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BIO 3100
Key Lecture Exam I-A
February 11, 2016
1. Which of the following is true about the two molecules shown below?

(a) They have same configuration

(b) They are cis-trans isomers
(c) They are enantiomers
(d) They have a chiral center
(e) C and D
2. The synthesis of a polypeptide chain from simple amino acid precursor
molecules:
(a) Is accompanied by a decrease in entropy
(b) Is against first law of thermodynamics
(c) Requires an input of free energy
(d) All of the above
(e) A and C
3. Which of the following is true about the two molecules shown below?

(a) They are different conformations formed due to freedom of rotation

about C=C double bond
(b) The carbon double bonds in each are chiral centers.
(c) They are different configurations formed due to rigidity of C=C
double bond
(d) They can be interconverted without breaking any covalent bonds
4. Synthesis of nucleotides, which are small molecule building blocks of
nucleic acids, takes place in every living organism from bacteria to

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humans. Based on this information, which of the following statements is

true:
(a) Biosynthesis of nucleotides is a primary metabolic pathway
(b) Biosynthesis of nucleotide in cells represent a secondary metabolic
pathway
(c) Nucleotides are macromolecules
(d) Tryptophan is a nucleotide
5. On a field trip to Yellowstone National Park, a researcher isolated a
unicellular microbe from hot springs that did not have a well-defined
nucleus and lacked the membrane-bound organelles. Further analysis
revealed that the transcription and translation machineries of the microbe
were unlike that of bacteria, but were more like that of eukaryotes. The
isolated microbe is likely:
(a) A eubacteria
(b) An archaea
(c) A fungi
(d) A protista
(e) None of the above
6. Which of the following is a list of organelles?

(a) Mitochondria, chromatin, chloroplast

(b) Golgi bodies, lysosomes, plasma membrane
(c) Cell wall, peroxisomes, lysosomes
(d) Mitochondria, chloroplast, golgi bodies
(e) All of the above
7. Which one of the following has the cellular components arranged in order
of increasing size?
(a) Amino acid < protein < mitochondrion < ribosome
(b)
Amino acid < protein < ribosome < mitochondrion
(c) Amino acid < ribosome < protein < mitochondrion
(d)Protein < amino acid < mitochondrion < ribosome
(e) Protein < ribosome < mitochondrion < amino acid
8. Which of these statements about hydrogen bonds is not true?
(a) Hydrogen bonds account for the anomalously high boiling point of
water.
(b) In liquid water, the average water molecule forms hydrogen bonds
with three to four other water molecules.
(c) Individual hydrogen bonds are much weaker than covalent bonds.
(d)
Individual hydrogen bonds in liquid water exist for many
seconds and sometimes for minutes.
(e) The strength of a hydrogen bond depends on the linearity of the
three atoms involved in the bond.

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9. Proline residues play an important role in folding of polypeptides because:

(a) peptide bonds involving proline have a relatively higher
tendency to be in cis configuration
(b) peptide bonds involving proline have a relatively higher tendency to
be in trans configuration
(c) proline can form disulfide bonds with cysteine
(d) All of the above
(e) None of the above
10. What is the concentration of H+ in a solution of 0.001M NaOH?
(a) 0.01M
(b) 2 M
(c) 10-12 M
(d) 10-11 M
11. A true statement about hydrophobic interactions is that they:
(a) Are the driving force in the formation of micelles of
amphipathic compounds in water
(b) Do not contribute to the structure of water-soluble proteins
(c) Are stronger than covalent bonds
(d) Involve the ability of water to denature proteins
(e) Primarily involve the effect of polar solutes on the entropy of
aqueous systems
12. Which of the following statement is true about the amino acid shown
below:

(a)
(b)

It is one of the 20 standard amino acids in proteins

The hydroxyl group is added to this amino acid at 5-C position
after its incorporation into the polypeptide chain
(c)
It is a constituent of collagen
(d)
A and B only
(e)
B and C only
13. The pKa value of compound A is 5.0, while that of compound B is 7.0.
What is the difference in proton-donating capacities of two compounds:
(a) Proton-donating capacity of A is 10 times more than that of B
(b) Proton-donating capacity of B is 100 times more than that of A
(c) Proton-donating capacity of A is 100 times more than that of B
(d) There is no difference in proton-donating capacity of two
compounds

