Pre-rRNA Processing and Ribosomal Assembly
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Questions and Answers

What nucleotide modification involves the conversion of uridine?

  • Formation of pseudouridine (correct)
  • Addition of methyl groups
  • Cleavage of rRNA
  • Base pairing with snoRNA

    • Which components are primarily involved in the processing of pre-rRNA?

  • RNA polymerase I and 5S rRNA
  • Pre-rRNA and large ribosomal subunits
  • Cytoplasmic ribosomal proteins only
  • Nucleolus proteins and snoRNA (correct)

    • Where are ribosomal proteins transcribed?

  • In the cytoplasm by RNA polymerase II (correct)
  • In the rough endoplasmic reticulum
  • In the nucleolus by RNA polymerase I
  • In the nucleolus by RNA polymerase III

    • What function do snoRNPs serve in pre-rRNA processing?

    <p>They direct the enzymes for rRNA modifications</p> Signup and view all the answers

    What is true about the assembly of preribosomal particles?

    <p>More than half of ribosomal proteins bind prior to rRNA processing</p> Signup and view all the answers

    Where are chromosomes that are rich in genes located within the nucleus?

    <p>In the center</p> Signup and view all the answers

    What effect does histone acetylation have on chromatin structure?

    <p>It neutralizes the charge of lysine.</p> Signup and view all the answers

    What is the primary role of chromatin remodeling factors?

    <p>To alter DNA and histone interactions</p> Signup and view all the answers

    How does DNA methylation affect gene expression?

    <p>It represses transcription.</p> Signup and view all the answers

    What is a characteristic of miRNAs in gene regulation?

    <p>They inhibit translation of homologous mRNAs.</p> Signup and view all the answers

    What is the function of histone acetyltransferase (HAT)?

    <p>To add acetyl groups to histones</p> Signup and view all the answers

    What role does gene H19 play in genomic imprinting?

    <p>It is expressed only from the maternal copy.</p> Signup and view all the answers

    How are ribosomal RNAs derived in prokaryotes?

    <p>From a single long pre-rRNA molecule</p> Signup and view all the answers

    What is the visual representation of nucleosomes linked together?

    <p>A necklace of beads</p> Signup and view all the answers

    What is the diameter of the 30 nm chromatin fiber during its formation?

    <p>30 nm</p> Signup and view all the answers

    Which regions are associated with the attachment of chromatin loops to the protein scaffold?

    <p>A and T rich regions</p> Signup and view all the answers

    What happens to the degree of DNA packaging during mitosis?

    <p>It increases to form chromatids</p> Signup and view all the answers

    What is histone acetylation primarily associated with?

    <p>Transcriptional activation</p> Signup and view all the answers

    Which modification of histones can lead to chromatin compaction?

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

    What structure results from the rearrangement of the 30 nm chromatin fiber?

    <p>300 nm fiber</p> Signup and view all the answers

    How much more compact is the DNA when it reaches the chromatid level compared to its original 2 nm fiber?

    <p>10,000 x</p> Signup and view all the answers

    What is the primary function of the nuclear pore complex?

    <p>To facilitate selective trafficking of proteins and RNA</p> Signup and view all the answers

    Which characteristic is true of the outer nuclear membrane?

    <p>It is continuous with the endoplasmic reticulum.</p> Signup and view all the answers

    What proteins make up the nuclear lamina?

    <p>Lamin A, B, and C</p> Signup and view all the answers

    How do lamins assemble to form the nuclear lamina?

    <p>Lamins dimerize and then associate head to tail.</p> Signup and view all the answers

    What is the role of ribosomes on the outer nuclear membrane?

    <p>To bind to the cytoskeleton</p> Signup and view all the answers

    What is the primary structure that allows small polar molecules to pass through the nuclear envelope?

    <p>Nuclear pore complexes</p> Signup and view all the answers

    What kind of proteins are specific to the inner nuclear membrane?

    <p>Integral membrane proteins</p> Signup and view all the answers

    Which of the following statements best describes the relationship between the nuclear lamina and the inner nuclear membrane?

    <p>Lamins interact with integral proteins of the inner membrane.</p> Signup and view all the answers

    What is the effect of deletions affecting residues 126 to 132 in the SV40 T antigen?

