1
Q
The central dogma of molecular biology states that
A
DNA encodes RNA which in turn encodes for protein sequences.
2
Q
Which statement does not correctly complete the following sentence: Non-covalent interactions …? (a) Are essential in maintaining the folded structure of a protein. (b) Are responsible for the hydrophobic effect. (c) Hold the primary structure of a protein together. (d) Connect the strands in a DNA double helix
A
Hold the primary structure of a protein together
3
Q
Which interaction will result in the shortest distance between two atoms? (a) A hydrogen bond between a carbonyl oxygen group and an amide nitrogen in an α-helix. (b) A peptide bond. (c) A salt bridge between the carboxylate oxygen of a negatively-charged glutamate side chain and the positively-changed amino terminus of a protein? (d) A dipole-dipole interaction between two carbonyl groups
A
b) peptide bond
4
Q
Consider a weak acid in a solution with a pH of 5.0. Which of the following statements is true?
a) The weak acid is a proton acceptor. (b) The weak acid has a weaker affinity for its proton than does a strong acid. (c) At its pK a , the weak acid will be totally dissociated. (d) The [H + ] of the solution is 10-5 M
A
The [H + ] of the solution is 10-5 M
5
Q
. For a chemical reaction, which of the following combinations is the most thermodynamically favorable at room temperature (298 K)? (a) positive ∆ H, negative ∆ S (b) positive ∆ H, positive ∆ S (c) negative ∆ H, negative ∆ S (d) negative ∆ H, positive ∆ S
A
(d) negative ∆ H, positive ∆ S
6
Q
2D gel electrophoresis requires that proteins be separated in the following order
A
Based on charge, followed by molecular mass
7
Q
Which of the following is not an accurate description of the protein folding process? A. Proteins fold by rapidly sampling a vast number of different conformations to select the most stable one. B. Proteins fold by first forming secondary structures, which self-associate to form tertiary structures. C. Protein folding is thermodynamically favorable only when the entropy of the surrounding solvent is taken into account. D. Chaperones assist protein folding by protecting hydrophobic regions from associating; in the absence of chaperones some proteins can aggregate and/or misfold
A
A. Proteins fold by rapidly sampling a vast number of different conformations to select the most stable one
8
Q
The major factor that determines the mobility of proteins in SDS-PAGE is their _____________. A. overall charge B. molecular mass (size) C. shape D. isoelectric point
A
Molecular mass/ Size
9
Q
- Which of the following methods of structural determination will not provide an atomic resolution structure of a 15 kDa (small) enzyme? A. x-ray crystallography B. electron microscopy C. nuclear magnetic resonance spectroscopy D. all three of these methods would be equally effective in obtaining a high resolution structure
A
B. electron microscopy
10
Q
- Which of the following statements about the Michaelis constant, K M , is correct? A. The K M is equal to the concentration of substrate when all enzyme binding sites are filled. B. The larger the K M , the higher the affinity of the enzyme for substrate. C. The half-maximum velocity (V max /2) of a reaction is reached when the substrate concentration is equal to the K M . D. The K M for a given enzyme is independent of nature of the substrate.
