Chapter 10: DNA Synthesis Flashcards
A method of replication where each replicated DNA molecule would consist of one “old” and one “new” strand.
Semiconservative Replication of DNA
A method of replication where two newly created strands then come together, and the parental strands reassociate.
Conservative Replication
A method of replication where the parental strands are dispersed into two new double helices following replication.
Dispersive Replication
True or False. Conservative Replication is the most complex of the three possibilities and is therefore considered to be least likely to occur
False. Dispersive Replication
Samples are forced by centrifugation through a density gradient of a heavy metal salt, such as cesium chloride.
Sedimentation equilibrium centrifugation (Meselson-Stahl Experiment) - an experiment providing strong evidence that semiconservative replication is the mode used by bacterial cells to produce new DNA molecules.
Is a common technique that, when applied cytologically, pinpoints the location of a radioisotope in a cell.
Autoradiography
At each point along the chromosome where replication is occurring, the strands of the helix are unwound, creating what structure?
Replication Fork
Refers to the length of DNA that is replicated following one initiation event at a single origin.
Replicon
The region in E. coli DNA where replication is initiated
oriC
True or False. DNA synthesis in bacteriophages and bacteria originates at a single point, the entire chromosome constitutes one replicon.
True
True or False. Replication in bacteria and viruses is bidirectional, moving away from oriC in both directions
True
Terminal region in a replicating bacterial or viral DNA.
ter
A single polypeptide containing 928 amino acids initially isolated from E. coli that is able to direct DNA synthesis in a cell-free (in vitro) system.
DNA polymerase I
Two major requirements for in vitro DNA synthesis under the direction of DNA polymerase I:
- All four deoxyribonucleoside triphosphates (dNTPs)
2. template DNA
True or False. As the two terminal phosphates of the deoxyribonucleoside triphosphate precursor are cleaved during DNA synthesis, the remaining phosphate attached to the 5′-carbon is covalently linked to the 3′-OH group of the deoxyribose to which it is added.
True
A mutant strain of E. coli that was deficient in polymerase I activity.
polA1
An existing RNA strand that can be elongated by polymerases I, II, and III.
Primer
True or False. Polymerase I, II, and III can initiate chain synthesis.
False. They all can’t.
True or False. Polymerase I, II, and III exhibit 5’-3’ polymerization.
True
True or False. Polymerase I, II, and III do not exhibit 3′ to 5′ exonuclease activity.
False. They all exhibit 3′ to 5′ exonuclease activity.
True or False. Only Polymerase I exhibit 5’-3’ exonuclease activity.
True
Encoded by a gene whose transcription is activated by disruption of DNA synthesis at the replication fork.
Polymerase II
Are involved in various aspects of repair of DNA that has been damaged by external forces, such as ultraviolet light.
DNA polymerase II, IV and V
The active form of the DNA Polymerase III.
Holoenzyme
Imparts the catalytic function of the holoenzyme and is made of the alpha subunit, along with subunits epsilon and theta.
Core enzyme
Subunit of the holoenzyme that is responsible for DNA synthesis along the template strands (5’-3’ polymerization activity).
Alpha subunit
Subunit of the holoenzyme (DNA polymerase III) that is responsible for 3’-5’ exonuclease activity that is essential for proofreading
Epsilon subunit
Pairs with the core enzyme and facilitates the function of a critical component of the holoenzyme called the sliding DNA clamp. Is formed by the gamma, delta, delta prime, chi, and nu subunits
Sliding clamp loader (y complex)
Made up of multiple copies of the beta subunit, taking on the shape of a donut, whereby it can open and shut, to encircle the unreplicated DNA helix. It leads the way during synthesis, maintaining the binding of the core enzyme to the template during the polymerization of nucleotides.
Sliding DNA clamp
Measure the length of DNA that is replicated by the core enzyme before it detaches from the template.
Processivity
The helicase that is responsible for the initial step in unwinding the helix.
