[BIO 110 LAB] Quiz_Exam Reviewer (_).pdf

Lab 1: Writing a scientific report Title: First record of hybridization between green Chelonia mydas and hawksbill Eretmochelys imbricata sea turtles in the Southeast Pacific Authors: Kelez, Velez-Zuazo, Pacheco (2016) Questions: 1. Problem 2. Purpose...

Lab 1: Writing a scientific report Title: First record of hybridization between green Chelonia mydas and hawksbill Eretmochelys imbricata sea turtles in the Southeast Pacific Authors: Kelez, Velez-Zuazo, Pacheco (2016) Questions: 1. Problem 2. Purpose 3. Hypothesis 4. Clearly conducted? Why? 5. Results related to hypothesis? 6. Discussion consistent with findings? 7. Consistent reference format? 8. Clearly written and understandable? 9. Strengths and weaknesses? 10. Abstract Summary: Hybridity between C. mydas and E. imbricata in southeast Pacific regions may be due to… 1. Overlapping habitats 2. The disparity of population sizes, with C. mydas being more abundant, which may lead to hybridization, given the scarcity among E. imbricata during the breeding season. Evidence/s: Hybrid sea turtle sample found in El Ñuro had similar morphological characteristics as C. mydas and E. impricata, as well as similar lineage identification and origin with the latter Importance: ○ Communication: To clearly communicate your key message about why your scientific findings are meaningful ○ Documentation: To document the research process and results for future reference, allowing others to replicate the study or build upon the findings ○ To establish hypotheses in order to create a framework/guide in conducting an experiment Lab 2: Transport of Substances Across the Cell Membrane Importance: To discuss the different factors affecting the movement of molecules across the cell membrane Notes on lab activity: ○ Diffusion in water: - Materials/methods: 1. 2 half-filled test tubes: Distilled, tap 2. 2 crystals of potassium permanganate (KMnO4) 3. Wait until purplish, light color - Results: 1. Occurred faster in distilled water than in tap water 2. Distilled water does not contain impurities; whereas  3. Tap water contains other molecules from impurities, which can hinder diffusion ○ Diffusion in colloid: - Materials/methods: 1. 3 test tubes filled with hardened 5% gelatin solution 2. 1 mL of each reagents into separate tubes: (1) potassium permanganate (2) methylene blue (3) congo red 3. Observe and record the time required for the stains to reach the bottom of each tube - Results: Methylene blue diffused the farthest (less viscosity = quicker diffusion time) - Affecting factors: 1. Molecular weight 2. Concentration gradient 3. Temperature 4. Viscosity 5. Solubility 6. Surface area; and 7. Agitation are pointed to implicate diffusion time ○ Dialysis - Purpose: To test the presence of chloride and calcium ions - Materials/methods: 1. Combine 3 mL of calcium chloride (CaCl2) solution and 2 mL of methylene blue 2. Seal the mouth of the test tube with a piece of dried longganisa skin (secure with thread or a rubber band) 3. Face test tube down and immerse in 20 mL distilled water 4. Aspirate about 2-4 drops of water from the beaker every 30 seconds; place a drop of it in each of two separate test tubes 5. 1st test tube: Add a drop of silver nitrate; 2nd test tube: Add a drop of ammonium oxalate 6. Repeat until the appearance of a white, cloudy precipitate - Results: 1. First to diffuse: Chloride test tube (silver nitrate solution) and methylene blue solution 2. Second (last) to diffuse: Calcium test tube (ammonium oxalate solution) - Affecting factors: 1. Molecular size = Can affect its velocity as it travels through the membrane; 2. Larger molecules move slower than smaller molecules during cell transport ○ Osmosis (longganisa skin) - Materials/methods: 1. 5 mL of 30% sucrose solution in a small test tube 2. Cover the mouth of the test tube with a piece of longganisa skin (secure with thread or a rubber band) 3. Record the weight of this test tube 4. Carefully invert the test tube and mark the level of the liquid inside 5. Immerse the test tube with the sealed mouth oriented downwards in 30 mL of distilled water 6. Leave the tube immersed in this position for about 2 hours. 