flashcards for exam
What is the key feature of semi-conservative DNA replication?
Each new DNA molecule contains one original strand and one new strand.
During which phase of the cell cycle does DNA replication occur in eukaryotes?
It occurs during the S phase.
What factors carry out DNA replication in prokaryotes?
Sigma factors.
Are the enzymes involved in DNA replication in eukaryotes similar to those in prokaryotes?
Yes, many similar enzymes are required in eukaryotes.
What does semi-conservative DNA replication mean?
Each new DNA molecule contains one original (parent) strand and one newly synthesized strand.
How does semi-conservative replication differ from conservative and dispersive replication?
Conservative: Keeps the original DNA intact, producing a completely new molecule.
Dispersive: Produces DNA with interspersed original and new segments.
Semi-conservative: One strand of the original DNA is retained in each new molecule.
What key experiment demonstrated the semi-conservative nature of DNA replication?
The Meselson-Stahl experiment using isotopes of nitrogen (N-15 and N-14) and density gradient centrifugation.
What is the role of the parent DNA strands during semi-conservative replication?
The parent strands act as templates for synthesizing the new complementary strands.
What enzyme is primarily responsible for adding new nucleotides during semi-conservative replication?
DNA polymerase.
What is the role of helicase in DNA replication?
Helicase unwinds the double helix to separate the two parent strands.
How is the leading strand synthesized during semi-conservative replication?
It is synthesized continuously in the 5’ to 3’ direction.
How is the lagging strand synthesized during semi-conservative replication?
It is synthesized in short fragments called Okazaki fragments, which are later joined by DNA ligase.
Why is DNA replication considered accurate and reliable?
DNA polymerase has proofreading ability, correcting errors during replication.
What stabilizes the single-stranded DNA during replication?
Single-stranded binding proteins (SSBs).
What is the role of primase in DNA replication?
Primase synthesizes RNA primers, which provide a starting point for DNA polymerase.
Why do eukaryotes use semi-conservative replication?
Eukaryotes use semi-conservative replication to maintain a high degree of similarity between generations. With such large genomes, low fidelity could be fatal.
What is semi-conservative replication?
Semi-conservative replication is the process where each new DNA molecule consists of one original (parental) strand and one newly synthesized strand.
Why is semi-conservative replication important?
It ensures genetic stability by preserving one original DNA strand, minimizing errors during DNA replication, and maintaining fidelity across generations.
How does semi-conservative replication help eukaryotes with large genomes?
It maintains high fidelity during DNA replication, preventing errors that could be fatal given the size and complexity of eukaryotic genomes.
What are the key enzymes involved in semi-conservative replication?
Key enzymes include DNA helicase (unwinds DNA), DNA polymerase (synthesizes new strand), and DNA ligase (seals fragments).
How was the semi-conservative nature of DNA replication proven?
It was proven through the Meselson-Stahl experiment, which used isotopes of nitrogen to demonstrate that new DNA molecules retain one original strand and one new strand.
What could happen if DNA replication had low fidelity in eukaryotes?
Low fidelity could lead to mutations and errors in the genome, potentially causing fatal consequences for the organism.
What is genetic integrity, and why is it essential in replication?
Genetic integrity ensures the accurate inheritance of nucleic acid sequences, preserving stability and minimizing harmful mutations in both somatic and germ-line cells.
What role do germ-line sequences play in a population?
Germ-line sequences introduce genetic variation within a population while mechanisms exist to limit replication errors that could lead to changes in germ-line DNA.
How do errors in replication affect germ-line and somatic cells differently?
Errors in germ-line cells can be passed to offspring and affect the entire lineage, while errors in somatic cells only impact the individual.
What mechanisms are in place to maintain genetic integrity during replication?
DNA repair systems, proofreading by DNA polymerase, and other cellular mechanisms ensure errors are minimized and genetic integrity is maintained.
How does genetic integrity balance stability and variation?
It preserves essential DNA sequences for survival while allowing controlled genetic variation through mutations in germ-line cells, supporting evolution and adaptability.
What happens when there are changes in nucleic acid sequences?
Changes in nucleic acid sequences can lead to:
* No changes in the amino acid sequence.
* Changes in amino acid sequences, which may affect protein shape, function, or expression.
What are the possible outcomes of changes in amino acid sequences?
Changes in amino acid sequences can:
* Alter protein shape, affecting molecular interactions.
* Change protein function, disrupting metabolic pathways or signaling.
* Modify protein expression levels, leading to overactivity or underactivity.
Why can changes in protein shape be problematic?
