DNA, enzymes, and energy can make RNA {transcription, DNA}| {DNA transcription}.
process: strand separation
RNA polymerase binds to DNA double helix locations {promoter, DNA}. RNA polymerase separates DNA strands for one complete double-helix turn, little more than three nucleotides. RNA polymerase separates two deoxyribonucleotide chains by breaking hydrogen bonds, starting at one double-helix point and going in one direction only. Transcription uses DNA strand lying in third carbon to fifth carbon direction. Direction that chains separate is opposite to chain phosphodiester-bond direction.
process: polymerase
Eukaryotic 5.8S, 18S, and 28S rRNA use RNA polymerase I. Eukaryotic mRNA and snRNA use RNA polymerase II. Eukaryotic 5S rRNA and tRNA use RNA polymerase III. RNA types have different promoters. RNA polymerase does not need primer.
process: matching
Free ribonucleotides in solution hydrogen-bond to matching chain deoxyribonucleotides. Adenine and thymine hydrogen-bond. Adenine and uracil hydrogen-bond. Guanine and cytosine hydrogen-bond. Error rate is 10^-4 to 10^-5.
process: linking
Using phosphodiester bonds, RNA polymerase links ribonucleotides to make RNA sequence. Phosphodiester bonds invert compared to original-DNA-strand phosphodiester bonds. Nucleotides link at rate 50 nucleotides per second.
process: termination
RNA transcription terminates just after poly-uracil region, using RNA chain-terminating proteins. Using rho protein, region near tRNA end curves around to hydrogen bond with itself using paired A and U or C and G ribonucleotides to make a hairpin loop.
process: separation
RNA polymerase leaves DNA, and RNA separates from DNA. Double helix reforms.
product
Transcription makes one rRNA, tRNA, or mRNA strand. In higher animals, mRNA intron regions can make protein, and exons do not. Introns can be separate or overlap.
blocking
Actinomycin can block transcription by sliding between and separating guanines and cytosines. Mushroom poisons block RNA polymerase from making histone protein.
DNA
DNA operons have gene for repressor, promoter where RNA polymerase binds, operator where repressor can bind and inducer can remove repressor, and one or more genes, typically in that order. RNA or protein binding at regulatory regions controls RNA amount.
DNA: repressor
Repressor prevents RNA polymerase from binding at promoter, because operator is next to promoter. Bacteriophage lambda has repressor-gene {cro gene} repressor. Cro and other repressors typically are dimers that have alpha-helix binding in DNA-helix major groove. Repressors can affect several transcriptions {trans-acting control}.
DNA: promoter
Promoters affect downstream transcription {cis-acting control}. Catabolite activator protein binds to cAMP to make cAMP-CAP complexes, which bind to promoter for lactose and galactose breakdown genes. If glucose is low, cAMP builds up.
Enzymes {RNA polymerase} can bind to DNA double-helix promoters.
Three nucleotides {termination sequence} end transcription.
Special enzymes {nuclease} can modify free-floating RNA. Nuclease adds methyl groups to nucleotides. Nucleases make other modified bases, such as inosine. In eukaryotes, nuclease adds adenines to mRNA 3' end to stabilize RNA and protect 3' end. In eukaryotes, nuclease adds nucleotides to mRNA to protect 5' end.
Endonuclease can split long RNA into functional pieces. For example, nuclease divides chain that contains all rRNA types into different ribosomal RNAs. Photolyase restores UV-induced dimers, using light.
Using enzymes {rho protein}, region near tRNA end curves around to hydrogen bond with itself, using paired A and U or C and G ribonucleotides.
Proteins induced from other sites control RNA transcription {transcriptional control}.
E. coli tryptophan operon (trp) has five genes, but, if tryptophan is at high levels, only short transcription {leader, DNA} can happen {attenuation}. Leader makes hairpin that stops transcription. If tryptophan is low, full operon transcribes, because different hairpin has few tryptophans.
5-Chemistry-Biochemistry-Nucleic Acid
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Date Modified: 2022.0225