BIOC 384 TEST PAPER QUESTIONS AND ANSWERS
GRADED A+
the TRUE statement below regarding the melting temperature (Tm) of DNA.
1. The melting temperature is the temperature at which every DNA molecule is half
denatured to the single-stranded state and half folded in the double stranded state.
2. The melting temperature is the temperature at which half of the DNA molecules are
denatured to the single-stranded state, and half of the molecules are double stranded.
3. The melting temperature of DNA occurs at the midpoint of a plot of DNA
concentration vs. absorbance.
4. The melting temperature of DNA occurs at the midpoint of a plot of temperature vs.
substrate concentration. - ✔✔Half of the DNA mols are denatured
✔✔The restriction enzymes EcoRI and MfeI have recognition sequences and cleavage
products as shown.
Can DNA cleavage products from an EcoRI reaction be specifically ligated (joined) to
cleavage products from an MfeI reaction?
1. No, since both enzymes generate complementary ends, their products cannot be
specifically ligated together.
2. No, since the recognition sequences are not the same, their products cannot be
specifically ligated together.
3. Yes, since both enzymes have the same recognition sequences, their products can
be specifically ligated together
4. Yes, since both enzymes generate complementary overhangs, their products can be
specifically ligated together. - ✔✔Yes, both enzymes have complementary overhangs
✔✔If a Glu sidechain is in a hydrophobic environment, would you expect that the pKa of
this sidechain would be higher or lower than the pKa for the sidechain in aqueous
solution?
Higher or Lower - ✔✔Lower
✔✔The catalytic activity of an enzyme requires that the side chain of a specific histidine
residue be in its conjugate base form in order to act as a proton acceptor. That specific
His side chain in the protein has a pKa of 6.5.
For this imidazole group, what is the base/acid ratio at pH 7.5?
10
,0.1
none of the above
0
1 - ✔✔10
✔✔The conjugate base form of the His side chain carries what charge at pH 9.0?
(Assume the pKa of this side chain is 6.5)
1. Negatively charged
2. Positively charged
3. Half positively charged, half negatively charged
4. Neutral - ✔✔Neutral
✔✔A short polypeptide has the following phi/psi angles. What can you conclude about
this polypeptide's secondary structure?
1. It has an irregular structure with no identifiable secondary structure elements.
2. It is in a beta-conformation.
3. It is a combination of alpha-helix and beta-conformations.
4. It is a right-handed alpha-helix. - ✔✔Right handed alpha helix
✔✔The primary structure of a protein results from a combination of the hydrophobic
effect, electrostatic interactions, and hydrogen bonds.
True or False - ✔✔False
✔✔Select the correct amino acid sequence for the peptide shown.
1. Phe-Gly-Pro-Ser-Lys-Thr
2. Phe-Ala-Val-Cys-Lys-Asn
3. Phe-Ala-Thr-Ser-Arg-Ile
4. Tyr-Ala-Gly-Ser-Arg-Met
5. His-Ala-Val-Asn-Met-Trp - ✔✔Phe-Ala-Val
✔✔A protein with a pI of 8.1 will be positively charged at pH 5.4.
, True or False - ✔✔True
✔✔The following sequence of amino acids is known to form a stable alpha helix in a
protein:
Glu-Ser-Ile-Arg-Thr-Val-Glu
A mutation that results in a change of the Arg residue to an Asp residue would most
likely:
1. Have no effect on the stability of the helical structure
2. Destabilize the helix due to electrostatic repulsion
3. Make the helix a more stable structure due to favorable ionic interactions. -
✔✔Destabilize the helix
✔✔Protein folding occurs primarily due to a process called the hydrophobic effect.
Which statement about the hydrophobic effect is NOT true?
1. Polar and charged amino acid side chains are typically oriented towards the aqueous
solvent due to their ability to hydrogen bond with water.
2. Hydrophobic side chains are buried in the interior of the protein resulting in an
increase in the entropy of the aqueous solvent.
3. Hydrophobic side chains are localized in the interior of the protein, resulting in a
greater entropy for these side chains as they pack together. - ✔✔Hydrophobic side
chains are localized
✔✔Red blood cells lack mitochondria and so the levels of ATP and ADP may be altered
relative to their values in other cells. Assume a red blood cell has the internal
concentrations
[ATP]=1X10-3 M
[ADP]=4X10-3M
[Pi]=10X10-3M
Determine the value of deltaG for ATP hydrolysis at 25 degrees Celcius and pH 7 with
these concentrations.
The standard free energy change for hydrolysis of ATP is -30.5 kJ/mol
+48 kJ/mol
-48 kJ/mol
+38.5 kJ/mol
-38.5 kJ/mol
GRADED A+
the TRUE statement below regarding the melting temperature (Tm) of DNA.
