Chapter 6 Flashcards
What does it mean that DNA replication is semi-conservative?
- each product of DNA replication consists of 1 conserved strand (old), 1 newly synthesized strand
- one double helix is replicated to form 2 identical double helices
- original DNA strands remain intact through many generations
What are replication origins?
- places where dna replication begins (bacterial cells= single origin; human genome- 10000 origins spread out over the set of chromosomes)
- origin contains a specific sequence of nucleotides
- origin is recognized by a set of proteins that bind to nt sequence at origin
What are initiator proteins?
DNA replication begins with initiator proteins which pull apart the 2 strands of DNA by breaking the H-bonds between complementary bases
- this opens up the short stretch of DNA which exposes the bases of single strands
- this change in structure attracts a second set of proteins that start replication of DNA
What are some characteristics of replication forks?
- Y shaped junctions in DNA as it is being replicated
- at each origin there are 2 replication forks that move away
- at each origin there are 2 replication forks that move away from each other in opposite directions as replication proceeds
- replication is bidirectional
- as the forks are unzipped as the forks move
What is DNA polymerase?
- enzymes that synthesizes DNA
- adds nucleotides at 3’end of a growing DNA strand using old (parental) strand as a template
- catalyzes the formation of phosphodiester bonds between 3’OH of last nt with the 5’ phosphate incoming nt
Why is DNA polymerase is self-correcting?
- has proofreading activity
- it detects its own error
- after adding a nt DNA poly checks to make sure correct nt has added
- if correct DNA poly adds next nt
- if incorrect DNA poly remove incorrect nt by cutting a phosphodiester bond and the adds the correct nt
What does it mean for the replication fork to be asymmetrical?
- One DNA strand is growing overall at 3’ end while other strand is growing overall at 5’end
- DNA is only synthesized is 5’—3’
- the 2 new DNA strands are constructed in different ways
What are leading strands or lagging strand?
leading strand- DNA is synthesized continuously from 5’—-> 3’ end
lagging strand- DNA is synthesized discontinuously in separate Okazaki fragments which are synthesized 5’–>3’
What are characteristics of primase?
- required to start the synthesis of a new strand
- can begin a new strand by joining 2 nts
- makes a short stretch of RNA about 10 nts to template strand
- makes the short stretch of DNA primer, which allows for DNA polymerase to begin adding nts to 3’ end of primer
- 1 primer for the leading strand, and 1 primer for each okazaki fragment
What are nucleases?
- enzymes that remove primers
- they recognize RNA in the RNA/DNA duplex and excise it
- gap that is left behind is filled by DNA repair polymerase and uses the adjacent okazaki fragment as primer
What is the DNA ligase?
enzyme that joins together the completed fragments
- catalyzes the formation of phosphodiester bonds
- 3’OH of one DNA fragment and 5’ phosphate of adjacent DNA fragment
- hydrolyzes ATP, uses energy
What is the replication machine?
- large multisubunit protein complex
- present at replication fork
- contains the primase, dna polymerase, helicase, single stranded binding protein, and sliding clamp
- allows dna synthesis
What is helicase?
- enzyme that uses atp hydrolysis to move along DNA helix
- separates 2 strands to expose single stranded dna templates`
What are single stranded binding proteins?
proteins that bind to the single strand and prevents reformation of the base pairs; helps to keep dna in the state ready for DNA polymerase
What is the sliding clamp?
Keeps DNA polymerase attached to the DNA and forms a ring around the DNA
