Deck 3: Amino Acids, Peptides, and Proteins
1
Titration of valine by a strong base, for example NaOH, reveals two pK's. The titration reaction occurring at pK2 (pK2 = 9.62) 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.
D
2
The uncommon amino acid selenocysteine has an R group with the structure -CH2-SeH (pKa 5). In an aqueous solution, pH = 7.0, selenocysteine would:
A) be a fully ionized zwitterion with no net charge.
B) be found in proteins as D-selenocysteine.
C) never be found in a protein.
D) be nonionic.
E) not be optically active.
A
3
Two amino acids of the standard 20 contain sulfur atoms. They are:
A) cysteine and serine.
B) cysteine and threonine.
C) methionine and cysteine
D) methionine and serine
E) threonine and serine.
C
4
What is the approximate charge difference between glutamic acid and -ketoglutarate at pH 9.5?
A) 0
B) 1/2
C) 1
D) 11/2
E) 2
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5
Which statement 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.
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6
Of the 20 standard amino acids, only _____ is not optically active. The reason is that its side chain _____.
A) alanine; is a simple methyl group
B) glycine; is a hydrogen atom
C) glycine; is unbranched
D) lysine; contains only nitrogen
E) proline; forms a covalent bond with the amino group
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7
Amino acids are ampholytes because they can function as either a(n):
A) acid or a base.
B) neutral molecule or an ion.
C) polar or a nonpolar molecule.
D) standard or a nonstandard monomer in proteins.
E) transparent or a light-absorbing compound.
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8
In a highly basic solution, pH = 13, the dominant form of glycine is:
A) NH2-CH2-COOH.
B) NH2-CH2-COO-.
C) NH2-CH3+-COO-.
D) NH3+-CH2-COOH.
E) NH3+-CH2-COO-.
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9
An octapeptide composed of four repeating glycylalanyl units has:
A) one free amino group on an alanyl residue.
B) one free amino group on an alanyl residue and one free carboxyl group on a glycyl residue.
C) one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue.
D) two free amino and two free carboxyl groups.
E) two free carboxyl groups, both on glycyl residues.
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10
At the isoelectric pH of a tetrapeptide:
A) only the amino and carboxyl termini contribute charge.
B) the amino and carboxyl termini are not charged.
C) the total net charge is zero.
D) there are four ionic charges.
E) two internal amino acids of the tetrapeptide cannot have ionizable R groups.
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11
Which statement about aromatic amino acids is CORRECT?
A) All are strongly hydrophilic.
B) Histidine's ring structure results in its being categorized as aromatic or basic, depending on pH.
C) On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine.
D) The major contribution to the characteristic absorption of light at 280 nm by proteins is the phenylalanine R group.
E) The presence of a ring structure in its R group determines whether or not an amino acid is aromatic.
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12
The chirality of an amino acid results from the fact that its carbon:
A) has no net charge.
B) is a carboxylic acid.
C) is bonded to four different chemical groups.
D) is in the L absolute configuration in naturally occurring proteins.
E) is symmetric.
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13
At pH 7.0, converting a glutamic acid to -carboxyglutamate, will have what effect on the overall charge of the protein containing it?
A) It will become more negative
B) It will become more positive.
C) It will stay the same.
D) There is not enough information to answer the question.
E) The answer depends on the salt concentration.
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14
For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have:
A) a net negative charge.
B) a net positive charge.
C) no charged groups.
D) no net charge.
E) positive and negative charges in equal concentration.
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15
Which statement about cystine is CORRECT?
A) Cystine forms when the -CH2-SH R group is oxidized to form a -CH2-S-S-CH2- disulfide bridge between two cysteines.
B) Cystine is an example of a nonstandard amino acid, derived by linking two standard amino acids.
C) Cystine is formed by the oxidation of the carboxylic acid group on cysteine.
D) Cystine is formed through a peptide linkage between two cysteines.
