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DNA Replication (Chapter 11)
Genetics Exam III
Terms in this set (139)
original DNA strand used as a template for synthesis of a new DNA strand
original strands serving as templates
newly made strands; replicated so that these copies contain the same information as the template strand
List the three models of DNA replication. Put asteric next to correct model
1) conservation model
2) semiconservative model*
3) dispersive model
two parental strands stay together after replication, two daughter strands stay together
Newly made double-stranded DNA has one parent and one daughter strand.
segments of parent and daughter strands are dispersed throughout the newly made DNA strand
Discuss Meselson and Stahls experiment used to determine which model was correct.
Why as nitrogen used?
What were the steps?
How are results analyzed/interpreted?
What were the results? What was the conclusion?
Nitrogen is found within bases of DNA and occurs in both heavy (15N) and light (14N) form.
1) grow E. coli cells in 15N medium for many generations - produces population of cells with all heavy-labeled DNA
2) switch E. coli cells to a 14N medium
3) allow time for cell growth and DNA replication - incubate cells for various lengths of time
4) lyse cells
5) analyze the density of DNA by centrifugation, using cesium chloride as gradient
Interpretation of results:
By initially growing E. coli in 15N medium, all original DNA is heavily labeled. Thus, when switched to 14N medium, all daughter strands of DNA will be lightly labeled.
1) if both strands contained 14N, DNA would be light in density and would sediment near the top of the tube
2) if one strand contained 14N and the other contained 15N, intermediate density and would sediment in middle of tube
3) if both strands contained 15N, would be of heavy density and would sediment at bottom of tube
After two generations (two rounds of DNA replication), there was a mixture of light DNA and half-heavy DNA. This is consistent with the semiconservative hypothesis.
What also follows the semiconservative model of replication?
What is the name of the segment at which DNA synthesis begin? How long is this sequence typically?
origin of replication
100-150 bp long
How many origins of replication does a bacterial chromosome have?
How does the synthesis of DNA in bacterial chromosomes occur? What does this mean for the number of replication forks?
bidirectionally - in both directions
there are two replication forks, moving in opposite directions outwards from the origin, they meet on the opposite side of the bacteria chromosome
What ends bacterial DNA replication?
when replication forks meet at opposite side of bacterial chromosome
DNA unwinds at the replication forks, replication proceeds in clockwise and counterclockwise direction until they meet on opposite side.
intertwined strands of DNA are formed
What is needed to undo catenades?
Another name for topoisomerase II
What is the origin of replication called in E. coli?
origin of chromosomal replication = oriC
What three types of DNA sequences in oriC are functionally significant?
1) AT-rich region
2) DNaA boxes- play prime role in beginning replication; about 4 to 5 bp; responsible for starting replication (NOT helicase)
3) GATC methylation sites
What three steps occur at oriC to initiate DNA replication process?
1) DnaA proteins bind to the DnaA-boxes and to each other - result: with the assistance of other proteins (e.g., HU and IHF) the region wraps around the DnaA proteins, causing a break of AT-rich region (break of HB)
2) DnaB (helicase) binds to the origin, with the assistance of DnaC
3) DNA helicase separates DNA in both directions, result: two replication forks
Role of DnaC protein
aids DnaA in the recruitment of helicase to the origin
What happens as helicase unwinds DNA? What protein binds to fix this?
positive supercoiling occurs ahead of the DNA helicase
topoisomerase II binds to alleviate positive supercoiling
Function of DNA helicase
breaks HB between DNA strands
Function of topoisomerase II
alleviates positive supercoiling
Function of single-stranded binding protein
keeps parental strands apart
Function of primase
synthesizes RNA primer
Function of DNA pol III
synthesizes a daughter strand of DNA
Function of DNA pol I
excises the RNA primers and fills in with DNA
Function of DNA ligase
covalently links Okazaki fragments together
What is involved in catalyzing the synthesis of daughter strands, what is its limitation?
cannot initiate synthesis
What initiates the synthesis of daughter strands, how?
makes small strands of RNA, about 10-12 bp. = RNA primers
once this is done, DNA pol comes and binds and continues the synthesis
What is synthesized by DNA primase? How are these synthesized?
synthesized by linkage of nucleotides via primase
What direction does DNA pol work in?