Altered protein shape affects its ability to interact with other molecules, potentially disrupting biological processes and causing disease.
How do changes in protein function affect the body?
Changes in protein function can disrupt critical biological processes such as metabolism, signaling, and immune responses, leading to conditions like cancer or metabolic disorders.
What are the effects of altered protein expression levels?
Altered protein expression levels can:
* Cause imbalances in cellular functions.
* Lead to systemic health effects, such as overactive or underactive biological processes.
How can changes in nucleic acid sequences negatively impact the body?
Changes in nucleic acid sequences may:
* Alter codons, leading to production of faulty or nonfunctional proteins.
* Introduce premature stop codons, causing truncated proteins.
* Generate proteins with altered functions that disrupt biological pathways.
What are the possible biochemical reasons changes in amino acid sequences can be harmful?
Changes in amino acid sequences can:
* Disrupt protein folding, leading to misfolded proteins that cannot function.
* Alter active sites in enzymes, reducing or eliminating catalytic activity.
* Affect binding domains, preventing interactions with other molecules or receptors.
Why can protein misfolding be harmful?
Protein misfolding can:
* Lead to aggregation, forming toxic clumps (e.g., amyloids in Alzheimer’s disease).
* Prevent proteins from reaching their functional sites in the cell.
* Trigger cellular stress responses like the unfolded protein response (UPR).
How do changes in protein shape affect biochemical pathways?
Altered protein shape can:
* Impair interaction with other proteins or DNA, disrupting complex assembly.
* Prevent recognition by signaling molecules, halting cellular communication.
* Reduce the stability of the protein, increasing degradation rates.
What are the consequences of altered protein function due to amino acid changes?
Altered protein function can:
* Cause enzymes to lose specificity, leading to unregulated or inappropriate reactions.
* Create dominant negative effects where the altered protein interferes with normal protein functions.
* Enable proteins to gain toxic functions, damaging cells and tissues.
Why can changes in protein expression be detrimental?
Changes in protein expression can:
* Cause an overproduction of proteins, overwhelming cellular systems (e.g., cancer-promoting oncogenes).
* Lead to insufficient production of essential proteins, impairing normal functions (e.g., hormone deficiencies).
* Disrupt cellular balance, affecting energy metabolism and homeostasis.
How do biochemical changes in post-translational modifications affect protein function?
Altered post-translational modifications (e.g., phosphorylation, glycosylation) can:
* Impact protein stability and degradation.
* Modify protein localization within the cell.
* Impair or enhance protein interactions, altering cellular signaling networks.
What structures preserve DNA integrity by providing a protective environment for chromosomes?
The nuclear envelope.
What mechanism ensures accurate duplication of DNA during cell division?
Semi-conservative replication mechanism.
How does chromatin structure contribute to DNA preservation?
Chromatin condenses when genes are not active, protecting DNA from damage.
What are telomeres, and why are they important for DNA integrity?
Telomeres are repeating sequences of DNA at chromosome ends that shorten with age. They are replicated by a mechanism different from the rest of the chromosome to prevent loss of genetic material.
What role do centromeres play in DNA preservation?
Centromeres are repetitive sequences of DNA that are highly packaged to provide a robust attachment site to the mitotic spindle during cell division.
Why are telomeres and centromeres critical for chromosomal stability?
Telomeres prevent genetic material loss during replication, while centromeres ensure accurate chromosome segregation during cell division.
What happens to telomeres as organisms age?
Telomeres shorten with age, potentially impacting the cell’s ability to replicate its DNA accurately.
How does the nuclear envelope help preserve DNA integrity?
The nuclear envelope provides a protective environment for chromosomes, shielding DNA from damage caused by external factors such as harmful molecules or physical stress.
How does chromatin condensation preserve DNA?
Condensation of chromatin when genes are not active reduces exposure to enzymes and other factors that could damage or alter DNA, ensuring its stability.
How does semi-conservative replication preserve DNA integrity?
Semi-conservative replication ensures that each new DNA molecule retains one original strand, providing a template for accurate duplication and reducing errors during replication.
How do telomeres protect chromosome ends during replication?
Telomeres are repetitive DNA sequences at the ends of chromosomes that prevent the loss of essential genes during replication by acting as a buffer zone. They also protect DNA ends from being recognized as damage.
How does the unique replication mechanism of telomeres contribute to DNA integrity?
Telomeres are replicated by a specialized enzyme, telomerase, which helps maintain their length and prevents chromosome degradation over successive cell divisions.
