Molecular Biology: Nucleic Acids, Replication, Gene Expression, and Regulation

Comprehensive vocabulary flashcards covering the molecular mechanisms of nucleic acids, semi-conservative DNA replication, replisome enzymes, eukaryotic and prokaryotic transcription, mRNA processing, translation, genetic mutations, and operon-based gene regulation.

Nucleotide

The monomer building block of nucleic acids consisting of three parts: a pentose sugar (ribose in RNA or deoxyribose in DNA), a nitrogenous base attached to the $1'$ carbon, and one, two, or three phosphate groups attached to the $5'$ carbon.

Purines vs. Pyrimidines

The two structural classes of nitrogenous bases; purines (adenine and guanine) possess a double-ring structure, whereas pyrimidines (cytosine, thymine in DNA, and uracil in RNA) possess a single ring.

Chargaff's Rules

Two foundational rules established in 1950 stating that DNA base composition varies between species, but within any species, the percentage of adenine equals thymine ($\%A = \%T$) and the percentage of cytosine equals guanine ($\%C = \%G$).

Maurice Wilkins

The researcher who, alongside Rosalind Franklin in the early 1950s, used X-ray crystallography on DNA crystals to produce structural images that helped determine the double-helical structure of DNA.

Semiconservative Model

The confirmed model of DNA replication demonstrated by Meselson and Stahl in 1958, wherein the two parental strands separate and each serves as a template to build a complementary daughter strand, producing molecules composed of one old strand and one new strand.

Origin of Replication (ORI)

A specific sequence of DNA where replisome proteins bind and separate the two parental strands to initiate DNA synthesis, forming a replication bubble flanked by two Y-shaped replication forks.

Replication Fork Initiation Proteins

A set of enzymes including helicase, which unwinds parental strands; single-strand binding proteins (SSBs), which prevent single strands from reannealing; topoisomerase, which relieves overwinding strain ahead of the fork; and primase, which synthesizes an RNA primer.

DNA Polymerase III

The primary multisubunit prokaryotic enzyme that synthesizes new DNA strands by adding complementary nucleotides to a pre-existing $3'\text{-OH}$ group, elongating exclusively in the $5' \rightarrow 3'$ direction.

DNA Polymerase I

The bacterial enzyme that removes RNA nucleotides of the primer from the $5'$ end and replaces them with corresponding DNA nucleotides during replication and repair.

DNA Ligase

An enzyme that catalyzes the formation of covalent phosphodiester bonds to join Okazaki fragments of the lagging strand and connect replaced primer segments to the leading strand.

Okazaki Fragments

Short, discontinuously synthesized segments of DNA formed on the lagging strand ($1000\text{--}2000$ base pairs in E. coli, $150\text{--}200$ base pairs in eukaryotes) that are initiated by RNA primers and later joined together by DNA ligase.

Nucleotide Excision Repair

A DNA repair pathway in which a nuclease excises damaged or mutated segments of a DNA strand (such as UV-induced thymine dimers), followed by gap filling by DNA polymerase and sealing by DNA ligase.

Telomeres

Repetitive, non-coding nucleotide sequences (such as $\text{TTAGGG} \times 2500$ in humans) located at the ends of eukaryotic chromosomes that postpone gene erosion caused by incomplete lagging strand synthesis.

Telomerase

A ribonucleoprotein enzyme that uses an intrinsic RNA template to add telomeric repeat sequences to the $3'$ end of the template strand, maintaining chromosome ends in stem cells, germline cells, and approximately $90\%$ of cancer cells.

Promoter

A specific DNA sequence situated upstream ($5'$ on the coding strand) of a gene's transcription start site that binds and orients RNA polymerase, dictating which DNA strand serves as the template.

TATA Box

A conserved promoter DNA sequence located approximately $10$ base pairs upstream of the transcription start site in prokaryotes, and approximately $25$ base pairs upstream in eukaryotes where it binds general transcription factors.

Template Strand

The specific strand of double-stranded DNA read by RNA polymerase in the $3' \rightarrow 5'$ direction to synthesize a complementary, antiparallel RNA transcript in the $5' \rightarrow 3'$ direction.

5' Cap (7-methylguanosine) and 3' Poly-A Tail

Post-transcriptional modifications added enzymatically to eukaryotic pre-mRNAs: an $\text{m}^7\text{G}$ cap at the $5'$ end and a polyadenylate tail of $100\text{--}250$ adenines at the $3'$ end following an $\text{AAUAAA}$ cleavage signal, functioning to facilitate nuclear export, enhance stability, and promote translation.

