Molecular Biology: Gene Expression, DNA Replication, and Regulation

Vocabulary practice flashcards covering essential molecular biology terminology, nucleic acid structures, replication mechanisms, transcription, translation, and eukaryotic/prokaryotic gene regulation.

-35 and -10

Conserved binding sites for prokaryotic transcription. The sigma factor binds to -35, and the -10 site is rich in adenine and thymine where the DNA begins to unwind.

3' UTR

The non-coding region between the stop codon and the poly-A tail that aids in mRNA stability. Located on both pre-mRNA and mature mRNA.

5' cap

A modified guanine nucleotide added to the $5'$ end of the pre-mRNA during transcription that remains on mature mRNA.

5' UTR

The non-coding region located between the $5'$ cap and the start codon that helps with mRNA stability; present on both pre-mRNA and mature mRNA.

Acceptor Stem

The region of a tRNA molecule that acts as the binding site for aminoacyl-tRNA synthetase at the CCA tail.

Aminoacyl-tRNA

A transfer RNA chemically linked to its corresponding amino acid that delivers the amino acid to the ribosome during protein synthesis.

Aminoacyl-tRNA synthetase

The enzyme that attaches the correct amino acid to its cognate tRNA, producing an aminoacyl-tRNA.

Anti-codon

A three-nucleotide sequence on a tRNA molecule that base-pairs with a complementary mRNA codon during protein synthesis.

Anti-codon loop

The loop structure within a tRNA molecule where the anti-codon is situated.

Antiparallel

The opposite directional orientation of the two strands in a DNA double helix, running $5'$ to $3'$ and $3'$ to $5'$.

Antisense strand

The non-coding DNA template strand used by RNA polymerase to transcribe mRNA.

Bidirectional replication

DNA replication that proceeds simultaneously in two opposing directions away from the origin via two replication forks.

cDNA

Complementary DNA synthesized from an mRNA template via reverse transcriptase, consisting exclusively of coding sequences.

CDS

Coding DNA Sequence.

Cell differentiation

The process by which generic cells, such as stem cells, specialize into specific cell types in response to chemical signals, hormones, and other triggers.

Central Dogma

The principle describing the directional flow of genetic information: $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Proteins}$.

Chromatin Remodeling Complexes

Protein complexes that alter and remodel chromatin structure (histones and wrapped DNA) to expose or conceal DNA sequences, regulating gene expression and cell differentiation.

Clamp Loader

A complex that opens and positions the sliding clamp onto DNA, tethering DNA polymerase to the template to enhance processivity.

Combinatorial Control

The regulation of gene expression by combinations of multiple transcription factors (activators and repressors binding to enhancers and promoters) to modulate expression levels rather than acting as a binary switch.

Consensus Sequence

A calculated sequence representing the most frequent or ideal nucleotide bases found at each position of a specific functional site across conserved elements.

Conserved

A DNA, RNA, or amino acid sequence that remains essentially unchanged throughout generations or across different evolutionary species.

Deoxyribose

The five-carbon monosaccharide sugar component found in the sugar-phosphate backbone of DNA.

di-deoxy nucleotide triphosphate (ddNTP)

A modified nucleotide lacking a $3'\text{-OH}$ group compared to standard dNTPs, used to terminate chain elongation during Sanger sequencing.

Directionality of DNA synthesis

The universal rule that new DNA is synthesized strictly in the $5'$ to $3'$ direction.

DNA Unwinding

The process initiated at the ORI where DNA helicase breaks hydrogen bonds between base pairs, single-stranded binding proteins (SSBs) prevent strand reannealing, and topoisomerases relieve overwinding.

dNTP

Deoxynucleoside triphosphates (dATP, dTTP, dGTP, and dCTP) that serve as the fundamental building blocks for DNA synthesis.

Downstream

Toward the $3'$ end of the coding strand, following the direction in which RNA polymerase moves; denoted by positive ($$+$) numbers and including coding sequences, stop codons, and terminators.

E, P, and A sites

Ribosomal binding sites through which tRNAs cycle ($\text{A} \rightarrow \text{P} \rightarrow \text{E}$): the A site receives incoming aminoacyl-tRNA, the P site holds the peptidyl-tRNA forming peptide bonds, and the E site releases empty tRNAs.

End-replication problem

The progressive loss of terminal DNA sequences with each round of division because DNA polymerase requires a free $3'\text{-OH}$ primer; mitigated in cells by telomeres and telomerase.

Enhancer

A regulatory DNA sequence to which transcriptional activator proteins bind, increasing the probability and rate of transcription.

Epigenetic inheritance

Heritable changes in gene expression across generations that do not stem from alterations in the underlying DNA nucleotide sequence, often mediated by histone modifications or lncRNAs.

Long Non-Coding RNA (lncRNA)

A non-protein-coding RNA transcript involved in epigenetic regulation and chromatin remodeling complexes.

Exon

A expressed segment of a gene that is retained after RNA splicing and codes for amino acids in the final protein product.

