splice site(1) 8. Poly-a polymerase mediates polyadenylation in the termination of transcription eukaryotes(1 ). It adds about 200 As to the 3 end of the newly synthesized mRNA without a template(2) 9. Gre factors stimulate hydrolytic editing, a proofreading mechanism in the prokaryotic transcription (2 ). They also serve as elongation stimulating factors(1) 10. Cre-lox is a simple example of recombination by the tyrosine recombinase family Cre is an enzyme encoded by phage Pl, and lox sites are its recombination sites on the DNA (2). Only Cre protein and the lox sites are needed for completing recombination (1). Cre-lox is widely used as a tool in genetic engineering Part l 1. What is the relationship between DNa damage/lesion and mutation? Which repair mechanisms are error-free, and which are error-prone? Is the error-prone repair mechanism useful?(10 points) 1) The relationship between dna damage/lesion and mutation If dna damage/lesion is not repaired before the next round of replication, it may result in mutation because the incorrect nucleotides could be incorporated into the newly synthesized dna because of the damaged DNA structure. In another word mutation could be resulted from DNA damage/lesion. (2) 2)Error-free repair mechanisms include Mismatch repair(1), Direct reversal of DNA damage(e.g. photoreactivation, methyltransferase, etc. )(1), Base excision repair(1), Nucleotide excision repair(1 )and Recombination repair(1) Error-prone repair mechanism refers to the translesion DNA synthesis (1) 3)The error-prone repair mechanism(translesion DNA synthesis) is useful. It is a fail-safe mechanism that allows the replication machinery to bypass the damaged sites Although this repair mechanism tends to introduce mutations, it saves the cells from the worse fate of an incompletely replicated chromosome(chromosome broken).(2) 2. What are the possible causes of double stranded breaks in e coli cells? How does E. coli repair this kind ofdamage?(10 points) 1) The possible causes of double stranded breaks in E. coli lonizing radiation and other damaging agents(reactive oxygen species) directly break both strands of dna backbone Interfering with the progress of a replication fork(an unrepaired nick or lesion in template strand) indirectly causes double stranded breaks 2)The ways that E coli repairs double stranded breaks Homologous recombination via the DSB-repair pathway(major mechanism): the broken dNA retrieves sequence information from the sister chromosome. 4 Nonhomologous end joining(NHEJ): the two ends of the broken DNA are directly ined to each other by misalignment between single strands protruding from thesplice site (1’). 8. Poly-A polymerase mediates polyadenylation in the termination of transcription in eukaryotes (1’). It adds about 200 As to the 3’ end of the newly synthesized mRNA without a template (2’). 9. Gre factors stimulate hydrolytic editing, a proofreading mechanism in the prokaryotic transcription (2’). They also serve as elongation stimulating factors (1’). 10. Cre-lox is a simple example of recombination by the tyrosine recombinase family: Cre is an enzyme encoded by phage P1, and lox sites are its recombination sites on the DNA (2’). Only Cre protein and the lox sites are needed for completing recombination (1’). Cre-lox is widely used as a tool in genetic engineering. Part II 1. What is the relationship between DNA damage/lesion and mutation? Which repair mechanisms are error-free, and which are error-prone? Is the error-prone repair mechanism useful? (10 points) 1) The relationship between DNA damage/lesion and mutation: If DNA damage/lesion is not repaired before the next round of replication, it may result in mutation because the incorrect nucleotides could be incorporated into the newly synthesized DNA because of the damaged DNA structure. In another word, mutation could be resulted from DNA damage/lesion. (2’) 2) Error-free repair mechanisms include Mismatch repair (1’), Direct reversal of DNA damage (e.g. photoreactivation, methyltransferase, etc.) (1’), Base excision repair (1’), Nucleotide excision repair (1’) and Recombination repair (1’) Error-prone repair mechanism refers to the translesion DNA synthesis (1’) 3) The error-prone repair mechanism (translesion DNA synthesis) is useful. It is a fail-safe mechanism that allows the replication machinery to bypass the damaged sites. Although this repair mechanism tends to introduce mutations, it saves the cells from the worse fate of an incompletely replicated chromosome (chromosome broken). (2’) 2. What are the possible causes of double stranded breaks in E. coli cells? How does E. coli repair this kind of damage? (10 points) 1) The possible causes of double stranded breaks in E. coli: Ionizing radiation and other damaging agents (reactive oxygen species) directly break both strands of DNA backbone. 2’ Interfering with the progress of a replication fork (an unrepaired nick or lesion in template strand) indirectly causes double stranded breaks. 2’ 2) The ways that E. coli repairs double stranded breaks: Homologous recombination via the DSB-repair pathway (major mechanism): the broken DNA retrieves sequence information from the sister chromosome. 4’ Nonhomologous end joining (NHEJ): the two ends of the broken DNA are directly joined to each other by misalignment between single strands protruding from the