Biotechnology Presentation Exam Review

Comprehensive vocabulary flashcards covering molecular biotechnology topics from the presentation review, including PCR, electrophoresis, blotting, Sanger and next-generation sequencing, cloning vectors, therapeutic viruses, GMOs, DNA fingerprinting, CRISPR-Cas systems, personalized medicine, mRNA vaccines, bioinformatics, and synthetic biology.

Reverse Transcriptase PCR (RT-PCR)

A specialized polymerase chain reaction technique required when the target genetic material to be amplified is RNA rather than DNA.

Quantitative PCR (qPCR)

An established form of polymerase chain reaction, also known as Real-Time PCR, used to amplify and quantify target DNA sequences.

Polymerase Chain Reaction Reagents

The reaction components necessary for successfully amplifying target DNA, which include Taq polymerase, DNase-free buffer, free nucleotides, and target DNA primers.

Polymerase Chain Reaction Steps

The three thermal cycling stages of the PCR process, consisting of denaturing, annealing, and synthesizing.

Western Blot

The standard analytical blotting technique used specifically for detecting targeted proteins.

Gel Electrophoresis Fragment Mobility

The separation principle in gel electrophoresis whereby smaller fragments travel farther through the gel matrix than larger fragments.

Northern Blot

A blotting technique used to analyze RNA and compare the mRNA expression levels of a gene between healthy and diseased cells.

Southern Blot

A molecular method in which DNA fragments are separated by gel electrophoresis and transferred to a membrane to identify a specific target DNA sequence.

Sanger DNA Sequencing

A classical sequencing method whose primary purpose is to determine the precise order of nucleotides in DNA.

Capillary Electrophoresis in Sanger Sequencing

The separation process during modern Sanger sequencing in which shorter DNA fragments pass the detector before longer fragments.

Dideoxynucleotide (ddNTP)

A modified chain-terminating nucleotide that halts DNA synthesis because it lacks the $3'\text{-OH}$ group needed to add another nucleotide.

Fluorescent Dye-Labeled ddNTPs

The four distinct fluorophores attached to each of the four ddNTPs in modern Sanger sequencing to optically identify each nucleotide.

Sanger Sequencing Read Capacity Limit

A major limitation of traditional Sanger sequencing, which produces short reads restricted to approximately $800$ to $1{,}000\text{ base pairs}$.

Human Genome Project Metrics

A landmark sequencing achievement that utilized traditional methods, spanned $13\text{ years}$ to complete, sequenced $3\text{ billion base pairs}$, and cost approximately $\$3\text{ billion}$.

Illumina Next-Generation Sequencing Detection

The real-time base detection mechanism of Illumina NGS platforms that identifies nucleotides by detecting laser-excited fluorescence from color-coded nucleotides.

Reference Genome Alignment

The bioinformatic alignment in next-generation sequencing where short fragment reads are aligned to a known reference genome to reconstruct the complete continuous sequence.

Next-Generation Sequencing (NGS)

High-throughput sequencing technology whose core benefits include rapid whole-genome sequencing (within $24\text{ hours}$) at a very low cost per base.

Restriction Enzyme Recognition Site (Palindrome)

A specific nucleotide sequence recognized by restriction enzymes, identified in the review material as $5'\text{-GATTAG-}3'$.

Antibiotic Resistance Selection Markers

Genes conferring resistance to antibiotics that are utilized as selection markers in recombinant DNA cloning to identify cells carrying plasmids.

Recombinant Cohesive End Annealing

The hybridization of compatible sticky ends produced by digestion with the same restriction enzyme, such as annealing mouse tail length and rabbit fur color fragments both cut with EcoRI.

DNA Ligase in Recombinant Cloning

The essential enzyme in recombinant DNA cloning required to covalently join DNA fragments and seal a plasmid cloning vector.

Bacteriophage λ (Lambda) Vector

A cloning vector system in which recombinant DNA is packaged into phage particles and introduced into Escherichia coli by infection.

Yeast Artificial Chromosome (YAC)

A cloning vector specifically designed to replicate and function as an artificial chromosome in Saccharomyces cerevisiae (yeast).

Human Artificial Chromosome (HAC) Vector

A large-capacity mammalian artificial chromosome vector whose major practical limitation is that its construction and transfer into target cells are technically challenging.

Bacterial Artificial Chromosome (BAC)

A cloning vector derived from the bacterial fertility (F) factor that is suitable for cloning large inserts, such as a $250\text{-kb}$ DNA fragment, in E. coli.

Viral Tropism

A viral vector's natural preference or affinity for infecting specific types of host cells, such as neurons, hepatocytes, or lung epithelium.

Phage Therapy

A therapeutic approach that utilizes bacteriophages undergoing the lytic cycle to actively replicate inside and destroy target bacterial cells.

Luxturna

A landmark gene therapy for inherited retinal dystrophy caused by RPE65 gene mutations, administered via subretinal delivery of an engineered AAV2 vector carrying a functional gene copy.

1999 Jesse Gelsinger Clinical Trial

A gene therapy trial involving a high-dose adenoviral vector where viral capsids triggered a lethal cytokine storm, leading to safer AAV vectors and stricter dosing protocols.

Biofortification

The process of genetically modifying crops so that their nutritional value increases as they grow.

GMO Gene Delivery Mechanism

The process of transferring foreign genes into host cells during GMO creation, which does not rely on PCR for delivery.

