BIOL190L Midterm Exhaustive Study Guide

BIOL190L Midterm Examination Overview

• Examination Parameters:

  • Time Limit: $60\,\text{minutes}$.

  • Total Questions: $30$ multiple-choice questions.

  • $12$ practical station multiple-choice questions.

  • $18$ regular multiple-choice questions.

• Curriculum Scope:

  • Covers all course content from Syllabus, Safety, Metric System, and Measurement through Energy Metabolism.

  • Encompasses any and all bolded terms and graphs from course presentations.

• Mandatory Requirements:

  • Materials: Must bring a pencil and an eraser.

  • Dress Code: Strict adherence to course laboratory dress code is enforced; non-compliant students will be asked to leave.

Laboratory Safety, Metric System, and Measurement

• Syllabus Policies and Laboratory Procedures:

  • Policies regarding unexcused and excused absences, mandatory laboratory dress code, grading rubrics, assignment due dates, and general laboratory conduct expectations.

• Metric System Conversions and Prefixes:

  • Mega- ($M$): $10^6$

  • Kilo- ($k$): $10^3$

  • Deca- ($da$): $10^1$

  • Base Unit (meter, gram, liter): $10^0$

  • Deci- ($d$): $10^{-1}$

  • Centi- ($c$): $10^{-2}$

  • Milli- ($m$): $10^{-3}$

  • Micro- ($\mu$): $10^{-6}$

  • Nano- ($n$): $10^{-9}$

  • Pico- ($p$): $10^{-12}$

• Base Units of Measurement:

  • Length: Meter ($\text{m}$).

  • Mass: Gram ($\text{g}$).

  • Volume: Liter ($\text{L}$) or cubic decimeter ($\text{dm}^3$).

  • Temperature: Degrees Celsius ($^\circ\text{C}$) or Kelvin ($\text{K}$).

• Solution Concentration Calculations:

  • Molarity ($M$): Expressed as moles of solute per liter of solution ($\text{mol}\,\text{dm}^{-3}$).

  • Mass/Volume Percentage: $\frac{\text{mass of solute (g)}}{\text{volume of solution (cm}^3\text{)}} \times 100$

  • Dilution Equation: $C_1 V_1 = C_2 V_2$

• Temperature Conversions:

  • Celsius to Fahrenheit: $^\circ\text{F} = (^\circ\text{C} \times \frac{9}{5}) + 32$

  • Fahrenheit to Celsius: $^\circ\text{C} = (^\circ\text{F} - 32) \times \frac{5}{9}$

  • Celsius to Kelvin: $\text{K} = ^\circ\text{C} + 273.15$

• Micropipetting Protocols:

  • Pipette Types and Ranges:

  • P20: Measures volumes between $2.0\,\mu\text{L}$ and $20.0\,\mu\text{L}$.

  • P200: Measures volumes between $20.0\,\mu\text{L}$ and $200.0\,\mu\text{L}$.

  • P1000: Measures volumes between $100.0\,\mu\text{L}$ and $1000.0\,\mu\text{L}$.

  • Volume Setting Interpretation:

  • Reading digital volume indicators top-to-bottom for designated decimal placement per pipette model.

  • Step-by-Step Micropipette Operation:

  1. Select appropriate micropipette and set volume.

  2. Attach sterile disposable tip securely.

  3. Depress plunger to the first stop before immersing tip into liquid.

  4. Submerge tip beneath liquid surface and slowly release plunger to draw sample.

  5. Move tip to destination vessel; depress plunger to the first stop, then press to the second stop to blow out residual liquid.

  6. Withdraw pipette completely before releasing plunger; eject tip into waste container.

• Spectrophotometry:

  • Function: Quantifies light absorbance or transmittance through a liquid sample at specified wavelengths.

  • Absorbance and Concentration Relationship: Direct proportionality defined by Beer-Lambert Law ($A = \epsilon c l$).

• Light Microscopy:

  • Microscope Components: Ocular lenses, objective lenses, stage, stage clips, condenser, iris diaphragm, coarse adjustment knob, fine adjustment knob, light source.

  • Total Magnification Calculation:     $\text{Total Magnification} = \text{Ocular Magnification} \times \text{Objective Magnification}$

  • Image Orientation:

  • Specimen viewed through microscope appears inverted (upside down) and reversed (flipped laterally) relative to its physical slide orientation (e.g., letter 'e' slide view vs. inverted microscope view).