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14. Van der Waals interactions are possible:

(a) Between any two uncharged atoms that are 5 Ao apart or less
(b) Between any two polar, uncharged hydrophilic groups that are 100
Ao apart or more
(c) Between an anion and a cation that are completely hydrated by
water molecules
(d) All of the above
(e) None of the above
15. Which of the following statements about buffers is true?
(a) At pH values lower than the pKa, the salt concentration is higher
than that of the acid.
(b)The pH of a buffered solution remains constant no matter how
much acid or base is added to the solution.
(c) The strongest buffers are those composed of strong acids and
strong bases.
(d)
When pH = pKa, the weak acid and salt concentrations in
a buffer are equal.
16. The properties that make water the molecule of life include:
(a) It is a good solvent for polar and charged solutes
(b) It allows buffering action
(c) It supports weak interactions that are crucial for maintaining the
biologically active conformation of a number of macromolecules
(d) It is the driving force of hydrophobic interactions
(e) All of the above
17. Which of the following is true about pKa:
(a) pKa is the pH at which an acid or base is half dissociated
(b) pKa is the negative log of Ka
(c) pKa is the pH at which a conjugate acid-base pair system exhibits
maximum buffering capacity
(d) All of the above
(e) A and C only
18. Topoisomerase is an enzyme that is composed of 6 different polypeptides.
It has a globular structure. The active site of the enzyme has a
permanently attached Mg2+ion. Based on this information, which of the
following statements are true:
(a) Topoisomerase is a fibrous protein
(b) Topoisomerase is a conjugated protein
(c) Topoisomerase has a quaternary structure
(d) All of the above
(e) B and C only

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19. What observation led Linus Pauling and Robert Corey to conclude that
peptide bond has a partial double bond character?
(a) Bond length of C-N peptide bond
(b) Electron delocalization
(c) Resonance
(d) Rigidity of peptide bond
(e) B, C and D
20. Which of the following is true about the titration curves of solutions of
weak acids like acetic acid?

(a) The pH for optimal buffering power of a weak acid is always 7.00.
(b) You can calculate the pKa of an acid, given the pH and the
molar ratio of the acid and its conjugate base.
(c) The pKa of a weak acid is the pH at which the acid is completely
dissociated.
(d) At a pH below the pKa of a weak acid, its conjugate base will
predominate.
21. The principal form of an amino acid under physiological conditions is:
(a)
Acid form
(b)
Base form
(c)
Zwitter ion form
(d)
Unionized form
22. An amino acid strongly absorb in in the UV range (Amax ~ 280 nm). It has
an aromatic, weekly ionizable R-group. In all probability, this amino acid is:
(a) Phenylalanine
(b) Tyrosine
(c) Tryptophan
(d) All of the above
(e) B and C

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23. Titration of asparagine by a strong base, for example NaOH, reveals two
pKs. The titration reaction occurring at pK2 (pK2 = 8.8) is:
(a) COOH + OH
COO + H2O
(b)COOH + NH2
COO + NH2+
(c) COO + NH2+
COOH + NH2
+

