Molecular Biology: Transcription and Translation
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Questions and Answers

Which of the following processes directly involves RNA polymerase?

  • Reverse transcription
  • DNA replication
  • Transcription (correct)
  • Translation

    • During DNA replication, what is the role of the enzyme DNA ligase?

  • To unwind the DNA double helix
  • To add nucleotides to the 3' end of the leading strand
  • To synthesize short RNA primers
  • To seal the gaps between Okazaki fragments (correct)

    • Which of the following is a key difference between DNA replication and transcription?

  • Replication copies the entire genome, while transcription copies only specific genes. (correct)
  • Replication occurs in the nucleus, while transcription occurs in the cytoplasm.
  • Replication uses RNA nucleotides, while transcription uses DNA nucleotides.
  • Replication involves proofreading mechanisms, while transcription does not.

    • What is the function of ribosomes in the process of translation?

    <p>To catalyze the formation of peptide bonds between amino acids (C)</p> Signup and view all the answers

    Which of the following modifications is typically found on eukaryotic mRNA before it leaves the nucleus?

    <p>Attachment of a poly(A) tail to the 3' end (D)</p> Signup and view all the answers

    What is the primary function of the Origin Recognition Complex (ORC) in DNA replication?

    <p>To recognize and bind to the DNA origin of replication. (B)</p> Signup and view all the answers

    Why are replication forks considered asymmetrical?

    <p>Due to the antiparallel arrangement of DNA strands and the 5' → 3' directionality of DNA synthesis. (C)</p> Signup and view all the answers

    During DNA replication, what is the role of the sliding clamp protein, PCNA?

    <p>To load the DNA polymerase onto the DNA template and increase its processivity. (A)</p> Signup and view all the answers

    What is the function of topoisomerase during DNA replication?

    <p>To relieve torsional stress and prevent supercoiling of the DNA ahead of the replication fork. (D)</p> Signup and view all the answers

    Which statement best describes the key difference between DNA replication on the leading and lagging strands?

    <p>The leading strand is synthesized continuously towards the replication fork, whereas the lagging strand is synthesized discontinuously away from the replication fork. (D)</p> Signup and view all the answers

    What enzymatic activity is responsible for removing the RNA primers during DNA replication?

    <p>RNase H/FEN1 (A)</p> Signup and view all the answers

    What is the role of DNA ligase in DNA replication?

    <p>To join Okazaki fragments together to create a continuous DNA strand. (A)</p> Signup and view all the answers

    What is the significance of telomeres in DNA replication?

    <p>Telomeres protect the ends of chromosomes from degradation and shortening during replication cycles. (D)</p> Signup and view all the answers

    During mRNA transcription, what is the role of the transcription factors?

    <p>To recognize and bind to the promoter region, creating a platform for RNA polymerase II to bind. (D)</p> Signup and view all the answers

    Which of the following is NOT a stage of transcription?

    <p>Replication (B)</p> Signup and view all the answers

    Which enzyme is responsible for synthesizing mRNA during transcription?

    <p>RNA polymerase II (C)</p> Signup and view all the answers

    What is the function of the poly(A) tail added during post-transcriptional processing of pre-mRNA?

    <p>All of the above. (D)</p> Signup and view all the answers

    What happens to RNA polymerase II after it receives the signal to end transcription?

    <p>It detaches from the DNA-RNA hybrid, leading to termination. (A)</p> Signup and view all the answers

    What is the role of helicase in the initiation of mRNA transcription?

    <p>To unwind the DNA at the promoter region, allowing RNA polymerase II to access the template strand (D)</p> Signup and view all the answers

    The pre-initiation complex (PIC) is essential for transcription. Which components combine to form the PIC?

    <p>Transcription factors and RNA polymerase II (A)</p> Signup and view all the answers

    What is the direction of DNA synthesis during replication?

    <p>5' → 3' (B)</p> Signup and view all the answers

    Which enzyme is responsible for unwinding the DNA double helix?

    <p>Helicase (A)</p> Signup and view all the answers

    What type of bond joins newly added nucleotides during DNA replication?

    <p>Phosphodiester bond (C)</p> Signup and view all the answers

    Which of the following proteins acts as a scaffold during DNA replication?