Scientific Method and Experimental Design

• Fundamental Components:

  • Observation: Direct gathering of information regarding a natural phenomenon using senses or instruments.

  • Hypothesis: Testable, falsifiable proposed explanation for an observed phenomenon.

  • Independent Variable: Factor intentionally manipulated or varied by the experimenter.

  • Dependent Variable: Factor measured or observed to evaluate the effect of changing the independent variable.

  • Constant Variable: Unchanged experimental factors maintained uniformly across all treatments to prevent confounding results.

  • Controls:

  • Positive Control: Group receiving a treatment known to produce a positive outcome, validating test functionality.

  • Negative Control: Group receiving no treatment or a baseline substance (e.g., water) expected to yield no response, ruling out external variables.

• Graphing Principles:

  • X-axis (horizontal): Plot independent variable.

  • Y-axis (vertical): Plot dependent variable.

  • Include appropriate units, scaling, legend, and descriptive title.

• Rollie Pollies Experiment:

  • Application of the scientific method to test terrestrial isopod behavior and habitat preference.

  • Identification of environmental variables (e.g., moisture, light intensity, substrate type) as independent variables.

  • Quantifying directional movement or distribution over time as the dependent variable.

Basic Chemistry and Macromolecules

• Chemical Reactions:

  • Condensation (Dehydration Synthesis): Reaction combining monomers into polymers through covalent bonding, accompanied by the removal of a water molecule ($\text{H}_2\text{O}$).

  • Hydrolysis: Reaction breaking polymers down into individual monomers by adding a water molecule ($\text{H}_2\text{O}$).

• Biochemical Classes and Subunits:

  • Carbohydrates:

  • Monomers: Monosaccharides (e.g., glucose, fructose).

  • Polymers: Polysaccharides (e.g., starch, glycogen, cellulose).

  • Lipids:

  • Subunits: Glycerol and fatty acids, or steroid rings.

  • Non-polar hydrophobic macromolecular structures.

  • Proteins:

  • Monomers: Amino acids.

  • Polymers: Polypeptides.

  • Nucleic Acids:

  • Monomers: Nucleotides.

  • Polymers: DNA, RNA.

• Biochemical Testing Matrix:

  • Reagent testing and visual indications for biochemical assays:

• Benedict's Test (Reducing Sugars / Monosaccharides):

  • Positive result: Brick red, orange, or green precipitate.

  • Negative result: Clear blue.

• Iodine Test (Starch / Polysaccharides):

  • Positive result: Blue-black complex.

  • Negative result: Yellow-brown iodine color.

• Biuret Test (Proteins):

  • Positive result: Violet / purple color.

  • Negative result: Light blue.

• Sudan IV Test (Lipids):

  • Positive result: Formation of distinct red-stained layer on top of liquid.

  • Negative result: Uniform dark red suspension or unlayered dispersion.

  • Food Label and Sample Analysis:

• Predicting biochemical assay outcomes (test tube colors) based on nutritional facts panels.

• Matching experimental test tube visual profiles back to corresponding food matrices.

  • pH, Acids, Bases, and Buffers:

• pH Paper Interpretation: Quantitative measuring scale spanning $0$ to $14$.

• Acid: Substance increasing hydrogen ion concentration ($\text{H}^+$) with $\text{pH} < 7$.

• Base: Substance increasing hydroxide ion concentration ($\text{OH}^-$) or decreasing $\text{H}^+$ with $\text{pH} > 7$.

• Neutral: Solution maintaining equal $\text{H}^+$ and $\text{OH}^-$ concentrations with $\text{pH} = 7$.

• Buffer Systems:

  • Buffer: Solution comprising a weak acid and its conjugate base that resists drastic shifts in pH upon addition of small quantities of acid or base.

  • Buffering Capacity: Maximum amount of acid or base a buffered system can absorb before experiencing a significant change in pH.

Cell Structure, Transport, and Microscopy

• Transport Mechanisms:

  • Diffusion: Passive net movement of solute particles down a concentration gradient from high to low concentration.

  • Osmosis: Net movement of solvent molecules (water) across a selectively permeable membrane from lower solute concentration (higher water potential) to higher solute concentration (lower water potential).

  • Concentration Gradients & Water Flow:

  • Net movement of water continues until osmotic equilibrium is established across the selectively permeable barrier.

• Dialysis Tubing Experiment Analysis:

  • Selective permeability based on molecular size thresholds.

