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Transcript
DNA Structure - Just as amino acids are the monomers of proteins, nucleotides are the monomers of nucleic acid - Chargaff’s Rule: the ratio of pyrimidines: purines should be 1:1 (A:T = 1:1; C:G = 1:1) - Nucleic acids are made up of PONCHO (thanks Mr. Grimm!) while proteins are full of CHNOS - Pyrimidines: single-ringed nucleotides. Think CUT Pie, or cytosine, uracil, thymine and pie-rymidine - Purines: double-ringed fatties/nucleotides. Think of GAP jeans, or guanine, adenine, pur-jeans/purines - Adenine will form three hydrogen bonds with thymine/uracil; cytosine will form two hydrogen bonds with guanine - The backbone is made up of alternating sugars (deoxyribose or ribose) and phosphates that are joined by covalent phosphodiester bonds - DNA is antiparallel, meaning that its two strands run opposite of each other. 1) 5’ → 3’: will be the lagging strand because it is in the opposite direction that DNA pol III reads. 2) 3’ → 5’: will be the leading strand because it is in the direction DNA polymerase III reads 3) The 5’ end will be the end with a phosphate group while the 3’ will be the end with the sugar. 4) The names come from the nomenclature (naming system) of sugars. The 3’ end is what it is because the 3’ carbon is free and not bound to a phosphate. How it all comes together - Nucleotides, in their lonely, single forms, have a triphosphate tail that is rich in potential energy - e.g.: in DNA: dATP (free form) → dAMP (in DNA); dGTP → dGMP; dCTP → dCMP; dTTP → dTMP - “d” means “deoxy,” which differentiates the nucleotide from being a monomer for DNA versus RNA. - The nucleotides differ in that deoxyribose is one oxygen atom short of being ribose. - e.g.: in RNA: ATP → AMP; GTP → GMP; CTP → CMP; UTP →UMP - Energy coupling: The exergonic dephosphorylation of nucleotides fuels the endergonic reaction of building covalent bonds between nucleotides and the sugar-phosphate backbone (phosphodiester bonds) OR: dephosphorylation → build covalent bonds - What builds them? DNA pol III! DNA Replication - Cells need to divide in order to reproduce, so what happens to their DNA as they divide? It has already divided and prepared for binary fission/asexual reproduction through DNA replication during the S phase, or DNA synthesis phase of its life cycle. - Replication begins at the ORI, or origin of replication 1) Helicase unzips the dress ;) to reveal the antiparallel strands of DNA: one goes 3’ to 5’ while the other goes 5’ to 3’ a) since helicase is going up the dress, the orange side will be the leading strand since you will be going in the 3’ → 5’ direction which is easier for DNA polymerase III to follow b) helicase splits the double stranded DNA by breaking the hydrogen bonds between nucleotides 2) Topoisomerase keeps the strands from twisting together 3) Single-stranded DNA binding proteins keep the DNA strands from rebinding to each other 4) RNA primase synthesizes a section of complementary RNA/RNA primers that forms a section of dsDNA/double-stranded DNA that DNA pol III can attach to. a) The primers are identifiable by their unique nucleotide (uracil) b) Required for replication of both leading and lagging strands to occur c) RNA primers are on both leading & lagging strands but more often on the lagging strand 5) DNA polymerase III begins to replicate both the leading and lagging strands: a) The leading strand is easily replicated since it runs 3’ → 5’, which is the direction DNA pol III reads. The replicated strand, however, runs 5’ → 3’ since it is a copied strand. b) The lagging strand is not as easily replicated since it runs 5’ → 3’, which is opposite of the direction DNA pol III. To accommodate for this, RNA primase makes multiple primers for DNA pol III to hop onto and follow to form Okazaki fragments. Note: DNA pol III follows the replication fork on the leading strand, but it goes in the opposite direction on the lagging strand because of DNA’s antiparallel structure 5) DNA polymerase I eats up the RNA primers (cuz you don’t want RNA in your DNA!) 6) Ligase binds the Okazaki fragments together to form a cohesive lagging strand. Note: - The purple asterisk (next the bottom right ligase) is signifying another DNA pol III that should be there as it would be forming the leading strand. - The replication fork goes both ways because the ORI/origin of replication splits the DNA strands into two parts: a 5’ → 3’ strand and a 3’ → 5’ strand. Therefore, on opposite sides of the ORI, there will be a leading and lagging strand depending on the direction of the replication fork and strand orientation. DNA pol III will always read 3’ → 5’ and build 5’ → 3’, though. - DNA pol III needs a primer to form a section of dsDNA that it can begin DNA replication on (not shown, oops) Another visual aid: Bibliography: 1) Nucleotides and sugar-phosphate backbone: http://www.phschool.com/science/biology_place/biocoach/bioprop/images/dnachem2.gif 2) DNA structure: https://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&ved=0ahUKEwi3qp_jjL7SAhVB4CYKHW7HCuAQjBwIBA& url=http%3A%2F%2Fwww.compoundchem.com%2Fwp-content%2Fuploads%2F2015%2F03%2FChemical-structure-of-DNA.png&p sig=AFQjCNGjNoBFHCgEmPUOT0435HFfijDgYg&ust=1488759851610137 3) Deoxyribose v ribose: https://www.mun.ca/biology/scarr/iGen3_02-07_Figure-L.jpg