    <p>PCNA (C)</p> Signup and view all the answers

    Which polymerase is primarily responsible for lagging strand synthesis?

    <p>Polymerase ε (B)</p> Signup and view all the answers

    What major role does RNAse H play in DNA replication?

    <p>Removes the iRNA primer (C)</p> Signup and view all the answers

    How does DNA polymerase ensure the accuracy of DNA replication?

    <p>Through exonuclease activity (A)</p> Signup and view all the answers

    What process occurs during the initiation stage of DNA replication?

    <p>Unwinding of DNA strands (D)</p> Signup and view all the answers

    Which of the following describes the role of topoisomerase in DNA replication?

    <p>Reduces torsional stress (A)</p> Signup and view all the answers

    What is the primary role of ribosomes during translation?

    <p>Catalyze the formation of peptide bonds (A)</p> Signup and view all the answers

    Which type of tRNA is involved in the initiation stage of translation?

    <p>fmet-tRNAf (C)</p> Signup and view all the answers

    What is the primary function of the FEN1 protein in DNA replication?

    <p>Removes RNA primers (A)</p> Signup and view all the answers

    What is the requirement for a DNA polymerase to initiate DNA synthesis?

    <p>An existing RNA primer (B)</p> Signup and view all the answers

    What does the presence of a STOP codon signal during translation?

    <p>Completion of the polypeptide chain (C)</p> Signup and view all the answers

    What are the three main stages of translation?

    <p>Initiation, elongation, and termination (A)</p> Signup and view all the answers

    What defines an origin of replication?

    <p>A specific sequence of nucleotides where replication begins (C)</p> Signup and view all the answers

    What is the main function of the polymerase α/primase complex?

    <p>Initiating the synthesis of DNA with a primer (D)</p> Signup and view all the answers

    Which site on the ribosome is responsible for the binding of the newly arriving aminoacyl-tRNA?

    <p>A site (B)</p> Signup and view all the answers

    What is a replicon?

    <p>A fragment of replicated DNA from one origin (A)</p> Signup and view all the answers

    What is the function of chaperone proteins in post-translational modifications?

    <p>Facilitate protein folding (C)</p> Signup and view all the answers

    What type of chemical modification is phosphorylation?

    <p>Adding a phosphate group (A)</p> Signup and view all the answers

    During translation elongation, which enzyme is responsible for forming the peptide bond?

    <p>Peptidyl transferase (A)</p> Signup and view all the answers

    Which component recognizes the first AUG start codon during translation initiation?

    <p>Small ribosomal subunit (B)</p> Signup and view all the answers

    What happens to the polypeptide chain at the end of translation termination?

    <p>It is released from the ribosome (D)</p> Signup and view all the answers

    Which of the following correctly describes the components of a pre-initiation complex?

    <p>Small subunit, initiation factors, mRNA (D)</p> Signup and view all the answers

    Which factor is NOT necessary for the elongation phase of translation?

    <p>Release factors (C)</p> Signup and view all the answers

    What is the role of aminoacyl-tRNA synthetase during translation?

    <p>Attaching specific amino acids to their corresponding tRNAs (C)</p> Signup and view all the answers

    Flashcards

    DNA Replication

    The process of copying DNA to create two identical DNA molecules.

    Transcription

    The process of synthesizing RNA from a DNA template.

    Translation

    The process in which ribosomes read mRNA to synthesize proteins.

    mRNA

    Messenger RNA, a type of RNA that carries genetic information from DNA.

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    Ribosomes

    Cellular structures that perform protein synthesis by translating mRNA.

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    Semiconservative replication

    Each DNA strand serves as a template for a new, complementary strand.

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    Direction of DNA synthesis

    DNA synthesis occurs only in the 5’ → 3’ direction.

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    Phosphodiester bond

    A bond formed between nucleotides during DNA synthesis.

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    Helicase

    Enzyme that unwinds the DNA double helix by breaking hydrogen bonds.

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    Topoisomerases

    Enzymes that relieve torsional stress in DNA during replication.

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    Replication Protein A (RPA)

    Binds to single-stranded DNA to prevent re-annealing.

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    RFC

    Regulatory factor that opens and closes PCNA around DNA.

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    DNA polymerase

    Enzyme that synthesizes new DNA strands by adding nucleotides.

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    Primase

    Synthesizes an RNA primer to initiate DNA replication.