5' to 3'
What role do DNA polymerases play?
enzymes that catalyze the attachment of nucleotides to make new DNA; catalyze formation of covalent bonds between nucleotides to make daughter strands
synthesize leading and lagging strands
How many DNA pol do E. coli have?
DNA pol I, II, III, IV, and V
What are DNA pol I and III involved in?
most important because they are involved in replication of normal strands
What are DNA pol II, IV, and V involved in?
repair of damaged strands
DNA pol I
-how many subunits?
composed of a single subunit (polypeptide)
role: removes/digests RNA primers and replaces them with DNA
DNA pol III
-how many subunits?
What is the complex of all 10 subunits of DNA pol III referred to as?
DNA pol III holoenzyme
Function of alpha, beta and epsilon subunits of DNA pol III
alpha - synthesizes DNA; catalyzes covalent bond formation between incoming nucleotide and the preexisting nucleotide
beta - aka "clamp protein"; allows DNA pol to attach to template strand and slide along DNA without falling off
epsilon - involved in repair; 3' to 5' proofreading; removes mismatched nucleotides - will digest mismatched pairs and replace with normal ones
What are gamma proteins? How essential are they relative to beta proteins?
gamma proteins are "clamp loader proteins" - they do not stall or slow down the formation of DNA
a mutation in a gamma subunit is not detrimental, as its role can be taken over by other proteins
conversely, if you have a mutation in the beta subunit, nothing can take over its role
Is DNA pol I or III responsible for most of DNA replication?
Explain structure of catalytic subunit of all DNA polymerases, what does it resemble? What are the basics of how the daughter strand is formed?
resembles a human hand
template DNA is threaded through the palm of the had, the thumb and fingers are wrapped around the DNA.
incoming deoxyribonucleoside triphosphates (dNTPs) enter the catalytic side and bind to the template strand according to the AT/GC rule, then they are covalently attached to the 3' end of the growing strand
What role does the 3' exonuclease site of the DNA polymerase play?
removes mismatched bases between the incoming dNTPs and the DNA strand
What are two ways in which error is reduced during bacterial DNA replication?
1) alpha subunit will notice if there is a mismatched base pair and will prevent that nucleotide from forming a covalent bond with another nucleotide
2) if alpha subunit is not able to repair it, epsilon comes in
What are two unusual features of DNA polymerase? How are these two problems overcome?
1) cannot begin DNA synthesis by linking the first two nucleotides, solution: can elongate only a preexisting strand starting with an RNA primer, synthesized by primase
2) can only attach nucleotides in 5' to 3' direction, solution: synthesize 3' to 5' strand in small fragments
How are the the synthesis of the leading and lagging strand different?
leading strand = continuous synthesis
lagging strand = discontinuous synthesis
How is the lagging strand synthesized?
template strand is flipped to form loops, allowing DNA synthesis to occur in 5' to 3' direction
-DNA pol II must detach and jump from loop to loop - use RNA primers to synthesize small DNA fragments (1000-2000 nucleotides)
-multiple DNA primase are needed to make multiple RNA primers
-synthesis occurs away from replication fork
What are Okazaki fragments?
small DNA fragments (1000-2000 nucleotides in length) synthesized by DNA pol III using RNA primers
Compare eukaryote Okazaki fragment lengths to bacteria Okazaki lengths
we have many more origins of replication than bacteria, so our Okazaki fragments are much smaller, a few hundred nucleotides in length
What are lagging strands composed of?
How is leading strand formed?
DNA pol II comes in to 3' end and adds in 5' to 3' direction
synthesis is continuous and in direction towards replication fork
DNA pol III never detaches
only one DNA primase is necessary, it is made at the origin of replication
What three events are necessary to finalize the synthesis of Okazaki fragments?
1) removal of RNA primers
2) synthesis of DNA in area where primers have been removed
3) covalent attachment of adjacent DNA fragments
How are RNA primers removed?
DNA pol I removes RNA primers and fills resulting gap with DNA
uses its 5' to 3' exonuclease activity to digest RNA primers, and its 5' to 3' polymerase activity to replace it with DNA
How is covalent bond between two DNA fragments formed?
