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Biochemistry 403 > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

2019

Four vitalist statements are listed below. Each time one was disproved, vitalists took refuge in a less general, more restricted statement. Order the four statements from most restrictive to least restrictive.

  • a) The reactions constituting life occur only in living cells.
  • b) The substances composing living matter are qualitatively different from those of the non-living world.
  • c) Structure of “ferments” is too complex to be described in chemical terms, and the nature of catalysis is not comprehensible.
  • d) Organisms arise from non-living matter by spontaneous generation through the intervention of the “vital force.”
A

c, a, d, b

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2
Q

2019

The structure of 11-cis-retinal is shown below. The side chain carbon directly attached to the ring is #7, and the aldehyde carbon is #15. When the molecule isomerizes from cis to trans, for which of the following pairs of atoms would the interatomic distance change?

  • A. a methyl on the ring and carbon 12
  • B. carbon 13 and carbon 15
  • C. a methyl on the ring and the methyl at carbon 9
  • D. a ring carbon and the aldehyde carbon
  • E. more than one of the above
A

D. a ring carbon and the aldehyde carbon

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3
Q

2019

For a cell to convert glucose to acetate or ethanol, it is necessary that

  • A. the cell be able to live in an atmosphere containing molecular oxygen.
  • B. the cell has a nucleus.
  • C. the cell contains chloroplasts.
  • D. the cell contains mitochondria.
  • E. none of the above
A

E. none of the above

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4
Q

2019

A short peptide (an oligopeptide) consists of eleven amino acid residues. Asn and gln are not present. How many water molecules would be required to hydrolyze the oligopeptide to free amino acids? (Adapted from last year’s exam)

  • A. Ten
  • B. Nine
  • C. Eight
  • D. Twenty
  • E. none of these
A

A. Ten

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5
Q

2019

Given the data in the table below, estimate the number of residues in the muscle protein myosin.

  • A. 1100
  • B. 9900
  • C. 4500
  • D. 564,500
  • E. None of these is even close to correct.
A

C. 4500

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6
Q

2019

Which of the following reactions involves dehydration?

  • A. the formation of a polypeptide from amino acids
  • B. oxidation of two sulfhydryl groups to make a disulfide bond C. conversion of sugar molecules into starch
  • D. breakdown of a DNA to single nucleotides
  • E. more than one of the above
A

E. more than one of the above

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7
Q

2019

The enthalpy of dissolving hydrophobic material in water is less than zero, i.e. heat is released to the surroundings when a hydrophobe is shaken with water and some dissolves. Why, then, are hydrophobic materials like olive oil not appreciably soluble in water?

  • A. Hydrophobic substances actively repel water.
  • B. Hydrophobic molecules have a strong attraction for one another, stronger than any attraction they have for water.
  • C. Water molecules have a strong attraction for one another, stronger than any attraction they have for hydrophobes.
  • D. Hydrophobes reduce the number of possible arrangements of water molecules that are near them, an effect that opposes dissolving them in the water.
  • E. none of the above
A

D. Hydrophobes reduce the number of possible arrangements of water molecules that are near them, an effect that opposes dissolving them in the water.

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8
Q

2019

Water molecules have a diameter of approximately 2.8 Å. They are not exactly spherical, though, and the diameter is an average obtained from rotating the molecule through all possible orientations. The Van der Waals radii of hydrogen and oxygen are given in the table below, which was discussed in class. The Van der Waals radius is the closest atoms can come to one another without steric hindrance. The total of the radii does not add up to the approximate diameter, and the difference exceeds experimental error. Why? Van der Waals radii

  • A. Formation of the molecule shrinks the noncovalent radii.
  • B. The approximate diameter describes the closest approach of the oxygens of two water molecules
  • C. Hydrogens do not count in determining the molecular diameter.
  • D. The covalent O-H bond length has not been taken into account in the total value to the left.
  • E. none of the above.

The diagram to the left, also from class, may be helpful. Bear in mind that 1 nm = 10 Å.

A

D. The covalent O-H bond length has not been taken into account in the total value to the left.

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9
Q

2019

If a crystal of sodium chloride were to be placed in water, which of the following factors would NOT favor the dissolving of the crystal?

  • A. the entropy of departure of sodium ions from the crystal
  • B. the change in electrostatic interactions between sodium and chloride ions
  • C. the change in state of water
  • D. electrostatic interactions between the ions and water molecules
  • E. more than one of the above
A

E. more than one of the above

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10
Q

2019

Fully protonated glycine can be purchased as a white crystalline solid. Because it has a net charge of +1, the crystals must contain a compensating negatively charged ion, which is usually chloride. The bottle will be labeled ‘glycine hydrochloride.’ If a 0.1 M solution of glycine hydrochloride were to be prepared, the approximate concentration of gly+1 would be

A. slightly less than 0.1 M

B. 10-2.34 M

C. 10-9.6 M

D. 0.01 M

E. none of these

A

A. slightly less than 0.1 M

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11
Q

2019

Why does citric acid not have a pH at which it would migrate toward a cathode? (This is derived from a question posed on p. 1 of the Polyprotic Molecules hand-out.)

A. Its molecules always carry a negative charge.

B. Its molecules are always uncharged regardless of the pH.

C. Its molecules can never carry a positive charge.

D. It is always combined with an immobile protein molecule

E. more than one of the above

A

C. Its molecules can never carry a positive charge

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12
Q

2019

Why are proteins least soluble at their isoionic pH?

  • A. They do not bind counterions at the isoionic pH.
  • B. At any other pH they repel one another.
  • C. They bind counterions at the isoionic pH.
  • D. They do not bind proteins at the isoionic pH.
  • E. cannot tell from data given.
A

B. At any other pH they repel one another.

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13
Q

2019

DNA in cells is always found in association with other molecules, most of which are proteins. What characteristic of these proteins is primarily responsible for enabling this association?

A. Their shapes are complementary to the shape of the DNA.

B. Their size allows them to wrap around the DNA, fitting it into the cell.

C. Their charge cancels much of the charge on the DNA.

D. They prevent hydrolysis of the DNA to nucleotides.

E. None of the above contributes.

A

C. Their charge cancels much of the charge on the DNA

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14
Q

2019

Most salts, including those found in the cytoplasm of cells, are more soluble in hot water than in cold. If enough potassium chloride were to be dissolved in water at 60 C to make a saturated solution, and the solution were then cooled to 37 C, which of the following reactions would be spontaneous?

A. KClsolution → KClsolid

B. an overall decrease in entropy

C. the dissolving of more KCl

D. a reaction involving a decrease in enthalpy

E. more than one of the above

A

A. KClsolution → KClsolid

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15
Q

2019

It is often the case that molecules must cross membranes from a zone in which their concentration is less than the zone to which they go. Which of the following must be true?

A. The transfer must be coupled to a reaction whose free energy is positive.

B. The transfer must be coupled to a reaction whose free energy is zero.

C. The transfer must be coupled to a reaction whose free energy is negative.

D. Such transfers are not spontaneous and cannot occur.

E. Such transfers are spontaneous and need no “assistance.”

A

C. The transfer must be coupled to a reaction whose free energy is negative.

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16
Q

2019

Which term in the Gibbs equation for free energy is analogous to the pKa in the Henderson-Hasselbalch equation?

A. log([salt]/[acid])

B. ∆G

C. ∆Gº’

D. RT ln [C]c [D]d / [A]a [B]b

E. none of the above

A

C. ∆Gº’

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17
Q

2019

Of the twenty amino acids found in proteins, how many have only atoms of carbon and hydrogen in their side chains?

A. all twenty

B. seven

C. six

D. three

E. none of these is correct

A

B. seven

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18
Q

2019

Which of the reactions in the figure below is driven solely by the entropy?

