Lecture Notes on Cell Biology PDF

Lecture 2 (macromolecules, cell theory, microscopy) 1. Molecules of life Water: The solvent of life, dissolving polar and charged molecules due to its polarity. Types of Macromolecules: o Carbohydrates: Polymers of sugars (e.g., glucose). o Lipids: Not true polyme...

Lecture 2 (macromolecules, cell theory, microscopy) 1. Molecules of life Water: The solvent of life, dissolving polar and charged molecules due to its polarity. Types of Macromolecules: o Carbohydrates: Polymers of sugars (e.g., glucose). o Lipids: Not true polymers but hydrophobic molecules (e.g., fats, oils). o Proteins: Polymers of amino acids; their structure is determined by the sequence and properties of amino acids. o Nucleic Acids: Polymers of nucleotides (e.g., DNA, RNA). Polymerization: The process of linking monomers together (dehydration synthesis), while depolymerization (hydrolysis) involves breaking down polymers by adding water. Protein Structure: o Primary: Linear sequence of amino acids. o Secondary: Formation of α-helices and β-sheets through hydrogen bonding. o Tertiary: Folding of the polypeptide into a 3D structure determined by chemistry of amino acid sidechains. o Quaternary: Interaction of multiple proteins to form a complex. 2. Cell Theory Core Principles: o All living organisms are composed of one or more cells. o The cell is the basic unit of structure and function in living organisms. o All cells arise from the division of pre-existing cells. 3. Microscopy Types: o Light Microscopy: Uses light to view cells and tissues. Variants include: ▪ Brightfield: Direct light transmission, often requires staining for better contrast. ▪ Darkfield: Illuminates the sample from the side, so that only light that is scattered by the specimen reaches the objective lens. ▪ Phase-Contrast: Enhances contrast by shifting light phases. ▪ Differential Interference Contrast (DIC): Enhances contrast and gives a pseudo-3D appearance to specimens. o Electron Microscopy: ▪ Transmission Electron Microscopy (TEM): Provides detailed internal views of thinly sliced samples. ▪ Scanning Electron Microscopy (SEM): Produces detailed 3D images of surfaces. Concepts:  o Resolution: The ability to distinguish two objects as separate entities. o Magnification: increasing the apparent size of the specimen, as a lens does. Higher magnification increases resolution. o Contrast: Enhances the visibility of structures within the sample. Does not increase resolution. Lecture 3 (microscopy, Prokaryotes vs. Eukaryotes) 1. Microscopy Types of Microscopy: o Light Microscopy: Includes techniques such as brightfield, darkfield, phase- contrast, and Differential Interference Contrast (DIC), which enhance contrast by exploiting light-scattering properties. o Fluorescence Microscopy: Utilizes fluorophores to visualize specific structures by emitting light when excited by photons. This method allows observation of live specimens and specific cellular components. o Electron Microscopy (EM): Provides higher resolution due to the shorter wavelength of electrons. Includes: ▪ Transmission Electron Microscopy (TEM): Thin sections of specimens are imaged, creating 2D images with high detail. ▪ Scanning Electron Microscopy (SEM): Visualizes 3D surface contours of specimens, typically at lower magnifications. Key Concepts: o Fluorescence: Occurs when an electron absorbs light, moves to a higher energy state, and emits light at a longer wavelength. o Advantages of Fluorescence Microscopy: Visualization of specific cellular structures, ability to observe live cells, and applications in imaging molecules like proteins and actin filaments. o Resolution in Microscopy: Electron microscopes provide much higher resolution than light microscopes but require fixed (dead) specimens. 2. Prokaryotes vs. Eukaryotes Prokaryotes: o Typically small (1-3 µm), unicellular organisms such as bacteria and archaea. o Have a nucleoid instead of a nucleus and contain a single circular chromosome. o Lack membrane-bound organelles. Eukaryotes: o Larger cells (10-100 µm), which include animals, plants, fungi, and protists. o Contain membrane-bound organelles, including a nucleus that houses linear chromosomes. o Can be unicellular or multicellular.  