Molecular Biology: Eukaryotic Transcription and Replication

Unit 3: The Nucleus

• The nucleus is a compartment within eukaryotic cells
• Its function relates to cell structure and function
• Several subtopics are examined including the cell nucleus and DNA, the nuclear envelope, DNA replication, DNA transcription, traffic between the nucleus and cytoplasm, and nuclear bodies.

3.1: The cell nucleus and the DNA

• The nucleus acts as a storehouse for genetic information
• DNA replication occurs at the genomic level inside the nucleus
• RNA transcription and processing are controlled by processes regulating the transport of transcription factors into the nucleus from the cytoplasm

Chromosomes and chromatin

• Eukaryotic genomes are complex, organized on multiple linear chromosomes.
• DNA is associated with proteins, primarily histones, to form a highly organized structure for efficient storage and function called chromatin.
• The length of human DNA is 2 meters, but it must fit into a nucleus that is only 5-10 micrometers in diameter.

Chromosomes

• DNA is tightly packaged during cell division to form chromosomes
• Chromosomes are only seen during cell division
• DNA is not being used for macromolecule synthesis in chromosome form

Chromatin

• Chromatin is unpacked DNA
• It is unstructured DNA present during interphase
• DNA is being used for macromolecule synthesis in chromatin form

Heterochromatin and euchromatin

• Heterochromatin is a tightly condensed form of chromatin and is inactive in transcription
• Euchromatin is a loosely condensed form of chromatin and is active in transcription

Chromatin structure

• Chromatin is a complex structure of DNA and proteins
• Varying degrees of condensation occur during the cell cycle to maintain functionality
• There are different levels of DNA packaging, ranging in dimensions from 2 nm to 1400 nm (from double helix to chromosome)

Level 1: 11nm chromatin fiber

•  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.
•  A distance of approximately 200bp is present between two consecutively placed nucleosomes which results in a “beads-on-a-string” appearance under a microscope.

Level 2: 30 nm chromatin fiber

• 11nm fibers are rewound to form a 30nm chromatin fiber.
• about 6 nucleosomes are found per turn of this fiber.
• Most euchromatin during interphase is in the form of 30 nm fibers.

Level 3: 300nm chromatin fiber

• 30nm fibers undergo more packaging process steps.
• Chromatin loops are linked to a protein scaffold structure with specific A and T sequences called SAR (scaffold attachment regions).
• A 300 nm fiber structure is formed.

Level 3: 600-700nm chromatin fiber

• During mitosis, the 300nm fiber further condenses to form a 600-700 nm fiber structure.
• This represents the chromatid form

DNA packaging

• The degree of packaging reaches 10,000 times in cells.
• This demonstrates the compactness of DNA and its efficient packing within the nucleus.

Interaction between histones and DNA

• Histones have amino‐terminal tails that undergo various modifications such as acetylation, methylation, and phosphorylation.
• These modifications constitute a histone code that participates in DNA replication and expression.
• Acetylation is associated with transcriptional activation.

Chromosomes

• Each eukaryotic species has a characteristic number of chromosomes.
• Humans have 46 chromosomes (2n): 22 homologous pairs & 1 pair of sex chromosomes.
• Females have two X chromosomes (homogametic), while males have an X and a Y chromosome (heterogametic)

Chromosome structure

• In metaphase, both copies of the replicated DNA are held together by the centromere.
• Each copy of DNA is called a chromatid (sister chromatids).
• The centromere divides the chromatids into two arms that can have the same or different lengths.
• Telomeres are the ends of the chromatids.

Centromere

• Specialized region of a chromosome
• Critical for the correct distribution of duplicated chromosomes during mitosis
• Acts as a binding site for the mitotic spindle
• In yeast, centromeres are short (about 125 bp)
• In mammals, centromeres are composed of hundreds of kilobases (kb) of repetitive DNA.

Telomeres

• Specialized structures of DNA and proteins
• Maintain structural integrity of chromosomes
• Position chromosomes in the nucleus
• Ensure complete DNA replication
• Constitute of tandem repeats of a single DNA sequence containing groups of G residues on one strand in humans
• The sequence of TTAGGG is repeated up to 3-20 kb

Telomere structure

• Telomeric DNA forms a loop on itself to form a circular structure
•  This structure is surrounded by a protein complex known as shelterin that protects the ends of the chromosomes.
• DNA polymerase cannot replicate the ends of the chromosomes; thus, a special enzyme, telomerase, is needed to complete replication of the telomeric DNA

Genes and genomes

• Genome: the complete set of genetic material in an organism.
• Genes: components of DNA essential to encoding a gene product, mainly mature RNA or protein.
• Some non-coding DNA plays a role in gene expression.

DNA quantity paradox

• The amount of DNA (base pairs) in a genome does not always correlate or correspond to the biological complexity or number of genes. An example is a correspondence between the amount of DNA and the organism complexity.

Gene structure: Introns and exons

• Exons are parts of a gene that are retained in mRNA
•  Introns are parts of a gene that are not retained in mRNA

Alternative splicing

• Generation of different mature RNA transcripts from one gene is possible by alternative splicing.
• It involves the omission of different combinations of exons during mRNA processing.
• Alternative splicing allows 21,000 human protein coding genes to specify nearly 85,000 different proteins.

Complexity in human DNA: Types of sequences in our genome

• The human genome contains 21,000 genes with many regulatory sequences
• Extragenic DNA includes repetitive sequences such as tandem repeats and sparse repeats

Noncoding RNA

• Various noncoding RNAs play fundamental roles in protein synthesis and gene regulation.
• microRNAs (miRNAs) are short noncoding RNAs that, among other functions, regulate gene expression or translation.
• Long noncoding RNAs (lncRNAs) are long noncoding RNAs that act as regulators of gene expression by interacting with chromatin-modifying proteins.