A. Reaction (a)

B. Reaction (b)

C. Reaction (c)

D. Reactions (a) and (c)

E. Cannot tell from data given.

A

C. Reaction (c)

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19
Q

2019

Which of the following characteristics of an atom other than hydrogen would allow it to participate in a hydrogen bond?

  • A. being bonded only to hydrogens or carbons
  • B. being part of a carbon to carbon double bond
  • C. having unshared pairs of electrons
  • D. being bonded to an oxygen atom
  • E. none of these (From last year’s exam)
A

C. having unshared pairs of electrons

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20
Q

2019

Sulfhydryl groups react with iodoacetic acid according to the following reaction, which we discussed in class: RSH + ICH2COO- → RSCH2COO- + H+ + I- . The group added to the sulfur atom is called a carboxymethyl group. A native protein is reacted with excess iodoacetic acid, whereupon three moles of carboxymethyl groups are found to be bound per mole of protein. In a second experiment a sample of the protein is completely unfolded and reacted with excess mercaptoethanol and then with excess iodoacetic acid. Thirteen moles of carboxymethyl groups are now found to be bound per mole of protein. How many disulfides does the native protein contain?

A. three

B. ten

C. eight

D. four

E. none of these is correct

A

E. none of these is correct

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21
Q

2019

Consider a solution of aspartic acid and lysine. At which pH would they migrate in opposite directions, one moving toward the cathode and one toward the anode? (Hint: remember that asp is acidic, while lys is basic.)

A. pH 2

B. pH 6

C. pH 11

D. all of these

E. none of these B. pH 6

A

B. pH 6

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22
Q

2019

At pH 6.5 ribonuclease has a net charge of +4. At pH 2 it has a net charge of +19. The most likely reason for this change in charge is

  • A. the protonation of 15 lysine side chains.
  • B. the deprotonation of 15 lysine side chains.
  • C. the protonation of 15 glutamic and/or aspartic acid side chains.
  • D. the deprotonation of 15 glutamic and/or aspartic acid side chains.
  • E. None of these could account for the change. (You may want to look at the table of pKa values at the end of this section of the exam.)
A

C. the protonation of 15 glutamic and/or aspartic acid side chains.

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23
Q

2019

Consider a carbon atom which is involved in a double bond to another atom and in single bonds to two other atoms. These four atoms

  • A. form a tetrahedron.
  • B. are co-linear.
  • C. lie in a plane.
  • D. form one half of an enantiomeric pair.
  • E. more than one of these answers is correct
A

C. lie in a plane

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24
Q

2019

Consider a carbon atom which is involved in single bonds to four other atoms, each of which is different from the others. These atoms

  • A. form a tetrahedron.
  • B. are co-linear.
  • C. lie in a plane.
  • D. form one half of an enantiomeric pair.
  • E. more than one of these answers is correct
A

E. more than one of these answers is correct

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25
Q

2019

What is the approximate pH of 10-10 M NaOH?

  • A. 10
  • B. 3
  • C. 14
  • D. 7
  • E. cannot tell from data given
A

D. 7

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26
Q

2019

When protein sequences from many species are studied, it is found that fibrinopeptides, which arise from hydrolysis of fibrinogen, show one amino acid difference per 100 residues every 2.1 million years. Hemoglobin, in contrast, requires 6.1 million years to show one amino acid change per 100 residues, while cytochrome c requires 21.4 million years for one such change. Which of the following is most likely to explain these results?

  • A. Mutations arise at different rates in the three proteins.
  • B. The proteins mutate at the same rate, but relatively few mutations are lethal in the fibrinopeptides, whereas most are lethal in cytochrome c, lethality in hemoglobin falling in between.
  • C. The three proteins arose on different branches of the evolutionary tree.
  • D. Cytochrome c interacts with many other different proteins, while hemoglobin interacts with a few small molecules, and the fibrinopeptides interact randomly with one another to make blood clots
  • E. more than one of the above.
A

E. more than one of the above.

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27
Q

2019

In class we examined the presence of glucose in the active site of hexokinase, the enzyme which catalyzes the first step of glycolysis. In this reaction the parts of a water molecule are removed from the glucose and the ATP to make glucose-6-phosphate. Imagine a mutant of hexokinase in which an alanine in the bottom of the active site is replaced by a leucine. What would be the likely effect on the reaction?

  • A. The mutation would cause the reaction to go faster because the isoleucine would push the product out of the site.
  • B. The active site is so big that the mutation wouldn’t matter, so there would be no effect.
  • C. The mutation would replace a large amino acid by a smaller one, so the glucose would be trapped and be unable to get out as glucose-6-phosphate.
  • D. The isoleucine would fill part of the site, causing the glucose to bind less well, thereby slowing or completely preventing reaction with the ATP.
  • E. None of the above.
A

D. The isoleucine would fill part of the site, causing the glucose to bind less well, thereby slowing or completely preventing reaction with the ATP.

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28
Q

2019

Some proteins contain no phenylalanine, no tyrosine and no tryptophan. Could the concentration of such a protein be determined by the absorbance at 280 nm using the Beer-Lambert law?

  • A. Yes, like any other protein
  • B. No.
  • C. Only at very high concentrations
  • D. It would depend on what other amino acids are present in the protein.
  • E. None of the above.
A

B. No.

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29
Q

2019

The annelid worm Glycera dibranchiata has an oxygen binding protein with the same folding pattern as myoglobin. Myoglobins and hemoglobins occur sporadically among invertebrate phyla. It is hard to see a clear, common line of descent from a single ancestor for these species let alone for annelids, insects and vertebrates. No other known protein form has oxygen binding capability. How might these observations best be explained?

  • A. The myoglobin fold evolved independently for the various evolutionary lines of descent.
  • B. The myoglobin fold evolved before the divergence of annelids, insect and vertebrates.
  • C. Some species since the divergence of annelids, insect and vertebrates lost the myoglobin fold, as they lived in ecological niches which did not require it.
  • D. B followed by C
  • E. All the above are plausible.
A

E. All the above are plausible.

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30
Q

2017

Which of the following vitalist statements was disproved by J. B. Sumner’s crystallization of the enzyme urease in 1926?

  • A. Structure of “ferments” is too complex to be described in chemical terms, and the nature of catalysis is not comprehensible.
  • B. The substances composing living matter are qualitatively different from those of the non-living world.
  • C. We may be able to make some of the substances of living matter, but the reactions constituting life occur only in living cells.
  • D. Living matter may be like non-living, but organisms arise from non-living matter by spontaneous generation through the intervention of the “vital force.”
  • E. none of the above
A

A. Structure of “ferments” is too complex to be described in chemical terms, and the nature of catalysis is not comprehensible.

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31
Q

2017

How many of the 20 standard amino acids have one or more atoms of nitrogen in their SIDE chains?

  • A. None
  • B. Four
  • C. Five
  • D. Seven
  • E. None of these is correct
A

E. None of these is correct

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32
Q

2017

How many hydrogen atoms are there in the side chain of isoleucine?

  • A. Three
  • B. Five
  • C. Seven
  • D. Nine
  • E. None of these is correct
A

D. Nine

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33
Q

2017

Consider the figure below, which is from the notes. How many of the carbon atoms in the figure have tetrahedral geometry of their bonds? Do not count the structures which have dots to represent electrons

  • A. Three
  • B. Five
  • C. Seven
  • D. Nine
  • E. None of these is correct
A

B. Five

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34
Q

2017

E. coli DNA contains about 4.6 million characters (nucleotides) and weighs approximately 10-10 g. Human DNA has 3.3 x 109 base pairs. If human DNA were to have the same information density as E. coli, what would be the weight in grams of the human genome? (Count a base pair as a single unit of information.)