  • Mass alterations: Dialysis bags increase in mass when placed in hypertonic external solution relative to bag interior due to water influx; dialysis bags decrease in mass when placed in hypotonic external solution relative to bag interior due to water efflux.

• Cell Categorization and Bacterial Morphology:

  • Prokaryotic vs. Eukaryotic Cells:

  • Prokaryotes: Lack membrane-bound organelles, lack membrane-bound nucleus, smaller cell size, circular DNA (e.g., bacteria, cyanobacteria).

  • Eukaryotes: Possess membrane-bound organelles, possess membrane-enclosed nucleus containing linear DNA, larger cell size (e.g., plant, animal, fungal cells).

  • Bacterial Shapes:

  • Bacillus: Rod-shaped bacterial cells.

  • Coccus: Spherical bacterial cells.

  • Spirillum: Spiral or helical bacterial cells.

• Prepared Microscope Slide Identification:

  • Cheek / Epithelial Cells: Animal eukaryotic cells featuring centered nucleus and irregular outer cell membrane.

  • Human Neuron / Nerve Cells: Complex eukaryotic cell bodies featuring distinct dendrites, axons, and central nuclei.

  • Human Skeletal Muscle: Striated eukaryotic muscle fibers featuring multiple peripheral nuclei and dark/light banding patterns.

  • Elodea: Fresh-water aquatic plant cells displaying rectangular rigid cell walls, large central vacuoles, and chloroplasts undergoing cytoplasmic streaming (cyclosis).

  • Anabaena: Filamentous photosynthetic cyanobacteria (prokaryotic) composed of chains of vegetative cells interspersed with heterocysts.

• Wet Mount Preparation Steps:

  1. Place clean glass slide on flat surface.

  2. Add single droplet of water or liquid stain to middle of slide.

  3. Position specimen sample into liquid droplet using forceps.

  4. Hold coverslip at a $45^\circ$ angle to slide surface touching liquid border.

  5. Gently lower coverslip over specimen to prevent trapping air bubbles.

• Plant vs. Animal Cells:

  • Plant Cells: Cell wall present, chloroplasts present, large central vacuole present, rigid shape, lack centrioles.

  • Animal Cells: Cell wall absent, chloroplasts absent, small transient vacuoles, variable flexible shape, centrioles present.

• Organelle Structures and Functions:

  • Nucleus: Contains genomic DNA, regulates transcription and cell function.

  • Mitochondria: Primary site of aerobic respiration and ATP generation via oxidative phosphorylation.

  • Chloroplast: Site of photosynthesis containing thylakoids and stroma.

  • Ribosome: Site of protein translation and polypeptide synthesis.

  • Endoplasmic Reticulum (ER):

  • Rough ER: Studded with ribosomes; synthesizes membrane-bound and secreted proteins.

  • Smooth ER: Synthesizes lipids, metabolizes carbohydrates, detoxicates chemicals.

  • Golgi Apparatus: Modifies, sorts, and packages macromolecules into membrane vesicles for export or cellular target.

  • Plasma Membrane: Phospholipid bilayer regulating selective passage of molecules.

  • Cell Wall: Outer rigid structural layer providing mechanical integrity and preventing osmotic lysis.

• Tonicity Dynamics:

  • Isotonic Condition: Equal solute potential between interior cell fluid and extracellular fluid. No net movement of water.

  • Red Blood Cells: Maintain normal biconcave disc shape.

  • Plant Cells: Flaccid condition.

  • Hypertonic Condition: Higher solute potential in extracellular fluid than cell cytoplasm. Net loss of water from cell.

  • Red Blood Cells: Undergo crenation (shriveling).

  • Plant Cells: Undergo plasmolysis (plasma membrane detaches and shrinks away from rigid cell wall).

  • Hypotonic Condition: Lower solute potential in extracellular fluid than cell cytoplasm. Net influx of water into cell.

  • Red Blood Cells: Undergo hemolysis (cell swelling and bursting).

  • Plant Cells: Maintain optimal turgor pressure (turgid state; rigid swelling contained by cell wall).

Enzyme Kinetics and Catalysis

• Principles of Enzyme Action:

  • Definitions:

  • Metabolism: Sum total of all anabolic and catabolic biochemical processes within an organism.

  • Enzyme: Biological protein catalyst that accelerates chemical reaction rates by lowering activation energy ($E_a$).

  • Activation Energy ($E_a$): Minimum kinetic energy required to initiate a chemical reaction.