DnaA protein
True or False. The binding of DnaA protein to the several 9mers of the oriC facilitates the subsequent binding of DnaB and DnaC proteins that further open and destabilize the helix.
True
A group of proteins responsible for the unwinding of DNA helix.
Helicase (DnaA, DnaB, DnaC proteins)
Stabilizes the DNA upon unwinding of the helicases.
Single-stranded binding proteins
This is produced due to coiling tension produced by the unwinding process.
Supercoiling
Relaxes supercoiling by making either a single- or double-stranded “cuts” and also catalyzes localized movements that have the effect of “undoing” the twists and knots created during supercoiling.
DNA gyrase
DNA gyrase is a member of larger group of enzymes referred to as?
topoisomerases
The DNA, the polymerase complex, and associated enzymes make up an array of molecules that participate in DNA synthesis. These molecules are collectively known as?
Replisome
A short segment of RNA (about 10 to 12 ribonucleotides long), complementary to DNA, is first synthesized on the DNA template. This molecule is called?
Primer
Directs the synthesis of the primer it does not require a free 3’ end to initiate synthesis.
Primase
Before terminating the replication process, the primer is clipped out and replaced with DNA nucleotides. This process is mediated by what polymerase?
DNA polymerase I
The strand at which replication is discontinuous.
Lagging strand
The strand that is being replicated in the 3’ – 5’ direction (same direction as the replication fork) and produces a continuous DNA product.
Leading strand
Segmented fragments of DNA resulting in discontinuous synthesis in the lagging strand.
Okazaki fragments
Capable of catalyzing the formation of the phosphodiester bond that seals the nick between the discontinuously synthesized strands (Okazaki fragments).
DNA ligase
Imparts the potential for polymerases to detect and excise a mismatched nucleotide (in the 3′ to 5′ direction).
3’ to 5’ exonuclease activity
True or False. To facilitate the rapid synthesis of large quantities of DNA, eukaryotic chromosomes contain multiple replication origins.
True
Two of the four subunits of this enzyme synthesize RNA primers on both the leading and lagging strands.
Pol a enzyme
True or False. Pol a possess a high processivity.
False.
Once the primer is in place, Pol alpha dissociates from the template and is replaced by Pol delta or epsilon. This process is called?
Polymerase switching
Synthesizes DNA in the lagging strand, has a much higher processivity and exhibits 3’ to 5’ exonuclease activity.
Pol d
Synthesizes DNA in the leading strand, has a much higher processivity and exhibits 3’ to 5’ exonuclease activity.
Pol e
Found exclusively in mitochondria, synthesizing the DNA present in that organelle.
Pol gamma
True or False. Before polymerases can begin synthesis, nucleosomes and other DNA-binding proteins must be stripped away or otherwise modified to allow the passage of replication proteins.
True
True or False. Nucleosomes form immediately after new DNA is synthesized at replication forks. Nucleosomes are disrupted just ahead of the replication fork and that the preexisting histone proteins can assemble with newly synthesized histone proteins into new nucleosomes.
True
Move along with the replication fork to assemble new nucleosomes
Chromatin assembly factors
True or False. In eukaryotic DNA, it is the 3’ ending that is the G-rich strand.
True
The G-rich single-stranded
tails are capable of looping back on themselves, forming
multiple G-G hydrogen bonds to create what is referred to as?
G-quartets
G-quartets form a looping structure known as? This structure, in combination with specific proteins that bind to them, essentially close off the ends of chromosomes and make them resistant to nuclease digestion and DNA fusions.
t-loop
What component of the telomerase serves as both a “guide” to proper attachment of the enzyme to the telomere and a “template” for the synthesis of its DNA complement.
telomerase RNA component
Synthesis of DNA using RNA as a template is called?
Reverse transcription
The catalytic subunit of the telomerase enzyme is called?
telomerase reverse transcriptase
