Biology End of Year Exam Revision Guide PDF
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This document is a revision guide for biology, focusing on cell structure, microscopy, and cell biology concepts. It covers topics such as prokaryotic and eukaryotic cells, organelles, and cell functions. It also introduces microscopy techniques, including light and electron microscopy.
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Cell Structure Prokaryotic vs. Eukaryotic Cells Prokaryotic Cells: ○ Size: 1-10 μm. ○ No nucleus; DNA is in a nucleoid region (single circular chromosome). ○ Plasmids: Small circular DNA, often carry antibiotic resistance genes. ○ Ribosomes: 70S ribosome...
Cell Structure Prokaryotic vs. Eukaryotic Cells Prokaryotic Cells: ○ Size: 1-10 μm. ○ No nucleus; DNA is in a nucleoid region (single circular chromosome). ○ Plasmids: Small circular DNA, often carry antibiotic resistance genes. ○ Ribosomes: 70S ribosomes for protein synthesis. ○ Cell wall: Made of peptidoglycan (murein). ○ Flagella: Simple structure for movement. ○ Pili: For attachment or conjugation. Eukaryotic Cells: ○ Size: 10-100 μm. ○ DNA within a membrane-bound nucleus (linear chromosomes). ○ Ribosomes: 80S ribosomes in cytoplasm; 70S in mitochondria and chloroplasts. ○ Organelles are compartmentalized by membranes. Organelles and Their Functions 1. Nucleus: ○ Double membrane with nuclear pores; contains nucleolus (site of rRNA synthesis). ○ Controls cell activities via transcription. 2. Mitochondria: ○ Site of ATP synthesis through aerobic respiration. ○ Inner membrane forms cristae; the matrix contains enzymes for the Krebs cycle. 3. Ribosomes: ○ Free in cytoplasm (proteins for internal use) or attached to rough ER (proteins for secretion). 4. Rough ER: ○ Processes and folds proteins synthesized by bound ribosomes. 5. Smooth ER: ○ Synthesizes lipids, steroids, and detoxifies harmful substances. 6. Golgi Apparatus: ○ Modifies, packages, and sorts proteins and lipids into vesicles. ○ Forms lysosomes. 7. Lysosomes: ○ Contain hydrolytic enzymes for digestion (autophagy, autolysis). 8. Chloroplasts (plant cells): ○ Photosynthesis occurs in the thylakoid membranes and stroma. 9. Vacuole (plant cells): ○ Contains cell sap (storage of ions, sugars). ○ Maintains turgor pressure for structural support. 10.Cytoskeleton: ○ Microtubules: Shape, intracellular transport, spindle formation. ○ Microfilaments: Cell movement, cytokinesis. ○ Intermediate filaments: Mechanical strength. Microscopy 1. Light Microscope: ○ Magnification: x1500; resolution ~200 nm. ○ Can observe live specimens. 2. Electron Microscopes: ○ Transmission Electron Microscope (TEM): High resolution, observes internal details. ○ Scanning Electron Microscope (SEM): 3D images of surfaces. 1.1 Cells are the Basic Units of Life Definition: Cells are the smallest structural and functional units of life. Cell Theory: ○ All living organisms are made of cells. ○ Cells arise from pre-existing cells. ○ The cell is the basic unit of structure and function. Types of Organisms: ○ Unicellular: Single-celled (e.g., bacteria, protozoa). ○ Multicellular: Organisms made of many specialized cells (e.g., plants, animals). 1.2 Cell Biology and Microscopy Microscopy is essential to studying cell structure. Light Microscopy: ○ Magnification: Up to x1500. ○ Resolution: ~200 nm (cannot resolve most organelles). ○ Stains enhance contrast (e.g., iodine for plant cells). 