Cell Nucleus Structure and Function

Structure of the Nucleus

• The nucleus contains chromatin, the nucleolus, the endoplasmic reticulum, intermediate filaments, an outer nuclear membrane, an inner nuclear membrane, the nuclear lamina, centrosome, microtubules, and nuclear pores

Nuclear Envelope

• The nuclear envelope comprises an outer (cytoplasmic) nuclear membrane, and an inner nuclear membrane
• Features a perinuclear space found between the two membranes
• Includes a nuclear lamina, which adheres to the inner nuclear membrane
• Nuclear pores allow molecules to exchange with the cytoplasm

Nuclear Lamina

• The nuclear lamina is composed of a network of protein filaments called lamins
• Lamins' structure and amino acid composition are similar to intermediate filaments
• The nuclear lamina provides shape to the cell nucleus
• The nuclear lamina participates in the structural organization of chromatin
• It provides a site of attachment for chromatin domains known as lamina-associated domains (LADs)
• Lamins are involved in fragmentation and reconstruction of the nuclear envelope during mitosis

Nuclear Pores

• A nuclear pore consists of three rings, each made of eight elements
• Elements form a cytoplasmic ring, a central pore, and a nuclear ring
• Eight filaments are anchored in both rings
• Nuclear filaments form a structure called the nuclear basket
• Nuclear pores enable two-way and selective transport of macromolecules between the nucleus and cytoplasm

Nuclear Matrix

• The nuclear matrix is a network of fibers located inside the nucleus
• It regulates DNA replication and gene expression
• The nuclear matrix is involved in transcription and maturation of pre-RNA
• It also transports ribosome precursors into the cytoplasm

The Nucleolus

• The nucleolus occupies 25% of the nucleus volume during interphase
• The nucleolus disappears in late prophase and is reconstructed in telophase
• Its primary components include RNA and proteins

Nuclear Chromatin

• Nuclear chromatin is the form of chromosomes during interphase
• Chromatin's chemical composition includes deoxyribonucleic acid (DNA) at 36.5%, histone proteins (basic) at 37.5%, non-histone proteins (acidic) at 10.5%, ribonucleic acid (RNA) at 9.5%, plus water, calcium and magnesium ions
• DNA molecules are 2 meters long in human cells, corresponding to 5.3 x10^9 base pairs
• In metaphase, a DNA molecule is 10,000 times shorter and occurs in a packed form, making up the chromosome
• DNA packing is a result of specific structural organization in space and the participation of histone and non-histone proteins
• Interphase chromosomes occupy a distinct space within the nucleus

Chromatin Types

• During interphase, chromatin is classified as euchromatin or heterochromatin
• Euchromatin is completely or partially relaxed, stains brightly, and is genetically active
• Heterochromatin is condensed, stains darkly, and is genetically inactive

Euchromatin

• Euchromatin forms through chromosome transformation from metaphase to interphase
• It consists of fully developed or lightly packed chromosomes with about 1,000x packing
• In interphase, euchromatin accounts for about 92% of the genome
• Euchromatin is genetically active and contains DNA that is transcribed
• Upon condensation of DNA strands, it can transform into packed (inactive) chromatin

Heterochromatin

• During interphase, heterochromatin contains DNA that is always in a condensed state
• Heterochromatin is within the confines of the nuclear envelope
• Heterochromatin decondenses only before DNA replication in the late S phase
• Heterochromatin is located at the ends of chromosomes (telomeric), within the centromere (centromeric), and in some parts of the chromosomes (intercalary)

Types of Heterochromatin

• Constitutive heterochromatin occurs at the centromeres and telomeres of chromosomes
• Facultative heterochromatin forms by the reversible condensation of euchromatin which contains genes when necessary

Nucleic Acids

• Nucleic acids comprise heterocyclic nitrogenous bases, a five-carbon sugar, and a phosphate group (phosphoric acid residue)
• A base-sugar unit is called a deoxyribonucleoside (DNA) or nucleoside
• A base-sugar-phosphate unit is called a deoxyribonucleotide (DNA) or nucleotide
• A [deoxyribo]nucleotide is the fundamental monomer unit of a nucleic acid chain