DNA ligase catalyzes phosphodiester bond, thereby connecting the DNA fragments.
List DNA ligase functional requirements in bacteria versus eukaryotes
bacteria - require NAD+, NAD+ is cleaved to form AMP and NMN (nicotinamide mononucleotide), which give energy to ligase
eukaryotes - requires ATP
How do incoming nucleotides come in?
in the form of deoxynucleoside triphosphate (3 phosphates)
Explain the reaction of DNA polymerase
DNA polymerase catalyzes a phosphodiester bond between the innermost phosphate group of the incoming deoxynucleoside triphosphate and the 3'-OH of the sugar of the previous deoxynucleotide.
The last two phosphates (terminal phosphates) of the incoming nucleotide are released in the form of pyrophosphate (PPi), which supplies energy for the formation of the ester bond.
What type of enzyme is DNA pol? What does this mean? What other subunit makes this possible?
a processive enzyme
means that DNA pol does not dissociate from the growing strand after it has catalyzed covalent bond of two nucleotides, it remains clamped to template primarily due to beta subunit
other associated subunit:
-gamma subunit is need for beta subunit to initially clamp onto DNA strand
What three subunits are essential for the optimal functioning of alpha and beta subunits DNA pol III?
epsilon, epsilon', and gamma subunits
Discuss the effect of processivity in the role of DNA pol III.
-in absence and presence of beta subunit...
how many nucleotides polymerized?
in the absence of the beta subunit:
-DNA pol III falls of DNA template after a few dozen nucleotides have been polymerized
-rate=20 nucleotides per second
in presence of beta subunit:
-DNA pol III stays on DNA template long enough to polymerize up to 50000 nucleotides
-rate=750 nucleotides per second
Where does termination of replication occur on E. coli?
a pair of termination sequences called ter sequences (designated as T1 and T2) on opposite side of oriC sequence
How does termination of replication occur?
tus protein (termination utilization substance) binds to ter sequence (one tus protein necessary to stop advancement of one replication fork)
tus protein stops movement of replication fork
complex formed by physically bound DNA helicase and primase
complex formed by physical association of primosome and DNA polymerase holoenzyme
Dimeric DNA polymerase
two DNA pol III proteins act in concert to replicate both the leading and lagging strands, and the two DNA pol holoenzymes form a complex that moves as a unit toward the replication fork
cells given radiolabeled compound for brief period of time (pulse), followed by excess unlabled compound (chase)
founded by Okazaki
DNA replication exhibits a high degree of what? What does this mean?
means that mistakes during the process are extremely rare
DNA pol III errors are one in one hundred million base pairs made
What are three reasons for high fidelity of DNA replication?
1) instability of mismatched base pairs
2) configuration of DNA polymerase active site
3) proofreading function of DNA pol - epsilon subunit; exonuclease cleavage of bonds, removes mismatched nucleotides; takes place after polymerization has happened
How does the instability of mismatched base pairs account for fidelity? Error rate?
the number of HB between A/T=2, G/C=3, this is unequal and causes instability
complementary base pairs have higher stability than mismatched base pairs
accounts for only part of the fidelity - has error rate of 1 per 1,000 nucleotdies
How does the configuration of DNA pol active site account for fidelity of DNA replication?
DNA pol is unlikely to catalyze bond formation between mismatched base pairs due to induced-fit phenomenon
active site preferentially binds nucleotides with correct bases; incorrect nucleotides are unable to undergo induced fit, which is necessary for catalysis; alpha subunit will prevent bond formation until the correct base pair comes along
decreases error rate to range of 1 in 100,000 to 1,000,000
How does proofreading function of DNA pol account for fidelity of DNA replication?
DNA pol can identify a mismatched nucleotide and remove it from the daughter strand, via epsilon subunit
enzyme uses its 3' to 5' exonuclease activity to remove the incorrect nucleotide
changes direction and resumes DNA synthesis in 5' to 3' direction
takes place after polymerization has happened - is HB instability and alpha subunit have not been able to contain error, epsilon comes in
At what rate do E. coli cells divide into two daughter cells?
20 to 30 minutes
What does the fast rate of bacterial cell division mean for bacterial DNA replication?
critical that DNA replication take place only when a cell is about the divide
How do bacterial cells regulate DNA replication process?
by controlling the initiation of replication at the oriC
What are the two mechanisms by which E. coli controls initiation at the oriC?
