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Questions and Answers
What is the primary function of DNA polymerase III in DNA replication?
What is the primary function of DNA polymerase III in DNA replication?
How do topoisomerases affect DNA supercoiling?
How do topoisomerases affect DNA supercoiling?
Which statement correctly describes the leading and lagging strands during DNA replication?
Which statement correctly describes the leading and lagging strands during DNA replication?
What is the role of ATP during the synthesis of the sugar phosphate backbone?
What is the role of ATP during the synthesis of the sugar phosphate backbone?
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Which of the following components is NOT a part of ATP?
Which of the following components is NOT a part of ATP?
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During which phase of the cell cycle does DNA replication primarily occur?
During which phase of the cell cycle does DNA replication primarily occur?
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What is the primary function of telomerase in DNA replication?
What is the primary function of telomerase in DNA replication?
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What are Okazaki fragments associated with during DNA replication?
What are Okazaki fragments associated with during DNA replication?
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Which component forms the sugar-phosphate backbone of DNA?
Which component forms the sugar-phosphate backbone of DNA?
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What type of molecule is DNA described as?
What type of molecule is DNA described as?
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What role do histones play in eukaryotic DNA packaging?
What role do histones play in eukaryotic DNA packaging?
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Which of the following accurately describes the orientation of DNA strands?
Which of the following accurately describes the orientation of DNA strands?
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What is the major groove in DNA structure?
What is the major groove in DNA structure?
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What is the primary activity of DNA polymerase I during DNA replication?
What is the primary activity of DNA polymerase I during DNA replication?
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Which of the following statements best describes the action of topoisomerase?
Which of the following statements best describes the action of topoisomerase?
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What distinguishes the leading strand from the lagging strand during DNA replication?
What distinguishes the leading strand from the lagging strand during DNA replication?
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Which of the following describes the role of ATP in DNA synthesis?
Which of the following describes the role of ATP in DNA synthesis?
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What type of fragments are formed on the lagging strand during DNA replication?
What type of fragments are formed on the lagging strand during DNA replication?
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What component is essential for the packaging of eukaryotic DNA?
What component is essential for the packaging of eukaryotic DNA?
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What is NOT a function of DNA replication?
What is NOT a function of DNA replication?
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Which of the following describes the structure of DNA?
Which of the following describes the structure of DNA?
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During which of the following processes do mutations primarily occur?
During which of the following processes do mutations primarily occur?
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What characteristic of DNA allows for easy breaking of hydrogen bonds during replication?
What characteristic of DNA allows for easy breaking of hydrogen bonds during replication?
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How is the orientation of DNA strands described?
How is the orientation of DNA strands described?
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Which type of bases form the sugar phosphate backbone of DNA?
Which type of bases form the sugar phosphate backbone of DNA?
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What is the primary structural form of DNA observed in eukaryotic cells?
What is the primary structural form of DNA observed in eukaryotic cells?
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What is the primary role of mRNA in the cell?
What is the primary role of mRNA in the cell?
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Which component is unique to RNA and not found in DNA?
Which component is unique to RNA and not found in DNA?
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During transcription, which enzyme is primarily responsible for synthesizing RNA?
During transcription, which enzyme is primarily responsible for synthesizing RNA?
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What distinguishes transcription from replication in terms of output?
What distinguishes transcription from replication in terms of output?
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Which of the following processes is NOT involved in RNA transcription?
Which of the following processes is NOT involved in RNA transcription?
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What is a key difference between RNA and DNA regarding mutation stability?
What is a key difference between RNA and DNA regarding mutation stability?
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What does the process of post-transcriptional modification include?
What does the process of post-transcriptional modification include?
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How do the strands of RNA and DNA differ in terms of their structural configuration?
How do the strands of RNA and DNA differ in terms of their structural configuration?
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What is the primary function of tRNA in the process of translation?
What is the primary function of tRNA in the process of translation?
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During which stage of transcription does RNA polymerase synthesize RNA in the 5'-3' direction?
During which stage of transcription does RNA polymerase synthesize RNA in the 5'-3' direction?
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Which modification is NOT part of the maturation process of pre-mRNA in eukaryotes?
Which modification is NOT part of the maturation process of pre-mRNA in eukaryotes?
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What is a key difference between transcription in prokaryotes and eukaryotes?
What is a key difference between transcription in prokaryotes and eukaryotes?
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Which of the following roles is NOT associated with the poly A tail in mRNA?
Which of the following roles is NOT associated with the poly A tail in mRNA?
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What is the complementary base pairing for the template DNA strand sequence 5'-ATCG-3' during transcription?
What is the complementary base pairing for the template DNA strand sequence 5'-ATCG-3' during transcription?
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What correctly describes the role of snRNA in eukaryotic cells?
What correctly describes the role of snRNA in eukaryotic cells?
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Study Notes
DNA Replication
- DNA replication occurs during late G1 and mostly during the S-phase of interphase.
