Molecular Genetics: DNA Structure, Replication, Transcription, Translation, Mutation, Repair, and Prokaryotic Gene Regulation

Comprehensive vocabulary flashcards covering the molecular biology of DNA structure, replication, transcription, post-transcriptional processing, translation, genetic mutations, DNA repair mechanisms, and prokaryotic gene regulation.

Tetranucleotide Hypothesis

A proposal made by Phoebus Levene in 1910 stating that DNA consists of equal amounts of four nucleotides repeating in identical groups, which incorrectly suggested DNA lacked the chemical diversity to store genetic information and led scientists to favor proteins as the genetic material.

Transformation

The process discovered by Frederick Griffith in 1927 in Diplococcus pneumoniae (Streptococcus pneumoniae), where living avirulent Type IIR bacteria acquired the ability to form capsules and cause fatal infection after being mixed with heat-killed virulent Type IIIS bacteria.

Transforming Principle

The macromolecular substance identified by Oswald Avery, Colin MacLeod, and Maclyn McCarty in 1944 as deoxyribonucleic acid (DNA), shown because enzymatic destruction with deoxyribonuclease (DNase) abolished the transformation of IIR cells into virulent IIIS cells, whereas ribonuclease and proteases had no effect.

Hershey-Chase Experiment

A 1952 experiment by Alfred Hershey and Martha Chase using bacteriophage T2 and Escherichia coli that labeled phage DNA with $^{32}\text{P}$ and phage protein with $^{35}\text{S}$, demonstrating that only $^{32}\text{P}$-labeled DNA enters bacterial cells and directs the production of progeny phage.

Phosphodiester Bond

The covalent linkage that connects adjacent nucleotides in a polynucleotide chain between the phosphate group attached to the $5'$ carbon of one pentose sugar and the hydroxyl ($-\text{OH}$) group on the $3'$ carbon of the adjacent sugar.

Chargaff's Rules

Quantitative relationships determined by Erwin Chargaff showing that in double-stranded DNA, the molar concentration of adenine equals thymine ($A = T$) and guanine equals cytosine ($G = C$), meaning the sum of purines equals the sum of pyrimidines ($A + G = C + T$), while $(G + C) \neq (A + T)$.

Photo 51

The famous X-ray diffraction photograph of the B-form of DNA produced on May 2, 1952, by Rosalind Franklin and Raymond Gosling, demonstrating that DNA is a double helix with a repeating periodicity of $0.34\,\text{nm}$ ($3.4\,\text{\AA}$).

B-DNA

The canonical, biologically significant right-handed double-helical conformation of DNA observed under aqueous, low-salt conditions, featuring a diameter of $2.0\,\text{nm}$ ($20\,\text{\AA}$), an axial rise of $3.4\,\text{nm}$ ($34\,\text{\AA}$) per complete helical turn, and approximately $10.4$ base pairs per turn with alternating major and minor grooves.

Semiconservative Replication

The mode of DNA replication wherein the two parental strands unwind, each serving as an individual template for the synthesis of a complementary daughter strand, resulting in daughter duplexes composed of one parental (old) strand and one newly synthesized strand.

Meselson-Stahl Experiment

A 1958 experiment by Matthew Meselson and Franklin Stahl utilizing $^{15}\text{N}$ heavy isotope labeling and CsCl density gradient centrifugation in E. coli, confirming semiconservative replication by demonstrating an intermediate-density $^{15}\text{N}/^{14}\text{N}$ band in Generation I and equal proportions of light ($^{14}\text{N}/^{14}\text{N}$) and intermediate bands in Generation II.

oriC

The unique origin of replication in the circular Escherichia coli chromosome consisting of a specific $245\text{-base-pair}$ sequence where DNA unwinding initiates and bidirectional replication forks assemble.

DNA Gyrase

A bacterial type II topoisomerase that introduces negative supercoils to relieve the positive torsional strain and supercoiling generated ahead of the advancing replication fork during double helix unwinding.

Okazaki Fragments

Short segments of newly synthesized DNA (roughly $1000\text{--}2000\,\text{bp}$ long in bacteria and $100\text{--}150\,\text{bp}$ long in eukaryotes) produced discontinuously along the lagging strand template in the $5'\rightarrow 3'$ direction, discovered by Reiji and Tsuneko Okazaki.

DNA Polymerase III Holoenzyme

The active, multi-subunit primary replicative enzyme complex in E. coli comprising a catalytic core ($\alpha$ for $5'\rightarrow 3'$ polymerization, $\epsilon$ for $3'\rightarrow 5'$ exonuclease proofreading, and $\theta$ for core assembly), a $\beta$ sliding clamp processivity factor, a $\gamma$ complex clamp loader, and a $\tau$ subunit that dimerizes the core complex.

DNA Polymerase I

A bacterial single-polypeptide DNA polymerase with $928$ amino acids that possesses unique $5'\rightarrow 3'$ exonuclease activity (to excise RNA primers), $5'\rightarrow 3'$ polymerase activity (to fill the resulting gaps with DNA), and $3'\rightarrow 5'$ exonuclease activity for proofreading.