1) regulating the amount of DnaA protein
2) methylating GATC methylation site
How is the amount of DnaA protein in a cell regulated (two ways)?
1) DnaA proteins must form complex with ATP in order to have affinity for DnaA-box.
DnaA-ATP complex hydrolyzes ATP and results in DnaA-ADP complex, which no longer has affinity for DnaA-boxes -->does not bind, initiation does not occur.
Therefore, once first replication has initiated, in order to prevent an immediate second round of replication, DnaA proteins hydrolyze ATP, resulting in DnaA-ADP complex.
2) some DnaA proteins degrade or inactivate, therefore there is insufficient DnaA proteins to initiate a second round of replicaiton
What happens to DnaA-boxes immediately after initiation of first replication? Why?
the concentration of DnaA proteins must be high enough to bind to all DnaA-boxes present, so by increasing number of DnaA-boxes, there are not enough DnaA proteins to bind and second replication cannot initiate
What occurs at GATC methylation site within oriC that stalls second round of replication?
DAM (DNA adenine methyltransferase) methylates GATC methylation site, by binding to the 5'-GATC-3' sequence, and attaching methyl group onto adenine base, forming methyladenine
takes several minutes for this process to occur, and second round of replication cannot occur until GATC methylation sites on both strands are methylated - DAM must be present in both strands (both strands must have methyl groups) for replication to occur
How does DAM affect parental versus daughter strands? What is the term for this?
parental strands have methyladenine, daughter strands only have methyl - not methyladenine
this makes it hemimethylated
Who studied in vitro DNA replication? What was he awarded for this? Dates?
Arthur Kornber, 1950's
Awarded Nobel Prize in 1959
Describe Arthur Kornbers in Vitro DNA replication experiment
Hypothesis: deoxynucleoside triphosphates are the precursors of DNA synthesis
1) Control: mix proteins and radiolabeled deoxyribonucleoside triphosphates
Experiment (complete system): mix proteins, template DNA that is not radiolabeled, and radiolabled deoxyribonucleoside triphosphates
2) incubate mixtures for 30 minutes to allow for DNA synthesis to occur
3) add perchloric acid to precipitate DNA (will not percipitate free nucleotides)
4) centrifuge - free nucleotides will remain in supernatant
5) collect pellet, which contains DNA and proteins
6) count amount of radioactivity in pellet using scintillation counter
Zero DNA was formed in the control experiment, whereas DNA was formed in the complete system. This indicates that this technique can be used to measure the synthesis of DNA in vitro. Shows that template DNA is necessary to make new daughter strands.
The isolation of _________ has been crucial in elucidating DNA replication.
Provide two examples of how mutants played key role in discoveries regarding DNA replication.
1) the activity of DNA pol I is so extensive that it was originally thought to be the only enzyme responsible for DNA replication, until a mutant with a nonfunctional DNA pol I continued to undergo replication - discovery of DNA pol II and III
2) discovery of enzymes involved in replication of leading and lagging strands
Why are most mutations that block DNA synthesis lethal? What does this mean in terms of the focus of research?
lethal because DNA replication is vital for cell division
means that researchers must screen for conditional mutants (loss of function mutations), which do not always express lethality, but rather only under nonpermissive conditions (extremes)
What is brute force genetic screening? Provide an example
= screening thousands of mutants to identify those involved in a certain function
E.g., E. coli has many vital genes that are not involved in DNA replication, so in order to identify those involved in DNA replication researchers had to screen thousands of ts mutants
What is a common type of conditional mutant?
temperature-sensitive (ts) mutant
What is the case regarding ts mutants of most vital genes?
ts mutant can survive at permissive temperature, but will fail to grow at nonpermissive temperatures
Explain a strategy for isolating mutants
1) bacteria are mutagenized, increasing liklihood of mutation
2) grown at permissive temperature
3) colonies are replica plated and grown at permissive and nonpermissive temperature
*ts mutants fail to grow at nonpermissive temperatures
4) appropriate colonies can be picked from permissive temperature plates and analyzed to see if DNA replication is altered at nonpermissive temperature
**result: enables researchers to identify ts mutations that are lethal at nonpermissive temperatures
What enzyme will cause immediate suspension of replication if mutated?
