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Flashcards in Chapter 6 Deck (24):

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


Replication of the ends of eukaryotic chromosomes problem: synthesis of the end of the lagging strand is hard since there is a gap

- there isn't a place to put down an RNA primer needed to start the Okazaki fragment
-if DNA can't be replicated chromosomes would get shorters with each round of replication


Solution to end of replication problem: telomeres and telomerase

-Telomeres= repeated sequences of DNA found at the ends of chromosomes which allow ends to be replicated
-Telomerase= enzyme that binds to telomeres and adds additional copies of the same DNA sequence to the end of the template strand
-Humans (GGGGTTA)
-has a short RNA complementary to telomere DNA repeat sequence.


What are the error rates of DNA polymerase w/ and w/o proofreading

w/o 1 in 10^5
w/ 1 in 10^7


What are mutations?

permanent change in nt sequence of DNA
effects of mutation depends on location


Mutations in different cells

germ cells- passed along to next generation
somatic cell- mutations will not be passed on but can result in uncontrolled cell reproduction


DNA mismatch repair

fixes error from replication and has an error rate of 1 in 10^21 nt, fixes 99 percent of errors that make it past proofreading
- repair system must be able to recognize the new strand based on its nicks that havent been sealed or chemical modifications which allow it to repair


Steps in DNA Mismatch repair

1- removal of newly synthesized strand in region of mismathc
2- resynthesis of missing strand using dna poly
3- lifate where dna ligase seals nicks in the backbone


Types of DNA Damage

1- depurination- spontaneous loss of purine (a or g), base is lost and often results in deletion
2- deamination- spontaneous loss of amino group
3- thymine dimer- covalent linkage between 2 adjacent pyrmidine bases because of uv radiation which blocks dna replication


Dna damage repair mechanism

-excision of damged dna leaving a small gap
- resynthesis= repair of DNA polymerase which fills in the gap
- ligate- seals nicks left in bottom