CHE316 3/16 notes

"Describe hydrogen bonds and their geometry."

"Hydrogen bonds are approximately 3 angstroms in length and have a specific geometry involving H bond donors like N-H and O-H, where hydrogen carries a partial positive charge, and acceptors such as N and O carry a partial negative charge."

"Explain the role of hydrophobic contacts in molecular interactions."

"Hydrophobic contacts, or van der Waals interactions, are influenced by the buried surface area of nonpolar groups that do not contain heteroatoms or heterocyclic aromatics, allowing them to compile together and create strong interactions that are concealed from water."

"Define salt bridges and their characteristics."

"Salt bridges are electrostatic attractions that combine hydrogen bonds and ionic bonds, with affinity decreasing with distance and no geometric restraints. An example is the interaction between glutamic acid's deprotonated carboxyl group and lysine's protonated amino group."

"How do pi stacking interactions occur between aromatic rings?"

"Pi stacking interactions are attractive, noncovalent interactions between aromatic rings, with over 30,000 observed pairs in the Protein Data Bank (PDB). The most common arrangement is T-shape, where the positively charged edge of one ring aligns with the pi electron cloud of another."

"Explain cation-pi interactions and their significance."

"Cation-pi interactions occur when the electron distribution and polarity of an aromatic ring interact with a cation, such as Na+, enhancing the stability and specificity of molecular interactions."

"Describe the concept of water bridges in molecular interactions."

"Water bridges involve water molecules interacting with two non-water atoms simultaneously, forming a bridge that can be critical for molecular interactions. The strength of these bridges is variable and can significantly impact the stability of structures."

"What are halogen bonds and how do they function?"

"Halogen bonds are attractive interactions between an electrophilic region associated with a halogen atom in one molecular entity and a nucleophilic region (sigma) in another, functioning similarly to hydrogen bonds."

"How do buried surface areas contribute to van der Waals interactions?"

"Buried surface areas consist of nonpolar groups that are uncharged and adept at making van der Waals interactions, allowing them to compile together and create strong interactions that are shielded from water."

"Explain the significance of salt bridges in protein interiors."

"Salt bridges are stronger when located within the interior of proteins, away from water, as this prevents water from masking the ionic interactions, thereby enhancing the stability of the protein structure."

"Describe the different arrangements of pi stacking interactions."

"Pi stacking interactions can occur in several arrangements: T-shape, where one ring's edge aligns with another's pi cloud; parallel staggered, where edges of two rings partially overlap while remaining parallel; and face-to-face, where two rings are flat and stacked directly on top of each other."

"Describe the interaction between halogens and electrons."

"Electrons are withdrawn from halogens, resulting in a partial positive charge at the tip of the halogen, known as a sigma hole."

"Explain the significance of the sigma hole in halogen bonding."

"The sigma hole must align perfectly with the donor for the halogen bond interaction to occur."

"Do receptors interact with ligands in a specific way?"

"Yes, receptors interact with ligands via non-covalent interactions, which are reversible and vary in strength and duration."

"Define the dissociation constant (K_d) in the context of ligand binding."

"K_d is the concentration of ligand at which 50% of the ligand binding sites on the receptor are occupied."

"How is affinity characterized in receptor-ligand interactions?"

"Affinity is characterized by the dissociation constant (Kd) or delta G, with a smaller Kd indicating higher affinity."

"Explain the relationship between Gibbs Free Energy and the dissociation constant."

"Delta G can be expressed as Delta G = H - TdeltaS and also as Delta G = RTln(K_d)."

"What does a smaller K_d value indicate about ligand affinity?"

"A smaller K_d value indicates a higher affinity between the ligand and the receptor."

"Describe the relationship between affinity and free energy."

"Very weak affinity corresponds to Kd values of 10^-3 to 10^-1 and delta G values of -4.3 to -1.4 kcal/mol, while high affinity corresponds to Kd values of 10^-9 to 10^-6 and delta G values of -13 to -8.5 kcal/mol."

"How are the units of the affinity constant related to the dissociation constant?"

"When the dissociation constant is in molar units, the affinity constant is expressed in units of M^-1."

"Explain the difference between dissociation and association in terms of their starting points."

"Dissociation starts with the whole complex, while association begins with two or more molecules forming a complex."

"What occurs during fluorescence polarization with small fluorescent biomolecules?"

