Midterm 1

Question 1

The central dogma of molecular biology states that

Answer 1

DNA encodes RNA which in turn encodes for protein sequences.

Question 2

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

Answer 2

Hold the primary structure of a protein together

Question 3

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

Answer 3

b) peptide bond

Question 4

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

Answer 4

The [H + ] of the solution is 10-5 M

Question 5

. 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

Answer 5

(d) negative ∆ H, positive ∆ S

Question 6

2D gel electrophoresis requires that proteins be separated in the following order

Answer 6

Based on charge, followed by molecular mass

Question 7

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

Answer 7

A. Proteins fold by rapidly sampling a vast number of different conformations to select the most stable one

Question 8

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

Answer 8

Molecular mass/ Size

Question 9

3. 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

Answer 9

B. electron microscopy

Question 10

4. 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.

Answer 10

C. The half-maximum velocity (V max /2) of a reaction is reached when the substrate concentration is equal to the K M

Question 11

1. Which of the following molecules has no net dipole moment? A. H 2 O B. glycine C. methane D. methyl alcohol E. acetic acid

Answer 11

Methane

Question 12

2. 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

Answer 12

C. has alternating single and double bonds resulting in delocalization of the electrons about the carbon ring

Question 13

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

Answer 13

A. Br-CH 2-CH 2-CH 3 can exist as both cis and trans isomers

Question 14

4. 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

Answer 14

e) disulfide bond

Question 15

5. 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

Answer 15

d) all the above

Question 16

6. 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.

Answer 16

B) . Hydrogen bonds are typically ~2 Å in length measured from the atom centers of the hydrogen bond donor and the acceptor

Question 17

A molecule of acetonitrile CH 3 CN contains ________ sigma bonds and ________ pi bonds

Answer 17

5, 2

Question 18

1. 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

Answer 18

d)

Question 19

2. 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

Answer 19

a)

Question 20

4. 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

Answer 20

c)

Question 21

5. 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

Answer 21

a)

Question 22

6. 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.

Answer 22

b)

Question 23

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

Answer 23

e) they are identical in energy and conformation whether an enzyme is present or not

Question 24

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

Answer 24

c) the addition of an exzyme will inc the keq of the rxn

Question 25

Which AA most likely to be found on interior of protein?

a) isoleucine
b) glutamine
c) arginine
d) aspartic acid
e) serine

Answer 25

a)

Question 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.

Answer 26

a) they have 2 left handed alpha helices that twist around each other

Question 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

Answer 27

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

Question 28

True or false, Water has a higher boiling point than methane.

Answer 28

true

Question 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

Answer 29

Aggregation of non-polar substances reduces their surface area and frees up ordered water
molecules, increasing the entropy of the system.

Question 30

What is the H+ concentration of a solution of acetic acid (Ka 1.74 x 10-5) at its titration
midpoint? (2)

Answer 30

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

Question 31

For the process of ice melting (or water freezing), at 0 oC (273 K) ΔH is 6 kJ/mol. What is
ΔS? (2

Answer 31

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)

Question 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:

Answer 32

tyrosine

lycine

Question 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)

Answer 33

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).

Question 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)

Answer 34

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.

Question 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)

Answer 35

–

Question 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

Answer 36

d)

Question 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.

Answer 37

a)

Question 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.

Answer 38

c)

Question 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.

Answer 39

a)

Question 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.

Answer 40

C. the more negative the ΔGo’.

Question 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.

Answer 41

d)

Question 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.

Answer 42

b)

Question 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.

Answer 43

c)

Question 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

Answer 44

d)

Question 45

Briefly describe the two thermodynamic terms that drive protein folding

Answer 45

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)

Question 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

Answer 46

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

Question 47

What effect does each of the following compounds have on proteins? (4)

(a) urea –
(b) β-mercaptoethanol –
(c) sodium dodecyl sulfate –

Answer 47

(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)

Question 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

Answer 48

(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

Question 49

Why is 2D electrophoresis better than 1D electrophoresis for proteomic studies?

Answer 49

Allows better separation of many proteins.

Question 50

Name two applications of antibodies for protein purification and analysis

Answer 50

Western blots (immunoblots), ELISA, immunofluorescence, affinity purification, immunoprecipitation, immunogold labeling

Question 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.

Answer 51

a)

Question 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.

Answer 52

b)

Question 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

Answer 53

b)

Question 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.

Answer 54

b)

Question 55

10. Which of the following is not an example of a globular protein?

(a) porin
(b) α-keratin
(c) RNase A
(d) myoglobin

Answer 55

b)

Question 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.

Answer 56

a)

Question 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

Answer 57

a)

Question 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

Answer 58

c)

Question 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

Answer 59

a)

Question 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

Answer 60

e)

Question 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

Answer 61

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].

Question 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?

Answer 62

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).

Question 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.

Answer 63

(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.

Question 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.

Answer 64

e)

Question 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.

Answer 65

a