Molecular Properties Lectures 1 & 2 Ford Flashcards
Briefly describe the differences between covalent and noncovalent bonds
covalent bonds- strong, short, and share electrons
non covalent- weak, long, and attraction only
Describe the types of bonds between
- carbohydrates
- lipids
- proteins
- nucleic acids
- glycosidic
- ester
- peptide
- phosphodiester
Describe electrostatic interactions
interaction between 2 charged ions
Define a dipole
molecule has a “partial charge”; can be permanent or induced
What are some examples of electrostatic interactions?
stacking of benzene rings, stacking of nucleotides, nucleotide base pairing
If the force between two ions is positive, what does that mean? If negative?
positive=repulsive
negative=attractive
Describe covalent bonds in terms of
- nature of interaction
- average bond distances
- average bond energies
- share an electron pair 2. 1 A
3. 355 kj/mol
Describe charge and or dipole interactions in terms of
- nature of interaction
- average bond distances
- average bond energies
- charge attraction
- 3 A
- 5.86 kJ/mol
Describe van der waals interactions in terms of
- nature of interaction
- average bond distances
- average bond energies
- charge attraction
- varies by atom sized
- 2-4 kj/mol
Describe the H bonds that are present in solids liquids and gasses
- solids have optimal H bonds; they perfect
- liquids have suboptimal H bonds; they are trying to be the best that they can be but are not quite there (me)
- gasses have no H bonds because they are too hyperactive and are not able to even interact with each other. they are too self absorbed to stop and say hello to their neighbors
Describe ice versus water in terms of hydrogen bonding
Water is more dense than the ice and has shorter distances between the molecules that does not allow for h bonding
Define specific heat capacity
the amount of heat needed to change the temperature of a 1g of a given substance by +/- 1 C
Define heat of vaporization
the amount of energy needed to change 1 g of a given substance from a liquid to a gas
Define cohesion
attraction of water molecules to each other
create surface tension
Define adhesion
attraction of water molecules to other polar substances
cohesion and adhesion make capillary action
Describe what a charged/polar molecule does in solution
It is hydrophilic and dissolves
Describe what non polar molecules do in solution
they are hydrophobic and separate
What is the relationship between Ka and a strong or weak acid?
A strong acid has a larger Ka and a weak acid has a smaller Ka
What is the relationship between pka and the strength of an acid
strong acids have a smaller pka and weak acids have a larger pka
What is the relationship between the energy of interaction and the strength of an acid?
Strong acids have smaller energies of interactions and weak acids have a larger energy
What is the relationship between Kb and the strength of a base?
The stronger the base, the larger the Kb and vice versa
What is the relationship between pkb and the strength of the base?
The stronger the base, the smaller the pkb and vice versa
What is the relationship between the energy of interaction and the strength of the bases?
The stronger the base, the larger the energy of interaction and vice versa
Define pH in terms of H+
pH=-log[H+]
Define pkw
pH+pOH
Define buffers
weak acids of bases that can stabilize pH
What is the Hendersen Hasselbalch derivation?
pH=pKa + log ([A-]/[HA])
OR
[A-]/[HA]=10^pH-pKa
If the pH
The molecule is protonated since
[HA]>[A-]
If the pH>pKa, what does it mean for the molecule itself?
That the molecule is deprotonated since [Ha]
What happens if the pH and pKa are equal?
Then the molecule is just as likely to be protonated as it is deprotonated
Describe gel electrophoresis
the direction of migration based on the net charge of molecule
Define isoelectric point and give the equation and the relationships between the pH and the pI
isoelectric point- the pH where aLL molecules of a given species in a solution have an overall charge of 0
pI=(pKa(+1) + pKa(-1)/2)
if pH< pI then the molecule has a positive charge
if pH>pI then the molecule has a negative charge
if they are equal, then there is no net charge
What is the first law of thermodynamics?
Energy is neither created nor destroyed in a closed system (energy cannot leave the system)
Define kinetic energy
motion
Define potential energy
position; potential to do work- the potential energy within chemical bonds
What is the second order of thermodynamics?
Disorder is increasing… catabolic reactions would be an increase in disorder because there are more individual molecules
Describe Gibbs Free Energy Equation
deltaG=deltaH-TdeltaS
delta G is the change in the available/usable energy
delta H is the change in the totally energy (enthalpy)
deltaS is the change in disorder
Define a state function and what is an example of a state function>
a state functions value depends only on the initial and final values, not the pathway to get there
delta G, S and H are state functions
What happens if the delta H is negative? positive? zero?
- negative: energy is released from the system
- positive: energy is added to the system
- zero: closed system
What happens if the delta S is negative? positive? zero?
Negative: disorder decreases
Positive: disorder increases
Zero: no net change
What happens if the delta G is negative? positive? or zero?
negative: free energy is released; exergonic reaction; favorable reaction; spontaneous reaction
positive: free energy is required; endergonic reaction; unfavorable reaction; driven reaction
zero: equilibrium