3.2: Nuclear envelope

• Acts as a selective barrier between the nucleus and cytoplasm
• Maintains both compartments metabolically independent
• Maintains the internal composition of the nucleus
• Plays a critical role in protein synthesis regulation; and regulates transcription

Nuclear envelope structure

• Composed of two membranes: an outer membrane and an inner membrane separated by a perinuclear space.
• The outer membrane is continuous with the endoplasmic reticulum membrane; the outer membrane may contain ribosomes
• The nuclear pore complex: acts as the selective channels allowing the passage of small molecules and macromolecules between the nucleoplasm and cytoplasm.

Nuclear lamina

• Network of protein filaments underlying both sides of the nuclear membranes; it provides structural support
• Constructed of lamin proteins (A, B,C; between 60-80 kDa)

Nuclear pore complex

• Junction of the two nuclear membranes
• Allows small polar molecules to pass through the nuclear envelope
• Responsible for the selective trafficking of proteins and RNA molecules between the nucleus and cytoplasm.

3.3: DNA replication

• The mechanism of DNA duplication that synthesizes an identical copy
• A semi-conservative mechanism of replication results in new strands from complementary strands.
• Each new double helix contains one of the original strands and a new complementary strand.

DNA polymerase

• Multiple DNA polymerases with different roles exist in prokaryotes and eukaryotes
• DNA polymerase III is the main polymerase responsible for replication in bacteria
• DNA polymerases α, δ, and ε carry out replication of nuclear DNA
• DNA polymerase γ takes on mitochondrial DNA replication
• All DNA polymerases share two fundamental properties

Origin of replication

• The DNA molecule opens like a zipper by breaking hydrogen bonds between complementary bases at specific points called origins of replication
• Initiator proteins recognize these sequences, facilitating the attachment of other proteins to form replication forks Mechanisms ensure complete and accurate DNA duplication across the entire chromosome

Origin of replication in prokaryotes

• Single origin in prokaryotes
• Binding of a specific initiator protein to initiate the unwinding of the DNA.
• The replication proceeds in both directions.

Origin of replication in eukaryotes

• Multiple origins of replication are required for rapid replication of the long chromosome.
• The high number of origins allows replication to happen in a fast manner

Replication fork

• Place in the DNA molecule where parental DNA strands are separated and new daughter strands are synthesized.
• DNA replication proceeds in the 5' to 3' direction, forming leading and lagging strands
• Okazaki fragments are small fragments of newly synthesized DNA on the lagging strand.
• DNA polymerase and DNA ligase enzymes are used to complete replication across the lagging and leading strands of DNA

DNA maintenance

• Accuracy of DNA replication is critical.
• The frequency of errors is less than one incorrect base for every 10^9 incorporated nucleotides, allowing DNA to maintain its integrity
• This accuracy is achieved by the DNA polymerase using double-reading activity.

Telomerase

• DNA polymerase involved in telomere formation
• It is only capable of synthesizing oligonucleotides with the telomeric sequence

3.4: DNA transcription

• Synthesis of RNA from DNA template using RNA polymerase
•  Antisense strand is used to synthesize a complementary RNA transcript or strand
• The RNA transcript is complementary to the DNA's sense strand with uracil replacing thymine in the RNA sequence and a hydroxyl group at the 2' carbon of pentose

RNA polymerase

• RNA polymerase is the main enzyme that catalyzes the reaction for RNA synthesis.
• (NMP)n + NTP → (NMP)n+1 + PPi where NMP is a nucleotide monophosphate and NTP is a nucleotide triphosphate , PPi being inorganic pyrophosphate.

Differences and similarities between DNA replication and DNA transcription

•  Replication involves duplicating an entire genome, while transcription involves copying some gene into RNA
•  Replication produces two complementary strands of DNA, while transcription produces a complementary RNA strand, which includes uracil
•  Both processes use one strand of DNA as a template; replication uses both strands while transcription uses only one.

Initiation

• Transcription commences with RNA polymerase binding to a promoter region before the transcription initiation site.
• Promoter regions contain conserved sequences of base pairs
• The DNA unwraps and polymerase undergoes conformational and chemical changes, inducing initiation of transcription.

Elongation

• Transcription factors are released.
• RNA polymerase advances in the 5' to 3' direction; the 3'OH group of the forming RNA reacts with the phosphate of the incoming ribonucleoside triphosphate
• the phosphodiester bond is formed

Termination

• RNA synthesis ends when RNA polymerase recognizes specific DNA sequences at the end of the genes.

Transcription in eukaryotes

• Eukaryotic cells have three types of RNA polymerases (I, II, and III)
• Transcription takes place in chromatin and regulation of chromatin structure is important
• Specific transcription factors are required

3.5: Traffic between the nucleus and cytoplasm

• Selective transport of proteins to and from the nucleus
• Regulation of protein transport to and from the nucleus
• RNA transport

Selective transport of proteins in and out of the nucleus

• Proteins, destined for the nucleus are labeled with specific aa sequences called nuclear localization signals (NLS)
• Importins recognize NLS
• Exportins recognize nuclear export signals (NES)
• Ran proteins and GTP hydrolysis are important in the transport processes

3.6: Nuclear bodies

• Differentiated organelles within the nucleus
• Serve to concentrate RNA and proteins involved in nuclear processes
• No membranes; dynamic structures are maintained by protein:protein and protein:RNA Interactions
• Active research field, but function not fully known

Types of nuclear bodies

• Nucleolus
• Cajal bodies
• Clastosomes
• Histone locus bodies
• Speckles
• PML bodies
• Polycomb bodies