Chem 153A - Lec 2 Midterm #1 Form D
Vivian Wong
TOTAL POINTS
peptide
QUESTION 1
+ 0.5 a 0.5 eq pt at 9.5 (instead of 8.5)
Question 1: Peptide and titration curve
+ 0.5 a 0.5 eq pt at 2 (instead of 3.5)
26 pts
+ 1 a 0.5 eq pt at pH = 10.5 based on above peptide
1.1 Draw peptide
1.4 pI
+ 4 Termini and peptide bonds are correct
+ 1 pKas used are in numerical order from their
+ 6 All amino acid side chains are correctly drawn
titration curve
+ 1 N-terminus is correctly drawn
+ 1 average included 6.0
+ 1 C-terminus is correctly drawn
+ 1 average included 4.2
+ 1 Carbonyl is correct in peptide bond
+ 1 Average Included 3.7 based on peptide above
+ 1 N-H is correct in pepetide bond
+ 0 Incorrect /Blank
+ 2 Histidine is drawn correctly
+ 2 valine is drawn correctly QUESTION 2
+ 2 glutamate is drawn correctly
Question 2: Protein Structure 28 pts
+ 0 Incorrect/Blank
2.1 A and B secondary H-bond
1.2 Q1 B-D
+ 2 A: Hydrogen bonds
+ 1 His is imidazole
+ 1 B: Drew a Hydrogen bond
+ 1 Val is an alkane/methyl/propyl
+ 1 B: H-bond include N-H
+ 1 Glu is carboxylic acid/carboxyl
+ 1 B: H-bond includes C=O
+ 1 C: correct net charge based on their peptide
+ 1 N-H is correctly identified on the backbone
(should be -1)
+ 1 C=O is correctly identified on the backbone
+ 1 20^3
+ 1 that N-H and C=O are in the correct position to
+ 0 Incorrect/Blank
form a H-bond
1.3 Titration Curve + 0 Incorrect/Blank
+ 1 direction: going down from ~14 to ~0
2.2 C and D tertiary structure
+ 1 0.5 eq points are shallowest part of the curve
+ 1 C: side chain of serine is correct
+ 1 Full eq points are steepest part of the curve
+ 1 C: facing the outside of the helix
+ 1 a 0.5 eq pt at pH = 8.5
+ 1 C: coming from an alpha carbon
+ 1 a 0.5 eq pt at pH = 6
+ 1 C: At the first alpha carbon from the N-terminal
+ 1 a 0.5 eq pt at pH = 4.2
side of the peptide (the bottom alpha carbon)
+ 1 a 0.5 eq pt at pH = 3.5
+ 1 D: Valine is in the core of the protein
+ 1 Buffer ranges are +/- 1 unit of graphed pKas and
+ 1 D: Serine would be near the surface of the
labeled on the graph with brackets
protein
+ 0 Incorrect/Blank
+ 0 Incorrect/Blank
+ 1 a 0.5 eq pt at pH = 3.7 based on your above
2.3 E Thermodynamics
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https://www.coursehero.com/file/24555659/CHEM153A-Midterm1-Tienson-Spring2017pdf/
, + 1 valine is hydrophobic + 1 B: free calcium ligand
+ 1 interacting with water would force water into + 1 B: your favorite protein
ordered structures + 1 B: associating with calmodulin
+ 1 Valine aggregates with other hydrophobic + 1 B: through a covalent bond (as the tag)
residues (in the center of the protein) + 1 B: buffer/water
+ 1 the aggregation increases the entropy of water + 0 incorrect/Blank
+ 1 serine is polar 4.2 basis of elution
+ 1 thus it interacts favorable with water (doesn't + 1 Protein-ligand binding is dynamic/transient
affect entropy of water) + 1 the protein will disassociate from the ligand
+ 1 doesn't have to fold away from water. + 1 the disassociation is not caused by anything
+ 0 Incorrect/blank + 1 protein-tag will bind free ligand
2.4 F physical Basis of Interactions + 1 blocking your favorite protein from rebinding
+ 1 hydrophobic interaction + 0 incorrect/blank
+ 1 interaction involves valine side chain
QUESTION 5
+ 1 with another amino acid side chain.
