For Questions #1-15, consider the peptide drawn below. Please use the pKa’s within Table 3-1 of the Lehninger text (6th ed.).
Question 1
The one-letter code for this peptide is ____________.
Question 2
The three-letter code for this peptide is ____________.
Question 3
At neutral pH:
The free amino terminus is ________________ protonated or deprotonated) and carries a ________
(-1, 0, or +1) charge.
The free carboxy terminus is __________________
(protonated or deprotonated) and carries a ________
(-1, 0, or +1) charge.
The side chain of Residue #1 is _________________
(protonated or deprotonated) and carries a _________
(-1, 0, or +1) charge.
The overall charge on this peptide is ___________
(-2, +4, etc.).
The ____________
side chain (indicate the residue #) could form an ionic bond with Cl-.
The _______________
side chain (indicate the residue #) could form a hydrogen bond with the hydrogen atom of a water molecule.
___________
is the most hydrophobic residue (indicate the residue #).
Question 4
At a pH of 5 (and using our rule of thumb), _______ retains the potential to act as an acid (at higher pH’s). Select any/all answers that apply.
A.A. The free amino terminus
B.TTh B. The side chain of Residue #1
C.C. The side chain of Residue #2
D.D. The side chain of Residue #5
E.E. The free carboxy terminus
Question 5
At a pH of 12 (and using our rule of thumb), _______ retains the potential to act as a base (at lower pH’s). Select any/all answers that apply.
A. The free amino terminus
B. The side chain of Residue #1
C. The side chain of Residue #2
D. The side chain of Residue #5
E. The free carboxy terminus
Question 6
________ is the strongest base in this peptide structure.
A.A. The free amino terminus
B.B. The side chain of Residue #1
C.C. The side chain of Residue #3
D.D. The side chain of Residue #5
E.E. The free carboxy terminus
Question 7
________ is the strongest acid in this peptide structure.
A.The free amino terminus
B.The side chain of Residue #1
C.The side chain of Residue #3
D.The side chain of Residue #5
E.The free carboxy terminus
Question 8
The side chain of Residue #________ is classified as aromatic.
A.1
B.2
C.3
D.4
E.5
F.6
Question 9
The side chain of Residue #________ is the amide derivative of the glutamate side chain.
A.1
B.2
C.3
D.4
E.5
F.6
Question 10
At pH 4, what percentage of the side chains of Residue #2 are deprotonated? Show all mathematical work.
______________________________________________________________________
Question 11
At pH 4, and using your answer to Question #10, what is the overall charge on the peptide? Support your answer by explaining the charge on each individual residue.
______________________________________________________________________
Question 12
Calculate an approximate pI for this peptide. Show all mathematical work and clearly explain your choice of pKa’s for the calculation.
__________________________________________________________________
Question 13
We would classify this peptide as slightly ___________ (acidic or basic) because the pI is ___________
(higher or lower) than 7.
Question 14
If this peptide sequence were part of a larger polypeptide/protein structure, it’s likely that:
this sequence would be part of an alpha-helix. _____________
(true or false)
this sequence would be part of a Type I beta turn. _______________ (true or false)
this sequence would reside within a hydrophobic pocket of a globular protein. ___________ (true or false)
one or more of the residues within this sequence would be part of a disulfide linkage. ___________
(true or false)
one or more of the residues within this sequence would engage in intramolecular and/or intermolecular hydrogen bonding. ____________ (true or false)
Question 15
In theory (don’t consider consensus sequences), which amino acid residue(s) within the peptide could be:
phosphorylated? _____________ (indicate the residue number(s) or “none”)
ubiquitinated? _____________
(indicate the residue number(s) or “none”)
N-linked glycosylated? _____________
(indicate the residue number(s) or “none”)
Question 16
Questions #16-19 are based on the Prusiner (2013) review article.
Which of the following proteins are considered to be prion proteins by Prusiner? Select any/all answers that apply.
A.SOD1
B.parkin
C.huntingtin
D.PrP
E.tau
Question 17
Which of the following statements is true? Select any/all answers that apply.
A.Any disease-associated prion protein exists in a different conformation than its normal cellular (wild-type) counterpart.
B.There are sporadic forms for all of the prion-based NDs (neurodegenerative diseases) that Prusiner describes.
C.Prusiner won the Nobel prize because he showed that mad cow disease was transmitted via a virus.
D.There are no known mutations to the PRNP gene that lead to the development of any NDs.
E.The A673T mutation in amyloid precursor protein is causative for familiar Alzheimer’s disease.
Question 18
Which of the following structures are (or include) oligomers or polymers of prion proteins? Select any/all answers that apply.
A.neurofibrillary tangles
B.amyloid plaques
C.micelles
D.GPI-anchors
E.Lewy bodies
Question 19
Huntingtin, [PSI+], and MAVS are all prion proteins that contain _________-rich domains.
A.glutamate
B.glutamine
C.asparagine
D.aspartate
E.leucine
Question 20
Questions #20-22 are based on the series of Nature Methods papers about targeted proteomics.
SRM analysis is best for analyzing ________ proteins at the same time.
A.7
B.70
C.700
D.7,000
E.70,000
Question 21
SISCAPA: (select any/all answers that apply)
A.relies on the use of antibodies.
B.is a hybrid approach for discovery proteomics.
C.relies on the use of mass spectrometry.
D.allows for the detection of small numbers of proteins.
E.is a hybrid approach for targeted proteomics.
Question 22
________ has been & continues to be the workhorse of shot-gun proteomics.
A.LC-MS/MS
B.Gas chromatography
C.SRM
D.SWATH
E.QQQ
Question 23
Match each type of protein purification strategy with its appropriate description. Any single description can be selected only once. Not all descriptions will be used.
Affinity chromatography
Cation exchange chromatography
ELISA
2D-gel electrophoresis
Hydrophobic interaction chromatography
Ammonium sulfate precipitation
Gel filtration chromatography
A. Used to “salt out” a subset of proteins, while other proteins remain in solution
B. The most hydrophobic proteins elute first while the most hydrophilic proteins elute last
C. An antibody-based method which measures enzymatic activity as an indicator of the abundance of the protein of interest
D. Separation technique that exploits a specific binding interaction between the protein of interest and its ligand
E. Smaller proteins elute first because they are less retarded by the matrix material within the column
F. Separation of proteins within a polyacrylamide gel, in the first dimension by pI and in the second dimension by standard SDS-PAGE
G. Used to “salt in” all the proteins, thereby keeping them all in solution
H. The stationary phase consists of an inert resin conjugated to a positively-charged species such as DEAE (diethylaminoethyl)
I. The stationary phase consists of an inert resin conjugated to a negatively-charged species such as CM (carboxymethyl)
J. A hydrophobic stationary phase is used to capture the most hydrophobic proteins in the sample
K. Larger proteins elute from the column first because smaller proteins are trapped within beads
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