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    Exonuclease activity

    Allows DNA polymerases to proofread and correct mistakes.

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    RNAse H

    An enzyme that removes RNA primers during DNA replication.

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    Ligase

    Enzyme that joins DNA fragments by forming phosphodiester bonds.

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    Stages of DNA replication

    Involves initiation, elongation, and termination.

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    Replication factories

    Sites in DNA where replication occurs simultaneously.

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    Pre-replication complex (pre-RC)

    A protein complex that initiates DNA replication at the origin.

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    Origin Recognition Complex (ORC)

    A six-protein complex that binds to the DNA origin for replication initiation.

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    Replication fork

    The area where DNA strands are separated and replication occurs.

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    Leading strand

    The DNA strand synthesized continuously during replication.

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    Lagging strand

    The DNA strand synthesized discontinuously in short sections (Okazaki fragments).

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    Okazaki fragments

    Short DNA segments synthesized on the lagging strand during replication.

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    RNase H and FEN1

    Enzymes that remove RNA primers during DNA replication.

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    Transcription factors

    Proteins that help initiate transcription by binding to promoters.

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    RNA polymerase II

    Enzyme that synthesizes mRNA from a DNA template during transcription.

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    Post-transcriptional processing

    Modifications made to pre-mRNA before it becomes functional mRNA.

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    Peptide bond

    A covalent bond formed between adjacent amino acids in a protein chain.

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    Polypeptide chain

    A sequence of amino acids linked by peptide bonds forming a protein.

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    Initiation factors

    Proteins required for the initiation stage of translation.

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    AUG codon

    The start codon for translation, signaling the beginning of protein synthesis.

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    Stop codons

    mRNA sequences that signal the termination of translation: UAA, UAG, UGA.

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    Translation elongation

    The stage where the polypeptide chain is lengthened by adding amino acids based on mRNA sequence.

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    Post-translational modifications

    Changes made to proteins after synthesis, enhancing their function.

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    Chaperone proteins

    Proteins that assist in the correct folding of newly synthesized polypeptides.

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    Peptidyl transferase

    An enzyme acting in the ribosome that forms peptide bonds between amino acids.

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    tRNA binding sites

    Sites on the ribosome where tRNA binds: A, P, and E sites.

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    Release factors

    Proteins that recognize stop codons and terminate translation.

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    Aminoacyl-tRNA synthetase

    Enzyme that attaches the correct amino acid to its corresponding tRNA.

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    Study Notes

    DNA Replication, Transcription and Translation

    • DNA Replication: A semiconservative process where each strand of the DNA double helix serves as a template for a new, complementary strand. DNA synthesis proceeds only in the 5' to 3' direction. This enzymatic process requires numerous protein complexes and energy input from the hydrolysis of high-energy phosphate bonds.

    Book Reference

    • Use Essential Cell Biology, 6th edition by Bruce Alberts, focusing on content covered in the lectures.
    • Refer to Chapter 6: DNA Replication and Repair.
    • Refer to Chapter 7: From DNA to Protein.

    DNA Replication Proteins

    • Helicase (MCM 2-7): A protein complex forming a ring around a single DNA strand and breaking hydrogen bonds between complementary bases to unwind the DNA. The MCM 2-7 proteins use ATP.
    • Topoisomerases (I and II): Enzymes that change topology of the DNA strand by reducing tension from the unwinding of the DNA helix.
    • Replication Protein A (RPA): Binds to single stranded DNA segments, preventing the formation of hydrogen bonds and allowing DNA polymerase to synthesize a complementary DNA strand.
    • Proliferating Cell Nuclear Antigen (PCNA): A ring-shaped homotrimer placed on the DNA strand with the participation of RFC. PCNA acts as a scaffold for recruitment of proteins involved in DNA replication, repair, chromatin remodeling, and epigenetic regulation. PCNA protects DNA polymerase from detaching and releases the DNA polymerase after each Okazaki fragment is synthesized.
    • Replication Factor C (RFC): A ring-applying protein that opens the PCNA protein trimer, introduces DNA into the center of the ring, and then closes the ring using ATP. RFC is involved in leading and lagging strand replication, where PCNA is placed multiple times on the DNA strand on the lagging strand synthesis due to Okazaki fragments.
    • DNA Polymerases (α, β, γ, δ, ε): Enzymes involved in DNA synthesis. DNA Polymerases δ (d) and ε (e) are composed of four subunits with specific molecular weights. Polymerase δ prefers leading strand replication, and Polymerase ε prefers lagging strand replication. Both polymerases exhibit 5' to 3' polymerase and 3' to 5' exonuclease activity.
    • RNase H (endonucleases): Removes RNA primers, except for the last ribonucleotide in the DNA chain.
    • FEN1 (exonuclease): Removes the last ribonucleotide of the iRNA primer.
    • Ligase: Joins deoxyribonucleotides to a DNA strand by forming phosphodiester bonds using ATP. Connects Okazaki fragments on the lagging strand.

