Lecture 1 Prep for Exam 1 Flashcards
What is the bond angle of a water molecule?
104.5
1 bond length equals about
1 Angstrom
The angle of a water molecule gives water what characteristic?
Polarity! Which then allows for hydrogen bonding
How many hydrogen bonds can H2O form?
4 bonds
Which are only hydrogen bond acceptors?
(a) water is both a donor and acceptor
(b) water is only an acceptor
(c) water only acts as a hydrogen acceptor
(d) water is only a hydrogen bond donor
What is the bond strength of a covalent bond?
400 kJ/mol
What is the bond strength for ionic interactions
80 kJ/mol
What is the bond strength for hydrogen bonding?
20 kJ/mol
What is the bond strength for dipole-dipole interaction?
10 kJ/mol
What is the bond strength for london dispersion forces?
0.3 kJ/mol
If Gibbs free energy is negative…that means
that the reaction is spontaneous
If Gibbs free energy is 0…that means
the reaction is at equilibrium
If Gibbs free energy is positive…that means
that the reaction is not spontaneous
Enthalpy (delta H) is
the change in heat produced
Entropy (delta S) is
the randomness of a system…the more greater the constant the more spontaneousness the more the bonding
What is the hydrophobic effect displaying?
The tendency of water to minimize its contacts with hydrophobic molecules
What effect allows for the membrane bilayer and micelles to exist?
the hydrophobic effect
What are the 3 reasons why protein structure is important?
life, disease, pharmaceuticals
How does a protein become active?
They must twist and fold into their final conformation.
Are amino acids that are derived from proteins chiral or achiral?
Chiral (except for Glycine)
All chiral amino acids have what type of stereochemistry?
L-stereochemistry
pH is the measure of
acidity or basicity of an aqueous solution
Ka (acid dissociation constant) is a quantitative measure of the…
strength of an acid
The lower the pKa the _____ the acid
stronger
What is the equation that shows the relationship between pKa and logKa
What is the pKa of an acid (in this class)?
4.5
What is the pKa of a base (in this class)?
9
pH < pKa…then the equilibrium shift to
a) deprotonated
b) protonated
c) depends
(b) protonated
pH=pKa…then the equilibrium is
a) in equilibrium (50 protonated/50 deprotonated)
b) 0
c) undefined
a) in equilibrium
Are ionized molecules more…
a) lipophilic
b) lipophobic
c) hydrophilic
d) hydrophobic
(C) hydrophilic
Are un-ionized molecules more…
A) lipophilic
B) lipophobic
C) hydrophilic
D) hydrophobic
(A) lipophilic
Uncatalyzed mechanism of keto-enol tautomerization:
What is keto-enol tautomerization?
The interconversion of ketones and enols by the transfer of a proton. The overall mechanism depends on pH of the solution.
General acid catalyzed mechanism of keto-enol tautomerization:
General base catalyzed mechanism of keto-enol tautomerization:
Why is the pK1 of COOH group 2.2? (when it is typically 4.5)
Due to the fact that amino acids are dipolar ions (Zwitterions). The pK is more acidic due to the electron withdrawing group making the acid stronger and the base weaker
(In the picture, at pH=7.4, the amino group is protonated and the COOH group is unprotonated)
What is the pK2 of alpha amino group?
9.4
What is the isoelectric point?
The pH at which molecule carries no net electric charge (total charge=0)…this is determined experimentally
What is unique about 2 cysteine residues? Why is it important?
Two cysteines can undergo oxidation and result in disulfide group formation. This is important for our survival!
If you have a difference of 1 unit between the pH and the pKa, what will the ratio of difference between COH% and CO-% be?
90% and 10%
If you have a difference of 2 units between the pH and the pKa, what will the ratio of difference between COH% and CO% be?
(Ionization will be more than 99%) therefore 99% and 1%CO-
What is the unique about this carboxylic acid?
It is called Gamma Carboxylic Acid and has a pKa of 4 unlike alpha carboxylic acid that has a pkA of 2.2.
Which carbon is most basic?
Epsilon carbon as it has a pKa of 10.5
In the scenario, why is the epsilon carbon most basic?
The epsilon carbon is electron donating and therefore, it will increase the basicity of the amine (higher pKa value).
Does hydroxyproline or proline make collagen more stronger? Why is that?
More bonds…stronger?
What will result from the reaction? What is the significance of the product?
The condensation of two amino acids will result in the formation of a peptide bond (CO-NH) with the elimination of a water molecule. Peptide bonds are very important as they form the backbone of polypeptide chains (amino acid residues).
What is the order of a polypeptide backbone?
N-terminus (amino terminus), alpha carbon, carbonyl terminus (c-terminus)
What structure is this?
glutathione! (short bioactive peptide)
Why is glutathione important and which amino acid is responsible for this molecule’s function?
Importance of Glutathione: It is a major antioxidant in our body as it helps protect cells from oxidative damage that are caused by free radicals and peroxides.
Cysteine allows for sulfur hydrogen groups to oxidize and form disulfide bonds. When free radicals and peroxides are encountered, GSH helps neutralize free radicals and convert organic peroxides into alcohols. GSH oxidizes itself when encountered with an organic peroxide, and thus a disulfide bridge is formed and the peroxide then reduces itself into an alcohol. in the case of a free radical, GSH neutralizes the free radical to then yield an alkyl group.
What was noted from the green fluorescent protein? (GFP)?
The ser, tyr, and gly, of the green fluorescent protein undergoes a reaction that includes peptide cyclization (to create a 5-membered imidazolone ring), dehydration of carbonyl oxygen and rate limiting oxidation step to then conjugate the ring. Altogether, the more conjugation allows for more stability and less light required to excite the electrons. This reaction demonstrates the creation of more conjugation in GFP.
What is the connection between this equation and Glutathione’s antioxidant characteristic?
2 GSH and an organic peroxide undergo oxidation to then yield glutathione disulfide (GSSG) and 2 alcohols (reduced)… GSH oxidizes itself essentially sacrificing itself
