bonds between oxygen and hydrogen. The oxygen atom is more electronegative, resulting in a partial negative charge on oxygen and partial positive charges on the hydrogen atoms.
This polarity enables water molecules to form hydrogen bonds with other water molecules and within large molecules.
Emergent properties of water significant to life:
Water's emergent properties, stemming from its polarity and extensive hydrogen bonding, are essential for life:
Ice is less dense than liquid water: This allows ice to float, insulating aquatic environments and preventing them from freezing solid, which is vital for aquatic life.
Excellent solvent: Water acts as a solvent for hydrophilic (water-loving) substances, such as salts and many biological molecules. Ionic compounds like NaCl dissociate and are solvated by surrounding water molecules, facilitating chemical reactions and transport within organisms.
These properties (e.g., high specific heat, high heat of vaporization, cohesion, adhesion) contribute to temperature regulation and transport in biological systems, which are foundational for sustaining life on Earth.
pH scale and its effects:
pH scale: A measure of the acidity or basicity of a solution, defined as the negative logarithm (base 10) of the hydrogen ion concentration ([H^+]). The formula is pH = -\log_{10} [H^+].
pH effects on organisms: pH is critically related to the concentration of hydrogen ions ([H^+]) and hydroxide ions ([OH^-]). Organisms maintain a narrow pH range (homeostasis) for metabolic processes to function correctly, as extreme pH values can denature proteins and disrupt cellular functions.
2.4 Carbon
Carbon's fundamentality and functional groups:
Carbon's fundamentality to life: Carbon is the chemical backbone of life and is present in all organic molecules. It is tetravalent, meaning it can form four stable covalent bonds with other atoms (including other carbon atoms) and functional groups.
This ability enables the formation of diverse carbon-based molecules that vary in length, branching, double bonds, and rings, providing the structural and functional complexity required for life.
Major chemical properties of biologically important functional groups: These groups attach to carbon backbones and determine the molecule's chemical reactivity.
Hydroxyl group (-OH): Found in alcohols (e.g., ethanol); makes molecules polar and soluble in water.
Carbonyl group (C=O): Found in ketones (if internal) and aldehydes (if terminal); contributes to reactivity.
Amino group (-NH$2$): Found in amines (e.g., amino acids); acts as a base by picking up H^+ from the surrounding solution, becoming -NH3^+ .
Phosphate group (-OPO_3^{2-}): Found in organic phosphates (e.g., glycerol phosphate, ATP); negatively charged and involved in energy transfer and nucleic acid structure.
Methyl group (-CH_3): A nonpolar group (e.g., 5-methylcytosine in DNA); can affect gene expression and molecular shape.
2.5 Macromolecules
Four major classes of biological macromolecules:
Carbohydrates:
Monomer: Monosaccharides (e.g., glucose).
Polymers: Disaccharides (e.g., sucrose, maltose) and polysaccharides (e.g., starch, glycogen for energy storage; cellulose, chitin for structural roles).
Characteristics: Serve as primary energy sources, energy storage, and structural components. Have an empirical (C1H2O1)n ratio.
Proteins:
Monomer: Amino acids (20 common types, each with an amino group, carboxyl group, hydrogen, central carbon, and a variable R group).
Polymer: Polypeptides (amino acids linked by peptide bonds).
Characteristics: Account for a large fraction of cell mass and perform diverse functions: enzymes (catalyze reactions), defense, energy storage, transport, signaling, movement, and structural support. Their function is determined by their 3D shape, which is dictated by the amino acid sequence.
Lipids:
Not true polymers: Diverse group of hydrophobic molecules.
Types:
Triglycerides (fats and oils): Composed of glycerol and three fatty acids; primarily for long-term energy storage and insulation.
Phospholipids: Composed of glycerol, two fatty acids, and a phosphate group; amphipathic (hydrophilic head, hydrophobic tails) and form the core of cell membranes (phospholipid bilayer).
Steroids: Characterized by four fused hydrocarbon rings (e.g., cholesterol); modulate membrane rigidity and serve as precursors for hormones.
Characteristics: Hydrophobic, largely nonpolar due to hydrocarbon chains. Functions include energy storage, membrane structure, and signaling.
Nucleic Acids:
Monomer: Nucleotides (each with a phosphate group, a pentose sugar (deoxyribose in DNA, ribose in RNA), and a nitrogenous base).
Polymer: Polynucleotides (DNA, RNA).
Characteristics: Encode and transmit genetic information. DNA stores genetic information, while RNA carries protein-encoding information, participates in protein synthesis, and can catalyze reactions. The Central Dogma describes the flow of genetic information.
Chapter 3: Cells, Membranes, and Homeostasis
Comparison of eukaryotic cells:
The provided notes primarily detail the structure and function of eukaryotic cells, including their various organelles and transport mechanisms. They do not directly compare eukaryotic cells with prokaryotic cells. However, all cells, including prokaryotic and eukaryotic, share fundamental components like a plasma membrane, cytoplasm, and ribosomes.
Major intracellular structures (organelles) found in eukaryotic cells and their functions:
Nuclear envelope: A double membrane with nuclear pores that regulates the passage of large molecules, requiring active transport.
