Everything about 3 End totally explained
Directionality, in
molecular biology, refers to the end-to-end chemical orientation of a single strand of
nucleic acid. The chemical convention of naming carbon atoms in the
nucleotide sugar-ring numerically gives rise to a
5' end and a
3' end (usually pronounced "five prime end" and "three prime end"). The relative positions of structures along a strand of nucleic acid, including
genes,
transcription factors, and
polymerases are usually noted as being either
upstream (towards the 5' end) or
downstream (towards the 3' end).
The importance of having this naming convention lies in the fact that nucleic acids can only be synthesized
in vivo in a 5' to 3' direction, as the
polymerase used to assemble new strands must attach a new nucleotide to the 3'
hydroxyl (-OH) group via a
phosphodiester bond. By convention, single strands of
DNA and
RNA sequences are written in 5' to 3' direction.
5' end
The 5' (pronounced "five prime") end designates the end of the DNA or RNA strand that has the fifth carbon in the
sugar-ring of the (deoxy)
ribose at its terminus. A
phosphate group attached to the 5' end permits
ligation of two
nucleotides, for example, the covalent binding of a 5'-phosphate to the 3′-hydroxyl group of another nucleotide, to form a
phosphodiester bond. Removal of the 5' phosphate prevents ligation. To prevent unwanted nucleic acid ligation (for example self-ligation of a
plasmid vector in
DNA cloning),
molecular biologists commonly remove the 5'-phosphate with a
phosphatase.
The 5' end is also the site at which
post-translational capping occurs, a process which is vital to producing mature
messenger RNA. Capping ensures the stability of the messenger RNA while it undergoes
translation, providing resistance to the degradative effects of
exonucleases. It consists of a
methylated nucleotide (methylguanosine) attached to the messenger RNA in a rare 5' to 5' triphosphate linkage.
The 5'
flanking region of a
gene often denotes a region of DNA which isn't transcribed into RNA. The 5'-flanking region contains the
gene promoter, and may also contain enhancers or other protein binding sites.
The
5' untranslated region (5' UTR) is a region of a gene which is transcribed into mRNA, and is located at the 5' end of the mRNA, but which doesn't contain protein-coding sequence. The 5'-untranslated region is the portion of the DNA starting from the cap site and extending to the base just before the ATG translation initiation codon. While not itself translated, this region may have sequences, such as the
ribosome binding site and Kozak sequence which determine the translation efficiency of the mRNA, or which may affect the stability of the mRNA.
3' end
The 3' (pronounced "
three prime") end of a strand is so named due to it terminating at the
hydroxyl (-OH) group of the third carbon in the
sugar-ring, and is known as the
tail end. The 3'-hydroxyl is necessary in the synthesis of new nucleic acid molecules as it's
ligated (joined) to the 5'-phosphate of a separate nucleotide, allowing the formation of strands of linked nucleotides.
Molecular biologists can use
nucleotides that lack a 3'-hydroxyl (dideoxyribonucleotides) to interrupt the replication of
DNA. This technique is known as both the
dideoxy termination method and the
Sanger method, and was used to determine the order of nucleotides in DNA.
The 3' end is also the site of
post-translational polyadenylation, which attaches a chain of 50 to 250
adenosine residues to
messenger RNA immediately after
translation. This chain helps in determining how long the messenger RNA lasts in the cell, and therefore how much protein is produced from it.
The 3'
flanking region is a region of DNA that isn't copied into the mature mRNA, but which is present adjacent to 3' end of the gene. It was originally thought that the 3' flanking DNA wasn't transcribed at all, but it was discovered to be transcribed into RNA and quickly removed during processing of the primary transcript to form the mature mRNA. The 3' flanking region often contains sequences that affect the formation of the 3' end of the message. It may also contain enhancers or other sites to which proteins may bind.
The
3' untranslated region (3' UTR) is a region of the DNA which IS transcribed into mRNA and becomes the 3' end or the message, but which doesn't contain protein coding sequence. Everything between the stop codon and the polyA tail is considered to be 3' untranslated. The 3' untranslated region may affect the translation efficiency of the mRNA or the stability of the mRNA. It also has sequences which are required for the addition of the poly(A) tail to the message (including one known as the "hexanucleotide", AAUAAA).
Further Information
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