Termination of transcription in prokaryotes (intrinsic termination) is mediated by special DNA secondary structures (stem and loop structures). Stem and loop structures have nucleotides that are complementary with the adjacent nucleotides. Along with a poly uracil sequence, these structures do not allow transcription to go further.In rho-dependent termination, rho binds to RNA until it reaches a RNA–DNA helical region, where it acts as a helicase and unwinds the complex. This in turn stops transcription. Sigma and TFIID are important in transcription in eukaryotes, not prokaryotes.

The correct answer is "six general transcription factors." RNA polymerase I is used to transcribe rRNAs, not mRNAs. The rho factor is used to initiate transcription in prokaryotes, not eukaryotes. Elongator is a factor used by eukaryotes to elongate transcripts and speed up transcription, but is not required to initiate transcription.

DNA replication occurs during the S phase of the cell cycle. Before DNA replication, the cell performs a check to ensure that there are no damages to the DNA molecules. One important molecule in this process is the cyclin-CDK complex. CDKs, or cyclin dependent kinases, are important kinases that facilitate the progression of cell through the cell cycle. Presence of CDK inhibitors will halt the progression of cell cycle and, subsequently, will halt DNA replication.

UV light is very damaging to DNA molecules. It changes the conformation of DNA molecules and prevents the activity of DNA replication enzymes; therefore, excessive UV light exposure will halt DNA replication.

Adenosine triphosphate, or ATP, is the main energy currency of the cell. It is used to power numerous energy consuming cellular processes. DNA replication requires lots of energy. Lack of energy, or ATP, will slow down DNA replication.

DNA methylation is an epigenetic process that involves the addition of a methyl group on DNA molecules. This makes the DNA molecule unavailable for and halts transcription. It does not stop DNA replication, however. Note that the methyl group added to the DNA here is different from the methyl cap added to RNA molecules during post-transcriptional processing.

The other epigenetic change that prevents transcription is the deacetylation of histones. Histones are proteins that facilitate the packaging and ordering of DNA molecules. Deacetylation of histones makes them more positive, strengthening the interaction between histones and negatively charged DNA molecules. This makes it harder for DNA molecules to open and be available for transcription.

CDKs are enzymes that facilitate the progression of a cell through the cell cycle. This involves the replication of DNA during the S phase. DNA polymerase is an important enzyme in DNA replication. It’s main function is to add complementary nucleotides to the growing daughter DNA strand. RNA polymerase serves a similar function as DNA polymerase; however, it is utilized only during transcription. All of the enzymes listed either enhance or have no effect on DNA replication.

The phases of cell cycle in order are as follows: G1 phase, S phase, G2 phase, and Mitosis. DNA replication occurs during the S phase; therefore, a checkpoint to ensure proper replication must occur before this phase, between the G1 and S phase. During this checkpoint, the cell checks for DNA damages that might have occurred. If the DNA is damaged, then the cell activates DNA repair enzymes. Upon repair, the cell undergoes the checkpoint one more time. If proper repairs have been made, the cell progresses into the S phase and undergoes DNA replication.

The nucleotide cytidine under certain chemical or heat conditions can be deaminated to form uracil. DNA repair mechanisms intervene at this point. Uracil is found only in RNA, so it needs to be removed and replaced with another cytosine molecule. The answers above are all steps in removing an uracil nucleotide from the DNA molecule. 

Among the proteins needed for RNA transcription are RNA polymerase, activators, and repressors. Corepressor proteins indeed bind to repressors, rather than DNA, in order to inhibit gene expression. Promoters are located toward the 5’ region of the sense strand (i.e., upstream). Normally, however, histone acetylation increases, rather than inhibits, gene expression (and hence transcription), by removing positive charges on the histone, thus decreasing the attractive interaction between the positively charged histones and negatively charged DNA. The decreased attraction allows room for transcription factors and RNA polymerase to bind promoter regions, increasing the incidence of transcription.

Untranslated regions never yield proteins, and thus do not attach to protein kinases. The 5’ end of pre-RNA is capped, and the 3’ end modified by poly A tails. Pre-RNA is, indeed, spliced when introns are removed. This is performed by spliceosomes, which only splice RNA, not DNA.

Transcription is the process of utilizing information in DNA molecules to make RNA molecules. It can occur in eukaryotes (such as humans) and in prokaryotes (such as bacteria). In eukaryotic transcription, the DNA is transcribed to RNA inside the nucleus. Upon completion, the synthesized RNA undergoes further post-transcriptional modifications such as addition of methyl cap, poly-A tail, and removal of introns. After these modifications, the RNA molecule leaves the nucleus, enters the cytoplasm, and undergoes translation (process of synthesizing proteins).

In contrast, bacterial transcription occurs in the cytoplasm and does not involve any of the post-transcriptional modifications. As a result, the transcribed RNA can immediately be used to synthesize proteins; therefore, translation immediately follows transcription in bacteria.

Recall that reverse transcriptase is a special enzyme that converts RNA to DNA (‘reverse’ of transcription). It is found in some viruses such as HIV.