What role do centromeres play in preserving DNA during cell division?
Centromeres serve as the attachment site for the mitotic spindle, ensuring accurate segregation of chromosomes during cell division and preventing loss or duplication of genetic material.
How do telomeres and centromeres together ensure chromosomal stability?
Telomeres prevent degradation at chromosome ends, while centromeres ensure proper alignment and separation during cell division, safeguarding the entire chromosome’s structure and function.
Why is chromatin structure critical for DNA preservation?
The tightly packed structure of chromatin protects DNA from enzymatic damage and mechanical stress, while also regulating access for replication and repair.
What four histones make up the core histone octamer in a nucleosome?
Two molecules each of H2A, H2B, H3, and H4 form the octamer core.
How many times does DNA wrap around the histone core, and how many nucleotides are involved in this wrap?
146 nucleotides of DNA wrap 1.65 times around the histone core to form the nucleosome.
Why are histones considered highly conserved across species?
Histones are considered highly conserved across species due to their essential role in DNA packaging and regulation of gene expression.
Why are histones considered highly conserved across species?
Histones have very similar amino acid sequences in different organisms, reflecting their fundamental role in DNA packaging and gene regulation.
What types of bonds help stabilize the interaction between DNA and the histone octamer?
Hydrogen bonds form between the DNA and the histone octamer, helping to maintain the structure of the nucleosome.
How are nucleosomes spaced along DNA, and what is the function of the DNA between nucleosomes?
Nucleosomes are separated from each other by up to 80 nucleotides of linker DNA.
The linker DNA connects one nucleosome to the next and provides sites where other proteins can interact or additional regulatory factors can bind.
What role does histone H1 play in nucleosome structure?
Histone H1 acts as a clamp, binding to the nucleosome where the DNA leaves and enters, thereby helping stabilize the higher-order structure of chromatin.
What is DNA packaging, and why is it important?
DNA packaging is the process of coiling and folding DNA into more compact forms. It is crucial for fitting large amounts of DNA into the limited space of the nucleus and for regulating access to DNA during processes such as transcription and replication.
What happens to the space DNA occupies as packaging becomes more complex?
The ‘room’ taken up by DNA gets smaller. However, as DNA becomes more tightly packed, it becomes harder for proteins to access the DNA for transcription and replication.
What does the ‘beads-on-a-string’ form of chromatin refer to?
This form represents DNA wrapped around histone protein cores (nucleosomes) connected by short segments of linker DNA, resembling ‘beads’ on a ‘string.’
What is a chromatin fiber of packed nucleosomes?
When nucleosomes coil and fold more tightly, they form a thicker, more compact fiber (often referred to as the 30 nm fiber). This additional packaging level further organizes the DNA, reducing its exposed length.
What happens when the chromatin fiber is folded into loops?
The 30 nm fiber forms looped domains attached to a scaffold, leading to an even higher level of compaction. These loops help regulate which sections of the DNA are more or less accessible to cellular machinery.
How does the fully condensed, mitotic chromosome relate to the earlier stages of packaging?
In preparation for cell division, the looped chromatin undergoes further coiling and compaction to form the fully condensed mitotic chromosomes visible under a microscope. This highest level of compaction ensures equal segregation of genetic material during mitosis.
Why is it harder for proteins to access DNA in highly compacted forms?
More compact structures shield DNA from proteins, reducing the likelihood that enzymes or transcription factors can bind. As a result, genes in tightly packed regions are often less actively transcribed or replicated.
How do cells overcome the challenge of tightly packaged DNA when they need to read or replicate it?
Cells use chromatin remodeling complexes and histone modifications (e.g., acetylation, methylation) to loosen specific DNA regions. These changes temporarily unwind or relax the chromatin structure to allow proteins to access genes for transcription or replication.
What is the function of DNA helicase in DNA replication?
DNA helicase unwinds the double helix by breaking hydrogen bonds between the complementary strands, creating the replication fork.
What role does DNA polymerase play during DNA replication?
DNA polymerase synthesizes new DNA strands by adding nucleotides complementary to the template strand. It also proofreads to correct errors in base-pairing.
Why is DNA primase necessary for replication?
DNA primase synthesizes short RNA primers that provide a 3ʹ hydroxyl group for DNA polymerase to start adding DNA nucleotides.
What does DNA ligase do in the replication process?
DNA ligase seals the nicks (breaks) in the sugar-phosphate backbone of the lagging strand, joining Okazaki fragments into a continuous strand.
How does topoisomerase aid in DNA replication?
