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.

Transcription is the process of transcribing RNA molecules from DNA. This is a normal cellular process that is required for cells to grow and function properly (because these RNA molecules are eventually converted to proteins, the building blocks of cells). Growth of cells occurs in G1 and G2 phases; therefore, transcription occurs during both of these phases.

Note that DNA replication occurs during S phase; therefore, no DNA molecules will be available for transcription during S phase and transcription will be halted.

Sigma factor is a special molecule in bacteria that is used to initiate transcription. In a bacterial cell, RNA polymerase is typically kept in its inactive form, called holoenzyme. When it is needed for transcription, RNA polymerase is converted to its active form by sigma factor. Sigma factor facilitates the binding of RNA polymerase to the gene sequence on the corresponding DNA molecule. Upon binding, RNA polymerase will carry out transcription and generate a new mRNA strand.

A Pribnow box is a type of promoter region in bacteria that contains a sequence similar to the eukaryotic TATA box.  5'- TATAAT -3' will be found in the Pribnow box and signifies that the particular section of DNA is a promoter region.  The eukaryotic TATA box typically contains the sequence 5'- TATAAA -3' and also serves as a promoter region, typically found upstream of a gene.

Transposable elements are those that can move around within the genome, which increases genetic diversity. Also, due to alternative splicing of introns, multiple distinct proteins can be synthesized from the same exact mRNA transcript. One example of this is antibody production. Segments of DNA can spontaneously switch to become new DNA coding regions (mutation). This also increases genetic diversity, if this occurs in the germ-line cells.