7. Record the level of the water inside the tube and of the weight of the tube - Results: Increase of weight and height - Affecting factors/Interpretation: 1. Osmosis: Movement of water from low to high solute concentration across a semipermeable membrane; unbalanced concentration 2. Semipermeable membrane = longganisa skin 3. Low solute concentration = Distilled water 4. High solute concentration = Sucrose solution ○ Osmosis in red blood cells - Materials/methods: 1. Blood from a willing volunteer 2. Slide A: 0.07M NaCl solution 3. Slide B: 0.15 M NaCl solution 4. Slide C: 0.30 M NaCl solution 5. Mix the blood and the NaCl solutions thoroughly, and smear the mixture evenly on the surface of the slides 6. View these slides under separate microscopes 7. Measure the diameter of the cells in each slide (using an ocular micrometer) every 5 minutes for about one hour - Affecting factors/Interpretation: 1. Slide A = Hypotonic solution 2. Slide B = Isotonic solution 3. Slide C = Hypertonic solution  Quick general notes: Cell transport system The movement of substances across the cell membrane either into or out of the cell Cell membrane ○ Made up of a phospholipid bilayer Hydrophilic (water-loving) head non-polar Made up of phosphate and glycerol Hydrophobic (water-fearing) tail non-polar Saturated fatty acids = Single bonds between hydrocarbon chains; solid at room temperature Unsaturated fatty acids = Double cis bonds between hydrocarbon chains (causes a bend or “kink” in chain); liquid at room temperature ○ Made up of membrane lipids Phospholipids (most abundant) Passage (1) Hydrophilic head (choline, phosphate, glycerol), (2) hydrophobic tail (2 fatty acid chains) Controls substances in and out of the cell Forms basic structure of membrane bilayer Cholesterol Maintenance, stability Hydroxyl group (-OH) Modulates fluidity Membrane stability Glycolipids (glycerol) Interaction and protection lipid part (similar to phospholipids), carbohydrate group Cell recognition and communication Adhesion and protection Immune responses; interacts with specific molecules on the surfaces of other cell Sphingolipids Structural integrity (1) Hydrophobic region (sphingoid long chain base, fatty acid chain attached by amide bond at carbon 2), (2) hydrophilic region (phosphate groups, sugar residues, and/or hydroxyl group)  Formation of lipid rafts (specialized membrane microdomains that organize and concentrate certain proteins and lipids) Signals pathways that regulate cell growth, apoptosis, and differentiation ○ Made up of membrane proteins (1) Integral membrane proteins Functions: ○ Penetrates the hydrophobic interior of the lipid bilayer ○ Molecule transfer (integral region) ○ Cell receptors Classes ○ Transmembrane proteins/Integral Polytopic Proteins Single-pass Transmembrane Proteins ○ Multi-pass Transmembrane Proteins ○ Integral Monotopic Proteins ○ Lipid-anchored integral proteins Transport proteins: ○ Carrier proteins ○ Channel proteins ○ ATP-powered pumps Na+/K+ ATPase (Sodium-Potassium Pump) Ca2+ ATPase (Calcium Pump) H+-ATPase (Proton Pump) (2) Peripheral proteins Functions: ○ Loosely bound to the surface of the membrane, often to exposed parts of integral proteins ○ Structural support ○ Signal transduction ○ Molecule transfer (surface of the membrane) (3) Lipid-anchored proteins Proteins located on the surface of the cell membrane that are covalently attached to lipids embedded within the cell membrane  Cholesterol Regulates the fluidity or viscosity of the cell membrane ○ Made up of membrane carbohydrates Glycoproteins - covalently bonded to proteins Glycolipids - covalently bonded to lipids ○ Extracellular fluid = Fluid surrounding the outside of the cell membrane ○ Intracellular fluid = Fluid within the cell membrane Parts of cell membrane transport Passive transport Does not require energy (ATP) Molecules move along the concentration gradient (higher to lower areas of water concentration)  Simple diffusion = Unassisted by membrane proteins ○ Osmosis = Movement of solvent from a region of lower solute concentration to a region of higher solute concentration through a semipermeable membrane Types Endosmosis ○ Hypotonic Exosmosis ○ Hypertonic Isotonic (equal concentration) Equal amounts of solute concentration No net movement of water particles in the cell Plant cells = Flaccid Hypertonic (higher