Replication Flashcards
What are the components of a nucleotide?
A nucleotide is composed of three components: a sugar molecule (deoxyribose in DNA, ribose in RNA), a phosphate group, and a nitrogenous base.
What is the significance of the sequence of bases in a nucleic acid chain?
The sequence of bases along a nucleic acid chain carries genetic information. The specific order of the bases encodes the instructions for the synthesis of proteins and other cellular functions.
How does DNA replication occur?
DNA replication occurs through a process called semi-conservative replication. Each DNA strand serves as a template for the creation of a new complementary strand. The result is two identical DNA molecules, each containing one original strand and one newly synthesized strand.
How is protein synthesis related to DNA and RNA?
DNA itself is not directly involved in protein synthesis. Instead, DNA is transcribed into mRNA through a process called transcription. The mRNA molecules then serve as templates for protein synthesis
What is the role of messenger RNA (mRNA) in protein synthesis?
Messenger RNA (mRNA) is a type of RNA molecule that carries the genetic information from DNA to the cellular machinery responsible for protein synthesis. mRNA acts as an intermediary, conveying the instructions encoded in DNA to guide the synthesis of proteins.
What is the relationship between transcription and translation?
Transcription is the process where DNA is copied into mRNA, while translation is the process where mRNA is used as a template to synthesize proteins according to the genetic instructions encoded in the mRNA.
What is the genetic code, and what does it define?
The genetic code defines the relationship between the sequence of bases in DNA (or its mRNA transcript) and the sequence of amino acids in a protein. It is nearly the same in all organisms and consists of codons, which are sequences of three bases that specify a particular amino acid.
Why are naturally occurring DNA molecules long?
Naturally occurring DNA molecules are long because they need to carry the genetic information necessary for the functioning of organisms, even in the simplest ones
Can you provide examples of DNA lengths in different organisms?
Polyoma virus: Two intertwined strands, each 5100 nucleotides long.
E. coli: A single DNA molecule consisting of two chains, each with 4.6 million nucleotides.
Human genome: Approximately 3 billion nucleotides in each chain of DNA, divided among 23 distinct chromosomes of different sizes.
Indian muntjac: The genome is nearly as large as the human genome but distributed on only 3 chromosomes. The largest chromosome has two chains of over 1 billion nucleotides each.
How many nucleotides are present in each chain of the human genome?
Each chain of the human genome contains approximately 3 billion nucleotides.
What is the significance of codons in the genetic code?
Codons are sequences of three bases (nucleotides) in DNA or mRNA that code for specific amino acids or serve as start or stop signals in protein synthesis. The genetic code is degenerate, meaning that multiple codons can code for the same amino acid.
Can you explain the concept of gene expression and its relationship to DNA, RNA, and proteins?
Gene expression refers to the process by which information encoded in genes is used to create functional proteins or other cellular products. It involves the transcription of DNA into mRNA and the subsequent translation of mRNA into proteins. Gene expression is a fundamental process for the functioning and development of organisms.
What proteins are involved in DNA replication?
DNA polymerases, primase, DNA helicase, DNA ligase, single-stranded binding proteins, and various other proteins that assist in the initiation, elongation, and termination stages of replication
What is the role of DNA polymerases in DNA replication?
DNA polymerases play a crucial role in DNA replication. They promote the formation of bonds between individual units of the DNA molecule, called nucleotides, and add them step by step to build a new DNA chain.
What are the activated precursors required for DNA synthesis?
deoxynucleoside 5’-triphosphates (dATP, dGTP, dCTP, and TTP) along with the presence of magnesium ions (Mg2+).
How is the new DNA chain assembled during replication?
The new DNA chain is assembled directly on a preexisting DNA template. The DNA polymerases read the template DNA strand and add complementary nucleotides to the growing DNA chain, ensuring that the bases on the incoming nucleotides match the bases on the template strand.
What is the function of primase in DNA replication?
Primase is an enzyme involved in DNA replication that initiates the synthesis of RNA primers. These primers provide a starting point for DNA polymerases to begin synthesizing a new DNA strand.
How is the accuracy of DNA replication maintained?
The accuracy of DNA replication is maintained through a multilayered system. Accurate DNA synthesis itself has a certain error rate, but it is reduced by proofreading processes during DNA synthesis. Additionally, postreplication mismatch repair further reduces errors by detecting and correcting mistakes after replication.
What is the error rate required to replicate the human genome without mistakes?
To replicate the human genome without mistakes, an error rate of less than 1 error per 3x10^9 base pairs must be achieved.
What are the different layers of the system that ensure accurate DNA synthesis?
The system that ensures accurate DNA synthesis involves multiple layers. It includes accurate DNA synthesis itself, which has an error rate of approximately 1 error per 10^3 to 10^4 inserted bases. There are also proofreading mechanisms during DNA synthesis that reduce the error rate to about 1 error per 10^6 to 10^7 base pairs.
Furthermore, postreplication mismatch repair processes further reduce the error rate to around 1 error per 10^9 to 10^10 base pairs.
