Deck 3: Amino Acids and the Primary Structures of Proteins

Question 1

Basic amino acids are positive, negative at pH 7 and acidic R group amino acids are positive, negative at pH 7.

A) negative; positive
B) negative; negative
C) positive; negative
D) positive; positive

Answer 1

positive; negative

Question 2

Disulfide bridges can form in proteins .

A) only between cysteine residues side-by-side in the protein sequence
B) between cysteine residues that are close in three-dimensional space, but not necessarily close in the primary structure
C) between two cystine residues in proteins
D) between any two methionines or cysteines

Answer 2

between cysteine residues that are close in three-dimensional space, but not necessarily close in the primary structure

Question 3

An amino acid named for a plant from which it was first isolated is

A) proline.
B) methionine.
C) threonine.
D) asparagine.

Answer 3

asparagine.

Question 4

Ultraviolet UV) light can be used to estimate protein solution concentrations because

A) phenylalanine absorbs at 260 nm.
B) all the amino acids absorb UV light.
C) aromatic amino acids absorb at 280 nm.
D) tryptophan and tyrosine absorb at 280 nm.
E) All of the above

Question 5

The overall shape of a protein is greatly influenced by

A) amino acid R group properties.
B) charged amino acids.
C) hydrophobic amino acids.
D) pH.
E) hydrophilic amino acids.

Question 6

An amino acid with two chiral carbon atoms

A) is unstable.
B) can exist in 4 forms all of which are superimposable.
C) can form three possible stereoisomers.
D) can form four possible stereoisomers.
E) can form five possible stereoisomers.

Question 7

Amino acids with non-ionizable side chains are zwitterions when they are .

A) in any solution
B) at physiological pH, pH = 7.4
C) in acidic solutions only
D) in alkaline solutions only
E) All of the above

Question 8

The RS system of nomenclature describes

A) amino acids not easily described by the DL system.
B) the way the R groups are arranged.
C) the chiral carbon centers of amino acids.
D) the strength of the chemical groups in amino acids.

Question 9

Arginine is the most basic of the 20 amino acids because its side chain is under most cell conditions.

A) very highly charged
B) hydrophobic
C) titrated
D) protonated
E) negatively charged

Question 10

If the R group of an amino acid is -CH₃, then the name of this compound is

A) methyl amino acid.
B) 2-aminopropanoic acid.
C) alanine.
D) All of the above
E) B and C

Question 11

The amino acids in polypeptide chains which contain sulfur S) are

A) cysteine, cystine, and methionine.
B) cystine.
C) methionine only.
D) cysteine only.
E) cysteine and methionine.

Question 12

Concentrations of some proteins cannot be estimated by UV spectrophotometry because they are

A) high in non-absorbing amino acids.
B) low in tryptophan and tyrosine.
C) low in protein.
D) high in aromatic amino acids.

Question 13

The R group of an amino acid determines if it is

A) hyrophilic or hydrophobic.
B) polar or nonpolar.
C) charged or uncharged.
D) an acid or a base.
E) All of the above

Question 14

Amino acids are named that because each one

A) is a unique carboxylic acid.
B) has a standard configuration.
C) is a carboxyl derivative of an amide acid.
D) is an amino derivative of a carboxylic acid.

Question 15

The last common ancestor of modern organisms must have used

A) both D and L amino acids.
B) D amino acids.
C) L amino acids.
D) either D or L amino acids.

Question 16

Although the hydroxyl groups in serine and threonine are uncharged, they can react within active sites of some enzymes .

A) precisely because they are uncharged
B) because the hydroxyl group is polar
C) because the hydroxyl group is small and fits into the site
D) All of the above

Question 17

Proline is distinct among the 20 commonly found amino acids because

A) it is a ring compound.
B) it is hydrophilic and ionic.
C) the nitrogen of the amino group is in a ring.
D) the carbon of the carboxyl group is in a ring.
E) it has little effect on protein structure.