Rapid-stop versus slow-stop mutations
rapid-stop=inactivated genes code enzymes need during DNA replication process, and so when in nonpermissive temperatures, they rapidly arrest DNA synthesis
slow-stop=inactivated genes are code for enzymes needed to initiate replication at the origin, so the round of replication can be completed but a second round cannot start
In what three ways was the isolation of dna mutants important?
1) allowed for identification of proteins that were defective in the mutant
2) allowed for mapping of these mutations along E. coli chromosome
3) provided important starting point for subsequent cloning and sequencing of these genes
How many origins of replication do eukaryotes have, why?
multiple, due to shape of chromosomes
long and linear, so to ensure that DNA can be replicated in reasonable time, must have multiple origins
Who provided evidence for multiple origins of replication, when?
1968 - Huberman and Riggs
In eukaryotes, how does DNA replication proceed in relation to the origin?
bidirectionally, from many origins
List three reasons that DNA replication in eukaryotes is more complex than in bacteria
1) large linear chromosomes
2) tight packaging within nucleosomes
3) more complicated cell cycle regulation
What is the origin of replication in Saccharomyces cerevisae (yeast)? Describe them
ARS elements = autonomously replication sequence
-50 bp in length (compared to 100-150 bp in bacteria)
-high percentage of A&T (greater than any other region of chromosomal DNA)
-have three or four copies of a specific sequence (similar to how bacteria has DnaA boxes)
How does eukaryotic cell replication begin? When does this occur?
with the assembly of 14 different proteins to form the prereplication complex
complex forms in G1 phase
Describe the ORC-protein complex (origin recognition complex)
-how many subunits?
-what is it's role?
-what is necessary for ORC to bind to ARS elements?
- 6 subunits
- acts as initiator of eukaryotic DNA replication
- requires ATP to bind to ARS elements
What stimulates ORC to hydrolyze ATP and bind with ARS elements?
single-strand of DNA stimulates this process
What protein is necessary to complete the process of initiating eukaryotic DNA replication?
MCM helicase - binds at the origin to complete DNA replication licensing, and only then can DNA synthesis begin
What occurs in the S phase?
22 proteins activate MCM helicase and assemble forks at the origins
What is so important about the role of those 22 proteins?
ensure that DNA replication occurs at the correct time during the cell cycle and only once per cell cycle
How many DNA polymerases do mammalian cells contain?
well over a dozen
What are the four polymerases we discuss in class (list)? What are their primary functions?
primary function = replicating DNA
What type of DNA to alpha, delta, and epsilon DNA pol replicate?
normal, nuclear DNA
What type of DNA does gamma DNA pol replicate?
What is beta involved in?
What is epsilon involved in?
replication of leading strand
What is delta involved in?
replication of lagging strand
Which DNA pol is the only polymerase to associate with primase?
DNA pol alpha
What is the role of the DNA pol alpha/primase complex? Why does it do this?
DNA pol alpha/primase complex synthesizes short RNA-DNA hybrid, containing 10 RNA nucleotides followed by 20-30 DNA nucleotides
This RNA-DNA complex is used by DNA pol delta or epsilon for the processive elongation of the leading and lagging strands, respectively. Alpha subunit pops off from the primase, and either delta or epsilon comes on.
What is a polymerase switch? When does it occur?
the exchange of DNA pol alpha for delta or epsilon
occurs only after RNA-DNA hybrid is made
Compare primer of eukaryotes to prokaryotes
primer in prokaryotic system is 10-12 bp of RNA nucleotides
in eukaryoes = 10 RNA nucleotides and 20-30 DNA nucleotides, so it is a hybrid
What initiates replication in eukaryotes?
primase, then alpha comes in and adds 20-30 DNA nucleotides
What is the clamp protein in eukaryotes that allows for processivity?
proliferating cell nuclear antigen (PCNA)
does the same function as beta subunit of pol III in prokaryotes
leading strand - PCNA allows pol to be bound to DNA
lagging strand - lot of hopping of DNA pol
What protein is involved in attaching segments in eukaryotes?
