Study Notes for BIO141 Exam

Chapter 6: Tour of the Cell

  • Fundamental Unit of Life

    • All organisms are composed of cells.

    • A cell is the simplest collection of matter that can be live.

    • All cells relate back to earlier cells.

    • Cells can differ substantially but share common features.

    • Even when organized into higher levels, cells remain the basic unit of structure and function.

  • Study of Cells through Microscopy

    • Cells are usually too small to see with the naked eye.

    • Microscopes are essential for visualizing cells.

  • Contributors to Cell Study

    • Robert Hooke:

    • Improved the compound microscope.

    • Observed nematodes, mites, mold filaments.

    • First to observe distinct units of living material, which he termed "cells".

    • Anton van Leeuwenhoek:

    • Observed bacteria with a single-lens microscope.

    • Developed stronger ground lenses than Hooke.

    • First to observe single-celled microbes.

    • His work revealed the microbial world.

  • Important Parameters of Microscopy

    • Magnification:

    • Ratio of an object's image size to its real size.

    • Resolution:

    • Measure of image clarity; the minimum distance between two distinguishable points.

    • Inversely related to wavelength of light (or electrons); shorter wavelengths yield better resolution.

    • Contrast:

    • Visible differences in brightness between parts of a sample.

  • Types of Microscopy

    • Electron Microscopy:

    • Two main types:

      • Scanning Electron Microscopes (SEMs):

      • Focus a beam of electrons onto a specimen's surface, yielding 3-D images.

      • Transmission Electron Microscopes (TEMs):

      • Focus a beam of electrons through a specimen, mainly used to study internal structures of cells.

  • Cell Fractionation

    • Process that takes cells apart and separates major organelles and subcellular structures.

    • Centrifuge:

    • Spins tubes at high speeds leading to the formation of a pellet with subsets of cell components, facilitating the study of specific cell functions.

  • Basic Features of Cells

    • Plasma Membrane:

    • A selective barrier.

    • Cytosol:

    • Semifluid substance where subcellular components are suspended.

    • Chromosomes:

    • Carriers of genes in the form of DNA.

    • Ribosomes:

    • Complexes responsible for protein synthesis.

    • **Cell Types: **

    • Prokaryotic Cells:

      • Found in Bacteria and Archaea.

      • DNA not surrounded by a membrane; located in an unbound region called the nucleoid.

    • Eukaryotic Cells:

      • Contain membrane-bound organelles.

  • Plasma Membrane Characteristics

    • Selectively allows passage of oxygen, nutrients, and waste.

    • Composed of phospholipids, proteins, and carbohydrates.

  • Differences Between Prokaryotic and Eukaryotic Cells

    • Prokaryotic Cells:

      • Cytoplasm bound by plasma membrane.

      • No organelles bound by membranes.

    • Eukaryotic Cells:

      • Contain membrane-bound organelles which divide the cell into compartments with different environments for various metabolic functions.

  • Cell Size

    • Metabolic requirements set upper limits on cell size.

    • Critical surface area to volume ratio; as cell size increases, volume grows more than surface area, limiting substance cross-membrane diffusion.

    • Larger organisms consist of more cells rather than larger cells.

  • The Nucleus: Information Center

    • Contains most of the cell's genes.

    • Nuclear Envelope:

    • Encloses the nucleus, consisting of a double membrane with lipid bilayers, equipped with pores lined with a pore complex that regulates molecular entry and exit.

    • Nuclear Lamina:

    • Net-like array of protein filaments lining the nuclear side, providing support.

  • Chromosomes and Chromatin

    • Chromosomes:

    • Discrete units of DNA associated with proteins.

    • Chromatin:

    • Condensed form of chromosomes during cell division.

    • Nucleolus:

    • Located within the nucleus, where ribosomal RNA (rRNA) synthesis occurs.

  • Ribosomes

    • Once mRNA reaches the cytoplasm, ribosomes translate it into the protein's primary structure.

    • Comprised of ribosomal RNA and proteins, they carry out protein synthesis either in cytosol (free ribosomes) or on the outside of endoplasmic reticulum or nuclear envelope (bound ribosomes).

  • Endomembrane System

    • Components:

    • Nuclear envelope, Endoplasmic reticulum, Golgi apparatus, Lysosomes, Vacuoles, Plasma membrane.

    • Functions to regulate protein traffic and metabolism, and detoxify poisons. Components may be continuous or connected via vesicle transfer.

  • Endoplasmic Reticulum (ER)

    • Extensive network of membranes, accounting for over half the total membrane in eukaryotic cells.

    • Divided into two regions:

    • Smooth ER:

      • Synthesizes lipids, metabolizes carbohydrates, detoxifies drugs and poisons, stores calcium ions.

    • Rough ER:

      • Contains bound ribosomes that synthesize secretory proteins, distributes transport vesicles, and synthesizes membranes through the addition of phospholipids and proteins.

  • Golgi Apparatus

    • Composed of flattened membranous sacs termed cisternae, involved in modification and storage of ER products, manufacturing macromolecules (e.g., polysaccharides), and sorting/packaging materials into transport vesicles.

