Microbial Genetics, Recombinant DNA Technology, and Microbial Control

Comprehensive vocabulary flashcards covering microbial genetics, molecular biology, recombinant DNA technology, genomics, and physical and chemical microbial control methods.

Levels of Genetic Study

The four hierarchical tiers of investigating heredity: organismal genetics (whole organism), cellular genetics (single cell), chromosomal genetics (structure and action of chromosomes), and molecular genetics (biochemistry of genes).

Genome

The sum total of genetic material of an organism, mostly existing as chromosomes, but also occurring in nonchromosomal forms such as plasmids or organellar DNA (mitochondria and chloroplasts).

Genomics

The comprehensive scientific study of an organism's entire genome.

Chromosome

A distinct cellular structure composed of a neatly packaged DNA molecule containing hereditary information.

Gene

A basic informational packet subdividing a chromosome that contains the necessary genetic code for a particular cellular function.

Genotype

The sum total of all gene types that constitute an organism's distinctive genetic makeup.

Phenotype

The physical expression of an organism's genotype that manifests as observable structural or functional traits.

Nucleotide

The basic structural unit of DNA, composed of a phosphate group, a deoxyribose sugar, and a nitrogenous base (adenine, thymine, guanine, or cytosine).

Antiparallel

The structural arrangement in the DNA double helix where one strand runs in the $5' \rightarrow 3'$ direction and the complementary strand runs in the $3' \rightarrow 5'$ direction.

Semiconservative Replication

The mechanism of DNA duplication in which each resulting daughter molecule consists of one original conserved parental template strand and one newly synthesized strand.

Replication Fork

The Y-shaped region in a DNA double helix where the parental strands are unwound and active replication proceeds.

Primer

A short sequence of RNA inserted onto a template strand during replication initiation before being replaced by DNA.

DNA Polymerase III

The primary enzyme responsible for synthesizing new daughter strands of DNA in the $5' \rightarrow 3'$ direction and proofreading the chain for mistakes.

DNA Polymerase I

The replication enzyme responsible for removing RNA primers, closing resulting gaps, and repairing base mismatches.

DNA Ligase

An enzyme that executes the final sealing of nicks in the sugar-phosphate backbone of DNA during replication and repair.

Leading Strand

The new strand of DNA that is synthesized continuously in the $5' \rightarrow 3'$ direction toward the replication fork.

Lagging Strand

The new strand of DNA that is synthesized discontinuously in short segments in the $5' \rightarrow 3'$ direction away from the replication fork.

Okazaki Fragments

Short fragments of DNA ($100\text{ to }1{,}000$ bases long) synthesized along the lagging strand that are subsequently joined by DNA ligase.

Topoisomerase I

An enzyme that produces single-stranded breaks in DNA to relieve supercoiling tension at the replication origin.

Topoisomerase II (DNA Gyrase) and IV

Enzymes that create double-stranded DNA breaks to remove supercoiling ahead of the replication fork and separate replicated circular daughter chromosomes.

Central Dogma

The foundational principle stating that genetic information flows from DNA to RNA via transcription, and from RNA to protein via translation.

Proteomics

The scientific study of the complete complement of expressed proteins produced by an organism.

Messenger RNA (mRNA)

A single-stranded RNA transcript of the DNA code that delivers instructions directly to the ribosome for translation into protein.

Transfer RNA (tRNA)

A cloverleaf-structured adaptor RNA containing an anticodon loop and a $3'$ amino acid attachment site that carries specific amino acids to the ribosome.

Ribosomal RNA (rRNA)

Large structural RNA molecules that associate with proteins to construct the ribosomal subunits and participate in catalytic protein synthesis.

Promoter Region

An adenine- and thymine-rich sequence of DNA preceding a gene that signals RNA polymerase to bind and initiate transcription.

DNA Scrunching

A process during transcription initiation in which RNA polymerase draws the early portions of DNA into itself to gather energy before advancing down the template strand.

Codon

A three-nucleotide sequence in mRNA that dictates a specific amino acid to be added during polypeptide synthesis.

Anticodon

The specific trinucleotide sequence located on the bottom loop of a tRNA molecule that pairs complementarily with an mRNA codon.

Redundancy (Degeneracy)

A property of the master genetic code in which a particular amino acid can be specified by multiple different codons.

Wobble

The relaxation of base-pairing rules at the third nucleotide position of a codon, allowing variations without changing the encoded amino acid.

Start Codon

The initial three ribonucleotides of an mRNA transcript ($\text{AUG}$) that signal the beginning of translation and code for formyl methionine in bacteria.

Nonsense Codon (Stop Codon)

One of three specific codons ($\text{UAA}$, $\text{UAG}$, or $\text{UGA}$) that lacks a corresponding tRNA and signals termination of translation.

