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M1.1 Evolution is ongoing and is constrained by its past
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M1.2 The most abundant chemical element in the human body dry weight is hydrogen
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M1.3 A non spontaneous process will proceed spontaneously in the reverse direction
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M1.4 A distance of 22.1 nm is 2.21 A.
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M1.5 If the enthalpy change of a process is negative and the entropy change is positive, the, reaction is Spontaneous at any temperature.
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M1.6 Weak acids are not very soluble in water
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M1.7 Kw is the ionization constant of water, is 10^(-14) at 25 degrees celsius
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M1.8 the amino acid V has a hydrophobic side chain
true/false |
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M1.9 Amphiphilic molecules have both acidic and basic groups
true/false |
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M1.10 The cell compartment eliminates any exchange between the inside of the enclosed system and the external environment
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M1.11 The 3D structure of water, including the lone pairs, forms a bended geometry of "H-O-H" in a planar
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M1.12 When tossing sugar with strawberries, the fruit will shrink because osmosis pressure drives the juice to drain out
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M1.13 Urey and Miller conducted and experiment that involved sparking a mixture of NH3, CH4, H2O, and H2 gases to yield amino acids, some of the fundamental building blocks of life
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M1.14 The 23.1 ms equals 2.31E13 fs
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M1.15 The pH of a 0.00005 M NaOH solution is 8.5
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| M1.16 What does it mean when q and w are positive? |
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| A) It means the energy of the system increased and it did work to the surrounding |
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M1.17 Which arrow points at the phosphate esther bond?
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M1.18 Which arrow points at the glycosidic bond?
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| M1.19 What is the relationship between right hand and a left hand glove? |
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M1.20 In the following reaction
4NH3(g)--> 2N2(g)+6H2(g), the... |
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M1.21 Identify the Cahn-Ingold-Prelog stereochemistry of the following molecule, which is drawn in a Fischer projection.
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| M1.22 In a hydrogen bond between a water and another biomolecule: |
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| C) The hydrogen bond will typically form between a hydrogen atom and either a nitrogen, sulfur, or oxygen atom. |
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| M1.23 What is the geometry of water molecule? |
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| B) tetrahedron with two invisible oxygen lone electron pairs |
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| M1.24 Which of the following are a pair of acid and conjugate base: |
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| M1.25 Which of the following amino acids has a sulfur atom in its side chain? |
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| M1.26 The pH at the midpoint of a weak acid base titration is: |
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| A) equal to the pK of the corresponding acid |
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| M1.27 What is the three letter code for the amino acid N? |
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| M1.28 What is the pKa of the C-terminus of a polypeptide? |
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| M1.29 Hydrogen bonds are approximately _% of the bond strength of a covalent C-C or C-H bonds? |
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| M1.30 What form of this amino acid cannot exist in any pH? |
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M1.31 What is the identity of the following organic functional group?
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| M1.32 Which molecular structure below is the predominant form of Aspartic acid at pH 1 |
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| M1.33 the isoelectronic point of an amino acid is the point where: |
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Definition
| E) the amino acid carries no net electrical charge |
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| M1.34 Entropy is a measure of |
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Definition
| D) the disorder of a system |
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| M1.35 what will the pH change when 0.5 M of NaAc is added into water solution at pH 7? |
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Definition
| C) pH will increase because Ac- embraces some H+ |
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| M1.36 Calculate the pI of the amino acid Lys. The side chain Pk is 10.54. |
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| M1.37 What is the value of delta G knot for the reaction A+B<-> C+D at 25 degrees celsius when the equilibrium conditions are [A]=1 uM; [B]=5 uM; [C]=10 uM; [D]=2 uM? |
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| M1.38 What is the chemical energy needed to form one ATP at 298K (ADP+Pi->ATP), if ATP=10M, ADP=0.8M, and Pi=4M |
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Definition
| B) delta G=delta G knot +RTln(10/(4*0.8)) |
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| M1.39 Consider the reaction with delta H=15kJ/mol and delta S=50 J/(K*mol). The following statements are TRUE: |
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Definition
E) both b and c
B)It is spontaneous at 80 degrees C
C) It is not spontaneous at 10 degrees C |
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| M1.40 Calculate the pH of a mixing solution containing 300 mL of 3M acetic acid and 200 mL of 2M sodium acetate? The pKa of acetic acid is 4.76. |
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| M1.41 If you add HCl to water to a final concentration of 0.01M, the pH of the solution becomes |
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| M1.42 What is the [H+] concentration of 0.1 M HAc (pk=4.7) if the pH is adjusted to 4? |
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| M1.43 indicate the predominate ionic species of phosphoric acid at pH 9. |
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| M1.44 What is the pK of the weak acid HA if the solution containing 0.2M HA and 0.1M A- exhibits a pH of 6.5? |
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| M1.45 What percentage of the histidine imidazole group is protonated at pH 7.2? (pKa is 6.04) |
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M1.46 Identify the sequence of the following peptide:
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| M1.47 _____ is exceptionally soluble in water due to the formation of hydrogen bonds |
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| M1.48 ATP <-> ADP+Phosphate, delta G= -30.5 kJ/mole, which graph describes this reaction? |
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| M1.49 When two amino acids form a peptide bond what molecule is eliminated ? |
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| M1.50 Which of the following amino acids has a charged polar side chain at pH 7? |
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M2.1 The order of amino acids (Arg, Glu, Val) eluted from a carboxymethyl column at pH 4 should be VRE.