Nitrogenous Bases

• Nitrogenous bases are heterocyclic, aromatic compounds that contain carbon and nitrogen atoms within their ring structures for nucleic acids
• They are derivatives of pyrimidine or purine
• Pyrimidine is a heterocyclic compound containing four carbon and two nitrogen atoms in the 1 and 3 carbon positions
• Purine is a compound consisting of a pyrimidine ring connected to an imidazole ring

Pyrimidine and Purine Bases

• Pyrimidine bases (single-ring) include cytosine (C), thymine (T), and uracil (U)
• Purine bases (two-ring) include adenine (A) and guanine (G)

Pentose Sugars

• In RNA nucleotides, the sugar component is a pentose called ribose
• In DNA deoxyribonucleotides, the sugar component is a pentose called deoxyribose
• Both pentoses have an oxygen within the ring and the 5' carbon is outside of the ring
• Deoxyribose is devoid of a hydroxyl group at the 2' carbon

Phosphate Group

• Nucleic acids contain a phosphoric acid (V) residue, which gives nucleic acid molecules acidic properties and a negative charge through cleavage of the hydrogen cation (proton)

DNA Structure: Deoxyribonucleoside

• Nitrogenous bases are Cytosine, Guanine, Adenine and Thymine
• The sugar is deoxyribose
• In a nitrogenous base, the nitrogen atom links to a carbon atom of the sugar residue via a N-glycosidic bond
• The C₁ carbon of the sugar is bonded to the N₁ nitrogen in pyrimidines and the N, nitrogen in purines

DNA Structure: Deoxynucleotide

• Nitrogenous bases are Cytosine, Guanine, Adenine and Thymine
• The sugar is deoxyribose
• Phosphate group: via a phosphodiester bond with the 5' carbon in the sugar ring

Nucleosides and Nucleotides in DNA

• Cytosine (C) base has the nucleoside Deoxycytidine
• The Cytosine nucleotide is Deoxycytidine 5'-monophosphate (dCMP)
• Guanine (G) base has the nucleoside Deoxyguanosine
• The Guanine nucleotide is Deoxyguanosine 5'-monophosphate (dGMP)
• Adenine (A) base has the nucleoside Deoxyadenosine
• The Adenine nucleotide is Deoxyadenosine 5'-monophosphate (dAMP)
• Thymine (T) base has the nucleoside Deoxythymidine
• The Thymine nucleotide is Deoxythymidine 5'-monophosphate (dTMP)

DNA Structure: Nucleoside Triphosphates

• The substrates in nucleic acid synthesis are nucleoside triphosphates

Primary Structure of DNA

• Information is contained according to the order of the nitrogenous bases (C, G, A, T) in the nucleotides
• The DNA polynucleotide chain is formed by phosphodiester linkages with the 5' and 3' deoxyribose carbon atoms of neighbouring nucleotides
• The DNA chain has two different ends: the 5' end is terminated by a phosphate group, and the 3' end is terminated by a hydroxyl group

Sequence of Bases

• Chemical differences in phosphodiester bonds at the 5' carbon of one nucleotide and at the 3' carbon of the adjacent nucleotide confer polarity (directionality) of the DNA molecule
• The sequence of bases is written in the 5' → 3' direction

Secondary Structure of DNA

• DNA exists in a double-stranded form composed of two complementary strands
• Nitrogenous bases are oriented toward the inside of the double strand and form base pairs linked by hydrogen bonds such as A=T and G=C
• Hydrogen bonds between nitrogenous bases form referred to as Watson-Crick-type base pairs, showing complementary base pairing
• The sugar and phosphate residues linked to each other by 3',5'-phosphodiester bonds are on the outside of the chain

DNA Double Helix

• Two complementary DNA chains wrap around a common axis to form a double helix
• One strand runs in the 5' → 3' direction, and another strand runs in the 3' → 5' direction
• This arrangement is referred to as antiparallel
• The DNA double helix has two different orientations: one from the 5' end to the 3' end, and another from the 3' end to the 5' end