1.3 Plant and Animal Cells as Seen with a Light Microscope Plant Cells: ○ Visible structures: Cell wall, plasma membrane, nucleus, cytoplasm, chloroplasts, large central vacuole. Animal Cells: ○ Visible structures: Plasma membrane, nucleus, cytoplasm (organelles not visible unless stained). Comparison: Feature Plant Cells Animal Cells Cell wall Present (cellulose) Absent Chloroplasts Present in photosynthetic cells Absent Vacuole Large, central, permanent Small, temporary if present 1.4 Measuring Size and Calculating Magnification Magnification Formula: Magnification=Image sizeActual size\text{Magnification} = \frac{\text{Image size}}{\text{Actual size}}Magnification=Actual sizeImage size Ensure units are consistent (e.g., convert mm to μm: 1 mm = 1000 μm). Micrometer Measurements: ○ 1 mm = 1000 μm. ○ 1 μm = 1000 nm. Using an Eyepiece Graticule: ○ Calibrate using a stage micrometer. ○ Measure specimen size directly. 1.5 Electron Microscopy Advantages over Light Microscopy: ○ Higher resolution (~0.1 nm). ○ Greater magnification (up to x500,000). Limitations: ○ Specimens must be dead (vacuum environment). ○ Time-consuming preparation and staining (e.g., heavy metals). Plant and Animal Cells as Seen with an Electron Microscope Visible organelles include: ○ Nucleus: Double membrane, nucleolus visible. ○ Mitochondria: Cristae and matrix visible. ○ Chloroplasts: Grana (stacks of thylakoids) and stroma visible. ○ Endoplasmic Reticulum: Rough (with ribosomes) and Smooth. ○ Golgi Apparatus: Series of flattened sacs. ○ Lysosomes: Membrane-bound vesicles. ○ Ribosomes: Smaller dots (80S). Bacteria Structure: ○ Cell wall: Peptidoglycan. ○ Plasma membrane: Regulates entry and exit. ○ Cytoplasm: Contains 70S ribosomes and enzymes. ○ Nucleoid: Circular DNA, no nucleus. ○ Plasmids: Small, additional DNA molecules. ○ Flagella: For motility. ○ Pili: Attachment and conjugation. Reproduction: Binary fission (asexual). Comparing Prokaryotic Cells with Eukaryotic Cells Feature Prokaryotic Cells Eukaryotic Cells Size 1-10 μm 10-100 μm Nucleus Absent Present DNA Circular, naked, in nucleoid region Linear, associated with histones Organelles Non-membrane-bound only (e.g., ribosomes) Membrane-bound (e.g., nucleus, ER) Ribosomes 70S 80S Cell Wall Peptidoglycan Cellulose (plants), absent in animals Viruses Non-cellular Structure: ○ Size: 20-300 nm (smaller than bacteria). ○ Protein coat (capsid) surrounds nucleic acid (DNA or RNA). ○ Some have a lipid envelope derived from the host cell. Examples: ○ DNA viruses: Adenoviruses. ○ RNA viruses: Influenza, HIV. Reproduction: ○ Obligate intracellular parasites (cannot replicate without a host). ○ Lifecycle: Attachment → Entry → Replication → Assembly → Release. Biological molecules: Biochemistry Definition: Biochemistry studies chemical processes within and relating to living organisms. Biomolecules are essential for life and include carbohydrates, lipids, proteins, nucleic acids, and water. Importance: ○ Provide structural components (e.g., cellulose, phospholipids). ○ Act as energy stores (e.g., starch, glycogen). ○ Serve functional roles (e.g., enzymes, hormones, DNA replication). The Building Blocks of Life Elements in Biomolecules: 1. Carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur (CHONPS). 2. Carbon’s ability to form four covalent bonds enables diverse structures like chains, rings, and branched molecules. Four Key Biomolecules: 1. Carbohydrates: Energy storage and structural roles. 2. Lipids: Energy storage, membrane structure, insulation. 3. Proteins: Enzymes, structural components, transport. 4. Water: Universal solvent, participates in metabolic reactions. Monomers, Polymers, and Macromolecules Monomers: Small, basic molecular units. ○ Examples: Glucose (monosaccharide), amino acids, nucleotides. Polymers: Large molecules made of repeating monomer units, formed by condensation reactions. ○ Examples: Starch, proteins, DNA. Macromolecules: Large, complex molecules (e.g., proteins, polysaccharides). Condensation Reaction: Forms covalent bonds between monomers, releasing water. Hydrolysis Reaction: Breaks covalent bonds, using water. Carbohydrates Structure: Contain carbon (C), hydrogen (H), and oxygen (O) in