Building the Script: Transcription Elongation Process

If the cell needs to construct a complementary copy of a gene, then an enzyme must catalyze the addition of ribonucleotides. If RNA polymerase is that enzyme, then its job is building the RNA strand.

If RNA polymerase can only add new nucleotides to the 3' hydroxyl group of the existing chain, then the overall growth of the molecule must proceed from the 5' end toward the 3' end.

If RNA does not contain the base thymine, then a different partner must be used for adenine. If uracil is the specific base used in RNA, then it is the one paired with adenine.

If the enzyme needs to read the bases, it must open the DNA. If the DNA must remain protected for future use, then the enzyme must close (rewind) the helix once it has passed.

If the reaction requires both material and fuel, then NTPs serve both roles. If they contain three phosphate groups, then their hydrolysis provides the energy to link the A, U, C, and G building blocks.

If only one side of the DNA contains the "blueprint" for the current gene being copied, then that side serves as the guide. If it serves as the guide, then it is the template strand.

If the DNA sequence is the "instruction manual," then the RNA must be a direct translation. If A pairs with U and C pairs with G, then the enzyme uses those chemical rules to select the next correct base.

If transcription typically adds 40 to 60 nucleotides per second in eukaryotes, it is actually quite fast, though still slightly slower than some DNA replication speeds; however, it is a highly efficient and rapid process.

If the RNA must be paired with the DNA to be synthesized, but then peels away as the enzyme moves, then a temporary "mixed" helix is formed. If it is mixed, then it is a hybrid.

If the enzyme hits a difficult sequence or runs low on building blocks (NTPs), it will slow down. If helper proteins are present to keep it moving, then the speed will increase.

If the DNA helix must rewind behind the enzyme, then the RNA cannot stay attached. If the DNA zips back up, then the RNA strand is pushed out and trails behind the moving polymerase.

If a cell needs a large amount of a specific protein quickly, then it must make many RNA copies. If one enzyme moves down the gene, then another can start right behind it, creating a "train" of polymerases.

If the new RNA is built 5' to 3' and DNA strands are antiparallel, then the enzyme must be physically tracking the template in the opposite direction, which is 3' to 5'.

If the enzyme holds about 10 to 20 base pairs of DNA open at any given time to read them, then that open section creates a small bulge. If transcription happens there, then it is the transcription bubble.

If the enzyme does not have the same level of proofreading as DNA polymerase, then errors are more common; however, since RNA is temporary, a mistake only affects that one message, not the master DNA code.

If the template strand is the "mirror image" of the RNA, then the other (unused) DNA strand must be the "matching" sequence. If it matches the RNA, then it is appropriately called the coding strand.

If the energy is stored in the chemical bonds of the triphosphate tail, then those bonds must be broken to release that energy. If they are shared-electron bonds, then they are covalent bonds.

If alpha-amanitin binds to RNA polymerase and stops it from moving, then no new RNA messages can be built. If no messages are built, then no proteins can be made, and the cell will stop functioning.

If the enzyme reaches the end of the gene, then it receives a signal to stop. If it stops, then it releases the RNA and the DNA closes up entirely. It does not replicate DNA or change its chemical class.

If the DNA is the permanent "master file" in the nucleus, then the RNA is the "mobile copy." If elongation builds that copy base-by-base, then it is turning the code into a portable message.