DNA Helix Dimensions

• The distance between consecutive nucleotides in the DNA helix is 0.34 nm (3.4Å)
• There are 10 base pairs per twist of the helix in the DNA helix
• The twist of the helix in the DNA helix is 3.4 nm (34Å)
• Two depressions called major and minor grooves exist on the surface of the DNA helix
• These grooves form because the bonds connecting the base and the sugar of complementary bases (glycosidic linkages) are not exactly opposite to each other
• The distance between C1 atoms of two chains is 1.1 nm, A-T distance is 1.11nm, G-C distance is 1.08 nm, and the distance between nucleotides is 0.34 nm

Histones

• Two types of histones are involved in the construction of DNA
• They are called core histones and linker histones
• The core histones are H2A, H2B, H3, and H4
• Interactions between H2A and H2B, as well as, H3 and H4 lead to the formation of two dimers and then an octamer
• Each core histone has a long amino acid "tail" at the N-terminus that extends beyond the core particle of the nucleosome
• The linker histones, H1 and H5, hold the DNA strands together

Nucleosome

• A nucleosome is the basic structural unit of DNA packaging in eukaryotes and is formed by eight histones and a section of DNA
• The nucleosome core is made up of eight histones, with two molecules each of H2A, H2B, H3, and H4
• A section of DNA is ~200 nucleotide pairs long wound around the core

Chromatosome

• A chromatosome is a structural unit of chromatin consisting of a nucleosome and histones H1/H5 (linker histones)
• Histones H1/H5 are responsible for the formation and stabilization of the chromatosome
• Chromatosomes are connected by a ~50 nucleotide pair-long DNA linker

The 30 nm Fiber

• The 30 nm fiber (filament) is a higher-order structure of which the presence of histones H1/H5 is important to form
• The resulting chromatin fiber has a diameter of about 30-nm and contains six nucleosomes per turn
• The packing of nucleosomes in the 30-nm fiber allows the DNA contained within it to be shortened by about 40 times

Chromosome Loops and Domains

• The 30-nm fiber together with the nuclear matrix forms chromosome loops
• Chromosome loops are created by non-histone proteins that bind to specific DNA sequences creating a clamp are established by special non-histone proteins that bind to specific DNA sequences forming a clamp at the base of each loop
• Chromosome loops are then folded into looped domains

DNA Packing in Chromosomes

• DNA packing levels in chromosomes have these average diameters:
  • double-stranded DNA helix (2 nm)
  • Nucleosome - DNA wrapped around histones (11 nm)
  • 30 nm fiber (30 nm)
  • loops (in dispersed form - 300 nm)
  • domains (in condensed form - 700 nm) -mitotic chromosome (1400 nm)
• A metaphase chromosome is 10,000 times shorter than an extended DNA helix

RNA Structure: Ribonucleoside

• Nitrogen bases: G, C, A, U
• Sugar: ribose
• In a nitrogenous base, the nitrogen atom links to a carbon atom of the sugar residue via a N-glycosidic bond
• Each C₁ carbon of the pentose ring is bonded in pyrimidines to N₁ nitrogen, and in purines to the N, nitrogen

RNA Structure: Ribonucleotide

• Ribonucleotide nitrogen bases are Guanine, Cytosine, Adenine, and Uracil
• The sugar is ribose
• A phosphodiester bond forms between the phosphate group and the 5' carbon of the sugar ring
• Phosphodiester bonds in RNA are less stable than those in DNA

Nucleosides and Nucleotides in RNA

• The Cytosine (C) base has the Nucleoside Cytidine, and the Cytidine 5'-monophospharane (CMP) Nucleotide
• The Guanine (G) base has the Nucleoside Guanosine, and the Guanosine 5'-monophosphate (GMP) Nucleotide
• The Adenine (A) base has the Nucleoside Adenosine, and the Adenosine 5'-monophosphate (AMP) Nucleotide
• The Uracil (U) base has the Nucleoside Uridine, and the Uridine 5'-monophosphate (UMP) Nucleotide

Primary Structure of RNA

• The primary structure's information is contained according to the order of the nitrogenous bases within the nucleotides (G, C, A, U)
• The RNA polynucleotide chain is formed by phosphodiester linkages between the 5' and 3' ribose carbon atoms of neighboring nucleotides
• The RNA chain has two different ends, where the 5' end is terminated by a phosphate group and the 3' end is terminated by a hydroxyl group

