Genes, Genomes, and Gene Expression

Comprehensive vocabulary flashcards covering classical DNA inheritance experiments, DNA structure, replication machinery, transcription, translation, mutations, prokaryotic and eukaryotic gene regulation, chromatin structure, and genome organization.

Bacterial Transformation

The process demonstrated by Frederick Griffith in $1928$ where non-virulent R strain Streptococcus pneumoniae acquired hereditary information from heat-killed virulent S strain bacteria in the environment, converting into live, disease-causing S strain cells.

Transforming Substance

The hereditary material identified in $1944$ by Oswald Avery, Colin MacLeod, and Maclyn McCarty through purification experiments, proving conclusively that DNA (and not protein or polysaccharide) is the molecule that transforms the R strain into the virulent S strain.

Hershey-Chase Experiment

A $1952$ experiment that infected bacterial cells with bacteriophages labeled with radioactive $^{35}\text{S}$ in protein capsules or $^{32}\text{P}$ in viral DNA; centrifugation showed that only $^{32}\text{P}$ entered the bacterial pellet while $^{35}\text{S}$ remained in the supernatant, confirming DNA as the genetic material.

Chargaff's Rules

The biochemical principle establishing that in double-stranded DNA, total purines equal total pyrimidines, specifically with the molar ratio of adenine equaling thymine ($\text{A} = \text{T}$) and guanine equaling cytosine ($\text{G} = \text{C}$).

Rosalind Franklin's Photo 51

The X-ray crystallography diffraction pattern of DNA produced by Rosalind Franklin that revealed critical dimensions of the double helix: $0.34\,\text{nm}$ spacing between base pairs, a width of $2.0\,\text{nm}$, and a full helical turn every $3.4\,\text{nm}$.

Antiparallel Strands

The structural arrangement of the double helix where one phosphodiester strand runs in the $5' \rightarrow 3'$ direction and the complementary strand runs in the reverse $3' \rightarrow 5'$ direction, with nitrogenous bases held together in the center by hydrogen bonds.

Semiconservative Replication

The mode of DNA replication confirmed by the Meselson-Stahl experiment using heavy isotope $^{15}\text{N}$ and light $^{14}\text{N}$, where each newly replicated double helix retains one intact parental strand and one newly synthesized daughter strand.

DNA Polymerase

The enzyme responsible for synthesizing new DNA polymers by covalently adding incoming deoxynucleotide triphosphates (dNTPs) exclusively to the exposed $3'\text{-OH}$ group of an existing complementary strand, releasing pyrophosphate and energy.

Helicase

The replication enzyme that unwinds the DNA double helix at the replication fork by breaking the hydrogen bonds between complementary base pairs.

Primase

An RNA polymerase enzyme that synthesizes a short complementary RNA sequence (a primer) on the template DNA, providing the essential free $3'\text{-OH}$ group required for DNA polymerase to initiate synthesis.

DNA Ligase

The enzyme that catalyzes phosphodiester bond formation to covalently seal nicks between adjacent Okazaki fragments on the lagging strand during DNA replication.

Origin of Replication

A specific, typically $\text{A-T}$-rich DNA sequence where initiator proteins and helicase first unwind the double helix to establish bidirectional replication forks.

Leading Strand

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

Lagging Strand

The discontinuous strand synthesized away from the replication fork in short discontinuous stretches known as Okazaki fragments, each initiated by an individual RNA primer.

Central Dogma of Molecular Biology

The framework describing the directional flow of genetic information inside a biological system: DNA is transcribed into messenger RNA (mRNA), which is then translated into functional polypeptides.

Promoter

A specific DNA sequence upstream of a gene that acts as the physical binding site for RNA polymerase (or the RNA polymerase holoenzyme in prokaryotes) to initiate transcription.

Template Strand

The strand of DNA read and copied by RNA polymerase in the $3' \rightarrow 5'$ direction to synthesize an antiparallel, complementary RNA molecule extending $5' \rightarrow 3'$.

Coding Strand

The non-template DNA strand whose nucleotide sequence matches the transcribed mRNA transcript directly in sequence and orientation ($5' \rightarrow 3'$), with thymine (T) in DNA in place of uracil (U) in RNA.

