Bioc Quiz 1

• Oxygen has a partial negative charge, and the hydrogens have a partial positive charge. The uneven distribution of charge gives rise to the large dipole moment of water.
• The polar nature of water largely determines its solvent properties. Ionic compounds with full charges, such as potassium chloride (;  and  in solution), and polar compounds with partial charges (i.e., dipoles), such as ethyl alcohol  or acetone , tend to dissolve in water
• Dipole–Dipole Interactions

  These forces occur between molecules that are dipoles, with the partial positive side of one molecule attracting the partial negative side of another molecule
• Dipole–Induced Dipole Interactions

  A permanent dipole in a molecule when it comes into close contact with any molecule, even those that have no dipoles, can induce a transient dipole in the other
• nduced Dipole–Induced Dipole Interactions

  In the same way that a dipole can create a momentary dipole in another molecule, any two molecules can effectively do the same thing. When two molecules lacking dipoles bump into each other, they distort each other’s electron cloud, thereby creating a brief interaction between these induced dipoles
•  London dispersion force. This type of force is the reason that all molecules are attracted to one another to a very small degree and explains why nonpolar molecules would have attractions for one another.
• Induced Dipole-Induced Dipole Interactions.

  Also called London dispersion forces, these attractions arise when otherwise nonpolar molecules bump into each other and distort each other’s electron shells, forming induced dipoles. Once the dipoles are formed, the molecules are momentarily attracted to one another.
• The favorable ion–dipole and dipole–dipole interactions responsible for the solubility of ionic and polar compounds do not occur for nonpolar compounds, so these compounds tend not to dissolve in water.
• biologically useful definition of an acid is a molecule that acts as a proton (hydrogen ion) donor.
• A base is similarly defined as a proton acceptor
• A new constant, , the ion product constant for water, has just been defined, where the concentration of water has been included in its value.
• pH = -log10 [H+]
• Henderson–Hasselbalch equation and is useful in predicting the properties of buffer solutions used to control the pH of reaction mixtures.
• The transfer of genetic information requires the recognition of RNA by DNA. The ability of RNA to form templates with DNA is due to H-bonding between RNA and DNA monomers.
• Electrostatic (ionic or salt bridges) non-covalent interactions are between distinct electrical charges on atoms.
• covalent bond (O-H) strength: 110 kcal/mol, 460 kJ/mol.
• Covalent bond strength (C-H): 105 kcal/mol, 413 kJ/mol.
• ionic interactions strength: 1-20 kcal/mol, 4-80 kJ/mol.
• ion-dipole strength: 5 kcal/mol, 20 kJ/mol.
• hydrogen bond strength: 5 kcal/mol, 20 kJ/mol.
• Van der Waals strength: 1 kcal/mol, 4 kJ/mol.
• entropy: a thermodynamic quantity representing the unavailability of a system's thermal energy for conversion into mechanical work, often interpreted as the degree of disorder or randomness in the system
• Primary structure is the order in which the amino acids are covalently linked together.
• The process of forming a peptide bond involves the condensation reaction, also known as dehydration synthesis, in which a molecule of water is eliminated as the bond is formed.
• Peptide bonds are characterized by their partial double-bond character, which restricts rotation around the bond and contributes to the stability of the protein structure.
• Peptide bond conformation is most commonly trans due to steric clashes of R-groups.
• X-Pro peptide bond are cis, which introduces kinks.
• The interactions present in the primary structure mainly involve the covalent peptide bonds that link one amino acid to the next along the chain.
• Secondary structure is the arrangement in space of the atoms in the peptide backbone. The alpha helix and beta pleated sheet arrangements are two different types of secondary structure.
• Secondary structures have repetitive interactions resulting from hydrogen bonding between the amide and the carbonyl groups of the peptide backbone. The conformations of the side chains of the amino acids are not part of the secondary structure.
• Overall, the primary structure of proteins is the foundation upon which their higher-order structures and functions are built. Understanding and analyzing the primary structure is essential for unraveling the complex biological processes that proteins participate in and for developing therapeutic interventions for diseases and disorders.
• In both the alpha-helix and beta-sheet structures, hydrogen bonds stabilize the folding pattern and contribute to the overall stability of the protein's secondary structure
• The arrangement of subunits with respect to one another is the quaternary structure. Interaction between subunits is mediated by noncovalent interactions, such as hydrogen bonds, electrostatic attractions, and hydrophobic interactions.
• Tertiary structure includes the three-dimensional arrangement of all the atoms in the protein, including those in the side chains and in any prosthetic groups (groups of atoms other than amino acids).
• domains play a critical role in determining the structure, function, and regulation of proteins.
• Hydrogen bonds, electrostatic interactions, and hydrophobic interactions occur in most proteins.
• Hydrophobic interactions are non-covalent interactions between non-polar molecules or regions of molecules in an aqueous environment.
• The hydrophobic effect refers to the tendency of non-polar molecules or regions of molecules to aggregate or associate with each other in an aqueous environment.
• The hydrophobic effect is driven by the desire to minimize the disruption of water molecules' hydrogen bonding network and maximize the entropy of the surrounding water molecules.
• entropy: the degree of disorder or randomness in the system