What is the effect of histone protein acetylation?
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D. Increase the transcription of target genes.
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What is the effect of histone protein acetylation?
D. Increase the transcription of target genes.
Which enzymes are responsible for removing RNA primers in eukaryotes?
Rnase H and FEN1.
Which protein is known for its ability to break hydrogen bonds?
D. DNA helicase
What are the three categories of nucleotides?
What are the three key components of nucleotide structure?
What can happen if the template strand has hairpins during DNA replication?
DNA polymerase may skip some sequence, causing deletion mutations.
How is zidovudine (ZDV) phosphorylated in the body?
By the kinases that normally phosphorylate nucleosides and nucleotides.
At which temperature does the bacterial mutant accumulate short segments of newly synthesized DNA?
At 42°C.
Which enzyme is most likely to be defective at the nonpermissive temperature in this mutant?
DNA polymerase.
What is the correct statement regarding histone proteins?
D. Nuclear DNA associates with histone proteins to form chromatin.
What can dideoxynucleosides be converted to in cells?
Dideoxynucleoside triphosphates.
What regulatory proteins control cell cycle progression into S phase?
Cyclin dependent kinases (CDKs), cyclins, p53, RB, Ras, c-myc, and E2F.
What is the key factor that the investigator neglected to include in the DNA replication reaction?
E. Topoisomerase II
What was the risk of death for twins with the shortest telomeres compared to their co-twins with the longest telomeres?
Twins with the shortest telomeres had a three times greater risk of death during the follow-up period than their co-twins with the longest telomere measurements.
What is the effect of adding ZDV to the growing 3'-end of the viral DNA chain?
It terminates the chain elongation of the DNA.
How is the leading strand synthesized in DNA replication?
Continuously in the direction of replication fork movement.
What specific function do topoisomerases perform at the replication fork?
Stabilize single-stranded DNA in the region of the replication fork.
What is the role of single-strand binding protein in DNA replication?
It prevents hairpins from forming and also prevents re-annealing of the parental strands.
What induces the cell to exit G1 phase and begin DNA synthesis in S phase?
Growth factor signaling cascade.
What is the process of DNA synthesis also known as?
DNA replication.
What is the function of DNA ligase?
To covalently join DNA fragments together by forming phosphodiester bonds.
How does DNA ligase join two polynucleotide chains?
By joining one chain with a free 3'-OH group and one chain with a free 5'-phosphate group.
Describe the process of semiconservative replication of DNA.
The two strands of parental DNA separate, and each serves as a template for synthesis of a new daughter strand by complementary base pairing.
What are the main enzymes involved in the synthesis of both leading and lagging strands of DNA in E. coli replication fork?
Helicase, primase, and two molecules of DNA Polymerase III.
What is associated with the clamp-loading protein at the E. coli replication fork?
Both molecules of DNA polymerase.
What is the role of helicase in DNA replication?
To unwind DNA.
What becomes active in S phase and phosphorylates components of the pre-replicative complex?
S-Cdk.
What enzyme covalently joins neighboring DNA fragments after RNA removal and replacement with DNA?
Ligase.
What is a nucleosome?
A repeating unit of chromatin.
What are telomeres?
Repetitive DNA sequences found at the ends of chromosomes.
What is the function of telomeres?
To facilitate the attachment of chromosomes to kinetochore during cell division.
ZDV have a higher affinity for reverse transcriptase than normal human cellular DNA polymerases, what does this allow? ?
To enable the drug to target viral replication more specifically than cellular replication.
How does each new DNA strand grow?
By the addition of nucleotides to its 3' end.
Name two pentose sugars used in nature.
Ribose and deoxyribose.
How is the lagging strand synthesized in DNA replication?
In small pieces (Okazaki fragments) backward from the overall direction of replication.
Where does the initiation of DNA replication occur?
Only at licensed origins.
What removes RNA primers in prokaryotes?
DNA Pol I.
When are RNA primers removed?
Before the joining of Okozaki fragments.
What is the relationship between stress and telomeric DNA?
Stress, including psychological stress, has been shown to increase the rate of loss of telomeric DNA.
