10_Nucleus and Chromosome

NUCLEAR LAMINS

are type V intermediate filament proteins that are critically important for the structural properties of the nucleus.

Lamins

may regulate nuclear functions by direct interactions with chromatin and determining the spatial organization of chromosomes within the nuclear space.

NUCLEUS

• The chromosomes are localized and replicated and where the DNA (genetic information) is transcribed.

• The machinery for DNA replication and RNA transcription and processing.

• The nucleus of a non-dividing cell is called interphase cell (gap phases 0, 1, 2)

• Components: chromatin, nucleolus, nuclear envelope, nucleoplasm

• Evaluation of its size, shape, structure : significant in tumor diagnosis (karyolysis, pyknosis, karyorrhexis)

• ensures that these controlled cell activities will be efficiently transmitted to daughter cells

interphase cell

The nucleus of a non-dividing cell is called __

chromatin, nucleolus, nuclear envelope, nucleoplasm

Nucleus components

pyknosis

process where the cell’s nucleus shrinks and the chromatin becomes densely packed and dark under a microscope

Chromatin

The nuclear material organized as euchromatin or heterochromatin; DNA + Histones (nuclear proteins) needed for DNA’s functionality.

Nucleolus

• is a small area that also has DNA in the form of transcriptionally active ribosomal RNA (rRNA) genes, RNA, and proteins; site of rRNA synthesis & contains regulatory cell-cycle proteins

• Non-membranous nuclear region; Site of ribosomal RNA (rRNA) synthesis and initial ribosomal production & assembly.

• Surrounds transcriptionally active ribosomal RNA (rRNA) genes

• Prominent in cells with active protein synthesis (ex: neurons)

nuclear envelope

is the membrane system surrounding the nucleus; double membranes: inner nuclear & outer nuclear membranes, separated by a perinuclear cisternal space and perforated by nuclear pores.

outer membrane nuclear envelope

The ___is continuous with the rough endoplasmic reticulum (rER) with ribosomes.

Nucleoplasm

• Is nuclear content other than the chromatin and nucleolus

• An amorphous material enclosed by the nuclear envelope exclusive of the chromatin and the nucleolus.

Chromatin packaging

permits the transcriptional machinery to access regions of the chromosomes that are required for gene expression

5 histones along with other nonhistone proteins

Chromatin proteins:

heterochromatin (condensed) and euchromatin (dispersed)

2 forms of chromatin:

Heterochromatin

What form of chromatin:

• Clumps of densely staining material & highly condensed

• Stains: Hematoxylin and basic dyes (basophilic nucleus); Feulgen stain (deoxyribose of DNA); Fluorescent vital dyes (Hoechst dyes & Propidium iodide)

• Nuclear Location: Marginal chromatin (periphery of the nucleus; formerly referred to as the nuclear membrane)

  • Karyosomes (discrete bodies irregular in size & shape throughout the nucleus)

  • Nucleolar-associated chromatin (association with the nucleolus)

• Cells: Predominates in metabolically inactive cells: Circulating lymphocytes; Sperm; Plasma cells that typically produce one major product

Euchromatin

What form of chromatin:

• Dispersed & Light-staining material (contains the transcribed genes); less tightly packed

• Not evident in the light microscope

• Present within the nucleoplasm appear as “clear” areas between & around heterochromatin

• In metabolically active cells: Neurons and Hepatocytes

The constitutive heterochromatin

(highly condensed form virtually all times) made of short DNA tandems that are not transcribed – the telomeres & centromeres of chromosomes

the facultative heterochromatin

appears as chromosomal regions that become specifically inactivated in a specific cell type; during embryonic development, facultative form is a means of inactivating entire blocks of genetic information

Nucleosomes

• Smallest units of chromatin structure consist of macromolecular complexes of DNA and histones.

• (+) euchromatin; heterochromatin; chromosomes.