Telomerase

A ribonucleoprotein enzyme complex consisting of an RNA component (TERC) that serves as a guide and template, and a catalytic protein reverse transcriptase (TERT) that synthesizes repetitive G-rich DNA sequences at the $3'$ overhangs of linear eukaryotic chromosomes to prevent end-shortening.

Holliday Structure

A characteristic cross-shaped (chi form) four-way DNA junction generated during homologous recombination following endonuclease nicking, strand invasion/displacement, branch migration, and duplex rotation.

Pribnow Box

A conserved hexameric cis-acting consensus sequence (TATAAT) situated at the $-10$ position upstream from the transcription start site ($+1$) in prokaryotic promoters, responsible for facilitating initial unwinding of DNA by RNA polymerase.

Sigma ($\sigma$) Factor

A regulatory subunit of the prokaryotic RNA polymerase holoenzyme ($\alpha_2 \beta \beta' \omega \sigma$) that recognizes specific promoter consensus sequences at $-35$ and $-10$ to direct transcription initiation, dissociating from the core enzyme once promoter clearance occurs.

Rho-Dependent Termination

A prokaryotic transcription termination mechanism mediated by the Rho ($\rho$) factor, a hexameric helicase that binds to an upstream cytosine-rich rut (rho utilization) sequence on nascent mRNA, migrates toward the $3'$ end, and unwinds the DNA-RNA hybrid when RNA polymerase pauses at a hairpin loop.

TATA Box (Goldberg-Hogness Box)

A conserved eukaryotic core promoter element located approximately $-30$ base pairs upstream of the transcription initiation site with the consensus sequence $\text{TATA(A/T)AAR}$, recognized and bound by TATA-binding protein (TBP) of the TFIID complex.

$5'$ Cap ($\text{m}^7\text{G}$ Cap)

A modified 7-methylguanosine residue added post-transcriptionally to the $5'$ end of eukaryotic pre-mRNA via an unusual $5'\text{--to--}5'$ triphosphate bridge, which protects the transcript from enzymatic degradation and promotes ribosome binding during translation initiation.

Spliceosome

A large multi-megadalton ribonucleoprotein complex composed of small nuclear RNAs (snRNAs U1, U2, U4, U5, and U6) and associated proteins (snRNPs) that recognizes conserved $5'$ splice donor (GU), branch point (A), and $3'$ splice acceptor (AG) motifs to excise introns via a lariat intermediate.

RNA Editing

A post-transcriptional process in eukaryotes that alters specific nucleotide sequences in pre-mRNA, including substitution editing via deaminases (such as C-to-U deamination in ApoB and A-to-I editing in GluR) as well as insertion/deletion editing.

Wobble Hypothesis

Francis Crick's proposal stating that spatial flexibility at the third base ($3'$ position) of an mRNA codon allows non-standard hydrogen bonding with the first base ($5'$ position) of a tRNA anticodon, allowing a single tRNA (such as one containing inosine) to recognize multiple synonymous codons.

Peptidyl Transferase

The ribozyme activity intrinsic to the large ribosomal subunit rRNA ($23\text{S}$ rRNA in prokaryotes and $28\text{S}$ rRNA in eukaryotes) that catalyzes peptide bond formation by transferring the growing polypeptide chain from the peptidyl-tRNA in the P site to the amino acid on the aminoacyl-tRNA in the A site.

Transfer RNA (tRNA)

An adaptor RNA molecule of $75\text{--}90$ nucleotides possessing post-transcriptionally modified bases, a secondary cloverleaf folding pattern, an anticodon loop for mRNA codon recognition, and a conserved $3'\text{-CCA-OH}$ terminal sequence where a specific amino acid is covalently attached.

Aminoacyl-tRNA Synthetase

One of 20 highly specific amino acid-activating enzymes that couples a particular amino acid to its cognate tRNA through a two-step reaction consuming ATP, generating an aminoacyl-AMP intermediate before transferring the amino acid to the $3'\text{-OH}$ of the terminal adenosine.

Shine-Dalgarno Sequence

A conserved purine-rich bacterial mRNA leader motif ($5'\text{-AGGAGG-}3'$) located upstream of the AUG start codon that hybridizes with a complementary pyrimidine-rich sequence ($3'\text{-UCCUCC-}5'$) on the $16\text{S}$ rRNA of the $30\text{S}$ ribosomal subunit to properly align the ribosome.

N-Formylmethionine (fMet)

The specialized, formylated methionine derivative delivered by initiator $\text{tRNA}^{\text{fMet}}$ to the ribosomal P site in response to the AUG start codon during translation initiation in bacteria.

Kozak Sequence

A consensus sequence in eukaryotic mRNAs ($5'\text{-(GCC)GCC(A/G)NNAUGG-}3'$) surrounding the initiator AUG codon that interacts with eukaryotic initiation factors to optimize recognition of the correct start codon by the scanning small ribosomal subunit.