Golden Rice

A genetically modified crop engineered with two genes, one from maize and one from a soil bacterium, to produce beta-carotene to combat Vitamin A deficiency.

PRRS Resistance in Pigs

A genetic modification engineered in pigs by removing a specific cell receptor to prevent porcine reproductive and respiratory syndrome virus from latching onto pig cells.

Restriction Fragment Length Polymorphism (RFLP) Analysis

A genetic analysis technique that compares differences in the lengths of DNA fragments produced by restriction enzyme digestion.

Single Nucleotide Polymorphism (SNP)

A point genetic variation occurring when a single nucleotide differs at a specific position in the DNA sequence.

Short Tandem Repeats (STRs)

Short repeated DNA sequences consisting of $2\text{ to }6\text{ nucleotides}$ whose repeat count is highly variable among individuals.

STR Allelic Variability

The high degree of variation in the number of repeat units at STR loci among individuals, making them ideal genetic markers for distinguishing between people.

Bacterial DNA Fingerprinting in Outbreaks

A molecular typing application critical for identifying bacterial pathogens and tracing contaminated food sources during a foodborne illness outbreak.

STR Paternity Testing Principle

The genetic evaluation principle where an alleged father is considered biologically compatible at an STR locus if he shares the child's non-maternal allele.

Whole-Genome Sequencing (WGS) Outbreak Investigation

The comprehensive genomic tracking of related bacterial pathogens (such as Salmonella) combined with patient interviews and food tracing to identify an outbreak source.

Bacterial CRISPR-Cas Immune System

An adaptive immune defense mechanism naturally occurring in bacteria and archaea that protects against invading genetic material such as bacteriophages.

Guide RNA (gRNA)

An engineered RNA component designed to direct the Cas9 endonuclease to a target DNA sequence through complementary base pairing.

Non-Homologous End Joining (NHEJ)

A cellular DNA repair pathway that rejoins double-strand breaks generated by Cas9, often introducing small insertions or deletions that disrupt a gene.

Prime Editing

A precise genome editing method that utilizes a pegRNA containing the desired edit along with a Cas9 nickase fused to a reverse transcriptase to insert short DNA sequences.

Casgevy

An FDA-approved (as of $2026$) CRISPR-based ex vivo cell therapy designed to treat sickle cell disease and beta-thalassemia.

Ex Vivo Gene Editing

A therapeutic strategy involving the removal of patient cells, editing them outside the body in a laboratory setting, and returning them to the patient.

In Vivo Gene Editing

A therapeutic approach that delivers gene-editing components directly into the patient's body, such as using lipid nanoparticles targeted to the liver.

Transthyretin (ATTR) Amyloidosis CRISPR Therapy

An in vivo gene-editing treatment that utilizes lipid nanoparticles to deliver editing components directly to hepatic cells inside the liver.

Human Embryo Gene Editing Regulation

Regulatory frameworks (such as the UK's HFEA) that permit editing IVF-donated embryos under license for research destroyed within $14\text{ days}$, while prohibiting their use to establish a pregnancy.

CAR-T Cell Therapy

A personalized cancer immunotherapy that successfully treated pediatric leukemia in patient Emily Whitehead.

Genomic Profiling

The analysis of a patient's specific tumor mutations to facilitate targeted and more effective individualized cancer therapies.

Targeted Monoclonal Antibodies

Personalized therapeutic agents generated by genetically engineering mice with human antibody genes to produce humanized antibodies.

Personalized Medicine Implementation Challenges

Major logistical and ethical hurdles in precision medicine, specifically ensuring genetic data privacy and avoiding discrimination.

Pseudouridine Modification

A synthetic nucleoside substitution replacing uridine with pseudouridine in synthetic mRNA (discovered by Katalin Karikó and Drew Weissman, earning the $2023$ Nobel Prize) to reduce immune inflammation.

SARS-CoV-2 mRNA Vaccine Mechanism

The immunization pathway in which ribosomes translate delivered mRNA into spike proteins displayed on the cell surface, prompting an immune response and antibody production.

Universal Influenza Vaccine Concept

A long-term vaccine development goal aimed at broad, durable protection against diverse influenza strains, rather than a seasonal shot reformulated every two to three years.

Intismeran

A therapeutic mRNA vaccine for melanoma that, when combined with Keytruda, reduced the chance of disease recurrence or death.

Bioinformatics

The scientific discipline focused on using computers to store, organize, and analyze complex biological data.

BLAST (Basic Local Alignment Search Tool)

A primary bioinformatics tool utilized for comparing query DNA or protein sequences against existing databases to identify similarities and match organisms.

AlphaFold

An artificial intelligence system that predicts the three-dimensional structures of proteins directly from their amino acid sequences.

JCVI-syn1.0 Project

A synthetic biology project that determined approximately $100\text{ genes}$ in Mycoplasma genitalium were non-essential and transplanted a chemically synthesized genome into a recipient bacterial cell.

Stéphane Leduc

The scientist who coined the term 'Synthetic Biology' in the publication 'Théorie physico-chimique de la vie et générations spontanées'.

Synthetic Biology Artificial Organs

Engineered replacement organs that are currently not cheap to manufacture and are not produced globally.

tTAV Protein

A transactivator protein expressed in genetically modified Aedes aegypti mosquitoes that is specifically inhibited by tetracycline.