Molecular Biology Terms Starting With C
Molecular Biology Glossary: C
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Cap Structure
/ kap STRUK-cher / · English: cap + structure
Cap Structure is the 7-methylguanosine residue linked through an unusual 5-prime-to-5-prime triphosphate bridge to the first transcribed nucleotide of a eukaryotic mRNA, added co-transcriptionally to protect the transcript and mark it for processing.
Capping enzymes are recruited to the phosphorylated C-terminal domain of RNA polymerase II shortly after transcription begins, and the cap is added before the nascent transcript reaches 30 nucleotides in length. Once in place, the cap protects the mRNA from 5-prime exonucleases, is recognized by the nuclear cap-binding complex that coordinates splicing and nuclear export, and is bound by the translation initiation factor eIF4E to recruit ribosomes to the mRNA. The 5-prime-to-5-prime linkage is chemically distinct from all other phosphodiester bonds in the transcript, making the cap resistant to the exonucleases that degrade RNA from the 3-prime end.
Influenza virus exploits this chemistry through a cap-snatching mechanism, cleaving the capped 5-prime ends from host mRNAs and using them to prime viral transcription.
Trypanosomes such as Trypanosoma brucei add a hypermethylated cap called cap 4 to their mRNAs, in which the first four transcribed nucleotides each carry additional methyl groups beyond the standard 7-methylguanosine. This elaborated cap structure is linked to a trans-splicing mechanism that trypanosomes use instead of conventional promoter-driven transcription, a strategy found in no vertebrate cell.
Translation Biology →MRNA is ready for translation the moment it is transcribed. Eukaryotic mRNAs require co-transcriptional capping, splicing of introns, and 3-prime polyadenylation before they are competent for export and translation.
Human mRNAs synthesized by RNA polymerase II receive a 7-methylguanosine cap within seconds of transcription initiation, before the transcript reaches 30 nucleotides. The translation initiation factor eIF4E binds this cap with a dissociation constant in the nanomolar range, making cap recognition one of the highest-affinity protein-RNA interactions in the cell.
Chromatin Remodeling
/ KROH-muh-tin REE-mod-el-ing / · Greek: chroma (color) + remodeling
Chromatin Remodeling is the ATP-dependent repositioning, ejection, or restructuring of nucleosomes by multisubunit complexes to alter DNA accessibility for transcription, replication, and repair.
Remodeling complexes fall into four major families, SWI/SNF, ISWI, CHD, and INO80, each using ATP hydrolysis to slide or eject histone octamers and expose or conceal regulatory sequences. These complexes work alongside histone-modifying enzymes to establish and maintain active or repressed chromatin states across the genome. A single SWI/SNF complex can reposition a nucleosome by more than 50 base pairs in a single ATP-hydrolysis cycle, dramatically changing which transcription factor binding sites are accessible.
Mutations in SWI/SNF subunits, particularly SMARCA4 and ARID1A, are among the most frequently detected alterations in human cancers, appearing in roughly 20 percent of all tumor types.
The yeast (Saccharomyces cerevisiae) SWI/SNF complex was first identified in the early 1990s through genetic screens for genes required for mating-type switching and sucrose fermentation, giving the complex its name. Subsequent work revealed that human cells carry a closely related complex, now linked to tumor suppression, demonstrating that the core remodeling machinery has been conserved for more than a billion years of eukaryotic evolution.
DNA accessibility is fixed once chromosomes are assembled. Chromatin-remodeling complexes can dynamically expose or occlude specific DNA regions within seconds in response to signaling events, without altering the underlying nucleotide sequence.
During the activation of heat-shock genes in fruit flies (Drosophila melanogaster), SWI/SNF-related remodeling complexes rapidly reposition nucleosomes at promoter regions within minutes of temperature stress. Nucleosome occupancy at the Hsp70 promoter drops by more than 80 percent during this response, allowing RNA polymerase II to engage the gene.
Cloning
/ KLOH-ning / · Greek: klon (twig)
Cloning is the process of producing many genetically identical copies of a DNA fragment, cell, or organism, with molecular cloning referring specifically to the insertion of a DNA fragment into a vector and its propagation in a host organism for study or expression.
The classic workflow involves cutting a DNA fragment and a vector with restriction enzymes, ligating them together, transforming the recombinant plasmid into bacteria, selecting colonies that carry the insert, and confirming the correct sequence. Modern approaches including Gibson assembly, Golden Gate cloning, and recombination-based methods such as Gateway offer greater flexibility and precision than restriction-ligation strategies. Cloning underpins the production of recombinant therapeutics: the human insulin gene was cloned into Escherichia coli in 1982, making recombinant insulin the first approved recombinant protein drug and replacing animal-derived insulin for millions of patients with diabetes.
Before recombinant DNA cloning, the only source of human growth hormone for treating children with growth deficiency was pituitary glands collected at autopsy, and the supply was severely limited. After the human growth hormone gene was cloned and expressed in bacteria in 1979 by researchers at Genentech, a reliable and scalable supply became available, eliminating dependence on cadaveric tissue entirely.
Cloning always means creating a genetically identical copy of a whole organism. Molecular cloning refers to copying a specific DNA sequence inside a microbial or cellular host, a routine laboratory procedure entirely distinct from reproductive cloning.
Designer Babies Pros and Cons →The gene encoding human erythropoietin was cloned into Chinese hamster ovary cells, which secrete the correctly glycosylated protein into culture medium. Recombinant erythropoietin produced this way has been used since 1989 to treat anemia in patients with chronic kidney disease.
Recombinant Proteins →Coding Strand
/ KOH-ding strand / · English: coding + strand
Coding Strand is the DNA strand whose sequence matches the mRNA produced during transcription, with thymine in place of uracil, and is the strand conventionally used to read and report gene sequences.
RNA polymerase does not read the coding strand directly; it reads the complementary template strand and synthesizes an RNA whose sequence is identical to the coding strand except that uracil replaces thymine. Gene sequences in databases such as GenBank and Ensembl are presented as coding strand sequences running 5-prime to 3-prime from left to right, a convention that makes the written sequence directly comparable to the mRNA. Because both DNA strands are present in every double-stranded molecule, which strand is the coding strand depends on the gene: on a circular bacterial chromosome, some genes use one strand as their coding strand while neighboring genes use the other.
In some double-stranded RNA viruses, the concept of a coding strand does not apply in the same way as in cellular DNA, because both strands can be transcribed or serve as templates depending on the viral replication strategy. This distinction highlights that the coding strand convention is specific to double-stranded DNA genomes and is a notational convenience rather than a chemical property of the strand itself.
Building Blocks of Nucleic Acids →RNA polymerase reads the coding strand directly to produce mRNA. RNA polymerase reads the template strand, which is antiparallel and complementary to the coding strand, and the resulting RNA matches the coding strand sequence.
When researchers report the BRCA1 gene sequence, they write the coding strand from 5-prime to 3-prime across the gene on chromosome 17. BRCA1 spans roughly 81,000 base pairs, and the corresponding mRNA matches the coding strand except that uracil replaces thymine.