How is shorter telomeric DNA associated with aging-related diseases?
Shorter telomeric DNA is associated with an increased risk of aging-related diseases.
What is the role of zidovudine (ZDV) in antiviral treatment?
It terminates the chain elongation of viral DNA by lacking a 3'-OH group, preventing additional nucleotides from being attached.
What is the role of topoisomerases in eukaryotic DNA replication?
Cut and reseal DNA in advance of the replication fork to eliminate supercoiling.
Which activity of topoisomerases helps in eliminating supercoiling during DNA replication?
Cutting and resealing DNA in advance of the replication fork.
What are dideoxyribose-containing nucleotides commonly used for?
Therapeutic agents or in laboratory techniques such as DNA sequencing.
What is the consequence if the base pair mismatch in the TP53 gene is not repaired prior to DNA replication?
Both daughter cells will have one copy of mutated TP53.
What is the effect of preventing the release of topoisomerase?
DNA can't be religated.
What is the 'winding problem' in DNA replication?
The supercoiling of DNA ahead of the replication fork causing torsional stress.
What is the role of telomerase in maintaining telomere length?
Telomerase maintains telomere length.
What is the directional DNA synthesis?
5' to 3' only.
What are the Draw It to Know It resources related to DNA Replication?
DNA Replication: Part I and DNA Replication: Part II.
What is the protein that makes reversible nicks in the DNA ahead of the replication fork?
Topoisomerase.
What is the characteristic feature of dideoxynucleotides?
They do not have a hydroxyl group on either the 2- or 3-carbon.
What does telomere length at advanced age predict?
Telomere length at advanced age is a biomarker that predicts survival beyond the impact of early familial environment and genetic factors.
What is the role of RNA primers in the initiation of Okazaki fragments?
RNA primers are used to initiate the synthesis of Okazaki fragments during DNA replication.
During which phase of the cell cycle does DNA synthesis occur?
S phase.
How does the lack of a 3'-hydroxyl group in dideoxynucleotides affect DNA replication?
It prevents further addition of nucleotides and terminates DNA synthesis.
What type of breaks do Type I topoisomerases make?
Single-strand nicks.
Which antibiotics inhibit bacterial topoisomerase (gyrase)?
Fluoroquinolone antibiotics like ciprofloxacin.
major workhorse in bacteria replication? mammalian cells?
bacteria pol III, mammals pol beta.
Which enzyme is missing from most cells in the body and contributes to organ failure with aging?
Telomerase.
What is a major function of telomerase?
Preserve the 3’ overhang at the ends of chromosomes during replication.
What is the characteristic of a pentose sugar?
It has 5 carbon atoms.
What type of breaks do Type II topoisomerases make?
Double-strand breaks.
What can happen if the torsional stress in DNA supercoiling is not relieved?
It can lead to a double-strand break.
What happens to telomeres with age?
They shorten.
What is the function of Gyrase in DNA replication?
Gyrase is a bacterial Type II topoisomerase, so it makes double-strand breaks..
Where can the Draw It to Know It resource for Bacteria: Growth and Genetics be found?
Which piece of DNA has the lowest melting point?
Option C: TAACCTTGGACA
How do dideoxynucleotides terminate chain growth when incorporated into DNA?
By causing chain termination due to the absence of a hydroxyl group on the 3-carbon.
When does DNA synthesis occur?
During the S phase of the cell cycle.
What happens when topoisomerase is inhibited?
It causes cell death.
What is the key structural difference between dideoxynucleotides and regular nucleotides?
Dideoxynucleotides lack a 3'-hydroxyl group.
What is semiconservative replication of DNA?
It involves retaining half of the parent molecule in each daughter molecule.
What are the two types of newly synthesized strands in DNA replication?
Leading strand and lagging strand.
What are the functions of Polymerase I (Pol I)?
Removing RNA primers, proofreading, DNA repair, and filling in gaps left by DNA pol III.
What is the role of Cdc6 and Cdt1 in G1 phase?
They recruit Mcm helicase in G1.