A
C. The half-maximum velocity (V max /2) of a reaction is reached when the substrate concentration is equal to the K M
11
Q
- Which of the following molecules has no net dipole moment? A. H 2 O B. glycine C. methane D. methyl alcohol E. acetic acid
A
Methane
12
Q
- Which of the following statements correctly describes benzene? A. has 6 sp 3 carbons B. has 12 hydrogens C. has alternating single and double bonds resulting in delocalization of the electrons about the carbon ring D. is a flexible molecule that can adopt both boat and chair conformations E. is highly unstable and very reactive
A
C. has alternating single and double bonds resulting in delocalization of the electrons about the carbon ring
13
Q
Which of the following statements is not true regarding stereochemistry? A. Br-CH 2-CH 2-CH 3 can exist as both cis and trans isomers. B. cis-2-pentene and trans-2-pentene have identical formulas but are different molecules. C. A chiral center has 4 different substituents. D. Chiral compounds have non-superimposable mirror images. E. Glycine is the only non-chiral amino acid
A
A. Br-CH 2-CH 2-CH 3 can exist as both cis and trans isomers
14
Q
- Which of the following interactions/bonds requires the most energy to break? A. a hydrogen bond between a methylamine and methyl alcohol B. a hydrophobic interaction between two non-polar molecules in water C. a charge-induced:dipole interaction between an amine group and a benzene ring D. an electrostatic interaction between an amine group and a carboxyl group E. a disulfide bond
A
e) disulfide bond
15
Q
- The magnitude of the force between two point charges increases as A. the distance between the point charges decreases. B. the dielectric constant of the solution decreases. C. the magnitudes of the charges on each species (ie. atom or molecule) increases. D. All of the above. E. None of the above
A
d) all the above
16
Q
- Which of the following statements is not correct with respect to hydrogen bonds? A. Hydrogen bonds are formed between a hydrogen on one electronegative donor atom and a lone electron pair on another electronegative atom. B. Hydrogen bonds are typically ~2 Å in length measured from the atom centers of the hydrogen bond donor and the acceptor. C. Hydrogen bonds are weaker than covalent bonds but are generally stronger than van der Waals (dipole:dipole) interactions.
A
B) . Hydrogen bonds are typically ~2 Å in length measured from the atom centers of the hydrogen bond donor and the acceptor
17
Q
A molecule of acetonitrile CH 3 CN contains ________ sigma bonds and ________ pi bonds
A
5, 2
18
Q
- Which of the following statements correctly describes benzene? A. has 6 sp3carbonsB. has 12 hydrogensC. has alternating single and double bonds about the carbon ringD. has delocalized electrons that form a closed ring making it a very stable molecule
A
d)
19
Q
- Which of the following statements is not trueregarding stereoisomers? A. cis-2-pentene and trans-2-pentene are identical molecules. B. A chiral center has 4 different substituents. C. Chiral compounds have non-superimposable mirror images. D. Glycine is the only naturally occurring amino acid with a non-chiral C
A
a)
20
Q
- The attraction between two oppositely-charged ions increases asA. the distance between the point charges increases.B. the magnitudes of the charges on each ion decreases.C. the dielectric constant of the solution decreases.D. All of the above are correct
A
c)
21
Q
- Which of the following statements is not correctwith respect to hydrogen bonds?A. Hydrogen bonds are formed between a hydrogen on an electropositive donor atom and a lone electron pair on an electronegative atom. B. Hydrogen bonds are typically ~3 Å in length measured from the atom centers of the hydrogen bond donor and the acceptor.C. Amine groups and hydroxyl groups can both act as H bond donors and acceptors.D. Hydrogen bonding explains the high melting and boiling points of water
A
a)
22
Q
- Weak acids are good buffers atA. a pH that is much higher than the pKa of the buffer.B. a pH that is close to the pKa of the buffer.
A
b)
23
Q
Which of the following is not true of transition states?
a) they are distorted from the substrate ground state conformation
b) they provide optimal bonding conformation for the enzyme
c) they are high-energy intermediates
d) they can be converted to products or back to reactants
e) they are identical in energy and conformation whether an enzyme is present or not
A
e) they are identical in energy and conformation whether an enzyme is present or not
24
Q
For the free nrg diagram of an uncatalyzed rxn, which of the following statements is not correct?
a) the reaction is thermodynamically favourable (its exothermic)
b) the addition of an enzyme will lower the delta G of the transition state
c) the addition of an exzyme will inc the keq of the rxn
d) the addition of an enzyme will inc the rate of rxn
e) at equilibrium the rxn may proceed in both directions
A
c) the addition of an exzyme will inc the keq of the rxn
25
Which AA most likely to be found on interior of protein?
a) isoleucine
b) glutamine
c) arginine
d) aspartic acid
e) serine
a)
26
Which of the following statements not correct regarding coiled coil proteins
a) they have 2 left handed alpha helices that twist around each other
B. The coiled coils are held together by hydrophobic interactions.
C. Some coiled coil proteins are leucine zippers.
D. α-keratin is an example of a coiled coil protein.
E. All of these statements are correct.
a) they have 2 left handed alpha helices that twist around each other
27
18. Which statement is incorrect regarding loops and turns?
A. Turns are typically comprised of 3 or 4 amino acids whereas loops can be many amino
acids long.