+ 1 held together by attractive force between Hemoglobin 16 pts
opposite charges 5.1 A, B and binding curve from part D
+ 1 involve partial charges + 1 A: X-Axis: pO2
+ 1 assymetric distribution of the electron cloud + 1 A: X-axis: torr or other unit of pressure
+ 1 produces transient dipoles (induces dipoles) + 2 A: Y-axis: fractional (or degree) saturation
+ 0 incorrect/blank/illegible + 1 A: only theta
+ 1 D: curve ends at 1.0
QUESTION 3
+ 1 D: curve is sigmoidal
buffer 6 pts + 1 D: curve is shifted to the left (lower p50)
3.1 Buffer + 0.5 B: pO2
+ 1 buffer D + 0.5 50% of something is bound
+ 2 buffer (D-F) have a pKa within 1 pH unit of 6.9) + 1 50% of the binding sites are occupied
+ 1 A-:HA ratio would make it a good buffer + 0 Incorrect/Blank
+ 1 more weak acid than conjugate base 5.2 C and written part of D
+ 1 pH of buffer will be less than pKa 7.21 (thus closest + 1 C: a number between 25-28
to 6.9) + 1 C: units of pressure same as x-axis
+ 0 Blank/Wrong answer/illegible + 1 D: protons stabilize the T-state
+ 1 D: this decreases the affinity of Hb for oxygen
QUESTION 4
+ 1 D: causing less O2 to be bound by Hb
Purification 14 pts + 1 D: Hb will deliver more oxygen (or less O2)
4.1 diagram and elution + 1 D: in areas with lower pH (in areas of higher pH)
+ 1 A:calmodulin is attached to your protein + 0 Incorrect/Blank
+ 1 A:calcium is attached to the column
+ 1 A:calmodulin interacts with calcium QUESTION 6
+ 1 A:calmodulin-calcium interaction is what attaches Glycerophospholipid 6 pts
protein to the column 6.1 Glycerophospholipidstructure and
This study source was downloaded by 100000810073548 from CourseHero.com on 03-24-2022 10:09:53 GMT -05:00
https://www.coursehero.com/file/24555659/CHEM153A-Midterm1-Tienson-Spring2017pdf/
Vivian Wong
TOTAL POINTS
peptide
QUESTION 1
+ 0.5 a 0.5 eq pt at 9.5 (instead of 8.5)
Question 1: Peptide and titration curve
+ 0.5 a 0.5 eq pt at 2 (instead of 3.5)
26 pts
+ 1 a 0.5 eq pt at pH = 10.5 based on above peptide
1.1 Draw peptide
1.4 pI
+ 4 Termini and peptide bonds are correct
+ 1 pKas used are in numerical order from their
+ 6 All amino acid side chains are correctly drawn
titration curve
+ 1 N-terminus is correctly drawn
+ 1 average included 6.0
+ 1 C-terminus is correctly drawn
+ 1 average included 4.2
+ 1 Carbonyl is correct in peptide bond
+ 1 Average Included 3.7 based on peptide above
+ 1 N-H is correct in pepetide bond
+ 0 Incorrect /Blank
+ 2 Histidine is drawn correctly
+ 2 valine is drawn correctly QUESTION 2
+ 2 glutamate is drawn correctly
Question 2: Protein Structure 28 pts
+ 0 Incorrect/Blank
2.1 A and B secondary H-bond
1.2 Q1 B-D
+ 2 A: Hydrogen bonds
+ 1 His is imidazole
+ 1 B: Drew a Hydrogen bond
+ 1 Val is an alkane/methyl/propyl
+ 1 B: H-bond include N-H
+ 1 Glu is carboxylic acid/carboxyl
+ 1 B: H-bond includes C=O
+ 1 C: correct net charge based on their peptide
+ 1 N-H is correctly identified on the backbone
(should be -1)
+ 1 C=O is correctly identified on the backbone
+ 1 20^3
+ 1 that N-H and C=O are in the correct position to
+ 0 Incorrect/Blank
form a H-bond
1.3 Titration Curve + 0 Incorrect/Blank
+ 1 direction: going down from ~14 to ~0
2.2 C and D tertiary structure
+ 1 0.5 eq points are shallowest part of the curve
+ 1 C: side chain of serine is correct
+ 1 Full eq points are steepest part of the curve
+ 1 C: facing the outside of the helix
+ 1 a 0.5 eq pt at pH = 8.5
+ 1 C: coming from an alpha carbon