Similarities: Both prokaryotes and eukaryotes share fundamental features like a plasma membrane, cytoplasm, ribosomes, and a cytoskeleton. Lecture 4 (Prokaryotes vs. Eukaryotes, Methods, and Organelles) 1. Prokaryotes vs. Eukaryotes Shared Features: Both cell types have essential components like DNA (genetic material), ribosomes for protein synthesis, a plasma membrane, and cytoplasm. Differences: Prokaryotic cells lack a true nucleus and membrane-bound organelles, while eukaryotic cells have a nucleus, mitochondria, and other organelles. 2. Cellular Organelles and Structures Plasma Membrane: Composed of a phospholipid bilayer with embedded proteins, regulating the entry and exit of substances. Cytoplasm: Contains the cytosol (liquid component) and organelles where many metabolic reactions occur. Ribosomes: Complexes of proteins and RNA that synthesize proteins from mRNA; prokaryotic ribosomes (70S) are smaller than eukaryotic ribosomes (80S). Cytoskeleton: A network of filaments in the cytoplasm responsible for maintaining cell shape, aiding in cell division, and transporting substances within the cell. 3. Research Methods Differential Centrifugation: A technique used to separate cell components based on size and density. Involves spinning samples at different speeds to isolate organelles of interest (e.g. nuclei, mitochondria). Green Fluorescent Protein (GFP): A protein derived from jellyfish that emits green light when exposed to blue light. GFP is widely used in biology to visualize cellular structures, processes, and dynamics in living specimens. LECTURE 5 (nucleus, endomembrane) 1. The Nucleus Structure: o Surrounded by a double membrane called the nuclear envelope, which contains nuclear pores to regulate the entry and exit of molecules, which is gated by the nuclear pore complex.  o Chromatin: DNA and associated proteins within the nucleus. o Nucleolus: A region responsible for assembling ribosomal subunits. o Nucleoplasm: The "cytoplasm" within the nucleus. Function: o Stores genetic material (DNA) and coordinates activities such as growth, metabolism, and protein synthesis. 2. The Endomembrane System A network of membranes that compartmentalizes the cell and regulates the movement of molecules within cells. Components: o Nuclear Envelope: Continuous with the rough endoplasmic reticulum. o Endoplasmic Reticulum (ER): ▪ Rough ER: Studded with ribosomes; involved in protein synthesis, folding, and modification. ▪ Smooth ER: Lacks ribosomes; involved in lipid synthesis and detoxification. o Golgi Apparatus: Modifies proteins received from the ER, adds finishing touches like sugars, and sorts them for delivery. o Vesicles: Transport materials between different parts of the endomembrane system, such as from the ER to the Golgi. o Lysosomes: Contain digestive enzymes to break down waste materials and cellular debris. o Plasma Membrane: Regulates what enters and exits the cell. Concepts: o Compartmentalization: Different metabolic processes can occur in specific, controlled environments within the cell. o Membrane Trafficking: Movement of proteins and other molecules through vesicles between organelles. o Protein Processing: Proteins are synthesized in the ER, modified in the Golgi, and transported to their final destinations. 3. Vesicle Trafficking Process: o Exocytosis: Vesicles move materials from the ER to the Golgi and then to the plasma membrane to be secreted from the cell. o Endocytosis: The plasma membrane engulfs external materials and brings them into the cell in vesicles. Example: Neurotransmitter release (exocytosis) and viral entry into cells (endocytosis). Lecture 6 (endomembrane, semi-autonomous, cytoskeleton) 1. Endomembrane System Components: o Nuclear Envelope: Controls what enters and exits the nucleus. o Endoplasmic Reticulum (ER): ▪ Rough ER: Protein synthesis and folding. ▪ Smooth ER: Lipid synthesis and detoxification. o Golgi Apparatus: Modifies proteins and sorts them into vesicles for transport. o Vesicles: Transport materials between cellular compartments. o Lysosomes: Digestive organelles that break down waste and engulfed materials. o Vacuoles: Large structures in plants and fungi that regulate turgor pressure and store nutrients. o Plasma Membrane: Regulates what enters and leaves the cell. 2. Semi-Autonomous Organelles Mitochondria and Chloroplasts: o Generate energy (ATP in mitochondria, sugars in chloroplasts). o Mitochondria are involved in respiration, and chloroplasts perform photosynthesis. o Both organelles have their own DNA and ribosomes, replicate independently, and have double membranes. o They originated from ancient prokaryotic symbionts. 