Histones & Nucleosomes: Structure, Modification & Function

This section covers molecular interactions in cells. DNA has a negative charge due to phosphate groups. Proteins binding to DNA must have positive charges from basic amino acids (lysine, arginine). Histones contain many basic amino acids for electrostatic binding to DNA. Proteins embedded in the hydrophobic interior of the lipid bilayer must be hydrophobic, containing amino acids with hydrophobic side chains (valine, leucine, phenylalanine) to interact favorably with lipid tails.

Charged amino acids (positively charged: lysine, arginine; negatively charged: aspartate, glutamate) participate in electrostatic interactions (salt bridges) with oppositely charged groups. Histones, which package DNA, are rich in positively charged amino acids that interact with negatively charged DNA phosphate groups. Amino acids contain ionizable groups with pKa values (pH at 50% protonation). At physiological pH (~7), carboxyl groups are deprotonated (negative) while amino groups are protonated (positive). The isoelectric point (pI) is the pH where net charge is zero. Changes in pH alter charge distribution, potentially disrupting electrostatic interactions and causing protein denaturation. The central dogma of molecular biology describes genetic information flow: DNA replicates and transcribes to RNA, which translates to proteins. DNA stores genetic information and replicates faithfully. RNA carries genetic information from DNA to protein synthesis machinery. Proteins are functional molecules performing cellular activities. The genetic code is read in triplets (codons), with each codon specifying an amino acid. The code is degenerate (multiple codons specify same amino acid), providing mutation protection. Translation begins at start codons (AUG, methionine) and ends at stop codons (UAA, UAG, UGA). Proteins perform diverse functions: catalytic (enzymes), transport (hemoglobin), structural (collagen, keratin), protective (antibodies), regulatory (hormones), and motor functions. The three-dimensional structure determines protein function. Proteins have four levels of structural organization: (1) Primary structure is the linear sequence of amino acid residues connected by peptide bonds; (2) Secondary structure involves local folding patterns (alpha-helices, beta-sheets, turns) formed by hydrogen bonding between backbone atoms; (3) Tertiary structure is the three-dimensional arrangement of the entire polypeptide chain, stabilized by interactions between amino acid side chains (hydrophobic interactions, electrostatic interactions, hydrogen bonds, disulfide bonds); (4) Quaternary structure occurs when multiple polypeptide chains associate into a single functional protein complex. The native conformation is the specific three-dimensional structure in which a protein performs its biological function.

Basic amino acids have amino groups in their side chains, giving them a net positive charge at physiological pH. They include lysine, arginine, and histidine. Lysine has a long aliphatic side chain with an amino group, arginine has a guanidino group, and histidine has an imidazole ring. These amino acids are important for protein structure and function, particularly in enzyme active sites and protein-DNA interactions.

Lysine is a basic amino acid characterized by its positively charged side chain at physiological pH. It contains an alpha amino group common to all amino acids plus an additional primary amino group on its side chain, attached to the epsilon carbon (the fifth carbon in the side chain). This unique structure gives lysine exceptional chemical versatility. The pKa of lysine's epsilon amino group is approximately 10.5, meaning at physiological pH (7.4), lysine predominantly exists in its protonated form (-NH3+), carrying a positive charge that enables it to form salt bridges with negatively charged acidic amino acids like aspartate and glutamate, stabilizing protein structures and facilitating protein-DNA interactions.

Amino acid side chains are classified as nonpolar, polar, or charged based on their chemical structure: nonpolar side chains contain only C-H bonds with equal electron sharing and no partial charges, so they interact only with other nonpolar side chains and are found in protein interiors; polar side chains contain oxygen atoms with higher electronegativity than hydrogen, creating partial charges that allow interactions with other polar side chains, charged side chains, and water, placing them on protein exteriors; charged side chains carry full electrical charges due to proton loss, enabling ionic interactions with oppositely charged side chains and interactions with polar molecules and water, also positioning them on protein exteriors.

Eukaryotic genomes are more complex than prokaryotic genomes due to multicellularity, requiring sophisticated chromatin organization where DNA wraps around histone proteins to form nucleosomes (the basic unit of chromatin), which then pack into 30-nanometer fibers and looped domains to create visible chromosomes during metaphase; this organization enables differential gene expression through histone tail modifications that control DNA accessibility for transcription.