E) Two cystines are released when a -CH2-S-S-CH2- disulfide bridge is reduced to -CH2-SH.
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16
The formation of a peptide bond between two amino acids is an example of a(n) _____ reaction.
A) cleavage
B) condensation
C) group transfer
D) isomerization
E) oxidation reduction
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17
The peptide alanylglutamylglycylalanylleucine has:
A) a disulfide bridge.
B) five peptide bonds.
C) four peptide bonds.
D) no free carboxyl group.
E) two free amino groups.
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18
All of the amino acids that are found in proteins, except for proline, contain a(n) _____ group.
A) amino
B) carbonyl
C) carboxyl
D) ester
E) thiol
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19
At pH 7.0, converting a proline to hydroxyproline, will have what effect on the overall charge of the protein containing it?
A) It will become more negative
B) It will become more positive.
C) It will stay the same.
D) There is not enough information to answer the question.
E) The answer depends on the salt concentration.
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20
Which two amino acids differ from each other by only one atom?
A) Ser and Thr
B) Leu and Ile
C) Ala and Ser
D) Asp and Asn
E) Ser and Cys
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21
The functional differences, as well as differences in three-dimensional structures, between two different enzymes from E. coli result directly from their different:
A) affinities for ATP.
B) amino acid sequences.
C) roles in DNA metabolism.
D) roles in the metabolism of E. coli.
E) secondary structures.
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22
Even when a gene is available and its sequence of nucleotides is known, chemical studies of the protein are still required to determine:
A) molecular weight of the protein.
B) the amino-terminal amino acid.
C) the location of disulfide bonds.
D) the number of amino acids in the protein.
E) whether the protein has the amino acid methionine in its sequence.
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23
Identify the pair of peptides below that CANNOT be distinguished by tandem mass spectrometry.
A) VTSPLYANEGK and VTCPLYANEGK
B) VTSPLYANEGK and VTSPLYADEGK
C) VTSPLYANEGK and VTSPIYANEGK
D) VTSPLYANEGK and VSTPLYANEGK
E) All of the answer choices are correct.
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24
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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25
All of the 20 common amino acids contain an R-group that is attached to the:
A) carboxyl group.
B) amino group.
C) carbon.
D) carbon.
E) It depends on the amino acid
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26
Compare the following sequences taken from four different proteins, and select the answer that BEST characterizes their relationships. A
B
C
1 DVEKGKKIDIMKCS
HTVEKGGKHKTGPNLH
GLFGRKTGQAPGYSYT
2 DVQRALKIDNNLGQ
HTVEKGAKHKTAPNVH
GLADRIAYQAKATNEE
3 LVTRPLYIFPNEGQ
HTLEKAAKHKTGPNLH
ALKSSKDLMFTVINDD
4 FFMNEDALVARSSN
HQFAASSIHKNAPQFH
NLKDSKTYLKPVISET
A) Based only on sequences in column B, protein 4 reveals the greatest evolutionary divergence.
B) Comparing proteins 1 and 2 in column A reveals that these two proteins have diverged the most throughout evolution.
C) Protein 4 is the protein that shows the greatest overall homology to protein 1.
D) Proteins 2 and 3 show a greater evolutionary distance than proteins 1 and 4.
E) The portions of amino acid sequence shown suggest that these proteins are completely unrelated.
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27
Which type of structure describes the overall three-dimensional folding of a polypeptide?
A) primary structure
B) secondary structure
C) tertiary structure
D) quaternary structure
E) None of the answers is correct.
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28
In a mixture of the five proteins listed below, which should elute second in size-exclusion (gel- filtration) chromatography?