    DNA Polymerase

    • Characteristics: Require a DNA template; unable to initiate a new strand independently (need a primer). Possess 5' to 3' polymerase activity and 3' to 5' exonuclease activity (proofreading).

    Polymerase a/primase

    • Characteristics: Has both primase and DNA polymerase activity. Primase synthesizes a short RNA primer complementary to the template DNA strand. Polymerase a adds a section of DNA to the primer. Polymerases δ and ε then take over further DNA synthesis.

    Ribonucleases (RNAses)

    • Characteristics: Hydrolases that divide RNA molecules into smaller segments or single nucleotides by hydrolyzing phosphodiester bonds.
      • Endoribonucleases: Divide RNA molecules in the middle of the RNA chain.
      • Exoribonucleases: Detach nucleotides from the 3' or 5' end of RNA.

    Replication Proteins

    • RNase H: Removes RNA primers, except for last ribonucleotide, in synthesis of new DNA.
    • FEN1: An exoribonuclease that removes the final ribonucleotide from RNA primer.

    Limitations of DNA Replication

    • Unwinding the DNA double helix: Requires energy and specific proteins (helicases) to prevent strain and maintain the unwound and copied strands.
    • DNA polymerase's inability to initiate independent synthesis: A primer (often RNA) is needed to provide a starting point.
    • Addition of nucleotides only in the 5' to 3' direction: This creates issues because the DNA strands are antiparallel, leading to continuous and discontinuous synthesis.

    Stages of DNA Replication

    • Initiation: Recognition of specific sequences (origins of replication) by the pre-replication complex. The specific sequence is 10,000 base pairs in mammals. Forms replication bubbles which then form replication forks. The unwinding of the DNA helix occurs at origins of replication.
    • Elongation: The action of replication forks. Copies the parent DNA strands.
    • Termination: Completion and assembly of new DNA strands and meeting of the replication forks.

    Replication Forks

    • Antiparallel arrangement of DNA strands and 5’ → 3’ synthesis means replication forks are asymmetrical. One strand is synthesized continuously (leading strand); the other in sections (lagging strand), called Okazaki fragments.

    DNA Replication Elongation

    • Leading strand: Synthesized continuously in the 5' → 3' direction by δ-polymerase in eukaryotic processes.

    • Lagging strand: Synthesized discontinuously (Okazaki fragments). Uses ε-polymerase and has RNA primers. This needs replacement of RNA primers, and joining those fragments.

    Transcription

    • The process of rewriting genetic information from DNA to RNA (mRNA, tRNA, or rRNA).
    • Based on the complementarity rule: base pairing (A-U and C-G).
    • Promoter and terminator regions mark the start and end of the transcription unit.
    • DNA is read in the 3' → 5' direction.
    • RNA is synthesized from 5' to 3' direction by RNA polymerases I, II, or III.

    Transcription Stages

    • Initiation: Binding of RNA polymerase to a promoter region.
    • Elongation: RNA polymerase synthesizes a pre-RNA molecule.
    • Termination: RNA polymerase stops synthesizing and releases the pre-RNA.

    Initiation of mRNA Transcription

    • A complex of two proteins recognizes the promoter and forms a platform for subsequent factors (like helicase) and RNA polymerase II.
    • The complex forms a pre-initiation complex that binds the gene promoter, enabling RNA polymerase II to initiate transcription of pre-mRNA.

    Elongation of mRNA Transcription

    • After elongation begins, most transcription factors detach from the DNA.
    • The first step in freeing RNA polymerase II involves adding phosphate groups (phosphorylation) to its "tail".
    • More ribonucleotides are added, and the pre-mRNA molecule is synthesized.

