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