B. A turn can connect two parallel β-strands in a β-sheet whereas a loop would be required to
connect two anti-parallel β-strands
C. Turns, like α-helices and β-sheets, are stabilized by hydrogen bonds between the main
chain atoms.
D. β-turns (Type I and II) have 4 amino acids and are stabilized by a hydrogen bond between
the carbonyl oxygen of residue 1 and the amide nitrogen of reside 4.
E. Proline and glycine are often found in turns
B. A turn can connect two parallel β-strands in a β-sheet whereas a loop would be required to
connect two anti-parallel β-strands
28
True or false, Water has a higher boiling point than methane.
true
29
Non-polar substances spontaneously aggregate in aqueous solutions even though this process
increases their order and is thus entropically unfavorable. Why does this occur? (2
Aggregation of non-polar substances reduces their surface area and frees up ordered water
molecules, increasing the entropy of the system.
30
What is the H+ concentration of a solution of acetic acid (Ka 1.74 x 10-5) at its titration
midpoint? (2)
the pKa of acetic acid is –log Ka = 4.76
at the titration midpoint pH = pKa so the pH = 4.76
pH = -log [H+] so [H+] = 1.74 x 10-5 M
31
For the process of ice melting (or water freezing), at 0 oC (273 K) ΔH is 6 kJ/mol. What is
ΔS? (2
```
For the process of ice melting (or water freezing), at 0 oC (273 K) ΔH is 6 kJ/mol. What is
ΔS? (2) 0.022 kJ/mol⋅K (or 22 J/mol⋅K)
at 0 oC ΔG = 0 and ΔH = TΔS
6 kJ/mol = 273 K x ΔS
ΔS = 0.022 kJ/mol⋅K (or 22 J/mol⋅K)
```
32
Which single amino acid best fits the following descriptions? (4)
B. has an aromatic side chain with a hydroxyl group
D. has an amine functional group on its side chain:
tyrosine
| lycine
33
Histidine is a good buffer at physiological pH (~7) but it is even better at pH 6 - why?
Include in your answer how imidazole acts as a buffer. (6)
The pKa of the imidazole side chain is 6, so at pH 7 substantial amounts of the protonated
form (HA+, weak acid) and the deprotonated form (A, conjugate base) are present (2): HA+
can dissociate, providing H+ to absorb OH- if [OH-] is increased and A can associate with
H+ to form HA+ if the [H+] is increased (2). However, at pH 7 there is 10X more of the
conjugate base (1). At pH 6 [HA+] will equal [H], which will improve the buffering power
(1).
34
Silk fibroin is comprised of stacked β-sheets, with alternating Gly and Ala (or Ser) in the β-
strands. The glycines are located on one face of each β-sheet and the alanines are located on
the other. What do you think the effect would be if you were to replace many of the alanines
in fibroin with arginines? (3)
The sheets stack with the glycine faces sandwiched together and the Ala/Ser faces together,
with side chains intercalating between each other. If you substituted Ala with Arg you would
be introducing large positively charged side chains that would not pack as well (1) and would
repel each other (1) due to their positive charges, resulting in destabilization of the stacked β-
sheets (1). This would reduce the strength of the silk.
35
Draw out the dipeptide Asp-Arg at pH 2. Use R1 for the Asp and R2 for the Arg side chain
(2.5) (okay to not show the hydrogens) and show all charges (give full marks if they say the
α-carboxyl is only 50% protonated b/c slide uses a pKa of 1.82 for this group). Label each
amino acid. Indicate the peptide bond and the Arg φ and ψ bonds (1.5). What is the net
charge on the dipeptide at this pH? +2 (1) At approximately what pH will there be equal
concentrations of protonated and deprotonated Asp side chain? (1) ~pH 4 (b/c pKa is 4; 3 is
okay too) (6)
--
36
1. Which of the following statements correctly describes benzene?
A. has 6 sp3 carbons
B. has 12 hydrogens
C. has alternating single and double bonds about the carbon ring
D. has delocalized electrons that form a closed ring making it a very stable molecule
d)
37
. Which of the following statements is not true regarding stereoisomers?