- The process of adding nucleotides to a growing DNA strand is based on complementary base pairing: Adenine (A) pairs with Thymine (T) and Guanine (G) pairs with Cytosine (C).
- Okazaki fragments are short, newly synthesized DNA fragments that are formed on the lagging strand during DNA replication.
- Telomerase is an enzyme that adds repetitive nucleotide sequences to the ends of chromosomes, preventing the loss of genetic information during replication.
DNA Structure
- DNA stores genetic information and is responsible for replication, gene expression, and genetic variation.
- DNA is composed of nucleotides, which consist of a phosphate group, a deoxyribose sugar, and a nitrogenous base.
- There are two types of nitrogenous bases: Pyrimidines (cytosine and thymine) and Purines (adenine and guanine).
- DNA adopts a double helix structure, where two strands of nucleotides are held together by hydrogen bonds between the nitrogenous bases.
- The two strands of DNA are antiparallel, running in opposite directions (5' to 3' and 3' to 5').
- DNA has a major groove and a minor groove, which are important for protein binding.
DNA Packaging
-
Eukaryotic cells: DNA is packaged around histones (proteins) to form nucleosomes, which are further condensed into chromatin. Chromatin is condensed into chromosomes during cell division.
- Histone proteins are organized into octamers, consisting of two dimers of H2A and H2B, and two tetramers of H3 and H4.
- Histone H1 helps to further condense the DNA packaged around the histones.
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Prokaryotic cells: DNA is packaged by supercoiling, a process that compresses the DNA by twisting the double helix into a more compact structure.
- Topoisomerases help regulate supercoiling, with topoisomerase I relaxing negatively supercoiled DNA and topoisomerase II (gyrase) introducing negative supercoils and relaxing positive supercoils.
DNA and ATP in Replication
- ATP provides the energy necessary for DNA replication. During the process, ATP is hydrolyzed into AMP, releasing energy to form the phosphodiester bonds between nucleotides in the DNA backbone.
- DNA polymerase III, the main replication enzyme, adds nucleoside triphosphates (dNTPs) to the growing DNA strand. Two phosphate groups are released per dNTP, providing energy for bond formation and driving replication forward.
Leading and Lagging Strands
- The leading strand of DNA is synthesized continuously in the 5' to 3' direction, following the direction of the replication fork.
- The lagging strand of DNA is synthesized discontinuously due to its antiparallel orientation. Short Okazaki fragments are synthesized in the opposite direction of the replication fork, and then joined together by DNA ligase.
DNA Polymerases
- DNA polymerase I (Pol I): primarily involved in DNA repair, DNA gap filling, and removal of RNA primers during replication.
- DNA polymerase II (Pol II): involved in proofreading and editing, primarily in the lagging strand.
- DNA polymerase III (Pol III): the main replicative enzyme that synthesizes new DNA strands.
DNA Replication
- DNA replication takes place during the S phase of the cell cycle.
- DNA replication begins with the separation of the two strands of the DNA double helix.
- Each strand serves as a template for the synthesis of a new complementary strand.
- The process of DNA replication is carried out by enzymes called DNA polymerases.
- DNA polymerases add new nucleotides to the 3' end of a growing DNA strand.
- The addition of new nucleotides is based on complementary base pairing: adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C).
- DNA replication is semi-conservative, meaning that each new DNA molecule contains one original strand and one newly synthesized strand.
- The leading strand is synthesized continuously in the 5' to 3' direction.
- The lagging strand is synthesized discontinuously in short fragments called Okazaki fragments.
- These fragments are later joined together by DNA ligase.
DNA Structure
- DNA is composed of two antiparallel strands of nucleotides.
- Each nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base.
- The nitrogenous bases are adenine, thymine, guanine, and cytosine. The bases pair up (A with T, G with C) to form hydrogen bonds between the two strands of DNA
- The sugar-phosphate backbone of DNA is a polymer formed by phosphodiester bonds.
- DNA is packaged in the form of chromosomes, which are made of chromatin.
- Chromatin consists of DNA and proteins, including histones, which help to compact DNA.
Prokaryotic DNA Replication
- DNA is supercoiled in prokaryotic cells.
- Supercoiling changes tension in the DNA molecule.
- Supercoiling is regulated by topoisomerases, which can introduce or remove supercoils.
- The enzyme DNA gyrase introduces negative supercoils.
- Topoisomerase I relaxes negative supercoils.
Eukaryotic DNA Replication
- DNA wraps around histones to form nucleosomes.
- Histones are proteins that help to compact DNA.
- Nucleosomes are the basic unit of chromatin.
DNA & ATP
- ATP is a nucleotide that provides energy for DNA replication.
- The synthesis of the sugar-phosphate backbone of DNA requires energy.
- During DNA replication, the two phosphates are broken off of the nucleoside triphosphate, providing energy to form the phosphodiester bond between nucleotides.
