Molecular Biology: DNA Replication & Translation
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Questions and Answers

Which process converts the information encoded in DNA into a complementary RNA sequence?

  • Transcription (correct)
  • Translation
  • Translocation
  • Replication

    • During which process are proteins synthesized based on the information encoded in mRNA?

  • Transcription
  • Reverse Transcription
  • Translation (correct)
  • Replication

    • Which of the following processes involves creating an exact copy of a DNA molecule?

  • Replication (correct)
  • Transcription
  • Translation
  • Mutation

    • What is the main enzyme responsible for synthesizing new DNA strands during replication?

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

    Which of the following is NOT directly involved in the process of translation?

    <p>DNA Polymerase (D)</p> Signup and view all the answers

    What is the primary function of DNA helicase during replication?

    <p>Breaking hydrogen bonds between complementary nitrogenous bases. (D)</p> Signup and view all the answers

    What is the role of topoisomerases in DNA replication?

    <p>Reducing the torsional stress caused by unwinding DNA. (B)</p> Signup and view all the answers

    What is the function of Replication Protein A (RPA) during DNA replication?

    <p>Stabilizing single-stranded DNA to prevent hairpin formation (B)</p> Signup and view all the answers

    What is the main function of Proliferating Cell Nuclear Antigen (PCNA) in DNA replication?

    <p>Protecting DNA polymerase from falling off the template strand (C)</p> Signup and view all the answers

    What is the primary role of Replication Factor C (RFC) in DNA replication?

    <p>Opening and closing the PCNA ring around the DNA (B)</p> Signup and view all the answers

    Which of the following is a characteristic of DNA polymerases?

    <p>They require a DNA template to function. (D)</p> Signup and view all the answers

    What are the two activities associated with Polymerase α/primase?

    <p>Primase and DNA polymerase activity (D)</p> Signup and view all the answers

    What is the role of the 3’ → 5’ exonuclease activity of DNA polymerases?

    <p>Proofreading and removing incorrectly inserted nucleotides. (A)</p> Signup and view all the answers

    What is the function of RNase H in DNA replication?

    <p>Removing the iRNA primer, except for the last ribonucleotide. (B)</p> Signup and view all the answers

    What enzyme removes the last ribonucleotide of the iRNA primer in DNA replication?

    <p>FEN1 (Flap endonuclease 1) (B)</p> Signup and view all the answers

    What is the function of DNA ligase in DNA replication?

    <p>Joining Okazaki fragments and deoxyribonucleotides to a DNA strand. (D)</p> Signup and view all the answers

    Which of the following is a limitation of DNA polymerase?

    <p>It requires a primer to begin synthesis. (D)</p> Signup and view all the answers

    During which stage of DNA replication does the copying of parent DNA strands occur?

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

    What is a replicon?

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

    What is the significance of having multiple origins of replication in eukaryotic chromosomes?

    <p>To complete DNA replication more rapidly. (B)</p> Signup and view all the answers

    What is the primary function of aminoacyl-tRNA synthetase during translation?

    <p>Attaching specific amino acids to their corresponding tRNA molecules. (A)</p> Signup and view all the answers

    Which of the following events occurs during the termination stage of translation?

    <p>A release factor binds to a stop codon in the A site of the ribosome. (A)</p> Signup and view all the answers

    What is the role of chaperone proteins following translation?

    <p>To ensure correct folding of newly synthesized polypeptide chains. (A)</p> Signup and view all the answers

    Which of the following is NOT a post-translational modification?

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

    Which of the following is directly responsible for catalyzing the formation of peptide bonds during translation elongation?

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

    What event immediately follows the recognition of the AUG start codon during translation initiation?

    <p>The large ribosomal subunit binds, forming the complete ribosome. (A)</p> Signup and view all the answers

    What is the function of the E site on the ribosome during translation?

    <p>It is the exit site for tRNA that has delivered its amino acid. (B)</p> Signup and view all the answers

    Which of the following is a characteristic of the initiator tRNA in bacteria?

    <p>It can only bind to the P site in the absence of the large ribosomal subunit. (A)</p> Signup and view all the answers

    During translation elongation, what is the correct order of tRNA binding sites that a tRNA molecule occupies in the ribosome?