a 1:2:1 ratio (general formula: (CH2O)n(CH_2O)_n(CH2O)n). Monosaccharides: Single sugar units. ○ Examples: Glucose, fructose, galactose. ○ α-glucose vs. β-glucose: Differ in the orientation of the -OH group on carbon 1. Disaccharides: Two monosaccharides joined by a glycosidic bond. ○ Examples: Maltose: Glucose + Glucose. Sucrose: Glucose + Fructose. Lactose: Glucose + Galactose. Polysaccharides: Long chains of monosaccharides. ○ Starch: Energy storage in plants. Amylose: Unbranched, helical structure. Amylopectin: Branched, more easily hydrolyzed. ○ Glycogen: Energy storage in animals, highly branched for rapid energy release. ○ Cellulose: Structural component in plant cell walls; β-glucose chains linked by hydrogen bonds to form microfibrils. Lipids Structure: Contain carbon, hydrogen, and oxygen but have a lower proportion of oxygen than carbohydrates. Types: ○ Triglycerides: Glycerol + 3 fatty acids (joined by ester bonds through condensation reactions). Saturated fatty acids: No double bonds, solid at room temperature (e.g., butter). Unsaturated fatty acids: One or more double bonds, liquid at room temperature (e.g., olive oil). ○ Phospholipids: Glycerol, 2 fatty acids, and a phosphate group. Hydrophilic head (phosphate) and hydrophobic tails (fatty acids). Major component of cell membranes (phospholipid bilayer). ○ Steroids: Four fused carbon rings (e.g., cholesterol, hormones like estrogen and testosterone). Functions: ○ Long-term energy storage. ○ Insulation and protection. ○ Components of membranes. ○ Signaling molecules (e.g., hormones). Proteins Structure: Contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur. Monomer: Amino acids. ○ General structure: Central carbon atom bonded to an amino group (-NH2), carboxyl group (-COOH), hydrogen atom, and an R group (variable side chain). Formation: ○ Amino acids joined by peptide bonds through condensation reactions. Levels of Protein Structure: ○ Primary: Sequence of amino acids in a polypeptide chain. ○ Secondary: Folding into α-helices or β-pleated sheets (stabilized by hydrogen bonds). ○ Tertiary: 3D folding due to interactions between R groups (hydrogen bonds, ionic bonds, disulfide bridges). ○ Quaternary: Association of multiple polypeptide chains (e.g., hemoglobin). Functions: ○ Enzymes (e.g., amylase). ○ Structural (e.g., collagen, keratin). ○ Transport (e.g., hemoglobin). ○ Immune response (e.g., antibodies). Water Structure: Two hydrogen atoms covalently bonded to an oxygen atom. The molecule is polar due to the uneven distribution of charge. Properties and Importance: 1. Solvent: Dissolves polar molecules and ions (e.g., glucose, salts). Medium for biochemical reactions. 2. High Specific Heat Capacity: Absorbs large amounts of heat without a significant temperature change. Stabilizes aquatic environments and body temperature. 3. High Latent Heat of Vaporization: Evaporation of water (e.g., sweat) cools organisms. 4. Cohesion and Adhesion: Water molecules stick together (cohesion) and to surfaces (adhesion). Enables capillary action in plants. 5. Density: Ice is less dense than liquid water, allowing it to float and insulate aquatic life. What is an Enzyme? Definition: Enzymes are biological catalysts that speed up chemical reactions without being consumed. Structure: ○ Globular proteins with a specific 3D shape. ○ The active site is a region where substrates bind, complementary in shape to the substrate. Importance: ○ Lower activation energy, enabling reactions to proceed at a faster rate and under milder conditions (e.g., body temperature). ○ Highly specific to substrates due to their unique active sites. Mode of Action of Enzymes 1. Formation of Enzyme-Substrate Complex: ○ Substrate binds to the enzyme's active site. ○ Binding is specific and follows the lock-and-key model or the induced