"When a small fluorescent biomolecule is free in solution, it tumbles and emits depolarized light between excitation and emission."

"How does the binding of a fluorescent ligand to a larger molecule affect its rotational movement?"

"When a fluorescent ligand binds to a larger molecule, its rotational movement slows down, affecting the emission of light."

"Explain how a fluorimeter measures light intensity."

"A fluorimeter uses a light source that passes through a monochromator to select a wavelength, then the light goes through the sample, and the intensity is measured by a detector."

"Describe the relationship between fluorophore size and light polarization in proteins."

"Larger fluorophores tend to tumble slowly in large proteins, resulting in light emitted that is much more highly polarized compared to smaller fluorophores."

"What are the disadvantages of fluorescence polarization techniques?"

"Disadvantages include the requirement for a size difference and the use of a fluorophore, which can alter drug interactions, and viscosity issues at high protein concentrations."

"How do polarizers function in the context of fluorescence measurements?"

"Polarizers are placed before and after the sample to rotate, allowing only perpendicular and parallel light to pass through, which helps determine the polarization of the emitted light."

"Define the advantages of using fluorescence polarization techniques."

"Fluorescence polarization techniques are simple to execute and analyze, versatile for various applications like enzyme assays, and adaptable to high-throughput measurements."

"Explain the significance of histone proteins in eukaryotic cells."

"Histone proteins are the most abundant DNA-binding proteins in eukaryotic cells and play a crucial role in packaging DNA into nucleosomes."

"How do histones interact with DNA?"

"Histones bind to DNA primarily through salt-bridge interactions with the phosphates in the DNA backbone, facilitated by their large number of basic amino acids."

"Describe the structure of nucleosomes."

"Nucleosomes consist of 147 base pairs of DNA wrapped in almost two turns around an octamer of histone proteins, typically with a stoichiometry of H2A2, H2B2, H3.2, and H4.2."

"What is the role of H1 histone in nucleosomes?"

"H1 histone binds to the linker DNA between nucleosomes, helping to stabilize the structure of chromatin."

"Define the histone code hypothesis."

"The histone code hypothesis suggests that more than 100 different posttranslational modifications of histone proteins regulate chromatin states and transcription."

"List some types of histone modifications and their effects."

"Histone modifications include the addition of phosphates, methyl groups, acetyl groups, and ubiquitin, which can influence chromatin structure and gene expression."

"Explain the effect of lysine methylation on its charge."

"Methylation of lysine does not change its charge; even after trimethylation, the quaternary amine group remains positively charged but is surrounded by hydrophobic groups."

"Describe the variability of linker DNA length in nucleosomes."

"Linker DNA length varies between 10 to 90 base pairs depending on the organism, contributing to the overall structure of chromatin."

"Describe the role of lysine modification in gene expression."

"The degree of lysine modification regulates gene expression by influencing chromatin compaction and the interaction with effector proteins, which can change gene expression based on the extent and location of the modification."

"Explain the interaction mechanisms of di and mono methyl readers."

"Di and mono methyl readers interact through pi-cation interactions and salt bridges, such as those between tryptophan and glutamic acid."

"Define anisotropy in the context of light polarization."

"Anisotropy is often misused as a synonym for polarization; greater anisotropy may indicate increased polarization of light after it passes through a sample."

"How does isothermal titration calorimetry (ITC) work?"

"ITC works by titrating a protein solution with a ligand while monitoring the energy required to maintain temperature in the sample cell compared to a reference cell, typically containing just buffer."

"What is the significance of the curve generated in ITC experiments?"

"The curve of enthalpy generated in ITC experiments is fitted by an algorithm, where the steepness of the curve indicates the affinity of the binding, and stoichiometry can be determined from the moles required to complete the titration."

"Explain how enthalpy (delta H) is determined in ITC."

"Enthalpy (delta H) is determined by summing all the heats measured during the titration process in ITC."

"How can delta S be calculated using ITC data?"

"Delta S can be calculated if delta H, temperature, and delta G are known from the ITC technique."

"Describe the components of the sample and reference cells in ITC."

"The sample cell in ITC contains the protein solution, while the reference cell typically contains only the buffer."

"What type of interactions do tri methyl readers utilize?"

"Tri methyl readers utilize pi-cation interactions for their binding mechanisms."