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M2.2 Phenylisothiocynate is a reducing agent that carries out reductive cleavage of disulfide bonds
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M2.3 Given the amino acid sequence DAHGHFLKAGMT, trypsin reagent would cleave AGMT from the peptide
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M2.4 The phi dihedral angle of a peptide bond is described by rotation about the bond that is between the C alpha and N atoms
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M2.5 Hydrophobic chromatrography is a method of fractioning a protein mixture according to the different polarities of the proteins
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M2.6 The function of BPG is to decrease hemoglobin's oxygen affinity
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| M2.7 The NOESY method to detect hydrogens that are close to each other in space but not linked through bonds |
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M2.8 CO2 does not bind to the porphyrin ring Fe2+ ion in myoglobin
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M2.9 One of the early steps in the folding of disordered polypeptides into ordered functional protein is the formation of 2nd order structures such as alpha helices and beta sheets
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M2.10 Peptide A (Q-L-E-F-T-L-D-G-Y) has greater absorbance at 280 nm than peptide B (S-V-W-F-G-Y-W-A).
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M2.11 A good way to predict whether an amino acid side chain is on the outside or inside of a protein is to use its side chain hydrophobicity. For example, in trans-membrane proteins nonpolar amino cids are most likely to be in the region that are within the cell membrane
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M2.12 The collagen contains hydroxylated amino acids
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M2.13 If the hill coefficient for a protein that binds more than one copy of a ligand is 1.5, the protein exhibits positive cooperativity
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M2.14 The sickle cell anemia is due to only a single mutation from a Glu to an Asp that changes the interaction between the two hemoglobin beta-subunits
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M2.15 A fast way for nature to generate new proteins is shuffling protein modules
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| M2.16 In the IEF electrophoresis: |
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Definition
| C) the pH of the Gel increases smoothly from the anode (+) to the cathode (-) |
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M2.17 You wish to determine the sequence of a short peptide. Treatment with dansylchloride reveals the amino acid terminal is Val. Trypsin digestion generated the fragments of:
Val-Gly-Ala-His-Ala-Gly-Glu-Tyr-Gly-Ala-glu-Ala-Thr-Glu (a)
ala-Ala-Trp-Gly-Lys (b)
Val-Leu-Ser-Pro-ala-Lys (c)
thr-Asn-Val-Lys (d)
chymotrypsin digestion gave the fragments of:
Gly-ala-glu-Ala-Thr-Glu
Gly-Lys-val-Gly-Ala-His-Ala-gly-Glu-Tyr
Val-Leu-Ser-Pro-ala-Lys-Thr-Asn-Val-Lys-Ala-Ala-Trp
The sequence of the peptide is: |
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| M2.18 the length of an alpha helix of 20 amino acid residues is |
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M2.19 The meaning of planar amide bond is:
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| A) bonds 1,2 and 3 are in one plane |
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M2.20 Which carbons are the C alpha carbons?
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M2.21 Which bonds define the phi and psi angles?
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M2.22 Your best estimate of the angle phi value in this figure is:
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M2.23 Which residues in the seven residue repeat (abcdefg) of the alpha keratin helical wheel provides a hydrophobic interaction to associate two coiled coils?
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M2.24 The GFP structure is shown below. The major motif in this protein is
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M2.25 the following figure showed the binding curves of myoglobin, stripped hemoglobin, adult hemoglobin in whole blood at conditions of (normal, elevated CO2, elevated area). Curve a is hyperbolic and the others are sigmoidal. the binding curve in whole blood is d. the binding curves for myoglobin, whole blood with elevated CO2-, and whole blood in elevated are are:
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| M2.26 ____is an example of a very slowly evolving protein |
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| M2.27 In the absence of ascorbic acid, prolyl oxidase is unable to oxidize proline residues in collagen to hydroxyproline, resulting in: |
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| M2.28 The misfolding of amyloid Beta protein leads to: |
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| M2.29 Given the amino acid sequence FIAGTKMDAWGH, what reagent will cut this peptide in two equal length pieces? |
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| M2.31 Spontaneous oxidation of the heme-bound Fe(II) to Fe(III) is prevented in hemoglobin by: |
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Definition
| C) the surrounding protein structure in each subunit |
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| M2.32 For beta sheets, the terms 'parallel' and 'anti-parallel' refer to ___. |
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Definition
| A) the 'direction' of the associated peptide strands |
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| M2.33 The classic experiment demonstrating that reduced and denatured RNase A could refold into the native form demonstrates that: |
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Definition
| C) disulfide bonds can dictate the tertiary structure of folding |
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| M2.34 The reagent iodoacetate is to: |
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Definition
| B) react with cys residue to prevent reformation of disulfide bonds |
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M2.35 Fully identify the subunit compostion of a protein form the following info
Molecular mass by gel filtration: 350kD
Molecular mass by SDS-PAGE: 180kD and 170kD
Molecular mass by SDS-Page with 2-mercaptoethanol: 100kD, 80kD, 70kD
-S-S- is a disulfide bond and [][] are non-covalent associations |
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Definition
| B) [100-S-S-80] [100-S-S-70] |
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| M2.36 A crude enzyme extract exhibits an activity of 10,000,000 nkat per 50,000 mg extract; and after DEAE-cellulose column, the enzyme exhibits 3,750,000 nkat activity per 5000 mg. How to calculate the fold of purification? |
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Definition
| C) (3,750,000/10,000,000)*(50,000/5000) |
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