How are many chemotherapy regimens for cancer treatment related to topoisomerase?
They include a topoisomerase inhibitor.
What are the main types of bacterial DNA Polymerases?
I, II, III, IV & V.
What does DNA polymerase require in order to add a nucleotide?
It must have a 3’-OH on the target in order to add a nucleotide.
Does prokaryotic DNA replication occur in the cytoplasm or the nucleus?
Cytoplasm.
What is the function of the 3’ -> 5’ exonuclease activity of DNA polymerases?
To perform proofreading.
What is the function of the 3’ overhang of telomeres?
It folds back and provides structure for shelterin proteins to bind.
What is the energy requirement for the functioning of helicase?
ATP.
What happens after the replication bubble is created?
DNA polymerase and other replication proteins bind within the bubble and begin DNA replication.
What enzyme unwinds the DNA double helix during prokaryotic DNA replication?
Helicase.
Which polymerase is the major replicative polymerase for both leading and lagging strand synthesis?
Polymerase d.
What is the role of single-strand binding protein (RPA) in eukaryotic DNA replication?
Preventing hairpins and keeping parental strands from reannealing.
How do eukaryotes remove RNA primers during DNA synthesis?
Using FEN1 and RNaseH.
What is the function of DNA polymerase in eukaryotic DNA replication?
Binding to template DNA and the sliding clamp, synthesizing DNA 5’ to 3’.
What is the process of creating an identical copy of a DNA molecule?
DNA replication.
What do eukaryotes have at the ends of their linear DNA molecules?
Telomeres.
What is the process of DNA replication in prokaryotes called?
Prokaryotic DNA replication.
What is the primary function of DNA Polymerase III (Pol III)?
Synthesizing most of the DNA and has proofreading activity.
What happens to cells that do not express telomerase?
They generate progressively shorter telomeres and are likely to reach senescence.
What is the structure at the ends of eukaryotic chromosomes?
Telomeres and they consist of many tandem copies of a 6 bp DNA sequence, plus proteins that bind.
What is the function of single-strand binding proteins in DNA replication?
To bind to exposed single strands and stabilize the DNA for replication.
What is the function of topoisomerase in DNA replication?
To decrease supercoiling caused by unwinding.
Where is telomerase found?
In germline cells, stem cells, and over 85% of cancer cells examined.
What happens to origins that have the 'license' at the end of G1?
They can be activated.
What occurs after the completion of DNA replication?
The pre-replication complex is disassembled, and multiple redundant mechanisms ensure that it can't form again until the next G1, preventing re-replication of DNA.
What is the role of gyrase in DNA replication?
It is a type II topoisomerase used by bacteria.
What is the consequence of a mutation in helicase in relation to genomic stability?
High degree of genomic instability due to increased recombination.
What is the function of the protein Tert in the telomerase complex?
It acts as a reverse transcriptase.
What is the function of the clamp loader in DNA replication?
It hydrolyzes ATP as it loads the clamp onto a primer-template junction.
How does telomerase affect the telomeres in cells?
It stabilizes the telomeres, allowing the cells to proliferate indefinitely, making them immortal.
How many origins do eukaryotic chromosomes have?
Numerous origins.
In which phase of the cell cycle does DNA synthesis occur?
S phase.
What are the short, newly synthesized DNA fragments formed on the lagging strand during DNA replication?
Okazaki fragments.
What binds to origins to initiate DNA replication?
Initiator proteins.
What is the function of primase in DNA replication?
It synthesizes RNA fragments about 10 base pairs long using DNA as a template.
What happens to the RNA segment in DNA replication?
It is removed when the neighboring growing strand reaches the primer stretch.
What happens to cells lacking telomerase activity?
They undergo chromosome shortening every time they divide.
What is the function of helicases in eukaryotic DNA replication?
Unwinding the helix.
What is the name of the regulated sliding clamp in human cells?
PCNA (proliferating cell nuclear antigen).
During which phase of the cell cycle do eukaryotes undergo DNA synthesis?
S phase.
What can result in the reactivation of telomerase in a few cells?