Question 18

Glycine is not a stereoisomer because

A) it has no chiral carbon.
B) it does not form enantiomers.
C) it does not exist in two non-superimposable mirror-image forms.
D) All of the above
E) A and B only

Question 19

Tyrosine and tryptophan are less hydrophobic than phenylalanine because

A) phenylalanine has an indole group.
B) phenylalanine has no polar group in the side chain.
C) phenylalanine is a phenol.
D) tyrosine and tryptophan have smaller R groups.
E) All of the above

Question 20

Amino acids found in meteorites and near stars are

A) D isomers only.
B) L isomers only.
C) Both D and L isomers.
D) not isomers.

Question 21

The pK_aʹs of arginineʹs α-Carboxyl group, α-Amino group and side chain are 1.8, 9.0 and 12.5, respectively. Calculate the isoelectric point.

A) 7.8
B) 7.2
C) 10.8
D) 5.4

Question 22

The pK_aʹs of isoleucineʹs α-Carboxyl group and α-Amino group are 2.3 and 9.8, respectively. Calculate the isoelectric point.

A) 2.3
B) 6.0
C) 9.8
D) The isoelectric point cannot be calculated without the pK_a value for the side chain.

Question 23

Which structure below is appropriate for glycine at neutral pH?

A) H₂NCH₂COOH
B) H₂NCH₂COO^{-
C)( +}H₃NCH₂COO^{- )
D)( +}H₃NCH₂COOH)

Question 24

Which amino acid is ideal for the transfer of protons within the catalytic site of enzymes due to the presence of significant amounts of both the protonated and deprotonated forms of its side chain at biological pH?

A) Lysine
B) Asparagine
C) Tyrosine
D) Cysteine
E) Histidine

Question 25

The primary structure of a protein describes the .

A) number of each type of amino acid percent composition
B) linear sequence of amino acids
C) overall three-dimensional shape
D) Φ and Ψ angles for each amino acid

Question 26

A protein that contains more isoleucine, phenylalanine and leucine than asparagine, lysine and arginine is most likely

A) hydrophilic.
B) hydrophobic.
C) neutral.
D) low on the hydropathy index scale.

Question 27

How do the pK_a values of an ionizable side chain compare when the amino acid is free versus when it is in a polypeptide chain?

A) The pK_a of the side chain is independent of whether the amino acid is in a polypeptide chain or is free.
B) The pK_a of the side chain is always lower for the free amino acid.
C) The pK_a of the side chain may be lower or higher in a polypeptide chain due to weaker inductive effects and differences in their microenvironments.
D) The pK_a of the side chain is usually higher in a polypeptide chain due to stabilization from nearby residues in the three-dimensional structure.

Question 28

According to the Henderson-Hasselbalch equation, when the concentrations of proton acceptor and proton donor are the same, then

A) the carboxylic acid is totally neutralized.
B) only salt forms are present.
C) pH = pK_a.
D) pK_a = log[proton acceptor]/[proton donor].

Question 29

Amino acids which are not incorporated into polypeptides are converted into

A) neurotransmitters.
B) methyl donors.
C) antibiotics.
D) blood flow controllers.
E) All of the above

Question 30

The pK_a of a certain weak acid is 4.0. Calculate the ratio of proton acceptor to proton donor at pH 7.0.

A) 1000:1
B) 20:1
C) 3:1
D) 1:1
E) The ratio cannot be calculated without knowing the structure of the weak acid.

Question 31

A polypeptide chain may have abrupt changes in direction and restriction in geometry because of the presence of

A) arginine.
B) glycine.
C) proline.
D) leucine or isoleucine.

Question 32

Cystine is likely to be isolated from proteins that are

A) high in methionine.
B) high in peptide-linked cysteine.
C) intracellular.
D) extracellular.

Question 33

At the isoelectric pH of an amino acid which has two pK_a values the net charge is

A) 0.5.
B) 1.
C) 0.
D) -1.

Question 34

A sequence of amino acids with a relatively high hydropathy is very likely to function by

A) being at the active site of an enzyme.
B) being embedded in a cell membrane.
C) making a protein soluble.
D) being on the protein surface.