  • Lysosomes

    • Membranous sacs of hydrolytic enzymes capable of digesting macromolecules, active in acidic environments. Lysosomal enzymes are produced in the rough ER and transferred to the Golgi apparatus.

  • Phagocytosis:

    • Certain cells can engulf other cells by forming a food vacuole that fuses with lysosomes for digestion.

  • Autophagy:

    • Hydrolytic enzymes recycle the cell's own organic material, surrounded by double membranes that fuse with lysosomes to renew cellular components.

  • Vacuoles

    • Large vesicles derived from the ER and Golgi apparatus.

    • Functions:

    • Food vacuoles formed by phagocytosis.

    • Contractile vacuoles maintain water concentration and pump excess out.

    • Central vacuoles maintain turgor pressure and store inorganic ions, allowing cell growth without new cytoplasm investment.

  • Mitochondria and Chloroplasts

    • Sites for energy conversion: mitochondria convert chemical energy from food during cellular respiration, while chloroplasts convert solar energy to chemical energy during photosynthesis.

  • Endosymbiont Theory

    • Proposed that ancestral prokaryotic cells engulfed smaller, energy-providing cells (mitochondria and chloroplasts), leading to symbiotic relations and separations.

  • Mitochondrial Structure

    • Smooth outer membrane and convoluted inner membrane (cristae) yielding two compartments: intermembrane space and mitochondrial matrix, containing DNA and enzymes for cellular respiration.

  • Chloroplast Structure

    • Contain chlorophyll and enzymes crucial for photosynthesis; include thylakoids (stacked into granum) and stroma (the internal fluid with DNA, ribosomes).

  • Peroxisomes

    • Specialized compartments bounded by a single membrane that produce H2O2 and break down fatty acids while detoxifying harmful compounds.

  • Cytoskeleton

    • A network of fibers extending throughout the cytoplasm, organizing the cell's structures and activities, providing support, and enabling motility through interaction with motor proteins.

  • Components of Cytoskeleton

    • Microtubules:

    • Thickest, consisting of hollow rods made from tubulin polymers, providing shape and guiding organelles.

    • Microfilaments:

    • Thinnest, made of actin, supporting cell shape and aiding motility through cytoplasmic streaming.

    • Intermediate Filaments:

    • Intermediate diameter fibers, providing structural support and anchoring organelles.

  • Microtubule Functions

    • Shaping the cell, guiding organelle movement, and separating chromosomes during cell division.

  • Cilia and Flagella

    • Microtubule projections in eukaryotic cells, aiding movement of unicellular organisms or moving liquid across tissues.

    • Structurally characterized by the arrangement of microtubules in a 9+2 configuration, requiring dynein motor proteins for movement.

  • Extracellular Components and Connections

    • Cells synthesize and secrete materials outside the plasma membrane, which support numerous cellular functions.

  • Cell Walls in Plants

    • Distinct plant cell structures providing protection, shape maintenance, and prevention of excess water uptake, composed of cellulose fibers.

    • Composition:

    • Primary cell wall (thin/flexible), Middle lamella (pectin), and Secondary cell wall (in certain cells).

  • Extracellular Matrix in Animal Cells

    • Composed of glycoproteins including collagen, proteoglycans, and fibronectin forming a complex covering as animals lack cell walls.

  • Cell Junctions

    • Structures enabling cell adherence, interaction, and communication with neighboring cells.

  • Types of Cell Junctions

    • Tight Junctions:

    • Prevent leakage of extracellular fluid.

    • Desmosomes:

    • Fasten cells into strong sheets.

    • Gap Junctions:

    • Provide cytoplasmic channels similar to plasmodesmata in plants.

Chapter 7: Membrane Structure and Function

  • Plasma Membrane

    • Boundary separating living cells from their surroundings, exhibiting selective permeability allowing transit of some substances more readily than others.

  • Membrane Composition

    • Phospholipids are the most abundant lipids in membranes. These are amphipathic molecules with a hydrophobic region and hydrophilic heads.

  • Fluid Mosaic Model

    • Membrane structure is a mosaic of protein molecules bobbing within a fluid lipid bilayer.

    • Proteins are not randomly distributed across the membrane.

  • Factors Affecting Fluidity of Membranes

    • Temperature:

    • Transition from fluid to solid state at lower temperatures depends on lipid types (unsaturated fatty acids yield higher fluidity).

    • Cholesterol:

    • Alters membrane fluidity variably depending on temperature; it restrains movement at warm temperatures and prevents tight packing when cold.

  • Membrane Proteins

    • Integral proteins span the membrane, often forming transmembrane proteins. Peripheral proteins associate via non-covalent interactions.

    • Functions of membrane proteins include carrying channels, facilitating enzymatic activity, signal transduction, and cell-cell recognition.

  • HIV Resistance and Membrane Proteins

    • HIV targets cell-surface protein CD4 and co-receptor CCR5 for infection; resistance occurs in individuals lacking CCR5.