Genomic rearrangements.
What is the term for the process in which DNA replication occurs bidirectionally from a single origin?
Bi-directional replication.
What is the purpose of having multiple origins on each chromosome?
To replicate all base-pairs within the 6-8 hours of S phase of the cell cycle.
What is the enzyme responsible for adding repetitive nucleotide sequences to the ends of eukaryotic chromosomes?
Telomerase.
What is the function of ORC (Origin recognition complex) in the cell cycle?
It binds to the origin throughout the cell cycle.
What factors affect the rate of loss of telomeric DNA?
Genetic and environmental factors.
How do dNTPs and NTPs differ at their 2’ position?
Ribonucleotides have OH, while deoxyribonucleotides have just H.
Where is Polymerase y found?
Only in mitochondria.
What happens to phosphorylated ORC during DNA replication?
It is temporarily displaced but quickly rebinds to the replicated DNA, preventing the other components of the pre-replicative complex from binding to the phosphorylated form of ORC.
What can the end replication problem result in?
Disruption of the cell cycle or cell aging (senescence).
What is the non-proliferative state called when most cells enter due to loss of telomeric DNA?
Senescence.
How does the exonuclease activity of DNA polymerases contribute to proofreading?
It chews away misincorporated nucleotides.
What is the function of DNA Ligase in eukaryotic DNA replication?
Sealing the nicks.
What are the enzymes responsible for unwinding the DNA double helix during replication?
Helicases.
What is the approximate length of Okazaki fragments?
Approximately 1,000 nucleotides long.
What is the end replication problem in eukaryotes?
Primers cannot be placed at the very end of the parental linear DNA.
What enzyme joins the Okazaki fragments together in DNA replication?
DNA ligase.
How can increased numbers of senescent cells affect repair capacity?
It can cause decreased capacity for repair due to depletion of stem cell populations.
What is a key difference in the number of origins for DNA synthesis between eukaryotes and prokaryotes?
Eukaryotes have multiple origins, while prokaryotes have a single origin.
What are the functions of telomeres?
Protect ends of chromosomes from degradation and fusion, and distinguish ends of intact chromosomes from broken ones.
What is the function of the proofreading mechanism in DNA replication?
To correct misincorporated nucleotides.
What are the functions of Polymerase e?
DNA repair and replicative polymerase that may substitute for d in certain cases.
What are the specific sites on the DNA molecule where replication begins?
Origins of replication.
Is DNA replication unidirectional or bi-directional from each origin?
Bi-directional from each origin.
How do topoisomerases relieve supercoiling in DNA?
By making reversible nicks in the DNA.
What is the role of topoisomerase in E. coli replication?
It acts as a swivel ahead of the fork.
Which cells do not express telomerase at significant levels?
Most somatic cells.
What is the role of phosphorylated Mcm in DNA replication?
It acts as an active helicase, separating the strands to create the replication bubble and moving away from the origin with the replication forks.
What is the function of the sliding clamp in DNA replication?
It holds DNA polymerase to the template DNA as long as it's moving, but releases it when double-stranded DNA is reached.
What is the specific eukaryotic helicase involved in DNA replication?
MCM.
How can an increased rate of loss of telomeric DNA be related to disease?
It can be a cause and/or an effect of disease.
What structure does the sliding clamp form around DNA?
A ring-like structure.
What is the function of primase in eukaryotic DNA replication?
Making RNA primer.
What is the role of DNA Pol I in prokaryotic DNA synthesis?
To remove RNA primers.
What is the role of RNAse H & FEN1 in eukaryotic DNA replication?
Removing RNA primers, gaps filled by DNA pol.
How many origins do prokaryotic chromosomes typically have?
A single origin.
How many origins do humans have per chromosome?
Approximately 220 origins.
What are the enzymes responsible for relieving the strain of unwinding DNA during replication?
Topoisomerases.
What is the purpose of relieving supercoiling in DNA?
To release the tension and prevent double-strand breaks.
What happens behind the E. coli replication fork?
RNA primers are removed by DNA polymerase I and Okazaki fragments are joined by DNA ligase.