A) cytochrome c Mr = 13,000
B) immunoglobulin G Mr = 145,000
C) ribonuclease A Mr = 13,700
D) RNA polymerase Mr = 450,000
E) serum albumin Mr = 68,500
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29
A nonapeptide was determined to have the following amino acid composition: (Lys)2, (Gly) 2, (Phe) 2, His, Leu, Met. The native peptide was incubated with 1-fluoro-2,4-dinitrobenzene (FDNB) and then hydrolyzed; 2,4-dinitrophenylhistidine was identified by HPLC. When the native peptide was exposed to cyanogen bromide (CNBr), an octapeptide and free glycine were recovered. Incubation of the native peptide with trypsin gave a pentapeptide, a tripeptide, and free Lys. 2,4-Dinitrophenyl-histidine was recovered from the pentapeptide, and 2,4-dinitrophenylphenylalanine was recovered from the tripeptide. Digestion with the enzyme pepsin produced a dipeptide, a tripeptide, and a tetrapeptide. The tetrapeptide was composed of (Lys) 2, Phe, and Gly. The native sequence was determined to be:
A) Gly-Phe-Lys-Lys-Gly-Leu-Met-Phe-His.
B) His-Leu-Gly-Lys-Lys-Phe-Phe-Gly-Met.
C) His-Leu-Phe-Gly-Lys-Lys-Phe-Met-Gly.
D) His-Phe-Leu-Gly-Lys-Lys-Phe-Met-Gly.
E) Met-Leu-Phe-Lys-Phe-Gly-Gly-Lys-His.
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30
A major advance in the application of mass spectrometry to macromolecules came with the development of techniques to overcome which problem?
A) Macromolecules were insoluble in the solvents used in mass spectrometry.
B) Mass spectrometric analyses of macromolecules were too complex to interpret.
C) Mass spectrometric analysis involved molecules in the gas phase.
D) Most macromolecules could not be purified to the degree required for mass spectrometric analysis.
E) The specialized instruments required were prohibitively expensive.
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31
Which type of structure refers to particularly stable arrangements of amino acid residues in a protein that give rise to recurring patterns?
A) primary structure
B) secondary structure
C) tertiary structure
D) quaternary structure
E) None of the answers is correct.
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32
In a conjugated protein, a prosthetic group is:
A) a fibrous region of a globular protein.
B) a nonidentical subunit of a protein with many identical subunits.
C) a part of the protein that is not composed of amino acids.
D) a subunit of an oligomeric protein.
E) synonymous with "protomer."
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33
The term "proteome" has been used to describe:
A) regions (domains) within proteins.
B) regularities in protein structures.
C) the complement of proteins expressed by an organism's genome.
D) the structure of a protein-synthesizing ribosome.
E) the tertiary structure of a protein.
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34
One method used to prevent disulfide bond interference with protein sequencing procedures is:
A) cleaving proteins with proteases that specifically recognize disulfide bonds.
B) protecting the disulfide bridge against spontaneous reduction to cysteinyl sulfhydryl groups.
C) reducing disulfide bridges and preventing their re-formation by further modifying the -SH groups.
D) removing cystines from protein sequences by proteolytic cleavage.
E) sequencing proteins that do not contain cysteinyl residues.
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35
By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to:
A) determine a protein's isoelectric point.
B) determine an enzyme's specific activity.
C) determine the amino acid composition of the protein.
D) preserve a protein's native structure and biological activity.
E) separate proteins exclusively on the basis of molecular weight.
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36
Prosthetic groups in the class of proteins known as glycoproteins are composed of:
A) carbohydrates.
B) flavin nucleotides.
C) lipids.
D) metals.
E) phosphates.
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37
To determine the isoelectric point of a protein, first establish that a gel:
A) contains a denaturing detergent that can distribute uniform negative charges over the protein's surface.
B) exhibits a stable pH gradient when ampholytes become distributed in an electric field.
C) is washed with an antibody specific to the protein of interest.
D) neutralizes all ionic groups on a protein by titrating them with strong bases.
E) relates the unknown protein to a series of protein markers with known molecular weights, Mr.
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38
The first step in two-dimensional gel electrophoresis generates a series of protein bands by isoelectric focusing. In a second step, a strip of this gel is turned 90 degrees, placed on another gel containing SDS, and electric current is again applied. In this second step:
A) proteins with similar isoelectric points become further separated according to their molecular weights.
