BIO 173 Exam 1: Comprehensive Vocabulary

Vocabulary practice flashcards covering the scientific method, enzyme kinetics, polyphenoloxidase assays, laboratory calculations, the human gut microbiome, and PCR workflow.

Scientific Method

The systematic process of observing a pattern, asking a question, proposing a testable explanation (hypothesis), designing an experiment and predictions, collecting and analyzing data, drawing conclusions, and revising or repeating experiments when appropriate.

Hypothesis

A testable, falsifiable explanation for an observation that explains why something might happen, formulated as a statement rather than a question.

Prediction

The specific observable result expected under a proposed experimental procedure if a hypothesis is supported, describing outcomes for both experimental groups and relevant controls.

Falsifiability

The property of an explanation or hypothesis requiring that a conceivable, possible observation exists that would contradict it; without this, it cannot be tested scientifically.

Independent Variable (IV)

The factor deliberately manipulated or assigned by the investigator in an experiment, such as substrate concentration, enzyme concentration, temperature, or inhibitor treatment.

Dependent Variable (DV)

The measured response to experimental manipulation, such as initial reaction rate calculated from absorbance change over time.

Controlled Variables (Constants)

Factors kept unchanged across all experimental treatments so they do not confound or explain differences in the dependent variable, such as total volume, $\text{pH}$, temperature, timing, and wavelength.

Negative Control

An experimental reference sample expected to lack the response being tested, used to detect contamination, optical background signal, or non-enzymatic spontaneous reactions.

Positive Control

An experimental sample known to produce the expected response under assay conditions, confirming that the procedure, reagents, and instruments can detect the effect when present.

Replicates and Randomization

Experimental practices where repeated trials reveal natural variability to improve confidence, and randomizing sample measurement order prevents systematic artifacts such as instrument drift or enzyme decay from confounding treatment effects.

Enzyme

A biological catalyst (typically a protein, though some are $\text{RNA}$) that accelerates a biochemical reaction by lowering its activation energy barrier and is regenerated after catalysis.

Catalyst

A substance that speeds up the rate of a chemical reaction without being consumed overall, allowing it to participate in numerous successive reaction cycles.

Activation Energy ($E_a$)

The minimum energy barrier that reacting molecules must overcome to reach the transition state and be converted into products.

Active Site

The specific region of an enzyme molecule that binds the substrate and carries out catalysis, shaped and chemically configured to provide high specificity.

Enzyme-Substrate Complex ($ES$)

The temporary molecular association formed when substrate binds non-covalently to the active site of an enzyme ($E + S \rightleftharpoons ES \rightarrow E + P$).

Catalytic Cycle

The multi-step process in which substrate binds to the active site, the enzyme facilitates chemical conversion to product, the product is released, and the unchanged enzyme becomes available for another round.

$[S]$ and $[E]$

Standard biochemical notations enclosed in brackets representing the concentration of substrate ($[S]$) and the concentration of enzyme ($[E]$), rather than simply the total added volumes.

Polyphenoloxidase (PPO)

A plant enzyme extracted from tissues (such as potatoes) that catalyzes the oxidation of catechol to orthoquinone in the presence of oxygen, driving enzymatic browning.

Catechol

A polyphenolic compound utilized as the clear, colorless substrate for polyphenoloxidase ($\text{PPO}$) in the laboratory assay.

Orthoquinone

The immediate, direct oxidation product formed by polyphenoloxidase from catechol and oxygen, which subsequently undergoes non-enzymatic reactions to generate dark, colored pigments.

Absorbance ($A$)

A quantitative measurement of light attenuation by a solution; within the assay's linear dynamic range and at a constant path length, it is directly proportional to the concentration of the absorbing solute.

Transmittance ($T$)

The fraction of incident light that passes through a sample without being absorbed; higher absorbance directly yields lower transmittance.

Spectrophotometric Wavelength ($525\,\text{nm}$)

The specific green light wavelength used to monitor the polyphenoloxidase reaction because the colored secondary reaction products absorb strongly at this value.

Initial Reaction Rate ($v_0$)

The slope of the early, approximately linear portion of an absorbance-versus-time curve (defined in Lecture 4 using the first $0\text{--}2\,\text{minutes}$), representing reaction velocity before substantial substrate depletion occurs.