3. Cytoskeleton Components: o Microtubules: Polymers of tubulin that maintain cell shape, aid in cell division, and serve as tracks for organelle movement. o Microfilaments: Polymers of actin that support organelle movement, cell movement, division, and structural support. o Intermediate Filaments: Polymers of intermediate filament proteins; found in some eukaryotes like animals but not in plants or fungi. Functions: Maintain cell shape, provide mechanical support, cell adhesion. Lecture 7 (cytoskeleton, ECM) 1. Cytoskeleton Components:  o Intermediate Filaments: Provide structural support and adhesion. Found in animal cells, they are made of proteins like keratin and collagen. Plants and fungi lack intermediate filaments, relying on cell walls for structural support. o Microtubules: Composed of tubulin, these structures are involved in maintaining cell shape, enabling intracellular transport, and facilitating cell division. Motor proteins kinesins and dyneins move along microtubules, carrying vesicles and organelles. o Microfilaments: Made of actin, microfilaments support cell shape, movement, and division. Myosin motor proteins walk along microfilaments, playing a role in muscle contraction and cellular migration. Functions: o Cell shape and polarity: Microtubules and microfilaments help maintain cell shape. o Cell division: Microtubules organize chromosomes during mitosis, while microfilaments aid in cytokinesis. o Intracellular transport: Motor proteins use the cytoskeleton to transport organelles and vesicles. o Movement: Cilia and flagella, driven by microtubules and dynein, facilitate cell movement or fluid movement over cell surfaces. 2. Extracellular Matrix (ECM) Components: o Animals: ECM is composed primarily of proteins (e.g., collagen) and glycoproteins. It provides structural support, cell adhesion, cell shape. o Plants, Fungi, Bacteria: The ECM takes the form of cell walls. Plant cell walls are primarily composed of cellulose, fungi use chitin, and bacteria have peptidoglycan. ECM Functions: o Support: Provides structural integrity to tissues and organs. o Cell adhesion: Holds cells together or attaches them to surfaces. o Protection: Acts as a barrier against physical damage and pathogens. o Intercellular communication: Allows communication between cells and facilitates selective transport through structures like plasmodesmata (plants) and gap junctions (animals). Lecture 8: Membrane Structure and Function 1. Membrane Structure and Composition: o Phospholipid bilayer forms the basic structure, with hydrophilic heads facing water and hydrophobic tails avoiding water. o Membrane asymmetry: The outer and inner leaflets differ in lipid, protein, and carbohydrate composition. o Membranes are fluid, described by the "fluid mosaic model," allowing flexibility and the proper function of embedded proteins. 2. Membrane Fluidity: o Factors influencing fluidity: temperature, phospholipid composition (degree of unsaturation, tail length), and cholesterol. o Cholesterol acts as a "fluidity buffer," maintaining stability under temperature fluctuations. 3. Membrane Proteins: o Integral and peripheral proteins serve various roles such as transporters, enzymes, signal receoptors, and cell recognition. o Integral membrane proteins contain stretches of non-polar (and thus hydrophobic) amino acids that span the membrane. These are referred to as transmembrane domains. 