  • Role of Membrane Carbohydrates

    • Cell recognition often occurs through binding of carbohydrates on the extracellular surface, leading to variations among species and individual cell types.

  • Membrane Structure and Selective Permeability

    • Membrane selective permeability is essential for molecular traffic regulation. Hydrophobic molecules pass readily, while hydrophilic molecules struggle to diffuse across.

  • Transport Proteins

    • Facilitators of hydrophilic substance passage across the membrane, including channel proteins like aquaporins and carrier proteins that change shape.

  • Passive Transport

    • Movement of substances without energy investment; based on diffusion along concentration gradients.

  • Osmosis

    • Definition: Diffusion of water across a selectively permeable membrane from lower to higher solute concentration until reaching equilibrium.

  • Tonicity

    • Measures impact of surrounding solutions on cellular water balance:

    • Isotonic:

      • Equal solute concentration with no net water movement.

    • Hypertonic:

      • Higher external concentration, leading to cell shrinking.

    • Hypotonic:

      • Lower external concentration, leading to cell swelling and potential lysis.

  • Osmoregulation

    • Processes managing solute concentrations and water balance, critical for cells lacking rigid walls (e.g., Paramecium).

  • Facilitated Diffusion

    • Passive transport accelerated by specific proteins.

  • Active Transport

    • Energy-consuming process moving solutes against concentration gradients, generally using ATP hydrolysis, e.g., sodium-potassium pump.

  • Electrochemical Gradient

    • Combination of chemical force (ion concentration) and electrical charge difference across membranes driving ion diffusion.

  • Electrogenic Pumps

    • Proteins (e.g., sodium-potassium pump) generating voltage across membranes.

  • Cotransport

    • Active transport indirectly driving substances against their gradients through coupled movement.

  • Bulk Transport

    • Substance transport via larger vesicular mechanisms (exocytosis/endocytosis) requiring energy.

  • Exocytosis

    • Mechanism by which cells secrete molecules through vesicle fusion with the plasma membrane.

  • Endocytosis

    • Process forming vesicles to internalize molecules, divided into:

    • Phagocytosis:

      • Cell engulfs particles and forms food vacuoles.

    • Pinocytosis:

      • Cell gulps dissolved substances in vesicles.

    • Receptor-mediated Endocytosis:

      • Specific substance uptake via receptor clustering and vesicle formation.

Chapter 8: Introduction to Metabolism

  • Energy of Life

    • Living cells are chemical factories carrying out numerous reactions; cellular respiration extracts energy stored in fuels.

    • Bioenergetics: Study of energy flow through organisms.

  • Metabolic Pathways

    • Chemical reaction sequences transforming matter and energy, each step being catalyzed by specific enzymes.

    • Metabolism is the total of all chemical reactions within an organism.

  • Forms of Energy

    • Kinetic Energy: Energy of motion; Thermal Energy: random movement of molecules (“heat” in transfer);

    • Potential Energy: stored energy based on matter's position/structure. Chemical Energy: a type of potential energy vital in chemical reactions.

  • Laws of Energy Transformation

    • Thermodynamics: Study of energy transformations in systems.

    • Isolated systems cannot transfer energy/matter; open systems (like cells) can.

    • First Law of Thermodynamics: Energy of the universe is constant; it can change forms but not be created or destroyed.

    • Second Law of Thermodynamics: Energy transfers increase overall entropy in the universe; spontaneous processes increase disorder.

  • Free-Energy Change (ΔG)

    • Determining spontaneity of reactions involves assessing energy and entropy changes.

    • Formula: \Delta G = \Delta H - T \Delta S where ΔH is change in enthalpy, ΔS is change in entropy, and T is temperature.

  • Exergonic and Endergonic Reactions

    • Exergonic: Net release of free energy; spontaneous.

    • Endergonic: Absorption of free energy; nonspontaneous.

  • ATP in Cellular Work

    • ATP couples exergonic to endergonic reactions, powering cellular processes like chemical work, transport work, and mechanical work.

    • ATP Structure: consists of ribose, adenine, and three phosphate groups.

  • ATP Hydrolysis

    • Breaking terminal phosphate bonds releases energy; the reaction is \text{ATP} + \text{H}2\text{O} \rightarrow \text{ADP} + \text{P}i, with ΔG = −7.3 kcal/mol.

  • Enzymatic Reactions

    • Enzymes lower activation energy barriers in reactions, increasing spontaneity and specificity. The enzyme-substrate complex binds substrates at the active site, often altering the substrate’s form for better fit (induced fit).

  • Factors Affecting Enzyme Activity

    • Temperature and pH can affect enzymatic reactions; each enzyme has optimal conditions for maximum activity.

  • Regulation of Enzyme Activity

    • Regulatory molecules can modify enzyme functions, and allosteric regulation involves binding at sites other than the active site (inhibition or activation).

  • Feedback Inhibition

    • End-products of metabolic pathways inhibit enzymes early in the pathway, preventing resource waste.