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Chapter 2 PP

Terms in this set (56)

What are the 4 classes of biomolecules?
Proteins, Nucleic Acids, Saccharides, Lipids
Why are noncovalent interactions important?
They define structure and function of biomolecules
hGH binding
The binding of human growth hormone to its receptor transmits a signal across the cell membrane which, in turn, stimulates cell growth
Bond Energy between Noncovalent and Covalent
Covalent bonds: 150 - 400 kJ/mol
Noncovalent: 10 to 100 times weaker
Bond Energy between different Noncovalent Interactions
Charge-Charge: 13 to 17 kJ/mol
Hydrogen Bond: 2 to 21 kJ/mol
van der Waals: 0.4 to 0.8 kJ/mol
Strength of Noncovalent Interactions
1. Charge-charge
2. Charge-dipole
3. Dipole-dipole
4. Charge-induced dipole
5. Dipole-Induced dipole
6. Dispersion (van der Waals)
7. Hydrogen bond

Charge > Dipole > Induced Dipole
All Noncovalent interactions are ________ in essence.
electrostatic
What do permanent and induced dipoles give rise to?
Charge separation
What is a salt bridge?
The simplest electrostatic interactions are those between a pair of charged particles (Charge-charge)
What is Coulomb's Law?
It occurs during charge-charge interactions. The attraction of the oppositely charged ions is governed by this law:
F = k (q1q2/r^2)
This law applies in a vacuum
Coulomb's Law in a Cell
In a cell, charges are screened in solution by the medium that exists between the charges. The screening effect of a medium is represented by ε, the dielectric constant (water has a high dielectric constant, 80):
F = k (q1q2/εr^2)
In Coulomb's law, what happens when F is positive?
q1 and q2 have the same sign, so a positive value corresponds to repulsion
In Coulomb's law, what happens when F is negative?
q1 and q2 have opposite signs, so a negative value corresponds to attraction
What is the van der Waals radius?
The effective radius of an atom or a molecule that defines how close other atoms or molecules can approach; it is thus the effective radius for closest molecular packing.
Interaction energy and van der Waals radii?
At first, the attraction is the force pulling the atoms together. Soon, the repulsion starts to increase very rapidly. Soon after the distance of minimum energy, r0. The distance of closest approach comes, rv.
Hydrogen bond donor
The atom to which the hydrogen is covalently bonded
Hydrogen bond acceptor
The atom with the nonbonded electron pair.
Hydrogen bonds and van der Waals radii?
The hydrogen bond is much closer than would be predicted by the van der Waals interactions.
Energy of hydrogen bonds?
Relatively high compared to other noncovalent interactions
When are hydrogen bonds strongest?
When the angle defined by the donor atom, the shared H atom, and the acceptor atom is 180 degrees.
Unique properties of water that make it suitable as the medium of life?
1. 2 H-bond donor sites
2. 2 H-bond acceptor sites
3. Permanent dipole
4. High heat capacity
5. Density greater in liquid
6. Relatively high dielectric constant
Hydrophilic molecules in water?
The hydrophilic molecules with hydrogen bonds will often exchange these bond with the water molecules that are added to the solution. This breaks up the molecule. Hydration shells form in ionic compounds.
Hydrophobic molecules in water?
Forms clathrate structures around the material. Hydrophobic molecules tend to aggregate together in order to make it so the water only has to form a single clathrate, as their formation decreases the entropy.
What do amphipathic molecules form in water?
Monolayer, bilayer vesicle, or micelle
Macroions
Charged molecules such as proteins and nucleic acids that change their charge depending on the pH of a solution
Proteins and pH
Proteins are soluble at low and high pH because of the charge that is induced. At the isoelectric point, they are not soluble due to a net zero charge and tend to aggregate.
Influence of small ions
Each macroion collects about it a counterion atmosphere enriched in oppositely charged small ions, and this cloud tends to screen the molecules from one another. The larger the concentration, the more screening their is involved. Prevents protein aggregation.
Ionic strength in our cells and used in biochemical experiments?
0.1 M - 0.2 M
Bronsted-Lowry acid
H+ donor
Bronsted-Lowry base
H+ acceptor
Strong acid
Completely donates protons, resulting in protons and weak conjugate base.
Strong base
Entirely releasing OH- group
Weak acid
partially dissociates into protons and conjugate base
Weak base
partially associates with protons and therefore increases OH- concentration, making solution basic
Kw
Ion product of water
Kw=[H+][OH-] = 10^-14 M

Neutral conditions at 25°C
[H+]=[OH-]=10^-7 M
pH
pH = -log[H+]
The lower the pH, the higher the proton concentration
Physiological pH range
6.5 - 8.0
pKa>pH
[HA]>[A-]
pKa<pH
[HA]<[A-]
pKa=pH
[HA]=[A-]
Ka
Acid-dissociation constant
[H+][A-]/[HA]
Henderson-Hasselbalch Equation
pH = pKa + log ([A-]/[HA])
pKa
pKa = -log(Ka)
Low pH and Proteins
+ charge
High pH and Proteins
- charge
Buffers
These will resist pH change following the addition of acid or base within about +/- 1 pH unit of the pKa of a solution
How are buffer solutions able to minimize the change in pH following the addition of H+ or OH-?
The conjugate acid (HA) and conjugate base (A-) of the buffering compound are present in sufficient concentration to combine with the added H+ or OH- and neutralize them.
How to choose a buffer?
One that has a pKa value close to the value of the experiments pH
pI
The isoelectric point is the pH at which the average charge on the molecule is zero.
It is the average of the two pKa values surrounding the isoelectric species.
Below pI
+ charge
Above pI
- charge
ampholyte
A molecule that contains groups with both acidic and basic pKa
Polysaccharide agarose gel electrophoresis
Appropriate buffer solution is cast in a mold. Smaller samples travel further to the anode (+) end of the gel. This is good for larger molecules, such as DNA and RNA of size 50 - 30,000 bps.
Electrophoresis
A molecule with a net positive charge will migrate toward the cathode, whereas a molecule with a net negative charge will migrate toward the anode.
Acrylamide gel electrophoresis
Smaller pore size than agarose, making is good for smaller molecules, such as proteins (2 - 200 KDa) or short nucleotides (10-200 bases).
Isoelectric focusing
Put proteins on a stable pH gradient making them not attracted to either the cathode or anode and thus allowing them to accumulate at their pI value.
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