4. Membrane Transport: o Passive transport requires no energy and includes simple diffusion and facilitated diffusion. o Active transport requires energy (ATP) to move molecules against concentration gradients. Lecture 9: Membrane Transport 1. Types of Membrane Transport: o Passive Transport: Movement down concentration gradients (high to low); includes diffusion and facilitated diffusion. o Facilitated Diffusion: Requires transport proteins (channels, gated channels, carrier proteins) to help molecules cross the membrane. o Active Transport: Moves molecules against gradients using energy; two types: ▪ Primary Active Transport: Uses ATP (e.g., sodium-potassium pump). ▪ Secondary Active Transport: Uses energy from electrochemical gradients (e.g., sodium-glucose co-transporter). 2. Endocytosis and Exocytosis: o Endocytosis: Uptake of substances via vesicles (includes receptor-mediated endocytosis, pinocytosis, phagocytosis). o Exocytosis: Release of substances from cells through vesicle fusion with the membrane. Lecture 10: Osmosis and Active Transport 1. Osmosis: o The movement of water across a semi-permeable membrane toward regions of higher solute concentration. o Cells can shrink (hypertonic), swell (hypotonic), or remain stable (isotonic) based on the surrounding solution. 2. Active Transport Examples: o Primary Active Transport: Proton pumps and sodium-potassium pumps maintain concentration gradients by using ATP. o Secondary Active Transport: Utilizes ion gradients (e.g., sodium-glucose cotransport). 3. Signal Transduction: o Key roles of transporters, enzymes, and receptor proteins in transmitting signals across membranes. o Signaling pathways often involve phosphorylation cascades, amplifying very faint extracellular signals (e.g., hormones). Lecture 11: Signal Transduction and Energy Storage 1. Energy in Gradients: o Concentration gradients across membranes store potential energy, used to drive cellular processes (e.g., active transport). o Electrochemical gradients, such as those created by the sodium-potassium pump, generate voltage across membranes (important for nerve function). 2. Signal Transduction Pathways: o Signal transduction involves receptor proteins that activate intracellular pathways (e.g., phosphorylation cascades). o Small signals can be amplified to produce larger responses (e.g., hormone action). 1. Cell Cycle Overview: o The cell cycle is the life cycle of a cell, involving growth, DNA replication, and division. o Prokaryotes divide through binary fission, while eukaryotes undergo mitosis. 2. Stages of the Eukaryotic Cell Cycle: o Interphase: ▪ G1 phase: Cell grows and prepares for DNA synthesis. ▪ S phase: DNA is replicated. ▪ G2 phase: Cell prepares for mitosis. o G0 phase: Cells can exit the cycle and enter a state of terminal differentiation or re-enter the cycle. 3. Prokaryotic Cell Cycle: o Prokaryotes, which have a single circular chromosome, undergo binary fission. o DNA replication and cell division occur rapidly, with minimal separation of stages. 4. Mitosis: o Mitosis is the division of eukaryotic cells and consists of several phases: ▪ Prophase: Chromosomes condense, nuclear envelope begins breaking down. ▪ Prometaphase: Nuclear envelope breaks down and microtubules attach to chromosomal kinetochores and move them toward the middle of the spindle. ▪ Metaphase: Chromosomes align at the metaphase plate. ▪ Anaphase: Sister chromatids separate and move to opposite poles. ▪ Telophase: Chromosomes decondense, nuclear envelope reforms, spindle microtubules are lost. o Cytokinesis: Cytoplasm divides, producing two daughter cells. Typically overlaps to varying degrees with anaphase and telophase. 5. Chromosome Structure: o During replication, a chromosome forms two sister chromatids connected by a centromere. o Chromatin condenses into visible chromosomes during mitosis. o The mitotic spindle, composed of microtubules, organizes and moves chromosomes. 6. Microtubules and Spindle Assembly: o Microtubules play a critical role in chromosome movement during mitosis. o Kinetochore microtubules attach to chromosomes, while non-kinetochore and astral microtubules help in spindle positioning and maintaining spindle integrity. 7. Anaphase Mechanisms: o In Anaphase A, kinetochores shorten microtubules, pulling chromatids to poles. o In Anaphase B, non-kinetochore microtubules elongate the spindle.