Molecular Biology: DNA Replication Quiz
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Questions and Answers

Which DNA polymerases are responsible for the replication of nuclear DNA in eukaryotes?

  • DNA polymerases β, η, and ζ
  • DNA polymerases α, β, and γ
  • DNA polymerases α, δ, and ε (correct)
  • DNA polymerases γ, δ, and ε

    • What fundamental direction do all DNA polymerases synthesize DNA?

  • 5' to 3' (correct)
  • In both 5' to 3' and 3' to 5'
  • In a circular direction
  • 3' to 5'

    • What is the primary role of initiator proteins in the origin of replication?

  • To separate the DNA strands completely
  • To recognize specific nucleotide sequences (correct)
  • To directly unwind the DNA helix
  • To synthesize new DNA strands

    • How many origins of replication are typically found in mammalian genomes?

    <p>Multiple origins</p> Signup and view all the answers

    What is the role of miRNAs in the cell?

    <p>They inhibit translation or stimulate mRNA degradation.</p> Signup and view all the answers

    What mechanism do helicase and single-stranded DNA-binding proteins use during replication?

    <p>To unwind the DNA strands</p> Signup and view all the answers

    Why is multiple origins of replication necessary in eukaryotes?

    <p>To replicate long chromosomes in a reasonable time</p> Signup and view all the answers

    What is a characteristic feature of long non-coding RNAs (lncRNAs)?

    <p>They are involved in the regulation of gene expression.</p> Signup and view all the answers

    What is the consequence of using a single origin of replication for the mammalian genome?

    <p>Extended time of replication</p> Signup and view all the answers

    Which of the following statements accurately describes the nuclear envelope?

    <p>It acts as a selective barrier between the nucleus and cytoplasm.</p> Signup and view all the answers

    What is a key distinction between the origin of replication in prokaryotes and eukaryotes?

    <p>Eukaryotes require multiple origins for long chromosomes</p> Signup and view all the answers

    What role does the nuclear pore complex play?

    <p>It regulates the transport of transcription factors to the nucleus.</p> Signup and view all the answers

    What type of DNA sequence represents a significant portion of the human genome but does not encode functional genetic information?

    <p>Single sequence repeats</p> Signup and view all the answers

    What characteristic distinguishes the AT-rich and GC-rich sequences in the context of satellite DNA?

    <p>GC-rich sequences appear as denser bands in density gradient centrifugation.</p> Signup and view all the answers

    How do long non-coding RNAs such as Xist RNA function in females?

    <p>They block the transcription of one of the X chromosomes.</p> Signup and view all the answers

    Which structure underlies the inner nuclear membrane?

    <p>Nuclear lamina</p> Signup and view all the answers

    What impact do deletions in residues 126 to 132 have on the T antigen?

    <p>They retain the T antigen in the cytoplasm.</p> Signup and view all the answers

    Which sequence composition is typical for nuclear localization signals (NLS)?

    <p>Short and rich in Lysine and Arginine.</p> Signup and view all the answers

    What role do Importins play in the nuclear transport process?

    <p>They recognize the NLS of protein-cargo and aid in transport to the nucleus.</p> Signup and view all the answers

    What happens to the importin-cargo complex in the nucleus?

    <p>It dissociates when Ran/GTP binds to importin.</p> Signup and view all the answers

    What is the effect of high concentration of Ran/GTP in the nucleus?

    <p>It regulates the directionality of nuclear transport.</p> Signup and view all the answers

    What function do Ran proteins serve in nuclear transport?

    <p>They regulate exchanges between GDP and GTP based on location.</p> Signup and view all the answers

    What is a characteristic of proteins with bipartite nuclear localization signals, like nucleoplasmin?

    <p>NLS consists of two separate sequences interspersed with non-NLS residues.</p> Signup and view all the answers

    Which process occurs after importin is released from the cargo protein?

    <p>It is recycled to bind new cargo proteins.</p> Signup and view all the answers

    What role do snoRNAs play in pre-rRNA processing?

    <p>They guide enzymes to modify rRNA through base pairing.</p> Signup and view all the answers

    How are ribosomal proteins incorporated into preribosomal particles?

    <p>They are synthesized outside the nucleolus and transported there.</p> Signup and view all the answers

    What is the primary component of snoRNPs involved in rRNA processing?

    <p>Small nucleolar RNAs that contain sequences complementary to rRNA.</p> Signup and view all the answers

    Which type of RNA polymerase is responsible for transcribing the genes encoding ribosomal proteins?

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

    What modification occurs to uridine during pre-rRNA processing?

    <p>Conversion to pseudouridine.</p> Signup and view all the answers

    What is the primary function of telomerase?

    <p>To replicate telomeric DNA</p> Signup and view all the answers

    Which of the following correctly defines extragenic DNA?

    <p>DNA with non-coding sequences</p> Signup and view all the answers

    What is the significance of alternative splicing in gene expression?

    <p>It generates different RNA transcripts from a single gene</p> Signup and view all the answers

    How does the complexity of DNA relate to the number of genes and proteins?

