VSG #2 - Chapter 2 Review

Tryptophan contains an indole ring, which absorbs UV light at a specific wavelength. This property makes tryptophan useful for measuring protein concentration using UV spectrophotometry.

Disulfide bonds, formed between two cysteine residues, are covalent bonds that contribute to protein folding and stability. They create cross-links within the protein structure, increasing its resistance to unfolding and denaturation.

The pKa of an amino acid side chain is the pH at which half of the side chains are protonated and half are deprotonated. Histidine's pKa is near physiological pH, making it important for enzyme activity and pH sensing.

The strength of a hydrogen bond depends on the pKa values of the donor and acceptor. The closer these values are, the stronger the bond. This is because the shared proton is more evenly distributed, increasing the bond strength.

A hydrogen bond is a weak electrostatic interaction between a hydrogen atom covalently linked to a highly electronegative atom (like oxygen or nitrogen) and an electronegative atom on another molecule.

The strength of a hydrogen bond is influenced by the partial charges on the atoms involved. A greater separation of charges leads to a stronger bond.

The pKa of the donor and acceptor in a hydrogen bond determines the strength of the bond because it reflects their ability to donate or accept a proton.

When the pKa values of the donor and the protonated form of the acceptor are identical, they form a low barrier hydrogen bond, which is the strongest type of hydrogen bond due to increased covalent character.

The measure of the tendency of a compound to donate a proton.

A solvent that can form hydrogen bonds, making it good at dissolving polar molecules. It also increases the acidity of acetic acid.

A solvent that cannot form hydrogen bonds, making it less effective at dissolving polar molecules and decreasing the acidity of acetic acid. It weakens the acetate ion's stability.

The interactions within the protein interior that contribute to its overall stability.

The formation of a hydrogen bond between a positively charged amino acid side chain and a negatively charged amino acid side chain.

The ability of a protein to fold into its correct three-dimensional structure, which is determined by the sequence of amino acids and their interactions.

A model that suggests that hydrogen bonds serve to prevent misfolded protein structures by limiting the possible conformations.

The interactions that contribute to the stability of a protein structure, such as salt bridges, hydrogen bonds, hydrophobic interactions, and van der Waals forces.

The formation of salt bridges and hydrogen bonds in a folded protein releases energy, making the folding process more favorable.

A lower dG value indicates a more stable protein because it is more thermodynamically favorable for the folding process to occur.

Protein folding is not a simple two-step process (unfolded to folded). There are many intermediate states the protein can transition through.

The entropy of water plays a crucial role in driving protein to fold.

H-bonds and salt bridges can contribute to the stability of a folded protein by lowering the Gibbs Free Energy (dG), making the folding process more favorable.

The free energy of intermediate states during protein folding exists between the unfolded and native states.

H-bonds and salt bridges can help the protein transition from one intermediate state to another during the folding process.

A measure of a molecule's tendency to donate a proton (H+). Lower pKa values indicate stronger acids, meaning they more readily donate protons.

A species that can readily lose a proton (H+) in a chemical reaction. It can be a molecule, or part of a larger molecule.

A range of pH values where a solution resists changes in acidity. It is defined as one pH unit above and below the pKa of the weak acid/base in the solution.

A process that releases heat. The formation of hydrogen bonds between water molecules releases energy as heat.

The solvent influences the pKa of a protonatable group by affecting its protonation state. If the solvent promotes protonation, the pKa of the group will decrease, making it more acidic. If it promotes deprotonation, the pKa will increase, becoming less acidic.

The change in pKa values can directly influence protein folding, structure, and ultimately, function. The ability to donate or accept protons is fundamental to protein interactions and functions.

The process of adding a proton (H+) to a molecule.

The process of removing a proton (H+) from a molecule.

The unique 3D structure of a protein that enables it to perform its specific function.

The pKa values of amino acid side chains in a protein can be different in the folded state compared to their values in solution. This is because the environment within the folded protein can affect their tendency to donate or accept protons.

Hemoglobin is the protein in red blood cells responsible for transporting oxygen. It also plays a role in regulating blood pH.

Hemoglobin binds to excess hydrogen ions (H+) in the blood when it becomes acidic (low pH) and releases H+ ions when it becomes alkaline (high pH). This helps to maintain a stable pH balance in the blood.

An increase in carbon dioxide (CO2) levels in the blood leads to a decrease in pH, making the blood more acidic. Hemoglobin recognizes this change and binds to the excess H+ ions to maintain a stable pH balance.

Histidine is an amino acid that acts as a pH sensor in the body. Its pKa is close to physiological pH, which means it can easily exist in both protonated and deprotonated states, allowing it to respond to changes in blood acidity.

The pKa of histidine is close to the physiological pH of 7.45. This means that in the human body, histidine exists in almost equal proportions of its protonated and deprotonated states.

Protonation of histidine residues on hemoglobin molecules helps release oxygen to tissues when the blood becomes acidic. The binding of protons to hemoglobin pushes it into a tense state, making oxygen release easier.

The Lambert-Beer Law relates the absorbance (A) of a solution to its concentration (C), path length (L), and extinction coefficient (e). The equation is: A = eLC.

The extinction coefficient represents how strongly a molecule absorbs light at a specific wavelength. It is a unique property of each molecule and helps determine the molecule's concentration.

The path length is the distance that light travels through the solution being measured. It is typically measured in centimeters (cm).

The concentration of a solution is a measure of the amount of solute dissolved in a given volume. It is often expressed in units of moles per liter (M)

A leaving group is an atom or group of atoms that departs from a molecule during a reaction. Good leaving groups are weak bases and readily accept electrons. They are typically stable and can exist independently.