  • A. 4.6 x 10-15 g
  • B. 3.3 x 109 g
  • C. 7.2 x 10-7 g
  • D. 1.4 x 10-6 g
  • E. Cannot tell from data given
A

C. 7.2 x 10-7 g

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35
Q

2017

A short peptide (an oligopeptide) consists of ten amino acid residues. Asn and gln are not present. How many water molecules would be required to hydrolyze the oligopeptide to free amino acids? (Adapted from last year’s exam)

  • A. Ten
  • B. Nine
  • C. Eight
  • D. Twenty
  • E. none of these
A

B. Nine

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36
Q

2017

Which of the reactions in the figure below is driven solely by the enthalpy?

A. Reaction (a)

B. Reaction (b)

C. Reaction (c)

D. Reactions (a) and (c)

E. Cannot tell from data given.

A

B. Reaction (b)

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37
Q

2017

In which of the following solvents would the attraction between a positively charged group and a negatively charged group be weakest if the distance between the charged is the same in all cases? (ε is the dielectric constant.)

  • A. water, ε = 80
  • B. a vacuum, ε = 1
  • C. gasoline, ε = 4
  • D. methanol, ε = 20
  • E. cannot tell from data given
A

A. water, ε = 80

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38
Q

2017

What is the maximum number of hydrogen bonds in which the side chain of serine can participate?

  • A. none
  • B. one
  • C. two
  • D. three
  • E. more than three
A

D. three

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39
Q

2017

Which of the following characteristics of an atom other than hydrogen would allow it to participate in a hydrogen bond?

  • A. being bonded only to hydrogens or carbons
  • B. being part of a carbon to carbon double bond
  • C. having unshared pairs of electrons
  • D. being bonded to an oxygen atom
  • E. none of these
A

C. having unshared pairs of electrons

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40
Q

2017

Which of the following amino acids will stick to an anion exchanger if the pH equals the amino acid’s pI?

  • A. glycine
  • B. alanine
  • C. aspartic acid
  • D. arginine
  • E. none of these will stick
A

E. none of these will stick

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41
Q

2017

The absorbance of a buffered solution of “A” is measured under several conditions. In which of the following would it have the lowest absorbance?

  • A. in a 1 cm cell
  • B. in a 2 cm cell
  • C. in a 1 mm cell after its concentration has been doubled
  • D. in a 1 cm cell after an equal volume of buffer has been added
  • E. two of the above
A

C. in a 1 mm cell after its concentration has been doubled

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42
Q

2017

Sulfhydryl groups react with iodoacetic acid according to the following reaction, which we discussed in class:

RSH + ICH2COO- → RSCH2COO- + H+ + I-

The group added to the sulfur atom is called a carboxymethyl group. A native protein is reacted with excess iodoacetic acid, whereupon three moles of carboxymethyl groups are found to be bound per mole of protein. In a second experiment a sample of the protein is completely unfolded and reacted with excess mercaptoethanol and then with excess iodoacetic acid. Eleven moles of carboxymethyl groups are now found to be bound per mole of protein. How many disulfides does the native protein contain?

  • A. three
  • B. eleven
  • C. eight
  • D. four
  • E. none of these is correct
A

D. four

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43
Q

2017

At pH 2 ribonuclease has a net charge of +19. At pH 6.5 it has a net charge of +4. The most likely reason for this change in charge as the pH is raised from 2 to 6.5 is

  • A. the protonation of 15 lysine side chains.
  • B. the deprotonation of 15 lysine side chains.
  • C. the protonation of 15 glutamic and/or aspartic acid side chains.
  • D. the deprotonation of 15 glutamic and/or aspartic acid side chains.
  • E. None of these could account for the change.

(You may want to look at the table of pKa values at the end of this section of the exam.)

A

D. the deprotonation of 15 glutamic and/or aspartic acid side chains.

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44
Q

2017

Imagine that two aspartic acid residues are close to one another on the surface of a protein, where they interact with one another and the surrounding aqueous solvent. One loses its side chain COOH proton to the solvent. All other factors being equal, what effect will this have on the pKa of the second aspartic acid side chain?

  • A. Its pKa will be higher than normal.
  • B. Its pKa will be unchanged by the first asp’s dissociation.
  • C. Its pKa will be lower than normal.
  • D. The second asp’s carboxyl will become more acidic.
  • E. Cannot tell from data given
A

A. Its pKa will be higher than normal.

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45
Q

2017

The pH of a sample of blood is 7.4, while gastric juice is pH 1.4. The blood sample has:

  • A. 0.189 times the [H+] as the gastric juice.
  • B. 5.29 times lower [H+] than the gastric juice.
  • C. 6 times lower [H+] than the gastric juice.
  • D. 6,000 times lower [H+] than the gastric juice.
  • E. a million times lower [H+] than the gastric juice.
A

E. a million times lower [H+] than the gastric juice.

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46
Q

2017

Why are gaps introduced into alignments of protein sequences from multiple species?

  • A. They allow for residues whose identity was not determined in the sequencing experiment.
  • B. They show positions in which the polypeptide chain is broken into two sequences.
  • C. They maximize the degree of sequence identity or similarity among the species.
  • D. They are an aid in establishing evolutionary relationships among species.
  • E. More than one of the above.
A

E. More than one of the above.

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47
Q

2017

If the partial charge on the oxygen atom of a water molecule were -0.1 unit, the partial charge on each of its hydrogen atoms would be

  • A. +0.01 unit
  • B. +0.05 unit
  • C. +0.1 unit
  • D. +0.2 units
  • E. none of these
A

B. +0.05 unit

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48
Q

2017

  1. Forming a charged group in aqueous solution from a neutral group causes formation of a hydration sphere of water molecules around the charges, among other effects. The formation of this hydration sphere
  • A. involves a reduction in entropy of the water if other effects are ignored.
  • B. involves an increase in entropy of the water if other effects are ignored.
  • C. the change in entropy of the water contributes favorably to the free energy of charge formation.
  • D. the change in entropy of the water contributes unfavorably to the free energy of charge formation.
  • E. more than one of the above.
A

E. more than one of the above

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49
Q

2017

Which of the following is best described as an entropy driven reaction?

  • a) ∆H = -82 kJ/mol, -T∆S = -136 kJ/mol
  • b) ∆H = -1367 kJ/mol, -T∆S = +41 kJ/mol
  • c) ∆H = +110 kJ/mol, -T∆S = -140 kJ/mol
  • d) none of the above is entropy driven
  • e) all the above are entropy driven
A

c) ∆H = +110 kJ/mol, -T∆S = -140 kJ/mol

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50
Q

2017

Two different types of protein are present in a solution undergoing electrophoresis. Protein X migrates toward the cathode, while protein Y moves toward the anode. Which of the two proteins has the lower isoelectric point?

  • A. Protein X
  • B. Protein Y
  • C. They have the same pI.
  • D. Cannot tell from data given, as it depends on the pH.
A

B. Protein Y

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51
Q

2017

The molecular weight of hemoglobin is 64,500 daltons. A single molecule of the protein contains 574 amino acid residues. The molecular weight of collagen is 336,000 daltons. Estimate the number of amino acid residues in a single molecule of collagen.

  • A. 4,464
  • B. 112
  • C. 585
  • D. 336,000
  • E. 3,000
A

E. 3,000

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52
Q

2017

Consider the table to the right, which was discussed in class. If serum albumin (SA), hemoglobin (Hb) and chymotrypsinogen (CT) were to be applied to a cation exchange column at pH 11 and eluted with a buffer of decreasing pH, in which order would they elute?

  • A. SA, Hb, CT
  • B. CT, Hb, SA
  • C. Hb, CT, SA
  • D. They would all come out together immediately.
  • E. Cannot tell from data given.
A

D. They would all come out together immediately.

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53
Q

2017

If the proteins in the question above were to be applied to an anion exchange column at pH 11 and eluted with a buffer of decreasing pH, in which order would they elute?

  • A. SA, Hb, CT
  • B. CT, Hb, SA
  • C. Hb, CT, SA
  • D. They would all come out together immediately.
  • E. Cannot tell from data given.
A

THIS QUESTION WAS ASKED IN 2017 & 2015. HE HAS 2 DIFFERENT ANSWERS FOR IT ???????