• These 10-nm-diameter particles represent the first level of chromatin folding (coiling of the DNA molecule around a protein core.) – “BEADS ON A STRING”

Fibrillar centers

Distinct Regions of NUCLEOLUS (pl. NUCLEOLI):

• contain DNA loops of 5 different chromosomes (13, 14, 15, 21, and 22) containing rRNA genes, RNA polymerase I, & transcription factors.

Fibrillar material (pars fibrosa)

Distinct Regions of NUCLEOLUS (pl. NUCLEOLI):

• contain ribosomal genes for active transcription & large RNA amounts

Granular material (pars granulosa)

Distinct Regions of NUCLEOLUS (pl. NUCLEOLI):

• represents the site of initial ribosomal assembly and contains densely packed, pre-ribosomal particles

Fibrillar centers, Fibrillar material (pars fibrosa), Granular material (pars granulosa)

3 Distinct Regions of NUCLEOLUS (pl. NUCLEOLI):

NUCLEOLONEMA

Pars fibrosa + pars granulosa =

Nucleolus organizer region (NOR)

a stretch of DNA carrying multiple copies of rRNA genes.

Nucleostemin

• is a p53 binding protein that regulates the cell cycle and influences cell differentiation, As cellular differentiation progresses, the level of this protein decreases.

• The presence of ___ in malignant cells suggests their role in cells uncontrolled proliferation

Basophilia and metachromasia

related to the phosphate groups of the nucleolar RNA is confirmed by predigestion of specimens with ribonuclease (RNAse), which abolishes the staining

Metachromasia

over reaction to staining

Feulgen staining

ineffective for nucleolar DNA due to its low concentration (Feulgen-negative)

Cajal bodies (Ramon Cajal) & Gemini of Cajal bodies (GEMs; so named appear similar to Cajal bodies)

are involved in maturation and processing of small nucleolar RNA (snoRNA) and small nuclear RNA (snRNA)

Speckles (interchromatin granule clusters, rich in RNAs & proteins)

necessary for splicing of messenger RNA precursors into mature mRNAs

Promyelocytic leukemia bodies (PML bodies)

role in programmed cell death, genomic stability, antiviral effects & control in cell division

NUCLEAR ENVELOPE

• Formed by two membranes: outer & inner nuclear membranes with a perinuclear cisternal space between them, separates the nucleoplasm from the cytoplasm.

• It houses the chromatin; Selectively permeable between the nuclear compartment and the cytoplasm.

• 2 membranes are perforated at intervals by nuclear pores. The perinuclear cisternal space is continuous with the cisternal space of the rER.

perinuclear cisternal space

The nuclear envelope is Formed by two membranes: outer & inner nuclear membranes with a ____between them, separates the nucleoplasm from the cytoplasm

Nuclear pores

• the outer & inner nuclear membranes are perforated at intervals by ___The perinuclear cisternal space is continuous with the cisternal space of the rER.

• ____ mediate the active transport of proteins, ribonucleoproteins, and RNAs between the nucleus and cytoplasm

Nuclear membranes

• Comprise the Nuclear envelope

• Outer - continuous with rER membrane. Polyribosomes are often attached to ribosomal docking proteins present on the cytoplasmic side of the outer nuclear membrane

• Inner - rigid network of intermediate filaments attached to its inner surface called the nuclear (fibrous) lamina. It contains specific lamin receptors and lamina-associated proteins that bind to chromosomes and secure the attachment of the nuclear lamina

Outer nuclear membrane

continuous with rER membrane. Polyribosomes are often attached to ribosomal docking proteins present on the cytoplasmic side of the outer nuclear membrane

Inner nuclear membrane

rigid network of intermediate filaments attached to its inner surface called the nuclear (fibrous) lamina. It contains specific lamin receptors and lamina-associated proteins that bind to chromosomes and secure the attachment of the nuclear lamina.

nuclear (fibrous) lamina

Inner nuclear membrane - rigid network of intermediate filaments attached to its inner surface called the ___. It contains specific lamin receptors and lamina-associated proteins that bind to chromosomes and secure the attachment of the nuclear lamina

nuclear lamina and nuclear matrix (nucleoskeleton)