    <p>A → P → E (C)</p> Signup and view all the answers

    What is the role of release factors in translation termination?

    <p>They bind to stop codons and trigger the release of the polypeptide chain. (C)</p> Signup and view all the answers

    During translation initiation, the small ribosomal subunit binds to the mRNA. What is the next key event?

    <p>Scanning for the AUG start codon. (D)</p> Signup and view all the answers

    Which of the following modifications is most likely to directly affect protein-protein interactions?

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

    Which of the following is a key difference between the two types of tRNA that can bind methionine?

    <p>One participates in initiation while the other participates in elongation. (B)</p> Signup and view all the answers

    What is the consequence of adding water molecules to peptidyl-tRNA during translation termination?

    <p>Leads to the release of the full-length protein (D)</p> Signup and view all the answers

    The start codon AUG codes for methionine. However, the synthesis of every protein in bacteria begins with formylmethionine. What is the significance of this difference?

    <p>Formylmethionine is removed after translation (D)</p> Signup and view all the answers

    Which of the following components are directly involved in forming the pre-replication complex (pre-RC)?

    <p>Origin Recognition Complex (ORC), Cdt1, and Cdc6 (A)</p> Signup and view all the answers

    During DNA replication, what is the primary role of RPA proteins?

    <p>Stabilizing single-stranded DNA (ssDNA) templates (B)</p> Signup and view all the answers

    Why are replication forks considered asymmetric?

    <p>Because one strand is synthesized continuously (leading strand) and the other discontinuously (lagging strand) (B)</p> Signup and view all the answers

    What is the function of RFC (Replication Factor C) during DNA replication elongation?

    <p>To recognize the primer-template DNA hybrid and deposit PCNA (D)</p> Signup and view all the answers

    What is the role of pyrophosphate (PPi) hydrolysis in DNA replication?

    <p>It makes the polymerization reaction irreversible (A)</p> Signup and view all the answers

    Which enzyme is primarily responsible for removing iRNA and iDNA primers during the processing of Okazaki fragments?

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

    What is the primary function of DNA ligase in DNA replication?

    <p>Joining Okazaki fragments (A)</p> Signup and view all the answers

    In eukaryotes, how is DNA replication terminated?

    <p>When a pair of replication forks meet (C)</p> Signup and view all the answers

    What is the significance of telomeres in DNA replication?

    <p>They prevent the shortening of DNA strands after each division (B)</p> Signup and view all the answers

    What is the role of RNA polymerase I in transcription?

    <p>Transcription of genes encoding ribosomal RNA (rRNA) (D)</p> Signup and view all the answers

    During the elongation stage of mRNA transcription, what happens to most transcription factors?

    <p>They detach from the DNA (A)</p> Signup and view all the answers

    What enzyme plays a role in unwinding DNA during the initiation of mRNA transcription?

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

    What event marks the termination of mRNA transcription?

    <p>The recognition of a specific DNA sequence called the transcription terminator (A)</p> Signup and view all the answers

    Which of the following processing steps occurs during the maturation of pre-mRNA?

    <p>Adding a cap to the 5' end (C)</p> Signup and view all the answers

    What is the name given to the region of DNA between the promoter and terminator that is transcribed into RNA?

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

    Flashcards

    DNA Replication

    The process of creating two identical copies of DNA from one original DNA molecule.

    Transcription

    The process of copying a segment of DNA into RNA.

    Translation

    The process of converting RNA sequences into proteins.

    Molecular Biology

    The field of science that studies the molecular mechanisms of biological activity.

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    Essential Cell Biology

    A foundational textbook covering key concepts in cell biology and molecular processes.

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    Semiconservative replication

    Each strand of DNA serves as a template for a new strand.

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    Direction of DNA synthesis

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

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    Phosphodiester bond

    Bond formed between new nucleotides during DNA synthesis.

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    Helicase

    Enzyme that unwinds the DNA double helix.

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    Topoisomerase

    Enzyme that relieves torsional stress in DNA.

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    RPA (Replication Protein A)

    Binds to single-stranded DNA to prevent reformation of doubles.