Question 35

The pK_aʹs of the side chain group and the α-carboxyl group of glutamate are 4.1 and 2.1, respectively. Which statement accounts for this difference?

A) The side chain has more possible resonance structures.
B) The α-carboxyl group has less steric hindrance and is therefore ionized more easily.
C) The side chain is a different functional group than the α-carboxyl group.
D) The α-carboxyl group is closer to the α-amino group than the side chain is.

Question 36

For the amino acid lysine, the Henderson-Hasselbalch equation can be applied to ionization groups).

A) one
B) two
C) three
D) four

Question 37

Histidine has pK_a values of 1.8, 6.0 R-group and 9.3 . At pH 8.0, the net charge on histidine is

A) positive.
B) negative.
C) neutral uncharged.
D) insufficient information to tell.

Question 38

The isoelectric point of alanine is pH = 6.15. It is mixed with proline pH_COOH = 2.0; pH_NH2 = 10.6), and the mixture is placed in an electric field at pH 6.15. Which statement is true?

A) The two amino acids will be separated.
B) The two amino acids will not be separated.
C) Neither amino acid will move in the electric field.
D) Both amino acids will move from the origin and be separated.

Question 39

Proteins can be modified by adding to protein residues.

A) sugars and phosphate groups
B) hydroxyl and formyl groups
C) cystine
D) A and B
E) All of the above

Question 40

The pH inside cells is normally near pH 7. At pH 7 which statement is true about the charges ionization state of the α-Carboxyland α-Amino groups of an amino acid?

A) The α-Carboxyl group is 1- and the α-Amino group is 1+.
B) The α-Carboxyl group is 1+ and the α-Amino group is 1-.
C) The α-Carboxyl group is 1- and the α-Amino group is uncharged.
D) Both groups are uncharged not ionized) at pH 7.

Question 41

The liquid emerging from the bottom of a chromatography column is called the .

A) eluate
B) supernatant
C) solute
D) lysate

Question 42

Which is used as the basis of separation of proteins by affinity chromatography?

A) The net charge and pI of the protein at the pH of the column.
B) The proteinʹs molecular weight.
C) The proteinʹs density.
D) The selective binding of the protein to a ligand on the column matrix.

Question 43

What is the net charge on the dipeptide Arg-Pro at pH 9.0? The table below gives the pKa?s of the ionizable groups on the free amino acids. $\begin{array}{|l|c|c|c|}\hline \text { Free amino acid } & \begin{array}{c}\text { pKa of } \\\alpha \text {-Carboxyl group }\end{array} & \begin{array}{c}\text { pKa of } \\\alpha \text {-amino group }\end{array} & \begin{array}{c}p \text { Ka of side } \\\text { chain }\end{array} \\\hline \text { Arginine } & 1.8 & 9.0 & 12.5 \\\hline \text { Proline } & 2.0 & 10.6 & \cdots \\\hline\end{array}$

A) -1
B) -0.5
C) 0
D) +0.5
E) +1

Question 44

Which is used to hydrolyze the peptide bonds of a protein to yield free amino acids?

A) PITC
B) SDS
C) CNBr
D) HCl

Question 45

Which amino acids are linked in phenylalanylglycine?

A) phenyline, alanine and glycine
B) phenol, alanine and glycine
C) phenylalanine and glycine
D) phenol, adenine and glycine

Question 46

In a biochemistry laboratory a student added ammonium sulfate to a tube containing a buffered protein solution. The student then centrifuged the solution. What was the student probably trying to do?

A) change the pH of the buffer solution to solubilize all proteins
B) hydrolyze the proteins into their constituent amino acids to determine the percent composition
C) derivatize the N-terminal amino acid of all proteins
D) selectively precipitate and purify a certain protein

Question 47

During the fractionation process which of the following remain in the supernatant?

A) membrane proteins
B) the less soluble impurities
C) the Target protein and other more soluble proteins
D) the remaining unbroken whole) cells

Question 48

Which substance is used to fractionate proteins based on differences in their solubility as a function of salt concentration?