Eukaryotic DNA is longer and consists of multiple linear molecules, unlike bacterial circular DNA. Human diploid cells contain approximately 2 meters of DNA compressed into a nucleus only 10 micrometers in diameter—a 1 million-fold compression. Chromatin, the DNA-protein complex, appears as bead-like structures under electron microscopy. Each nucleosome, the basic chromatin unit, consists of 146 base pairs of DNA wrapped around an octamer of histone proteins.

Eukaryotic cells are larger than bacteria (about 10 times the size) and contain membrane-bound organelles, including a nucleus. The nucleus stores and protects DNA, acting like a secure file cabinet where genetic material is kept safe while copies are made for use elsewhere. The nucleus has a double membrane with large pores allowing DNA copies and ribosome components to pass in and out. The nucleolus within the nucleus produces ribosomes, which are molecular machines that build proteins. This organization allows eukaryotic cells to compartmentalize their functions and efficiently manage genetic information.

Eukaryotic cells contain multiple membrane-bound organelles: nucleus (genetic control center), mitochondria (energy production), endoplasmic reticulum (protein and lipid synthesis), Golgi apparatus (protein modification and sorting), lysosomes (digestion), vacuoles (storage), and cytoskeleton (structural support). The cell size scale ranges from atoms (~0.1 nm) to cells (10-100 μm). Light microscopes image 1 μm and above, while electron microscopes image the entire scale.

A eukaryotic cell is defined as a cell possessing a true nucleus containing genetic material (DNA) surrounded by a nuclear envelope. The nucleus is the control center containing DNA organized into chromosomes (23 pairs in humans, totaling 46 chromosomes). The cytoplasm is the second major compartment, consisting of cytosol (the liquid portion where metabolic reactions occur) and various organelles. The plasma membrane separates the intracellular environment from the extracellular environment and regulates exchanges between them. The cytoskeleton consists of protein filaments (microfilaments, microtubules, and intermediate filaments) that organize the cell's three-dimensional structure and facilitate intracellular transport.

The central dogma describes how genetic information flows from DNA to RNA to protein. Transcription begins when transcription factors assemble at a promoter region, followed by the mediator complex bringing RNA polymerase to the DNA. The transcription initiation complex requires activator proteins binding to enhancer regions to activate copying. RNA polymerase unzips DNA and synthesizes mRNA using one strand as a template. After transcription, mRNA undergoes splicing where introns are removed and exons are joined. The resulting mRNA carries the genetic message from the nucleus to ribosomes for protein synthesis.

The Central Dogma describes genetic information flow: DNA stores information, RNA transmits it, and proteins execute functions. DNA uses 4 bases for stable storage, RNA uses 4 bases for mobility, and proteins use 20 amino acids for diverse functions. Transcription begins at promoters where RNA polymerase unwinds DNA and selects a template strand. The enzyme reads DNA 3' to 5' while synthesizing RNA 5' to 3' using complementary base pairing (C-G, G-C, A-U, U-A). The resulting RNA is complementary and antiparallel to the template. One DNA molecule can produce multiple RNA copies. In prokaryotes, transcription occurs in the cytoplasm; in eukaryotes, it occurs in the nucleus before RNA export.

RNA polymerase requires transcription factors to initiate transcription. In eukaryotes, RNA polymerase II requires general transcription factors (such as TFIID, TFIIH) to recognize promoter sequences and initiate transcription. These factors help position RNA polymerase at the correct location on the DNA template.

Transcription is the process by which RNA polymerase copies a gene from DNA to RNA, starting at a promoter and ending at a transcriptional stop signal, producing a single-stranded RNA molecule that is complementary to the template DNA strand; this process, along with translation, forms the central dogma of molecular biology (DNA → RNA → protein), with key differences between DNA and RNA being the sugar (deoxyribose vs. ribose) and the base (thymine vs. uracil).

Transcription is the process of synthesizing RNA from a DNA template. RNA polymerase is the key enzyme that catalyzes this process. Before RNA polymerase can begin transcription, transcription factors must first bind to specific DNA sequences to position the enzyme correctly at the start site. Transcription factors are proteins that bind to specific DNA sequences and help recruit RNA polymerase to the correct location. RNA polymerase then binds to the transcription factors and the DNA, forming a complex that will initiate transcription. This assembly ensures that transcription begins at the correct location and in the correct direction.