Topoisomerase relieves the supercoiling and torsional strain that develop ahead of the replication fork by cutting and rejoining the DNA strands.
Why must DNA replication occur before cell division?
To ensure each new daughter cell inherits a complete, accurate copy of the genome. Without prior replication, cells would not have the correct genetic material to pass on.
How does the original DNA strand function during replication?
The original strand serves as a template to produce a complementary copy of the genomic DNA.
What is the first major step in DNA replication?
The double helix is unwound and separated into two strands, forming a replication fork. This step is essential for exposing the bases on each strand, allowing them to serve as templates.
What role does DNA primase play in the replication process?
DNA primase synthesizes short RNA primers that provide a starting point for DNA polymerase. On the leading strand, a single primer is typically needed to initiate replication.
How do free nucleotide bases participate in forming the new DNA strand?
Free nucleotide bases pair with the exposed template bases according to complementary base-pairing rules (A with T, G with C). DNA polymerase then joins these nucleotides together, synthesizing the new strand.
What happens on the lagging strand during replication?
On the lagging strand, DNA primase creates primers every 100–200 bp. DNA polymerase extends these primers, forming Okazaki fragments. DNA ligase then joins the fragments to create a continuous DNA strand.
Why is replication said to be ‘based upon the formation of base-pairs’?
DNA replication relies on complementary base pairing (A-T, G-C). Each strand of the original double helix acts as a template for generating its complementary strand.
What is the first step of DNA replication?
The double helix must be unwound and separated into two strands, generating a replication fork where the bases become exposed.
What is the second step of DNA replication?
DNA primase synthesizes short RNA primers, which provide a starting platform (3′ hydroxyl group) for DNA polymerase to begin DNA synthesis.
What is the third step of DNA replication?
DNA polymerase recognizes the exposed bases on the template strands and adds complementary nucleotides, building the new DNA strand in the 5′ to 3′ direction.
How does replication differ on the lagging strand (fourth step)?
On the lagging strand, DNA primase lays down multiple RNA primers every 100–200 nucleotides. DNA polymerase extends these segments (Okazaki fragments). DNA ligase then joins the fragments, forming one continuous strand.
What must happen before DNA replication can begin?
The double helix must be separated into two template strands. This is done by DNA helicase, which unwinds the helix.
How does DNA helicase separate the two strands of DNA?
DNA helicase binds to one strand of DNA and spins around it. Using energy from ATP hydrolysis, it breaks the hydrogen bonds between complementary bases.
What is the energy source for DNA helicase activity, and why is it needed?
ATP hydrolysis provides the energy. This energy is needed for DNA helicase to physically unwind the double helix and move along the DNA strand.
Why is the action of DNA helicase essential for replication?
By unwinding and separating the strands, it exposes the bases on each template strand. This exposure is required for the next steps in replication, where DNA polymerase can begin synthesizing new strands.
What happens to the single-stranded DNA immediately after the double helix is unwound?
Single-stranded binding (SSB) proteins bind to the separated DNA strands. This stabilizes the single strands and prevents the formation of secondary structures (e.g., hairpins).
Why are single-stranded binding proteins especially important for the lagging strand?
The lagging strand is synthesized in short fragments, leading to more frequent exposure of single-stranded DNA. SSB proteins maintain the strands in an extended form so replication enzymes can access them efficiently.
How do single-stranded binding proteins help replication proceed smoothly?
By preventing single-stranded DNA from re-annealing or forming loops, SSB proteins ensure that DNA polymerase and other replication factors can quickly bind and replicate the exposed strands.
What is ‘cooperative binding’ in the context of single-stranded binding (SSB) proteins?
Cooperative binding means that the binding of one SSB protein to single-stranded DNA increases the likelihood that additional SSB proteins will bind nearby. This cooperative effect helps stabilize the DNA in an extended conformation, preventing secondary structures and ensuring efficient replication.
What is the replication fork, and how is it formed?
The replication fork is a Y-shaped region created when the DNA double helix is unwound by helicase. This unwinding exposes the individual template strands, allowing replication enzymes to access and copy the DNA.
Why does DNA replication need an RNA primer?
DNA polymerases can only add nucleotides to an existing 3′ hydroxyl (3′-OH) group. RNA primers, made by DNA primase, provide the initial 3′-OH so that DNA polymerase can start synthesizing the new DNA strand.
How long are the RNA primers synthesized by DNA primase, and what do they do?
The RNA primers are typically about 10 nucleotides in length. They base-pair with the DNA template at the replication fork, creating a short stretch of double-stranded nucleic acid for DNA polymerase to bind and initiate DNA synthesis.