    <p>They cause increased cytoplasmic localization of the antigen.</p> Signup and view all the answers

    What characterizes the nuclear localization signal (NLS) of many nuclear proteins?

    <p>It is often bipartite, consisting of separated basic amino acids.</p> Signup and view all the answers

    Which proteins are primarily responsible for the transport of proteins into the nucleus?

    <p>Importins and Ran proteins.</p> Signup and view all the answers

    What occurs after Importin binds to the NLS of the cargo protein?

    <p>The complex undergoes structural changes and gets transported through the pore.</p> Signup and view all the answers

    How does Ran/GTP facilitate protein release in the nucleus?

    <p>It displaces the cargo protein from the importin complex.</p> Signup and view all the answers

    Where are the enzymes that stimulate GDP to GTP exchange located?

    <p>On the nuclear side of the nuclear envelope.</p> Signup and view all the answers

    What will happen to importin after it releases the cargo protein inside the nucleus?

    <p>It forms a complex with Ran/GTP for re-exportation.</p> Signup and view all the answers

    What is a common feature of the basic amino acids found in many NLS?

    <p>They are often non-contiguous in the sequence.</p> Signup and view all the answers

    What is the primary function of the LINC complex formed by SUN and KASH proteins?

    <p>Connecting the nuclear lamina with the cytoskeleton</p> Signup and view all the answers

    Which statement accurately describes the nuclear pore complex?

    <p>It has a central channel that can vary in diameter from 9 nm to 40 nm.</p> Signup and view all the answers

    What is the approximate molecular weight of the nuclear pore complex?

    <p>125 million Da</p> Signup and view all the answers

    In the context of DNA replication, what does the term 'semi-conservative' mean?

    <p>Existing strands serve as templates for new strands.</p> Signup and view all the answers

    Which type of DNA polymerase is primarily responsible for replication in bacteria?

    <p>DNA polymerase III</p> Signup and view all the answers

    What is the role of nucleoporins within the nuclear pore complex?

    <p>Facilitate the exchange of ions and proteins</p> Signup and view all the answers

    What characteristic property allows DNA to reproduce identically during replication?

    <p>Base complementation</p> Signup and view all the answers

    What structures extend from the cytoplasmic ring of the nuclear pore complex?

    <p>Cytoplasmic filaments</p> Signup and view all the answers

    Study Notes

    Unit 3: The Nucleus

    • This unit focuses on the cell nucleus and its functions within cellular structure and function.

    Index

    • The cell nucleus and DNA
    • Nuclear envelope
    • DNA replication
    • DNA transcription
    • Traffic between the nucleus and the cytoplasm
    • Nuclear bodies

    3.1 The Cell Nucleus and DNA

    • Function: Storehouse for genetic information
    • Genomic level functions:
      • DNA replication
      • RNA transcription and processing
    • Regulates gene expression by controlling the transport of transcription factors from the cytoplasm to the nucleus.

    Chromosomes and Chromatin

    • Eukaryotic genomes are complex, with DNA organized on multiple linear chromosomes.
    • DNA associates with histone proteins, compacting it into a structure called chromatin.
    • This compaction is essential to fit the enormous length of human DNA into the nucleus (2 meters into 5-10 micrometers).

    Chromosomes and Chromatin (continued)

    • Chromosomes: Tightly packaged DNA visible during cell division.
    • Chromatin: Unwound DNA throughout interphase, active in macromolecule synthesis.

    Chromatin: Heterochromatin and Euchromatin

    • Heterochromatin: Condensed chromatin, inactive in transcription.
    • Euchromatin: Loose chromatin, active in transcription.

    Chromatin Packaging Levels

    • Level 1: DNA double helix (2 nm) coils around histone octamers forming nucleosomes (“beads-on-a-string”).
    • Level 2: Nucleosomes coil into 30 nm chromatin fiber.
    • Level 3: 30 nm fibers form loops attached to a protein scaffold forming 300 nm fibers.
    • Higher levels: Further condensation during mitosis to form 600-700 nm fibers (chromatids).

    Level 4 DNA Packing:

    • The DNA double helix (about 147 bp) coils around a core or octamer of histones (two molecules of each of the histones H2A, H2B, H3 and H4) in a structure known as a nucleosome.