A) cellophane
B) sodium dodecyl sulfate
C) phenylisothiocyanate
D) ammonium sulfate

Question 49

The peptide bond is which of the following?

A) an amide bond
B) an ester bond
C) an ether bond
D) an amine bond

Question 50

What is the net charge on the tripeptide Gly-Arg-Lys at pH 7? The table below gives the pK_a?s of the ionizable groups on the free amino acids. $\begin{array}{|l|c|c|c|}\hline \text { Free amino acid } & \begin{array}{c}\mathrm{pKa} \text { of } \\\alpha \text {-Carboxyl group }\end{array} & \begin{array}{c}p \mathrm{k} \text { of } \\\alpha \text {-amino group }\end{array} & \begin{array}{c}\mathrm{pK} \mathrm{a} \text { of side } \\\text { chain }\end{array} \\\hline \text { Glycine } & 2.4 & 9.8 & \cdots \\\hline \text { Arginine } & 1.8 & 9.0 & 12.5 \\\hline \text { Lysine } & 2.2 & 9.1 & 10.5 \\\hline\end{array}$

A) -1
B) 0
C) +1
D) +2

Question 51

What is the purpose of SDS in SDS-PAGE?

A) to selectively bind the target protein
B) to maintain buffer pH in the gel
C) to cause the separation to be on the basis of molecular weight only
D) to initiate polymerization of acrylamide to form a gel

Question 52

In which technique is a protein solution a pumped through a metal needle at high voltage to create tiny droplets that are analyzed for their mass/charge ratio?

A) electrospray mass spectrometry
B) MALDI-TOF
C) aerosol microscopy
D) Millikan analysis
E) SDS-PAGE

Question 53

Which technique is used less for protein purification and more for the determination of molecular weights?

A) affinity chromatography
B) SDS-PAGE
C) gel filtration
D) ion exchange chromatography

Question 54

What is the N-terminal for the pentapeptide Val-Ile-Glu-Arg-Tyr?

A) the NH₃⁺ group on the side chain of Arg
B) valine
C) tyrosine
D) tryptophan

Question 55

Even though mass spectrometry has been in use for over a hundred years, it had only limited use with proteins until the 1980ʹs because

A) not many proteins had been discovered and purified before the 1980ʹs.
B) it was not possible to disperse charged proteins into a gaseous stream of particles.
C) many proteins are difficult or impossible to crystallize.
D) proteins decompose too quickly into their component amino acids.

Question 56

Which technique is most sensitive and accurate for the determination of a proteinʹs molecular weight?

A) SDS-PAGE
B) Gel filtration chromatography
C) mass spectrometry
D) X-ray crystallography
E) osmotic pressure

Question 57

The ionic charges associated with a protein molecule are .

A) mostly contributed by the side chains of constituent amino acids
B) determined by the contribution from the α-carboxyl group, α-amino group and side chain of every amino acid in the protein
C) contributed by only the N-terminal and C-terminal residues
D) independent of the amino acid composition and depend only on pH

Question 58

A mixture of four proteins X, Y, Z and N is applied to a gel-filtration column. Given the information supplied, which will elute first? $\begin{array}{|c|c|}\hline \text { Protein } & \text { Molecular Weight g/mol) } \\\hline X & 35,000 \\\hline Y & 26,000 \\\hline Z & 146,000 \\\hline \mathrm{N} & 26,000 \\\hline\end{array}$

A) Z
B) Y and N elute together
C) X
D) cannot answer without information about the isoelectric point

Question 59

Gel-filtration chromatography separates a mixture of proteins on the basis of .

A) charge
B) size
C) affinity for ligands in the column matrix
D) density

Question 60

A mixture of two proteins with the same pI and molecular weights MW) of 10,000 and 15,000 daltons, respectively, are applied to a gel filtration column. What happens during elution?

A) Both elute together.
B) The one with MW of 10,000 elutes first.
C) The one with MW of 15,000 elutes first.
D) More information is needed about the specificity of the column matrix to tell what happens.