  • 2017: B. CT, Hb, SA
  • 2015: D. They would all come out together immediately
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54
Q

2017

Which of the following observations in the course of protein purification is consistent with the sample being pure?

  • A. A single band is observed on an SDS polyacrylamide gel.
  • B. Additional purification steps leave the specific activity unchanged.
  • C. The protein elutes from a molecular sieve column in a single fraction.
  • D. The protein elutes from an ion exchange co
  • E. All the above are consistent with purity
A

E. All the above are consistent with purity

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55
Q

2017

A peptide is digested with trypsin, yielding three shorter peptides whose sequences are determined by Edman degradation. T1 (tryptic peptide 1) is FSAR. T2 is VAYEK, while T3 is QDWGN. Digestion of a fresh sample of the original peptide with chymotrypsin yields four shorter peptides whose sequences are C1 = EKF, C2 = GN, C3 = VAY and C4 = SARQDW. What is the sequence of the original peptide?

  • A. VAYEKFSARQDWGN
  • B. NGWDQRASFKEYAV
  • C. FSARVAYEKQDWGN
  • D. EKFGNVAYSARQDW correct sequence
  • E. None of these is the
A

A. VAYEKFSARQDWGN

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56
Q

2017

A protein isolated from six species, and the amino acid sequences are aligned. If one reads down one residue position for the six species, one finds the following amino acids: ILLVFI. What property, if any, is conserved at this sequence position? (Give the best possible answer.)

  • A. The position is polar
  • B. There is no conservation at this position.
  • C. Only small amino acids fit in this position
  • D. The position is nonpolar
  • E. None of these describes this position.
A

D. The position is nonpolar

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57
Q

2017

Upon aligning polypeptide sequences of a protein as found in several species, the best alignment requires a nine residue gap in several of the sequences. This means that

  • A. Each sequence with the gap consists of two polypeptides which associate to make the native protein in that species.
  • B. Species whose sequences have the gap are more closely related to one another than they are to those without the gap.
  • C. Species whose sequences lack the gap are more closely related to one another than they are to those with the gap.
  • D. B and C
  • E. Cannot tell from data given
A

D. B and C

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58
Q
A
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59
Q

2015

How many of the 20 standard amino acids have one or more atoms of oxygen in their SIDE chains?

  • A. None
  • B. Four
  • C. Five
  • D. Seven
  • E. None of these is correct
A

D. Seven

60
Q

2015

At pH 2 ribonuclease has a net charge of +19. At pH 6.5 it has a net charge of +4. The most likely reason for this change in charge as the pH is raised from 2 to 6.5 is

  • A. the protonation of 15 lysine side chains.
  • B. the deprotonation of 15 lysine side chains.
  • C. the protonation of 15 glutamic and/or aspartic acid side chains.
  • D. the deprotonation of 15 glutamic and/or aspartic acid side chains.
  • E. None of these could account for the change. (You may want to look at the table of pKa values at the end of this section of the exam.)
A

D. the deprotonation of 15 glutamic and/or aspartic acid side chains.

61
Q

2017

What is meant when one says that two biochemical reactions are coupled?

  • A. Neither occurs without the other occurring at the same time.
  • B. Both reactions proceed in the same direction.
  • C. The reactions each occur on an enzyme, the two enzymes being coupled together.
  • D. Energy yielded by one of the reactions drives the other, which requires energy to proceed.
  • E. more than one of the above
A

E. more than one of the above

62
Q

2015

In which of the following methods are proteins are separated based on their size?

  • A. molecular sieve (gel filtration) chromatography
  • B. SDS gel electrophoresis
  • C. affinity chromatography
  • D. more than one of these
  • E. none of these
A

D. more than one of these

63
Q

2015

The Buchner funnel, which you may have used in organic chemistry lab, was named after the Buchner brothers Edward and Hans, who were brewers of beer. Their experiments with yeast disproved which of the following vitalist statements?

  • A. Structure of “ferments” is too complex to be described in chemical terms, and the nature of catalysis is not comprehensible.
  • B. The substances composing living matter are qualitatively different from those of the non-living world.
  • C. We may be able to make some of the substances of living matter, but the reactions constituting life occur only in living cells.
  • D. Living matter may be like non-living, but organisms arise from non-living matter by spontaneous generation through the intervention of the “vital force.”
  • E. none of the above
A

C. We may be able to make some of the substances of living matter, but the reactions constituting life occur only in living cells.

64
Q

2015

The structure of acetyl-coenzyme A is shown below. Which of the numbered items is the acetyl group?

  • A. 1
  • B. 2
  • C. 3
  • D. 4
  • E. none of these
A

A. 1

65
Q

2015

A polypeptide contains 59 amino acids, as does pancreatic trypsin inhibitor. If the polypeptide contains no asparagine or glutamine, how many water molecules would be needed to hydrolyze it to its component amino acids?

  • A. 58
  • B. 116
  • C. 59
  • D. 118
  • E. none of these
A

A. 58

66
Q

If the protein in the question immediately above were to contain two asparagines and one glutamine, the number of water molecules needed for its complete hydrolysis would change by

  • A. 0
  • B. +1
  • C. +2
  • D. +3
  • E. none of these
A

D. +3

67
Q

2015

A polysaccharide contains 59 glucose residues. How many water molecules would be required to hydrolyze it fully to glucose?

  • A. 58
  • B. 116
  • C. 59
  • D. 118
  • E. none of these
A

A. 58

68
Q

2015

An anerobic ancestral eukaryote required capture of which of the following to become a photosynthetic plant cell?

  • A. an aerobic bacterium
  • B. a bacterium from the Archaea
  • C. a cyanobacterium
  • D. more than one of these
  • E. none of these
A

D. more than one of these

69
Q

2015

What is the maximum number of hydrogen bonds in which the side chain of threonine can take part?

  • A. one
  • B. two
  • C. three
  • D. four
  • E. none of these
A

C. three

70
Q

2015

Imagine two proteins which have opposite net ionic charge, one positive and one negative. All other factors being equal, in which of the following solutions would the force of attraction between them be strongest?

  • A. plain water
  • B. 0.01 m NaCl
  • C. 0.05 M NaCl
  • D. 0.1 M NaCl
  • E. The attractive force will be the same for all these solutions.
A

A. plain water

71
Q

2015

Sulfhydryl groups react with iodoacetic acid according to the following reaction, which we discussed in class: RSH + ICH2COO- → RSCH2COO- + H+ + I- . The group added to the sulfur atom is called a carboxymethyl group. A native protein is reacted with excess iodoacetic acid, whereupon two moles of carboxymethyl groups are found to be bound per mole of protein. In a second experiment a sample of the protein is completely unfolded and reacted with excess mercaptoethanol and then with excess iodoacetic acid. Eight moles of carboxymethyl groups are now found to be bound per mole of protein. How many disulfides does the native protein contain?

  • A. None
  • B. Two
  • C. Three
  • D. Four
  • E. cannot tell from data given
A

C. Three

72
Q

2015

Which of the following techniques would NOT be useful in estimating a protein’s molecular weight?

  • A. Gel filtration chromatography
  • B. SDS gel electrophoresis
  • C. isoelectric focusing
  • D. ion exchange chromatography
  • E. more than one of these
A

E. more than one of these

73
Q

2015

If the yield in the Merrifield solid state synthesis were to be 90% for each amino acid addition, what would be the yield after ten amino acids had been added?

  • A. 90%
  • B. 9%
  • C. ~35%
  • D. nearly zero
  • E. ~8%
A

C. ~35%

74
Q

2015

Why is it harder to stretch silk, which is made up primarily of beta pleated sheets, than to fold it?