B) the individual bands become stained so that the isoelectric focus pattern can be visualized.
C) the individual bands become visualized by interacting with protein-specific antibodies in the second gel.
D) the individual bands undergo a second, more intense isoelectric focusing.
E) the proteins in the bands separate more completely because the second electric current is in the opposite polarity to the first current.
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39
The term specific activity differs from the term activity in that specific activity:
A) is measured only under optimal conditions.
B) is the activity (enzyme units) in a milligram of protein.
C) is the activity (enzyme units) of a specific protein.
D) refers only to a purified protein.
E) refers to proteins other than enzymes.
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40
For the study of a protein in detail, an effort is usually made to first:
A) conjugate the protein to a known molecule.
B) determine its amino acid composition.
C) determine its amino acid sequence.
D) determine its molecular weight.
E) purify the protein.
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41
According to the diagram, how many titratable groups does this amino acid have?
A) 0
B) 1
C) 2
D) 3
E) It cannot be determined by this diagram.
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42
Which of the following CORRECTLY matches the amino acid name with its one letter abbreviation?
A) tyrosine, T
B) lysine, L
C) phenylalanine, P
D) aspartic acid, D
E) proline, R
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43
According to the diagram, which pH range offers the GREATEST buffering power for this amino acid?
A) 0.5-1.5
B) 0-1
C) 1-2
D) 2-3
E) 1-3
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44
According to the diagram, at pH 2, what is the average net charge on this amino acid?
A) +1
B) + 0.5
C) 0
D) -0.5
E) -1
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45
By convention, polypeptides are read in which order?
A) N- to C-terminus
B) C- to N-terminus
C) 5 to 3
D) 3 to 5
E) smallest to largest amino acid by molecular weight
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46
Which pair of amino acids can be used to measure the concentration of proteins based on absorption of UV light?
A) proline and valine
B) serine and threonine
C) aspartate and glutamate
D) lysine and histidine
E) tyrosine and tryptophan
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47
According to the diagram, does this amino acid have a titratable R-group?
A) yes, as evidenced by the steep center of the curve
B) yes, as evidenced by the two relatively flat parts of the curve
C) no, as evidenced by only two relatively flat parts of the curve
D) no, as evidenced by the steepness of the center of the curve
E) It cannot be determined from this graph.
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48
When the ribosome forms a peptide bond, which two atoms form a covalent bond?
A) the carbon and the amino nitrogen
B) the amino nitrogen and carboxylic acid carbon
C) the carbon and the carboxylic acid carbon
D) the amino nitrogen and the carbon
E) It depends on the amino acids being joined.
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49
Which compound is a side-product of a peptide bond formation?
A) water
B) phosphate
C) ammonium
D) carboxylic acid
E) None of the answers is correct.
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50
Why can only some amino acids be used to measure protein concentration based on absorption of UV light?
A) Only some amino acids are aromatic.
B) Only some amino acids are positively charged.
C) Only some amino acids are strongly hydrophobic.
D) Only some amino acids are strongly hydrophilic.
E) Only some amino acids are negatively charged.
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51
According to the diagram, at pH 1, what is the average net charge on this amino acid?
A) + 1
B) + 0.5
C) 0
D) -0.5
E) -1
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52
According to the diagram, which estimate is BEST of this amino acid's isoelectric point?
A) 0.5
B) 1
C) 1.5
D) 6
E) 11
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53
According to the diagram, which pH is the one at which this amino acid will have a net charge of 0?
A) 11
B) 6
C) 1.5
D) 1
E) 0.5
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54
Amino acids without ionizable R-groups can act as a zwitterion in a(n) _____ solution.
A) nonpolar
B) boiling
C) acidic
D) basic
E) neutral
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55
The pKa of lysine's carboxyl group, amino group, and side chain are 2.2, 9.0, and 10.5, respectively. If lysine is in a pH 13 solution, what is the net charge on each lysine molecule?