A. cis-2-pentene and trans-2-pentene are identical molecules.
B. A chiral center has 4 different substituents.
C. Chiral compounds have non-superimposable mirror images.
D. Glycine is the only naturally occurring amino acid with a non-chiral Cα.
a)
38
4. The attraction between two oppositely-charged ions increases as
A. the distance between the point charges increases.
B. the magnitudes of the charges on each ion decreases.
C. the dielectric constant of the solution decreases.
D. All of the above are correct.
c)
39
5. Which of the following statements is not correct with respect to hydrogen bonds?
A. Hydrogen bonds are formed between a hydrogen on an electropositive donor atom and a lone electron pair on an electronegative atom.
B. Hydrogen bonds are typically ~3 Å in length measured from the atom centers of the hydrogen bond donor and the acceptor.
C. Amine groups and hydroxyl groups can both act as H bond donors and acceptors.
D. Hydrogen bonding explains the high melting and boiling points of water.
a)
40
. The larger the equilibrium constant of a reaction,
A. the less thermodynamically favorable the reaction.
B. the more quickly the reaction will reach equilibrium.
C. the more negative the ΔGo’.
D. the less product will be produced.
C. the more negative the ΔGo’.
41
. Which of the following statements is not correct regarding the polypeptide backbone?
A. Electrons are delocalized about the peptide bond, restricting rotation.
B. Rotation is allowed about phi (φ) and psi (ψ) bonds.
C. A protein with mixed β-sheet and α-helical secondary structure will have peaks in the top left and bottom left quadrants of a Ramachandran plot
D. Most combinations of phi/psi angles are allowed and equally favored.
d)
42
Which statement is not correct regarding loops and turns?
A. Turns are typically comprised of 3 or 4 amino acids whereas loops can be many amino acids long.
B. A turn could connect two parallel β-strands in a β-sheet whereas a loop would be required to connect two anti-parallel β-strands
D. Turns are stabilized by hydrogen bonds between main chain atoms.
E. Proline and glycine are often found in turns.
b)
43
Which statement best describes the process of protein folding in a cell?
A. Protein rapidly sample all possible conformations before adopting their final folded conformation.
B. Proteins folding is directed by the main chain atoms of the polypeptide.
C. Proteins fold post-translationally, with secondary structures forming first.
D. Disulfide bonds must form before the protein adopts its final conformation.
c)
44
```
Which of the following methods cannot be used as a preparative step to purify an enzyme of interest from whole cell lysate?
