Molecular Biology Terms Starting With B
Molecular Biology Glossary: B
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B Form DNA
/ BEE FORM dee-en-ay / · B form (Watson-Crick right-handed form); Deoxyribonucleic Acid
B Form DNA is the predominant right-handed double-helical conformation of DNA found in cells under physiological conditions, characterized by base pairs stacked perpendicular to the helix axis and approximately 10.5 base pairs per complete turn.
DNA can adopt several distinct helical conformations depending on sequence context, hydration, and ionic environment. B-form predominates under the high-water-activity conditions found inside cells, with a helical rise of about 3.4 angstroms per base pair and a diameter of roughly 20 angstroms. Its right-handed spiral positions the base pairs inside the helix like ladder rungs, with the sugar-phosphate backbones on the outside forming a major groove wide enough to accommodate transcription factor binding and a narrower minor groove.
A-form DNA, which is wider and shorter with about 11 base pairs per turn, appears in dehydrated conditions and in RNA-DNA hybrid duplexes, while Z-form DNA, a left-handed helix, forms transiently in GC-rich sequences under torsional stress.
Rosalind Franklin's X-ray diffraction image known as Photo 51, taken in 1952 at King's College London, provided critical evidence for the B-form helical structure. The characteristic X-shaped diffraction pattern in that image directly indicated a helix with a repeat of 34 angstroms, corresponding to 10 base pairs per turn.
The DNA double helix always has exactly the same geometry. B-form is the most common conformation, but DNA also adopts A-form in RNA-DNA hybrids and Z-form in GC-rich regions under negative superhelical stress, each with distinct dimensions and groove geometries.
In the bacterium Escherichia coli, the 4.6-million-base-pair circular chromosome is maintained predominantly in B-form while being negatively supercoiled by DNA gyrase. The chromosome carries about one negative supercoil per 200 base pairs, which helps compact DNA and regulate promoter opening.
Base Excision Repair
/ bays ek-SIZH-un reh-PAIR / · English: base + Latin: excisio (cutting out) + repair
Base Excision Repair is a DNA repair pathway that removes and replaces single damaged bases, including oxidized, alkylated, and deaminated bases, through a sequence of enzymatic steps that excise the lesion and restore the correct nucleotide using the complementary strand as a template.
The pathway begins with a damage-specific DNA glycosylase that cleaves the N-glycosidic bond between the damaged base and its deoxyribose sugar, leaving an abasic site called an AP site. AP endonuclease then incises the phosphodiester backbone 5-prime to the AP site, and DNA polymerase beta fills the resulting single-nucleotide gap using the complementary strand as template. DNA ligase seals the final nick to restore the intact double strand.
Human cells encode at least 11 distinct DNA glycosylases with overlapping but distinct substrate specificities, allowing the pathway to recognize dozens of chemically different base lesions; OGG1, for example, specifically removes 8-oxoguanine, one of the most common oxidative lesions produced by reactive oxygen species.
Cells repair an estimated 10,000 to 20,000 oxidative base lesions per cell per day in humans, the majority of which are processed by base excision repair. This rate reflects the continuous exposure of DNA to reactive oxygen species generated as byproducts of mitochondrial respiration.
Every DNA repair pathway fixes the same kind of damage. Base excision repair is specialized for small, non-helix-distorting base lesions such as oxidation and deamination, while bulky helix-distorting adducts are instead handled by nucleotide excision repair.
The human MUTYH glycosylase removes adenine when it is mispaired with 8-oxoguanine, preventing G-to-T transversion mutations that would otherwise arise during replication past oxidized guanine. Individuals who inherit two defective copies of MUTYH develop MUTYH-associated polyposis, a condition characterized by dozens to hundreds of colorectal polyps and a markedly elevated lifetime risk of colorectal cancer.
Are Enzymes Proteins? →Blotting
/ BLOT-ing / · English: blot (stain)
Blotting is a family of techniques in which nucleic acids or proteins are separated by electrophoresis, transferred to a membrane, and detected by hybridization with a labeled probe or by antibody binding.
Southern blotting detects specific DNA sequences, northern blotting detects specific RNA sequences, and western blotting detects specific proteins, each following the same three-step principle of separation, transfer, and detection. Dot blotting and slot blotting apply samples directly to membranes without prior electrophoresis for rapid semi-quantitative detection. Edwin Southern developed the original DNA blotting method in 1975 at the University of Edinburgh, and researchers named the RNA and protein variants by analogy.
Together, these techniques gave molecular biologists a straightforward way to detect and size specific molecules within complex biological mixtures.
The naming of blotting techniques follows a geographic and compass-point pattern: Southern blot was named after its inventor Edwin Southern, and researchers then named Northern blot (RNA) and Western blot (protein) by compass-point analogy. A "Eastern blot" has been proposed for lipid-modified proteins but has never been standardized.
Building Blocks of Nucleic Acids →All blotting methods detect the same type of molecule. Southern blots detect DNA, Northern blots detect RNA, and Western blots detect proteins, each requiring a different detection reagent.
In a Northern blot of pancreatic tissue, insulin mRNA appears as a distinct band at approximately 600 nucleotides. A band of that size confirms transcript identity, while its intensity across 2 or more sample lanes estimates relative abundance.
Branch Point
/ BRANCH poynt / · English: branch + point
Branch Point is a conserved adenosine residue within an intron that attacks the 5-prime splice site during the first transesterification step of pre-mRNA splicing, forming a lariat-shaped RNA intermediate.
The branch point adenosine typically sits 20 to 50 nucleotides upstream of the 3-prime splice site, and its 2-prime hydroxyl group carries out a nucleophilic attack on the phosphodiester bond at the 5-prime splice site. U2 small nuclear RNA base-pairs with the branch point sequence to position this hydroxyl group precisely for catalysis. Mutations at the branch point consensus sequence reduce U2 binding affinity by 10- to 100-fold, causing exon skipping or intron retention.
Branch point position can vary from 15 to 100 nucleotides upstream of the 3-prime site, and this variability contributes to regulatory control of alternative splicing. Approximately 15 percent of human genetic diseases involve mutations at splice-site sequences, including branch point variants that impair spliceosome assembly.
Computational tools that scan human pre-mRNA sequences for branch points identify tens of thousands of candidate sites across the transcriptome, yet only a subset are used in any given cell type. The choice among competing branch points is one mechanism by which cells generate transcript diversity without altering the underlying DNA sequence.
Introns are removed by random cleavage events. Splicing depends on precise sequence signals, including the branch point adenosine, the 5-prime splice site, and the polypyrimidine tract, all of which are recognized by specific spliceosomal components.
In the human beta-globin gene, a single nucleotide change near the branch point region of intron 2 can disrupt normal splicing and cause beta-thalassemia. Aberrant transcripts from this defect can reduce functional beta-globin output enough that severe patients require transfusions every 2 to 5 weeks.