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    PCNA (Proliferating Cell Nuclear Antigen)

    Ring-shaped protein that acts as a scaffold during DNA replication.

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    RFC (Replication Factor C)

    Helps load the PCNA onto DNA to initiate replication.

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    DNA polymerase

    Enzyme that synthesizes new DNA strands from a template.

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    Primase

    Synthesizes RNA primers needed for DNA replication.

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    Okazaki fragments

    Short DNA fragments synthesized on the lagging strand.

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    Exonuclease activity

    The ability to remove incorrect nucleotides from DNA.

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    RNAse H

    Removes the RNA primer during DNA replication.

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    Ligase

    Joins DNA fragments by forming phosphodiester bonds.

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    Stages of DNA replication

    Includes initiation, elongation, and termination.

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    Origin Recognition Complex (ORC)

    A protein complex that binds to the origin of replication to start DNA replication.

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    Pre-replication Complex (pre-RC)

    A complex formed by ORC, Cdt1, Cdc6, and helicase that prepares the DNA for replication.

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    Helicase Function

    Unwinds the DNA double helix to allow replication to occur.

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    Topoisomerase Role

    Enzymes that relieve the tension and supercoiling in DNA ahead of the replication fork.

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    Replication Forks

    Y-shaped structures that form during DNA replication where the DNA strands separate.

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    Leading Strand

    The strand of DNA that is synthesized continuously during DNA replication.

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    Lagging Strand

    The strand of DNA that is synthesized in short fragments called Okazaki fragments.

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    RNA Primer Removal

    The process of replacing RNA primers with DNA after replication.

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    Ligase Function

    An enzyme that joins together Okazaki fragments to create a continuous DNA strand.

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    Transcription Terminator

    A DNA sequence that signals the end of transcription process.

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    Post-transcriptional Processing

    The modifications made to pre-mRNA before it becomes functional mRNA.

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    RNA Polymerase II

    An enzyme responsible for synthesizing mRNA from a DNA template during transcription.

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    Mature mRNA

    mRNA that has been processed and is ready for translation after introns are removed.

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    Ribosome structure

    Ribosomes consist of two subunits (small and large) made of proteins and rRNA, connecting during translation.

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    tRNA binding sites

    Ribosomes have three tRNA binding sites: A (aminoacyl), P (peptidyl), and E (exit).

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    Stages of translation

    Translation occurs in three stages: initiation, elongation, and termination.

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    Initiation of translation

    The start of translation involving formation of a pre-initiation complex and initiator tRNA.

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    fmet-tRNAf

    The tRNA that binds to the P site during initiation, carrying formylmethionine.

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    Translation elongation

    The phase where amino acids are added one by one to the growing polypeptide chain.

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    Peptide bond formation

    A reaction where amino acids are linked together, catalyzed by peptidyl transferase in the ribosome.

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    STOP codons

    Codons UAA, UAG, and UGA signal the end of translation and are not recognized by tRNA.

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    Release factors

    Proteins that bind to STOP codons, causing termination of translation by hydrolyzing the bond of tRNA and the polypeptide.

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    Post-translational modifications

    Chemical changes to a protein after synthesis, necessary for functional activity.

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    Chaperone proteins

    Helper proteins that assist in proper folding of newly synthesized polypeptide chains.

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    Biochemical modifications

    Processes that include phosphorylation, glycosylation, and others that alter proteins for activity.

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    Translation termination

    The final phase of translation where the completed polypeptide is released and the ribosome disassociates.

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    Study Notes

    DNA Replication, Transcription, and Translation

    • This is a summary of the processes of DNA replication, transcription and translation.
    • The lectures will focus on these processes as outlined in Essential Cell Biology, 6th Edition by Bruce Alberts.
    • Key chapters are 6: DNA Replication and Repair and 7: From DNA to Protein.

    DNA Replication

    • Replication is a semiconservative process, meaning each strand of the double helix acts as a template for a new, complementary strand.
    • DNA synthesis proceeds only in the 5' to 3' direction.
    • Newly added nucleotides are connected by a phosphodiester bond.
    • The process is enzymatic due to the numerous protein complexes required.
    • Energy input is necessary, supplied by the hydrolysis of high-energy phosphate bonds.

