Fundamentals of RNA Polymerase and Viral Replication

RNA polymerases are enzymes responsible for synthesizing RNA from a DNA template. In eukaryotes, RNApol I synthesizes ribosomal RNA (rRNA), RNApol II transcribes protein-coding genes and messenger RNA (mRNA), and RNApol III transcribes transfer RNA (tRNA) and other small RNAs. Therefore, options 1, 2, and 3 are incorrect as they do not accurately describe the functions of the different RNA polymerases.

The correct answer involves the interaction between viral and cellular factors during the initiation process, RNApolII recognition of the core promoter (TATA and +1), formation of the initiation complex leading to nascent RNA synthesis by RNApol I. The incorrect answers provide plausible but incorrect information related to various factors and processes in transcription initiation.

The PolII promoter structure consists of various elements that regulate gene transcription, including TATA box, transcription start site, and regulatory sequences. It is essential for initiating the transcription of genes by RNA polymerase II.

The PolII promoter structure plays a crucial role in transcription by utilizing cellular proteins, recognizing specific regions, and enhancing gene transcription through enhancer-binding proteins. The incorrect answers provided do not accurately describe the function of PolII promoter structure.

Transcription factors play a crucial role in gene expression by binding to specific DNA sites and regulating the transcription process. While viral transcription factors may share similarities with cellular transcription factors, they are not configured in exactly the same way. Additionally, DNA binding by transcription factors does not solely involve protein-protein interactions, as DNA sites are specifically targeted. It is important to note that cellular transcription factors may not always be sufficient for viral transcription, which may require additional viral transcription factors.

In-vitro transcription refers to the reconstitution of cellular transcription using purified transcription factors in a tube, with the flexibility of adding viral regulatory proteins or altering promoter/templates.

The correct methods for measuring protein-DNA interactions are gel shift and DNAse footprinting for in-vitro studies, and ChiP (chromatin Immunoprecipitation) for in-vivo studies.

The 4 modes of transcription for DNA viruses involve different factors that influence the transcription process. Retroviruses integrate into the cellular genome and do not express viral regulatory proteins; Lentiviruses, however, do express regulatory proteins. The correct answer focuses on the complicated promoter/enhancer region, availability of factors in the cell, and the physical state of chromatin in the integration region.

Cascade regulation is a mode of transcription where viral genes are expressed in a cascading effect, starting with cellular promoters that have complex regulatory regions. This process involves activating regulatory proteins that then trigger the transcription of other genes, leading to DNA replication and activation of late viral genes.

Transcription of DNA viruses involves various mechanisms, where some viruses interact with cellular pathways to alter transcription factors and gene expression.

The correct answers highlight the roles of HIV enhancer and TAT in the transcription process of HIV. Option 1 incorrectly states the function of TAT, while Option 2 and 3 provide inaccurate information about the roles of HIV enhancer and TAT respectively.

Transcription of HIV is a complex process where the interplay of factors like enhancers, TAT, Pol, and phosphorylation affect the outcome. HIV transcription is initiated by an enhancer leading to the expression of TAT. In cases where Pol falls off, the process can be disrupted, impacting the binding of TAT to TAR, recruitment of cellular kinases, and the processivity of RNApol II.

The correct sequence of events in adenovirus transcription involves the E1 region being transcribed first, followed by activation of remaining E transcription units by E1A, and then activation of late transcription unit by E1A and late genes for cascade regulation.

E1A binds to RB, releasing E2F to activate transcription of Adenovirus genes. This process is essential for viral replication and production of viral proteins.

HSV has a linear genome with each gene having its own promoter, allowing for individual regulation of gene expression. The lack of introns in HSV genes prevents splicing and allows for the direct transcription of unspliced genes.

VP16 is a late protein packaged with mature virion. It performs a structural role and is located in the tegument region of the virion, between the envelope and nucleocapsid.

During the lytic cycle of the virus, VP16 mainly activates the remainder of HSV genes. While ICP4 may have different functions mentioned, it is VP16's activation role that is emphasized in this context.

Ori is a specific DNA sequence where DNA replication begins, and replication proteins are required to bind to Ori for the replication process to initiate. It is not involved in breaking down DNA strands, DNA repair, or cell division regulation during replication.

The correct answer explains the roles of alpha, sigma, and epsilon in DNA replication, highlighting their high fidelity and processivity. The incorrect answers provide different functions of DNApol that do not align with its actual role.

The correct types of replication are bidirectional replication, where the 3' OH group of primer and RNA primers are recognized, and non-RNA primer replication where replication occurs on a single strand.

In SV40 replication, the correct mode involves recognizing the origin, binding to the core origin, and forming a hexamer to encase the DNA. Options 2, 3, and 4 do not accurately describe the modes of replication according to SV40 replication.