ligase, same as prokarytoes
lagging strands - attaches many small segments
leading strands - attaches two long strands
What is the role of DNA pol beta? What subunit does beta compare to in prokaryote replication?
plays role in base-excision repair, meaning it removes incorrect bases from damaged DNA
does NOT play a role in DNA replication, as it does in prokaryotes
similar to alpha subunit of prokaryotes
involved in the replication of damaged DNA
synthesize a complementary strand over the abnormal region
lesion polymerases understand what the complementary base should be, so it is able to detect errors in nucleotide sequences - when it does, replication stops and lesion-replicating pol comes in and replicates segment in correct way
only come into play when alpha, epsilon or delta encounter abnormalities in DNA that they cannot replicate over
What is a major difference between eukaryotic and prokaryotic polymerases?
eukaryotic pol are DNA dependent, meaning they need a DNA strand to be present in order to function
prokaryotic pol are NOT DNA dependent
How are RNA-DNA primer hybrids removed in eukaryotes?
Once all delta polymerase replicates all okazaki fragments, PCNA enables delta pol to hop off and fall backwards to the very first okazaki fragment, where it begins adding to the first fragment in an effort to attach the two fragments
1) polymerase delta runs into primer of adjacent okazaki fragment, pushing a portion of the primer into a short flap
2) flap endonuclease (FEN1) removes the primer
3) DNA ligase formes final covalent bond between two fragments
When FEN1 removes the flap, some of the DNA is removed as well. How is this accounted for?
Delta pol builds back those pieces of the nucleotides based on complementary nature of strand.
What is a limitation of FEN1 and how is this accounted for?
can only digest small sequences
DNA2 nuclease/helicase is capable of digesting larger sequences, so they come in and cleave the large flaps into shorter flaps, which are then removed by FEN1
Which DNA pol in eukaryotes is always at its maximum activity?
Replication doubles the amount of DNA. What must the cell synthesize more of to accommodate for this increase in DNA?
must synthesize more histones
When does the synthesis of histones occur? What is their structure and where do they associate with DNA?
occurs during S phase
histones assemble into an octamer structure and associate with newly made DNA very near the replication fork
What model does histone replication fork follow?
follows semiconservative model - retainment of old and new histones
each daughter strand has a mixture of old and new histones following DNA replication
What is a telomere and where is it located?
telomere= complex of telomeric DNA sequences and bound proteins
located on both ends of linear eukaryotic chromsomes
What do telomeric sequences consist of (4)?
1) moderately repetitive tandem arrays
2) 3' overhang that is 12-16 nucleotides in length
3) several guanines
4) many thymines
Tandem repeat versus array
repeat = longer (multiple repeats of tandem arrays)
arrays = shorter (9-16 pb long)
Are telomeric regions heterochromatic or euchromatic?
What two features of DNA polymerase make telomeric repeat sequence necessary?
1) cannot synthesize in 3' to 5' direction
2) cannot start synthesis without RNA primer
because the overhang is on 3', DNA pol cannot synthesize
What happens if this problem is not solved?
linear chromosome will become progressively shorter with each round of replication
this is seen with aging as well
Why is does chromosome length shorten with age? Is this due to reduction of telomerase activity or reduction in the number of telomerase enzymes?
do not have this answer for this still
children have higher telomerase activity, but not known if this is due to activity or presence of enzyme units
What is the function of telomerase?
prevents chromosome shortening
How does telomerase function, what are the three steps?
1) binding - binds to 3' overhang in such a way that the terminal 3 nucleotides are complementary to the RNA strand of the telomerase
2) polymerization - RNA sequence functions as a template, allowing synthesis of 6-nucleotide sequence at the end of the DNA strand; this is catalyzed by two identical protein subunits = telomerase reverse transcriptase (TERT)
3) translocation - telomerase moves to new end of DNA and attaches 6 more nucleotides
What is TERT? What is its role?
telomerase reverse transcriptase
two subunits of TERT catalyze polymerization of incoming 6 nucleotides to end of DNA sequence
What happens after telomerase adds sequence to end of DNA?
complementary strand is synthesized by primase, DNA pol, and DNA ligase
At what point does polymerization stop?
only occurs until the DNA length has been returned to original length
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