    Replication Proteins

    • Helicase (MCM 2-7): A protein complex forming a ring around a single DNA strand; it breaks hydrogen bonds between complementary base pairs, unwinding the DNA helix. The MCM 2-7 proteins use ATP hydrolysis to move along the strand and separate the complementary strands.
    • Topoisomerases: Enzymes that relieve torsional stress (twisting tension) in DNA during unwinding. Topoisomerases change the topology of the DNA molecule, reducing tension. There are two main types: Topoisomerase I and II.
    • Replication Protein A (RPA): Binds to single-stranded DNA to prevent the formation of secondary structures, making the DNA available for replication.
    • Proliferating Cell Nuclear Antigen (PCNA): A ring-shaped homotrimer that acts as a scaffold for proteins involved in replication and repair, chromatin remodeling, and epigenetic regulation. It protects DNA polymerase from falling off the template strand and releases it after each Okazaki fragment is synthesized.
    • Replication Factor C (RFC): A ring-applying protein required for loading PCNA onto the DNA strand during replication. The process depends on ATP in both the leading and lagging strand.
    • DNA Polymerases: Enzymes responsible for synthesizing new DNA strands using existing DNA as templates. Specific types such as alpha (α), beta(β), gamma (γ), delta (δ), and epsilon (ε) have differing roles, which will be covered in detail during the lectures.
    • RNase H (endonucleases): Removes RNA primers except for the final ribonucleotide in the newly formed DNA chain.
    • FEN1 (exonuclease): Removes the final ribonucleotide of the RNA primer.
    • Ligase: Seals the gaps (nicks) between Okazaki fragments on the lagging strand, connecting them using a phosphodiester bond, and using ATP as energy source.

    DNA Polymerase

    • DNA polymerases need a DNA template for synthesis.
    • They cannot initiate synthesis without a primer.
    • DNA polymerases have a 5' → 3' polymerase activity and a 3' → 5' exonuclease activity (proofreading).

    Polymerase α/primase

    • Plays a combined primase and DNA polymerase role.
    • Primase synthesizes RNA primers, short strands of RNA complementary to the DNA template.
    • Polymerase α adds a short section of DNA (initiator DNA) to these primers.

    Ribonucleases

    • Enzymes that divide RNA molecules into shorter chains or individual nucleotides, by hydrolyzing phosphodiester bonds.
    • Endo-RNases cut RNA molecules in the middle.
    • Exo-RNases remove nucleotides from either ends.

    DNA Replication Limitations

    • Need to unwind the double helix.
    • DNA polymerase's inability to initiate synthesis independently.
    • Addition of nucleotides can only occur in the 5′ -> 3′ direction.

    DNA Replication Stages

    • Initiation: Unwinding the DNA helix at origins of replication which involve specific sequences of ~10,000 base pairs. Replication occurs simultaneously at many sites. Clusters occur in what are called replication factories, or foci.
    • Elongation: Process of replication forks and copying of parent DNA strands.
    • Termination: Completion and assembly of new DNA strands once replication forks meet.

    Limitations of Replication

    • Primer synthesis for initiating new DNA strands, by primase. Polymerase a synthesizes short strands of 10 nucleotides of iRNA. Polymerase a synthesizes the first ~20-30 deoxynucleotides of DNA (IDNA). Polymerase δ or ε takes over.
    • The need to unwind the double helix by helicase
    • The inability of DNA polymerase to independently initiate the synthesis of a new DNA strand.
    • Addition of nucleotides occurs in a 5' → 3' direction.

    Replication Forks

    • Due to the antiparallel nature of DNA strands and the synthesis direction, replication forks are asymmetric.
    • Leading strand synthesizes continuously.
    • Lagging strand synthesizes in short sections, Okazaki fragments.

    DNA Replication Elongation (Leading Strand)

    • Hydrolysis of one phosphate bond from dNTP provides energy for attachment.
    • Formation of a phosphodiester bond between the last deoxyribonucleotide of DNA and 5′ end of new deoxynucleotide.
    • Release of pyrophosphate (PPi) makes the reaction irreversible.