A) -2
B) -1
C) 0
D) +1
E) +2
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56
Which statement is TRUE about the pKa values for ionizable R-group of amino acids within a polypeptide?
A) The pKa values for R-groups do not change from free amino acids.
B) The pKa values for R-groups are 1 pH unit higher than free amino acids.
C) The pKa values for R-groups are 1 pH unit lower than free amino acids.
D) The pKa values for R-groups vary depending on the local environment of the side chain.
E) The pKa values for R-groups depend on how close the R-group is to the N- or C-terminus of the polypeptide.
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57
On the molecule below, the arrow is pointing to the _____ carbon.
A) amino
B)
C)
D)
E) carboxylic acid
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58
The MOST useful way to classify amino acids is by:
A) molecular weight.
B) pKa.
C) polarity.
D) propensity in proteins.
E) alphabetical order.
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59
The protein bovine serum albumin (BSA), has a MW of about 66,400. Using the Lambert-Beer Law, calculate the concentration of a sample of BSA with an absorbance at 280 nm of 1.3, assuming the molar extinction coefficient at 280 nm is 43,824 M-1cm-1.
A) 0.51 mg/mL
B) 0.86 mg/mL
C) 1.97 mg/mL
D) 2.56 mg/mL
E) 3.78 mg/mL
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60
The amino acid proline is unique because the R group:
A) has a phosphate attached.
B) is cyclical.
C) is attached to the carboxylic acid carbon.
D) is positively charged.
E) None of the answers is correct.
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61
If protein A has a pI of 3.1, protein B has a pI of 6.8, and protein C has a pI of 8.9, which protein would elute FIRST from a cation exchange column at pH 7?
A) protein A
B) protein B
C) protein C
D) All three proteins would elute at the same time from the column.
E) Not enough information about the proteins is given in the problem.
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62
How are sequential reactions controlled in the Edman degradation procedure?
A) A high salt step is followed by a low salt step.
B) A low salt step is followed by a high salt step.
C) A high pH step is followed by a low pH step.
D) A low pH step is followed by a high pH step.
E) None of the answers is correct.
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63
The structure below is a molecule used in the sweeteners Equal® and NutraSweet®. When heated, the peptide bond will hydrolyze into methanol and which two amino acids?
A) asparagine and tyrosine
B) aspartic acid and phenylalanine
C) glutamic acid and phenylalanine
D) aspartic acid and tryptophan
E) glutamic acid and histidine
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64
Iodoacetamides, maleimides, benzyl halides, and bromomethyl ketones can all be used to modify the _____ group on _____ residues.
A) amino; basic
B) phenyl; Tyr and Trp
C) carboxyl; acidic
D) sulfhydryl; Cys
E) hydroxyl; Ser and Tyr
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65
Which item is NOT a biochemical use/function of peptides of small molecular weight?
A) artificial sweetener
B) hormone
C) poison
D) antibiotics
E) All of the answer choices are correct.
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66
Which of the lanes in the gel below would represent an "uninduced" sample?
A) 1
B) 2
C) 3
D) 4
E) 5
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67
Describe the structures of the amino acids phenylalanine and aspartate in the ionization state you would expect at pH 7.0. Why is aspartate very soluble in water, whereas phenylalanine is much less soluble?
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68
According to the table, size-exclusion (gel-filtration) chromatography could NOT be used to separate which protein mixture? Protein
MW
PI
A
12,500
3)2
B
13,200
5)7
C
13,500
10)5
D
25,200
6)3
E
36,900
5)8
F
78,400
6)1
A) proteins A, D, and F
B) proteins C, E, and F
C) proteins B, E, and F
D) proteins A, B, and C
E) All of the answers are correct.
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69
The gel below illustrates the purification of the RecA protein from E. coli. This gel was loaded from the top. Which statement BEST describes how proteins "run" in an SDS gel?