1. The melting temperature is the temperature at which every DNA molecule is half
denatured to the single-stranded state and half folded in the double stranded state.
2. The melting temperature is the temperature at which half of the DNA molecules are
denatured to the single-stranded state, and half of the molecules are double stranded.
3. The melting temperature of DNA occurs at the midpoint of a plot of DNA
concentration vs. absorbance.
4. The melting temperature of DNA occurs at the midpoint of a plot of temperature vs.
substrate concentration. - ✔✔Half of the DNA mols are denatured
✔✔The restriction enzymes EcoRI and MfeI have recognition sequences and cleavage
products as shown.
Can DNA cleavage products from an EcoRI reaction be specifically ligated (joined) to
cleavage products from an MfeI reaction?
1. No, since both enzymes generate complementary ends, their products cannot be
specifically ligated together.
2. No, since the recognition sequences are not the same, their products cannot be
specifically ligated together.
3. Yes, since both enzymes have the same recognition sequences, their products can
be specifically ligated together
4. Yes, since both enzymes generate complementary overhangs, their products can be
specifically ligated together. - ✔✔Yes, both enzymes have complementary overhangs
✔✔If a Glu sidechain is in a hydrophobic environment, would you expect that the pKa of
this sidechain would be higher or lower than the pKa for the sidechain in aqueous
solution?
Higher or Lower - ✔✔Lower
✔✔The catalytic activity of an enzyme requires that the side chain of a specific histidine
residue be in its conjugate base form in order to act as a proton acceptor. That specific
His side chain in the protein has a pKa of 6.5.
For this imidazole group, what is the base/acid ratio at pH 7.5?
10
,0.1
none of the above
0
1 - ✔✔10
✔✔The conjugate base form of the His side chain carries what charge at pH 9.0?
(Assume the pKa of this side chain is 6.5)
1. Negatively charged
2. Positively charged
3. Half positively charged, half negatively charged
4. Neutral - ✔✔Neutral
✔✔A short polypeptide has the following phi/psi angles. What can you conclude about
this polypeptide's secondary structure?
1. It has an irregular structure with no identifiable secondary structure elements.
2. It is in a beta-conformation.
3. It is a combination of alpha-helix and beta-conformations.
4. It is a right-handed alpha-helix. - ✔✔Right handed alpha helix
✔✔The primary structure of a protein results from a combination of the hydrophobic
effect, electrostatic interactions, and hydrogen bonds.
True or False - ✔✔False
✔✔Select the correct amino acid sequence for the peptide shown.
1. Phe-Gly-Pro-Ser-Lys-Thr
2. Phe-Ala-Val-Cys-Lys-Asn
3. Phe-Ala-Thr-Ser-Arg-Ile
4. Tyr-Ala-Gly-Ser-Arg-Met
5. His-Ala-Val-Asn-Met-Trp - ✔✔Phe-Ala-Val
✔✔A protein with a pI of 8.1 will be positively charged at pH 5.4.
, True or False - ✔✔True
✔✔The following sequence of amino acids is known to form a stable alpha helix in a
protein:
Glu-Ser-Ile-Arg-Thr-Val-Glu
A mutation that results in a change of the Arg residue to an Asp residue would most
likely:
1. Have no effect on the stability of the helical structure
2. Destabilize the helix due to electrostatic repulsion
3. Make the helix a more stable structure due to favorable ionic interactions. -
✔✔Destabilize the helix
✔✔Protein folding occurs primarily due to a process called the hydrophobic effect.
Which statement about the hydrophobic effect is NOT true?
1. Polar and charged amino acid side chains are typically oriented towards the aqueous
solvent due to their ability to hydrogen bond with water.
2. Hydrophobic side chains are buried in the interior of the protein resulting in an
increase in the entropy of the aqueous solvent.
3. Hydrophobic side chains are localized in the interior of the protein, resulting in a
greater entropy for these side chains as they pack together. - ✔✔Hydrophobic side
chains are localized
✔✔Red blood cells lack mitochondria and so the levels of ATP and ADP may be altered
relative to their values in other cells. Assume a red blood cell has the internal
concentrations
[ATP]=1X10-3 M
[ADP]=4X10-3M
[Pi]=10X10-3M
Determine the value of deltaG for ATP hydrolysis at 25 degrees Celcius and pH 7 with
these concentrations.
The standard free energy change for hydrolysis of ATP is -30.5 kJ/mol
+48 kJ/mol
-48 kJ/mol
+38.5 kJ/mol
-38.5 kJ/mol