  • A. Stretching requires rotation about single bonds, whereas bending bends and stretches single bonds.
  • B. Bending requires rotation about single bonds, whereas stretching bends and stretches single bonds.
  • C. Stretching requires cis-trans isomerization about peptide bonds, whereas bending does not.
  • D. Bending requires cis-trans isomerization about peptide bonds, whereas stretching does not.
  • E. None of these is correct
A

B. Bending requires rotation about single bonds, whereas stretching bends and stretches single bonds.

75
Q

2015

Non-covalent interactions are comparable in energy to the thermal energy available at room temperature. Thermal energy is approximately equal to RT, where R is the gas constant and T is the absolute temperature. R = 2 calories/(mole-degree). Let T = 300 K. Stabilizing interactions in a biological molecule are often of the order of 600 kilocalories per mole. How many non-covalent interactions are needed to provide this much stabilizing free energy? (This is much easier than it may appear at first sight….) (From a posted exam)

  • A. 0.6
  • B. 10
  • C. 100
  • D. 10,000
  • D. 1000
  • E. None of these
A

D. 1000

76
Q

At which of the following pH values would the buffering capacity of glycine be worst? (pK1 = 2.35; pK2 = 9.6)

  • A. 2.5
  • B. 1.95
  • C. 6
  • D. 9.2
  • E. Glycine’s buffering capacity is the same at all these pHs.
A

C. 6

77
Q

2015

When the free energy change of a reaction is zero,

  • A. both ∆H and ∆S must also be zero.
  • B. no molecules of reactants are being converted to products nor are any product molecules being converted back to reactant molecules.
  • C. the reaction is far from equilibrium.
  • D. the system is at equilibrium.
  • E. none of the above.
A

D. the system is at equilibrium.

78
Q

2015

On comparing the molecular weight of a free amino acid in solution with that of the same amino acid as a nonterminal residue in a protein, one finds that

  • A. the free amino acid exceeds the residue weight by 18 daltons.
  • B. the residue’s weight exceeds that of the free amino acid by 18 daltons.
  • C. the difference depends on which amino acid one considers.
  • D. the free amino acid and the residue have the same weight.
  • E. none of the above is true.
A

A. the free amino acid exceeds the residue weight by 18 daltons.

79
Q

All other factors being equal, a rise in the dielectric constant will have what effect on the strength of the repulsion between two positive charges?

  • A. It will reduce the repulsion.
  • B. It will increase the repulsion.
  • C. It will leave the repulsion unchanged.
  • D. It will create an attraction between the charges.
  • E. Cannot tell from data given.
A

A. It will reduce the repulsion

80
Q

The free energy of a reaction which is not at equilibrium, such as is the case in nearly all cellular reactions, involves two terms: the standard free energy at equilibrium and a term expressing the deviation of the actual conditions from equilibrium. In the Henderson-Hasselbalch equation governing buffers, the equivalent of the standard free energy term occurs at the pH at which

  • A. the weak acid is fully dissociated.
  • B. the weak acid is fully in the undissociated form.
  • C. the pH = the pI.
  • D. half the weak acid is dissociated.
  • E. none of the above.
A

D. half the weak acid is dissociated.

81
Q

2010

Which of the following represents an increase in the entropy of water?

  • A. dissolving an aliphatic hydrocarbon
  • B. dissolving sodium chloride
  • C. forming a salt bridge between lys and asp side chains on the surface of a protein
  • D. unfolding a protein
  • E. none of the above.
A

C. forming a salt bridge between lys and asp side chains on the surface of a protein

82
Q

2010

Cations such as Ca++, Mn++, Zn++, and a number of others are frequently found in globular proteins as cofactors. In some cases they participate in catalysis, while in others they serve a structural role, helping to hold parts of the polypeptide chain in the native conformation. Which of the following pairs of side chains would be most likely to coordinate the cation?

  • A. asp and glu
  • B. ala and phe
  • C. lys and asp
  • D. arg and his
  • E. none of the above
A

A. asp and glu

83
Q

2010

Which of the bonds listed below would be the weakest?

  • A. a carbon-oxygen double bond
  • B. a carbon-carbon bond in an aromatic ring
  • C. a carbon-carbon single bond
  • D. a hydrogen bond
  • E. all the above are of about the same strength
A

D. a hydrogen bond

84
Q

2010

The “hard sphere” behavior of the atoms in biological molecules - in all molecules for that matter - arises from

  • A. the interactions of ionic groups with one another
  • B. the third power dependence on the interatomic distance of interactions between permanent dipoles
  • C. the twelfth power dependence on the interatomic distance of interactions of overlapping electron clouds.
  • D. the fact that pi clouds are easily polarized by nearby charged groups
  • E. none of the above
A

C. the twelfth power dependence on the interatomic distance of interactions of overlapping electron clouds.

85
Q

2010

What is removed when biopolymers are formed from their monomers?

  • A. enthalpy
  • B. entropy
  • C. water
  • D. some of the monomers
  • E. none of the above
A

C. water

86
Q

2010

The open lattice-like structure of liquid water is maintained primarily by

  • A. enthalpy
  • B. entropy
  • C. the large size of the oxygen atoms F. none of the above
  • D. the small size of the hydrogen atoms
  • E. hydrogen bonding
  • F. none of the above
A

E. hydrogen bonding

87
Q

2010

The dielectric constant of some parts of the protein interior is approximately 10, while that of water is 80. Where would the repulsive interaction between two positively charged groups be greatest?

  • A. in the part of the protein interior of dielectric constant 10
  • B. in bulk water
  • C. at the surface of the protein
  • D. The dielectric constant has nothing to do with the matter.
  • E. Cannot tell from data given.
A

A. in the part of the protein interior of dielectric constant 10

88
Q

2010

All other factors being equal, the entropy of the water hydrating a leucine side chain would be expected to be

  • A. greater than that of bulk water
  • B. the same as that of bulk water
  • C. less than that of bulk water
  • D. indeterminate: one cannot know anything about the entropy of this water
A

C. less than that of bulk water

89
Q

2010

A reduction in the hydrogen ion concentration in an aqueous solution would lead to

  • A. a reduction in the hydroxide ion concentration
  • B. an increase in the hydroxide ion concentration
  • C. a change in Kw, the ion product of water
  • D. none of the above
A

B. an increase in the hydroxide ion concentration

90
Q

2010

How many amino acids have one or more atoms of oxygen in their side chains?

  • A. One
  • B. Three
  • C. Five
  • D. Seven
  • E. none of these.
A

D. Seven

91
Q

2010

In an entropy driven reaction

  • A. T∆S is negative and larger in magnitude than ∆H.
  • B. ∆H is negative and larger in magnitude than T∆S.
  • C. T∆S is positive and larger in magnitude than ∆H.
  • D. ∆H is positive and larger in magnitude than T∆S.
  • E. ∆G is positive.
A

C. T∆S is positive and larger in magnitude than ∆H.

92
Q

2010

Rank the following vitalist statements in order of decreasing breadth of their claims about the living world.

  1. Living matter may be composed of the same materials as non-living matter, but organisms arise from non-living matter by spontaneous generation by intervention of the “vital force.”
  2. The substances composing living mater are qualitatively different from those of the non-living world.
  3. The structure of enzymes is too complex to be described in chemical terms, and the nature of biological catalysis is not comprehensible.
  4. We may be able to make some of the substances of living matter, but the reactions which constitute life occur only in living cells.
  • A. 1,2,3,4
  • B. 4,3,2,1
  • C. 2,1,4,3
  • D. 3,2,4,1
  • E. none of these
A

C. 2,1,4,3

93
Q

2010

The components of poison ivy and poison oak that produce the characteristic rash are catechols substituted with long-chain alkyl groups. Catechols are benzene rings with two hydroxyl groups substituted for ring hydrogens. These hydroxyls are weak acids like the hydroxyl of tyrosine. The poison ivy/oak catechol is shown below. Its first pKa is 8.0. If you were exposed to poison ivy, which of the treatments below if applied immediately would best reduce or eliminate the itchy rash in the affected area? (From the end of chapter 2 in the text and used, as well, on last year’s exam)

  • A. Wash the affected area with cold water.
  • B. Wash the area with dilute vinegar or lemon juice.
  • C. Wash the area with soap and water.
  • D. Wash the area with soap, water and baking soda (sodium bicarbonate).
  • E. Nothing can reduce or eliminate the rash
A

D. Wash the area with soap, water and baking soda (sodium bicarbonate).

94
Q

2010

The dielectric constant of water is approximately 80, while that of the interior of a biological membrane is approximately 5. If two charged groups, one positive and the other negative are at a certain distance in water and if the same two charges are at the same distance in a membrane, which pair will experience the greater force of attraction?