A) The proteins are separated primarily by molecular weight-the largest MW proteins are on the bottom, and the smallest are on the top.
B) The proteins are separated primarily by molecular weight-the smallest MW proteins are on the bottom, and the largest are on the top.
C) The proteins are separated primarily by charge-the protein with the smallest pI is on the top, and the protein with the largest pI is on the bottom.
D) The proteins are separated primarily by charge-the protein with the largest pI is on the top, and the protein with the smallest pI is on the bottom.
E) The proteins are separated primarily by their propensity to precipitate-as electrophoresis progresses, the heat generated by the current denatures proteins faster or slower. The slowest to denature is on the bottom, and the fastest to denature is on the top.
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70
A protein with a high percentage of lysine and arginine residues would be BEST purified and concentrated with which type of column?
A) cation exchange
B) anion exchange
C) size-exclusion chromatography
D) affinity chromatography
E) reverse-phase chromatography
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71
What does the molecule SDS do to proteins?
A) It neutralizes any charged residues on the protein.
B) It denatures large portions of proteins.
C) It distributes a large negative charge throughout the protein.
D) It neutralizes any charged residues on the protein and denatures large portions of proteins.
E) It denatures large portions of proteins and distributes a large negative charge throughout the protein.
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72
Only one of the common amino acids has no free -amino group. Name this amino acid.
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73
A protein with a high percentage of aspartate and glutamate residues would be BEST purified and concentrated with which type of column?
A) cation exchange
B) anion exchange
C) size-exclusion chromatography
D) affinity chromatography
E) reverse-phase chromatography
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74
Selective precipitation of a protein from a crude extract is MOST effective by which molecule?
A) ammonium sulfate
B) urea
C) sodium dodecyl sulfate
D) EDTA (ethylenediaminetetraacetic acid)
E) All of the answers are correct.
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75
The "signature sequence" shown below represents a portion of a protein from four different organisms. a. At which position(s) are amino acid residues invariant?
b. At which position(s) are amino acids limited to positively charged residues?
c. At which position(s) are amino acids limited to negatively charged residues?
d. At which position(s) are amino acids limited to nonpolar residues?
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76
The "signature sequence" shown below represents a portion of a protein from four different organisms. The proteins can be classified as:
A) homologs.
B) orthologs.
C) paralogs.
D) both homologs and orthologs.
E) both homologs and paralogs.
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77
According to the table, ion-exchange chromatography would be the LEAST effective method to separate which protein mixture? Protein
MW
PI
A
12,500
3)2
B
13,200
5)7
C
13,500
10)5
D
25,200
6)3
E
36,900
5)8
F
78,400
6)1
A) proteins A, B, and C
B) proteins A, C, and E
C) proteins B, E, and F
D) proteins B, C, and E
E) All of the answers are correct.
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78
R. Bruce Merrifield provided an innovation to synthesize peptides. Which statement does NOT describe part of his technology?
A) One end of the peptide is attached to a solid support.
B) At each step in the cycle, protective chemical groups block unwanted reactions.
C) The peptide product must be purified between each step of the cycle.
D) The support for the peptides is similar to a chromatography column.
E) All of the statements describe part of Merrifield's technology.
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79
What are the structural characteristics common to all amino acids found in naturally occurring proteins?
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80
Briefly describe the five major groupings of amino acids.
79.
A
B
C
D
E
Tyr-Lys-Met
Gly-Pro-Arg
Asp-Trp-Tyr
Asp-His-Glu
Leu-Val-Phe
Which one of the above tripeptides:
____ (a) is most negatively charged at pH 7?
____ (b) will yield DNP-tyrosine when reacted with l-fluoro-2,4-dinitrobenzene and hydrolyzed in acid?
____ (c) contains the largest number of nonpolar R groups?
____ (d) contains sulfur?
____ (e) will have the greatest light absorbance at 280 nm?
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