Consider the synthetic RNA-DNA transcription bubble illustrated here. Let us refer to the coding DNA strand, the template strand, and the RNA strand as strands 1,2 and $3,$ respectively. (a) Suppose that strand 3 is labeled with ${}^{32}\mathrm{P}$ at its $5^{\prime }$ end and that polyacrylamide gel electrophoresis is carried out under nondenaturing conditions. Predict the autoradiographic pattern for(i) strand 3 alone,(ii) strands 1 and $3,(\text{ iii })$ strands 2 and $3,(\text{ iv })$ strands $1,2,$ and $3,$ and $(\mathrm{v})$ strands $1,2,$ and 3 and core $\mathrm{RNA}$ polymerase.(b) What is the likely effect of rifampicin on RNA synthesis in this system?(c) Heparin blocks elongation of the RNA primer if it is added to core RNA polymerase before the onset of transcription but not if added after transcription starts. Account for this difference.(d) Suppose that synthesis is carried out in the presence of ATP, CTP, and UTP. Compare the length of the longest product obtained with that expected when all four ribonucleoside triphosphates are present.

Step by Step Solution: Step 1. Analyze the given RNA-DNA transcription bubble. Step 2. Predict the autoradiographic pattern for the given strands as follows: Step 3. {'i': 'When strand 3 alone undergoes nondenaturing polyacrylamide gel electrophoresis, the autoradiographic pattern will show a single band, indicating that it is a single-stranded RNA molecule.', 'ii': 'When strands 1 and 3 are exposed to nondenaturing polyacrylamide gel electrophoresis, the autoradiographic pattern will show two distinct bands, one for the single-stranded RNA molecule and another more slowly migrating band due to the double-stranded DNA.', 'iii': 'When strands 2 and 3 are exposed to nondenaturing polyacrylamide gel electrophoresis, the autoradiographic pattern will show a single band for the single-stranded RNA molecule.', 'iv': 'When strands 1, 2 and 3 undergo nondenaturing polyacrylamide gel electrophoresis, the autoradiographic pattern will show three distinct bands - one for single-stranded RNA, one for the double-stranded DNA and another one for hybrid RNA-DNA molecules.', 'v': 'When strands 1, 2, and 3 along with core RNA polymerase are exposed to nondenaturing polyacrylamide gel electrophoresis, the autoradiographic pattern will show four bands as in (iv), with an additional slowly migrating band for the RNA-DNA-polymerase complex.'} Step 4. Rifampicin is an antibiotic that inhibits bacterial RNA polymerase and likely prevents the initiation of RNA synthesis in this system. Step 5. When heparin is added before transcription, it can bind to the core RNA polymerase and prevent the access of template DNA, thereby blocking elongation of the RNA primer. However, if heparin is added after transcription has initiated, RNA polymerase has already displaced the sigma factor and shifted to elongation mode, thereby rendering it insensitive to heparin. Step 6. In the presence of ATP, CTP and UTP, the length of the longest product obtained will be less than the expected maximum length, which would have been possible with the presence of all four ribonucleoside triphosphates. This is because the absence of GTP will lead to premature termination of RNA synthesis as the polymerase will stall at the first G residue encountered in the template strand.