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175 Cards in this Set
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LECTURE 7
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LECTURE 7
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During mitosis, chromatin is ? packed
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tightly
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when packed tightly, the chromatin ? in length, but ? in width
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Decrease
Increases |
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10nm fiber is the
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smallest
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30nm fiber is the
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largest
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DNA is packed into
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nucleosomes
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what makes up a nucleosome
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DNA+histone core
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Core DNA is
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the DNA wrapped around the histone
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Linker DNA is
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the DNA between histones
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The Histone core is composed of 4 proteins named
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H2A
H2B H3 H4 |
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The four proteins are ? charged
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+
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There is one other Histone and it is called
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H1
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What does H1 do?
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It binds to the linker DNA
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What does it do once bound to the linker DNA
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It can help condense the histones
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What makes the DNA stick to the Histones
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The DNA is - and the Histone core is + charged
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First step in forming a histone
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H3 and H4 come together to form a tetramer
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After the H3-H4 teramer is formed, what happens?
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H2A and H2B come together to form a dimer and they join the tetramer
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3 things make up a total Histone core
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2 H2A H2B dimers
1 H3 H4 tetramer |
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Complete histone core assembles ONLY when
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DNA is present
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Two models for nucleosome compaction are
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solenoid
zig zag |
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The solenoid model has its nucleosomesstacked on
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the edge
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Where is the linker DNA in the solenoid model
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burried in the middle of the superhelix, but never passes through the center
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The zig zag model has it nucleosomes stacked in
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a zig zag array
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The linker DNA must ? in a zigzag model
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pass straight through the central axis of the fiber
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What are the N-Terminal tails crucial for
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forming the 30nm fiber
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Two ways that the N-terminal tails are modified to regulate Histone function
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Acetylation
Methylation |
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What is the first step in Histone Acetylation
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Histone acetyl transferase adds acetyl groups to the N terminal tails
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What happens after these tails have been acetylated
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Bromodomain proteins associate with the acetylated tails
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Histone acetylation means
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transcriptionally ACTIVE
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What associates with acetylated histone tails?
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Bromodomain proteins
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What is the first step to Hoistone Methlyation
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histone methyl transferase adds methyl groups to the N terminal tails
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Once the N terminal tails are methlyated, what happen
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Chromodomain proteins recognize the methlyated histones and associate
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Histone methlyation means
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Transcriptionally REPRESSED
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What associates with methlyation?
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Chromodomain proteins
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After DNA replication, new nucleosome inheritance follows two rules. The rule for the H3 H4 tetramer is
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the old H3 H4 tetramer will associate with one of the daughter starnd and the other daughter strand will get a new H3 H4 tetramer
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The rule for the H2A H2B dimer
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The old H2A H2B dimer is released, so the daughter starnd can get either an old or new H2a H2B dimer
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LECTURE 8
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LECTURE 8
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First two things needed for DNA synthesis
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-dNTPs
-Primer template junction |
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what does the template strand do
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provides the ssDNA that will direct the addition of nucleotides
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What does the primer do
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it is complemntary to the template strand but shorter and it is where you start from
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The RNA primer must have ? on its end
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3'-OH group
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What does this 3'-OH group do
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it is extended by the additional of other nucleotides
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How is DNA replication powered?
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pyrophosphate hydrolysis
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The structur and function of the DNA polymerase can be visualized using three strucutres
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Palm
Fingers Thumb |
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The Palm does 2 things
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-Binds metal ions at the catalytic site (where the magic happens)
- Monitors the accuracy of base pairing |
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The Fingers do three things
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- Bind incoming dNTPs
-Then they close and form the bonds once proper dNTPs have been bound - It bends the template strand to make sure only one dNTP will be added to the next available base |
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The Thumb does two things
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- Maintains the correct position of the Primer:Template junction
- Maintains a strong interaction between the Polymerase and the template strand |
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What does this strong interaction between the enzyme and substrate do for the RNA polymerase
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it allows the polymerase to slide along the template strand and continually bind new dNTPs processivly
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What does the proofreading exonuclease do and where does it do it
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It removes incorrectly paired bases from the 3' DNA end
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Which strand of DNA is replicated?
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BOTH
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DNA Polymerase functions ONLY in the
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5'-3' direction
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What does the Primase do
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it adds small RNA primers to the template strand
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How many primers does the leading strand need?
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1
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How many primers does the lagging strand need?
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many
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Okazaki fragments are
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the stretches of DNA replicated between RNA primers on the lagging strand
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How are RNA primers removed?
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By RNAse H
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What does RNAse H do
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It cleaves the bonds between the ribonucleotides
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this makes RNAse a ?
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Exonuclease because it can only cleave at the end where there is not bond between DNA and RNA at the primer
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What happens after the primer is removed?