Translocation

The enzyme-mediated shifting of the ribosome down the mRNA strand by one codon in the $5' \rightarrow 3'$ direction during translation elongation.

Cotranscriptional Translation

The simultaneous occurrence of transcription and translation on the same mRNA strand, exclusive to bacteria and archaea.

Introns

Intervening noncoding sequences of bases within a eukaryotic gene that do not code for protein and are removed prior to translation.

Exons

The coding regions of a eukaryotic gene that remain after splicing to form the mature mRNA molecule translated into protein.

Spliceosome

An enzymatic RNA-protein complex that recognizes exon-intron junctions, cuts out introns into lariat shapes, and joins exons end to end in eukaryotic cells.

Operon

A coordinated set of genes regulated as a single unit under the control of an operator and promoter, found exclusively in bacteria and archaea.

Inducible Operon

An operon whose default state is 'off' that is turned 'on' (induced) by a specific substrate nutrient that binds and inactivates the repressor protein.

Repressible Operon

An operon whose default state is 'on' that is turned 'off' (repressed) when an accumulated end product acts as a corepressor to activate the repressor.

Phase Variation

A regulatory mechanism in which bacteria reversibly switch specific genes on or off, resulting in heritable phenotypic changes such as surface antigen alterations.

Recombinant

Any organism that contains and expresses genes that originated in another organism.

Horizontal Gene Transfer

Any transfer of DNA resulting in organisms acquiring new genes that did not originate directly from parent organisms.

Conjugation

A direct mode of horizontal genetic transfer between living donor and recipient bacterial cells via a pilus bridge.

Transformation

An indirect horizontal genetic transfer process where a competent bacterial cell absorbs fragments of soluble naked DNA from the surrounding environment.

Transduction

An indirect method of genetic exchange in which a bacteriophage carries donor bacterial DNA to a recipient bacterial cell of the same species.

Transposons (Transposable Elements)

Specialized DNA segments ('jumping genes') capable of excising and shifting from one genomic site to another, between chromosomes, or between plasmids and chromosomes.

Pathogenicity Islands (PAIs)

Large coordinated gene clusters flanked by transposable element sequences that confer virulence properties to bacteria, such as toxin production or iron scavenging.

Point Mutation

A small alteration in genetic code that affects only a single base pair within a gene through addition, deletion, or substitution.

Missense Mutation

A base substitution mutation that alters a codon so that it directs the incorporation of a different amino acid.

Nonsense Mutation

A mutation that converts a normal amino-acid-specifying codon into a stop (nonsense) codon, terminating protein synthesis prematurely.

Silent Mutation

A base substitution that alters a codon but does not change the resulting amino acid due to redundancy in the genetic code.

Frameshift Mutation

A mutation resulting from the insertion or deletion of bases in numbers other than multiples of three, which shifts the reading frame and changes every downstream amino acid.

Ames Test

A rapid bacterial screening assay using a histidine-requiring mutant of Salmonella typhimurium to determine whether a chemical induces back-mutations and acts as a potential carcinogen.

Restriction Endonucleases

Enzymes that selectively cleave foreign DNA crosswise at specific palindromic sequences of $4\text{ to }10$ base pairs, breaking phosphodiester bonds.

Sticky Ends

Staggered, single-stranded overhangs produced by restriction enzyme cleavage that base-pair with complementary tails on other DNA fragments.

Restriction Fragment Length Polymorphisms (RFLPs)

Differences in the lengths of DNA fragments produced when identical restriction enzymes cut different individuals' genomes at polymorphic sites.

Reverse Transcriptase

A retroviral enzyme that converts an RNA template into a complementary strand of DNA.

Complementary DNA (cDNA)

DNA synthesized in vitro from processed eukaryotic mRNA using reverse transcriptase, representing an expressed gene free of noncoding introns.

CRISPR-Cas9

A molecular endonuclease system derived from bacterial adaptive immunity that utilizes guide RNAs to recognize and cleave precise targeted DNA sequences.

Polymerase Chain Reaction (PCR)

A molecular amplification method that uses repeated cycles of denaturation ($94^\bot\text{C}$), priming ($50^\bot\text{C}\text{ to }65^\bot\text{C}$), and extension ($72^\bot\text{C}$) with heat-stable polymerases to rapidly produce billions of DNA copies.

pUC19

A classic $2{,}686\text{ bp}$ plasmid cloning vector carrying an ampicillin resistance gene ($\text{Amp}^R$), an origin of replication ($\text{ori}$), and a multiple cloning site ($\text{MCS}$) within the $\text{lacZ}\alpha$ gene.

Synthetic Biology

The scientific discipline focused on the design and artificial construction of entirely new biological parts, molecules, and organisms from scratch.