Polyribosome (Polysome)

A structural assembly consisting of a single mRNA molecule undergoing simultaneous translation by multiple active ribosomes spaced along its coding sequence.

Prion

An infectious proteinaceous particle that causes transmissible spongiform encephalopathies (such as scrapie, BSE, CJD, and kuru) by inducing a conformational transition in the host normal $\alpha$-helical $\text{PrP}^C$ protein into an aggregated, insoluble $\beta$-sheet-rich $\text{PrP}^{Sc}$ isoform.

Somatic Mosaicism

A condition in an individual who possesses genetically distinct populations of somatic cells originating from a post-zygotic de novo mutation early in embryonic development, exemplified by the $G\rightarrow A$ mutation in the AKT1 gene causing Proteus syndrome.

Haploinsufficiency

A dominant loss-of-function genetic mechanism in which a single functional wild-type allele fails to produce an adequate quantity of protein product to maintain normal phenotype, such as FBN1 mutations causing Marfan syndrome.

Transition

A specific point substitution mutation in DNA involving the replacement of a purine with another purine ($A \leftrightarrow G$) or a pyrimidine with another pyrimidine ($C \leftrightarrow T$).

Transversion

A specific point substitution mutation in DNA in which a purine is replaced by a pyrimidine, or a pyrimidine is replaced by a purine ($A/G \leftrightarrow C/T$).

Frameshift Mutation

A gene mutation caused by the insertion or deletion of any number of nucleotides not divisible by three within a coding region, which alters the translational triplet reading frame and changes all downstream amino acids until a premature stop codon is encountered.

Luria-Delbrück Fluctuation Test

A 1943 experiment demonstrating that genetic mutations in E. coli conferring resistance to bacteriophage T1 arise randomly and spontaneously prior to exposure to the selective environmental agent, rather than as an adaptive response induced by the phage.

Apurinic (AP) Site

A lesion in a DNA strand created by depurination—the spontaneous cleavage of the N-glycosidic bond linking an adenine or guanine base to the $1'$ carbon of deoxyribose, leaving an intact sugar-phosphate backbone devoid of a purine base.

Thymine Dimer

A bulky, helix-distorting covalent lesion formed between adjacent thymidine bases on the same DNA strand upon the absorption of non-ionizing ultraviolet (UV) radiation at an intensity peak near $260\,\text{nm}$.

Nucleotide Excision Repair (NER)

A light-independent DNA repair pathway mediated in bacteria by uvrA, uvrB, and uvrC gene products (and in humans by XPA through XPG proteins) that recognizes bulky distorting lesions like thymine dimers, excises a short single-stranded oligonucleotide containing the lesion, and fills the gap using DNA polymerase and ligase.

Ames Test

A biological assay designed by Bruce Ames that utilizes histidine-auxotrophic ($\text{his}^-$) Salmonella typhimurium strains and metabolic activation by rodent liver enzymes to evaluate the mutagenic and carcinogenic potential of chemical compounds by measuring reverse mutations to $\text{his}^+$.

Transposable Elements (TEs)

Mobile genetic elements capable of changing their location within the genome via cut-and-paste or copy-and-paste transposition, first discovered in maize by Barbara McClintock through mutable alleles in the Ac-Ds system.

Retrotransposon

A class of mobile transposable element (comprising approximately $42\%$ of the human genome, including autonomous LINEs and non-autonomous SINEs/Alu) that transposes via a 'copy-and-paste' mechanism requiring an RNA intermediate, reverse transcriptase, and integrase.

Operon

A contiguous cluster of bacterial structural genes with related metabolic functions transcribed together under the control of a single promoter and operator as a single polycistronic mRNA.

Allolactose

The physiological inducer of the lac operon, produced as a side reaction by $\beta$-galactosidase upon the entry of lactose into E. coli cells, which binds directly to the lac repressor protein causing an allosteric shift that abolishes its affinity for the operator.

Constitutive Mutant

A bacterial mutant in which structural genes of an operon are continuously expressed regardless of environmental conditions or inducer concentration, caused either by a repressor gene mutation ($lacI^-$) that prevents operator binding or an operator sequence alteration ($lacO^c$).

Catabolite-Activating Protein (CAP)

A bacterial transcriptional activator that exerts positive control over the lac operon; when glucose is absent, intracellular cyclic AMP (cAMP) levels rise, forming a CAP-cAMP complex that binds to the promoter to recruit RNA polymerase and stimulate transcription.

Attenuation

A regulatory mechanism in bacterial amino acid biosynthetic operons (such as the trp operon) where transcription initiates normally but is prematurely terminated in the leader sequence when charged $\text{tRNA}^{\text{Trp}}$ is abundant, causing the leader mRNA to fold into a 3-4 terminator hairpin loop.

Riboswitch

A regulatory segment within the $5'$ untranslated region of an mRNA molecule composed of an aptamer domain that binds a specific small ligand and an expression platform domain that undergoes conformational rearrangement to form either an antiterminator or terminator hairpin, altering transcription or translation.