BIOT 062 Exam 1

Vocabulary practice flashcards covering biomanufacturing concepts, quality control standards, laboratory equipment, solution chemistry, aseptic techniques, bacterial and mammalian cell culture, bioreactor modes, and protein analysis methods.

Biotechnology

The use of living organisms, cells, or biological systems to develop products, processes, and technologies.

Biomanufacturing

The use of biological systems—such as cells and enzymes—to produce commercial products on a large scale.

Biopharmaceutical

A medicinal product that is manufactured using biological sources or biotechnology.

Therapeutic protein

A protein used as a medicine to treat, prevent, or manage a disease or medical condition.

Upstream processing

The initial biomanufacturing phase focused on growing cells and producing the desired biological product, ending with a culture containing the product.

Downstream processing

The biomanufacturing stage focused on recovery, purification, and preparation of the product, separating it from cells and debris.

SOPs (Standard Operating Procedures)

Written instructions that explain exactly how a specific manufacturing or laboratory task should be performed.

GMP (Good Manufacturing Practice)

A system of regulations and quality practices designed to ensure medicines are consistently produced and controlled according to quality standards.

Change control

A formal process for retrieving, approving, documenting, and implementing changes to manufacturing processes, equipment, materials, or procedures.

Cleaning

The physical removal of dirt, product residue, and other soils from equipment and surfaces.

Sanitization

The reduction of microorganisms on surfaces to an acceptable level.

Sterilization

The complete elimination of all viable microorganisms, including spores.

CIP (Clean-In-Place)

A method of cleaning internal surfaces of equipment without taking the equipment apart.

SIP (Sterilize-In-Place)

A method of sterilizing internal surfaces of equipment without taking the equipment apart prior to use.

Data integrity

The principle that all manufacturing actions and additions must be recorded accurately at the time they occurred.

Spectrophotometer

A laboratory instrument that measures light absorbance at a specific wavelength, often used to determine cell density.

Laminar-flow biological work area

A clean workbench that uses HEPA-filtered air to protect samples and products from biological contamination during aseptic work.

Chemical fume hood

A safety enclosure that protects workers from hazardous chemical vapors by pulling air away, typically without a HEPA filter.

Molarity

A measure of solute concentration defined as $\text{Molarity} = \frac{\text{moles}}{\text{Liters}}$.

pH

A logarithmic measure of the hydrogen ion concentration in a solution, defined as $\text{pH} = -\text{log}_{10}([\text{H}^+])$.

Buffer

A solution typically containing a weak acid and its conjugate base that resists large changes in pH when small amounts of acid or base are added.

pKa

The pH value at which a weak acid and its conjugate base are present at equal concentrations.

Henderson-Hasselbalch equation

The mathematical relationship between pH and buffer components, expressed as $\text{pH}=\text{p}K_{a}+\text{log}\begin{pmatrix}\frac{[\text{A}^-]}{[\text{HA}]}\end{pmatrix}$ .

Aseptic technique

Procedures designed to prevent contamination by blocking the transfer of microorganisms from the environment, equipment, or personnel to a sterile field.

Quadrant streaking

A serial dilution technique performed on an agar plate to isolate individual bacterial colonies.

E. coli

A common rod-shaped (bacillus), gram-negative bacterial cloning host valued for its rapid growth rate, simple genetics, and cost-effectiveness.

Selectable marker

A gene on a plasmid, such as antibiotic resistance genes like bla, used to identify and select cells that have successfully taken up the plasmid.

Restriction digestion

A laboratory technique that uses restriction enzymes to cut DNA molecules at specific sequence recognition sites.

Ligation

The enzymatic joining of two DNA strands by forming covalent phosphodiester bonds using DNA ligase.

Transformation

The process by which recipient bacterial cells take up foreign DNA from their surroundings and begin expressing its genes.

Binary fission

A form of asexual reproduction in prokaryotes where one cell replicates its DNA, enlarges, and splits into two identical daughter cells.

Lag phase

The initial bacterial growth phase where cells adapt, repair, and synthesize machinery, resulting in little net population increase.

Log phase

The bacterial growth phase during which population size doubles exponentially at a steady maximal rate.

Stationary phase

The bacterial growth phase where cell division roughly equals cell death due to nutrient exhaustion and waste accumulation.

Death phase

The final bacterial growth phase where viable cell counts decline because the rate of cell death exceeds the rate of division.

Obligate aerobes

Organisms that require oxygen to live and grow at the top of an undisturbed culture tube.

Obligate anaerobes

Organisms that cannot survive in the presence of oxygen and grow at the bottom of an undisturbed culture tube.

Facultative anaerobes

Organisms that grow faster in the presence of oxygen but can also grow without it.

Psychrophiles

Cold-loving microorganisms that have an optimal growth temperature at $15^\text{o}\text{C}$ or lower.

Mesophiles

Moderate-temperature-loving microorganisms that grow optimally between $20^\text{o}\text{C}$ and $45^\text{o}\text{C}$.