Gel Electrophoresis

A technique that separates DNA fragments embedded in an agarose gel by subjecting them to an electrical gradient, moving negatively charged fragments toward the positive pole according to size.

Gene Probe

A short, labeled single- or double-stranded oligonucleotide of known sequence used to detect and hybridize with complementary target nucleic acid sequences.

Fluorescent In Situ Hybridization (FISH)

A diagnostic technique that applies fluorescently tagged probes directly to intact cells to identify specific genetic marker sequences without prior culturing.

Contig

A continuous, larger set of overlapping nucleotide sequences reconstructed computationally during shotgun whole-genome sequencing.

Single Nucleotide Polymorphism (SNP)

A single nucleotide variation at a specific genomic locus among individuals of a species, often serving as a marker for traits or disease predispositions.

DNA Microarray Analysis

A high-throughput technology consisting of microscopic DNA sequences affixed to a solid grid, used to quantify and track the simultaneous expression of thousands of genes.

Somatic Cell Gene Therapy

A clinical gene transfer procedure that corrects genetic defects in specific non-reproductive body tissues, rendering the correction permanent in the patient but not heritable.

Germline Therapy

A gene therapy approach in which therapeutic genes are inserted into an egg, sperm, or early embryo, resulting in heritable genetic changes passed to offspring.

Sterilization

The complete destruction or absolute removal of all viable microorganisms, including bacterial endospores and viruses, from inanimate objects.

Disinfection

A physical process or chemical treatment that destroys vegetative microorganisms and toxins on inanimate objects, but does not eradicate bacterial endospores.

Antisepsis (Degermation)

The application of chemical agents to exposed body surfaces, wounds, and surgical incisions to destroy or inhibit vegetative microbes on living tissue.

Decontamination (Sanitization)

The mechanical cleansing process that removes microorganisms and debris from surfaces to reduce contamination to safe public health levels.

Microbial Resistance Hierarchy

The relative spectrum of microbial resistance ranging from the most resistant forms (prions and bacterial endospores) down to the least resistant forms (enveloped viruses such as SARS-CoV-2).

Microbicidal Agent

Any chemical or physical agent whose primary mode of action is to directly kill microorganisms (e.g., bactericide, fungicide, sporicide).

Microbiostatic Agent

An agent that prevents microbes from multiplying and growing without immediately killing them.

Surfactants

Polar amphipathic molecules that bind and disrupt the hydrophobic lipid core of cell membranes, causing loss of selective permeability and fatal leakage.

Thermal Death Time (TDT)

The shortest duration of time required to kill all test microbes in a liquid sample at a specified constant temperature.

Thermal Death Point (TDP)

The lowest temperature required to completely kill all microorganisms in a sample within an exposure time of 10 minutes.

Autoclave

A sterilization chamber that subjects materials to pressurized steam at $15\,\text{psi}$, achieving a temperature of $121^\circ\text{C}$ for 20 minutes to destroy all microbes and endospores.

Pasteurization

A moist heat treatment applied to consumable liquids to kill potential agents of infection and spoilage while retaining flavor and nutritional value.

Lyophilization

A method of microbial preservation combining rapid freezing and instantaneous dehydration under high vacuum (freeze-drying).

Ionizing Radiation

High-energy radiation (gamma rays, X-rays, cathode rays) that ejects orbital electrons from atoms, creating toxic ions and free radicals that break DNA strands.

Pyrimidine Dimers

Abnormal cross-links formed between adjacent pyrimidines (thymine or cytosine) in DNA upon absorption of ultraviolet radiation, disrupting replication and transcription.

Tinctures

Antimicrobial chemical solutions formulated by dissolving the active chemical solute in pure alcohol or a water-alcohol mixture.

Iodophors

Stable complexes of elemental iodine bound to a polymer or alcohol that release free iodine slowly, decreasing staining and tissue irritation.

Phenol Coefficient

A quantitative numerical rating that compares the bactericidal efficacy of a chemical disinfectant to that of standard phenol.

Chlorhexidine

A bis-biguanide antiseptic consisting of chlorine and two phenolic rings that targets cell membranes and walls, widely used in surgical prep and hand scrubs.

Quaternary Ammonium Compounds (Quats)

Cationic detergents carrying a positively charged nitrogen that bind negatively charged bacterial surface proteins and disrupt the cytoplasmic membrane.

Oligodynamic Action

The property of heavy metals (such as silver and mercury) to exert microbicidal effects in extremely minute concentrations by inactivating enzyme functional groups.

Ethylene Oxide (ETO)

A potent, explosive, and carcinogenic gas used in specialized chemiclaves to achieve gaseous sterilization of prepackaged medical devices by alkylating DNA and proteins.