+ 1 a 0.5 eq pt at pH = 6
+ 1 C: At the first alpha carbon from the N-terminal
+ 1 a 0.5 eq pt at pH = 4.2
side of the peptide (the bottom alpha carbon)
+ 1 a 0.5 eq pt at pH = 3.5
+ 1 D: Valine is in the core of the protein
+ 1 Buffer ranges are +/- 1 unit of graphed pKas and
+ 1 D: Serine would be near the surface of the
labeled on the graph with brackets
protein
+ 0 Incorrect/Blank
+ 0 Incorrect/Blank
+ 1 a 0.5 eq pt at pH = 3.7 based on your above
2.3 E Thermodynamics
This study source was downloaded by 100000810073548 from CourseHero.com on 03-24-2022 10:09:53 GMT -05:00
https://www.coursehero.com/file/24555659/CHEM153A-Midterm1-Tienson-Spring2017pdf/
, + 1 valine is hydrophobic + 1 B: free calcium ligand
+ 1 interacting with water would force water into + 1 B: your favorite protein
ordered structures + 1 B: associating with calmodulin
+ 1 Valine aggregates with other hydrophobic + 1 B: through a covalent bond (as the tag)
residues (in the center of the protein) + 1 B: buffer/water
+ 1 the aggregation increases the entropy of water + 0 incorrect/Blank
+ 1 serine is polar 4.2 basis of elution
+ 1 thus it interacts favorable with water (doesn't + 1 Protein-ligand binding is dynamic/transient
affect entropy of water) + 1 the protein will disassociate from the ligand
+ 1 doesn't have to fold away from water. + 1 the disassociation is not caused by anything
+ 0 Incorrect/blank + 1 protein-tag will bind free ligand
2.4 F physical Basis of Interactions + 1 blocking your favorite protein from rebinding
+ 1 hydrophobic interaction + 0 incorrect/blank
+ 1 interaction involves valine side chain
QUESTION 5
+ 1 with another amino acid side chain.
+ 1 held together by attractive force between Hemoglobin 16 pts
opposite charges 5.1 A, B and binding curve from part D
+ 1 involve partial charges + 1 A: X-Axis: pO2
+ 1 assymetric distribution of the electron cloud + 1 A: X-axis: torr or other unit of pressure
+ 1 produces transient dipoles (induces dipoles) + 2 A: Y-axis: fractional (or degree) saturation
+ 0 incorrect/blank/illegible + 1 A: only theta
+ 1 D: curve ends at 1.0
QUESTION 3
+ 1 D: curve is sigmoidal
buffer 6 pts + 1 D: curve is shifted to the left (lower p50)
3.1 Buffer + 0.5 B: pO2
+ 1 buffer D + 0.5 50% of something is bound
+ 2 buffer (D-F) have a pKa within 1 pH unit of 6.9) + 1 50% of the binding sites are occupied
+ 1 A-:HA ratio would make it a good buffer + 0 Incorrect/Blank
+ 1 more weak acid than conjugate base 5.2 C and written part of D
+ 1 pH of buffer will be less than pKa 7.21 (thus closest + 1 C: a number between 25-28
to 6.9) + 1 C: units of pressure same as x-axis
+ 0 Blank/Wrong answer/illegible + 1 D: protons stabilize the T-state
+ 1 D: this decreases the affinity of Hb for oxygen
QUESTION 4
+ 1 D: causing less O2 to be bound by Hb
Purification 14 pts + 1 D: Hb will deliver more oxygen (or less O2)
4.1 diagram and elution + 1 D: in areas with lower pH (in areas of higher pH)
+ 1 A:calmodulin is attached to your protein + 0 Incorrect/Blank
+ 1 A:calcium is attached to the column
+ 1 A:calmodulin interacts with calcium QUESTION 6
+ 1 A:calmodulin-calcium interaction is what attaches Glycerophospholipid 6 pts
protein to the column 6.1 Glycerophospholipidstructure and
This study source was downloaded by 100000810073548 from CourseHero.com on 03-24-2022 10:09:53 GMT -05:00
https://www.coursehero.com/file/24555659/CHEM153A-Midterm1-Tienson-Spring2017pdf/