fit model: Lock-and-Key Model: The active site is a perfect fit for the substrate. Induced Fit Model: The active site molds to the substrate for a better fit. 2. Catalysis: ○ Enzymes catalyse the reaction, breaking or forming bonds. ○ Products are released from the active site. 3. Reusability: ○ Enzymes remain unchanged after the reaction and can be reused. Example: Catalase catalyzing the decomposition of hydrogen peroxide into water and oxygen. Investigating the Progress of an Enzyme-Catalyzed Reaction Measure how quickly substrate is consumed or product is formed over time. Key Techniques: 1. Measuring Gas Production: Collect oxygen released during the catalysis of hydrogen peroxide by catalase. 2. Color Change: Use colorimetric assays (e.g., starch breakdown by amylase monitored with iodine). 3. Mass Loss: Record the loss of mass in reactions producing gaseous products. Reaction Phases: 1. Initial rate: Rapid due to a high concentration of substrate. 2. Plateau: Reaction rate decreases as substrate is consumed and fewer enzyme-substrate complexes form. Factors that Affect Enzyme Action 1. Temperature: ○ Optimal Temperature: Maximum enzyme activity. ○ Too high: Enzymes denature (loss of 3D structure). ○ Too low: Reduced kinetic energy slows reactions. 2. pH: ○ Enzymes have an optimal pH (e.g., pepsin in the stomach: pH 2; amylase in saliva: pH 7). ○ Deviation from optimal pH disrupts ionic bonds, altering the active site. 3. Substrate Concentration: ○ Increases reaction rate up to a saturation point where all active sites are occupied. 4. Enzyme Concentration: ○ Directly proportional to reaction rate, provided substrate is not limiting. 5. Presence of Cofactors: ○ Non-protein molecules or ions (e.g., zinc, magnesium) that assist enzyme activity. Comparing Enzyme Affinities Enzyme Affinity: Refers to how strongly an enzyme binds to its substrate. Michaelis-Menten Constant (KmK_mKm): ○ Represents the substrate concentration at which the enzyme works at half its maximum velocity (VmaxV_{max}Vmax). ○ Low KmK_mKm: High affinity (enzyme binds substrate strongly). ○ High KmK_mKm: Low affinity (enzyme binds substrate weakly). Using Lineweaver-Burk Plot: Double reciprocal graph to determine KmK_mKmand VmaxV_{max}Vmax. Enzyme Inhibitors 1. Competitive Inhibitors: ○ Compete with substrate for binding to the active site. ○ Can be overcome by increasing substrate concentration. ○ Example: Malonate inhibits succinate dehydrogenase. 2. Non-Competitive Inhibitors: ○ Bind to an allosteric site (not the active site), changing the enzyme’s shape and reducing its activity. ○ Cannot be overcome by increasing substrate concentration. ○ Example: Cyanide inhibits cytochrome c oxidase. 3. Irreversible Inhibitors: ○ Form covalent bonds with the enzyme, permanently disabling it. ○ Example: Nerve gas inhibits acetylcholinesterase. Immobilizing Enzymes Definition: Enzymes are fixed to a solid support or trapped in a gel to restrict movement. Methods: ○ Adsorption onto inert surfaces (e.g., glass beads). ○ Entrapment in alginate beads or a cellulose matrix. ○ Covalent bonding to a carrier. Advantages: ○ Enzymes can be reused. ○ Products are enzyme-free (easier separation). ○ Increased stability and resistance to denaturation. Applications: ○ Industrial Processes: Lactase to hydrolyze lactose in milk. ○ Biosensors: Glucose oxidase immobilized in blood sugar monitors. The Importance of Membranes Definition: Membranes are selectively permeable barriers that control the movement of substances into and out of cells and organelles. Functions: 1. Compartmentalization: Separate cellular environments (e.g., cytoplasm from the extracellular environment). Maintain conditions for specific biochemical reactions (e.g., enzymes in lysosomes). 2. Communication: Facilitate cell signaling through receptors and recognition. 