concentration) Outside > Inside Water particles move out of the cell, causing crenation (shrivel/contraction) Plant cells = Plasmolyzed Hypotonic (lower concentration) Outside < Inside Water particles enter the cell, causing the cell to expand and eventually, lyse (breakdown) Plant cells = Turgid Facilitated diffusion = Assisted by membrane proteins ○ Channel proteins Passive transport Creates a hydrophilic hole or a pore in the cell membrane ○ Carrier proteins Passive and active transport Transport specific molecules like glucose, amino acids, and ions across cell membranes Embedded in the cell membrane and remain open at one side Active transport Requires energy (ATP) Molecules move against the concentration gradient (lower to higher areas of water concentration) Types ○ Primary Uses ATP as an energy source  ○ Secondary Does not use ATP as an energy source Symport = Movement of two substances in the same direction Antiport = Movement of two substances in opposite directions ○ Vesicles (Bulk) = Sacs that move substances into or out of the cell across the cell membrane Exocytosis Movement of particles out of the cell Endocytosis Movement of particles into the cell Phagocytosis Ingestion of solid particles Pinocytosis Ingestion of liquid particles Receptor-mediated endocytosis A selective form of endocytosis where specific molecules bind to receptors on the cell membrane, triggering internalization Pumps ○ A kind of active transport which pumps ions and molecules against their concentration gradient ○ Sodium-Potassium pump Goes through cycles of shape changes to help maintain a negative membrane potential In each cycle, 3 sodium (Na+) ions exit the cell, while 2 potassium (K+) ions enter the cell Lab 3: Action Potential (Inhibitory and Excitatory Responses) Importance: Transmission of electrical signals along our nerves under the effect of inhibitory and excitatory neurotransmitters General notes: ○ Resting potential: (of a neuron) - -70mV - Established by the permeability of the membranes and the sodium-potassium pump - Maintained through differences in concentration and permeability of Na, K, and Cl ions through a leak channel (type of ion channel; randomly gated) - More sodium inside, more potassium outside  ○ Graded potential: - Stimulation from neurotransmitters of connected neurons - Created as neurotransmitters from adjacent cells that are either excitatory or inhibitory ○ Action potential: If the neuron reaches the threshold of -55mV, an opening of voltage-gated sodium channels triggers an all-or-none action potential that may affect other connected neurons Notes on lab experiment: ○ The dependent variable is the membrane potential of Neuron 1 and Neuron 2 ○ The membrane potential is measured at the axon hillock of each neuron (units are in millivolts) ○ Neuron 1: - Interneuron of the Central Nervous System (CNS) - Two antagonistic neurotransmitters bind to the receptors on the dendrites of Neuron 1: 1. Glutamic acid = Most common excitatory (towards the threshold) neurotransmitter in the CNS 2. GABA = Most common inhibitory (away from the threshold) neurotransmitter in the CNS - Process of depolarization (less negative due to rush of positive charge): 1. Glutamic acid → Binds to glutamic acid protein receptor 2. Receptor changes shape and sodium ions (Na+) diffuse into the dendrite 3. Membrane potential depolarizes (negative to positive voltage) - Factors for action potential: 1. Enough excitatory neurotransmitters bind to these ligand-gated sodium channels  2. Electrical potential at the trigger zone (i.e. axon hillock) reaches +55 mV 3. Action potential is carried down the length of the axon - Action potential reaches the axon terminals → Vesicles there dump their neurotransmitters into their synaptic spaces toward other neurons' dendrites - Process for hyperpolarization (becomes more negative; returns to resting potential): 1. GABA → Binds to a GABA protein receptor 2. Protein changes shape, allowing chlorine ions (Cl-) to diffuse into the dendrite 3. Resting membrane potential of a neuron is -70mV → Negatively charged ions diffuse into dendrite → membrane hyperpolarizes 4. Hyperpolarization → membrane is even more negatively charged → inhibits neuron from depolarizing ○ Neuron 2: - Motor neuron of the peripheral nervous