Absorbance-versus-Time Plateau

The late leveling off of measured absorbance in a single reaction cuvette, reflecting a cessation of product accumulation due to substrate/oxygen depletion, enzyme inactivation, or exceeding the spectrophotometer's upper linear range.

Dilution Equation ($C_1 V_1 = C_2 V_2$)

The formula used to calculate simple dilutions, where $C_1$ is stock concentration, $V_1$ is required stock volume, $C_2$ is final desired concentration, and $V_2$ is final total solution volume.

Diluent Volume

The volume of solvent or buffer added to a stock reagent to achieve the final volume, calculated explicitly as $\text{Diluent Volume} = V_2 - V_1$.

Twofold Dilution

A dilution procedure in which one volume of starting stock is combined with one equal volume of diluent, halving the concentration ($\frac{1}{2}$ of original).

Tenfold Dilution

A dilution procedure in which one volume of stock is mixed with nine volumes of diluent (yielding a 1:10 ratio of stock to total volume), producing one-tenth ($\frac{1}{10}$) of the starting concentration.

Serial Dilution

A sequence of consecutive stepwise dilutions where each dilution is prepared from the immediately preceding diluted sample using the same dilution factor at each step.

Micropipette First Stop

The initial resistance position reached when depressing a micropipette plunger, used to measure and slowly aspirate the precise calibrated volume of liquid.

Micropipette Second Stop

The full-depression blowout position of a micropipette plunger, used solely during dispensing to expel remaining liquid droplets from the tip; liquid must never be aspirated from this stop.

Spectrophotometer Blank

An optical reference containing the cuvette, solvent, and nonreacting components used to calibrate the instrument to zero absorbance and subtract background absorbance.

Enzyme Kinetics

The quantitative study of chemical reaction rates catalyzed by enzymes and how those rates are influenced by substrate concentration, enzyme amount, inhibitors, and environmental conditions.

$$V_{\max}$$

The maximum initial reaction velocity approached asymptotically as substrate concentration approaches saturation for a given quantity of active enzyme under specified conditions.

$K_m$ (Michaelis Constant)

The specific substrate concentration ($[S]$) at which the initial reaction velocity reaches half of maximum ($v_0 = \frac{V_{\max}}{2}$); a lower $K_m$ indicates a higher apparent affinity for substrate.

Michaelis-Menten Equation

The rate equation $v_0 = \frac{V_{\max}[S]}{K_m + [S]}$ relating initial catalytic rate ($v_0$) to substrate concentration ($[S]$) for enzymes exhibiting hyperbolic saturation kinetics.

Competitive Inhibitor

A substance that binds reversibly to an enzyme's active site in direct competition with substrate, causing an increase in apparent $K_m$ while leaving $V_{\max}$ unchanged.

Noncompetitive Inhibition (Course Broad Definition)

An inhibition mechanism where the inhibitor binds outside the active site, inducing conformational distortion that lowers $V_{\max}$ and cannot be overcome by adding substrate, while $K_m$ may or may not change.

Pure Noncompetitive Inhibition

A strict allosteric model in which the inhibitor binds free enzyme and enzyme-substrate complex with identical affinity, decreasing $V_{\max}$ while leaving $K_m$ unchanged and displaying constant percent inhibition across all $[S]$.

Mixed Inhibition

An enzyme inhibition mode where the inhibitor binds to an allosteric site but alters both the catalytic efficiency and substrate affinity, leading to a decreased $V_{\max}$ and an altered $K_m$.

Percent Inhibition

The quantitative metric describing inhibitor efficacy, calculated as $\left(\frac{\text{Rate}_{\text{no inhibitor}} - \text{Rate}_{\text{inhibitor}}}{\text{Rate}_{\text{no inhibitor}}}\right) \times 100$.

Cofactor

A non-protein chemical component (such as a divalent metal ion or an organic coenzyme) essential for or supportive of an enzyme's catalytic activity and structural stability.

Chelator

A chemical compound that coordinates and binds metal ions with high affinity, rendering them biologically unavailable to determine whether an enzyme requires a specific metal cofactor.

