Chapter Six vocab
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Because each parental strand serves as the template for one new strand, each of the daughter dan double helices ends up with one of the original (old) strands plus one strand that is completely new; this style of replication is said to be ___________.
The process of DNA synthesis is begun by_______ that bind to specific dan sequences called ___________ ________.
Once the double helix is unzipped, the initiator proteins attract other proteins for DNA replication called ________ ________ that copy the DNA and each protein has its specific function.
At each replication origin, how many replication forks form?
DNA molecules in the process of being replicated contain Y-shaped junctions called _____ _____________.
2 y-shaped junctions, replication forks form where?
At the replication origin.
DNA replication in bacterial and eukaryotic chromosomes is (hint: both directions).
What happens at the replication fork (process of DNA synthesis)?
The movement of a replication fork is driven by the action of _________ _______.
Protein machines moe along the DNA, opening up the two strands of the double helix and using each strand as a template to make a new daughter strand.
At the heart of the protein machine is an enzyme called _____ ______ catalyzes the addition of nucleotides to the 3' end of a growing DNA strand using one of the original strands as a template.
What does DNA polymerase do?
Adds deoxyribonuclotide to the 3' hydroxy of the growing strand.
Describe formation of the new strand, use of DNA Polymerase.
DNA Polymerase guides the deoxyribonucleoside triphosphate to the template strand.
Pairs with the complementary base.
Breakage of the phosphate bond by release of pyrophosphate (2 phosphates) provides energy for polymerization reaction.
DNA Polymerase adds the 5'-deoxyribonucleotide to the 3'-hydroxyl of the growing DNA chain.
The DNA strand that appears to grow in the 3'-5', how is it actually synthesized? Is it made in 5'-3' still?
- The lagging strand is made 5'-3'.
- 1. DNA Polymerase moves backward relative to the replication fork making new short DNA strands (discontinuous or separate small pieces) called Okazaki fragments.
- 2. The fragments are later joined to form a continuous strand by DNA Polymerase, in a backstitching mechanism.
DNA disasters can be avoided because DNA Polymerase has two special qualities that increase the accuracy of replication. What are they?
- 1. Enzyme carefully monitors the base-pairing between each incoming nucleotide and the template strand and only when the match is correct does DNA Polymerase catalyze the nucleotide=addition reaction to 3'-end.
- 2. Proofreading allows the correction of wrong nucleotide addition.
When does proofreading happen?
How many domains does DNA Polymerase have, and what are they?
What happens when an incorrect nucleotide is added and does DNA Polymerase continues on?
How is the cleaving of the incorrect nucleotide from the strand done?
At the same time as DNA synthesis occurs.
Polymerization domain and Proofreading domain.
DNA polymerase cleaves the incorrect nucleotide from the strand and replaces it with the correct one before continuing.
The new (synthesized) DNA strand transiently unpairs from the template strand and the 3' end moves into the error-correcting catalytic site (E) to be removed.
Why is it important for DNA Polymerase to proceed from 5'-3'?
What happens if it worked 3'-5'?
Because that is the only way that DNA Polymerase can function as a self-correcting enzyme that removes its own polymerization error.
It wouldn't need to do the backstitching but when it correct the incorrect nucleotide, it will cause chemical dead end where the chain can't be elongated.
How are RNA polymerases (primase) and DNA polymerases similar?
Which direction does the primase work?
What is different?
- DNA polymerase makes a strand of DNA.
- RNA polymerase makes a strand of RNA serving as an RNA primer for DNA synthesis.
RNA polymerase joins together two polynucleosides together making a polynucleotide without the need for a base-paired 3' end as a starting point as in the case for DNA polymerase.
How to get DNA synthesis started at the replication fork.
It first combines two nucleosides together making a polynucleotide thenmakes a short length, 10 nucleotides long, of closely related nucleic acids (RNA) using the DNA strand as a template, is base-paired to the template providing the 3' end as a starting point for DNA polymerase thus serving as an ____________ for DNA synthesis.
- An enzyme that can begin a new polynucleotide strand simply by joining two nucleotides together without the need for a base-paired end.
- RNA polymerase or primer.
Procedure for DNA replication at the lagging strand.
After the old RNA primer and okazaki fragments have been added.
- 1. New RNA primer is added by primase.
- 2. DNA polymerase is added to the 3' end of the RNA primer.
- 3. DNA polymerase finishes the DNA fragment.
- 4. Nuclease makes the old RNA primer is erased and replaced by DNA using DNA repair polymerase.
- 5. Nick sealed by DNA ligase joining new Okazaki fragment to the growing DNA strand.
- Process repeats.
What is used to power DNA ligase to join together the Okazaki fragments on the lagging strand during DNA synthesis.
In other words,
What is used by the ligase enzyme to activate the 5'-phosphate end to the 3'-hydroxyl end of the other fragment.
- ATP on step one.
- AMP released on step two forming continuous strand.
Proteins at a ________ _________ cooperate to form a replication machine.
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