How does postreplication mismatch repair reduce the error rate in DNA replication?
Postreplication mismatch repair is a mechanism that detects and corrects errors after DNA replication. It helps reduce the error rate in DNA replication to approximately 1 error per 10^9 to 10^10 base pairs.
How does primase initiate synthesis without a primer, and what is its role in DNA replication?
Primase initiates synthesis without a primer by synthesizing a short RNA primer complementary to the DNA template. The RNA primer provides a starting point for DNA polymerases to bind and begin DNA synthesis.
How does the presence of magnesium ions (Mg2+) contribute to the DNA synthesis reaction?
Magnesium ions (Mg2+) play a crucial role in DNA synthesis. They stabilize the negatively charged phosphate groups of the dNTPs, facilitating the bonding reaction between the incoming nucleotide and the growing DNA chain. Mg2+ ions also help in the proper positioning of the dNTP within the active site of DNA polymerases.
What are the specific proofreading mechanisms employed by DNA polymerases during DNA synthesis?
DNA polymerases employ proofreading mechanisms to ensure accuracy during DNA synthesis. These mechanisms include exonuclease activity, where the polymerase can remove mismatched nucleotides from the growing DNA chain and replace them with the correct ones.
What are the specific functions of each protein in the DNA Replicase system or Replisomes?
DNA polymerases: Catalyze the synthesis of new DNA strands by adding nucleotides.
Primase: Initiates the synthesis of RNA primers.
DNA helicase: Unwinds the double-stranded DNA to create a replication fork.
DNA ligase: Joins the Okazaki fragments on the lagging strand during DNA replication.
Single-stranded binding proteins: Stabilize and protect the single-stranded DNA regions during replication.
How does the catalytic activity of DNA polymerases promote the formation of bonds in the DNA backbone?
DNA polymerases have an active site that can catalyze the formation of phosphodiester bonds between nucleotides. They use the energy from the incoming deoxynucleoside 5’-triphosphate (dNTP) to join the 3’-hydroxyl group of the growing DNA chain with the 5’-phosphate group of the incoming nucleotide, thereby forming the bond in the DNA backbone.
What’s the site of DNA replication
Replication fork
It is formed by the newly synthesized daughter helices and resembles a two-pronged fork.
How are the leading and lagging strands synthesized during DNA replication?
The leading strand is synthesized continuously during DNA replication, while the lagging strand is synthesized in small fragments called Okazaki fragments.
What is the direction of DNA synthesis by DNA polymerases?
DNA polymerases synthesize DNA in the 5’ to 3’ direction. They cannot synthesize DNA in the opposite direction (3’ to 5’).
How are Okazaki fragments joined together during replication?
together during replication by an enzyme called DNA ligase. DNA ligase catalyzes the formation of covalent bonds between the fragments, resulting in a continuous daughter strand.
What is the difference between the leading and lagging strands?
The leading strand is synthesized continuously in the same direction as the replication fork, while the lagging strand is synthesized discontinuously in the opposite direction. The leading strand is synthesized without interruption, while the lagging strand is synthesized in fragments.
How does the discontinuous assembly of the lagging strand
The discontinuous assembly of the lagging strand enables overall growth because the fragments are still synthesized in the 5’ to 3’ direction at the nucleotide level. When the fragments are joined together, they form a continuous strand.
What is the role of DNA ligase in DNA replication?
DNA ligase plays a crucial role in DNA replication by sealing breaks in double-stranded DNA molecules. It catalyzes the formation of phosphodiester bonds between the 3’-hydroxyl group of one DNA chain and the 5’-phosphoryl group of the other, resulting in the connection of DNA fragments.
What energy source drives the bond formation catalyzed by DNA ligase in different organisms?
ATP is typically used as the energy source, while in bacteria, NAD+ is commonly utilized.
What can DNA ligase seal in double-stranded DNA molecules?
DNA ligase can seal breaks in double-stranded DNA molecules. It is not able to link two molecules of single-stranded DNA or circularize single-stranded DNA. Its main function is to join the ends of DNA strands during replication or repair processes.
Can you explain the mechanism of DNA ligase in joining Okazaki fragments during DNA replication?
DNA ligase joins Okazaki fragments during DNA replication by catalyzing the formation of phosphodiester bonds between the adjacent fragments. It seals the nicks (unjoined ends) in the DNA backbone, resulting in the formation of a continuous daughter strand.
Can you explain the role of single-stranded binding proteins (SSBs) in DNA replication?
Single-stranded binding proteins (SSBs) stabilize and protect single-stranded DNA regions during DNA replication. They bind to the exposed single-stranded DNA, preventing it from forming secondary structures and being degraded by nucleases. SSBs also help to keep the DNA strands separated, allowing for efficient replication.
What are the functions of helicase in DNA replication, and how does it contribute to the unwinding of the DNA double helix?
