Which of the following is NOT an example of a biopolymer?

a. phosphatidyl serine

b. starch

c. myoglobin

d. DNA

Which of the following statements is generally TRUE?

a. Eukaryotic cells are larger and less compartmentalized than prokaryotic cells

b. Eukaryotic cells are smaller and more compartmentalized than prokaryotic cells

c. Eukaryotic cells are larger and more compartmentalized than prokaryotic cells

d. Eukaryotic cells are smaller and less compartmentalized than prokaryotic cells

Which of the following organelles is NOT present in animal cells?

a. lysosome

b.mitochondrion

c. nucleus

d. chloroplast

Which of the following is always TRUE about a reaction that happens spontaneously?

a. ΔG is negative

b. ΔH is negative

c. ΔS is positive

d. ΔH is negative and ΔS is positive

As ice melts into water, how does the entropy and enthalpy change?

a. entropy increases, enthalpy decreases

b. entropy increases, enthalpy increases

c. entropy decresases, enthalpy increases

d. entropy decreases, enthalpy decreases

Which of the following statements is TRUE about open systems?

a. Only reactions with positive ΔS are spontaneous

b. A reaction with ΔG= -20 kJ/mol will always proceed faster than one with ΔG= -10 kJ/mol

c. Reactions with a negative ΔS may be spontaneous

d. A reaction that occurs spontaneously at T=273K will occur spontaneously at T=300K

Which of the following do you expect to have highest entropy?

a. ammonia (NH3) gas

b. liquid ammonia

c. solid ammonia

d. all of the above have the same entropy

In which of the following are the types of interactions sorted from STRONGEST to WEAKEST?

a. dipole-dipole, covalent interactions, van der Waals

b. dipole-dipole, van der Waals, covalent interactions

c. covalent interactions, dipole-dipole, van der Waals

d. van der Waals, dipole-dipole, covalent interactions

Given what you know about nonbonded interactions, which of the following do you expect to have the LOWEST boiling point?

a. methane (CH4)

b. mehtanol (CH3OH)

c. methylamine (CH3NH2)

d. formaldehyde (CH2O)

Which of the following statements about hydrogen bonding in water is TRUE?

a. An average water molecule makes <4 hydrogen bonds as ice and <4 as a liquid

b. An average water molecule makes <4 hydrogen bonds as ice and 4 as a liquid

c. And average water molecule makes 4 hydrogen bonds as ice and 4 as a liquid

d. An average water molecule makes 4 hydrogen bonds as ice and <4 as a liquid

Which of the following molecules have BOTH a hydrogen bond donor and acceptor?

a. formaldehyde (CH2O)

b. methanol (CH3OH)

c. acetonitrile (CH3CN)

d. ethane (C2H6)

Hydrophobic molecules (like oil) tend to self-associate in water rather than dissolve.  What is the MAJOR energetic contribution to this property?

a. The self-associations maximizes the entropy of the oil molecules

b. The self association minimizes the enthalpy of the oil molecules

c. The self-association minimizes the enthalpy of the oil/water interactions

d. The self association maximizes the entropy of the water molecules

The pKa of acetic acid (CH3COOH) is 4.76. What is the ratio of [CH3COO-] to [CH3COOH] at a pH of 6.76?

a. 100:1

b. 2:1

c. 1:2

d. 1:100

Sort the pH of the following mixtures from LOWEST (most acidic) to HIGHEST (most basic):

• (I) 0.001 mol of HCl added to 1 L water
• (II) 0.001 mol HCl added to a buffer solution of 0.1 M HCOOH and 0.1 M NaHCOO (pKa=3.75)
• (III) 0.001 mol HCl added to a buffer solution of 0.1 M NH4Cl and NH3 (pKa=9.25)

a. I, II, III

b. II, I, III

c. II, III, I

d. III, II, I

Which of the following statements is TRUE about a protein with an isoelectric point (pI) of 5.5?

