Web Development Fundamentals Quiz

Alternating single and double bonds in benzene result in delocalized pi bonds.
Molecular orbital theory explains the distribution of pi electrons.
Benzene's resonance hybrid structure signifies the delocalization of pi electrons.
3 molecular orbitals, 4 pi cloud electrons

Intramolecular forces include ionic interactions, dipole-dipole interactions, ion-dipole interactions, and ionic bonds.
Intermolecular forces are weaker than intramolecular forces and include hydrogen bonding, van der Waals forces, and London forces.

Arrhenius acids produce hydrogen ions (H⁺) in water.
Arrhenius bases produce hydroxide ions (OH⁻) in water.
Brønsted-Lowry acids act as proton donors.
Brønsted-Lowry bases act as proton acceptors.
The hydronium ion (H₃O⁺) is formed when a proton is donated by an acid to water.
Brønsted-Lowry acids don't necessarily have to be in a water solution to exhibit acidity.
Not all Brønsted-Lowry acids are Arrhenius acids because Brønsted-Lowry acids can be proton donors in any solution.

Water is amphoteric (can act as both an acid and a base).
Water autoionizes, meaning it can react with itself to form hydronium (H₃O⁺) and hydroxide (OH⁻) ions.
The equilibrium constant for water autoionization (Kw) at 25°C is 1.0 x 10⁻¹⁴.
The product of the concentrations of H₃O⁺ and OH⁻ is Kw.
pH is a measure of the concentration of hydronium ions in a solution.
pH = -log₁₀[H₃O⁺]
pOH = -log₁₀[OH⁻]

Calculate the pH of a 0.3 M NH₃/0.36 M NH₄Cl buffer solution given Kb = 1.76 x 10⁻⁵.
pKa = -log₁₀Ka = -log₁₀ (1 x 10⁻¹⁴ / 1.76 x 10⁻⁵) = 9.2455.
pH = 9.166

A process is spontaneous if the total entropy of the universe increases.
Gibbs Free Energy accounts for enthalpy and entropy changes in a system at constant pressure.
AG = ΔH - TΔS.
A negative ΔG indicates a spontaneous process

Look for carbon atoms bonded to four different groups to determine whether they are chiral centers.
Usually only one of two enantiomers is found in nature to be biologically active (D-Isomers) + (L-Isomers)
Enantiomers are molecules that are non-superimposable mirror images of each other.
Enantiomers have the same physical properties, but they rotate plane-polarized light in opposite directions.
Diastereomers are stereoisomers that are not enantiomers.
Fischer Projections are used to represent the spatial arrangement of molecules.
Enantiomer = all stereo swapped.
Diastereomer = only one stereo swapped

Sequence similarity, phylogenetic relationships, and environmental factors guide the selection of template proteins with known structures.
Sequence alignments are used to align the target protein with template proteins while making appropriate adjustments for the alignments.
Model building follows the amino acid sequence.
Loops modeling is important to ensure accuracy.
Model optimization & validation is often required to ensure the quality of the model reflects functions.

Metal ions can form complex ions with molecules or ions (ligands).
A ligand is a molecule or an ion that donates an electron pair to a metal ion.
Lewis acids are electron pair acceptors.
Lewis bases are electron pair donors.
The number of ligands in a complex ion can vary.
The overall charge of a complex ion is the sum of the charges of the metal ion and the ligands.
Examples are Cu2+, Zn2+

Myoglobin binds oxygen as a ligand and the dissociation constant (Kd) explains how readily an oxygen molecule can be released when more oxygen is not actively needed.

Hemoglobin is a protein in red blood cells that carries oxygen.
2,3-BPG lowers hemoglobin's affinity for oxygen.
The Bohr effect describes how changes in pH affect hemoglobin's oxygen-binding affinity.

Protein folding occurs on a relatively quick timescale. Most proteins spontaneously refold into native conformation under favorable conditions, but some proteins can't regain their functions on their own.
Molecular chaperones are proteins that assist other proteins in folding. Proteins can aggregate if they are not correctly folded
The hydrophobic effect is important for the stabilization of folded protein structure.
Disulfide bonds are important in maintaining tertiary structure. Allosteric proteins can switch among conformations, leading to changes in their function, are often quite involved in regulating metabolic processes).
Protein structure can be determined through homology modeling & experimental methods such as x-ray crystallography.

Proteins at high concentrations often aggregate in misfolded states(which may lead to diseases such as Mad Cow Disease)
Chaperones can help prevent protein misfolding + aggregation.
Diseases like Mad Cow Disease are linked to misfolded protein aggregation.

Homology modeling uses known protein structures as templates to model the structures or function of similar but unknown proteins.

Peptide bonds are intermediate between single and double bonds.
Rotation limited about the peptide bonds
Partial double bond character.
cis configuration is generally not favored by steric hinderance/energy considerations.

Alpha helices are right-handed helical structures stabilized by hydrogen bonding between the backbone amide (-NH) and carbonyl (C=O) groups of the peptide chain.
Beta sheets are formed by two or more extended beta strands arranged either parallel or antiparallel and stabilized by hydrogen bonds between backbone NH and C=O groups of different strands.

Proteins' tertiary+ quaternary structures are directly responsible for determining the protein's function.
proteins are composed of multiple folded polypeptide chains.

Water molecules can form relatively strong hydrogen bonds
hydrophilic molecules are polar molecules and can form hydrogen bonds with water molecule.
Hydrophobic interactions are non-covalent interactions that occur between nonpolar molecules or parts of molecules in an aqueous solution, reducing the entropy of water to a minimum
Many hydrogenated compounds have lower solubility and tendency to avoid/reduce contact with water.

Water can act as both an acid and base, autoionizing to form hydronium (H₃O⁺) and hydroxide (OH⁻) ions.
The equilibrium constant(Kw) is the product of [H₃O⁺] and [OH⁻].

Equilibrium constants (K) describe the ratio of products to reactants at equilibrium in a chemical reaction.

pH is used as a measure of hydrogen ion concentration.
pOH is used as a means to measure hydroxide ion concentration.
These concepts relate directly to equilibrium concentrations and thus relate to equilibrium constants.

A state of reaction is reached when the rate of the forward reaction is equal to the rate of the reverse reaction.
Equilibrium constants quantify the relative concentrations of reactants + products at equilibrium.
At equilibrium, ΔG = 0.

Many chemical reactions can be described by a constant, K, which is the quotient of the product to reactant concentrations at equilibrium for the specific reaction.