    <p>The amount of DNA specifies both number of genes and complexity</p> Signup and view all the answers

    Which type of RNA is known for playing fundamental roles in protein synthesis?

    <p>tRNA and rRNA</p> Signup and view all the answers

    Which type of sequences in human DNA are responsible for regulating gene expression?

    <p>Regulatory sequences such as promoters and enhancers</p> Signup and view all the answers

    What is the approximate number of different proteins that can be generated from 21,000 human protein-coding genes?

    <p>85,000 different proteins</p> Signup and view all the answers

    Which of the following features is NOT part of a gene structure?

    <p>Telomeres</p> Signup and view all the answers

    What specific amino acid sequence is used to tag proteins for export from the nucleus?

    <p>Nuclear export signal (NES)</p> Signup and view all the answers

    What role does Ran-GEF play in the nucleus?

    <p>Converts Ran-GDP to Ran-GTP</p> Signup and view all the answers

    Which exportin is specifically responsible for the transport of tRNA from the nucleus?

    <p>Exportin-T</p> Signup and view all the answers

    How is NF-kB prevented from entering the nucleus in unstimulated cells?

    <p>Binding to a cytoplasmic protein</p> Signup and view all the answers

    What event allows the transport of Pho4 to the nucleus?

    <p>Dephosphorylation allowing NLS exposure</p> Signup and view all the answers

    What is the role of the hydrolysis of GTP in protein export from the nucleus?

    <p>It causes dissociation of the target protein</p> Signup and view all the answers

    What distinguishes mRNA export from tRNA and rRNA export?

    <p>Use of exportin proteins</p> Signup and view all the answers

    Which of the following proteins directly binds to RNA for export?

    <p>Exportin-5</p> Signup and view all the answers

    Study Notes

    Unit 3: The Nucleus

    • The nucleus serves as a storehouse for genetic information
    • DNA replication takes place at the genomic level
    • RNA transcription and processing occur
    • Gene expression is regulated by controlling the transport of transcription factors from the cytoplasm to the nucleus

    Index

    • 3.1: The cell nucleus and the DNA
    • 3.2: Nuclear envelope
    • 3.3: DNA replication
    • 3.4: DNA transcription
    • 3.5: Traffic between the nucleus and the cytoplasm
    • 3.6: Nuclear bodies

    3.1 The cell nucleus and the DNA

    • Functions:
      • Stores genetic information
      • Site of DNA replication
      • Site of RNA transcription and processing
      • Regulates gene expression by controlling the transport of transcription factors

    Chromosomes and chromatin

    • Eukaryotic genomes are complex, organized on multiple linear chromosomes
    • DNA is packaged with small proteins called histones
    • The length of human DNA is 2 meters, but it must fit in a core of 5-10 micrometers within the nucleus

    Chromosomes

    • Tightly packaged DNA
    • Found only during cell division
    • DNA is not used for macromolecule synthesis

    Chromatin

    • Unwound DNA
    • Found throughout interphase
    • DNA is being used for macromolecule synthesis

    Heterochromatin and euchromatin

    • Heterochromatin: condensed chromatin, inactive for transcription
    • Euchromatin: loose chromatin, active for transcription

    Levels of DNA packaging

    • Level 1: DNA double helix (2nm) coils around histone core to form nucleosome ("beads-on-a-string")
    • Level 2: Nucleosomes coil to form 30nm chromatin fiber
    • Level 3: 30nm fibers form loops attached to a protein scaffold, forming a 300nm fiber
    • Level 4: 300nm fibers condense forming a 700nm fiber or chromatid which is further condensed

    DNA polymerase

    • Eukaryotes and prokaryotes contain DNA polymerases with different roles
    • Bacterial DNA polymerase III is the main polymerase responsible for replication
    • In eukaryotes, DNA polymerases α, δ and ε function in nuclear DNA replication, and DNA polymerase γ is for mitochondrial DNA replication
    • DNA polymerases synthesize DNA 5' to 3'

    Origin of Replication

    • DNA molecule unwinds at specific points called origins of replication
    • Initiator proteins recognize specific nucleotide sequences to facilitate the attachment of other proteins to form two replication forks
    • A large replication complex (replisome) is assembled consisting of multiple enzymes and proteins

    Origin of Replication in Prokaryotes

    • Replication begins at one single origin
    • Initiator protein unwinds the DNA, recruiting other replication enzymes
    • Replication proceeds in both directions from the single origin

    Origin of Replication in Eukaryotes

    • Eukaryotes require multiple origins of replication to replicate long chromosomes in a reasonable time
    • The rate of DNA replication is slower in eukaryotes than in bacteria due to DNA packaging in chromatin

    Replication Fork

    • The DNA molecule unwinds to separate parental strands forming two replication forks.
    • One strand is synthesized continuously (leading strand) whereas the other in short fragments (lagging strand)

    DNA Maintenance

    • High accuracy in DNA replication is crucial for cell reproduction
    • Error frequency is less than one incorrect base per 10,000 nucleotides
    • Mechanisms for DNA polymerase fidelity include:
      • Selecting correct bases
      • Proofreading activity (3' to 5' exonuclease excises incorrect base)