DNA Polymerases
- There are several types of DNA polymerases, including Pol I, Pol II, and Pol III.
- DNA Polymerase III is a key enzyme responsible for the synthesis of new DNA during DNA replication.
- DNA polymerase I is involved in DNA repair.
- DNA polymerase II is involved in proofreading and is primarily active during lagging strand synthesis.
RNA Structure
- RNA consists of a phosphate group, a sugar (ribose), and a base (adenine, uracil, guanine, cytosine)
- Ribose differs from deoxyribose in DNA by having a hydroxyl (-OH) group at the 2' carbon instead of a hydrogen (-H)
- RNA is single-stranded, unlike DNA’s double-stranded structure
- RNA forms loops due to base interactions, influencing its various functions
DNA vs RNA
- DNA has two strands while RNA has one strand
- DNA contains thymine as a base while RNA contains uracil
- DNA has deoxyribose as its sugar while RNA has ribose
- DNA primarily stores genetic information, while RNA transfers genetic information
- Mutations in DNA have more serious consequences compared to RNA
- DNA is more stable and accurate with less frequent mutations, while RNA is more prone to mutations and less stable
Transcription vs Replication
- Both processes occur in the 5'-3' direction
- Both involve multiple proteins in their processes
- Both have three steps: initiation, elongation, and termination
- Both involve a temporary unwinding of the DNA double helix to form a transcription bubble
- Transcription involves RNA polymerase while replication involves DNA polymerase
- Transcription copies only one strand of DNA, while replication copies both
- Transcription only copies a specific region of DNA
- Transcription uses nucleoside triphosphates (NTs) while replication uses deoxyribonucleoside triphosphates (dNTs)
RNA Functions
- Facilitate the translation of DNA into proteins
- Act as adapter molecules during protein synthesis
- Carry genetic information
- Function as the primary genetic material for some viruses
- Involved in RNA editing, regulation, and interference
Specific RNA Types
- Messenger RNA (mRNA) carries genetic information for protein synthesis; It is quickly degraded by nucleases
- Transfer RNA (tRNA) delivers amino acids to ribosomes during translation; tRNA is a stable molecule
- Small nuclear RNA (snRNA) forms complexes with proteins involved in eukaryotic RNA processing and splicing
- Ribosomal RNA (rRNA) is the most abundant RNA type and forms a major component of ribosomes; rRNA is stable
DNA Transcription
- Process of synthesizing RNA as a copy of DNA (one strand only)
- Transfers genetic information from DNA to RNA
- Template strand of DNA is 3'-5', while RNA polymerase synthesizes in the 5'-3' direction
- RNA polymerase catalyzes the transcription process
- Transcription bubble is temporary and small
- Template strand of DNA is the non-coding strand (+ strand), and the non-template strand (- strand) is the coding strand; The coding strand has the same sequence as mRNA (except T is replaced with U)
- In prokaryotes, transcription and translation happen simultaneously in the cytoplasm
- In eukaryotes, these processes occur in different locations within the cell
Stages of Transcription
- Initiation: Basal transcription factors bind to promoter regions, aiding RNA polymerase binding; topoisomerase unwinds DNA and then restores it; Positive supercoiling forms in front of the bubble while negative supercoiling occurs behind it; A short RNA primer is synthesized
- Elongation: Ribonucleotide bases (A+U, C+G) are added in the 5'-3' direction, complementary to the template strand DNA
- Termination: RNA synthesis halts at CG-rich sites in DNA in prokaryotes; The termination mechanism varies between prokaryotes and eukaryotes
RNA Modifications
- After transcription, RNA undergoes modifications to become mature RNA
- 5' Cap: GTP (guanine triphosphate) is added to the 5' end, protecting it from degradation; The cap protects RNA from nucleases and aids in translation
Poly A Tail
- A polyA tail is added to the 3' end of the mRNA, increasing its stability by protecting it from exonucleases
- The polyA tail aids in translation
Splicing
- Introns (non-coding regions) are removed from the pre-mRNA, and exons (coding regions) are joined together to form mature mRNA
- Splicing involves snRNPs (snurps) that bind to splice junctions and a branch point on the 5' end of the intron
- Splicing forms a spliceosome where the intron is excised from the exons
- Exons are then joined back together, and the intron is degraded
- Alternative splicing allows for different mRNA sequences from a single DNA strand, resulting in various protein isoforms
Transcription Termination in Prokaryotes
- Rho-dependent Factor: Rho enzyme binds to a specific RNA sequence and dislodges the holoenzyme, resulting in termination
- Rho-independent Factor: Hairpin loops form in the RNA, destabilizing the DNA-RNA hybrid and causing RNA polymerase to detach from the DNA strand
Regulation of Protein Production
- There are six levels at which protein production can be regulated, including:
- Transcriptional control
- RNA processing control
- RNA transport control
- Translational control
- Protein activity control
- Protein degradation control
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