|Why is DNA important?
|molecular basis for inheritance contains the code for all other cellular molecules its complementary structure allows it to be replicated and the code to be read variations in DNA sequence lead to phenotypic differences and susceptibility to disease defects in DNA replication and repair lead to many diseases
|What is a DNA nucleotide made out of?
|phosphate deoxyribose sugar organic nitrogenous base (GCAT)
|What can be said about the strands of DNA?
|double stranded DNA strands in antiparallel directions linked through hydrogen bonding A and T = 2 H bonds C and G = 3 H bonds A and G = 2 rings, purines T and C = 3 rings, pyrimidines
|What is the 5' end?
|free phosphate group at the 5' position on the sugar backbone
|What is the 3' end?
|unlinked OH group at 3' position on sugar
|Explain the compaction of DNA
|DNA exists as double helix wraps around histones to form nucleosomes undergoes further folding to form 30nm chromatin fibre compacted further to form chromosome
|Describe the differences in compaction at interphase and metaphase
|each cell has 2m of DNA 1,000x compaction at interphase 10,000x compaction at metaphase
|What is the role of linker histones?
|histone H1 keeps DNA wrapped around the histones in place by binding nucleosome at exit and entry sites binds to linker DNA region between nucleosomes, helping stabilize the zig-zagged 30nm chromatin fibre
|Why are histones abundant in the nucleus?
|form the framework around which DNA is wrapped
|What are core histones?
|four different types H2A H2B H3 H4 these all exist as dimers form octameric nucleosome core which DNA strands wrap around twice
|With chromosomes in interphase nucleus what do you see?
|you don't see separate chromosomes but rather chromosome families
|What is the difference between the sense and anti-sense strand?
|sense - runs from 5' to 3' antisense - runs from 3' to 5'
|What is the difference between the lagging and leading strand?
|lagging - synthesized discontinuously leading - synthesized continually
|Explain the process of DNA replication in terms of leading and lagging strands
|replication starts at the point of origin here DNA polymerase moves in opposite directions continuous synthesis if DNA polymerase is moving in 5' to 3' direction (in terms of new strand) - leading strand if polymerase is moving in the 3' to 5' direction simple replication not possible as no free OH 3' end for polymerase to bind replication needs to happen in chunks thus forming okazaki fragments that are then fused together by DNA ligase - lagging strand
|Explain the role of DNA topoisomerases
|any protein that propels itself alone along a DNA strand of a double helix e.g. helicase tends to generate superhelical tension DNA topoisomerase enzymes rapidly remove this tension prevents DNA supercoiling
|What targets topoisomerases? What is the result of this?
|quinolones this leads to supercoiling of DNA so double strand breaks
|Some antibiotics interfere with DNA replication in bacteria. Give some examples
|fluoroquinolones e.g. gemifloxacin target topoisomerases in aerobic gram negative and positive species trimethoprim targets nucleotide synthesis in aerobic gram negative and positive species
|There are three ways to repair single strand defects. Explain base excision repair
|each DNA glycosylases can recognise a specific type of altered base in DNA and catalyse its hydrolytic removal flipping out of altered nucleotide base from helix DNA glycosylase probes all faces of base for damage once an enzyme finds damaged base it recognises it and removes base from sugar sugar phosphate with missing base cut out by the sequential action of AP endonucleases and phosphodiesterase DNA polymerase adds new nucleotide DNA ligase seals nick
|There are three ways to repair single strand defects. Explain nucleotide excision repair
|multienzyme complex recognises pyrimidine dimer one cut is made on each side of lesion DNA helicase removes entire portion of damaged strand leaves a gap of 12 nucleotides gap in DNA helix repaired by DNA polymerase and DNA ligase
|What is a pyrimidine dimer and what is it caused by?
|pyrimidines become chemically bonded together e.g. T-T, C-T, C-C caused by sunlight
|What is the major concern with double strand breaks?
|means no intact template strand to enable accurate repair if not repaired leads to breakdown of chromosomes into smaller fragments and loss of genes when the cell divides
|Double strand breaks can be joined by end-joining. Explain how non-homologous end-joining works
|broken ends brought together and joined by DNA ligation with a loss of nucleotides at sight of joining due to degradation from ends common in mammalian somatic cells although there's a change in DNA sequence alright for chromosomes as little of genome is essential for life
|Double strand breaks can be joined by end-joining. Explain how homologous end-joining works
|occurs in newly replicated DNA uses sister chromatid as template only happens in S and G2 phases (when SC available to serve as templates) the copying process involves homologous recombination a complete sequence restored by copying second chromosome
|Draw a table depicting some examples of inherited DNA repair defects. Include name, phenotype and affected processes
|BRCA2 breast and ovarian cancer repair by homologous recombination MutS, MutL colon cancer mismatch repair Xeroderma pigmentosum (XP) skin cancer, cellular UV sensitivity, neurological abnormalities nucleotide excision repair