The ____ are supporting structures of the nucleus.

nucleoskeleton (matrix)

is associated with 3H-thymidine (radioactive precursor for DNA synthesis) suggesting that it is involved in anchoring chromatin fibers locations where DNA or RNA is being synthesized; orienting the DNA for orderly replication & transcription; and providing tracks /pathway for new mRNA, being guided and propelled to the nuclear pores for transport to the cytoplasm

lamins

• The nuclear lamina is constructed from ___, intermediate filament proteins (lamin A and lamin C.) crosslinking lamin B protein to the inner nuclear membrane through its interactions with lamin receptors.

• disassemble during mitosis and reassemble when mitosis ends.

Hutchinson–Gilford progeria

Inherited abnormalities in these proteins have been linked human diseases, including severe muscle wasting or premature aging. Ex: _____, has a single base mutation in one lamin gene, appear in young children and usually cause death by the early teenage years having symptoms of old age— such as hair loss, cardiovascular disease, and degeneration of skin, muscle, and bone. The cells of such individuals exhibit severe abnormalities in nuclear shape.

pre-mature aging

nuclear lamina

• serve as scaffolding for chromatin, chromatin-associated proteins, nuclear pores, and the membranes of the nuclear envelope.

• It is involved in nuclear organization, cell-cycle regulation, differentiation, and gene expression.

• The ___ is constructed from lamins, intermediate filament proteins (lamin A and lamin C.) crosslinking lamin B protein to the inner nuclear membrane through its interactions with lamin receptors.

Emerin, Nurim & Lamin B receptor (LBR)

Lamin receptors:

Emery-Dreifuss muscular dystrophy (EDMD)

have been associated with mutations in either lamins or lamin receptors.

mutations of emerin

The X-linked recessive EDMD is caused by

X-linked recessive EDMD

The ____ is caused by mutations of emerin

mutations in lamin A/C.

the autosomal dominant EDMD is caused by

autosomal dominant EDMD

the ___ is caused by mutations in lamin A/C.

Nuclear Pores

• 70- to 80-nm “openings” along nuclear envelope

• Made of NUCLEOPORINS

• (+) Central plug/transporter : Nuclear translocation

• Translocation – involves importation & exportation cellular products & exchange between cytoplasm & nucleus

Translocation

involves importation & exportation cellular products & exchange between cytoplasm & nucleus

Nucleoporins of NPC

• Collective term for nuclear pore proteins

• This central framework is inserted between the cytoplasmic ring and the nuclear ring.

• From the cytoplasmic ring, eight short protein fibrils protrude into the cytoplasm and point toward the center of the structure.

• The nucleoplasmic ring complex anchors a nuclear basket (or nuclear “cage” that resembles a fish trap) assembled from eight thin 50-nm-long filaments joined distally by an adjustable terminal ring 30 to 50 nm in diameter.

• The cylinder-shaped central framework encircles the central pore of the NPC, which acts as a close-fitting diaphragm or gated channel.

• Each NPC contains one or more water-filled channels for transport of small molecules

cytoplasmic ring and the nuclear ring

Nucleoporins of NPC, the central framework, is inserted between the _____

nuclear basket

The nucleoplasmic ring complex anchors a ____ (or nuclear “cage” that resembles a fish trap) assembled from eight thin 50-nm-long filaments joined distally by an adjustable terminal ring 30 to 50 nm in diameter

central pore

The cylinder-shaped central framework encircles the ___of the NPC, which acts as a close-fitting diaphragm or gated channel

Nuclear Pore Complex (NPC)

• regulates the passage of proteins between the nucleus and the cytoplasm; GTP energy-dependent mechanism

