Review Questions-2Energy and Metabolism ATP, its role in metabolism, generation of ATP by different mechanisms.Mention the number of high energy bonds in each of the following molecules: ATP; PEP; 1,3 BPG; ADP; AMPcatabolism, anabolism, endergonic, exergonic reactions. Redox reactions*. Role of electron carriers: NAD+, NADP+, etcEnzymes*: mechanism of action, effect of environment, inhibition, regulation.Overview of metabolismGlucose to pyruvate: Glycolysis, Pentose Phosphate pathway**TCA cycle, ETC:Oxidative Phosphorylation, anaerobic phosphorylation.Fermentation: organic e- acceptors, their role. How is NAD+ regenerated in: Oxidative phosphorylation, fermentation? Why is it necessary to regenerate NAD+?Photosynthesis (Calvin/Dark cycle), GluconeogenesisOrganization of synthetic pathways DNA structure & replication Explain the flow of genetic information in a diagram. (Include the exceptions if any).How did Griffith’s expt with S. pneumoniae demonstrate the transformation of non-virulent strainto virulent strain. Be familiar with the double helical structure for DNA. Know the structures of DNA, RNA and proteins.What polarity do the strands have? What bond is it between complementary N-bases?What are Chargaff’s rules? Can these be used for single stranded polynucleotides?For different DNA forms - A, B, and Z forms, which are right- handed? Which are left- handed? What is the role of Z form, if any, in human beings? Complementarity rules, H-bond, covalent bond, phosphodiester linkage (Sugar-Phosphate backbone), antiparallel, Name the bond that links adjacent nucleotides (in the same strand) in nucleic acids Peptide; Beta(1->4) glycosidic; 5’-3’ phosphodiester ; hydrogen bond What is the most common form of DNA found in cells? What are the other forms? What gives Z DNA its zig- zag structure? Which of the following are true about the structure of DNA?a. Purine and pyrimidine bases are attached to the C1 of the deoxyribose sugarsb. The bases extend towards the middle of the cylinder formed by the two chainsc. The bases are stacked on top of each other in the center with the rings forming parallel planesd. All of the above are true.1How did Messelson and Stahl prove that DNA replication is semi conservative?How many replicons does E. coli have? Is the chromosomal DNA replication bidirectional in both prokaryotes and eukaryotes?Both DNA replication and transcription proceed in the 5’ to 3’ direction. Mention one important difference between DNA polymerases and RNA polymerases with respect to initiation of polymerization. True / False: Many prokaryotes have only one origin of replication per DNA molecule, while most eukaryotes have multiple origins per DNA molecule. What is required in the initiation of DNA replication? What is the origin of replication? What characteristic elements does it contain?What is the role of: Ori C, DnaA, Dna helicase, DNA Pol I, and Pol III in chromosomal DNA replication in E. coli? Why do you need a free 3’-OH for chain elongation? E. coli DNA Pol III: core and holoenzyme. What are the different subunits and what are their functions? Which subunit accounts for polymerizing? Which subunit accounts for 3’- 5’ exonuclease activity? Which subunit accounts for processivity?What is proof reading? How would DNA replication differ in a cell with a mutant epsilon subunit?What properties do DNA polymerase I and III share? Which property is unique to DNA polymerase I? Why is DNA polymerase I considered “distributive” and polymerase III “processive”? What is the main difference between how the leading strand is synthesized and how the lagging strand is synthesized?What are Okazaki fragments? How and why are they formed? What is the role of beta clamp? Is it a part of the core polymerase, or of the holoenzyme? In leading strand synthesis, DNA pol III can proofread the newly formed DNA; this function is performed by ________ subunit of the enzyme. It recognizes errors, removes the wrong nucleotide through ____ to ___ exonuclease activity. E.coli makes an error of only 1 in 1010 bp during DNA replication. What accounts for this extreme fidelity?What are the functions of the following molecules in the replication of E.coli genome:DnaADnaBDnaCSSBDNA topoisomerase IDNA gyraseDNA primaseDNA ligaseDNA pol IDNA pol III (holoenzyme)2What are the important functions of telomerases? Are they necessary in prokaryotes? Would it help E. coli to have telomeres? Explain. What is semi – conservative replication? What is bidirectional replication? How many replicons does the bacterial chromosome have? dNTP’s provide energy for chain elongation during replication. True/False. What is the role of Type I and Type II topisomerases?How would you distinguish between template DNA and newly synthesized DNA? Gene organization in Phage PhiX174 is rather unusual. What is it that makes it so unusual?** Tau and gamma subunits of DNA PolIII holoenzyme are a product of the same gene, dnaX. This is an example of one gene 2 products: How do you think these are formed? [Dr. Walker’s work on DNA replication! Result of ribosomal frame shifting] Draw ds DNA. Use each of the two strands, strand 1 and 2 as template strands. Fork movement is from left to right for strand 1. Strand 1 : 3’ _______________________ 5’ Strand 2 : 5’ _______________________ 3’ Which strand is the template for the synthesis of the leading strand? Which one is the template for the synthesis of the lagging strand? Name the proteins/ enzymes required for the synthesis of the leading strand. Name the proteins/ enzymes required for the synthesis of the lagging strand. RNA structure & transcriptionStructure of m, r, t RNAs.Special features of tRNA: Unusual nucleotides, H-bonded, ds regions. What kind of effect will be observed in cells that contain a mutant sigma 70 factor (the predominant sigma factor in the cell)? Explain your answer. How many RNA polymerases do the prokaryotes have? How many do the eukaryotes have? What do you understand by the term Ribozymes? Mention some functions of the ribozyme. What is the role of sigma factor in transcription? What is the advantage of having more than one sigma factor in a cell? What is the role of different subunits of E. coli RNA polymerase in transcription? What is the difference between core polymerase and holoenzyme in case of RNA