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DNA polymerase binds the free 3'OH end of the DNA and fills the gap
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What seals the nick left behind by DNA polymerase?
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DNA ligase
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How does DNA ligase seal this nick?
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By forming phosphodiester bonds between the 3' OH end and 5' P end
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What does the unwinding of the DNA?
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DNA helicase
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Once the Helicase goes through and unwinds the DNA and there is only ssDNA left, what happens
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The DNA must remain free of base pairing
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How is the DNA reamin free of base pairing?
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Single stranded DNA binding proteins bind the bases and dont allow other proteins to bind
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These SSBs bind, how
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cooperatively - once one binds it helps another and another and another
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What helps to releave the tension created by unwinding the DNA?
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Topo II bc it cuts both strands
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LECTURE 9
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LECTURE 9
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What is an apoenzyme
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and enzyme that require a co -factor, but does not have one
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An example of an apoenzyme is
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just the DNA polymerase core enzyme
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what is a holoenzyme
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an apoenzyme with all it's co-factors that
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what do these co-factors do?
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enhance its productivity
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What is an example of a holo enzyme
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DNA Polo III
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The main goal of DNA Pol I is
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to remove the RNA primers
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Is DNA Pol I processive?
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No
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Is DNA Pol III processive?
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yes
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What helps to increase the processitivity
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The DNA sliding Clamp
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How does the sliding clamp increase the processtivity
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by encircling dsDNA and holding the DNA polymerase onto the DNA primer:Template junction
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On the lagging strand, how does the sliding clamp opperate
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Once DNA Pol reaches the end of an Okazaki fragment the clamp is released
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First step in loading the sliding clamp
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The sliding clamp loader starts off closed
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Why does it matter that thesliding clamp loader is closed, and what happens
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If it is closed it cannot bind the sliding clamp. ATP binds the loader and it opens
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what do these co-factors do?
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enhance its productivity
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What is an example of a holo enzyme
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DNA Polo III
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The main goal of DNA Pol I is
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to remove the RNA primers
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Is DNA Pol I processive?
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No
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Is DNA Pol III processive?
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yes
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What helps to increase the processitivity
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The DNA sliding Clamp
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How does the sliding clamp increase the processtivity
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by encircling dsDNA and holding the DNA polymerase onto the DNA primer:Template junction
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On the lagging strand, how does the sliding clamp opperate
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Once DNA Pol reaches the end of an Okazaki fragment the clamp is released
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First step in loading the sliding clamp
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The sliding clamp loader starts off closed
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Why does it matter that thesliding clamp loader is closed, and what happens
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If it is closed it cannot bind the sliding clamp. ATP binds the loader and it opens
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Once the loader is opened what happens
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It binds the sliding clamp
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Once the loader has bound the sliding clap what happens
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The sliding clamp will open
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Pnce the sliding clamp is open what happens
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the sliding clamp binds around the DNA q
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once the open Sliding clamp has bound the DNA what happens
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The clamp loader hydrolyzes ATP and the loader closes, causing the Clamp to close around the DNA as well
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LECTURE 10
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LECTURE 10
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The Polymerase chain reaction is
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a powerful way to amplify DNA sequences
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First step of the PCR
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the template DNA strands must be denatured into ssDNA
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Once the ssDNA is made, what happens
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Primers are added
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why are the Primers added?
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PCR cant start without Primers
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After the Primers are added, what happens
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DNA Pol is added to extend the Primers
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This process is then..
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repeated over and over
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How many times are eukaryotic chromosomes replicated per cell divison
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once
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Chromosome replication occurs only during the ? Phase
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S
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Once an origin has been copied, it must..
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remain inactive until the cell divides
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Eukaryotic DNA replication is initiated by
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Pre-Replicative Complex (Pre-RC)
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Where is the Pre-RC formed
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G1 phase
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When is the Pre-RC activated?
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S phase
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What activates the Pre-RC
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CDKs and DDKs
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What happens after the Pre-RC is activated by the CDKs and DDKs
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DNA helicase begins to unwind the the dsDNA
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After the helicase unwinds the dsDNA what happens
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a DNA Pol/Primase complex comes in
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What does the DNA Pol/Primase complex do
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adds a primer and extends and breifly entends it with a short stretch of DNA
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Then what happens
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The primase exits breifly
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Once the Primase exits, what happens
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The sliding clamp loader and sliding clamp come in and assemble at the primer template junction and begin synthesizing the lagging and leading strand
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Will the DNA Pol/Primase come back?