Frameshift mutation

A mutation caused by the insertion or deletion of nucleotides not in multiples of three, shifting the triplet reading frame of the coding sequence.

Functional RNA

RNA molecules that carry out cellular or catalytic tasks directly rather than serving as translation templates, including rRNA, tRNA, and miRNA.

Gene Expression

The total cellular process by which information encoded in a gene is transcribed and translated, regulated at transcriptional, post-transcriptional, translational, and post-translational stages.

General Transcription Factors (GTFs)

Proteins that assemble at the transcription start site (TSS) / promoter to recruit and position RNA Polymerase II for transcription initiation.

Helicase

An enzyme that separates double-stranded DNA by breaking the hydrogen bonds between complementary base pairs, establishing the replication fork.

Histone acetyltransferases

Enzymes that transfer acetyl groups to lysine residues on histone tails, neutralising charges to loosen chromatin structure and facilitate gene expression.

Histone Deacetylase

Enzymes that remove acetyl groups from lysine residues on histones, leading to chromatin compaction and transcriptional repression.

Histone tail

The flexible, N-terminal extension of a histone protein projecting outside the nucleosome core that interacts with nearby DNA and serves as a site for regulatory modifications.

Housekeeping genes

Genes that are constitutively active ('always on') in all cells to maintain fundamental, everyday cellular metabolism and survival.

Induced pluripotent stem cells

Mature adult somatic cells (e.g., skin or blood cells) that are genetically reprogrammed in the laboratory to regain embryonic-like pluripotency.

Intron

A non-coding sequence of DNA within a gene that is transcribed into pre-mRNA and subsequently excised by the spliceosome before translation.

Lariat

The looped, lasso-shaped RNA intermediate structure generated during the excision of an intron by the spliceosome.

Library

A comprehensive collection of cloned DNA fragments, RNA, or chemical compounds stored in host organisms (such as bacteria or yeast) or multi-well plates for screening.

Ligase

An enzyme that seals nicks in the phosphodiester backbone by joining adjacent nucleotides, such as connecting Okazaki fragments on the lagging strand.

Major Groove

The wider and deeper of the two helical grooves along the outer surface of a double-stranded DNA molecule.

Mediator

A multi-protein complex that conveys signals from DNA-bound transcriptional regulatory factors directly to RNA Polymerase II to drive transcription.

Melting Temperature

The temperature ($T_m$) at which $50\%$ of a double-stranded nucleic acid duplex dissociates into single strands.

Minor Groove

The narrower of the two helical grooves on the exterior surface of a double-stranded DNA helix.

miRNA

Small non-coding RNA molecules that down-regulate gene expression post-transcriptionally by binding complementary mRNAs, leading to cleavage or translational repression.

Mismatch repair

A DNA repair pathway that identifies replication errors distorting the helical backbone, unwinds DNA using helicase, excises the incorrect base, and resynthesizes using DNA polymerase and ligase.

Missense mutation

A point mutation in which a single base substitution alters the codon to specify a different amino acid.

mRNA

Single-stranded RNA produced by RNA polymerase from a DNA template in the nucleus that carries the genetic sequence to cytoplasm ribosomes for protein translation.

mRNA processing

The series of nuclear modifications made to pre-mRNA—including $5'$ capping, intron splicing, and addition of a $3'$ poly-A tail—yielding mature mRNA.

Nonsense mutation

A point mutation that converts an amino acid-specifying codon into a premature stop codon, terminating translation early.

Operator

A prokaryotic regulatory DNA sequence situated between the promoter and downstream structural genes that serves as an on/off binding site for repressors or activators.

Operon

A genetic regulatory unit found in prokaryotes consisting of a promoter, an operator, and multiple co-regulated structural genes transcribed as a single polycistronic mRNA.

ORF (open reading frame)

A continuous span of nucleotide triplets starting with an initiation codon and terminating at a stop codon, capable of coding for a protein.

Peptidyl-tRNA

The tRNA molecule occupying the ribosomal P site that remains covalently linked to the nascent growing polypeptide chain.

Phosphoanhydride

A high-energy chemical bond linking adjacent phosphate groups in ATP that releases significant energy upon hydrolysis to ADP.

Plasmid

A small, circular, double-stranded extrachromosomal DNA molecule capable of autonomous self-replication within a host cell.

Vector

Any DNA molecule utilized as a vehicle to artificially deliver foreign genetic material into a recipient host cell.

Point mutation

A genetic alteration where a single nucleotide base pair is substituted, inserted, or deleted.

PolyA tail

A tract of approximately 250 adenine residues enzymatically added to the $3'$ terminus of eukaryotic pre-mRNA to protect against degradation.

DNA Polymerase

The enzyme that synthesizes new DNA strands in the $5'$ to $3'$ direction, requiring a primer, free $3'\text{-OH}$ group, helicase, and topoisomerase, while providing proofreading ability.

RNA Polymerase

The enzyme responsible for transcribing RNA from a DNA template in the $5'$ to $3'$ direction without requiring a primer.

Polymerization

The biochemical reaction where individual monomers are covalently linked together to form high-molecular-weight polymers.