What does the combination of ORC and Mcm form in G1 phase?
Pre-RC (pre-replicative complex) which 'licenses' the origin at the end of G1.
Do telomeric DNA encode any proteins?
No, telomeric DNA doesn’t encode any proteins.
What effect do high levels of reactive oxygen species have on telomere attrition?
They increase the rate of telomere attrition.
What prevents further proliferation in response to loss of telomeric DNA?
Cell cycle checkpoint mechanisms.
What is the term for the process of making two identical DNA molecules from one original DNA molecule?
Semi-conservative replication.
What happens once the G-rich strand has been lengthened by telomerase?
Primase activity of DNA pol α can use it as a template to synthesize an RNA primer.
What are the enzymes responsible for synthesizing new DNA strands during replication?
DNA polymerases.
What is the function of helicase in DNA replication?
Unwinds strands of DNA at the replication forks.
What increases DNA polymerase processivity?
A sliding clamp.
What is the shape of the prokaryotic DNA replication origin?
Circular.
What is the role of Polymerase a?
It is involved with the initial synthesis of DNA strands off RNA primers.
What is the function of DNA polymerase in prokaryotic DNA replication?
To synthesize new DNA strands.
What are the symptoms of Bloom syndrome?
Short stature, photosensitivity, multiple health problems, and increased risk of cancer.
What happens if the cell cycle checkpoint fails in response to loss of telomeric DNA?
Cells continue to proliferate without telomeres, leading to genomic instability and crisis.
What is the function of the RNA Terc in the telomerase complex?
It acts as a template for reverse transcriptase activity.
What do eukaryotes need to do during DNA synthesis that prokaryotes do not?
Displace and reassemble nucleosomes.
What type of DNA tends to be replicated early in S phase?
Transcriptionally active DNA (euchromatin).
How are gaps left by removal of primers filled in at the ends of linear DNA?
By DNA polymerase using adjacent newly synthesized DNA to provide the 3’OH.
How often is an incorrect nucleotide incorporated during DNA replication?
About 1 in 100,000 nucleotides.
What triggers cellular senescence?
Loss of telomeric DNA.
What is Bloom syndrome?
A rare disorder caused by mutation of a helicase.
What is required for the assembly of the clamp around the DNA?
A clamp loader.
What is the role of clamp loader in eukaryotic DNA replication?
Loading sliding clamp around 3’ end of the primer.
How does the C-rich RNA template in telomerase base-pair with telomeric DNA?
It base-pairs with the G-rich, single-stranded 3′-end of telomeric DNA.
In which direction does the reverse transcriptase in telomerase synthesize DNA?
In the usual 5′→3′ direction.
What is the usual structure of prokaryotic genomes in relation to DNA ends?
Circular and do not have telomeres.
How is the primer extended after being synthesized by DNA pol α?
It is extended by DNA pol α and then removed by nucleases.
What ensures that each origin is activated only once per cell cycle?
Licensing of origins in G1, and removal of the license from origins already used.
What type of DNA tends to replicate late in S phase?
Constitutive heterochromatin.
What type of bond links each successive nucleotide to the growing DNA chain?
Phosphodiester bond between the phosphate group on its 5' carbon and the hydroxyl group on the 3' carbon of the nucleotide added in the previous step (5'-> 3').
How do ddNTPs and dNTPs differ at their 3’ position?
Dideoxyribonucleotides have just H, while deoxyribose has OH.
what are the main types of eukaryotic DNA polymerase?
alpha, beta, delta, gamma, epsilon
which disease is ZDV used against?
patients with AIDS.
DNA polymerase provides what?
high accuracy, high speed and processivity.
what does fidelity requires?
proofreading.
what does double-strand breaks lead to?
cell death by apoptosis.
What is the role of RNA primers in DNA replication?
They initiate DNA replication.
What can start synthesis from scratch?
RNA polymerases.
in bacteria, primase part of a complex is called?
primosome.
In eukaryotic cells, where is primase found? what is its purpose?
in the DNA Polymerase alpha complex. it initiates DNA replication.
