Nucleic Acid Synthesis: Replication and Transcription

Vocabulary practice flashcards covering nucleic acid synthesis mechanisms, DNA replication, and RNA transcription, including energetics, enzymatic machinery, and eukaryotic RNA processing.

Central Dogma

The framework describing the flow of genetic information in biological systems: DNA replication ($\text{DNA} \rightarrow \text{DNA}$), transcription ($\text{DNA} \rightarrow \text{RNA}$), and translation ($\text{RNA} \rightarrow \text{protein}$), each proceeding through initiation, elongation, and termination phases.

Phosphoanhydride Bond Hydrolysis

A spontaneous, exergonic reaction ($-\Delta G$) involving the cleavage of high-energy phosphate bonds in nucleotide triphosphates (NTPs or dNTPs) that provides the chemical energy required for nucleic acid synthesis.

Pyrophosphate ($\text{PP}_i$) Hydrolysis

The rapid, essentially irreversible hydrolysis of inorganic pyrophosphate into two orthophosphates ($\text{PP}_i + \text{H}_2\text{O} \rightarrow 2\,\text{P}_i$), which thermodynamically pulls nucleic acid polymerization reactions forward, consuming $2$ ATP equivalents per incorporated nucleotide.

DNA Polymerase

The enzyme that catalyzes DNA replication by extending a growing nucleic acid chain in the $5' \rightarrow 3'$ direction via nucleophilic attack of a terminal 3' OH on an incoming dNTP substrate complementary to the template strand.

Helicase

An enzyme that couples ATP hydrolysis to the mechanical unwinding and separation of the double-stranded DNA helix at the replication fork. Unzipping the DNA

Topoisomerase

An enzyme that uses the energy of ATP hydrolysis to relieve torsional strain caused by overwinding (supercoiling) of the double helix ahead of the advancing replication fork.

Single-Stranded Binding Proteins (SSBs)

Proteins that bind to exposed single strands of DNA at the replication fork to prevent them from reannealing back into a double helix before replication can occur.

Primase

A specialized RNA polymerase that synthesizes a short RNA primer complementary to the template strand, providing the free 3' OH group required by DNA polymerase to initiate DNA synthesis.

Origin of Replication

A specific genomic locus where DNA replication begins by forming a replication bubble with two bidirectional forks; characteristically rich in A-T base pairs due to their fewer hydrogen bonds and lower thermal stability relative to G-C pairs.

Leading Strand

The continuously synthesized DNA strand formed in the $5' \rightarrow 3'$ direction toward the opening replication fork.

Lagging Strand

The discontinuously synthesized DNA strand synthesized in the $5' \rightarrow 3'$ direction away from the replication fork in short segments known as Okazaki fragments.

Okazaki Fragments

Short, discontinued segments of newly synthesized DNA (approximately 1,000 to 2,000 base pairs in length) generated on the lagging strand, each initiated by an RNA primer.

DNA Clamp

A multimeric ring-shaped protein structure that encircles the DNA double helix and binds DNA polymerase, preventing it from dissociating and thereby increasing its processivity.

Processivity

The operational capacity of a polymerase enzyme to remain bound to its template and continuously catalyze thousands of consecutive nucleotide addition steps without detaching.

$3' \rightarrow 5'$ Exonuclease Proofreading

A proofreading activity inherent to DNA polymerase that checks the geometric fit and hydrogen-bond acceptor positioning in the minor groove of the newly added base-pair, cleaving incorrectly incorporated terminal nucleotides to achieve an error rate as low as 1 in 1 billion base pairs.

DNA Ligase

The enzyme responsible for sealing single-strand phosphodiester nicks between adjacent Okazaki fragments after RNA primer excision, driven by ATP (or $\text{NAD}^+$) hydrolysis and $\text{PP}_i$ cleavage.

Telomeres

Repetitive, non-coding hexameric DNA sequences (such as TTAGGG) capping the ends of eukaryotic linear chromosomes to prevent information loss resulting from the end-replication problem.

Telomerase

An RNA-dependent DNA polymerase (reverse transcriptase) containing an intrinsic RNA template that extends the 3' overhanging ends of eukaryotic linear chromosomes in dividing cells.

Dideoxynucleotide (ddNTP)

A synthetic nucleotide analog lacking both 2' and 3' hydroxyl groups; can be incorporated into growing DNA by its 5' triphosphate, but permanently terminates chain elongation due to the absence of a free 3' OH.

Messenger RNA (mRNA)

The primary coding RNA molecule transcribed from the genomic DNA template that directs the amino acid sequence during translation at the ribosome.

Transfer RNA (tRNA)

Small adapter RNA molecules that carry specific amino acids one at a time to the ribosomal complex, translating codon sequences into polypeptides.

Ribosomal RNA (rRNA)

The structural and catalytic RNA components of the ribosome that function as a ribozyme to synthesize peptide bonds during translation.

Coding (Sense) Strand

The strand of duplex DNA whose base sequence is identical in direction and order to the transcribed mRNA (with uracil substituting for thymine); it does not serve as the template for RNA polymerase.

Antisense (Template) Strand

The strand of duplex DNA that RNA polymerase physically reads in the $3' \rightarrow 5'$ direction to synthesize an antiparallel, complementary single-stranded RNA transcript.

Promoter

A DNA regulatory region situated within the 5' flanking region (5' UTR) upstream of the transcription start site (+1) that contains conserved sequence elements (such as the TATA box) required for transcription factor binding and RNA polymerase recruitment.

Histone Lysine Acetylation

A post-translational modification wherein acetyl groups are added to the basic amino groups of histone lysines, converting them to neutral amides; this eliminates electrostatic salt bridges to negatively charged DNA phosphates, unpacking nucleosomes for transcription.

RNA Polymerase CTD Phosphorylation

Phosphorylation of the C-terminal domain of RNA polymerase that disrupts electrostatic and steric interactions with general transcription factors (GTFs) at the promoter, triggering the transition from transcription initiation to elongation.

Intrinsic (RNA-Dependent) Termination

A transcription termination mechanism in which the nascent RNA transcript folds into a stable self-complementary hairpin (stem-loop) structure that mechanically stalls and disrupts the RNA polymerase elongation complex.

Rho-Dependent Termination

A protein-dependent transcription termination pathway wherein the hexameric protein Rho binds a designated recognition sequence on the nascent RNA, moving along the transcript to disrupt RNA polymerase from the DNA template.

Spliceosome

The macromolecular ribonucleoprotein complex responsible for eukaryotic pre-mRNA (hnRNA) processing, catalyzing the excision of noncoding introns and the precise ligation of coding exons.

Introns

Non-coding intervening sequences within eukaryotic primary transcripts (hnRNA) that are spliced out and excluded from the mature mRNA product.

Exons

Coding regions of a eukaryotic gene that are retained and joined together during pre-mRNA splicing to form the mature mRNA translated into protein.