  • A. the pair in water
  • B. the pair in the membrane interior
  • C. the attraction will be the same in both locations
  • D. cannot tell from data given
A

B. the pair in the membrane interior

95
Q

2010

The fact that non-covalently bonded atoms do not interpenetrate appreciably is expressed mathematically in

  • A. Coulomb’s law.
  • B. the weakness of non-covalent interactions compared to covalent bonds.
  • C. the term in the “6-12” potential which depends on the inverse sixth power of the interatomic distance.
  • D. the term in the “6-12” potential which depends on the inverse twelfth power of the interatomic distance.
  • E. none of the above
A

D. the term in the “6-12” potential which depends on the inverse twelfth power of the interatomic distance.

96
Q

2010

The fact that oil and water don’t mix, otherwise called the hydrophobic effect, is due to

  • A. repulsive enthalpic interactions between water molecules and hydrophobic molecules.
  • B. attractive enthalpic interactions between water molecules and hydrophobic molecules.
  • C. an increase in the ordering of water molecules around hydrophobic molecules when the latter dissolve in water.
  • D. a decrease in the ordering of water molecules around hydrophobic molecules when the latter dissolve in water.
  • E. none of the above.
A

C. an increase in the ordering of water molecules around hydrophobic molecules when the latter dissolve in water.

97
Q

2010

In what order would the amino acids glu, gln, ala, his, lys, arg elute from an anion exchange resin as the pH is raised from 2 to a high value?

  • A. glu, gln, ala, his, lys, arg
  • B. the reverse of A above
  • C. gln, glu, ala, lys, his, arg
  • D. glu, gln, ala, his, arg, lys
  • E. none of the above; they don’t stick to the resin at pH 2.
A

E. none of the above; they don’t stick to the resin at pH 2.

98
Q

2010

In what order would the amino acids glu, gln, ala, his, lys, arg elute from a cation exchange resin as the pH is raised from 2 to a high value?

  • A. glu, gln, ala, his, lys, arg
  • B. the reverse of A above
  • C. gln, glu, ala, lys, his, arg
  • D. glu, gln, ala, his, arg, lys
  • E. none of the above; they don’t stick to the resin at pH 2.
A

A. glu, gln, ala, his, lys, arg

99
Q

2010

In what order would the amino acids glu, gln, ala, his, lys, arg elute from an anion exchange resin as the pH is lowered from 13 to 2?

  • A. glu, gln, ala, his, lys, arg
  • B. the reverse of A above
  • C. gln, glu, ala, lys, his, arg
  • D. glu, gln, ala, his, arg, lys
  • E. none of the above; they don’t stick to the resin at pH 13.
A

B. the reverse of A above

100
Q

2010

The formation of a tetrasaccharide from four glucose molecules involves the removal of ___ molecules of water in a dehydration reaction.

  • A. none
  • B. one
  • C. two
  • D. three
  • E. more than three
A

D. three

101
Q

2010

Which of the following would produce the best buffering at a pH near 7?

  • A. acetic acid, pK = 4.76
  • B. carbonic acid, pK1 = 6.37
  • C. ammonium chloride, pK = 9.3
  • D. formic acid, pK = 3.75
  • E. cannot tell from data given
A

B. carbonic acid, pK1 = 6.37

102
Q

2010

“Salting in” is a phenomenon in which addition of salt ions to a solution increases the solubility of a protein. Which of the following is most likely to explain salting in?

  • A. The salt ions bind to the protein molecules, reducing the repulsion between them.
  • B. The protein molecules contain a variety of positive and negative charges which cause one molecule to attract another in the absence of salt. The ions of the added salt interact with the protein charges, screening one protein from another, thus enabling the protein molecules to separate from one another and dissolve.
  • C. The salt ions cause the protein to unfold.
  • D. Rapid diffusional motion of the salt ions causes them to bombard the solid protein, chipping molecules away into the solution.
  • E. None of the above
A

B. The protein molecules contain a variety of positive and negative charges which cause one molecule to attract another in the absence of salt. The ions of the added salt interact with the protein charges, screening one protein from another, thus enabling the protein molecules to separate from one another and dissolve.

103
Q

2010

“Salting out” is a phenomenon in which addition of salt ions decreases the solubility of a protein, causing it to precipitate. The precipitate contains many salt ions. Which of the following is most likely to explain salting out?

  • A. The salt ions form “ion atmospheres” around the protein charges, thus screening the repulsion of one protein molecule from another and allowing them to come into contact with one another, forming the precipitate.
  • B. The salt ions cause the protein molecules to unfold.
  • C. Rapid diffusional motion of the salt ions causes them to bombard the dissolved protein molecules, driving them into colliding with one another.
  • D. The salt ions cause the protein molecules to fold.
  • E. None of the above
A

A. The salt ions form “ion atmospheres” around the protein charges, thus screening the repulsion of one protein molecule from another and allowing them to come into contact with one another, forming the precipitate.

104
Q

2011

Which will show the greater degree of dissociation: formic acid (pKa = 3.75) or acetic acid (pKa = 4.76) if dissolved in water at 0.1 M concentrations?

  • A. Formic acid
  • B. Acetic acid
  • C. Within the accuracy of measurement they will be equally dissociated.
  • D. Cannot tell from data given.
A

A. Formic acid

105
Q

2011

Which will show the greater degree of dissociation: formic acid (pKa = 3.75) or acetic acid (pKa = 4.76) if dissolved at 0.1 M concentrations in solutions whose pH is 11.0?

  • A. Formic acid
  • B. Acetic acid
  • C. Within the accuracy of measurement they will be equally dissociated.
  • D. Cannot tell from data given.
A

C. Within the accuracy of measurement they will be equally dissociated.

106
Q

2011

The information density (ID) of a material is the ratio of the number of pieces of information in it divided by its weight: information per unit weight. Information may be expressed as the number of characters in the material. The Prism of Senacherib, made in approximately 700 B.C., contains 20,000 characters and weighs 50 kilograms. The single chromosome of an E. coli bacterial cell contains 10 million characters (bases) and weighs 1 x 10-10 grams. Which of the following is NOT correct?

  • A. The ID of the Prism is 0.4 information units per gram.
  • B. The ID of the E.coli chromosome is 1 x 10+17 information units per gram.
  • C. The ratio of the E.coli chromosome’s ID to that of the Prism is 2.5 x 10+17 to 1.
  • D. Being made of heavy stone, the Prism has a higher information density.
  • E. Cannot tell from data given.
A

D. Being made of heavy stone, the Prism has a higher information density.

107
Q

2011

Imagine two groups each of which carries a single positive charge. In one situation they are fully exposed to the aqueous solvent, while in another they are buried in the interior of a folded protein and unable to contact the solvent at all. In both situations they are separated by the same distance, r. The dielectric constant of water is 80, while that of the protein interior is 20. It follows that

  • A. the force of attraction between the two groups is four times greater in water than in the protein interior.
  • B. the force of repulsion between the two groups is four times greater in water than in the protein interior.
  • C. the force of repulsion between the two groups is four times greater in the protein interior than in water.
  • D. the two groups do not interact in either situation.
  • E. none of the above is true.
A

C. the force of repulsion between the two groups is four times greater in the protein interior than in water.

108
Q

2011

Which of the following is best described as an entropy driven reaction?