RNA Splicing

A eukaryotic post-transcriptional process within the nucleus where non-coding intervening sequences (introns) are excised from the primary RNA transcript and coding segments (exons) are joined together.

$5'\text{ Cap}$ and $3'\text{ Poly(A) Tail}$

Eukaryotic mRNA modifications consisting of a modified guanine ($\text{m}^7\text{G}$) added to the $5'$ end and a tract of adenine residues added to the $3'$ end, required for nuclear export, transcript stability, and ribosome binding.

Transfer RNA (tRNA)

Non-coding RNA molecules comprising roughly $15\%$ of cellular RNA that carry specific amino acids at their $3'$ acceptor stem and contain a three-base anticodon to base-pair with codons on mRNA.

Ribosomal RNA (rRNA)

Catalytic RNA making up approximately $80\%$ of cellular RNA that forms the enzymatic and structural core of the ribosome responsible for catalyzing peptide bond formation during translation.

Silent Mutation

A point mutation where a nucleotide substitution results in a new codon that specifies the identical amino acid, causing a change in genotype without altering the polypeptide sequence or phenotype.

Missense Mutation

A point mutation where a nucleotide change replaces one amino acid codon with a codon specifying a different amino acid, altering the primary structure of the encoded protein.

Nonsense Mutation

A point mutation that converts a sense codon specifying an amino acid into a premature stop codon ($\text{UAA}$, $\text{UAG}$, or $\text{UGA}$), yielding a truncated and typically non-functional polypeptide.

Frameshift Mutation

The addition or deletion of a number of nucleotides not divisible by three within a protein-coding region, completely shifting the downstream triplet reading frame and causing extensive missense alterations.

Constitutive Promoter

An unregulated promoter possessing an optimal DNA consensus sequence that allows RNA polymerase to bind efficiently on its own without assistance, driving continuous baseline transcription.

Regulatory Element

A specific non-coding DNA sequence (switch) bound by sequence-specific transcription factor proteins (activators or repressors) to control spatial and temporal gene expression.

Positive Regulation

A mechanism of transcriptional control where a regulatory protein (activator) binds to a DNA regulatory element to recruit general transcription factors and RNA polymerase, stimulating transcription.

Negative Regulation

A mechanism of transcriptional control where a regulatory protein (repressor) binds to a DNA operator or regulatory element, physically obstructing RNA polymerase access and shutting off transcription.

Chromatin Remodeling

The dynamic condensation and decondensation of DNA-histone complexes mediated by histone acetyltransferases (HATs, which add acetyl groups to relax chromatin) and histone deacetylases (HDACs, which remove acetyl groups to condense chromatin and silence genes).

Alternative Splicing

A eukaryotic gene regulatory process wherein different combinations of exons from a single pre-mRNA transcript are spliced together, producing distinct mature mRNA isoforms and multiple tissue-specific protein variants from one gene.

Operon

A cluster of contiguous prokaryotic genes transcribed from a single promoter into a continuous polycistronic mRNA possessing multiple start and stop codons, enabling coordinated co-regulation.

Regulon

A group of separate, dispersed prokaryotic genes or operons controlled by the same regulatory protein because each gene shares an identical DNA regulatory element near its promoter.

Pitx1 Gene

A developmental transcription factor gene in stickleback fish whose tissue-specific expression depends on modular regulatory switches (jaw, pituitary, pelvic); deletion of the pelvic switch causes loss of pelvic spines in freshwater sticklebacks while preserving essential jaw and pituitary functions.

C-value Paradox

The observation in eukaryotes that total haploid genome size does not correlate with organismal complexity or total number of protein-coding genes.

Transposable Elements

Mobile DNA sequences (including LINEs, SINEs, LTR retrotransposons, and DNA transposons) capable of moving throughout the genome, accounting for approximately $44\%$ of the total human genome.

Exome Sequencing

A targeted genomic sequencing method that selectively sequences only the protein-coding exons of all genes (the exome, representing approximately $2\%$ of the human genome), offering a cost-effective way to identify disease-causing mutations.

XIAP Gene

An X-linked gene regulating apoptosis and gut immunity in which a missense substitution ($\text{TGT} \rightarrow \text{TAT}$ changing an evolutionarily conserved cysteine to tyrosine) was identified by exome sequencing as the cause of fatal bowel ulceration in patient Nic Volker.