    Histone Modifications

    • Histone tails can be modified (acetylated, methylated, phosphorylated).
    • These modifications constitute a histone code influencing DNA accessibility and gene expression.
    • Acetylation relaxes chromatin, increasing DNA accessibility for transcription.
    • Methylation can be associated with both active and repressed chromatin.

    Chromosomes: Characteristics and Structure

    • Each eukaryotic species has a characteristic chromosome number (diploid [2n] or haploid [n]).
    • Humans have 46 chromosomes (2n), 22 pairs of autosomes and 2 sex chromosomes (XX or XY).
    • Homologous chromosomes: Similar in size, shape, and genetic information, one from each parent.
    • Sister chromatids: Identical copies of replicated chromosomes, held together by the centromere.
    • Telomeres: Protective caps at the ends of chromosomes.

    Centromere

    • Specialized region of the chromosome.
    • Crucial for proper chromosome segregation during mitosis and meiosis.
    • Attachment site for the mitotic spindle.

    Telomeres

    • Specialized structures at chromosome ends.
    • Protect the ends from degradation or fusion.
    • Crucial for DNA replication and stability during cell division.

    Genes and Genomes

    • Genome: The complete set of genetic material in an organism.
    • Gene: The fundamental unit of heredity, containing the information for a specific protein or RNA molecule.
    • Extragenic DNA: DNA sequences that do not code for proteins, but are important for gene expression and regulation.
    • Human genome approximately 3200 Mb.

    DNA Quantity Paradox

    • Complexity and number of genes are not uniformly related to the amount of DNA.

    Gene Structure: Introns and Exons

    • Exons: Coding regions of a gene that are part of the mature mRNA.
    • Introns: Non-coding regions that are removed during RNA processing.

    Alternative Splicing

    • Alternative splicing creates multiple mRNA isoforms from a single gene, leading to a wide range of protein products.

    Complexity in Human DNA: Types of Sequences in Our Genome

    • Regulatory sequences (promoters, silencers, enhancers)
    • Non-coding RNA genes (multiple RNA types).
    • Repetitive DNA sequences (transposons, satellite DNA, short tandem repeats, and long interspersed nuclear elements)

    Noncoding RNA

    • Non-coding RNAs are molecules of RNA that do not encode proteins but play crucial roles in gene regulation and other cellular processes.
    • microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are examples of non-coding RNAs important for gene expression regulation.

    3.2 Nuclear Envelope

    • Double membrane surrounding the nucleus.
    • Nuclear pore complexes.
    • Nuclear lamina.
    • Outer membrane continuous with endoplasmic reticulum.

    Nuclear Envelope Structure

    • Two membranes (Outer and Inner)
    • Nuclear pore complex (NPC)
    • Nuclear lamina.

    3.3 DNA Replication

    • DNA replicates semi-conservatively.
    • Replication proceeds in both directions from multiple origins.
    • Okazaki fragments, DNA polymerase, primase, helicase.
    • Components of the replisome.

    DNA Polymerase

    • Enzymes that synthesize new DNA strands.
    • 5' to 3' direction.

    Origin of Replication

    • Specific sites on the DNA molecule where replication begins.
    • Initiator proteins recognize these sites.
    • Prokaryotic origins are typically single in the chromosome.
    • Eukaryotic origins are multiple to speed up the replication process.

    DNA Maintenance

    • Accuracy of replication. Error rate is high; mechanisms correct errors.
    • Proofreading and repair mechanisms are critical aspects of DNA maintenance.
    • DNA polymerase proofreading activity.

    Telomerase

    • Enzyme that maintains telomeres, preventing the erosion of chromosomes.

    3.4 DNA Transcription

    • Synthesis of RNA from a DNA template.
    • RNA polymerase catalyzes synthesis.
    • Semi-conservative mechanism doesn't apply.

    RNA Polymerases

    • Enzyme that synthesizes RNA from DNA template.

    Differences and Similarities between Replication and Transcription

    • Enzymes needed differ slightly.
    • Pre-mRNA processing steps are needed in transcription, but DNA replication does not need that process.
    • The end products are different (DNA vs RNA).