  • A. ∆H = -82 kJ/mol, -T∆S = -136 kJ/mol
  • B. ∆H = -1367 kJ/mol, -T∆S = +41 kJ/mol
  • C. ∆H = +110 kJ/mol, -T∆S = -140 kJ/mol
  • D. none of the above is entropy driven
  • E. all the above are entropy driven
A

C. ∆H = +110 kJ/mol, -T∆S = -140 kJ/mol

109
Q

2011

The standard free energy change for the conversion of glucose-6-phosphate (G6P) to fructose-6-phosphate (F6P) is +1.7 kJ/mol. In an equilibrium mixture of the two compounds

  • A. there will be more F6P than G6P.
  • B. there will be equal amounts of G6P and F6P.
  • C. there will be more G6P than F6P.
  • D. there will be no G6P
  • E. cannot tell from data given
A

C. there will be more G6P than F6P.

110
Q

2011

  1. In the conversion of glucose-6-phosphate (G6P) to fructose-6-phosphate (F6P), the actual free energy change will be least sensitive to changes in the fraction of G6P (or F6P) in the reaction mixture when
  • A. the ratio of [G6P] to [F6P] is very large.
  • B. the ratio of [F6P] to [G6P] is very large.
  • C. the concentrations of G6P and F6P are nearly but not exactly equal.
  • D. the concentrations are such that ∆G λ ∆Go ’
  • E. cannot tell from data given.

(Hint: remember that the forms of the free energy equation, the Henderson-Hasselbalch equation and the Nernst equation are the same.)

A

D. the concentrations are such that ∆G λ ∆Go ’

111
Q

2011

The pKa values for glutamic acid are: α-carboxyl, 2.19; side chain carboxyl, 4.25; α-amino, 9.67. At what pH will glutamic acid not move in an electric field?

  • A. 2.19
  • B. 3.22
  • C. 4.25
  • D. 6.44
  • E. none of the above
A

B. 3.22

112
Q

2011

The formation of a Schiff’s base involves

  • A. a dehydration
  • B. a hydrolysis
  • C. an oxidation
  • D. a reduction
  • E. more than one of these
A

A. a dehydration

113
Q

2011

Which of the following experimental observations disproved the vitalist claim that the substances of which living matter is composed are qualitatively different from those which compose the non-living world?

  • A. the demonstration by the Buchner brothers that broken and therefore dead yeast cells could convert sugar into ethanol
  • B. the crystallization by Sumner of the enzyme urease
  • C. Pasteur’s proof that living organisms arise only from other living organisms rather than by spontaneous generation caused by the “vital force”
  • D. Wöhler’s synthesis of urea from ammonium cyanate
  • E. none of the above
A

D. Wöhler’s synthesis of urea from ammonium cyanate

114
Q

2011

Which of the following amino acids has the smallest side chain?

  • A. asp
  • B. ala
  • C. asn
  • D. cys
  • E. ser
A

B. ala

115
Q

2011

Iodoacetic acid reacts with free sulfhydryl groups according to the following reaction:

RSH + ICH2COOH → RSCH2COOH + H+ + I-

The disulfides of an unfolded protein which contains no free sulfhydryls are fully reduced with dithiothreitol, following which the protein is reacted with a large excess of iodoacetic acid. It is found that eight molecules of iodoacetic acid are bound per molecule of protein. How many disulfides does the protein contain?

  • A. none
  • B. two
  • D. four
  • B. one
  • C. three
  • E. more then four
A

D. four

116
Q

2011

How many water molecules would it take to hydrolyze a pentapeptide which contains no asparagines and no glutamines among its constituent amino acids?

  • A. one
  • B. two
  • C. three
  • D. four
  • E. more than four
A

D. four

117
Q

2011

Consider the table to the right, which was discussed in class. If the proteins listed were to be dissolved in a buffer of pH 7.0 and subjected to electrophoresis, how many would migrate toward the anode?

  • A. None
  • B. All
  • C. Three
  • D. Six
  • E. Cannot tell from available data.
A

D. Six

118
Q

2011

A protein preparation is assayed and shown to have 50,000 units of activity in a volume of 25 mL. The protein concentration in the preparation is found to be 4 mg/mL. What is the specific activity of the preparation?

  • A. 500 U/mg
  • B. 50,000 U/mg
  • C. 2,000 U/mg
  • D. 4 U/mg
  • E. Cannot tell from the data given.

Is the protein preparation in the problem above pure?

  • A. Yes
  • B. No
  • C. No, but it would be if it were passed through an ion exchange column.
  • D. No, but it would be if it were passed through a size exclusion column.
  • E. Cannot tell from data given.
A
  • A. 500 U/mg
  • E. Cannot tell from data given.
119
Q

2011

Consider the pentapeptide gly lys ser glu ala. How many buffering regions would the titration curve of this peptide show if it were dissolved in water?

  • A. none
  • B. two
  • C. three
  • D. four
  • E. more than four
A

D. four

120
Q

2011

In biochemistry we often study “model systems” because they illustrate principles which are broadly applicable. Why is formic acid a useful model system for studying buffering in biochemical systems?

  • A. It is a simple compound which shows all the buffering properties of a weak acid.
  • B. It is cheap and easy to work with in the laboratory.
  • C. Its multiple carboxyl groups are a good model for proteins.
  • D. Its pKa, 3.75, is in the physiological range very near neutrality.
  • E. It is toxic to baboons.
A

A. It is a simple compound which shows all the buffering properties of a weak acid.

121
Q

2011

In biochemistry we often study “model systems” because they illustrate principles which are broadly applicable. Why is formic acid a useful model system for studying buffering in biochemical systems?

  • A. It is a simple compound which shows all the buffering properties of a weak acid.
  • B. It is cheap and easy to work with in the laboratory.
  • C. Its multiple carboxyl groups are a good model for proteins.
  • D. Its pKa, 3.75, is in the physiological range very near neutrality.
  • E. It is toxic to baboons.
A

A. It is a simple compound which shows all the buffering properties of a weak acid.

122
Q

2011

If the dielectric constant is doubled, the force of interaction between charged groups is

  • A. doubled
  • B. cut in half
  • C. multiplied by four
  • D. divided by four
  • E. unaffected
A

B. cut in half

123
Q

2011

Pancreatic trypsin inhibitor has a molecular weight is 6,500 Daltons and is made up of 59 amino acid residues. Hemoglobin’s molecular weight is 64,500 Daltons, and the protein has 574 amino acids. Estimate the number of amino acids in the muscle protein myosin if its molecular weight is 500,000 Daltons.

  • A. 111
  • B. 500,000
  • C. 4500
  • D. 50,000
  • E. Cannot tell from data given.
A

C. 4500

124
Q

2013

Protein sulfhydryl groups as found in cysteine react with iodoacetic acid according to the following reaction:

RSH + I–CH2–COO-  RSCH2–COO- + H+ + I-

iodoacetate Reaction of an unfolded protein with excess iodoacetate results in two moles of acetate being bound per mole of protein. Treatment of a fresh sample of the unfolded protein with excess mercaptoethanol or dithiothreitol followed by excess iodoacetate results in six moles of acetate being bound per mole of protein. How many disulfides does the protein contain?

  • A. none
  • B. one
  • C. two
  • D. four
  • E. six
A

C. two

125
Q

2013

Lysine, aspartic acid, and asparagine are introduced onto a cation exchange column at pH 2, and the column is eluted with a buffer gradient of increasing pH. All other factors being equal, in which order will the amino acids elute?