Untranslated Regions (UTRs)

Expressed sequences situated at the $5'$ and $3'$ ends of mature mRNAs that are transcribed from DNA but not translated into amino acids, serving crucial regulatory roles in mRNA localization, stability, and translation efficiency.

Spliceosome

A massive ribonucleoprotein complex composed of small nuclear ribonucleoproteins (snRNPs) and proteins that recognizes conserved boundary sequences of introns and catalyzes their excision as ribozymes while ligating flanking exons.

Alternative RNA Splicing

A eukaryotic regulatory mechanism by which different combinations of exons from a single pre-mRNA transcript are spliced together, enabling one gene to encode multiple distinct protein isoforms.

doublesex (dsx) Gene

An insect gene exhibiting sex-specific alternative splicing that yields distinct female (DSX-F) and male (DSX-M) transcription factors, directly determining sexual differentiation in insects such as mosquitoes.

Transfer RNA (tRNA)

An adaptor RNA molecule roughly $80$ nucleotides long containing a specific $3' \rightarrow 5'$ anticodon that base-pairs with an mRNA codon, and a covalently linked specific amino acid attached at its $3'$ CCA terminus.

Aminoacyl-tRNA Synthetase

A family of $20$ distinct enzymes that accurately couple each of the $20$ amino acids to their corresponding tRNAs through high-energy covalent bonds, establishing fidelity in translation.

Ribosomal A, P, and E Sites

The three functional tRNA binding chambers in the assembled ribosome: the A site binds incoming aminoacyl-tRNA, the P site holds the peptidyl-tRNA with the growing polypeptide, and the E site holds uncharged tRNAs before their release.

Translation Initiation Complex

The assembled apparatus comprising the small ribosomal subunit, an mRNA, and an initiator tRNA carrying methionine positioned at the AUG start codon, joined by the large ribosomal subunit in an energy-dependent process fueled by GTP hydrolysis.

Release Factor

A specialized protein shaped like a tRNA that binds directly to a stop codon (UAA, UAG, or UGA) in the ribosomal A site, hydrolyzing the ester bond linking the polypeptide to the tRNA in the P site.

Wobble Base Pairing

Relaxed Watson-Crick base-pairing rules at the third ($3'$) position of an mRNA codon and the first ($5'$) position of a tRNA anticodon, allowing a single tRNA to recognize multiple synonymous codons.

Transgenesis

The introduction of an exogenous gene from one organism into the genome of an entirely different species, made possible by the near-universal nature of the genetic code (e.g., bacteria producing human insulin).

Silent Mutation

A point mutation that substitutes a single nucleotide in a protein-coding sequence without altering the specified amino acid due to redundancy in the genetic code.

Missense Mutation

A point mutation in which a nucleotide-pair substitution changes an mRNA codon such that it codes for an incorrect amino acid, such as the GAG (Glu) to GTG (Val) change causing sickle-cell disease.

Nonsense Mutation

A base substitution that prematurely converts an amino-acid-specifying codon into a stop codon (UAA, UAG, or UGA), resulting in truncated, usually non-functional polypeptides.

Frameshift Mutation

An insertion or deletion of nucleotides not occurring in multiples of three within a protein-coding region, shifting the reading frame established by the AUG start codon and altering downstream amino acids.

In-Frame Mutation

An insertion or deletion of nucleotides in exact multiples of three (3, 6, 9, etc.) that adds or deletes amino acids without disrupting the downstream triplet reading frame.

Enhancer

A eukaryotic distal regulatory DNA sequence, often located hundreds to thousands of base pairs away from the promoter, that binds activator proteins and interacts with the promoter via DNA-bending proteins and the Mediator complex.

Operon

A functional prokaryotic genetic unit consisting of a promoter, an operator, and a cluster of functionally related structural genes transcribed together as a single polycistronic mRNA.

Polycistronic mRNA

A single bacterial transcript containing coding sequences for multiple distinct proteins, possessing internal ribosome entry sites that allow independent initiation of translation at each cistron.

Inducible Operon

An operon that is typically inactive (OFF) due to an active repressor bound to the operator, but can be switched on (induced) when an inducer molecule binds and inactivates the repressor (e.g., the lac operon).

trp Operon

A repressible prokaryotic operon governing tryptophan synthesis that is constitutively ON by default, but is shut OFF when tryptophan accumulates, acts as a corepressor, and activates the trp repressor to bind the operator.

lac Operon Dual Regulation

The dual regulatory system governing lactose catabolism requiring both the derepression of the operator by allolactose (lactose isomer) and positive transcriptional activation by cAMP-bound catabolite activator protein (CRP) when glucose levels are low.