Microbial Genetics and Recombinant Technologies

Comprehensive vocabulary flashcards covering microbial genetics, DNA replication, gene expression, operon regulation, horizontal gene transfer, mutations, and recombinant DNA technologies.

Genome

The sum total of genetic material in an organism; consists exclusively of DNA in cellular organisms (chromosomes, plasmids, mitochondria, and chloroplasts) and of either DNA or RNA in viruses.

Genotype vs. Phenotype

Genotype is an organism's full collection of inherited genes, whereas phenotype refers to the observable physical traits and functions manifested when those genes are expressed.

Nucleotide

The fundamental building unit of nucleic acids, consisting of a phosphate group, a 5-carbon pentose sugar (deoxyribose in DNA or ribose in RNA), and a nitrogenous base (adenine, thymine/uracil, guanine, or cytosine).

Antiparallel Strands

The structural orientation of double-stranded DNA where one strand runs in the $5' \rightarrow 3'$ direction and the complementary strand runs in the opposing $3' \rightarrow 5'$ direction.

Semiconservative Replication

The mode of DNA synthesis in which the parental double helix separates so that each original strand serves as a template, producing two daughter molecules that each retain one parental strand and one newly formed strand.

Replication Fork Enzymes

The coordinated enzymatic system duplicating DNA: helicase unzips the double helix, primase lays down short RNA primers, DNA polymerase III synthesizes new DNA in the $5' \rightarrow 3'$ direction, DNA polymerase I replaces RNA primers with DNA nucleotides, and DNA ligase seals backbone nicks.

Leading Strand vs. Lagging Strand

The leading strand is synthesized continuously toward the advancing replication fork in the $5' \rightarrow 3'$ direction, whereas the lagging strand is synthesized discontinuously away from the fork in short segments called Okazaki fragments.

Okazaki Fragments

Short stretches of newly synthesized DNA formed along the lagging template strand during replication, which are subsequently connected into a continuous strand by DNA ligase.

Transcription

The first major stage of gene expression, wherein RNA polymerase binds to a gene's promoter region, unwinds DNA, and synthesizes a complementary single-stranded RNA transcript using one DNA template strand.

Transfer RNA (tRNA)

A folded, cloverleaf-shaped RNA molecule containing three hairpin loops, a specific triplet anticodon that pairs with complementary mRNA codons, and a $3'$ terminal amino acid attachment site.

Ribosomal Binding Sites (A, P, and E Sites)

Three functional ribosomal cavities: the A (aminoacyl) site welcomes incoming aminoacyl-tRNAs, the P (peptidyl) site holds the tRNA bearing the growing peptide chain, and the E (exit) site releases uncharged tRNAs.

Codon

A specific sequence of three consecutive nucleotides on an mRNA molecule that directs the incorporation of a specific amino acid or dictates the termination of translation.

Bacterial Start Codon

The initiation codon, almost universally $\text{AUG}$, which sets the translational reading frame and codes for the modified initiator amino acid formylmethionine ($\text{fMet}$) in bacteria.

Stop Codons

The three non-coding mRNA codons ($\text{UAA}$, $\text{UAG}$, and $\text{UGA}$) that lack matching aminoacyl-tRNAs and signal the completion of translation and release of the nascent polypeptide.

Polyribosomal Complex (Polysome)

A bacterial structure enabling rapid protein synthesis where multiple ribosomes simultaneously translate an mRNA transcript as it is still being actively transcribed by RNA polymerase.

Introns and Exons

Components of eukaryotic split genes: exons are coding regions that are transcribed and expressed into functional protein, whereas introns are noncoding intervening segments excised by spliceosomes into lariat structures before translation.

Operon

A genetic regulatory mechanism found solely in Bacteria and Archaea consisting of a coordinated cluster of structural genes transcribed together into a single unbroken polycistronic mRNA under the control of a common promoter and operator.

lac Operon

An inducible bacterial operon governing lactose catabolism; in the absence of lactose, an allosteric repressor binds the operator locus to block transcription, but when lactose enters, it binds the repressor, changing its conformation so RNA polymerase can proceed.

Inducible vs. Repressible Operons

Inducible operons are normally turned off and are activated only when a specific substrate (inducer) is present, whereas repressible operons are normally active and are turned off when excessive metabolic end-products accumulate.

Horizontal Gene Transfer (HGT)

The non-reproductive acquisition of foreign DNA by an organism from another cell within the same generation, distinct from vertical inheritance from parent to offspring.