3. Transport: Regulate entry and exit of nutrients, waste, and signaling molecules. 4. Site of Biochemical Reactions: Provide surfaces for reactions (e.g., ATP synthesis in mitochondria). Structure of Membranes Fluid Mosaic Model (proposed by Singer and Nicolson, 1972): 1. Phospholipid Bilayer: Hydrophilic (polar) heads face outward. Hydrophobic (nonpolar) tails face inward. 2. Proteins and lipids are embedded within the bilayer, forming a dynamic structure. Key Components: 1. Phospholipids: Form the bilayer; provide flexibility and create a hydrophobic barrier. 2. Proteins: Integral (embedded) and peripheral (on the surface). Involved in transport, signaling, and enzymatic activity. 3. Cholesterol: Embedded within animal cell membranes. Provides stability, reduces fluidity at high temperatures, and prevents solidification at low temperatures. 4. Glycolipids and Glycoproteins: Lipids or proteins with carbohydrate chains. Involved in cell recognition and signaling. Roles of the Molecules Found in Membranes 1. Phospholipids: ○ Form a semi-permeable barrier. ○ Allow passage of small, nonpolar molecules (e.g., oxygen, carbon dioxide). 2. Proteins: ○ Channel Proteins: Facilitate diffusion of specific ions or molecules. ○ Carrier Proteins: Involved in active transport and facilitated diffusion. ○ Receptor Proteins: Bind signaling molecules and initiate cellular responses. 3. Cholesterol: ○ Modulates membrane fluidity and mechanical stability. 4. Glycoproteins and Glycolipids: ○ Serve as antigens for immune recognition. ○ Facilitate cell adhesion and communication. Cell Signaling Definition: The process by which cells communicate to coordinate responses and activities. Process: ○ Reception: A signaling molecule (ligand) binds to a specific receptor on the membrane. Examples: Hormones, neurotransmitters. ○ Transduction: The receptor undergoes a conformational change, triggering a cascade of intracellular events. Example: Activation of secondary messengers like cAMP. ○ Response: A specific cellular activity is triggered (e.g., gene expression, enzyme activation). Types of Signaling: ○ Autocrine: Signal acts on the same cell that produced it. ○ Paracrine: Signal acts on nearby cells. ○ Endocrine: Signal travels through the bloodstream to distant cells. Receptor Examples: ○ Ion Channel Receptors: Open or close in response to a ligand. ○ G-Protein Coupled Receptors: Activate intracellular pathways via G-proteins. ○ Enzyme-Linked Receptors: Activate enzymatic activity upon ligand binding (e.g., tyrosine kinases). Movement of Substances Across Membranes 1. Passive Transport (does not require energy): ○ Diffusion: Movement of molecules from a high to low concentration gradient. Examples: Oxygen, carbon dioxide. ○ Facilitated Diffusion: Involves channel or carrier proteins for polar molecules (e.g., glucose). ○ Osmosis: Diffusion of water across a semipermeable membrane from low solute to high solute concentration. 2. Active Transport (requires energy in the form of ATP): ○ Moves substances against their concentration gradient. ○ Involves carrier proteins. Example: Sodium-potassium pump. 3. Bulk Transport: ○ Transport of large molecules or particles. Endocytosis: Phagocytosis: Engulfing solid particles (e.g., bacteria by white blood cells). Pinocytosis: Engulfing liquids or small solutes. Exocytosis: Vesicles fuse with the membrane to release contents outside the cell (e.g., secretion of enzymes). 