a. it has a net negative charge at pH 4 and net negative charge at pH 9

b. it is neutral at pH 4 and has a net negative charge at pH 9

c. it has a net negative charge at pH 4 and net positive charge at pH 9

d. it has a net positive charge at pH 4 and net negative charge at pH 9

There are only three naturally occurring amino acids that do not have EXACTLY one chiral center. Which are they?

a. GLY, ILE, THR

b. ALA, ILE, TYR

c. ASP, GLU, GLY

d. PHE, TYR, TRP

a. GLY, ILE, THR

What is the charge of the peptide EHK at pH=3, pH=5, and pH=7, respectively? (Note: only consider the most populated protonation state)

a. +1, +1, 0

b. +1, 0, -1

c. +2, +1, -1

d. +3, +1, 0

Which of the following sequences is cleaved by BOTH trypsin and chymotrypsin?

a. MSFESTVL

b. AKSDYGRD

c. DFGSRPGG

d. EGHVVIKL

What is the sequence of the illustrated peptide?

[image]

a. QGDF

b. EGNF

c. QADW

d. EANW

Which of the following peptides sequences has NO spectroscopic signal at 280 nm wavelength?

a. NHYLK

b. FEFDL

c. WVIAS

d. PYWGG

Which amino acid is chemically modified to form a key component of the connective tissue protein collagen?

a. lysine

b. serine

c. proline

d. cysteine

Which amino acid substitution is MOST likely to disrupt the function of a protein (that is, which mutation is least conservative)?

a. R to K

b. W to S

c. D to E

d. I to L

Which post-translational modification is encoded genetically?

a. Phosphorylation of a serine residue

b. Formation of a disulfide bridge from two cysteine residues

c. Acetyllation of a lysine residue

d. None of the above

What is the ΔG of FORMATION of a peptide bond?

a. >0

b. 0

c. <0

Which of the following BEST describes the geometry of an alpha helix?

a. A left-handed helix with ~3.6 residues per turn

b. A right-handed helix with ~3.6 residues per turn

c. A left-handed helix with ~3.0 residues per turn

d. A right-handed helix with ~3.0 residues per turn

In which secondary structure arrangement does a single residue make TWO hydrogen bonds with the SAME residue?

a. Alpha helix

b. 3 10 helix

c. Parallel beta strands

d. Antiparallel beta strands

Ramachandran maps are similar for all amino acids with two exceptions: glycine and proline. How do the Ramachandran maps of these two compare to the general case?

a. Glycine has more allowed conformation, proline has fewer

b. Glycine has fewer allowed conformations, proline has more

c. Both have more allowed conformations

d. Both have fewer allowed conformations

Which of the following are NOT an example of fibrous protein?

a. alpha keratin

b. collagen

c. myoglobin

d. all of the above are fibrous proteins

Which of the following proteins do NOT contain alpha helices?

a. myoglobin

b. collagen

c. alpha keratin

d. triosephosphate isomerase

Which of the following sequences would you expect to find in the CORE of a globular protein?

a. DERST

b. GQERR

c. KYSKT

d. VLFAI

Which of the following statements are TRUE regarding the energetics of globular protein folding?

a. Folded proteins bury hydrophobic residues in the protein core to maximize the entropy of solvent (water)

b. In going from random coil to a folded protein, the entropy of the polypeptide chain decreases

c. The enthalpy changes that occur in protein folding are mostly due to noncovalent interactions

d. All of the above are true 

Which of the following methods is NOT a method for denaturing a folded protein?

a. Addition of urea

b. Decreasing the protein concentration

c. Changing the pH

d. Increasing the temperature

Which of the following experimental methods can NOT be used for protein purification:

a. affinity chromotography

b. tandem mass spectrometry

c. ion exchange chromotography

d. gel filtration

You have a solution containing a mixture of three proteins:

(i) 100 Kda protein with pI = 3
(ii) 100 Kda protein with pI = 7 
(iii) 100 Kda protein with pI = 11

How would you purify protein (iii)?

a. run a gel filtration column, and take the first band

b. run an anion exchange column at pH=9 and take the earliest elution

c. run a gel filtration column, and take the last band

d. run a cation exchange column at pH=9 and take the earliest elution

In size exclusion chromatography, smaller proteins elute through the column:

a. slower than larger proteins

b. faster than larger proteins

c. at the same speed as larger proteins

d. there is not enough information to answer this question

A protein of interest is bound to the matrix of a cation exchange column.  Which of the following techniques would successfully elute this protein from the column?