  • Substrate: Specific reactant molecule bound by an enzyme at its active site.

  • Active Site: Distinct catalytic pocket formed by protein tertiary structure where substrate binding and chemical transformation occur.

  • Enzyme Properties: Highly specific to substrates; unchanged and reusable after catalyzing reactions.

• Tyrosinase Biochemistry:

  • Biological Role: Copper-containing enzyme responsible for catalyzing the oxidation of monophenols/diphenols into quinones, leading to melanin production.

  • Real-World Applications: Enzymatic browning in fruit/vegetables, skin pigmentation mechanisms, target for pharmacological and agricultural inhibitors.

• Spectrophotometric Quantitation of Enzyme Activity:

  • Spectrophotometer reads optical absorbance of reaction product over time.

  • Absorbance rate directly correlates with enzyme reaction velocity and activity levels.

• Environmental and Kinetic Influences on Enzyme Function:

  • Temperature: Increases collision rates up to optimal temperature; extreme high temperatures cause thermal denaturation (loss of tertiary structural integrity).

  • pH: Deviations from optimal pH alter ionization states of active site amino acid side chains, compromising substrate binding or inducing denaturation.

  • Enzyme Concentration: Direct proportional increase in catalytic rate when substrate is in excess.

  • Substrate Concentration: Catalytic rate increases until substrate saturation of active sites occurs (reaching maximum velocity $V_{\max}$).

• Competitors and Inhibitors in Laboratory Systems:

  • Target Enzyme: Tyrosinase.

  • Primary Substrate: Pyrocatechol or Tyrosine.

  • Competitive Substrate: Hydroxyquinone (competes directly with substrate for active site occupancy).

  • Inhibitor: Phenylthiourea (PTU; acts as a potent inhibitor by chelating essential copper cofactors within the active site of Tyrosinase, preventing catalytic activity).

  • Experimental Outcomes: Addition of Phenylthiourea reduces optical absorbance to baseline levels due to complete suppression of Tyrosinase activity.

Energy Metabolism: Cellular Respiration and Photosynthesis

• Cellular Respiration:

  • General Summary Reaction:     $\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} + \text{ATP}$

  • Pathways:

  • Glycolysis (Cytosol)

  • Pyruvate Oxidation & Citric Acid / Krebs Cycle (Mitochondrial Matrix)

  • Oxidative Phosphorylation & Electron Transport Chain (Inner Mitochondrial Membrane)

  • Experimental Design & Measurement: Measuring oxygen ($\text{O}_2$) consumption rate using respirometers or measuring carbon dioxide ($\text{CO}_2$) release rate.

• Fermentation Pathways:

  • Anaerobic conversion of pyruvate into reduced metabolic end-products to regenerate $\text{NAD}^+$ for continued glycolysis.

  • Alcoholic Fermentation: Produces ethanol and ethanol-associated carbon dioxide ($\text{CO}_2$) gas production in yeast.

  • Lactic Acid Fermentation: Produces lactate in animal muscle tissues and specific microbes without producing $\text{CO}_2$ gas.

  • Experimental Outcomes: Quantifying fermentation velocity by measuring vertical gas volume displacement in fermentation tubes under varying carbohydrate substrate conditions.

• Interrelationship Between Photosynthesis and Respiration:

  • Photosynthesis converts light energy into chemical potential energy (glucose), generating $\text{O}_2$ as a byproduct.

  • Aerobic cellular respiration breaks down glucose in the presence of $\text{O}_2$ to yield chemical energy ($\text{ATP}$), releasing $\text{CO}_2$ and $\text{H}_2\text{O}$ as metabolic waste.

  • Outputs of photosynthesis serve as direct inputs for cellular respiration and vice versa.

• Photosynthesis:

  • General Summary Reaction:     $6\text{CO}_2 + 6\text{H}_2\text{O} + \text{light energy} \rightarrow \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2$

  • Light Reactions: Take place in thylakoid membranes; consume water, yield $\text{O}_2$, $\text{ATP}$, and $\text{NADPH}$.

  • Calvin Cycle (Light-Independent Reactions): Takes place in stroma; consumes $\text{CO}_2$, $\text{ATP}$, and $\text{NADPH}$ to synthesize triose phosphates and glucose.

  • Experimental Results: Observation of leaf disk flotation driven by $\text{O}_2$ accumulation during photosynthetic light exposure; color shifts in pH indicator solutions (e.g., phenol red) due to uptake of dissolved $\text{CO}_2$.