Terms in this set (67)
- accurate duplication of the genetic information carried in its DNA.
- DNA replication: occur before a cell can produce two genetically identical daughter cells.
permanent changes of DNA caused by copying errors and accidental damage.
Differences in DNA over time leads to...
How does the DNA strand can serve as a template?
the complementary nature of the DNA double helix allows a strand of DNA to serve as a template for the formation of a new, complementary strand of DNA
occurs between pairs of nucleotides (A with T, and G with C) that can form base pairs.
What does preferential binding enable?
This enables each strand to act as a template for forming its complementary strand.
How does DNA acts as a template for its own duplication?
- Both S strand and its complementary S' strand -can serve as a template to specify the sequence of nucleotides in its complementary strand.
- This complementarity allows for the double-helical DNA to be copied precisely.
- The copy must be carried out with speed and accuracy: in about 8 hours, a dividing animal cell will copy the equivalent of 1000 books like ECB and get no more than a letter or two wrong.
- This feat is performed by a cluster of proteins that together form a replication machine.
- each parental strand serves as the template for one new strand, and thereby each daughter DNA double helix is composed of one of the original (old) strands plus one strand that is completely new.
- Each of the two strands of DNA is used as a template for the formation of a complementary DNA strand.
What must happen in order to initiate DNA replication?
a DNA double helix is opened at its replication origin
Replication initiator proteins:
recognize specific sequences of DNA at replication origins and locally pry/pull apart the two strands of the double helix by breaking the hydrogen bonds that hold the base pairs together.
Origins of replication create a "replication fork" which is due to the antiparallel nature of the DNA double helix (think about the polarity of the DNA molecule moving 5'--> 3'in opposite directions). Replication forks move away in opposite directions from multiple replication origins in a eukaryotic chromosome
DNA is synthesized in the 5'-to-3' direction
Addition of a deoxyribonucleotide to the 3'-hydroxyl end of a polynucleotide chain is the fundamental reaction by which DNA is synthesized.
What do the nucleotides enter the reaction as?
as nucleoside triphosphates (the 5-C sugar attached to the nitrogenous base and 3 phosphate groups).
What guides the formation of a new strand of DNA that is complementary in nucleotide sequence to the template chain?
Base paring between the incoming deoxyribonucleotide and the template strand
An enzyme that catalyzes the addition of nucleotides to the free 3' hydroxyl on the growing DNA strand.
a phosphoanhydride bond
bond between the phosphate groups on the nucleoside tri-phosphate
What does the breakage of a phosphoanhydride bond create?
releases a large amount of free energy and thus provide the energy for the polymerization reaction
At a replication fork, the two newly synthesized DNA strands are of what polarities?
opposite (antiparallel nature of the DNA molecule)
Are DNA replication forks symmetrical or asymmetrical?
Why are DNA replication forks asymmetrical?
DNA polymerase can only catalyze the addition of incoming nucleotides in one direction (the 5-->3' direction, adding nucleotides to the free 3' end of the molecule). Since DNA pol can only move in one direction, but the strands are running in opposite directions, we encounter a problem within the cell. So how does the cell handle this problem? This asymmetrical characteristic establishes a discontinuity in the replication of the parental strands, creating a leading strand and a lagging strand. This is due to the fact that DNA is replicated in the 5'3' direction.
Why are Okazaki fragments formed?
Because both the new strands are synthesized in the 5'-to-3' direction, the lagging strand of DNA must be made initially as a series of short DNA strands called Okazaki fragments that later joined together.
the lagging strand
The DNA strand that is synthesized discontinuously
the leading strand
The DNA strand that is synthesized continuously
How does DNA polymerase proofread its own work?
- If an incorrect nucleotide is added to a growing strand, the DNA polymerase will cleave it from the strand and replace it with the correct nucleotide before continuing.
- First, the DNA polymerase carefully monitors the base-paring between each incoming nucleotide and the template strand. Only when the match is correct does DNA polymerase catalyze the nucleotide addition reaction.
- Second, when DNA polymerase makes a rare mistake and add the wrong nucleotide, it can correct the error through an activity called proofreading.
What is a reason that DNA is synthesized only in the 5' to 3' direction?
Does DNA polymerase contains the same or separate sites for DNA synthesis and proofreading?
How does DNA polymerase correct an error?
When an incorrect nucleotide is added, the newly synthesized DNA (red) transiently unpairs from the template (orange), and the polymerase undergoes a conformational change that moves the error-correcting catalytic site into a position where it can remove the most recently added nucleotide.
How is DNA synthesized on the lagging strand?
What can DNA Polymerase not do?
DNA polymerase cannot start a completely new DNA strand.
(an RNA polymerase)
In eukaryotes, RNA primers are made at intervals of about 200 nucleotides on the lagging strand by primase
Each RNA primer is about how many nucleotides long?
remove primers by recognizing an RNA strand in an RNA/DNA helix and degrade it
DNA repair polymerase
fills gaps left by nuclease
Join complemented fragments together by catalyzing the formation of a phosphodiester bond between the 3'-OH end of one fragment and the 5'-phosphate end of the next, thus linking up the sugar-phosphate backbones.