Question 61

Ultraviolet (UV) light can be used to estimate concentrations of proteins in solutions because tryptophan and tyrosine absorb light at a wavelength of 280 nm.

Question 62

Which will react with amino acids to yield derivatives that can be detected by monitoring the absorbance at 254 nm?

A) PITC
B) SDS
C) CNBr
D) HCl

Question 63

Most proteins contain an approximately equal amount of each of the standard amino acids.

Question 64

The distribution of amino acids in a protein often cannot be determined precisely by acid hydrolysis. Why?

A) The side chains of asparagine and glutamine are also hydrolyzed.
B) The amine groups on lysine and arginine neutralize much of the acid.
C) The side chain of phenylalanine is almost totally destroyed by acid hydrolysis.
D) All of the above

Question 65

Asparagine and glutamine are both amides of aspartic acid and because they have uncharged sidechains are often found on the interior of proteins.

Question 66

Cation-exchange resins have negatively charged groups covalently attached to the column matrix.

Question 67

All 20 common amino acids exist in nature equally as both the D and L stereoisomers.

Question 68

All amino acids have mirror-image pairs designated D and L.

Question 69

What is the purpose of treating a protein with 2-mercaptoethanol?

A) to hydrolyze the protein into its amino acids
B) to cleave the disulfide bonds
C) to derivatize any free sulfhydryl groups to prevent them from reforming disulfide bonds
D) to derivatize the N-terminal amino acid during the Edman degradation

Question 70

Amino acids are neutral at the isoelectric pH.

Question 71

All 20 common amino acids have an amino group and a carboxyl group bonded to the same carbon atom.

Question 72

Most purification procedures for proteins are carried out at room temperature.

Question 73

The isoelectric point of amino acids is the average of the values pK_COOH + pK_NH2.

Question 74

Amino acids and amino acid derivatives can be used to modify proteins.

Question 75

Affinity chromatography can be used to save many purification steps compared to other techniques due to its high specificity for the target protein.

Question 76

Uncharged R groups of amino acids are not polar.

Question 77

What information can be gained by comparing the sequences of proteins that have the same or similar function in different species?

A) to determine evolutionary relationships and relatedness of species
B) to determine sequences that are conserved among species since they are likely to be important to the function and stability of the proteins
C) to locate highly variable residues which contribute little to the structure and function of the protein
D) All of the above

Question 78

An octapeptide was determined to have the following amino acid composition: Lys 2), Phe 2), Gly 1), His 1), Leu 1), Met 1). The native peptide was run through one cycle of the Edman degradation and the PTH-leucine derivative was identified by HPLC. When the native peptide was exposed to cyanogen bromide CNBr), a heptapeptide and free glycine were recovered. Incubation of the native protein with trypsin gave a tetrapeptide, a tripeptide, and free lysine. The peptides were separated and each run through one cycle of the Edman degradation. The tetrapeptide yielded the PTH-leucine derivative, and the tripeptide yielded the PTH-phenylalanine derivative. Incubation of the native protein with pepsin produced a dipeptide and two tripeptides. The amino acid composition of the tripeptides not the order) were determined to be Phe, Gly, Met) and Phe, Lys, Lys). What is the sequence of the octapeptide?
Specificities of Proteases
BrCN cuts at the C-terminal side of Met Trypsin cuts at the C-terminal side of Lys or Arg
Pepsin cuts at the N-terminal side of Phe, Trp or Tyr

A) Leu-His-Phe-Lys-Lys-Phe-Met-Gly
B) Gly-Met-Phe-Lys-Lys-Phe-His-Leu
C) Met-Leu-Phe-Lys-Phe-Gly-Lys-His
D) Leu-His-Lys-Lys-Phe-Phe-Gly-Met
E) His-Phe-Leu-Lys-Lys-Phe-Met-Gly

Question 79

The hydropathy of amino acids can help determine the folding of protein chains.

Question 80

In gel electrophoresis the molecules with the highest molecular weight migrate the farthest from the starting wells.