Nuclear Structure

The Nucleus

  • Structure

    • Largest organelle in the cell

    • Components include

    • Nuclear envelope

    • Nucleolus

    • Nucleoplasm

    • Chromatin associated with chromosomes

      • Chromosomes consist of deoxyribonucleic acid (DNA)

  • Function

    • Acts as the cell's control center

    • Stores genetic material (DNA)

    • Coordinates cell activities like growth, division, and protein synthesis

    • Contains:

    • Genes

    • Messenger ribonucleic acid (mRNA)

    • Transfer ribonucleic acid (tRNA)

    • rDNA coding for ribosomal RNA

    • Other ribonucleic acids including regulatory RNAs (noncoding RNAs)

Interphase Cell Nucleus Consists of

  • Chromatin

    • Nuclear material comprising DNA and proteins

    • Organized as

      • Euchromatin (active)

      • Heterochromatin (inactive)

  • Nucleolus

    • Contains transcriptionally active DNA for ribosomes

    • Site of rRNA synthesis

    • Contains regulatory proteins for the cell cycle

  • Nuclear Envelope

    • Double membrane that surrounds the nucleus

    • Comprised of

    • Inner membrane

    • Outer membrane

    • Separated by a perinuclear cisternal space

  • Nuclear Pores

    • Openings in the nuclear envelope connecting the nucleus and cytoplasm

  • Nucleoplasm

    • Nuclear content excluding chromatin and nucleolus

Nuclear Envelope or Nuclear Membrane

  • Surrounds nuclear material

  • Comprised of two membranes separated by a narrow perinuclear cisterna

  • Membranes fuse at the nuclear pores

  • Outer Nuclear Membrane

    • Faces the nuclear material but separated by the nuclear lamina

    • Continuous with rough endoplasmic reticulum (rER) at certain sites

    • Ribosomes on the cytoplasmic surface synthesize proteins that enter the perinuclear cisterna

Nuclear Lamina

  • Composed of nuclear lamins A, B1, B2, and C (Type V intermediate filament)

  • Involves lamin-associated proteins or receptors

    • Lamin B receptor (LBR)

    • Nurim binds lamin A

    • Emerin binds both lamin A and B

  • Functionality

    • Organizes nuclear envelope and chromatin

    • Directs formation of nuclear pore complexes (NPCs)

    • Responsible for disassembly/reassembly of nuclear envelope during mitosis

    • Phosphorylation of lamins leads to disassembly; dephosphorylation results in reassembly

  • Clinical Application

    • Mutation in LMNA gene leads to abnormal protein progerin which results in unstable nuclei, accelerated telomere shortening, and cellular decline

    • Related to progeria, causing rapid aging and notably affecting heart muscle leading to dilated cardiomyopathy

Nuclear Pores (NPs)

  • Approximately 80 nm in diameter; numbers range from dozens to thousands

  • More abundant in metabolically active cells

  • Associated with protein subunits called the nuclear pore complex (NPC)

  • Functions

    • Permits passage of certain molecules in either direction

  • Clinical Applications

    • NPC dysfunction leads to conditions such as:

    • Triple A Syndrome (Allgrove Syndrome)

      • Caused by mutations in AAAS gene encoding nucleoporin protein ALADIN

      • Symptoms: alacrima, achalasia, adrenal insufficiency

    • Links to neurodegenerative diseases (e.g., ALS, frontotemporal dementia) due to altered RNA export and protein mislocalization

    • Viruses hijack NPC to facilitate their life cycle (e.g., HIV, influenza, herpesvirus)

Structure of the Nuclear Pore Complex

  • Composed of nearly 100 proteins (nucleoporins)

  • Features include

    • Nuclear Basket on nucleoplasm side

    • Cytoplasmic Filaments extending into the cytoplasm

    • Four rings:

    • Cytoplasmic ring

    • Luminal spoke ring

    • Nuclear ring

    • Distal ring

  • Cytoplasmic Ring

    • Eight subunits with cytoplasmic filaments made of Ran-binding proteins

    • Acts as a staging area for protein transport

Transport Mechanisms of the Nuclear Pore Complex

  • Passive Movement

    • Simple diffusion through open channels of nuclear envelope (9 to 11 nm wide)

  • Receptor-mediated Transport

    • Facilitated by transporter proteins called exportins and importins, regulated by Ran GTP-binding proteins

    • Recognizes transport signals known as nucleocytoplasmic shuttling signals

    • Exportins facilitate export of proteins with nuclear export sequences

    • Importins facilitate import of proteins with nuclear localization sequences

Nucleolus - Structure

  • Observed in interphase cells; actively synthesizing proteins

  • Composed of

    • rRNA

    • Nucleostemin

    • Nucleolin

    • Fibrillarin

    • Small amount of DNA

  • Contains four distinct regions:

    1. Fibrillar Centers (FC)

      • Composed of nucleolar organizer regions (NORs), ribonucleoprotein signal recognition particle (SRP), RNA polymerase I

    2. Pars Fibrosa (F)

      • Surrounds fibrillar centers; contains transcriptionally active DNA and substantial rRNA

    3. Pars Granulosa (G)

      • Composed of maturing ribosomal precursor particles, assembly of 18S rRNA and 28S rRNA subunits

    4. Nucleolar Matrix

      • Fiber network involved in the organization of the nucleolus

Nucleolus - Functions

  • Produces ribosomes; disappears during prophase of mitosis

  • Produces nucleostemin for cell cycle checkpoint signaling

  • Prominent nucleolus indicates high protein synthesis activity observed in plasma cells and neurons

  • Clinical application

    • RNA viruses hijack nucleolar machinery; enlarged nucleoli seen in cancer due to increased protein synthesis demand

  • Genetic Disorders

    • Robertsonian translocations may involve NORs leading to balanced translocation and possible Down/Patau syndromes due to chromosomal fusions

Nucleoplasm

  • Viscous matrix containing chromosomes and nucleoli

  • Composed of macromolecules, ions, transcriptional processing apparatus

  • Nucleoplasmic Reticulum

    • Continuous with nuclear envelope and endoplasmic reticulum

    • Contains nuclear calcium regulating gene expression

  • Clinical Importance

    • Involved in cancer, aging, muscular dystrophy, and infertility

Nuclear Particles

  • Interchromatin Granules

    • Clusters containing ribonucleoproteins and various enzymes

  • Perichromatin Granules

    • Dense granules surrounded by a less dense halo, containing 4.7S RNA and peptides

  • Heterogeneous Nuclear Ribonucleoproteins (hnRNPs)

    • Complexes of precursor mRNA and proteins crucial in mRNA processing

  • Small Nuclear RNPs (snRNPs)

    • Involved in RNA splicing or cleavage reactions

DNA Overview

  • A long double-stranded helical molecule of nucleotides storing genetic information

    • If stretched, 46 chromosomes measure almost 6 ft

  • Nucleotides consist of

    1. Base (purine or pyrimidine)

    2. Deoxyribose sugar

    3. Phosphate group

    • Purines: Adenine (A), Guanine (G)

    • Pyrimidines: Cytosine (C), Thymine (T)

  • Double Helix

    • Made of two complementary DNA strands held by hydrogen bonds between base pairs A–T and G–C

DNA Terminology

  • Exons: Coding regions of DNA

  • Introns: Non-coding regions; regulatory roles

  • Codon: Sequence of three bases coding for one amino acid

  • Gene: Segment of DNA containing information for encoding a single mRNA molecule, includes regulatory sequences

  • Genome: Complete set of hereditary information

    • Genes classified as protein-coding or noncoding, with only about 2% coding for proteins

DNA Supercoiling

  • Mitochondrial DNA and bacterial DNA are circular structures that may be relaxed or supercoiled