system (PNS) - Stimulated by the neurotransmitter acetylcholine (ACh) - ACh 1. Most common excitatory neurotransmitter secreted by motor neurons 2. ACh → binds to the ACh protein receptor → protein changes shape → Na+ diffuses into the dendrite - Acetylcholinesterase (AChE) 1. Destroys ACh 2. Prevents the neurotransmitter ACh from continuously stimulating Neuron 2 ○ Other neurotransmitters and neurotoxins: - GABA: Added to the dendrites of Neuron 1. - Glutamic acid: Can also be added to the dendrites of Neuron 1. - TTX 1. Neurotoxin in pufferfish and can be lethal; 2. Blocks the opening of voltage-gated sodium channels. - Sarin Nerve Gas: 1. Neurotoxin used in chemical warfare as a weapon of mass destruction 2. Sarin blocks the active site of the enzyme AChE; 3. Prevents AChE from breaking down its substrate ACh in the synaptic space - Botulinum toxin 1. Neurotoxin that destroys the proteins that help move ACh vesicles in the axon terminals; and therefore 2. Inhibit ACh release from Neuron 1 Lab 4: arghhhhhhh Diploidy ○ The condition of being diploid, which is a term meaning that there are two sets of chromosomes in the same cell nucleus ○ Significance of the appearance of diploidy is… - “a fundamental hallmark of eukaryotic evolution and bisexual reproduction because diploidy offers the basis for the bisexual life cycle, allowing for oscillation between diploid and haploid phases” - Diploidy is advantageous/aids in evolution, especially during the process of meiosis - Meiosis: The sexual reproduction of sperm and egg cells - Meiosis produces haploid (a single set of chromosomes) gametes; - Through the process of fertilization, gametes merge into diploid cells, forming a zygote, and eventually, a new life - The diploid cells then ensure pluripotency, cell proliferation, and functions Homologous chromosomes ○ Pairs of chromosomes in a diploid organism ○ Arranged in the same order, but do not always have the same alleles due to variations between them ○ During meiosis, these homologous chromosomes line up and the process of recombination occurs between them; ○ Resulting in gametes with unique combinations of alleles on each chromosome and therefore the creation of unique individuals Genetic variability ○ Advantages: Natural selection (evolution for survival; adjust to shifting environmental conditions)/can be developed to survive in adverse conditions, more resistant to diseases, also it creates diversity ○ Disadvantages: Can also cause some undesired effects like genetic disorder, diseases, etc. Lab 5: DNA extraction from fruit Purpose: To extract DNA from a chosen fruit sample; understanding its composition can provide insights into its breeding and preservation Materials/methods: 1. Preparation - Label the test tubes or cups to keep track of the samples. - Gather all the materials and read through the procedure. 2. Mashing the fruit - Place 2-3 ripe strawberries in the zipper-lock bag. - Seal the bag and gently mash the fruit using your hands. 3. Creating the Extraction Solution - In a cup, mix 1/4 teaspoon of dishwashing detergent, 1/4 teaspoon of table salt, and 1/2 cup of water. Stir gently until dissolved.  - Add the extraction solution to the mashed strawberries in the bag. Seal the bag again and mix gently. 4. Filtering the Extract - Place a coffee filter or cheesecloth over another cup or beaker. - Pour the strawberry mixture through the filter to collect the liquid. 5. Precipitating the DNA - Pour the filtered liquid into a test tube or cup, filling it about 1/4 full. - Tilt the test tube and carefully layer rubbing alcohol on top of the liquid. - Observe the DNA strands that form at the interface between the rubbing alcohol and liquid layers. 6. Collecting the DNA - Use a stirring stick or wooden stick to gently wind the DNA strands around it. - Carefully lift the DNA out of the test tube and observe its appearance. Uses of materials: ○ Lysis buffer = dishwashing soap + salt (sodium chloride) + water ○ Dishwashing soap: helps in bursting open the fruit’s cell and nuclear membranes, releasing the DNA ○ Salt: ensures the separation of proteins from the DNA ○ Isopropyl alcohol: DNA is insoluble in alcohol = causes clumping = visibility; Cold temperatures = DNA is less soluble = DNA is more precipitated/visible