Midterm Questions Flashcards
In the alpha helix, the hydrogen bonds are:
Mainly between EN Atoms of the BACKBONE
What experiment provided the first evidence that the amino acid sequence of a polypeptide chain contains all the information required to fold the chain into its native, 3D Structure?
When denatured ribonuclease was allowed to renature, it gained its catalytic activity.
What is one catalytic method not provided by any amino acids?
Electrophilic Catalysis
What two structural properties make some amino acids prefer beta pleated sheets?
1.) The branch on the B-carbon of the side chain
2.) They are typically large and bulky.
Briefly explain why it is important to have a few strategically placed breaker amino acids in a protein sequence?
Secondary Structure breakers allow the globular structure to fold upon itself, causing it to be more compact as the breakers form loops and turns, allow interactions via Van Der Walls forces.
To which family of protein tertiary structures does the myoglobin protein belong?
ALL ALPHA HELICES
Matching: The binding pocket of a large amino acid in the binding pocket of chymotrypsin positions the bond to be broken
Orientation and Proximity
Matching: Water is deprotonated, leaving it with three lone pairs of electrons in its valence shell.
Nucleophilic Catalysis
Matching: The binding pocket of chymotrypsin is the right size to fit a large amino acid
Van Der Waals Forces
Matching: Chymotrypsin breaks the natural reaction into two easy steps
Lowering the activation energy
His-57 donates or accepts protons during catalysis
Acid/Base Catalysis
The binding pocket of chymotrypsin is lined with non-polar amino acids?
Hydrophobic Effect
Asp-102 delocalizes the charge on protonated His-57
Ionic Interactions
The Peptide substate binds in a groove on the surface of chymotrypsin
H - Bonds
The oxyanion hole binds to the tetrahedral carboxyanion
Complementary to the Transition State.
Why does trypsin not hydrolyze a peptide bond containing proline?
The constained structure of proline does not fit.
What atom does not have a lone pair of electrons?
A general acid.
What properties of proteins are the basis of separation of SDS Page?
Based on size solely
Why does ninhydrin stain give a yellow colour only on proline?
Proline posses a secondary alpha amino group.
At which pH will 20% of arginine side chain be protonated?
pH = 12.5 + log(0.2)
= 11.9
If an enzyme is functioning at 75% of its Vmax, what is the substrate concentration expressed as a multiple of Km?
Do:
0.75Km/1 - 0.75Km = 0.75/0.25 = 3
*Note: if gave the percent of Km do 1 + …
Which bonds are planar (cannot rotate) in planar?
N - H bonds
Which of the following amino acids prefer both a-helical and b-strand?
Phenylalanine
By what factor does a typical amino acid speed up reactions compared to uncatalyzed reactions?
10 000 000 000
(9 aminos)
What family fo protein does Green Fluorescent protein belong to?
beta barrel