    Telomerase

    • DNA polymerase involved in telomere formation
    • Contains 159-nucleotide RNA oligonucleotide that acts as a template for telomere synthesis
    • Replicates telomeric DNA

    Genes and Genomes

    • Genome: The complete set of genetic material in an organism
    • Gene: A segment of DNA that codes for a specific gene product, either RNA or protein
    • Extragenic DNA: DNA in a genome that does not contain protein-coding genes, but can have regulatory functions

    DNA Quantity Paradox

    • A larger genome does not necessarily correspond to a greater number of genes
    • Complexity is a multi-faceted parameter and not only a matter of DNA quantity

    Gene Structure: Introns and Exons

    • Exons: Regions of mRNA that are expressed and form protein-coding sequences
    • Introns: Non-coding regions of DNA that are removed during mRNA processing

    Alternative Splicing

    • Multiple mature mRNA transcripts can be generated from a single gene depending on which exons are included or excluded in the final mRNA
    • Increases the diversity of proteins encoded by a single gene and plays a critical role in development and differentiation.

    Complexity in Human DNA: Types of Sequences in our genome

    • Regulatory DNA sequences include promoters, silencers, and enhancers
    • Extragenic DNA includes repetitive sequences (tandem and sparse repeats), gene duplication, and pseudogenes

    Noncoding RNA

    • Diverse classes of noncoding RNAs play important regulatory roles in the cell (tRNAs, rRNAs, miRNAs, IncRNAs)
    • miRNA: 20-30 nucleotides, control gene expression by inhibiting translation
    • IncRNA: over 200 nucleotides, involved in regulating gene expression and chromatin structure

    RNA Processing

    • Bacterial mRNAs are used immediately for protein synthesis
    • Many types of RNA (rRNA, tRNA, mRNA) in eukaryotes are processed extensively before being used to synthesize proteins.

    Ribosomal RNAs

    • rRNA molecules of both prokaryotes and eukaryotes are derived from a single long pre-rRNA molecule (cleaved into smaller mature rRNA)
    • Each rRNA type (18S, 5.8S, 28S, 5S) is transcribed from a separate gene (except in the case of the 5.8S, 18S and 285 rRNAs, which are transcribed from a single long pre-rRNA molecule) in eukaryotes

    tRNAs

    • tRNA molecules are processed from longer precursors, requiring cleavage of both 5' and 3' ends
    • Modification of specific bases in precursor tRNA (10%)

    mRNA Processing (Eukaryotes)

    • 5' cap
    • 3' poly-A tail
    • Splicing: removal of introns

    Splicing

    • Splicing proceeds in two steps:
      1. Cleavage and joining
      2. Excising intron loop
    • Alternative splicing: multiple mature mRNAs from one gene

    Nuclear Envelope and Pore Complex

    • Double membrane structure surrounding the nucleus
    • Nuclear pore complex is the pathway for selective transport between the nucleus and cytoplasm
    • The nuclear lamina is a fibrous network that provides structural support to the nucleus

    Selective Transport of Proteins

    • Proteins required for nuclear functions are transported from the cytoplasm to the nucleus
    • NLS (nuclear localization signals): specific amino acid sequences targeting particular proteins to the nucleus
    • Importins: bind to NLSs, facilitating transport
    • Ran proteins: regulate the directionality of transport

    RNA Transport

    • RNA molecules are transported through the nuclear pore complex, associated with proteins to form RNPs
    • Different RNA types (tRNA, mRNA, rRNA, miRNA) use various mechanisms

    Other Small Noncoding RNAs

    • snRNAs (small nuclear RNAs): act in pre-mRNA splicing
    • snoRNAs (small nucleolar RNAs): involved in rRNA processing

    Nucleolos

    • Large structure in the nucleus
    • Site of ribosome biogenesis

    Histone Modifications

    • Acetylation: adding acetyl groups, relaxing chromatin, increasing transcriptional activity
    • Methylation: adding methyl groups, affecting transcriptional activity

    Chromatin Remodeling Factors

    • Protein complexes that alter interactions between DNA and histones, impacting transcription

    DNA Methylation

    • Epigenetic mechanism for controlling transcription (often leads to repression)
    • Methylation of cytosine bases preceding guanines (CpG dinucleotides)

    Regulation of Transcription

    • Mechanisms for regulating gene expression in eukaryotes by:
      • Binding of regulatory proteins
      • Chromatin structure modifications
      • DNA methylation
      • Noncoding RNA regulation

    Nuclear Bodies

    • Specific subnuclear structures that concentrate specific proteins and RNAs
    • Include the nucleolus, cajal bodies, speckles, histone locus bodies, etc

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    Unit 3. The Nucleus PDF

    Description

    Test your knowledge on the key processes in DNA replication, focusing on eukaryotic systems. Explore the roles of DNA polymerases, initiator proteins, and the significance of origins of replication. This quiz also delves into the functions of miRNAs and the structural characteristics of nuclear components.

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