A. affinity exchange chromatography
B. salting out with ammonium sulfate
C. ultracentrifugation
D. SDS-PAGE
```
d)
45
Briefly describe the two thermodynamic terms that drive protein folding
negative ΔH (or favorable ΔH), due to formation of weak non-covalent bonds (2)
positive ΔS (or favorable ΔS), due to increasing disorder of the surrounding water molecules when hydrophobic regions become buried in the protein interior (or the surrounding water becomes more disordered) (3)
46
The enzyme PLC hydrolase catalyzes the hydrolysis of a phospholipid. The substrate binding site of PLC hydrolase contains a hydrophobic pocket that binds to one hydrocarbon chain of the phospholipid and a lysine that interacts with its negatively charged phosphate. Assuming catalysis occurs at pH 7, indicate with a circle whether each of the following amino acid changes in the substrate binding site will likely result in tighter or weaker binding or will not affect binding. Briefly explain each answer. (6)
(a) a Val in the hydrophobic pocket is changed to Asn: tighter / weaker / no affect
(b) an Ala in the hydrophobic pocket is changed to a Trp: tighter / weaker / no affect
(c) Lys is changed to an Asp: tighter / weaker / no affect
a) weaker; Asn is polar so pocket will not be as hydrophobic
b) weaker; Trp much bigger than Ala, the HC chain won’t fit as well (1)
c) weaker; negatively charged Asp will repel the negatively charged phosphate
47
What effect does each of the following compounds have on proteins? (4)
(a) urea –
(b) β-mercaptoethanol –
(c) sodium dodecyl sulfate –
(a) urea – denatures/unfolds proteins (1)
(b) β-mercaptoethanol – reduces disulfide bonds (1)
(c) sodium dodecyl sulfate – denatures proteins (1), coats them with a negative charge (1)
48
You have three proteins, A, B and C, with the following properties, in a buffer at pH 7.4. (4)
```
Protein MW (kDa) Net charge at pH 7.4
Properties
```
Protein A 120 -2 has an N-terminal hexa-histidine (His6) tag
Protein B 20 0 binds to maltose
Protein C 75 +4 is a DNA binding protein
(a) Which protein will bind to a nickel-NTA column? A
(b) Which protein will bind to a cation exchange column (has carboxymethyl functional group)? C
(c) Which protein will elute first from a size exclusion column? A
(d) Which protein will run the furthest/fastest on SDS-PAGE (i.e. will appear at the bottom, closest to the + terminal)? B
49
Why is 2D electrophoresis better than 1D electrophoresis for proteomic studies?
Allows better separation of many proteins.
50
Name two applications of antibodies for protein purification and analysis
Western blots (immunoblots), ELISA, immunofluorescence, affinity purification, immunoprecipitation, immunogold labeling
51
Which of the following hydrogen bonding schemes stabilizes an α-helix?
(a) Intrachain H-bonds between the carbonyl oxygen on residue i and the amide nitrogen on residue i+4.
(b) Intrachain H-bonds between the amide nitrogen on residue i and the carbonyl oxygen on residue i+4.
(c) Intrachain H-bonds between the amide nitrogen on residue i and the carbonyl oxygen on residue i+3.
(d) Intrachain H-bonds between the side chains of residue i and the carbonyl oxygen on residue i+4.
a)
52
Protein folding is entropically unfavorable but occurs spontaneously. Why?
(a) Because reactions that are entropically unfavorable are thermodynamically favorable.
(b) Because the overall entropy of the system increases by releasing the surrounding water molecules from hydration spheres around exposed hydrophobic regions of the protein.
(c) Because the increase in enthalpy of folding counteracts the decrease in entropy.
(d) Because water molecules that interact weakly with polar groups on the protein are released, increasing the entropy of the system.
b)
53
Which of the following statements is not true about protein folding?
(a) Proteins fold in stages, with local secondary structures forming first, followed by interactions between the secondary structures.
(b) Cysteines must form disulfide bridges prior to the protein adopting its tertiary structure.
(c) Protein folding is initiated co-translationally, before the complete amino acid sequence of the protein is synthesized.
(d) The amino acid sequence of a protein dictates its tertiary structure
b)
54
Which of the following statements is not true for enzymes?
(a) Enzymes enhance the rate of a chemical reaction by stabilizing the transition state.
(b) Enzymes shift the equilibrium of a reaction such that the formation of products is favoured.
(c) Enzymes can enhance the rate of both forward and reverse reactions.
(d) Enzymes are most effective when they bind more tightly to the transition state than the substrate.
b)
55
10. Which of the following is not an example of a globular protein?
(a) porin
(b) α-keratin
(c) RNase A
(d) myoglobin
b)
56
Which of the following statements is not correct regarding irreversible inhibitors?
(a) They bind to and stabilize the transition state of a substrate.
(b) They compete with the substrate for binding to the active site on an enzyme.
(c) They often mimic the transition state of an enzyme.
