Molecular Biology: DNA Replication, Gene Regulation, Transcription, Translation, and Chromatin Structure

Flashcards covering key vocabulary terms, definitions, and concepts across all five lecture topics on molecular biology, including DNA replication, gene regulation, transcription, translation, and chromatin structure.

Semi-Conservative Replication

A mechanism of DNA replication in which each strand of the original double-stranded DNA molecule serves as a template for the synthesis of a new complementary strand, resulting in two daughter molecules that each contain one original parental strand and one newly synthesized strand.

Replication Fork

A Y-shaped structure created during DNA replication where DNA Helicase unwinds double-stranded parental DNA into two single template strands for active synthesis.

Replisome

The multi-protein complex assembled at the origin of replication that contains all enzymes and factors necessary for carrying out DNA replication, including DNA Polymerase, DNA Helicase, Primase, and Topoisomerase.

Topoisomerase

An enzyme that moves ahead of the replication fork to relieve supercoiling tension caused by helicase unwinding by introducing temporary cuts in the DNA backbone, unwinding the strands, and resealing the breaks.

Okazaki Fragments

Short, newly synthesized DNA segments formed on the lagging template strand during DNA replication, which are synthesized discontinuously in the $5'$ to $3'$ direction and subsequently joined together by DNA Ligase.

Telomeres

Repetitive, non-coding nucleotide sequences located at the ends of linear eukaryotic chromosomes that prevent the loss of critical coding genetic sequence during successive rounds of replication.

Nucleotide Excision Repair

A DNA repair mechanism that removes larger structural DNA lesions, such as UV-induced thymine dimers, by using an endonuclease to cleave the damaged backbone strand, helicase to unwind it, and DNA polymerase to rebuild the gap.

Non-Homologous End Joining

An error-prone DNA repair mechanism that directly ligates the broken ends of double-strand DNA breaks together without requiring a homologous template, resulting in nucleotide loss.

Lac Operon

An inducible operon in bacteria consisting of structural genes ($lacZ$, $lacY$, $lacA$) and regulatory elements that enable substrate-induced transcription of lactose-metabolizing enzymes in response to lactose availability.

Polycistronic mRNA

A single mRNA transcript that carries coding information for the translation of multiple distinct proteins, driven by a single shared promoter region.

Cis-Acting Regulatory Element

A DNA sequence, such as a promoter or operator, that regulates the expression of genes situated on the same physical strand of DNA in close proximity.

Trans-Acting Regulatory Element

A diffusible regulatory factor, such as a repressor or transcription factor protein, that can move through the cell to regulate target genes regardless of their chromosomal location.

Enhancer

A distal cis-acting DNA sequence that binds activator transcription factors to stimulate the rate of transcription at a target promoter via DNA looping.

CpG Island

A DNA region rich in cytosine-guanine dinucleotide repeats, commonly located near gene promoters, where cytosine methylation represses transcription by inhibiting RNA Polymerase recruitment and recruiting HDACs.

Proteasome

A multi-protein barrel-shaped complex in the cytoplasm and nucleus that degrades unwanted, damaged, or regulatory proteins that have been post-translationally tagged with polyubiquitin chains.

Central Dogma

The core concept of molecular biology describing the direction of genetic information transfer from DNA to RNA via transcription, and from RNA to functional protein via translation.

Promoter

A specific sequence of consensus DNA located near the start site of a gene that recruits RNA Polymerase and associated transcription factors to initiate transcription.

TATA-Binding Protein

A general transcription factor subunit of TFIID that specifically binds to the TA-rich TATA box sequence in eukaryotic promoters, bending the DNA to assist preinitiation complex assembly.

Spliceosome

A complex composed of small nuclear RNAs (snRNAs) and proteins that identifies conserved consensus sequences at intron boundaries to excise introns and ligate exons together in pre-mRNA.

Alternative Splicing

A regulated post-transcriptional process in eukaryotes where different combinations of exons are selectively included or excluded from a single pre-mRNA, generating diverse functional protein isoforms from a single gene locus.

Codon

A sequence of three consecutive nucleotides in mRNA that specifies a single amino acid or signals translation termination during protein synthesis.

Open Reading Frame

A continuous triplet sequence of codons starting with an AUG start codon and terminating at a stop codon, translated uninterruptedly into a polypeptide sequence.

Frameshift Mutation

A mutation caused by the insertion or deletion of a number of nucleotides not divisible by three, altering the triplet reading frame for all downstream codons during translation.

Aminoacyl-tRNA Synthetase

An enzyme that catalyzes the ATP-dependent covalent attachment of a specific amino acid to its corresponding tRNA molecule at its $3'$ hydroxyl attachment site.

Wobble Position

The third base of an mRNA codon (and first base of a tRNA anticodon) that exhibits relaxed base-pairing rules, enabling a single tRNA species to recognize multiple synonymous codons.

Polyribosome

A complex formed by multiple ribosomes simultaneously translating a single mRNA strand in the $5'$ to $3'$ direction to generate multiple copies of a polypeptide.

Nucleosome

The basic structural repeating unit of eukaryotic chromatin, consisting of approximately $146$ base pairs of double-stranded DNA wrapped around a core octamer of basic histone proteins.

Euchromatin

A loosely packed, transcriptionally active form of chromatin that allows RNA polymerase and regulatory transcription factors access to genomic DNA.

Histone Acetyltransferase

An enzyme that transfers acetyl groups to basic lysine residues on histone tails, neutralizing their positive charge, opening chromatin, and increasing transcription factor accessibility.

Nuclear Localization Signal

A short, specific amino acid sequence within a protein that targets it for recognition by importin transport proteins for active passage through nuclear pore complexes into the nucleus.