Helicase plays a crucial role in DNA replication by unwinding the double-stranded DNA at the replication fork. It uses energy from ATP hydrolysis to break the hydrogen bonds between the base pairs, separating the DNA strands and creating the single-stranded DNA templates needed for DNA synthesis.
What is the function of topoisomerases in DNA replication, and how do they relieve torsional stress during replication?
Topoisomerases are enzymes involved in DNA replication that help relieve torsional stress and prevent DNA supercoiling. They achieve this by cutting and rejoining the DNA strands, allowing for controlled rotation of the DNA during replication.
What are topoisomerases and what role do they play in DNA processes?
Topoisomerases are enzymes that are involved in DNA processes such as replication, transcription, and recombination. They help regulate the degree of supercoiling in DNA, which is the twisting and winding of the DNA strands.
What is the difference between negative and positive supercoiling of DNA?
Negative supercoiling refers to the underwinding of DNA, which prepares it for processes like replication. Positive supercoiling, on the other hand, condenses DNA but makes strand separation more difficult.
How do Type I and Type II topoisomerases differ in their actions on DNA?
Type I topoisomerases cleave one strand of DNA and relax supercoiled DNA. Type II topoisomerases cleave both strands of DNA and utilize ATP energy to introduce negative supercoils into DNA.
What are some antibiotics that target bacterial topoisomerase II (DNA gyrase)?
Antibiotics such as novobiocin, nalidixic acid, and ciprofloxacin target bacterial topoisomerase II (DNA gyrase). Novobiocin blocks the binding of ATP to gyrase, while nalidixic acid and ciprofloxacin interfere with the breakage and rejoining of DNA chains.
How does camptothecin inhibit human topoisomerase I and what effect does it have on DNA?
Camptothecin inhibits human topoisomerase I by stabilizing the form of the enzyme covalently linked to DNA. This prevents DNA re-ligation and leads to DNA damage, ultimately causing apoptosis (programmed cell death).
What are autonomously replicating sequences (ARS) or replicators, and where have they been extensively studied?
Autonomously replicating sequences (ARS) or replicators are specific sequences in DNA that act as origins of replication. They have been extensively studied in eukaryotes, particularly in yeast
What is the function of the origin recognition complex (ORC) in initiating DNA replication?
The origin recognition complex (ORC) is a multisubunit protein complex that plays a crucial role in initiating DNA replication. It binds to several sequences within the replicator and helps recruit other proteins involved in replication.
How does the rate of replication fork movement differ between eukaryotes and E. coli?
The rate of replication fork movement in eukaryotes is slower compared to E. coli. Eukaryotes replicate at a rate of approximately 50 nucleotides per second, which is only one-twentieth of the rate observed in E. coli.
How long would it take to replicate an average human chromosome from a single origin at the rate observed in eukaryotes?
Replicating an average human chromosome from a single origin at the rate observed in eukaryotes (~50 nucleotides per second)
What are some potential applications or implications of understanding the mechanisms of topoisomerases and DNA replication?
Understanding the mechanisms of topoisomerases and DNA replication has several implications and applications. It helps in understanding genetic processes, developing antibiotics that target bacterial topoisomerases, studying diseases related to DNA replication errors, and exploring potential therapeutic strategies for cancer treatment. Additionally, knowledge of DNA replication is crucial for advancements in genetic engineering, biotechnology, and synthetic biology
What are the specific mechanisms by which Type I and Type II topoisomerases cleave and reseal DNA strands?
Type I topoisomerases cleave one strand of the DNA, forming a transient covalent bond between the enzyme and the DNA. The DNA strand is then passed through the break, and the enzyme reseals the nicked DNA strand.
Type II topoisomerases cleave both strands of the DNA, creating a double-stranded break. They form a covalent protein-DNA intermediate, allowing them to pass another segment of DNA through the break. Finally, the enzyme reseals the double-stranded break.
What are some of the key sequences recognized by the origin recognition complex (ORC) during DNA replication initiation in eukaryotes?
The origin recognition complex (ORC) recognizes specific sequences within the replicator during DNA replication initiation in eukaryotes. These sequences, known as origin recognition sites, vary among species but generally contain conserved DNA motifs that serve as binding sites for ORC.
How do different types of autonomously replicating sequences (ARS) or replicators function, and what factors determine their efficiency and specificity?
The slower rate of replication fork movement in eukaryotes compared to E. coli can be attributed to multiple factors, such as the larger size and complexity of eukaryotic genomes, the need for coordination with chromatin structure, and the requirement for more complex protein-protein interactions during replication.
What are the potential long-term consequences of DNA replication errors caused by topoisomerase dysfunction?
DNA replication errors caused by topoisomerase dysfunction can have various long-term consequences. They can lead to mutations, genomic instability, and the development of genetic diseases or predisposition to certain cancers. Additionally, errors in DNA replication can result in impaired cellular function and contribute to aging processes.
How does replication of human chromosomes occur?(direction)
Replication of human chromosomes occurs bidirectionally from multiple origins, with each origin initiating the replication process in both directions.