Endoplasmic Reticulum (ER):
Rough ER: Involved in protein synthesis, especially for proteins destined for secretion or insertion into membranes.
Smooth ER: Responsible for lipid synthesis, detoxification of drugs and poisons, and storage of calcium ions.
Golgi apparatus: Modifies, sorts, and packages proteins and lipids synthesized in the ER for transport to their final destinations.
Lysosomes: Contain hydrolytic enzymes that degrade damaged macromolecules, waste materials, and cellular debris.
Peroxisomes: Break down fatty acids into smaller molecules and synthesize other molecules, often producing hydrogen peroxide as a byproduct.
Mitochondria: Double-membraned organelles that are the primary sites of ATP production through the harvesting of energy from chemical compounds (e.g., sugars) via cellular respiration.
Chloroplasts (in plant cells): Double-membraned organelles with an inner thylakoid membrane system that capture light energy to fix atmospheric carbon and synthesize simple sugars through photosynthesis.
Ribosomes: Synthesize proteins based on genetic instructions (found both freely in the cytoplasm and attached to the Rough ER).
Cytoskeleton: An internal structural network composed of microfilaments, intermediate filaments, and microtubules that supports the cell, maintains shape, and enables movement of substances.
Comparison of plant and animal cells:
Shared features: Both plant and animal cells are eukaryotic and possess a nucleus, an endomembrane system (ER, Golgi, vesicles, plasma membrane), ribosomes, mitochondria, cytoskeleton, and peroxisomes.
Plant-specific features:
Cell wall: Provides structural support and protection, maintaining cell shape.
Chloroplasts: Sites of photosynthesis.
Large central vacuole: Contributes to turgor pressure, stores water and nutrients, and helps maintain cell rigidity.
Plasmodesmata: Channels through the cell wall that connect the cytoplasm of adjacent plant cells.
Animal-specific features:
Lysosomes: (While plants do have vacuoles with hydrolytic functions, lysosomes are typically highlighted as animal-specific for this comparison).
Lack a cell wall.
Possess two vacuole systems (simplified in the notes).
Structure and function of biological membranes:
Structure: Biological membranes are described by the Fluid Mosaic Model, consisting of a fluid bilayer of phospholipids with embedded and associated proteins. Phospholipids are amphipathic, having hydrophilic heads and hydrophobic tails, which spontaneously form bilayers in water. The fluidity of the membrane is influenced by the saturation of fatty acid tails (saturated tails pack tightly, unsaturated tails with kinks reduce packing) and by cholesterol, which modulates membrane fluidity at different temperatures. Proteins within the membrane can be integral (transmembrane), spanning the entire bilayer, or peripheral, associating with the membrane surfaces.
Function: The plasma membrane defines the cell boundary and plays a crucial role in maintaining cellular homeostasis through selective permeability, controlling the movement of substances into and out of the cell.
Concepts of osmosis and diffusion:
Diffusion: The passive movement of substances (e.g., small nonpolar molecules) down their concentration gradient, from an area of higher concentration to an area of lower concentration, without requiring cellular energy.
Osmosis: The specific type of diffusion involving the movement of water across a semi-permeable membrane from an area of lower solute concentration (higher water concentration) to an area of higher solute concentration (lower water concentration).
Mechanisms of transport across the cellular membrane:
Passive processes (no energy required; substances move down their concentration gradient):
Simple diffusion: Small, nonpolar molecules move directly across the lipid bilayer without the aid of transport proteins (e.g., O2, CO2).
Osmosis: The passive movement of water across a selectively permeable membrane.
Facilitated diffusion: Ions or polar molecules move across the membrane down their concentration gradient with the help of specific transport proteins. This can be:
Channel-mediated diffusion: Ions move through protein channels.
Carrier-mediated diffusion: Polar molecules bind to a carrier protein, which then changes shape to move them across.
Active processes (require cellular energy; substances move against their concentration gradient):
Primary active transport: Utilizes energy directly from ATP hydrolysis to move substances against their gradient (e.g., the Na^+/K^+ pump, which pumps 3 Na^+ out and 2 K^+ in per ATP hydrolyzed).
Vesicular transport (Bulk transport): Involves the movement of large quantities of substances or large molecules across the membrane via vesicles.
Exocytosis: Secretion of substances from the cell; vesicles fuse with the plasma membrane.
Endocytosis: Uptake of substances into the cell; the plasma membrane engulfs material to form a vesicle.
Analysis and interpretation of experimental data:
The provided notes describe the theoretical concepts of osmosis, diffusion, and membrane transport but do not include specific experimental data or examples for analysis and interpretation.
10.2 Cytoskeleton
Role of cytoskeletons and microtubules in the cell:
Cytoskeleton: An internal structural network that supports the cell and enables the movement of substances within it.
Microtubules: These hollow tubes radiate from the centrosome, help maintain cell shape, and are crucial for several key roles:
Cell division and chromosome segregation.
Vesicle transport and organelle positioning.
Movement of cells via cilia and flagella.
They exhibit dynamic instability (cycles of growth and shrinkage) and use motor proteins (Kinesin and Dynein) for cargo movement toward their plus (+) and minus (-) ends, respectively.