Secondary Structure of RNA

• Formed by the folding of single-stranded RNA into motifs comprising hairpin loops, stems (helices), internal-loops, and bulges

Double Stranded Regions of RNA

• Double-stranded regions of RNA form an A-form helix
• The formation of a B-form double-stranded helix typical of DNA molecules is prevented in RNA molecules due to a -OH group on the 2' carbon of the ribose
• Regular A-type double-stranded RNA helices contain minor and major grooves and feature Watson-Crick base pairs (A-U and G-C )
• Proteins bind to RNA in the minor groove region

Double Stranded RNA Helix

• Double-stranded RNA helices include canonical pairs of two bases (Watson-Crick type), non-canonical pairs of two bases (so-called, "non-Watson-Crick"), and non-canonical pairs of three bases
• More than 20 types of non-canonical pairs of bases that are connected by two, three or more hydrogen bonds have been characterized

Types of RNA

• There are coding and non-coding ribonucleic acids
• Coding features messenger RNA (mRNA)
• Non-coding features transfer RNA (tRNA), ribosomal RNA (rRNA), short non-coding RNA (sncRNA) which is less than 200 nucleotides and long non-coding RNA (lncRNA) which is more than 200 nucleotides

MRNA

• Messenger RNA (mRNA) is produced in the nucleus
• Pre-mRNA is produced, containing exons (coding sequence) and introns (non-coding sequence)
• Pre-mRNA undergoes a multi-stage maturation process
• mRNA migrates to ribosomes in the cytoplasm

TRNA

• Transport RNA (tRNA), are small base pair molecules (from 63 to 94 base pairs) which occur mainly in the cytoplasm of cells
• Constituting about 10 to 15% of the total RNA present in the cell, where are 60 types of tRNA exist in eukaryotic cells
• tRNA performs two basic functions that include the protein synthesis process, where it recognises the correct amino acid, and transfers that amino acid to the polypeptide

Primary TRNA Structures

• It comprises nucleotides with canonical nitrogenous bases and nucleotides with modified nitrogenous bases
• Modified bases in tRNA can be dihydrourydine - UH2, pseudourydine - Ψ, inosine - I, methylguanosine - mG, ribotidine - T, N6-isopentenyl adenosine - 16A, and 2(4)-thiouridyne - s2(4)U

Secondary TRNA Structures

• Contain three loops, a T (TΨC loop) and a D (D loop) and anticodon loop, and three stems (double-stranded areas, helices) - T, D and anticodon
• Features an acceptor arm, and additional arm (variable loop)

Loops in TRNA

• Known as the pseudouridine loop, the T-loop (TΨC) contains pseudouridine (Ψ)
• The T-loop helps in recognizing ribosomes by tRNA, by helping temporarily immobilize TRNA during the recognition process
• Known as the dihydrouridine loop, the D-loop (DHU) contains dihydrouridine (UH 2) and recognizes aminoacyl-tRNA synthetases that attach appropriate amino acids to the appropriate tRNA molcules
• The D-loop catalyses aminoacyl-tRNA synthetases by creating aminoacyl-tRNA

Anticodon Loops

• Contains a 7-nucleotide sequence that form the anticodon
• Aids in the anticodon bonds to the bases of complementary 3 nucleotides found in mRNA codes

Stems in TRNA

• Involve double stranded regions (helixes)
• T stem: is a short five base pair segment
• D stem: short three or four base pair segments
• Anticodon stem: short-paired segment of five base pairs

TRNA Structures

• The acceptor arm consists of seven base pairs
• The shorter 5' end will always terminate with a guanine nucleotide
• The longer 3' end will always ends with the CCA series of codes
• The amino acid is attached to the adenine nucleotide of the 3' arm, and is transported by tRNA to mRNA during the protein synthesis process
• The additional (variable) arm, is short containing or long, containing 13-21 nucleotides, performing auxiliary functions

Tertiary TRNA Structures

• Molecule in general include interactions that engage coaxial with or between acceptor and T.
• The D-stem interacts coaxially with the anticodon stem (AS), resulting in the formation of a second double helix
• During formation these helices for arms arranged relative to in such a way that the 3D resembles the shape of the letter L