(d) Increasing the amount of substrate will have no effect on inhibition.
a)
57
Experiments on denaturation and renaturation after the reduction and reoxidation of the –S-S- bonds in the enzyme ribonuclease (RNase) have shown that:
a) the primary sequence of RNase is sufficient to determine the formation of a specific secondary and tertiary structure
b) the enzyme, dissolved in water, is thermodynamically stable relative to the mixture of amino acids whose residues are contained in RNase
c) native ribonuclease does not have a unique secondary and tertiary structure
d) the completely unfolded enzyme, with all –S-S- bonds broken, is still enzymatically active
e) the folding of denatured RNase into the native, active conformation, requires the input of energy in the form of heat
a)
58
Thermodynamics of protein folding (the ΔG for folding) is a balance of several thermodynamic factors:
a) positive conformation entropy, positive enthalpy contribution, negative entropy contribution from salt bridges
b) positive conformation entropy, negative enthalpy contribution, negative entropy contribution from salt bridges
c) positive conformation entropy, negative enthalpy contribution, negative entropy contribution from hydrophobic effect
d) negative conformation entropy, negative enthalpy contribution, positive entropy contribution from hydrophobic effect
e) negative conformation entropy, positive enthalpy contribution, positive entropy contribution from salt bridges
c)
59
Protein domains:
a) are locally folded and stable regions within proteins
b) are not often associated with a particular function
c) with interiors that may consist entirely of polar residues
d) are the same as protein subunits
e) may come together to form protein quaternary structure
a)
60
A sequence of amino acids in a certain protein is found to be –Ser-Gly-Pro-Gly-. This sequence is most probably part of a(n):
a) γ turn
b) parallel β sheet
c) α helix
d) φ sheet
e) β turn
e)
61
2 marks) For the pH values listed below, write the values for [A-]/[HA] for a weak acid. What trend do you observe in dissociation of HA to H+ and A- as the pH values go from being above the pKa to below the pKa?
(a) pKa+3, [A-]/[HA] = 1000
(b) pKa+2, [A-]/[HA] =100
(c) pKa+1, [A-]/[HA] =10
(d) pKa, [A-]/[HA] =1
(e) pKa-1, [A-]/[HA] =0.1
(f) pKa-2, [A-]/[HA] =0.01
(g) pKa-3, [A-]/[HA] =0.001
As the pH goes from well above the pKa to well below the pKa the weak acid goes from being almost fully dissociated to being hardly dissociated (1). At the halfway point where pH = pKa, [A-] = [HA].
62
For the following free energy diagram explain in terms of the enzyme-substrate complex why there are two peaks. What form do these peaks represent in chymotrypsin catalysis of a peptide? What does the dip in the curve represent for this reaction?
The peaks represent high energy (or transition state) intermediates where the enzyme is bound to the transition state (2). This interaction is unstable and will collapse back to the substrate-enzyme conformation or to the more stable intermediate (dip) or the product. In serine protease catalysis, the peaks represent the two tetrahedral intermediates and the dip represent the acyl enzyme intermediate (2).
63
(5 marks) For the main chain of the peptide shown, about which bonds can atoms rotate (i.e. which bonds are flexible and which are not): (1) N-Ca, (2) Cα-C and/or (3) C-N? Explain.
(1) and (2) are flexible, (3) is not (1 mark each). (3) is the peptide bond (1 mark). It has partial double bond character because of the resonance (delocalization) of electrons between the carbonyl oxygen, the carbonyl carbon and the amide nitrogen (1 mark). This gives the bond rigidity.
64
The major reason that antiparallel β-stranded protein structures are more stable than parallel β-stranded structures is that the latter___________________________________________.
a) are in a slightly less extended configuration than antiparallel strands.
b) do not have as many disulfide crosslinks between adjacent strands.
c) do not stack in sheets as well as antiparallel strands.
d) have weaker hydrogen bonds laterally between adjacent strands than antiparallel strands.
e)
65
Which of the following statements is false?
A) Collagen is a protein in which the polypeptides are mainly in the alpha-helix conformation.
B) Disulfide linkages are important for keratin structure.
C) Gly residues are particularly abundant in collagen.
D) Silk fibroin is a protein in which the polypeptide is almost entirely in the beta conformation.
E) alpha-keratin is a protein in which the polypeptides are mainly in the -helix conformation.
a
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