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yes to help synthesize the lagging strand
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What are the CDK levels like in G1
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Low
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If the CDK levels are low in G1, what does this mean
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allows Pre-RC to form, but not enough to activate it
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How are CDK levels in S phase
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high
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If the CDK levels are high is S phase, what does this mean
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Signals for DNA replication to begin at existing pre-RC complexes
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High CDK levels also prevent
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the formation of new pre-RCs
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CDK remains high until
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the cell divides into and enters G1 phase again
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When the last RNA primer is removed in the lagging strand, how can DNA Pol fill the gap?
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IT CANT
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this means that since it cant fill the gap at the end of every single round of replication
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linear chromosomes gets shorter and shorter
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Some cells have ? that are used to ?
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Proteins that are used as primer to synthesize the last okazaki fragment
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Another way to get around this problem is by utilizing
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Telomeres and Telomerases
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At the very end the ? end extends farther then the ? end
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3' end extends farther than the 5' end
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What extends the 3'
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Telomerases
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Telomerase is actually called a
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riverse transcriptase
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It is called reverse transcriptase because
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it uses an RNA strand to synthesis a DNA strand
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Once the Telomerase synthesizes the DNA from the RNA
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it moves 6 nucleotides forward and does the same thing
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Now normal replication can take place by
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Primase
DNA Pol Primer degradation |
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LECTURE 11
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LECTURE 11
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What is a Transitions mutation
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is the change of a pyrimidine-pyrimidine, or purine-purine
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What is a Transversion mutation
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pyrimidine-purine , or purine-pyrimidine
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The mismatch repair system does what
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Increase the accuracy of DNA synthesis
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Whats the first step in this process
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MutS (scans) dimer scans the DNA of kinks produce by mismatch bases
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What does MutS do once it finds a kink
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It binds and distorts it even further
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Once this kink is more distorted, what happens
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MutL (localizes) localizes to the site
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Once MutL gets to the site, what does it do
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it recuirts MutH
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What does MutH do once it gets to the kink
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It nicks near the mismatch
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What happens once MutH nicks near the mismatch
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UvrD is a helicase and it unwinds the DNA from the nick to the mismatch
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What is the final step
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DNA Pol III and ligase close the gap
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With the help of ? , MutH will know which strand is the newly synthesized one
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Dam Methlyase
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What does Dam Methlyase do
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it adds methyl groups to A with the 5'-GATC-3' sequence of the parent strand
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how does this relate
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When DNA is newly synthesized Dam methylase has not methylated it yet
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So that means MutH binds
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to the non methlyated strand of the Hemimethylated DNA (Hemi = MutH)
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LECTURE 12
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LECTURE 12
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Three types of CSSR Recombination
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Insertion
Deletion Inversion |
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During insertion, what happens
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DNA is inserted into specific sites
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During deletion, what happens
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Deletion of a DNA segment
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The arrows are point in what direction for deleltion to occur
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Same way
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What happens in inversion
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The DNA segment is inverted, or flipped
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For inversion to occur the arrows have to be facing
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towards each other
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What do Transposons do
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They move certain genetic elements from one DNA site to another
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Transposons are present in the genome of
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All organisms
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They do/do not require duplication?
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Do not require duplication
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Why are Transposons the most common source of new mutations in organisms?
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They show very little sequence selectivity
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Three classes of Transposons
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DNA Transposons
Viral-like retrotransposons/retroviruses Poly-A retro transposons |
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If the Transposon encodes for Transposase, what happens
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It is autonomous
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What does autonomous means
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on its own
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If DNA Transposons encode for ? and ? they will be autonomous
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Transposase
Inverted repeats (Arrows facing the opposite way) |
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If a DNA Transposon does not have Transposase ...
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It will not be non-autonomous (stuck)
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Viral-like Retrotransposons/Retroviruses have ? repeats and encode for ?
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Inverted repeats (like DNA Transposons)
Reverse Transcriptase |
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Poly-A Retrotransposons have ? repeats and encode for
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DO NOT have inverted repeats (theirs face the same way)
Encode for reverse transcriptiase and endonuclease activity |
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Poly-A Retrotransposons have a distinct ? and they are know as ? and ?
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Termini
5'UTR & 3'UTR |
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LECTURE 13
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LECTURE 13
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The most simple type of DNA Transposition is
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Cut and Paste transposition
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First step of Cut and Paste
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Transposase binds the inverted repeats
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After Transposase bind the inverted repeats..
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It brings the ends together
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bring the end together forms the
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synaptic complex
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Once the synaptic complex is formed the transposons are
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cut out
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When the transposons are cut out it forms
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2 free 3'OH groups
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what do these freed 3'-OH groups do
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attach the phosphodiester bonds in the middle of the new insertion
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this new insertion is called the
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target DNA
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Once this target DNA is loaded onto the old DNA the 3' ends serve as
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primers
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the remaining nicks are
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ligated
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