Water, Weak Bonds - Chapter 2 Flashcards
What is Brownian motion? Why is it important for cells?
random movement of gases and liquids powered by the background thermal energy
Brownian motion inside the cell supplies energy for many interactions required of a functioning biochemical system.
What causes Brownian motion?
random fluctuation of energy content of the environment (thermal energy changes)
What evidence is there of Brownian motion?
Water and gas molecules bounce at rate determined by temperature and collide into pollen or dust particles, causing them to move randomly too.
What is a hydrogen bond?
a bond formed when two relatively electronegative atoms, such as oxygen or nitrogen, unequally share a hydrogen atom that is covalently bonded to one of the electronegative atoms
What is the hydrophobic effect?
when nonpolar or hydrophobic molecules encounter water and sequester themselves away
What relevance does the hydrophobic effect have on cellular biology?
The hydrophobic effect allows the plasma membranes of cells and organelles to form, allowing for cells to compartmentalize and have specific functions.
What is pH?
measure of the hydrogen ion concentration; between 0 and 14
What are buffers?
an acid-base conjugate pair that resists changes in the pH of a solution
What is Coulomb’s law? What do the variables stand for?
describes the energy of an electrostatic interaction between two ions
k - proportionality constant
q1 and q2 - charges on 2 atoms
D - dielectric constant
r - distance between two atoms in angstroms
What kind of environment weakens electrostatic interactions? Strengthens them?
The polarity of water causes salt bridges to be weaker because charged ions dissolve more by partially charged O and H in water. Uncharged environments are more fertile for electrostatic interactions.
What is dielectric constant in a vacuum? Does this lead to weaker or stronger electrostatic interactions?
D = 1 in a vacuum; electrostatic interactions are strongest here
What is the dielectric constant of water? Does this lead to weaker or stronger electrostatic interactions?
D = 80; electrostatic interactions are weak here
What are van der Waals interactions?
attraction between two molecules based on transient electron asymmetry around an atom that induces a complementary asymmetry in a nearby molecule
How long is a van der Waals contact distance?
3-4 angstroms
What happens to van der Waals forces when atoms are at a distance shorter than 3-4 angstroms? Why?
Very strong repulsive forces dominate because outer electron clouds overlap.
What kind of bonds are between bae pairs in DNA, stabilizing the double helix?
hydrogen bonds
Why are weak bonds biochemically important?
They can be easily broken and reformed.
What is the second law of thermodynamics?
The total entropy of a system and its surroundings always increases in a spontaneous process.
What is entropy?
a measure of randomness
What is the hydrophobic effect? How does it comply with the 2nd law of thermodynamics?
process in which nonpolar molecules in aqueous solutions are driven together because of a resulting increase in entropy of water molecules
Although the nonpolar molecules are congregating, they are causing the water molecules to be less ordered than they were when in a solvation shell around the individual nonpolar molecules.
How does the introduction of a single nonpolar molecule, like a benzene ring, decrease the entropy of water?
While it temporarily disrupts some hydrogen bonds, water molecules reorient themselves to try to form as many hydrogen bonds with the benzene as possible (which is very few). The water molecules around the benzene are more ordered than elsewhere in the solution.
Do nonpolar solute molecules have an affinity for each other?
No, but they are driven together because associating releases water molecules, leading to an increase in entropy.
Are hydrophobic interactions spontaneous? Why or why not?
Yes, they are. They do not require an input of energy because they increase the entropy of water when they form.
What is an amphipathic mor amphiphilic molecule?
molecule with two distinct chemical personalities (hydrophobic and hydrophilic)
What stabilizes the hydrophobic tail groups of the lipid bilayer?
van der Waals interactions between hydrophobic tails
Folding proteins inherently decreases the entropy of the system. How can protein folding proceed spontaneously anyway?
Nonpolar amino acids experience the hydrophobic effect and tend to associate with one another in the interior of the folded protein. The increased entropy of water due to this helps compensate for entropy loss inherent in folding.
Describe an aromatic functional group
hydrocarbons in a ring structure with multiple double bonds
Describe a hydroxyl group.
alcohols
Describe the aldehyde functional group
C double bonded to an O
Describe a keto functional group.
C double bonded to an O and single bonded to an R group
Describe a carboxyl group.
COOH
Describe an amino group.
R-NH2
Describe a phosphate group.
Describe a sulfhydryl group.
R-SH
What does aliphatic refer to?
hydrocarbon chains
Waht is an acid?
a proton donor
What is a base?
a proton acceptor
What is the species formed by the ionization of an acid called?
conjugate base
The acid is stronger is the Ka is larger or smaller?
larger
What is a pKa?
the pH at which the acid is half dissociated
What happens above the pKa?
the A- (base) predominates
What happens below the pKa?
the Ha (acid) predominates
How to tell what the pKa is on a titration curve?
Look at the inflection point.
What is most effective at buffering against pH changes?
a weak acid