What does a nick-sealing reaction require energy in the form of?
ATP or NADH
DNA synthesis is carried out by a group of...
During DNA synthesis where are the DNA polymerases?
One DNA polymerase is on the leading strand and the other polymerase on the lagging strand.
What holds the polymerases together and what does this allow them to do?
- a circular protein clamp
- allows the polymerase to slide.
Located at the head of the fork, uses the energy of ATP hydrolysis to propel itself forward and thereby separate the strands of the parental DNA double helix.
Single-strand DNA-binding proteins (SSBPs)
maintain these separated strands as single-stranded DNA to provide access for the primase and polymerase.
What would happen if the SSBPs were not present?
the DNA would hydrogen bond the strands back together after the helicase enzyme was propelled forward.
Why is the DNA on the lagging strand is folded? (2)
- to bring the lagging-strand DNA polymerase molecule in contact with the leading-strand DNA polymerase molecule
- This folding also brings the 3' end of each completed Okazaki fragment close to the start site for the next Okazaki fragment.
-Therefore, the lagging strand DNA polymerase can be reused to synthesize successive Okazaki fragments.
allow the completion of DNA synthesis at the ends of eukaryotic chromosomes
An enzyme that adds a series of repeats of a DNA sequence to the 3' end of the template strand, which then allows the lagging strand to be completed by DNA polymerase.
What causes the disease sickle-cell anemia?
A single nucleotide change
How could sickle-cell anemia possibly be beneficial?
People with the disease, or those who carry one normal gene and one sickle-cell gene, are more resistant to malaria than unaffected individuals, because the parasite that causes malaria grows poorly in red blood cells that contain the sickle-cell form of hemoglobin.
Why does the likelihood of cancer increase dramatically as function of age?
Because cells are continually experiencing accidental changes to their DNA that accumulate and are passed on to progeny cells, the chance that a cell will become cancerous increases greatly with age.
What do DNA mismatch repair proteins do?
correct errors that occur during DNA replication
In eukaryotes, newly replicated DNA strands are...
What are the most frequent chemical reactions known to create serious DNA damage in cells?
Depurination and deamination
What is the purpose of nicks?
- to provide the signal that directs the mismatch repair machinery to the appropriate strand.
-A DNA mismatch distorts the geometry of the DNA.
-The distortion is subsequently recognized by the DNA mismatch repair proteins, which then remove the newly synthesized DNA.
- The gap in the newly synthesized DNA is replaced by a DNA polymerase that proofreads as it synthesizes and is sealed by DNA ligase.
Where are nicks known to occur?
in the lagging strands but also occur, although less frequently, in the leading strands (discontinuous synthesis vs continuous synthesis).
Chemical modifications of nucleotides, if left unrepaired, produce mutations
What does deamination of cytosine, if uncorrected, result in?
the substitution of one base for another when the DNA is replicated.
Depurination, if uncorrected, can lead to...
the loss of a nucleotide pair
DNA damage can be caused by:
The ultraviolet radiation in sunlight
When two adjacent thymine bases have become covalently attached to one another
The basic mechanism of DNA repair involves three steps:
excision, resynthesis, and ligation
Step 1: excision
the damage is cut out by one of a series of nucleases, each specialized for a type of DNA damage.
Step 2: resynthesis
the original DNA sequence is restored by a repair DNA polymerase, which fills in the gap created by the excision events.
Step 3: ligation
DNA ligase seals the nick left in the sugar-phosphate backbone of the repaired strand.
What does Nick sealing require?
energy from ATP hydrolysis to remake the broken phosphodiester bond between the adjacent nucleotides
How can cells repair double-strand breaks?
nonhomologous end-joining (the quick-and-dirty method)
- Most common repair method in humans
- two broken ends are simply brought together by a specialized group of enzymes and rejoined by DNA ligation.
This "quick and dirty" mechanism alters the original DNA sequence during the process of repairs
The alterations are usually short deletions
Homologous recombination allows
(more exact and precise than non-homologous end joining) the flawless repair of DNA double-strand breaks
How does homologous recombination occur?
Homologous recombination is often initiated when a double-strand break occurs shortly after a stretch of DNA has been replicated;
At that time, the duplicated helices are still in close proximity to one another (A).
A nuclease generates single-stranded ends at the break by chewing back one of the complementary DNA strands (B).
With the help of specialized enzymes, one of these single strands then invades the homologous DNA duplex by forming base pairs with its complementary strand (C).
If this sampling results in extensive base pairing, a branch point is created where the two DNA strands -one from each duplex -cross (C).
The invading strand is elongated by a repair DNA polymerase, using complementary strand as a template (D).
The branch point then 'migrates' as the base pairs holding together the duplexes break, and new ones form (E). Repair is completed by additional DNA synthesis, followed by DNA ligation (F).
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