Copper ($\text{Cu}^{2+}$)

The essential divalent metal cofactor located within the active site of polyphenoloxidase ($\text{PPO}$) required to mediate oxygen-dependent catechol oxidation.

Protein Denaturation

The loss of a protein's native three-dimensional tertiary/secondary folding due to environmental stress (such as high heat), distorting the active site and eliminating catalysis without cleaving peptide bonds.

Gut Microbiome

The dense, diverse ecological community of commensal, symbiotic, and pathogenic microorganisms inhabiting the gastrointestinal tract, especially the large intestine.

Dietary Fiber

Complex plant-derived carbohydrates (e.g., resistant starch, inulin) that escape host enzymatic digestion in the small intestine and reach the colon intact to fuel microbial fermentation.

Short-Chain Fatty Acids (SCFAs)

Principal organic end-products of anaerobic bacterial fiber fermentation in the colon, predominantly consisting of acetate, propionate, and butyrate.

Butyrate

A specific four-carbon short-chain fatty acid produced by bacterial fermentation of resistant starch that serves as the primary metabolic energy source for colonocytes.

Methanogens

Specialized anaerobic microorganisms within the domain Archaea that inhabit the gut and consume fermentation products, utilizing the pathway $\text{CO}_2 + 4\text{H}_2 \rightarrow \text{CH}_4 + 2\text{H}_2\text{O}$.

End-Expiratory Breath Sampling

A collection method targeting the final portion of exhaled breath to selectively capture alveolar gas in equilibrium with pulmonary blood while bypassing anatomical dead-space air.

Quintron Instrument

The specialized gas chromatography breath analyzer utilized to quantify concentrations of hydrogen ($\text{H}_2$) and methane ($\text{CH}_4$) gases produced by colonic microbial fermentation.

Spread Plating

A microbiological technique where an evenly distributed liquid aliquot is spread across the surface of an agar plate to allow discrete colony formation and viable cell quantification ($\text{CFUs}$).

Streak Plating

A dilution procedure in microbiology where an inoculation loop is dragged across successive sectors of an agar plate to progressively separate individual cells and isolate pure single colonies.

Aseptic Technique

A standardized set of sterile handling practices designed to prevent contamination of cultures, reagents, and sterile equipment by unwanted ambient microorganisms.

Bacterial Freezer Stock

A culture suspension prepared with a cryoprotectant (such as glycerol) and frozen at ultra-low temperatures to maintain bacterial cell viability for long-term archival storage.

Polymerase Chain Reaction (PCR)

An enzymatic in vitro technique that exponentially amplifies a designated target DNA segment across thermal cycles consisting of denaturation, annealing, and extension.

PCR Denaturation Step

The initial high-temperature phase of a $\text{PCR}$ cycle ($94\text{--}98\,^\circ\text{C}$) that breaks hydrogen bonds between complementary bases to yield single-stranded DNA templates.

PCR Annealing Step

The second thermal phase of a $\text{PCR}$ cycle ($50\text{--}65\,^\circ\text{C}$) that enables sequence-specific forward and reverse primers to hybridize to their complementary flanking sites on single-stranded template DNA.

PCR Extension Step

The phase of a $\text{PCR}$ cycle ($\approx 72\,^\circ\text{C}$ for Taq) where thermostable DNA polymerase synthesizes nascent complementary strands in the $5' \rightarrow 3'$ direction by incorporating dNTPs.

Taq Polymerase

A heat-tolerant DNA polymerase originally derived from Thermus aquaticus that synthesizes new DNA without denaturing during repeated high-temperature $\text{PCR}$ cycles.

Deoxynucleotide Triphosphates (dNTPs)

The equimolar mixture of four nucleotide monomer building blocks ($\text{dATP}$, $\text{dTTP}$, $\text{dCTP}$, $\text{dGTP}$) consumed during polymer chain extension in $\text{PCR}$.

No-Template Control (NTC)

A negative control $\text{PCR}$ mixture containing all reaction reagents except template DNA (replaced with nuclease-free water) to confirm the absence of DNA contamination.

16S rRNA Gene

The conserved prokaryotic gene encoding the small ribosomal subunit RNA, containing alternating universal sequence regions for primer binding and variable regions used to identify bacterial taxa.