202 MT 1 Flashcards
Properties of water? Why is it a good solvent for polar or charged molecules?
Bent shape making it polar and able to form multiple hydrogen bonds.
Cohesive - Water molecules bonding with each other.
How does water affect electrostatic interactions?
Water molecules compete for their charge reducing electrostatic interactions by 80x.
First and second laws of thermodynamics
Energy can not be created or destroyed only modified.
The total entropy of a system always increases for a spontaneous process.
How can entropy decrease locally?
Entropy can be decreased locally in the formation of ordered structures only if the entropy of the universe is increased by an equal or greater amount.
I.e. Heat being released
Enthalpy
H, Heat content of the system.
Gibbs Free energy equation and spontaneity
ΔG = ΔH - T ΔS
0 > ΔG = Spontaneous
If ΔH < 0 (releasing heat) ΔG becomes more spontaneous
Cage effect
Non-polar molecules tend to cluster together.
Water molecules form a cage around the hydrophobic molecules.
Fewer water molecules are needed to form one big cage as opposed to multiple small cages.
Increases entropy.q
Buffers
Mixture of weak acid and conj base. Resists change sin pH because both forms are present and able to donate/accept protons.
What are the charges of carboxy and amide groups between
2-9 pH?
Zwitter ions - COO- and NH3+
Positive and negative charge.
Peptide bond
Linkage of an alpha-carboxyl linked to the amino group of another amino acid. h20 byproduct.
Where would you find the amino-terminal end versus the free carboxyl group?
Amino-terminal end (N) is on the left
Free carboxyl group on the right (C)
What would K 614 P denote?
The 614th residue from the N termincal end would change from Lysine to Proline.
Phi vs Psi angle
Phi angle is the rotation about the Alpha carbon - nitrogen bond.
Psi angle is the rotation about the alpha carbon - carbonyl.
Why is there no rotation about the peptide bond?
Peptide bond has double bonding characteristics due to resonance between peptide bond and carbonyl.
What produces flexibility, allowing the backbone to fold?
The bonds between αC-N and αC-Carboxyl are free to rotate.
Length added per residue for parallel, anti-parallel and α-helix?
Parallel 3.25 and anti-parallel = 3.5
A-helix = 1.5
Parallel B-Strand bonding
N-H of residue i bonds with j carbonyl and carbonyl of i bonds with N-H of j+2.
Has to “reach over”
