CH 16- S: Pathogenic strain. - R: Non-pathogenic strain - He injected pathogenic strain in mouse and they died. When injected R strains, the one without the capsule, their immune system fought it. - Non-pathogenic strain into pathogenic strain=living S cells, mouse died.- After 20 years, what transformed? They added some enzymes, and found thatwhen they killed the DNA, there was no transformation and the mouse lived. - Bacteriophage: virus that attacks bacteria. - In the experiment: the radioactive showed u in liquid versus and not in the pellet. Second one, the radioactive was shown in pellet and not in mitochondria. This shows DNA was being transformed. - DNA:o DNA has one less sugar than RNAo A&G: purineso C&T: pyrimidine o 4 nucleotideso Double stranded- RNA:o Have uracil instead of thiamine o Uracil is a pyrimidine o Single stranded- A+T=C+G but Erwin didn’t know why they were equal?- After the DNA structure was figured out the answer was given. - Rosalind: whenever rays passed through DNA they bent into a certain shape. Gave an idea that DNA had a helical structure. There was an equal width/distance no matter where she looked at. Her x-ray photography gave some initial say if it had a helical structure or uniform diagram.- James Watson and Francis crick observed DNA: said it was double stranded and helical. They pretty much confirmed what Rosalind had said.o They were trying to pair these bases. Tried 2 purines together, didn’t give the 2nm and put 2 pyrimidine and got a narrow structure. Then they decided to put a purine and pyrimidine and it was always 2nm wide. There has to be a specific base pairing. o Bases/the ladder are held together by: hydrogen. Covalent bonds: keeping backbone of sugar together. Phosphodiaster bonds are the covalent bonds in the backbone.o A&T= 2 hydrogen bonds. C&G= 3 hydrogen bonds.o The strands were antiparallel. - Rosalind saw these things but were figured out after they built the structure:o 3.4 nm was the distance for each turn of DNA strand - DNA is in nucleus: nucleus diameter is probably 10 micrometer. You’re fitting 2 meter long DNA in that. - Whenever the DNA has to be replicated:o The 2 strands of DNA have to be separated. Each acts as a template to make a new strand. o Conserving part of the parent strand and making a new one- Matthew Meselson and Franklin Stahl did this experiment.- DNA separation; semiconservative model. 1 strand is new and 1 is from parent. - Helicase: unzips 2 parents strand so they can bind to a new strand. Single strand binding protein: stabilizes the 2 parent strands until a replication is done. Topoisomerase: avoids the parent strands over-coiling as its being unwinding. If the strain is coiling too much, it will break the DNA. - DNA polymerase: 11 kinds in eukaryotes. It starts adding the nucleotides to the DNA, requiring a starting point, which is created with the help of RNA primer (made by primase) - When it says going from 5 prime end to 3 prime, it’s talking about the daughter strand. Or if it says 5 prime to 3 prime end. - DNA polymerase 3 adds the nucleotides to the new strands but it cant make the new strands by itself. It only adds and needs help to take off. Primase helps DNA polymerase add those nucleotides. - RNA primer (A=U). DNA polymerase adds nucleotides from 3 prime end and cant add anything from the 5 prime end.- Lagging strand: because DNA polymerase can’t add any nucleotides from the 5 prime end. So it happens it intervals. Understand what leading (continuous) or lagging (discontinuous) is. - DNA polymerase 1: all the primers are going to be removed here and replaced with DNA nucleotides. - dNTP’s are added at the 3 prime end by DNA polymerase 3. - ATP: ribose sugar. dNTP: deoxyribose sugar- Primase that makes RNA primer is what starts the addition of nucleotides while working with DNA polymerase.- There are always going to be gaps between these fragments. DNA ligase connects the two okazarki fragments.- Whenever we’re talking about one prime to some other prime end, we’re talking about the synthesis of a new strand. - DNA polymerase 3 can also proofread itself in addition to adding nucleotides.Most of the times, it will actually put up in a way where there are not many errors. However, if it makes a mistake, then that nucleotide will be wrongly paired. If DNA polymerase doesn’t do the job, then Nucleotide excision repair are floating around fixing things. Some of these damages are not just from DNA polymerase 3 but also from any other things outside. - The process of nucleotide excision repair: Nuclease picks up the damaged part and chops it off, once it removes it, it asks DNA polymerase 3 to replace it and then DNA ligase comes and binds. - Pyrimidine dimer: when dimers are formed, they start messing up the rest of the DNA and there are a lot of mutations that occur. Dimers are related to skin cancer. - The gene doesn’t get copied if there are extra spaces left where the lagging strand doesn’t reach a primer end. So the 5 prime end is a problem. This means the chromosomes would get shorter each time it would replicate and eventually there would be nothing left to copy. This is where Telomere come into play.- You’re going to extend your lagging strand by adding telomeres at the end (repeating extra sequence that doesn’t code for anything). The telomeres will shorten too but its okay because there’s no major protein that is being coded in that particular region. It is active in gametes because they go into fertilization (conserve your DNA so they can be carried to other cells). In somatic: you tend to lose genes over time (gene erosion, relates to aging process) because there’s less telomere. - Telomere activity in cancer cells is high because then it doesn’t stop cell division. - Telomere carries its own template so it doesn’t have to copy form anyone else. It slows down the process of gene erosion. - How does the 2m long DNA fit in the nucleus?o Bacterial chromosomes are double stranded and circularo In eukaryotic: DNA needs to be packed to fit in the nuclei- Packing: start with 2m DNA, then Histone protein (made up of positively charged amino acids because DNA wraps around histone proteins. DNA has a – charge so they are together). - There are 5 diff types of histones. A nucleosome: know which nuclear proteins are used. H1 holds the two nucleosomes/DNA together outside (it’s 30 nm).- After this packing, it forms scaffolds. These are called
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