Molecular Biology Terms Starting With L
Molecular Biology Glossary: L
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Leader Sequence
/ LEE-der SEE-kwens / · English: leader + sequence
Leader Sequence is the 5-prime untranslated region of an mRNA, spanning from the 5-prime cap to the AUG start codon and containing regulatory elements that influence ribosome binding and translation initiation efficiency.
Leader sequences range from tens to thousands of nucleotides in length and can contain upstream open reading frames, internal ribosome entry sites, RNA secondary structures, and binding sites for regulatory proteins. Short upstream open reading frames within the leader can attenuate translation of the downstream main ORF, providing a mechanism for sensing cellular stress through changes in translation initiation factors. In bacteria, the Shine-Dalgarno sequence in the leader region base-pairs with 16S rRNA to recruit ribosomes directly to the start codon.
This direct ribosome recruitment distinguishes bacterial translation initiation from the scanning mechanism used by eukaryotic ribosomes.
The leader sequence of the tobacco mosaic virus (TMV) RNA, called the omega sequence, boosts translation so efficiently that molecular biologists borrowed it to enhance protein production in plant expression systems.
Noncoding mRNA regions have no function. Leader sequences directly affect ribosome binding, mRNA stability, and the rate at which the coding region is translated.
The bacterial trp operon mRNA carries a 162-nucleotide leader region that forms alternative RNA secondary structures depending on tryptophan availability. When tryptophan is abundant, the leader folds into a terminator hairpin within this 162-nucleotide segment, halting transcription before the structural genes are reached.
Ligase
/ LY-gays / · Latin: ligare (to bind) + -ase
Ligase is an enzyme that catalyzes the formation of a covalent bond between two substrate molecules using energy derived from ATP or NAD+ hydrolysis, joining broken or separate molecular ends into a continuous chain.
DNA ligases seal nicks in DNA by forming phosphodiester bonds between adjacent 3-prime hydroxyl and 5-prime phosphate termini, completing DNA replication and repair. RNA ligases join RNA fragments and contribute to some non-spliceosomal intron removal pathways. T4 DNA ligase, derived from bacteriophage T4, is the most widely used enzyme in recombinant DNA technology because it efficiently joins both cohesive and blunt DNA ends.
Each ligation reaction consumes one molecule of ATP per phosphodiester bond formed, with the energy driving the otherwise thermodynamically unfavorable condensation reaction.
Aminoacyl-tRNA synthetases are a class of ligases that attach each amino acid to its correct tRNA, consuming ATP in the process. Without these enzymes, accurate translation of the genetic code would be impossible.
Every ligase works only on DNA. Ligases join many kinds of biological molecules, including RNA strands, amino acids to tRNA, and ubiquitin to target proteins, depending on the specific enzyme.
Are Enzymes Proteins? →During base excision repair in human cells, DNA ligase III, working with its partner protein XRCC1, seals the final nick after a damaged base has been removed and replaced by DNA polymerase beta. This sealing step restores 1 missing phosphodiester bond and completes the repair.
Ligation
/ ly-GAY-shun / · Latin: ligatio (a binding)
Ligation is the enzyme-catalyzed joining of two DNA or RNA fragments by formation of a phosphodiester bond between the 3-prime hydroxyl end of one fragment and the 5-prime phosphate end of another.
Efficient ligation requires that both ends have compatible chemistries, either matching single-stranded overhangs generated by restriction enzyme cleavage or blunt ends, and that they are positioned adjacent to each other on the same molecule. Cohesive-end ligation proceeds 10 to 100 times more efficiently than blunt-end ligation because the complementary overhangs hold the fragments in proximity before the bond forms. In cells, DNA ligase I seals the nick at the junction of each completed Okazaki fragment during lagging-strand synthesis, while DNA ligase III handles nicks generated during base excision repair.
Each bond formation consumes one ATP molecule, with the adenylate group transiently transferred to the enzyme before attacking the nick.
T4 RNA ligase, originally characterized in bacteriophage T4-infected Escherichia coli, joins single-stranded RNA ends and is now widely used in small RNA library preparation for next-generation sequencing.
Are Enzymes Proteins? →DNA fragments automatically stay joined after they are placed in contact. Without covalent bond formation by a ligase, the two strands are held together only by weak hydrogen bonds between complementary bases and will separate under physiological conditions.
In recombinant DNA cloning, ligation joins a restriction-digested plasmid vector to a foreign DNA insert carrying compatible sticky ends. Sticky-end ligation can be 10 to 100 times more efficient than blunt-end ligation because complementary overhangs hold the DNA ends together before the covalent bond forms.
Long Non-Coding RNA
/ long non-KOH-ding ar-en-ay / · English: long + non-coding + RNA abbreviation
Long Non-Coding RNA is a non-coding RNA transcript longer than 200 nucleotides that regulates gene expression, chromatin organization, and other cellular processes without encoding a protein.
LncRNAs are transcribed by RNA polymerase II, are capped and polyadenylated like mRNAs, but are not translated into protein. XIST, the best-characterized lncRNA, coats the inactive X chromosome and recruits Polycomb repressive complexes to silence thousands of X-linked genes during X inactivation in female mammals. More than 16,000 lncRNA genes have been annotated in the human genome, outnumbering protein-coding genes, though the functions of most remain under active investigation.
Some lncRNAs, such as HOTAIR, act in trans by guiding chromatin-modifying complexes to genomic loci on different chromosomes from the one that produced them.
The lncRNA NEAT1 forms the structural scaffold of nuclear bodies called paraspeckles, which sequester specific RNA-binding proteins and regulate their availability. Paraspeckles disassemble during cell division and reform when division is complete, making NEAT1 a dynamic organizer of nuclear architecture.
Building Blocks of Nucleic Acids →RNA matters only when it codes for protein. Long non-coding RNAs regulate gene expression, guide chromatin-modifying complexes, and organize nuclear structure without ever producing a protein product.
XIST is a long non-coding RNA, approximately 17,000 nucleotides in length, that coats the inactive X chromosome in female placental mammals. During early embryonic development, XIST expression from one X chromosome triggers silencing of most genes along that chromosome in each cell, a process that becomes permanent in the cell's descendants.