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DNA Synthesis
| Question | Answer |
|---|---|
| What is required to start polymerization to begin? | A primer strand |
| What is the DNA polymerase said to be shaped like? | A hand |
| Which end does the deoxynucleoside triphosphate bind to? | 3' OH |
| When the 5' triphosphate binds, what is a product of this binding? | pyrophosphate (2 bound phosphates) and H2O |
| Where is this reaction said to take place on the "hand"? | The palm |
| When nucleotide is attached, what happens to the DS DNA? | It translocates |
| What two sites exist on the polymerase? | Editing and proofreading |
| What happens when two bases are mis-matched? | Moves DNA from polymerizing site to editing site, removes nucleotide, and moves back to polymerizing site |
| What is a nick? | A break in the sugar-phosphate backbone |
| What is the repair of nicks called? | Exonuclease activity |
| Who studied the replication fork? | Reiji Okazaki |
| What is the pulse chase experiment? | 3-H thymine was added to dividing DNA right before a replication fork. 30" pulse showed two distinct regions of long and short DNA, which became one large group of long DNA after 20 minutes |
| What does primase do? | Adds an RNA primer to the SS lagging strand as an attaching site for DNA polymerase III |
| What does DNA polymerase III do? | Adds to the lagging strand from the primer |
| What does DNA polymerase I do? | Goes back to the RNA primers and erases the, and replaces with DNA sequence |
| What does DNA ligase do? | Joins together breaks in the sugar phosphate backbone between okazaki fragments |
| How does the ligase catalyze reactions? What does it need to do this? | It needs ATP to catalyze into AMP. The 2-phosphates are released. The AMP binds to the 5'-P end of the nick and then releases itself when a full chain is formed |
| What does DNA helicase surround? | It surrounds the single stranded leading strand of DNA, and breaks hydrogen bonds between bases. |
| What is the difference between bacterial and eucaryotic helicase? | Bacterial - 5' to 3' Eucaryotic - 3' to 5' |
| How is helicase powered? | ATP hydrolysis |
| What proteins straighten out chains? | Single-strand binding protein monomers |
| How are single strand binding proteins beneficial, other than keeping a rigid structure | They keep the DNA from misfolding and binding to itself |
| What is a series of binding proteins called? | Cooperative protein binding |
| What are binding proteins called in eukaryotes? | Replication Protein A (RPA) |
| What is a sliding clamp's function? | Helps the polymerase stay attached to the SS DNA |
| What is a clamp loader's function? | Threads SS DNA into the polymerase, and then detaches |
| What does Topoisomerase I do, in short? | Covalently attaches to the phosphate-sugar backbone, breaks the linkage, allows the structure spin once to relieve strain , and binds the backbone together |
| How are circular DNA replicated? | T-antigen |
| What attaches to the tAntigen, in order? | Topoisomerase, polymerases/primers, RPA, which eventually fall off |
| When a loop is formed, what is in the leading end? | Clamp and clamp loader |
| What attaches after the clamp and clamp loader? | The topo I and RPA again. |
| After topo I and RPA are bound to loop, what binds next and what does it do? | Poly delta attaches in front of clamp and extends the SS DNA for more copying to happen |
| After loop is being extended, what happens? | Polymerase and primer work on synthesizing a new loop |
| In short, what does topoisomerase II do? | Finishes replication of circular DNA by covalently binding to them and making them not interlocked in the end |
| What happens in the G1 phase? | Origin Recognition Complex finds origin and binds, while proteins bind to form a preReplicative complex. |
| What happens in the S phase? | CDC phosphorylates proteins to dissociate and replication begins |
| What happens in G2 phase? | DNA replication is completed |
Created by:
neeck
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