    • Negative supercoiling is loose, while positive is tight

  • Topoisomerases: Enzymes involved in supercoiling

  • Clinical Importance: Targets for antibiotics and anticancer drugs

Nucleosomes and Chromatin

  • Nuclear DNA forms chromatin, with nucleosomes as basic packaging units

  • A nucleosome consists of histones and non-histone proteins

    • Histones: H2A, H2B, H3, H4 arranged in octamer

DNA Packaging

  • DNA winds around histones forming nucleosomes

  • Series of nucleosomes form a "beads on a string" structure

  • Histone H1: Associates with linker DNA between nucleosomes

  • Condensed chromatin forms a 30 nm fiber structure, further organized into thicker structures for chromosome formation

Telomeres

  • Repetitive DNA sequences at chromosome ends (TTAGGG)

    • Protect against degradation and fusion, shorten with cell divisions

    • Telomerase: Reverse transcriptase that elongates telomeres, active in germ, stem, and cancer cells

  • Clinical Applications:

    • Cancer reactivates telomerase for unlimited replication

    • Stem cells maintain telomere length

    • Mutations can lead to dyskeratosis congenita, signs of premature aging

  • Potential biomarker for aging, cancer prognosis, and diseases related to stress

Chromatin Types

  • Euchromatin

    • Transcriptionally active, less condensed; appears lightly stained

    • Histone acetylation associated with its formation

  • Heterochromatin

    • Condensed, transcriptionally inactive; darkly stained

    • Makes up about 90% of chromatin in the cell

    • Barr body: inactivated X chromosome in females, appears dense

  • Clinical Application: Malignant cells exhibit altered euchromatin/heterochromatin ratios

G-Banding and Karyotype

  • G-Banding

    • Chromosomes visible during mitosis after Giemsa staining; highlights adenine and thymine rich regions

    • Used to identify structural chromosomal anomalies

  • Karyotyping

    • Genetic test examining chromosome structure and number; forms visual karyotype map

    • The human genome includes 22 pairs of autosomes and 1 pair of sex chromosomes

RNA Overview

  • RNA: Single-stranded molecule containing ribose instead of deoxyribose, and uracil instead of thymine

  • Synthesized by transcription catalyzed by three RNA polymerases:

    • RNA polymerase I (for rRNA)

    • RNA polymerase II (for mRNA)

    • RNA polymerase III (for tRNA)

Messenger RNA (mRNA)

  • Carries genetic code to cytoplasm for protein synthesis

  • Codons complementary to DNA codons; contains one start codon (AUG) and three stop codons (UAA, UAG, UGA)

Transfer RNA (tRNA)

  • Involved in protein synthesis, cloverleaf shape

  • Contains approximately 80 nucleotides, terminal adenylic acid attaches amino acids

  • Anticodon recognition determines specified amino acid in polypeptide chain

Ribosomal RNA (rRNA)

  • Associates with proteins to form ribosomes, involved in protein synthesis within the nucleolus

  • Processed from a single 45S precursor rRNA to form ribosomal subunits: 28S, 18S, 5S rRNA

  • Clinical Application: ATG in DNA corresponds to the translation start, while repeat-associated non-ATG proteins associated with neurodegenerative diseases

Regulatory RNAs

  • Micro-RNA (miRNA)

    • Small segments (19-25 nt) regulating gene expression, may methylate DNA preventing transcription

  • Long Intergenic Noncoding RNA (lincRNA)

    • Over 200 nt in length; regulates gene transcription, competes with mRNAs for miRNA

  • Small Interfering RNAs (siRNAs)

    • 19-25 nt; act similarly to miRNAs inhibiting transcription

Comparison of DNA and RNA

  • DNA vs. RNA Differences
    1) Double-stranded vs. single-stranded
    2) Deoxyribose (DNA) vs. ribose (RNA)
    3) Thymine (DNA) vs. uracil (RNA)