Ribosomal proteins

Because the nucleus does not carry out protein synthesis, ____ are partially assembled into ribosomal subunits in the nucleolus and are transported through nuclear pores to the cytoplasm (Exportins)

exportin

RNA Proteins that possess the nuclear export sequence (NES) bind in the nucleus to ___ (a protein that moves molecules from nucleus into cytoplasm) and to a GTP molecule. Protein–exportin–GTP complexes pass through NPC into the cytoplasm where GTP is hydrolyzed and the NES protein is released.

nuclear import receptor (importin)

Large molecules (such as large proteins and macromolecular complexes) depend on the presence of an attached signal sequence called the nuclear localization signal (NLS) for passage through the pores. Labeled NLS proteins destined for the nucleus then bind to a soluble cytosolic receptor called a ___ that directs them from the cytoplasm to an appropriate NPC.

nucleoplasmic reticulum

Tubular invaginations of the nuclear envelope, collectively known as the _____projects into the internal nuclear space and increase the area of the nucleus that makes direct contact with the inner nuclear membrane.

Gene as a segment of DNA involved in producing a polypeptide chain

Old definition of Gene

GENE being a union of genomic sequences encoding a coherent set of potentially overlapping functional products.

New definition of Gene

Histone octamers

are created by joining together two H2A–H2B dimers and two H3–H4 dimers and that the DNA double helix is then wrapped around the resulting octamer

• a. Beads on a string

• 30-nm chromatin fiber

• Looped domains of the 30-nm chromatin fiber

• Heterochromatin

• A replicated chromosome (two attached chromatids)

Levels of Chromatin packing

CHROMOSOMES

[Gr., colored bodies]: During mitotic division, chromatin fibers formed from chromatin loop domains attached to a flexible protein scaffold undergo condensation to form ____

Telomere

area located at each end of the chromosome; shorten with each cell division.

Telomere length

s an important indicator of the lifespan of the cell. To survive indefinitely (become “immortalized”), cells must activate a mechanism that maintains telomere length.

TELOMERASE

• In malignant cells: Cells transformed into malignant cells… Linked to Telomerase enzyme, present in the Telomere that adds repeated nucleotide sequences to the chromosomal ends.

• New Finding: Has been shown to extend the lifespan of cells

PROKARYOTES

• single chromosome plus plasmids

• circular chromosome made only of DNA

• found in cytoplasm

• copies its chromosome and divides immediately afterwards

EUKARYOTES

• many chromosomes

• linear chromosomes

• made of chromatin, a nucleoprotein (DNA coiled around histone proteins)

• found in a nucleus

• copies chromosomes, then the cell grows, then goes through mitosis to organise chromosomes in two equal groups

Bacterial Nucleoid

• Circular double helix

• Nucleoid - complexed with protein in a structure

• Attached to plasma membrane (+) Plasmids – small, circular, supercoiled, condensed molecules of DNA that carry genes both for their own replication and for other cellular functions (usually nonessential ones) used in genetic transformation

• Ex:(F factors during conjugation, R factors in drug resistance, virulence factors).

Gregor Mendel

inheritance patterns (pea plants) that is transmitted in the form of distinct units, genes.

Johann Friedrich Miescher

chemistry of the nucleus containing nuclein

Walther Flemming

chromosome ID

Frederick Griffith

Discovers that a factor in diseased bacteria can transform harmless bacteria into deadly bacteria.

Avery, MacLeod, McCarty

DNA as agent of genetic transformation

Hershey & Chase experiment

DNA is the ‘transforming principle’

Rosalind Franklin

double helical structure

Watson and Crick

described the physical structure of the DNA molecule

H.J. Muller

DNA as the genetic material

Adenine, Guanine

Purines

Thymine, Cytosine

Pyrimidines

Phosphate group, Deoxyribose sugar, Nitrogenous base

Components of DNA nucleotides

Hydrogen bonds

Paired nitrogenous bases are connected with

Phosphate bonds

DNA nucleotides are connected with

base pairs (bp)

Genome size is usually expressed as the total number of base paired nucleotides, or __

“jumping genes”

Interspersed repeated DNA – transposons, ___– establishes evolutionary adaptability of organisms