DNA Synthesis S Genes 09 23 2013 F Chromosomes are made of a combination of a DNA strand and two copies of each from each parent They look that way because each DNA molecule is wrapped around proteins called histones and knots up to form a condensed chromosomes The DNA is formed as a double helix with a sugar phosphate backbone and used complementary base pairs joined by hydrogen bonding T A G C o T and A are always paired together and the same goes for G and C DNA replication strands are semi conservative meaning that they go in the opposite direction forming two strands one is new and the other is an original based on the base pairing rules These strands are anti parallel and the sugar strands consist of carbonated phosphate that attaches to the backbone of the DNA The DNA molecules are surprisingly flexible and when ribose sugars bends it s bonds you will either get a chair conformation or a boat conformation The critical feature about forming DNA is forming the deoxyribonucleotides no oxygen and in RNA oxygen is present DNA polymerase builds new strands of DNA enforces base pairing rules and creates new phosphodiester bonds It will only work when you have a strand of DNA and then one 3 prime hydroxyl with some of the template missing The primes are the number of carbons in the sugar This allows DNA synthesis to start and the primers are normally RNA not DNA DNA synthesis only happens when the strands separate and this happens in multiple places on the double helix origins of replication used in the S phase of the cell cycle Helicase separates the strands of the double helix Single strand binding protein stabilizes DNA and keeps them from binding back together Topoisomerase relieves unwinding tension in the double helix by breaking one of the bonds of the two strands and flips it to relieve the tension and then connects it as the tension leaves Primase builds the RNA primer made of 8 10 bases to provide the initial 3 prime hydroxyl Leading strand is responsible for starting DNA synthesis and this is called continuous DNA replication The lagging strands is responsible for going in front of the leading strand and then connect back to the leading strand DNA polymerase III 5 to 3 synthesis primer builds off the hydroxyl DNA polymerase I chew out the RNA of the primer and fill it in with DNA DNA ligase creates the final bond closing off DNA synthesis Cancer 09 23 2013 Hallmarks of Cancer Self sufficiency for growth signals can turn on and keep the cell on activating the division Failure to respond to growth control signals Sustained angiogenesis they can grow their own blood supply by branching the blood vessels nearby into them in order to get oxygen and nutrients stopping oxygen nutrient diffusion Evasion of programmed cell death Rebuilds the end of their enzymes in order to keep growing Limitless replicative potential Some cancer cells when dividing can leave behind chromosomes and others can make 4 poles when getting to the metaphase and anaphase checkpoint instead of the normal 2 Over replication of the chromosomes have a mess of the genes and these cause major problems in the cell Tissue invasion and metastasis Metastasis cancer cells that have spread from the initial site either through the blood stream or through the rest of the body Genomic instability high mutation rate Don t copy chromosomes incorrectly and their genomes are wrong as well Resistant to treatment through mutation to the chemotherapy agent Metabolic changes Cachexia cancers of the esophagus and the lungs cause a wasting disorder where you are unable to eat and gain the nutrients you need you literally waste away and end up looking anorexic o Lung cancer patients have clubbing of the fingers and cachexia Remember that cancer is not just limited to humans but goes to other mammals Sun cancer different proteins that are responsible for repairing damage from harmful UV rays 9 central genes and when exposed to sunlight the genes are unable to repair the damage This type of cancer is inherited Double strand break of chromosomes It is identified by proteins that stick to the broken ends Non homologous ends ends that are near each other just rejoin to one another even though they are wrong Homologous recombine the correct chromosome to the other one and keeps the chromosome more or less the same P53 is responsible for this type of repair Benzo a pyrene potent carcinogen that is responsible for lung cancer Mutating the DNA genes and targets specific places on the chromosome does this Non random mutation Base 157 248 and 273 are the favorite places of this carcinogen Most cancer cells will target p53 first because it is responsible for programming cell death or DNA repair PCR 09 23 2013 Plasmids used in the cloning of DNA fragments and they contain multiple cloning sites MCS MCS they can be cut open with restriction enzymes and DNA fragments are then inserted into the site Ex pUC19 cloning site that contains BamH1 site and EcoR1 site 3 686 bp long In cloning there are individual molecules that you can make many copies of them and when put back into the MCS they can be put into different orientations depending on the way it was put in PCR amplifies DNA fragments Transcription factors and Enhancers 09 23 2013 Endo16 gene that contributes to the formation about a sea urchins gut and one of the first gene expressions we have seen Expressed early in time and space To do transcription the DNA strands have to be separated in order to provide a template and the RNA polymerase then creates a new molecule using the base pairing rules and references the template To build the RNA molecule you must have phosphodiester bonds using either the 5 or 3 base pairs RNA polymerase separates the DNA strands and builds the phosphodiester bonds using the base pairing rules It will only make one strand Arthur Kornberg won the Nobel Prize for figuring out DNA polymerase 1959 Roger Kornberg Arthur Kornberg s son won the Nobel Prize for RNA polymerase 200 The promoter or regulatory sequence is responsible for making binding sites for various transcription factors Combinatorial regulation or transcription Multiple transcription factors are required for gene expression Transcription factors activate or block gene expression in specific combinations DNA sequences of promoter regions of genes and the presence of absence of specific transcription factors determined by gene expression Promoter fusion gene promoter changes the location Tetra cyclin