4. Factors Affecting Transport: ○ Membrane permeability. ○ Concentration gradient. ○ Temperature. ○ Surface area to volume ratio. Growth and Reproduction Importance: ○ Growth: Increase in cell number through mitosis to build tissues and organs. ○ Reproduction: Single-celled organisms reproduce via mitosis to produce genetically identical offspring. ○ Tissue repair: Replacement of damaged or dead cells (e.g., skin regeneration). Asexual Reproduction: ○ Mitosis produces offspring without genetic variation (e.g., binary fission in bacteria). Chromosomes Structure: ○ DNA is tightly coiled around histone proteins, forming chromatin. ○ During cell division, chromatin condenses into visible chromosomes. Composition: ○ Each chromosome consists of two sister chromatids joined at a centromere. ○ Telomeres are repetitive sequences at the ends of chromosomes that protect genetic material. Ploidy Levels: ○ Diploid (2n2n2n): Two sets of chromosomes (e.g., somatic cells in humans). ○ Haploid (nnn): One set of chromosomes (e.g., gametes in humans). Human Chromosome Count: 46 chromosomes (23 pairs). The Cell Cycle Definition: The sequence of events that a cell undergoes from one division to the next. 1. Interphase (90% of the cycle): ○ G1 Phase (Gap 1): Cell growth, organelle production, and protein synthesis. ○ S Phase (Synthesis): DNA replication occurs, doubling the genetic material. ○ G2 Phase (Gap 2): Preparation for mitosis; synthesis of spindle proteins. 2. M Phase (Mitotic Phase): ○ Includes mitosis and cytokinesis. 3. Checkpoints: Ensure accuracy: ○ G1 Checkpoint: Verifies cell size, nutrients, and DNA integrity. ○ G2 Checkpoint: Ensures DNA replication is complete and accurate. ○ M Checkpoint: Confirms correct spindle attachment before anaphase. Mitosis Definition: Division of the nucleus resulting in two genetically identical daughter cells. Stages: ○ Prophase: Chromosomes condense and become visible. Nuclear envelope breaks down. Spindle fibers form and attach to centromeres. ○ Metaphase: Chromosomes align at the metaphase plate (center of the cell). ○ Anaphase: Sister chromatids are pulled apart by spindle fibers to opposite poles. ○ Telophase: Chromosomes decondense into chromatin. Nuclear envelopes reform around each set of chromosomes. Cytokinesis: ○ Division of the cytoplasm. ○ In animal cells: Cleavage furrow forms. ○ In plant cells: A cell plate forms, leading to new cell walls. The Role of Telomeres Definition: Telomeres are repetitive DNA sequences at the ends of chromosomes. Functions: ○ Protect chromosomes from degradation and fusion with other chromosomes. ○ Prevent loss of essential genes during DNA replication. Telomere Shortening: ○ Occurs with each cell division; associated with aging and the Hayflick limit (maximum number of divisions). ○ Telomerase enzyme extends telomeres in certain cells (e.g., stem cells, cancer cells). The Role of Stem Cells Definition: Undifferentiated cells capable of self-renewal and differentiation into specialized cell types. Types: ○ Embryonic Stem Cells: Pluripotent: Can differentiate into any cell type in the body. ○ Adult Stem Cells: Multipotent: Limited to differentiating into specific cell types (e.g., hematopoietic stem cells for blood cells). Functions: ○ Regeneration and repair of tissues. ○ Used in medical therapies (e.g., bone marrow transplants). Applications: ○ Research on treating diseases like Parkinson’s, diabetes, and spinal cord injuries. Cancers Definition: Uncontrolled cell division resulting in abnormal growths (tumors). Causes: ○ Mutations: Changes in genes that regulate the cell cycle (e.g., proto-oncogenes to oncogenes, tumor suppressor gene loss). ○ Carcinogens: Environmental factors like tobacco smoke, radiation, and certain chemicals. ○ Genetic Predisposition: Inherited mutations (e.g., BRCA1/BRCA2 in breast cancer). Types of Tumors: ○ Benign: Non-invasive, do not spread to other tissues. ○ Malignant: Invasive, metastasized to other parts of the body via blood or lymph. Treatments: ○ Surgery: Removal of tumors. ○ Chemotherapy: Drugs to kill dividing cells. ○ Radiation: Targets and destroys cancer cells. ○ Immunotherapy: Boosts the immune system to target cancer cells.