    Transcription Initiation

    • RNA polymerase binds to the promoter region.
    • Promoter sequences are often present far upstream in eukaryotic promoters; different transcription factor sequences than those in the prokaryotic promoters.
    • DNA unwinds and conformational changes in polymerase occur.

    Transcription Elongation

    • RNA polymerase synthesizes RNA in the 5' to 3' direction by adding nucleotides to the 3' end.
    • RNA polymerase moves sequentially along the DNA template.

    Transcription Termination

    • RNA synthesis ends when RNA polymerase reaches specific termination sequences in DNA.
    • Eukaryotic termination mechanisms are complex and not entirely understood.

    Transcription in Eukaryotes

    • Three RNA polymerases (I, II, III) are involved in eukaryotic transcription.
    • Different RNA polymerases require different sets of transcription factors.
    • Regulation of chromatin structure greatly influences gene expression.

    Transcription of Ribosomal RNA Genes

    • RNA polymerase I is responsible for transcription of the genes for rRNA.
    • Transcription of rRNA genes is typically in tandem repeats, located usually in the center of the nucleus
    • Ribosomal RNA is a key component of the ribosome.

    Transcription of RNA Polymerase III Genes

    • RNA polymerase III transcribes genes for tRNA and 5S rRNA.
    • Regulatory elements such as promoters play a pivotal role in RNA polymerase III-mediated transcription.

    Regulation of Transcription in Eukaryotes

    • Transcription is controlled by various factors including protein binding to specific sequences (regulatory sequences / promotors/ enhancers), chromatin modifications.

    Proteins in Eukaryotic Transcription

    • General transcription factors, which are essential for the binding of polymerase to the promoter.
    • Transcriptional activators and repressors, which regulate the transcription of specific genes.
    • Chromatin remodelers, which make DNA more or less accessible to the transcriptional machinery.

    Chromatin and Epigenetics

    • Chromatin packaging limits access to DNA influencing gene expression.
    • Histone modifications and nucleosome rearrangements are critical aspects of chromatin structure regulation and are stably inherited.

    Location of Chromatin and Transcriptional Activity

    • Euchromatin is usually located inside the center of the nucleus
    • Heterochromatin is typically located preferentially near the nuclear envelope.

    Histone Modifications

    • Acetylation and methylation are typical modifications of histones.
    • Acetylation typically activates gene transcription, while methylation often reduces accessibility to the DNA.

    Transcriptional Activators and Repressors

    • Transcriptional activators increase gene expression, while repressors decrease gene expression.

    Chromatin Remodeling Factors

    • These protein complexes regulate the accessibility of DNA.

    DNA Methylation

    • Addition of methyl groups to cytosine can alter gene expression.

    Genomic Imprinting

    • Expression of genes varies based on whether the gene is inherited from maternal or paternal ancestry.

    Non-coding RNAs

    • RNAs that do not produce proteins have regulatory roles in transcription.

    3.5 Traffic between the Nucleus and the Cytoplasm

    • Selective transport.
    • Passive diffusion (small molecules).
    • Active transport (larger proteins and RNAs)
      • Importin, Ran and nuclear localization signals (NLS)
      • Exportin and nuclear export signals (NES)

    3.6 Nuclear Bodies

    • Specialized structures in the nucleus.
    • Compartmentalize the nucleus allowing concentration of proteins and RNAs (ex: nucleolus)
    • Dynamic structures (exchangeable with the rest of the nucleus)
    • Active research area. (Roles still largely unknown).

    Nucleolus, Cajal Bodies, Speckles

    • Nucleolus: Sub-compartment within the nucleus crucial for ribosome biogenesis.
    • Cajal Bodies: Participate in snRNP assembly.
    • Speckles: Storage for splicing factors.

    Ribosome Assembly

    • Ribosomes are composed of ribosomal RNAs and proteins, assembled in the eukaryotic nucleolus.
    • Assembly involves a staged process of modification to ribosomal RNA transcripts.

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    Unit 3. The Nucleus PDF

    Description

    Test your knowledge on the intricate processes involved in pre-rRNA processing and the assembly of ribosomal components. This quiz covers nucleotide modifications, the role of snoRNPs, and the transcription of ribosomal proteins.

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