    DNA Replication Elongation (Lagging Strand)

    • Elongation is discontinuous: iRNA synthesis for primer strands.
    • Synthesis of subsequent iDNA strands in 5' → 3' direction using a-polymerase.
    • Recognition of the primer-template hybrid by RFC, which places PCNA at the site.
    • Exchange of a-polymerase for ε-polymerase.

    Okazaki fragments

    • After reaching the preceding primer, the first a-polymerase with primase detaches from the template.
    • DNA strand synthesis in the 5' → 3' direction is catalyzed by ε-polymerase.
    • Removal of the iRNA and iDNA fragments using RNase H and FEN1.
    • Exchange of ε-polymerase for α-polymerase.

    Overview

    • The lagging strand DNA synthesis requires multiple primers which are eventually removed.
    • In linear DNA molecules, the lagging strand is always shorter than the template, which occurs at the end of each chromosome, the telomeric part.

    Post-transcriptional Modifications

    • Adding a cap to the 5' end.
    • Cutting out introns and joining exons (splicing).
    • Adding a series of adenine nucleotides to the 3' end (polyadenylation).

    Transcription

    • Rewriting genetic information from DNA to RNA.
    • Based on the complementarity rule: A-U, C-G.
    • DNA strand read in 3' → 5' direction.
    • RNA synthesized in 5' → 3' direction.
    • Catalyzed by RNA polymerases (I, II, III).
    • Occurs in the nucleus in eukaryotes

    Initiation of mRNA Transcription

    • A complex of proteins recognizes the promoter and creates a platform.
    • Transcription factors (one of which is helicase) bind to the platform.
    • RNA polymerase II along with transcription factors form the pre-initiation complex that binds to the gene promoter.
    • This allows RNA polymerase II to begin transcription of pre-mRNA.

    Elongation of mRNA Transcription

    • Once elongation begins, most transcription factors detach.
    • Phosphate groups are added to the tail of RNA polymerase II, freeing it from the transcription factors.
    • More ribonucleotides are added, creating pre-mRNA on the template strand.

    Termination of mRNA Transcription

    • RNA polymerase II continues transcription until signal to stop.
    • Transcription terminator is a DNA fragment marking the end of the gene.
    • The steps are:
    • phosphodiester bond formation ceases.
    • Pre-mRNA dissociates from the DNA-RNA hybrid.
    • The unravelled DNA fragment joins to complete the termination.

    Translation

    • Synthesis of a polypeptide chain from mRNA.
    • Occurs in the cytoplasm or on membranes of the rough endoplasmic reticulum.
    • Catalyzed by ribosomes.

    Ribosome Structure

    • Ribosomes are made up of two subunits, small and large.
    • These subunits are made of proteins and rRNA (ribosomal RNA).
    • The small and large subunits are joined during translation.
    • mRNA binding site is in the small subunit only.
    • Both subunits participate in tRNA binding sites: A, P, E.

    Translation Stages

    • Initiation: Formation of a pre-initiation complex (small ribosomal subunit, initiation factors, initiator tRNA).
    • Elongation: Cycle with 4 stages:
    1. tRNA carrying the next amino acid binds to free A site
    2. Peptide bond is formed (peptidyl transferase).
    3. tRNA without amino acid moves to site E, peptidyl-tRNA moves from site A to site P.
    4. Small subunit moves 3 nucleotides, tRNA without amino acid is removed, site A released.
    • Termination: Signaled by a STOP codon; factors detach, the polypeptide chain detaches, and the ribosome disintegrates into its subunits.

    Post-Translational Modifications

    • Many proteins must undergo further modifications to become fully functional.
    • Proteolytic processing, formation of secondary structure, protein folding, and various other modifications are included.
    • So-called chaperone proteins help in the correct folding, degradation of incorrectly folded proteins.
    • Chemical processes can also modify proteins: phosphorylation, dephosphorylation, glycosylation, hydroxylation and methylation.

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    DNA Replication, Transcription, and Translation Lecture Notes PDF

    Description

    Test your knowledge on key processes in molecular biology, focusing on DNA replication and translation. This quiz covers enzyme functions, characteristics of DNA polymerases, and the roles of various proteins involved in these central biological processes.

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