Lecture 1-2 - Molecular Properties of Biological Molecules Flashcards
What is the name of the monomer, polymer, and bond between monomers for carbohydrates, lipids, proteins, and nucleic acids?
L1 S4
Carbohydrates:
-monosaccharides/di- or polysaccharide/glycosidic bond
Lipids:
-fatty acids/triacylglycerol + phospholipids/ ester bond
Proteins:
-amino acids/polypeptide/peptide bond
Nucleic acid:
-nucleotide/oligo- or polynucleotide/phosphodiester bond
In a lab you made an aqueous solution with magnesium ions and bromide ions. If you had made your solution in an organic solvent, say methanol, would the energy of the interaction:
(Dwater=80.1 and Dmethanol=30.7)
A. Increase (more negative)
B. Decrease (less negative)
C. Stay the same
A. Increase (more negative)
F=k (q1q2)/(Dr)
D is the dielectric constant and it is located in the denominator. Decreasing the dielectric constant would therefore increase the energy of interaction (make it more negative).
What effect would increasing each of the variables in the equation for the energy of interaction between substances have?
L1 S10
Equation: E= kq1q2/(Dr)
Directly related (E would increase):
- q1 (charge)
- q2
Inversely related (E would decrease):
- D (dielectric constant)
- r (distance between charges)
k is a constant and therefore cannot be changed
What is the order of chemical interactions by decreasing bond energy?
L1 S6;17
- covalent bond (~355kJ/mol)
- ionic bond (charge-charge)(~5.86kJ/mol)
- dipole-dipole (~5.86kJ/mol)
- hydrogen bonds (4-20kJ/mol)
- van der Waals interactions (~2-4kJ/mol)
What unusual properties are conferred to water due to its hydrogen bonding ability and why?
L1 S17-23
Ice is less dense than liquid water:
-optimal, longer hydrogen bonds form in ice than the suboptimal hydrogen bonds in liquid water
Water is a liquid over a wide range of temperatures:
-additional energy is needed to break all the hydrogen bonds formed by liquid water, resisting evaporation
Surface tension/capillary action:
- cohesion between water molecules results in surface tension
- cohesion and adhesion results in capillary action
Water is the universal solvent:
-water displays partial positive and negative charges allowing it to dissolved substance with either charge
A hydrogen bond length is __________ than a covalent bond length and __________ than van der Waal interaction contact distance.
L1 S15 (it was more stated verbally in class)
GREATER that covalent bond length
LESS than van der Waal interaction contact distance.
What is the equation for Ka and how does pKa relate to Ka?
L2 S33
Ka=[H+][A-]/[HA]
pKa=-log(Ka)
Would the Ka of a strong acid be larger or smaller than a weak acid?
What about for pKa?
L2 S34
Ka:
- larger for strong acid
- smaller for weak acid
pKa:
- smaller for strong acid
- larger for weak acid
What is Kw?
L2 S37
The dissociation constant for water; 10^-14 M
What is the physiological pH of the body?
L2 S38 (stated in class)
7.4
What is a buffer?
L2 S39
A weak acid or base that stabilizes pH
What is the Henderson-Hasselbalch equation and how does the relationship of concentration of acid with it’s conjugate base relate to pKa and pH?
L2 S42
pH=pKa + log ([A-]/[HA])
-or-
[A-]/[HA] = 10^(pH-pKa)
If pH is greater, then the concentration of conjugate base [A-] is greater than the acid [HA].
If pKa is greater, then the concentration of the acid [HA] is greater than the conjugate base [A-]
If pH=pKa, then the concentration of acid [HA] is equal to conjugate base [A-]
What is the pKa of the carboxyl group of an amino acid? What is its charge when pH is above its pKA and below its pKa?
What about with the amine group?
L2 S43
Carboxyl group:
- pKa= ~2
- pH less than 2; it is neutral (protonated)
- pH greater than 2; it is negative (deprotonated)
Amine group:
- pKa= ~9
- pH less than 9; it is positive (protonated)
- pH greater than 9; it is neutral (deprotonated)
What are isoelectric points? What happens when pH is above or below the isoelectric point?
L2 S46
The pH at which all local charges on a molecule average out to a net charge of 0.
It is the average of the pKa of the molecule when it has a +1 charge and a -1 charge.
- when pH is higher, there is a net negative charge
- when pH is lower, there is a net positive
What happens to a protein in solution when it is at it’s isoelectric point and why?
L2 S50
Because the proteins net charge is 0, it has regions of local negative and positive charges. This causes the protein to associate with other molecules of the same protein more than with the solvent causing the protein to precipitate.