    Termination of mRNA Transcription

    • RNA polymerase II continues transcription until a termination signal (terminator sequence) is encountered.
    • Phosphodiester bond formation ceases.
    • Pre-mRNA dissociates from the DNA–RNA hybrid, and the unraveled DNA fragment joins.

    Post-transcriptional Processing

    • Adding a cap to the 5' end.
    • Cutting out introns and joining exons (splicing).
    • Adding a poly-A tail to the 3' end.

    Translation

    • The process of synthesizing a polypeptide chain (protein) from an mRNA.
    • Takes place in the cytoplasm or on the rough endoplasmic reticulum.
    • Catalyzed by the ribosome.
    • Consists of synthesis of polypeptide chain according to the information in the DNA fragment; and peptide bond formation between consecutive amino acids.

    Ribosome

    • Composed of two subunits (small and large), both made of proteins and rRNA.
    • Subunits connect for translation.
    • The small subunit has an mRNA binding site.
    • Both subunits form tRNA binding sites: A (aminoacyl-tRNA), P (peptidyl-tRNA), and E (exit).

    Translation Stages

    • Initiation: Formation of the pre-initiation complex
      • Small ribosomal subunit
      • Initiation factors
      • Initiator tRNA
    • Elongation: A sequence of steps (Stage 1-4) repeated for each amino acid added to the growing polypeptide chain.
      • tRNA binds to the A site.
      • Peptide bond forms.
      • Ribosome moves along the mRNA.
    • Termination: The incorporation of STOP codons into the mRNA sequence.
      • Release factors bind to the A site.
      • Polypeptide chain releases.

    Initiator tRNA

    • fmet-tRNA and met-tRNA bind methionine.
    • fmet-tRNA initiates protein synthesis.
    • Only fmet-tRNAf binds the P site in the absence of the large ribosomal subunit.

    Attaching tRNA to Amino Acid

    • Aminoacyl-tRNA synthetase attaches the correct amino acid to its specific tRNA.

    Translation initiation

    • No signal sequences on mRNA to help locate start site.
    • Pre-initiation complex (small ribosomal subunit, initiator tRNA, and mRNA).
    • The complex scans the mRNA for AUG start codon.
    • Translation initiation factors detach, large subunit joins the complex, and the first tRNA (initiator tRNA) binds within the P site, where the polypeptide chain will begin to grow.

    Translation Elongation

    • tRNA carries the next amino acid and binds to the A site, ensuring codon–anticodon base complementarity to maintain the genetic flow.
    • Peptide bond formation occurs between the amino acid on site A with the peptide on site P.
    • Ribosome moves one codon position along the mRNA.
    • tRNA that previously was at site A moves to site P, and the tRNA that was at site P moves to site E (exit).

    Termination of Translation

    • STOP codon encountered.
    • Release factors bind the A site.
    • Polypeptide chain is released.
    • Ribosome disintegrates into two subunits.

    Post-translational modifications

    • Several processes modify proteins after translation to create functional proteins.

      • Proteolytic processing: Cutting proteins into smaller units.
      • Formation of secondary structure: Folding into specific shapes.
      • Protein folding: Using chaperone proteins to help proteins fold properly.

    • Chemical modifications: Phosphorylation of proteins (adding a phosphate group); dephosphorylation (removing a phosphate group).

    • Glycosylation (adding sugar residues), hydroxylation (adding a hydroxyl group), acetylation (adding an acetyl group), methylation (adding a methyl group), and formylation (adding a formyl group).

    • Chaperone are proteins that are involved in the correct folding of proteins. Newly synthesized polypeptide chains bind to these chaperone proteins to correctly fold. If incorrectly folded proteins are present, they can be degraded (broken down into smaller chains of amino acids). Additionally, chaperone proteins can also create isolation chambers in order to facilitate protein folding.

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    DNA Replication, Transcription, and Translation Lecture Notes PDF

    Description

    This quiz tests your understanding of key molecular biology processes, including transcription and translation. You'll explore the roles of RNA polymerase, DNA ligase, and ribosomes, alongside the modifications to eukaryotic mRNA. Perfect for students reviewing these fundamental concepts.

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