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Questions and Answers
During which phase of the cell cycle does DNA replication occur?
During which phase of the cell cycle does DNA replication occur?
What prevents the DNA strands from renaturing during replication?
What prevents the DNA strands from renaturing during replication?
Which of the following is not one of the major classes of RNA molecules produced by transcription?
Which of the following is not one of the major classes of RNA molecules produced by transcription?
What characteristic of A-T base pairs makes them easier to disrupt compared to G-C base pairs?
What characteristic of A-T base pairs makes them easier to disrupt compared to G-C base pairs?
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What happens when replication forks meet during DNA replication?
What happens when replication forks meet during DNA replication?
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What is the purpose of the gene regulatory elements found at the beginning and end of genes?
What is the purpose of the gene regulatory elements found at the beginning and end of genes?
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What type of replication occurs in eukaryotic DNA synthesis?
What type of replication occurs in eukaryotic DNA synthesis?
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Which phase immediately follows the S phase in the cell cycle?
Which phase immediately follows the S phase in the cell cycle?
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What type of gene directly codes for a protein molecule?
What type of gene directly codes for a protein molecule?
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Which RNA polymerase function is essential for recognizing a promoter?
Which RNA polymerase function is essential for recognizing a promoter?
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What is the result of transcription when the RNA polymerase encounters a transcription terminator?
What is the result of transcription when the RNA polymerase encounters a transcription terminator?
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In what direction is RNA synthesized during transcription?
In what direction is RNA synthesized during transcription?
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Which molecule is not a precursor for RNA synthesis?
Which molecule is not a precursor for RNA synthesis?
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What is the primary RNA transcript in eukaryotes subject to before translation?
What is the primary RNA transcript in eukaryotes subject to before translation?
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Which of the following statements about transcription in prokaryotes and eukaryotes is true?
Which of the following statements about transcription in prokaryotes and eukaryotes is true?
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What is the role of RNA polymerase during transcription?
What is the role of RNA polymerase during transcription?
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What is the role of DNA helicase in DNA replication in prokaryotes?
What is the role of DNA helicase in DNA replication in prokaryotes?
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Which component is essential for the synthesis of DNA and cannot be missing?
Which component is essential for the synthesis of DNA and cannot be missing?
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What structure is formed during the local denaturation of DNA at the origin of replication?
What structure is formed during the local denaturation of DNA at the origin of replication?
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What direction is new DNA synthesized during replication?
What direction is new DNA synthesized during replication?
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What is the function of the RNA primer in DNA replication?
What is the function of the RNA primer in DNA replication?
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In which organisms does DNA replication occur in a simpler manner compared to others?
In which organisms does DNA replication occur in a simpler manner compared to others?
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What enzyme is responsible for removing RNA primers during DNA replication?
What enzyme is responsible for removing RNA primers during DNA replication?
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Which of the following correctly describes the organization of DNA in eukaryotes compared to prokaryotes?
Which of the following correctly describes the organization of DNA in eukaryotes compared to prokaryotes?
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What is the primary function of the cap structure in mRNA processing?
What is the primary function of the cap structure in mRNA processing?
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How many possible codons can be generated using a three-letter code with four nucleotides?
How many possible codons can be generated using a three-letter code with four nucleotides?
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What characteristic demonstrates that the genetic code is nonoverlapping?
What characteristic demonstrates that the genetic code is nonoverlapping?
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Which of the following describes what the start codon does in protein synthesis?
Which of the following describes what the start codon does in protein synthesis?
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What does it mean that the genetic code is described as degenerate?
What does it mean that the genetic code is described as degenerate?
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What role do spliceosomes play in RNA processing?
What role do spliceosomes play in RNA processing?
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Which of the following is NOT a characteristic of the genetic code?
Which of the following is NOT a characteristic of the genetic code?
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Which of the following codons is classified as a stop codon?
Which of the following codons is classified as a stop codon?
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Study Notes
DNA Replication in Prokaryotes
- The DNA replication process in prokaryotes follows a semi-conservative model. This means that the two strands of the DNA double helix separate, and each strand serves as a template for the synthesis of a new complementary strand.
- Four crucial components are needed for DNA synthesis in vitro:
- All four deoxyribonucleoside 5' triphosphates (dNTPs): dATP, dGTP, dTTP, dCTP
- Magnesium ions (Mg2+)
- A DNA fragment as a template
- DNA polymerase
- The initiation of DNA replication in prokaryotes starts with the denaturation of the DNA at a specific sequence called the origin of replication. This denaturation exposes the bases, allowing new strands to be synthesized.
- In circular chromosomes, like those found in E. coli, this denaturation creates a replication bubble. E. coli has a single origin of replication called oriC. Replication proceeds bidirectionally from this origin.
- An initiator protein binds to the parental DNA at the origin of replication sequence, initiating the separation of the two strands. This process necessitates localized denaturation and the untwisting of the DNA, which is catalyzed by the enzyme DNA helicase.
- DNA helicase uses energy derived from ATP hydrolysis to untwist the DNA. Another enzyme, DNA primase, binds to the helicase and denatured DNA. Primase is derived from RNA polymerase.
- The initiation of DNA synthesis involves the synthesis of a short RNA primer, a process catalyzed by primase. This complex involving primase, helicase, and potentially other proteins, along with the DNA, is referred to as the primosome.
- The primer nucleotide serves as a substrate for DNA polymerase activity.
- Short DNA segments known as Okazaki fragments remove the RNA primers.
- The new DNA is synthesized in the 5' to 3' direction.