Thermophiles

Heat-loving microorganisms that grow optimally between $50^\text{o}\text{C}$ and $80^\text{o}\text{C}$.

Defined media

Culture media composed of pure, specific chemical compounds in precise known quantities, ensuring zero batch-to-batch variation. Cells often grow slower on it.

Complex media

Culture media containing nutrient-rich extracts or digests with unknown or variable exact chemical compositions. Fast, cheap and forgiving.

Selective media

Culture media formulated to promote the growth of specific desired microorganisms while inhibiting the growth of others.

Differential media

Culture media that allow multiple types of microorganisms to grow while visually distinguishing between them using indicators.

OD600

A fast, non-destructive optical measurement of light scattering at a wavelength of $600\text{ nm}$ used to estimate cell density.

Primary culture

A culture established directly from biological tissue, characterized by a finite lifespan and eventual senescence.

Continuous cell line

A cell population capable of proliferating indefinitely in culture, making it easy to scale up despite potentially losing specialized original functions.

Hayflick phenomenon

The biological limit wherein normal human embryonic cell strains divide a finite number of times before entering permanent growth arrest.

CHO cells

Chinese Hamster Ovary host cells capable of human-compatible protein folding and post-translational modifications like glycosylation.

Fed-batch operating mode

A bioreactor operation mode where concentrated nutrients are added progressively over time, raising vessel volume before one final harvest.

Perfusion operating mode

A bioreactor operation mode where cell culture media is continuously exchanged while cells are retained within the vessel.

SDS (Sodium Dodecyl Sulfate)

An anionic detergent in SDS-PAGE that denatures proteins and imparts a uniform negative charge-to-mass ratio to polypeptides.

Rf (Relative Mobility)

In gel electrophoresis, the ratio calculated as $R_f = \frac{\text{distance migrated by protein band}}{\text{distance migrated by dye front}}$.

Bioreactor

A controlled vessel and system used to grow biological cultures under specific conditions to produce a target biological product.

Impeller

A bioreactor component that rotates to mix the culture, maintaining cell suspension and aiding mass transfer.

Sparger

A bioreactor component used to introduce process gases into the culture medium.

Baffles

Internal vessel components in a bioreactor that reduce vortex formation and enhance mixing efficiency.

Bioreactor jacket

An outer layer surrounding a bioreactor vessel through which fluid flows to control culture temperature.

Bioreactor probes

Sensors in a bioreactor that continuously measure parameters like pH, dissolved oxygen, and temperature for automated control systems.

Bioreactor ports

Controlled access points on a bioreactor used for inoculation, adding feeds or reagents, and drawing samples.

Exhaust filter

A filter on the bioreactor off-gas line that allows gas to exit while maintaining sterile containment.

Reducing agents in SDS-PAGE (e.g., DTT or $\beta$-mercaptoethanol)

Reagents added to sample buffer to cleave covalent disulfide bonds into thiols, ensuring complete protein unfolding.

Polyacrylamide gel

A porous matrix in gel electrophoresis that acts as a molecular sieve, allowing smaller polypeptides to migrate faster than larger ones.

Protein ladder

A mixture of known molecular weight proteins run alongside samples in SDS-PAGE to serve as a reference for estimating polypeptide sizes.

Tracking dye

A small charged molecule added to SDS-PAGE samples that migrates ahead of proteins to show the progress of the electrophoresis run and provide the denominator for $R_f$ calculations.

Coomassie blue and silver stain

Reagents used after SDS-PAGE to visualize protein bands within the gel, with silver stain offering higher sensitivity than Coomassie.

Smiling bands in SDS-PAGE

A gel electrophoresis artifact usually caused by excess voltage, uneven heating, or ionic concentration differences across the gel.

Origin of replication (ori)

A specific DNA sequence on a plasmid that enables host bacteria to replicate the plasmid independently of the genomic chromosome.

bla gene

The selectable marker gene on the pGLO plasmid that confers resistance to ampicillin.

Arabinose promoter/regulator (\text{pBAD})

The DNA sequence on the pGLO plasmid that acts as an on/off switch, initiating transcription of the GFP gene only when arabinose is present.

\text{CaCl}_2 and heat shock

A laboratory procedure used to make $E.\text{ coli}$ competent by altering cell wall permeability, enabling uptake of plasmid DNA.

Transformation recovery step

An incubation phase following heat shock during which bacterial cells recover from physical stress and express antibiotic resistance genes before exposure to selective media.

-pGLO, LB control plate

A positive control agar plate showing heavy lawn growth of untransformed wild-type bacteria to confirm cell viability.

-pGLO, LB/amp control plate

A negative control agar plate where ampicillin prevents growth of non-transformed $E.\text{ coli}$, verifying antibiotic effectiveness.

+pGLO, LB/amp/ara experimental plate

A selective and inductive agar plate where transformed $E.\text{ coli}$ grow and produce green fluorescent protein (GFP) that glows under UV light.