Flashcards in Chapter 5 Deck (65):
What is a permanent change in a DNA sequence?
What is the mutation rate?
the rate at which mutations occur in the cell
What is a silent mutation?
a mutation that changes the codon but not the amino acid
what is the mutation rate of a bacteria?
one nucleotide change per 10^9 nucleotide per generation
What are fibrinogens?
proteins that do not depend on the amino sequence for survival so, you can insert any AA in their sequence and they will survive. you can use them to calculate mutations in proteins
What is the mutation rate of eukaryotic proteins?
once every 200,000 years of a protein of 400 AA
What are two ways to measure mutation rates for eukaryotes?
measure the amino acid sequence for changes
measure the DNA sequence of a closely related species
What are germ cells?
reproductive cells of sexually reproducing organisms
What are somatic cells?
any cell that is not a sex cell
What does a high mutation rate in somatic cells cause?
How fast is DNA replicated?
1000 nucleotides per second
What is DNA templating?
using the complementary strand to copy a strand of DNA.
What is the enzyme that polymerizes the hydrogen bond between a nucleotide and its complementary nucleotide?
free nucleotides serve as its substrate
What is the nucleotide that polymerized into DNA by DNA polymerase?
What is semiconservative replication of DNA?
during replication the daughter DNA receive one old strand and one new strand
What is the replication fork?
it is the y shaped area in DNA that DNA polymerase continually synthesizes complementary strands of DNA
Which way is DNA synthesis on the strands of DNA?
From the 5` to the 3` direction
What are Okazaki fragments?
sequence of DNA that is synthesized on the lagging strand about 1000-2000 base pairs long that synthesized in the 5` to 3` direction. allows for 3`to 5` direction on the lagging strand
What is the leading strand?
the strand of DNA that synthesized continuously from 5` to 3`
What is the lagging strand?
the strand that has chain growth from 3`to 5` but synthesizes only 5` to 3`. this is accomplished by discontinuous backstitching
What does the first step in proofreading the DNA sequence?
The DNA polymerase
the correct nucleotide has a higher affinity for the polymerase. it is more energetically favorable.
before the nucleotide covalently binds the correct nucleotide, it finger tightens around the active sight. this is done readily with the correct nucleotide (it double checks base pair geometry before catalyzing the bind)
What is exonucleolytic proofreading?
when a DNA polymerase cleaves of a mismatch nucleotide at the 3`OH. and inserts the correct base. tho is done by a separate domain called the 3` to 5` proofreading exonuclease. requires a previous 3` OH end of the primer strand
What are the self correcting properties of DNA polymerase dependent on?
perfectly base paired primer terminus
Why doesn't RNA require a primer terminus?
because mistakes are not passed on to the next generation. Mistakes in RNA are 100000 times higher
What is DNA primase?
a enzyme that lays down a short RNA primer that DNA polymerase needs to start DNA replication
How long are the RNA primer?
how far apart are the RNA primers on the lagging strand?
What is DNA ligase?
they remove* the RNA primer and ligate the Okazaki fragments together on the lagging strand. by sealing a broken phosphosdiester bond
What is DNA helicase?
uses ATP to pry apsrt the helix of DNA at 1000nucleotide per second
What direction does DNA helicase unwinds double-stranded DNA?
in both directions
In which direction does the helicase have the predominant?
The DNA helicase that is unwinding in the 5` to 3` direction on the lagging strand
What are Single Strand DNA-binding proteins also called?
What do Single Strand DNA-binding proteins do?
They stabilize the unwound single-stranded conformation
Straightens out the single strand on the lagging strand preventing short hair pins
What holds te DNA polymerase onto the DNA as it is moving on the strand?
How does the sliding clam prevent DNA polymerase from falling off the strand of DNA?
one part of the clamp is attached to the back of DNA polymerase. the whole ring slides along
What does the assembly of the sliding need to bind to DNA polymerase?
a clamp loader uses ATP to bind the sliding clamp onto DNA polymerase
Where is the sliding clamp for the DNA polymerase?
for the lagging strand the sliding clamp is assembled on the RNA primer. a new clamp is used for every fragment it makes
Is the protein that synthesize DNA in one single complex?
yes, the DNA moves as if it was a cloth moving along a sewing machine.
What is the strand directed mismatch repair in prokaryotes?
The A in the GATC sequence is methylated not until some time after it is incorporated into new DNA. this way the new strand can be distinguished from the old strand if repair is needed
educes errors by 100 fold
What is the directed mismatch repair in eukaryotes?
instad of methylation the DNA strands have nicks to tell the new strand from the old strand
What are DNA Topoisomerase's?
it swivels DNA so it wouldn't wind because DNA forms a helix every 10 base pairs
How does Topoisomerase's add add to the DNA?
They break the phosphodiester bond in a reversible reaction. it covalently links itself to phosphate in DNA
What does Topoisomerase 1 does?
Cleaves the phosphodiester bond and uses the bond opposite on the nick as a swivel point. Any tension will unwind the DNA in the opposite direction. use the energy in the phosphodiester bond to reseal the bond. doesn't use add. energy
What does Topoisomerase 2 does?
it binds to DNA strands that are crossed over each other. binds to both strands. uses ATP
1)breaks double helix reversibly
2)the second to cross through the gate
3)reseals break and dissociates from DNA
What is the mutation rate of DNA before proofreading?
What are the exonuclease activity of pol I?
5`-3` exonuclease (removes nucleotides)
3`-5` exonuclease (proofreading)
what is the exonuclease activity of pol II?
What is the exonuclease activity of Pol III (holoenzyme)?
3`-5` exonuclease activity
What are the subunits of holoenzyme Pol III?
Catalytic core of three subunits - alpha - epsilon-pmega
Clamp subunits - Beta Beta - for processivity
Clamp loader - Y complex
assembly subunits Theta theta
What are does the catalytic core of the holoenzyme do?
epsilon - exonuclease activity
omega- not well defines
What are the steps of DNA replication?
Unwinding by of DNA by helicase
stabilization by SSB and topoisomerases
primer sythesis by primase
leading and lagging strand synthesis
removal of RNA primer
sealing gaps by ligase
Which polymerase removes the RNA primer?
DNA pol I
What is the protein for dnaA?
what is the protein for dnaB?
what is the protein for dnaG
What is the protein for polA?
What is the protein for polB?
what is the protein for dnaE?
What resyricts the size of okazaki fragments in eukaryotes?
What are the DNA polymerases in mammals?
poly alpha (primase)
Which polymerase in mammals is used for the lagging strand?
Which polymerase in mammals is used for the leading strand?
What degrades RNA ?
how long are Okazaki fragments in mammals?