DNA Replication in Eukaryotes
- Similar to prokaryotes, DNA replication in eukaryotes involves the same fundamental processes: denaturation of the DNA double helix and semi-conservative, semi-discontinuous replication of the DNA. However, eukaryotes have the additional complexity of distributing DNA across multiple chromosomes.
- During each cell division cycle, every chromosome must be faithfully duplicated, with a copy distributed to each progeny cell.
- This process unfolds within the cell cycle: G1, S, G2, and M. DNA replicates during the S phase, and the progeny chromosomes segregate into daughter cells during the M phase.
- The replication of the eukaryotic chromosome involves replicating both the DNA and the histone core of the nucleosome, as well as doubling the non-histone components.
- Unlike prokaryotes, eukaryotes have multiple origins of replication per chromosome, which significantly speeds up the replication process. This is essential for efficient replication, given the much larger size of eukaryotic genomes.
- Replication proceeds bidirectionally from each origin, opening the DNA double helix to expose single strands that serve as templates for new DNA synthesis.
- Eventually, each replication fork encounters an adjacent fork, merging the replication process.
- A-T base pairs, with only two hydrogen bonds, break more easily than G-C base pairs with three hydrogen bonds.
- Single-strand binding (SSB) proteins prevent the DNA from renaturing and stimulate polymerase activity.
Transcription
- Transcription is the process of transferring information from a double-stranded DNA template molecule to a single-stranded RNA molecule.
- There are four major classes of RNA molecules or transcripts produced by transcription:
- messenger RNA (mRNA)
- transfer RNA (tRNA)
- ribosomal RNA (rRNA)
- small nuclear RNA (snRNA)
- The first three RNA types are found in both prokaryotes and eukaryotes, while snRNA is exclusively found in eukaryotes.
- Only the mRNA molecule is translated to produce a protein molecule.
- A gene that codes for an mRNA molecule and a protein is called a structural gene or a protein-coding gene.
- Transcription is catalyzed by an enzyme called RNA polymerase.
- The DNA double helix unwinds before transcription can begin, and only one of the two DNA strands is transcribed into RNA. This strand is called the template strand, while the other is the non-template or coding strand.
- During transcription, the RNA precursors are the ribonucleoside triphosphates: ATP, GTP, CTP, and UTP, collectively known as NTPs.
- RNA polymerization is very similar to the DNA polymerization reaction. The next nucleotide to be added to the chain is selected by the RNA polymerase based on its ability to pair with the exposed base on the DNA template strand. Like DNA replication, RNA is synthesized in the 5' to 3' direction.
- To initiate transcription of a gene, RNA polymerase binds to a transcription-controlling sequence adjacent to the start of the gene. This sequence is called the promoter.
- The sigma factor is essential for promoter recognition. Without sigma, the core enzyme initiates transcription randomly.
- Transcription ceases when a controlling element called a transcription terminator sequence or a terminator is encountered at the end of a gene.
- The RNA polymerase enzyme performs several functions:
- It recognizes the promoter on the double-stranded DNA.
- It initiates the denaturation and unwinding of the DNA into single strands at the promoter.
- It orients itself properly based on the promoter sequence and transcribes the entire template strand of the gene.
- It stops transcribing upon encountering and recognizing the terminator sequence.
- The sequence of the gene is as follows: promoter - RNA-coding sequence - terminator.
- Transcription in prokaryotes and eukaryotes share similarities but have key differences:
- Eukaryotes have multiple RNA polymerase enzymes, unlike prokaryotes.
- The transcription sequences (promoters and terminators) differ between prokaryotes and eukaryotes.
- Transcription can be broken down into three stages: initiation, elongation, and termination.
Translation
- Translation is the process of converting mRNA base sequence information into the amino acid sequence of a polypeptide in the cell.
- The DNA base-pair information that specifies the amino acid sequence of a polypeptide is known as the genetic code.
- mRNA molecules are read in groups of three called codons, which specify the amino acid sequence in proteins.
- The genetic code is a triplet code, meaning that three nucleotides (one codon) are needed to specify one amino acid.
- The code is comma-free, meaning that the mRNA is read continuously, three nucleotides at a time, without skipping any nucleotides.
- The code is non-overlapping, meaning that each nucleotide in mRNA is part of only one codon.
- The code is almost universal, which means that all organisms essentially share the same genetic language.
- The code is degenerate, which means that multiple codons can specify the same amino acid. Most amino acids are encoded by more than one codon, except for methionine and tryptophan, which have a single codon.
- The code has start and stop signals. Methionine is commonly used as the start codon for protein synthesis.
- 61 out of 64 codons specify amino acids and are known as sense codons. The remaining three codons (UAG, UAA, and UGA) represent stop codons, nonsense codons, or chain-terminating codons.
Post-Transcriptional Modifications
- In prokaryotes, the RNA copy of a gene is messenger RNA, ready for translation into protein. Translation can even begin before transcription is finished.
- In eukaryotes, the primary RNA transcript requires additional processing before it can be translated. This step is called RNA processing or post-transcriptional modifications.
- Eukaryotic mRNA must be transported out of the nucleus into the cytoplasm.
- rRNA links amino acids together to form proteins.
- The cap is 7-methylguanosine, which protects the mRNA from degradation by ribonucleases.
- Splicing is catalyzed by large protein complexes called spliceosomes, which are assembled from proteins and snRNA that recognize splice sites.
- The poly(A) tail protects the 3' end of mRNA from ribonuclease digestion.
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Description
Explore the intricate process of DNA replication in prokaryotes, focusing on the semi-conservative model, essential components required for synthesis, and the initiation at the origin of replication. Learn about the significance of the replication bubble in circular chromosomes, particularly in organisms like E. coli.