Bacterial Conjugation

A form of horizontal gene transfer requiring direct cell-to-cell contact, mediated by a pilus encoded by the fertility ($\text{F}$) factor plasmid transferring DNA from an $\text{F}^+$ donor to an $\text{F}^-$ recipient.

Transformation

A mode of horizontal gene transfer in which a competent bacterial cell captures and takes up free, naked DNA fragments released into the environment by dead or lysed cells.

Generalized Transduction

A viral gene transfer process wherein random host DNA fragments are mistakenly packaged inside a bacteriophage capsid during viral assembly, delivering bacterial donor genes into a new host upon subsequent infection.

Specialized Transduction

A highly specific phage-mediated gene transfer that occurs when an integrated prophage is excised imperfectly from the bacterial chromosome, carrying adjacent flanking host genes into newly packaged viral progeny.

Transposons

Transposable DNA elements ("jumping genes") containing transposase genes that allow them to excise and insert into alternate locations within a genome, chromosome, or plasmid.

Missense Mutation

A point mutation characterized by a single nucleotide substitution that replaces one codon with another, resulting in the substitution of a different amino acid in the synthesized protein.

Nonsense Mutation

A base substitution that converts an amino acid-specifying codon into a premature stop codon, terminating translation early and generating a nonfunctional truncated peptide.

Frameshift Mutation

The insertion or deletion of one or more base pairs in numbers not divisible by three, completely altering the downstream mRNA reading frame and nearly always producing a nonfunctional protein.

Silent Mutation

A point mutation altering a base that still specifies the exact same amino acid due to the degeneracy of the genetic code, resulting in an identical, functional protein.

Single Nucleotide Polymorphism (SNP)

A normal or pathological variation occurring at a single DNA base position within a population, such as the missense point mutation in clotting factor V altering position $506$.

Restriction Endonuclease

A bacterial defensive enzyme that recognizes foreign palindromic DNA sequences and cleaves phosphodiester bonds on both strands, generating sticky or blunt restriction fragments.

DNA Palindrome

A symmetrical sequence of double-stranded DNA that reads identically in the $5' \rightarrow 3'$ direction on one strand and the $5' \rightarrow 3'$ direction on the complementary antiparallel strand (e.g., $5'\text{-GAATTC-}3'$ cut by EcoRI).

Restriction Fragment Length Polymorphisms (RFLPs)

Variations in the length of DNA fragments produced when genomic DNA from different individuals is cut by specific restriction endonucleases, forming distinct banding patterns for DNA profiling.

Reverse Transcriptase (RT)

An enzyme found in retroviruses like HIV that synthesizes complementary DNA (cDNA) from an RNA template, yielding eukaryotic genes devoid of noncoding introns.

Polymerase Chain Reaction (PCR)

A molecular amplification technique that rapidly replicates a targeted region of DNA from a few starting copies to billions of amplicons within hours without culturing living cells.

PCR Primers

Short, single-stranded DNA oligonucleotides ($15\text{ to }30$ bases in length) designed to flank the specific target sequence and provide free $3'\text{-OH}$ groups for DNA synthesis.

Taq Polymerase

A heat-stable DNA polymerase isolated from the thermophilic bacterium Thermus aquaticus that retains functional enzymatic activity during the repeated high-temperature denaturation steps of PCR.

PCR Thermal Cycling Steps

The three-step cyclical process: Denaturation at $94^\circ\text{C}$ (strands separate), Priming/Annealing at $50^\circ\text{C}-65^\circ\text{C}$ (primers anneal to complementary templates), and Extension at $72^\circ\text{C}$ (Taq polymerase synthesizes complementary strands).

Gel Electrophoresis

A separation method wherein DNA samples migrate through an agarose gel under an electric current toward the positive pole due to their negatively charged phosphate groups, with smaller fragments traveling faster and farther than larger ones.

Cloning Vector

A self-replicating genetic vehicle (commonly a bacterial plasmid or virus) used to carry a cleaved donor gene into a cloning host cell for amplification and protein expression.

Metagenomics

The systematic study of all genomic material and microbial communities isolated directly from a specific environmental or ecological niche without culturing individual species.

Ex Vivo Gene Therapy

A therapeutic approach where patient cells (such as bone marrow) are harvested, transduced in vitro with a normal functional gene delivered by a retroviral vector, and subsequently reinfused into the patient.

CRISPR-Cas9

A targeted molecular gene-editing system that enables biotechnologists to cleave DNA at precise locations in the genome to repair defects or introduce desired mutations.

CAR T-Cell Therapy

A personalized cancer therapy in which a patient's T lymphocytes are genetically modified with synthetic chimeric antigen receptors to recognize and destroy specific tumor cell antigens.