(d)
NH3 + OH

NH2 + H2O

(e) NH2 + OH
NH + H2O
24. A protein retained on an affinity chromatography column is usually eluted
off the column by:
(a) gradually increasing the salt concentration of the elution buffer
(b) adding the protein's free ligand
(c) applying electric field to the column
(d) allowing the retained protein to naturally come off the column after the nonspecifically bound proteins have first passed through the resin.
25. What is the highest level of structural organization in collagen?
(a) Primary
(b) Secondary
(c) Tertiary
(d) Quaternary
26. Which of the following is correct with respect to the amino acid
composition of proteins?
(a) Larger proteins have a more uniform distribution of amino acids
than smaller proteins.
(b) Proteins contain at least one each of the 20 different standard
amino acids.
(c) Proteins with different functions usually differ significantly in
their amino acid composition.
(d) Proteins with the same molecular weight have the same amino acid
composition.
(e) The average molecular weight of an amino acid in a protein
increases with the size of the protein.
27. A protein binds very tightly to a cation exchanger and can be eluted from
the column only at extremely high ionic strength. On the basis of this
information, what can be concluded about the amino acid composition of
this protein?
(a)
It is rich in phenylalanine, isoleucine and valine
(b)
It is rich in lysine, arginine and histidine
(c)
It is rich in aspartic acid and glutamic acid
(d)
It is rich in proline and glycine

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28. In size exclusion chromatography, only those proteins get fractionated on

the basis of their size, which:
(a) Get excluded from the beads
(b) Get included into the beads
(c) Get crosslinked to the beads
(d) Get immobilized on the beads
29. The R group of which of the following amino acids has a strong tendency
to form H-bonds?
(a) Phenylalanine
(b) Isoleucine
(c) Asparagine
(d) Glycine

(a)
(b)
(c)
(d)

30. Which of the following is not true about SDS polyacrylamide gel
electrophoresis of proteins?
It separates proteins using an electric field
It makes the net charge equal on all proteins
Larger proteins move faster in the gel than smaller proteins
It separates proteins that differ in molecular weight.
31. Which of the following types of electrophoresis are you going to use to
analyze total proteins in a cell?
(a) Isoelectric focusing
(b) SDS-PAGE
(c) Two-dimensional-PAGE
(d) A and B
(e) B and C
32. The average molecular weight of the 20 standard amino acids is 138, but
biochemists use 110 when estimating the number of amino acids in a
protein of known molecular weight. Why?
(a) The number 110 is based on the fact that the average molecular
weight of a protein is 110,000 with an average of 1000 amino acids.
(b)
The number 110 reflects the higher proportion of small
amino acids in proteins, as well as the loss of water when the
peptide bond forms.
(c) The number 110 reflects the number of amino acids found in the
typical small protein, and only small proteins have their molecular
weight estimated this way.
(d)The number 110 takes into account the relatively small size of
nonstandard amino acids.
(e) The number 138 represents the molecular weight of conjugated
amino acids.

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33. Which of the following is true about glycine?

(a) It is an imino acid
(b) It frequently occurs in -turns
(c) It cannot exist L- and D- configurations
(d) All of the above
(e) B and C only
34. The major reason that antiparallel -stranded protein structures are more
stable than parallel -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 fewer lateral hydrogen bonds than antiparallel strands.
(e) have weaker hydrogen bonds laterally between adjacent
strands
35. Fibrous proteins differ from globular proteins in that
(a) fibrous proteins tend to serve structural functions, and
globular proteins are more likely to be enzymes
(b) fibrous proteins can often contain several types of secondary
structures, whereas globular proteins usually consist largely of a
single type of secondary structure
(c) globular proteins are insoluble in water, and fibrous proteins are
usually soluble
(d) globular proteins are more likely than fibrous proteins to have an
elaborate quaternary structure.
36. In a region of polypeptide, residue n is interacting with residue n+3 by Hbonds between backbone carbonyl and NH groups. The residues n+1
and n+2 are glycine and proline. What is the secondary structure in this
region of polypeptide?
(a) -helix
(b) -sheet
(c) -turn
(d) None of the above
37. Which of the following statements is true about the tertiary structure of a
protein in aqueous solution:
(a) Hydrophilic residues are inside and hydrophobic residues are
outside
(b) Hydrophilic residues are outside and hydrophobic residues
are inside
(c) Both hydrophilic and hydrophobic residues are present on the
surface as well as in the interior of protein
(d) All of the above
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38. In the diagram below, the plane drawn behind the peptide bond indicates
the:

(a) absence of rotation around the CN bond because of its partial doublebond character.
(b) plane of rotation around the CN bond.
(c) region of steric hindrance determined by the large C=O group.
(d) region of the peptide bond that contributes to a Ramachandran plot.
(e) theoretical space between 180 and +180 degrees that can be occupied
by the and angles in the peptide bond.
39. In a region of polypeptide, there are helical repeats with 3.6 residues per
turn of the helix and translational rise of 1.5 Ao. What is the secondary
structure in this region of polypeptide:
(a) -helix
(b) -conformation
(c) -turn
(d) collagenhelix
40. Which of the following is not true about a polypeptide chain:
(a) A polypeptide chain starts with N-terminus and ends with Cterminus
(b) A polypeptide chain has a main chain and a number of side chains
(c) A polypeptide chain is made up of residues
(d) The sequence of amino acids in a polypeptide chain reflects
its secondary structure
41. The difference between H-bond and salt bridge is that:
(a) In H-bond, both donor and acceptor are partially negatively charged
while in salt bridge they are partially positively charged
(b) In H-bond, both donor and acceptor are partially negatively charged
while in salt bridge they are completely positively charged
(c) In H-bond, both donor and acceptor are partially negatively
charged while in salt bridge they are completely negatively
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(d) In H-bond, both donor and acceptor are partially positively charged
while in salt bridge they are completely positively charged
42. Tertiary structure of proteins differ from quaternary structure in that:
(a) Tertiary structure is due to interaction of residues far apart on the
same polypeptide while quaternary structure is due to interaction of
residues on different polypeptides
(b) Tertiary structure is present in all globular proteins while quaternary
structure is present in only multi-subunit proteins
(c) All of the above
(d) None of the above
43. 3-dimensional structure of myoglobin obtained by X-ray diffraction
analysis demonstrated that:
(a) corners between -helical regions invariably lacked proline
residue.
(b)highly polar or charged amino-acid residues tended to be located
interiorally.
(c) myoglobin was completely different from hemoglobin, as expected.
(d)the structure was very compact, with virtually no internal
space available for water.
(e) the helix predicted by Pauling and Corey was not found in
myoglobin.
44. Which of the following is true about domains and motifs:
(a) They are supersecondary structures
(b) Domains maintain their structure and function when taken out
of their protein context, while motifs do not
(c) Motifs maintain their structure and function when taken out of their
protein context, while domains do not
(d) All of the above
(e) None of the above
45. When Anfinsen dialyzed denatured ribonuclease to remove urea in the
presence of traces of 2-ME, ribonuclease slowly regained its native three
dimensional structure and enzymatic activity. On the basis of this
experiment, Anfinsen concluded that:
(a) Ribonuclease can be renatured
(b) Primary structure of a polypeptide chain contains all the
information required to fold the chain into its native, threedimensional structure
(c) Dialysis can remove urea from protein
(d) The higher order structure of a protein is independent of its primary
structure
46. Which of the following is true about disulfide bonds?
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(a) They are formed by oxidation of two cysteine residues located

on the same or different polypeptides
(b) They are generally present in intracellular proteins
(c) They are weak interaction
(d) They stabilize secondary structure of proteins
47. Which of the following pairs of bonds within a peptide backbone show
free rotation around both bonds?
(a)
CC and NC
(b)C=O and NC
(c) C=O and NC
(d)NC and CC
(e) NC and NC
48. The three-dimensional conformation of a protein may be strongly
influenced by amino acid residues that are very far apart in sequence.
This relationship is in contrast to secondary structure, where the
interacting amino acid residues are:
(a) always side by side.
(b) generally near each other in sequence.
(c) invariably restricted to about 7 of the 20 standard amino acids.
(d)often on different polypeptide strands.
(e) usually near the polypeptide chains amino terminus or carboxyl
terminus.
49. Which of the following statements is false?
(a)
Collagen is a protein in which the polypeptides are
mainly in the -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 conformation.
(e) -keratin is a protein in which the polypeptides are mainly in the helix conformation.
50. Which of the following best represents the backbone arrangement of two
peptide bonds?
(a) CNCCCNCC
(b)CNCCNC
(c) CNCCCN
(d)
CCNCCN
(e) CCCNCCC

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