Molecular Biology: Translation, Gene Regulation, Mutations, and Biotechnology

Vocabulary practice flashcards covering protein translation, bacterial and eukaryotic gene regulation, DNA repair pathways, and biotechnology techniques derived from lecture notes.

Disulfide bond

A covalent linkage between cysteine R groups that serves as an example of protein tertiary structure.

Secondary protein structure

Conformations such as $\alpha$-helices and $\beta$-pleated sheets stabilized by hydrogen bonds between carboxyl and amino groups of different amino acids.

23S rRNA

The catalytic ribozyme component in bacteria that catalyzes peptide bond formation during translation elongation.

tRNA charging

The covalent linkage of a specific amino acid to its appropriate tRNA molecule.

Amino acid structure

A monomer composed of three central parts: an amino group, a carboxylic acid, and a side chain / R group.

Levels of protein structure

The hierarchical organization of proteins ordered from most basic to most complex: Primary $\rightarrow$ Secondary $\rightarrow$ Tertiary $\rightarrow$ Quaternary.

Polysome

A complex formed by a mature mRNA molecule bound simultaneously by multiple active ribosomes.

Aminoacyl-tRNA synthetase

An enzyme responsible for attaching the appropriate amino acid to its corresponding tRNA.

Synonymous codons

Codons with different nucleotide sequences that encode the same amino acid.

Ribosome tRNA binding sites

The sequential functional sites through which a tRNA moves during elongation: aminoacyl (A) $\rightarrow$ peptidyl (P) $\rightarrow$ exit (E).

Beadle and Tatum hypothesis

The principle formulated from experimentation with Neurospora fungus proposing that the role of a specific gene is to produce a specific enzyme.

Molecular chaperones

Proteins that mediate the folding process by preventing the formation of alternative incorrect folding patterns.

Ubiquitin

A molecular tag that marks misfolded, damaged, or unneeded proteins for degradation in the proteasome.

Shine-Dalgarno sequence

A bacterial mRNA ribosome binding site (RBS) that helps the ribosome identify and bind the translation start site.

Kozak sequence

A consensus sequence in eukaryotic mRNA that helps the eukaryotic ribosome locate the translation start site.

Closed loop translation

The circularized eukaryotic mRNA conformation formed by the interaction between the $5'$ cap and the $3'$ poly-A tail during translation initiation.

IF-1

A bacterial initiation factor that prevents aminoacyl-tRNA from binding to the ribosomal A site prematurely.

IF-2

A bacterial initiation factor that binds initiator fMet-tRNA and transfers it into the ribosomal P site.

IF-3

A bacterial initiation factor that binds the $30S$ ribosomal subunit to prevent premature association with the $50S$ subunit.

EF-Tu

An elongation factor that delivers an aminoacyl-tRNA to the A site of the ribosome.

EF-Ts

An elongation factor that regenerates and recharges EF-Tu.

EF-G

A GTP-dependent elongation factor that stimulates ribosomal translocation along mRNA.

RF1 and RF2

Bacterial release factors that recognize stop codons and catalyze the release of the polypeptide chain from tRNA.

RF3

A bacterial release factor that stimulates the release of RF1 and RF2 from the ribosome.

Constitutive gene expression

A pattern of transcription in which a gene is continuously active and turned on.

Negative gene regulation

A control mechanism in which gene expression proceeds unless actively halted by a repressor protein.

Corepressor

A small regulatory molecule that binds to a repressor protein to allow it to bind the operator and shut off transcription (e.g., tryptophan in the trp operon).

Inducer

A small molecule that binds to a repressor protein to remove it from the operator and allow gene transcription (e.g., allolactose/lactose derivatives in the lac operon).

lacI

The gene encoding the lac operon repressor; loss-of-function mutations cause constitutive lac operon expression.

Attenuator

A regulatory element in the trp operon that prematurely halts transcription when tryptophan levels are high.

Allosteric protein

A protein whose conformation and activity are altered upon binding an effector molecule at a specific regulatory site.

Riboswitch

An RNA regulatory domain comprising an aptamer that binds a specific ligand and an expression platform that modulates transcription or translation (such as forming a terminator hairpin).

Small non-coding RNA (sRNA)

Bacterial non-coding RNA molecules capable of regulating translation by concealing or revealing the ribosome binding site (RBS).

Insulator

A eukaryotic DNA regulatory element that blocks enhancer activity from stimulating transcription of adjacent non-target promoters.

RNA interference (RNAi)

A eukaryotic posttranscriptional regulatory mechanism where siRNAs or miRNAs silence specific genes by mRNA cleavage, degradation, or translational repression.

Histone acetylation

An epigenetic chromatin modification that relaxes DNA-protein interactions to regulate transcription, such as controlling flowering time in Arabidopsis.

Non-homologous end joining (NHEJ)

An error-prone DNA repair mechanism used prior to DNA replication to rejoin double-strand breaks without a homologous template, often causing insertions, deletions, or translocations.

Homologous recombination (HR)

A high-fidelity double-strand break repair pathway utilized after DNA replication that uses an intact sister chromatid as a repair template.

Gain-of-function mutation

A mutation that confers a novel or constitutively active function onto a gene product, usually inherited in a dominant manner.

Transition

A point mutation involving a base substitution between like bases, such as a purine replacing another purine (e.g., A to G) or a pyrimidine replacing another pyrimidine.

Haploinsufficiency

A condition in a diploid heterozygote where a single wild-type allele is insufficient to generate enough gene product to produce the wild-type phenotype.

Suppressor mutation

A secondary genetic alteration that counteracts or relieves the phenotypic consequences of a preexisting primary mutation.

Apurinic (AP) site

A DNA lesion characterized by the spontaneous spontaneous loss of a purine base from an intact deoxyribose-phosphate backbone.

Deamination

A chemical reaction involving the removal or conversion of an amino group on cytosine or adenine to a keto group.

5-bromouracil

A base analog of thymine that mispairs anomalously with guanine, inducing transition mutations.

Conservative mutation

A missense mutation that substitutes one amino acid for another with similar biochemical properties, preserving overall protein function.

Strand slippage

A DNA replication error causing repeats to expand or contract within repetitive sequence tracts.

Ames test

A biological assay evaluating the mutagenicity of compounds by measuring the rate of reverse mutations in auxotrophic bacteria.

Intercalating agent

A planar chemical compound that slips between stacked base pairs of the DNA double helix, commonly used for staining DNA gels.

Multiple Cloning Site (MCS)

A engineered plasmid region containing unique restriction endonuclease recognition sequences where foreign DNA fragments are inserted.

PAM site

A short motif adjacent to target phage DNA essential for Cas9 cleavage that is absent in the host bacterial genome to prevent self-targeting.

Single guide RNA (sgRNA)

An engineered synthetic RNA construct designed to direct the Cas9 endonuclease to a complementary target sequence for site-specific cleavage.