  • A. asp asn lys
  • B. asp lys asn
  • C. lys asp asn
  • D. lys asn asp
  • E. they won’t stick to the column at all
A

A. asp asn lys

126
Q

2013

Lysine, aspartic acid, and asparagine are introduced onto an anion exchange column at pH 11, and the column is eluted with a buffer gradient of decreasing pH. All other factors being equal, in which order will the amino acids elute?

  • A. asp asn lys
  • B. asp lys asn
  • C. lys asp asn
  • D. lys asn asp
  • E. they won’t stick to the column at all
A

D. lys asn asp

127
Q

2013

Lysine, aspartic acid, and asparagine are introduced onto an anion exchange column at pH 2, and the column is eluted with a buffer gradient of increasing pH. All other factors being equal, in which order will the amino acids elute?

  • A. asp asn lys
  • B. asp lys asn
  • C. lys asp asn
  • D. lys asn asp
  • E. they won’t stick to the column at all
A

E. they won’t stick to the column at all

128
Q

2013

Which of the following would produce the lowest pH if dissolved in water at a concentration of 0.1 M?

  • A. acetic acid, pK = 4.76
  • B. carbonic acid, pK1 = 6.37
  • C. citric acid, pK1 = 3.3
  • D. formic acid, pK = 3.75
  • E. cannot tell from data given
A

C. citric acid, pK1 = 3.3

129
Q

At pH 6.5 ribonuclease-A has a net charge of +4. At pH 2 the protein has a net charge of +19. If the protein is dissolved in 0.1 M KCl at both pHs, and if the solution contains no other solutes, in which case will the protein molecules have a larger number of chloride ions in their immediate vicinity?

  • A. pH 2
  • B. pH 6.5
  • C. a pH midway between 2 and 6.5
  • D. It will have the same number of chlorides at the two pHs.
  • E. cannot tell from data given.
A

A. pH 2

130
Q

2013

The protein myoglobin acts as an oxygen storage protein in muscle tissue. It contains 152 amino acids. If the side chains of asparagine and glutamine are ignored, how many water molecules would be required to hydrolyze myoglobin completely to its constituent amino acids?

  • A. None. Proteins are not hydrolyzable.
  • B. 152
  • C. 151
  • D. 204
  • E. 202
A

C. 151

131
Q

2013

When a weak monoprotic acid is titrated with one half mole of base per mole of acid,

  • A. the pH = the pI
  • B. [HA] = [A-]
  • C. the pH = the pKa
  • D. the pI = the pKa
  • E. none of the above
A

C. the pH = the pKa

132
Q

2013

When an organism dies, what happens to the entropy of its components?

  • A. It decreases.
  • B. It increases.
  • C. It remains unchanged.
  • D. Death and entropy have nothing to do with one another.
  • E. Cannot tell without further information.
A

B. It increases.

133
Q

2013

During embryological development from a fertilized egg to birth (or hatching), what happens to the entropy of the substances which become the new organism?

  • A. It decreases.
  • B. It increases.
  • C. It remains unchanged.
  • D. Birth and entropy have nothing to do with one another.
  • E. Cannot tell without further information.
A

A. It decreases.

134
Q

2013

A salt bridge occurs in a protein when a positively charged group of the protein interacts with a negatively charged group. When this occurs

  • A. the salt bridge is more heavily hydrated than the groups were before they interacted.
  • B. the entropy of water increases when the bridge forms.
  • C. the groups become hydrophobic.
  • D. the native protein conformation becomes less stable.
  • E. none of the above
A

B. the entropy of water increases when the bridge forms.

135
Q

2020

How many hydrogen atoms are there in the side chain of valine?

  • three
  • five
  • seven
  • none
  • none of these is correct
A

seven

136
Q

2020

The three pKa values of histidine are 1.82 and 9.17 for the amino and carboxyl groups respectively and 6.0 for the side chain? How would you compute the isoelectric pH of histidine?

  • (1.82 + 9.17) / 2
  • (9.17 + 6.0) / 2
  • (1.82 + 6.0) / 2
  • (1.82 + 6.0 + 9.17) / 3
  • cannot tell from data given
A

(9.17 + 6.0) / 2

137
Q

2020

Consider a protein whose isoelectric pH is 7.4 but which is dissolved in a solution of pH 3. Which of the following would be most likely to be found in the immediate vicinity of a molecule of the protein

  • a sodium ion
  • another protein molecule
  • A calcium ion
  • a chloride ion
  • none of the above
A

a chloride ion

138
Q

2020

Consider diffusion across a membrane. The reaction is Ain zone 1 ⇌ Ain zone 2. We showed in class that for this reaction Delta-Goverall = RT ln ([A]2 / [A]1). Under which of the following conditions will the reaction proceed spontaneously from right to left?

  • [A]2 > [A]1
  • [A]1 > [A]2
  • [A]1 = [A]2
  • The reaction will never go from right to left
  • Cannot tell from data given
A

[A]2 > [A]1

139
Q

2020

Which of the following correctly describes coupled biochemical reactions?

  • Both reactions run spontaneously from left to right
  • One reaction runs spontaneously from left to right, while the other runs spontaneously from right to left.
  • Neither reaction runs spontaneously from right to left.
  • Energy yielded by one reaction drives the other
  • more than one of the above.
A

more than one of the above.

140
Q

Consider a hydrocarbon, H. It can be thought of as being a solution of H dissolved in itself, as in Hoil. Some Hoil is shaken in a separatory funnel with water, giving us the reaction Hoil ⇌ Hwater, and the funnel is allowed to sit undisturbed afterward. Which of the following statements about the system at that time will be correct?

  • [Hoil] = [Hwater]
  • The number of H molecules in oil that move into the water per minute is the same as the number of H molecules in water that move into the oil phase per minute.
  • The free energy of this system is given by

Delta-G = Delta-Go’ + RT ln {[Hwater] / [Hoil]}

  • None of the three terms in this expression equals zero.
  • [Hwater] > [Hoil]
  • Cannot tell from data given.
A

The number of H molecules in oil that move into the water per minute is the same as the number of H molecules in water that move into the oil phase per minute.

141
Q

2020

A protein is isolated from six species, and the amino acid sequences are aligned. If one reads down one residue position for the six species, one finds the following amino acids: SGNYEQ. What property, if any, is mostly conserved at this sequence position? (Give the best possible answer.)

  • There is no conservation at this position
  • The position is polar
  • Only small amino acids fit in this position
  • The position is nonpolar
  • None of these describes this position.e
A

The position is polar

142
Q

A protein sample is treated exhaustively with cyanogen bromide, and a second sample of the protein is treated exhaustively with trypsin. If the protein contains five lysines, two arginines, three methionines and four tyrosines, how many Edman degradations would have to be done to determine the protein’s sequence?

  • None could be done, as the reactions described above would render the protein unreactive in Edman degradation.
  • ten
  • seven
  • eight
  • twelve
A

twelve

143
Q

2020

The maximum possible value relative migration can have

  • depends on the pH of the system in use.
  • depends on the molecular weight of the proteins involved.
  • equals one.
  • equals the log of the molecular weight of the smallest protein in the experiment.
  • none of the above
A

equals one.

144
Q

2020

Why are symmetry axes observed so often in biochemical structures?

  • They require fewer amino acids.
  • They are easier to find than unsymmetrical forms.
  • They are more stable than unsymmetrical forms.
  • They allow complex structures to be built from fewer different forms.
  • none of the above
A

They allow complex structures to be built from fewer different forms.

145
Q

2020

Tobacco mosaic virus is a long rod-shaped structure. The protein capsid of the virus is made up of molecules of a globular protein arranged to form a helix that winds around and covers the RNA genome. If one turn of the helix involves 72 capsid molecules, what is the angle of rotation about the viral axis per capsid protein?

  • 360 degrees
  • 10 degrees
  • 5 degrees
  • 60 degrees
  • Cannot tell from data given.
A

5 degrees

Biochemistry 403 (12 decks)

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