Understand regulation of transcription - AP Biology

Shine-Delgarno sequences are ribosomal binding sites slightly upstream of start codons on prokaryotic mRNA. Eukaryotic mRNA is more complicated (it does not contain Shine-Delgarno sequences) and contains promoter regions that are responsible for recruiting translation factors and ribosomal subunits.

The lack of a nuclear membrane in prokaryotes has the advantage of allowing the cell to translate RNA as it is transcribed from DNA. This means that even before the full RNA is produced, the protein coded by that RNA can start being made. Eukaryotes produce RNA inside the nucleus, so it must first be fully transcribed and undergo modifications before it can be moved to the cytoplasm, where translation occurs.

Inactive RNA polymerase must bind to a specific sigma factor in order to become active in gene transcription. Sigma factors are specialized transcription factors involved in recruiting and activating RNA polymerase. Only once RNA polymerase has bound the sigma factor can it identify promoter sequences and initiate transcription.

mRNA is the product of transcription and is not involved in prokaryotic RNA polymerase recruitment. An RNA primer is essential to recruiting DNA polymerase for DNA replication.

Prokaryotic transcription has three essential steps: initiation, elongation, and termination. The initiation process involves the binding of RNA polymerase to the correct region of DNA, and is characterized by the binding of the sigma factor to the RNA polymerase. Elongation occurs as the RNA strand is synthesized from the DNA template. Termination occurs when the RNA polymerase enzyme encounters a rho factor or particular DNA structure that causes it to release the DNA strand and cease RNA synthesis.

It is during the elongation process that RNA nucleotides are matched to the DNA template. The temporary DNA-RNA hybrid exists only briefly at the point of transcription before phosphodiester bonds form between adjacent ribonucleotides.

The sigma factor is an important part of initiation for prokaryotic transcription. Once transcription has been initiated, however, the sigma factor is released during elongation. RNA polymerase synthesizes the RNA product until it is interrupted in one of two ways. In rho-dependent termination, a rho factor protein interferes with RNA polymerase binding and causes it to release the DNA strand. In rho-independent termination, structural features of the DNA cause RNA polymerase to become detached. The structures include hairpin loops, which generate steric hindrance, and adenine-rich sequences, which lead to weak binding of the RNA product to the DNA template.

Prokaryotic transcription occurs in the cytosol, since prokaryotes lack a nucleus. This allows ribosomes to interact with RNA even while it is still be synthesized.

In contrast, eukaryotic transcription occurs in the nucleus. Once RNA has been synthesized it must be transported from the nucleus to the cytoplasm before it can interact with ribosomes. The newly-synthesized RNA undergoes splicing to remove introns, addition of a 5'-cap, and addition of a poly-A tail before it can exit the nucleus. These modifications help prevent degradation of the RNA. Only after these modifications can the RNA leave the nucleus and becomes functionally active.

RNA polymerase does not interact with the Shine-Delgarno sequence. The Shine-Delgarno sequence is present on some prokaryotic mRNAs and serves as a ribosomal binding site for the initiation of translation. RNA polymerase is only involved in transcription and will bind to DNA, not RNA.

The other answers are all true and unique to prokaryotic transcription. Eukaryotic transcription is much more tightly regulated by transcription factors and DNA packaging (chromatin), and is confined to the nucleus.

While prokaryotic and eukaryotic transcription processes are quite similar, there are some key differences. One significant difference is that prokaryotic transcripts can contain multiple genes, which will then transition as a single RNA strand to the ribosome. This is referred to as a polycistronic transcript. Eukaryotes have only one gene per transcript.

Both prokaryotes and eukaryotes use promoters. Prokaryotes do not have nuclei, though transcription and translation can occur simultaneously and in close proximity in these cells.

Plasmids are small pieces of DNA that are not part of a bacteria's genome. The genes contained on plasmids are not necessary for proper function of the bacteria. However, bacterial plasmids can carry genes to confer antibiotic resistance, and commonly do. Plasmids can be transferred between bacteria via conjugation, and can be integrated into their genomic DNA.. Plasmids are usually present in more than one copy per cell.

Bacteria organize some of their genes into operons. Operons contain genes of a similar function grouped together, and these genes are all transcribed together. For example, the lac operon involves the three genes required for breaking down lactose. There is no point in only transcribing one or two of the three genes since they are all required to break down lactose. Thus, they are under the control of a single operator and are all transcribed when the operator is active.

The correct answer is that prokaryotes only have exons, whereas eukaryotes have exons and introns. As a result, in eukaryotes, when mRNA is transcribed from DNA, the introns have to be cut out of the newly synthesized mRNA strand. The exons, or coding sequences, are then joined together. Prokaryotes do not have to process their mRNA to this extent.

The correct answer is operator. In most operons, repressors bind operators to prevent transcription of downstream genes.

Promoters are sequences of DNA upstream of genes that usually promote transcription by recruiting polymerases and other transcription factors. Enhancers are distant DNA sequences that promote transcription, whereas exons are the coding segments of a gene.

The correct answer is transcribe RNA from a DNA template. RNA polymerases are DNA-dependent, meaning that they require a DNA template; however, the new daughter strand that they create is composed of RNA. This RNA will then be translated into a functional protein by prokaryotic ribosomes.

Rho attaches to a Rho recognition site on the mRNA strand and uses ATP to move along the mRNA strand towards RNA polymerase. When RNA polymerase pauses at the terminator, Rho unwinds the DNA-RNA hybrid. RNA polymerase, Rho, and the newly synthesized mRNA are released.

Restriction Endonucleases, or otherwise known as restriction enzymes, allows biologist to “cut and paste” different DNA sequences together. The use of restriction endonucleases is critical for the creation of recombinant plasmids. Viral vectors is incorrect, as viral vectors are useful in the application of recombinant DNA plasmids, delivery to host cell, but not in forming.

DNA polymerase is not involved in the process of transcription. The incorrect answer could be corrected if it was rewritten as "a mutation in the promoter region where the RNA polymerase binds to."

In bacterial cells, binding of a sigma factor to RNA polymerase is required for the initiation of transcription. Once the sigma factor binds, RNA polymerase is referred to as a holoenzyme and begins to make the RNA transcript.

The operator region is the location where the repressor binds. Other parts of an operon include the promoter (where RNA polymerase binds), and structural genes.

Addition of 5’ cap, 3’ tail, and intron splicing occur in eukaryotes, not prokaryotes. Repressors bind to the operator region of the gene and prevent RNA polymerase from transcribing the gene, while activators bind to the promoter and increase transcription of the gene.