(i) increase pH above the protein's pI
(ii) decrease pH below the protein's pI
(iii) addition of an ionic salt to the elution buffer

a. (i) only

b. (ii) only

c. both (i) and (iii)

d. both (ii) and (iii)

Which of the following methods is commonly used for determining the sequence of a purified protein?

a. affinity chromotography

b. ion exchange chromotography

c. gel filtration

d. tandem mass spectrometry

A (His)6-tagged protein is bound to the matrix of a nickel column. Which of the following methods can be used to elute the protein from the column?

(i) run a high pH buffer through the column
(ii) run a low pH buffer through the column
(iii) run an imidizole-containing buffer through the column
(iv) run a urea-containing buffer through the column

a. (i) only

b. (ii) only

c. (i) or (iii)

d. (ii) or (iii)

e. (ii), (iii), or (iv)

Chaperones like GroEL/GroES facilitate protein folding by which of the following?

a. Preventing aggregation of proteins trapped in deep local minima of the free energy landscape

b. Modifying the energy landscape of folded protein so that otherwise high-energy states are stabilized

c. Catalyzing the breaking of incorrectly paired disulfide bonds in proteins

d. Catalyzing the formation of trans peptide bonds in proteins

Which enzyme or enzyme family is responsible for correcting incorrectly formed disulfides in misfolded proteins?

a. prolyl isomerase

b. GroEL/GroES

c. heat-shock proteins

d. protein disulfide isomerase

Which of the following symmetries is NOT an example of point symmetry?

a. C symmetry

b. helical symmetry

c. Cubic symmetry

d. icosahedral symmetry

A symmetric assembly is known to contain exactly FOUR identical subunits. Which of the following symmetry groups could the protein adopt?
(i) C2
(ii) C4
(iii) D2
(iv) D4

a. (i) only

b. (i) or (ii)

c. (iii) only

d. (ii) or (iii)

e. (iv) only

Which of the following statements about the "energy landscape model" of protein folding is NOT correct?

a. It provides a resolution of Leventhal's paradox

b. There may be several pathways of intermediate structures in going from an unfolded to a natively folded protein

c. A folding protein explores the majority of all possible conformations before reaching the native state

d. There are stable intermediates corresponding to local minima in the energy landscape

What is the most common symmetry seen in nature?

a. C2

b. C3

c. D2

d. helical

Which of the following statements about amyloid fibrils is NOT true?

a. They primarily consist of beta strands

b. They adopt a helical symmetric arrangement

c. They form rapidly following an initial nucleation event

d. They occur when a natively folded protein aggregates in the cell

Which of the following statements about the differences between myoglobin and hemoglobin is FALSE?

a. hemoglobin consists of four subunits, while myoglobin has one

b. at PO2 = 30 mg Hg, myoglobin binds oxygen at higher affinity than does hemoglobin

c. myoglobin has a sigmoidal oxygen binding curve, while hemoglobin has a hyperbolic binding curve

d. myoglobin binds one heme molecule, while hemoglobin binds four

Which of the following statements about the heme binding sites of hemoglobin is TRUE?

a. upon binding to oxygen, the heme group becomes more planar

b. each heme iron is coordinated by two histidine sidechains

c. upon binding to oxygen, two histidine sidechains coordinate the O2 molecule

d. ALL of the above are true 

Which of the following statements about the allostery of hemoglobin is TRUE?