What is the role of DNA primase in the initiation stage of replication?
DNA primase recognizes the exposed bases at the replication fork. It then synthesizes the short RNA primers needed for DNA polymerase to begin elongation of the new DNA strand.
Why is this primer-initiated process referred to as ‘initiation’?
It’s called ‘initiation’ because laying down the RNA primer is the critical first step in starting the synthesis of the new DNA strand, enabling other replication proteins to join and continue the process.
What is the overall role of DNA polymerase in DNA replication?
DNA polymerase adds deoxyribonucleotides to the growing DNA strand, using the existing template strand and an RNA primer. It forms phosphodiester bonds between the 3′ hydroxyl (3′-OH) of the primer and the 5′ phosphate (5′-P) of the incoming nucleotide.
In which direction does the newly synthesized DNA strand grow?
The new DNA strand always elongates in the 5′ to 3′ direction. DNA polymerase attaches each new nucleotide to the 3′-OH end of the growing chain.
How does the incoming nucleotide supply energy for bond formation?
The incoming nucleotide is a deoxyribonucleoside triphosphate (dNTP) (e.g., dATP, dTTP, dCTP, dGTP). When a nucleotide is added, pyrophosphate (PPi) is released. The hydrolysis of pyrophosphate provides energy that drives the formation of the phosphodiester bond.
What ensures the correct nucleotide is added during DNA synthesis?
Complementary base pairing (A–T, G–C) ensures the correct match. DNA polymerase also has a ‘checking’ mechanism (often proofreading) that helps correct mispaired bases.
What is meant by ‘phosphodiester bonds’ in DNA synthesis?
A phosphodiester bond is the linkage between the 3′ hydroxyl group of the existing strand and the 5′ phosphate of the incoming nucleotide. It creates the sugar-phosphate backbone of DNA.
What is the significance of the polymerase ‘hand’ shape shown in the diagram?
DNA polymerase is often depicted as a right-handed shape. The ‘palm’ region is where the catalytic site resides, binding DNA and checking base pairing. The ‘fingers’ help position the incoming dNTP, and the ‘thumb’ helps secure the DNA in place.
How does DNA polymerase proceed along the template once a nucleotide is incorporated?
After each correct nucleotide is added and the bond is formed, DNA polymerase translocates forward. It repositions so the next 3′-OH is aligned in the active site, ready to bind the next incoming nucleotide.
What happens to pyrophosphate after it is released?
Pyrophosphate is typically hydrolyzed into two phosphate ions (Pi). This hydrolysis makes the DNA synthesis reaction effectively irreversible under cellular conditions.
Why does the lagging strand require multiple primers during replication?
- DNA polymerase synthesizes DNA only in the 5′ to 3′ direction.
- On the lagging strand, the replication fork opens in the opposite direction, so DNA primase must repeatedly lay down new RNA primers to initiate each Okazaki fragment.
What are Okazaki fragments, and how are they formed?
- Okazaki fragments are short segments of newly synthesized DNA on the lagging strand.
- DNA polymerase uses each new RNA primer as a starting point, extending the DNA until it reaches the previous primer.
Once an Okazaki fragment is completed, what happens to the RNA primer?
- The RNA primer is removed (often by an exonuclease activity or specialized enzyme) and replaced with DNA by DNA polymerase.
- This replacement ensures the final strand is entirely made of DNA.
How do the individual Okazaki fragments become one continuous strand?
- DNA ligase forms a phosphodiester bond between the adjacent 3′ hydroxyl (from the newly synthesized DNA) and the 5′ phosphate (remaining from the replaced primer region).
- This “glues” all the fragments together into a continuous strand.
Why is the lagging strand referred to as ‘lagging’?
- Because it’s synthesized in a discontinuous manner, in short segments (Okazaki fragments), it lags behind the continuous synthesis on the leading strand.
- Nonetheless, both strands complete replication around the same time.
What is the significance of ‘3′ to 5′ direction’ limitation for DNA polymerase?
- DNA polymerase cannot synthesize DNA in the 3′ to 5′ direction.
- Therefore, the lagging strand must adopt a discontinuous approach, repeatedly using primers to allow 5′ to 3′ extension in small sections.
How does the process on the lagging strand ensure fidelity (accuracy) despite multiple steps?
- DNA polymerase has proofreading capability, removing incorrectly paired bases.
- Enzymes that remove RNA primers and DNA ligase also check and correct any structural or bonding errors during fragment joining.
