Chapter 2 Flashcards
What are the 3 fundamental noncovalent bonds?
-Ionic bonds (electrostatic interactions)
-Hydrogen bonds
-van der Waals interactions
Why are weak, non-covalent reversible reactions so important?
-Essential in the flow of energy and information
-Play roles in the replication of DNA, folding of proteins into 3D forms, specific recognition of reactants by enzymes and the detection of molecular signals
-Bonds are weak enough to be broken during DNA metabolism or protein conformational changes during molecular interactions, allowing the occurrence of diverse processes with little or no energy cost
-Weak bonds imply they may be formed or broken during a biological process, ensuring feasibility of reversibility
What is Coulumb’s Law?
E = kq1q2/Dr
-E is energy
-q1 and q2 are charges on ions
-D is dielectric constant (1 in vacuum, 80 in water)
-r is distance between the ions
-k is proportionality constant
The energy of an electrostatic interaction between two charges given
Describe the chemical properties of water
-Polar molecule, oxygen atom carrying a slightly negative charge and the hydrogen atoms each carrying slightly positive charges
-Very electronegative chemical element
-Each oxygen atom carries two lone pairs of electrons (crucial for hydrogen bonding)
What is Brownian motion?
-Movement of molecules powered by random fluctuations of environmental energy (thermal noise)
-Random Brownian motion of water initiates many biochemical reactions
Describe hydrogen bonding in water
-Water molecules may form up to four hydrogen bonds in liquid water
-Bonds are highly directional and transient
-Highly ordered, but open and dynamic in structure
-Hydrogen bonds in liquid water are constantly breaking and reforming as a result of Brownian motion of individual water molecules
How does water affect hydrogen bonding?
-Water can disrupt hydrogen bonds between two molecules by competing (substituting) for the hydrogen bonding position
What is the typical distance between two electronegative atoms in strong hydrogen bonds?
-2.4A < d < 3.4A
What are the types of hydrogen bonds that are important in biological systems?
N-H—-N
N-H—-O
O-H—-N
O-H—-O
(H-N and H-O covalent bonds are about 1A in length)
Describe van der Waals interactions and their importance
-Nonpolar and uncharged molecules can interact electrostatically at a specific distance or “sweet spot” (3.5A < d < 4.0A)
-Both permanent and transient asymmetry in the electron distribution of one molecule will induce complementary asymmetry in a nearby molecule
-Sum of weak dipolar electrostatic interactions
-Weaker than hydrogen bonds
-Typically many of these interactions, making them very important
Why are hydrogen bonds and VDW interactions so important despite their individually relative weakness to covalent bonds?
-Their power and importance lies in “strength in numbers”
-The dynamic properties of these plentiful bonds and interactions allow for an impactful result in the composition of biological systems
What is the hydrophobic effect?
-The inability of water to dissolve nonpolar molecules resulting in an important and powerful organizing principle
-Driven by the increase in the entropy of water causing hydrophobic molecules to cluster together and form phospholipid bilayers through protein folding