a. The cooperativity of oxygen binding is largely due to heme-heme interactions between subunits

b. Conformational changes between the R and T state are not believed to contribute to the cooperativity of oxygen binding

c. Cooperativity in oxygen binding gives rise to the sigmoidal oxygen binding curve

d. ALL of the above are true 

Which of the following statements about the interaction of BPG and hemoglobin is TRUE?

a. Oxygen delivery is enhanced at high altitudes by strengthening hemoglobin's affinity to oxygen

b. Oxygen delivery is enhanced at high altitudes by weakening hemoglobin's affinity to oxygen

c. BPG does not weaken or strengthen hemoglobin's affinity to oxygen, but modulates the cooperativity of binding

d. BPG does not weaken or strengthen hemoglobin's affinity to oxygen, but competes with hemoglobin for O2

Which of the following mutations would you expect to be MOST detrimental to hemoglobin's ability to bind oxygen?

a.  (alpha) F8 His -> Leu 

b. (beta) A3 Glu -> Val 

c. (alpha) HC3 Arg -> His 

d. ALL of the above would likely have the same effect on hemoglobin binding to O2

Which of the following statements about the Bohr effect is FALSE?

a. The pH responsiveness of hemoglobin is due to protonation of a histidine residue

b. The Bohr effect increases hemoglobin's ability to deliver oxygen in hypoxic conditions

c. At high pH, hemoglobin has a hyperbolic binding curve 

d. ALL of the above are TRUE 

Which of the following statements about sickle-cell hemoglobin is TRUE?

a. It dramatically weakens the binding of hemoglobin to oxygen 

b. It leads to oxydation of heme to Fe(3+) 

c. It reduces the pH-induced binding affinity changes of hemoglobin to oxygen

d. It involves a mutation far from the site of oxygen binding 

Which of the following statements about the symmetry model of allosteric change in hemoglobin is TRUE?

a. Binding of oxygen at one subunit increases oxygen affinity at neighboring subunits

b. Under this model, it is not possible to have a tetramer contain both R and T subunits

c. The model describes cooperativity of hemoglobin binding as largely a change in dynamics rather than in conformation

d. ALL of the above are true 

Catalysts primarily work by:

a. providing additional kinetic energy for a substrate to overcome free energy barriers

b. increasing the free energy of the substrate 

c. stablizing the transition state of a reaction 

d. decreasing the free energy of the product 

In a Lineweaver-Burk plot of a reaction without inhibition, if the x-intercept is -0.02 L/μmol and the y intercept is 0.01 L·min/μmol, what is Km?

a. 2 μmol/L 

b. 50 μmol/L 

c. 100 μmol/L 

d. 0.5 μmol/L 

In a Lineweaver-Burk plot of a reaction without inhibition, if the x-intercept is -0.02 L/μmol and the y intercept is 0.01 L·min/μmol, what is Vmax?

a. 0.5 μmol/(L·min) 

b. 2 μmol/(L·min) 

c. 50 μmol/(L·min) 

d. 100 μmol/(L·min) 

In the case of competitive inhibition, which of the following statements about the Lineweaver-Burk plot is TRUE?

a. The slope does not change as inhibitor is added 

b. The intersection point as inhibitor is added is given by [-1/α, 1/α]

c. The y intercept does not change as inhibitor is added

d. The x intercept does not change as inhibitor is added

In the case of uncompetitive inhibition, which of the following statements about the Lineweaver-Burk plot is TRUE?

a. The slope does not change as inhibitor is added 

b. The x intercept does not change as inhibitor is added

c. The y intercept does not change as inhibitor is added

d. The intersection point as inhibitor is added is given by [-1/α', 1/α']

If a Lineweaver-Burk plot of a reaction is not linear, which of the following is TRUE?

a. The reaction is performed with a competative inhibitor

b. The reaction is performed with an uncompetative inhibitor

c. The reaction is performed with a mixed inhibitor 

d. The reaction does not obey Michaelis-Menton kenetics