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Homeworks chapter 2 and 3
What is the first step in analysis of any cellular protein?
digestion of proteins
purification of proteins
identification of proteins
affinity chromatography
gel electrophoresis
purification of proteins
The X-ray analysis of a pure protein crystal is used to determine:
a helices of protein.
b sheets of protein.
secondary structure of protein.
tertiary structure of protein.
quaternary structure of protein.
tertiary structure of protein.
What is another name for molecular exclusion chromatography?
ion-exchange chromatography
affinity chromatography
gel-filtration chromatography
high-performance liquid chromatography
gel electrophoresis
gel-filtration chromatography
What method can be used to separate proteins only by their charge?
gel-filtration chromatography
affinity chromatography
gel electrophoresis
ion-exchange chromatography
dialysis
ion-exchange chromatography
What method can be used to separate proteins by specific binding with other molecules?
gel-filtration chromatography
affinity chromatography
gel electrophoresis
ion-exchange chromatography
dialysis
affinity chromatography
______ enables highly sensitive and reliable detection of masses of different molecules.
mass spectrometry
What compounds are used to reduce disulfide bonds? Select all that apply.
sodium dodecyl sulfate
polyacrylamide
β-mercaptoethanol
dithiothreitol
polyampholytes
β-mercaptoethanol
dithiothreitol
A medium for SDS-PAGE and isoelectric focusing is:
β-mercaptoethanol.
methylenebisacrylamide.
acrylamide.
polyacrylamide.
sodium dodecyl sulfate.
polyacrylamide.
In SDS-PAGE, the protein mass is inversely proportional to the:
velocity of protein migration.
frictional coefficient.
protein shape.
viscosity of the medium.
concentration of polyacrylamide.
velocity of protein migration.
What parameter of the molecule can be determined based on time it takes for the ion of that molecule to pass through the chamber of the TOF mass analyzer?
structure
size
mass
pI
pH
mass
_____ can be added prior to gel electrophoresis to fully denature proteins.
Coomassie blue
Polyacrylamide
SDS
β-mercaptoethanol
Cyanogen bromide
β-mercaptoethanol
What is the advantage of adding SDS to gel electrophoresis?
SDS colors the proteins for visualization.
SDS reduces disulfide bonds.
SDS allows proteins to be separated on the basis of approximate mass.
SDS participates in the creation of a three-dimensional mesh.
SDS changes the charge of the native protein.
SDS allows proteins to be separated on the basis of approximate mass.
What property can be identified from the recombination of scattered waves during X-ray analysis of the protein crystal?
size of protein
atomic arrangement of the protein crystal
charge of the protein molecule
protein activity
molecular weight of protein
atomic arrangement of the protein crystal
The method that reveals the atomic structure of proteins in a solution is:
MALDI.
electrophoresis.
X-ray crystallography.
ion-exchange chromatography.
NMR.
NMR
What is used during preparation of samples for SDS-PAGE to disrupt covalent bonds that support the spatial structure of the protein?
β-mercaptoethanol
polyacrylamide
sodium dodecyl sulfate
Coomassie blue
methylenebisacrylamide
β-mercaptoethanol
A method that can be used to separate proteins by their sedimentation coefficients is:
gel-filtration chromatography.
mass spectrometry.
dialysis.
zonal centrifugation.
electrophoresis.
zonal centrifugation.
The FIRST step in protein purification from a homogenate often is:
ion-exchange chromatography.
gel-filtration chromatography.
HPLC.
centrifugation.
gel electrophoresis.
centrifugation.
Molecular exclusion or gel-filtration chromatography separates molecules on the basis of:
structure.
size.
mass.
pI.
pH.
size
What technique can be used to determine the mass-to-charge ratio of a molecule?
Edman degradation
affinity chromatography
diagonal electrophoresis
MALDI-TOF
SDS-PAGE
MALDI-TOF
Two-dimensional electrophoresis is a combination of:
ion-exchange chromatography and affinity chromatography.
ion-exchange chromatography and SDS-PAGE.
SDS-PAGE and affinity chromatography.
isoelectric focusing and SDS-PAGE.
isoelectric focusing and ion-exchange chromatography.
isoelectric focusing and SDS-PAGE.
What is NOT a key property that enable proteins to participate in a wide range of functions?
Proteins have a high molecular weight.
Proteins contain different functional groups.
Some proteins are quite rigid, whereas others display considerable flexibility.
Proteins are linear polymers built of different amino acids.
Proteins can interact with one another and with other biological macromolecules to form complex assemblies.
Proteins have a high molecular weight.
What does an α-amino acid consist of?
carbonyl group, α carbon, amino group, oxygen atom, distinctive R group
carboxylic acid group, α carbon, amino group, hydrogen atom, distinctive R group
carboxylic acid group, ε carbon, nitro group, hydrogen atom
alcohol group, α carbon, amino group, nitrogen atom, distinctive R group, hydrogen atom
carboxylic acid group, δ carbon, imine radical, hydrogen atom, distinctive R group
carboxylic acid group, α carbon, amino group, hydrogen atom, distinctive R group
What isomers of amino acids are found in proteins and what absolute configuration do they have?
L isomer; R absolute configuration
D and L isomers; R absolute configuration
L isomer; S absolute configuration
D isomer; S absolute configuration
L and D isomers; S absolute configuration
L isomer; S absolute configuration
In an acidic solution (pH = 1), what is the ionization state of an amino acid?
The amino group is deprotonated; the carboxyl group is protonated.
The amino group is not dissociated; the carboxyl group is not dissociated.
The amino group is protonated; the carboxyl group is deprotonated.
The amino group is protonated; the carboxyl group is not dissociated.
The amino group is deprotonated; the carboxyl group is not dissociated.
The amino group is protonated; the carboxyl group is not dissociated
Choose the correct groups for Thr, Lys, His, Met, respectively, on the basis of general chemical characteristics.
polar but uncharged; negatively charged; positively charged; hydrophobic
polar but uncharged; positively charged; positively charged; hydrophobic
positively charged; hydrophobic; polar but not charged; positively charged
negatively charged; hydrophobic; positively charged; polar but not charged
positively charged; positively charged; polar but not charged; negatively charged
polar but uncharged; positively charged; positively charged; hydrophobic
Which amino acid has the one-letter abbreviation K?
histidine
asparagine
alanine
valine
lysine
lysine
The amide bond is a linkage between the:
β-amino group of one amino acid and the α-amino group of another amino acid.
β-carboxyl group of one amino acid and the β-amino group of another amino acid.
δ-carboxyl group of one amino acid and the α-carboxyl group of another amino acid.
α-amino group of one amino acid and the ε-amino group of another amino acid.
α-carboxyl group of one amino acid and the α-amino group of another amino acid.
α-carboxyl group of one amino acid and the α-amino group of another amino acid.
What is the amino-terminal residue and what is the carboxyl-terminal residue in the sequence of amino acids Gly-Tyr-Gly-Phe-Leu?
Leucine is N-terminal and glycine is C-terminal.
Glycine is N-terminal and leucine is C-terminal.
Tyrosine is N-terminal and leucine is C-terminal.
Phenylalanine is N-terminal and leucine is C-terminal.
There are no N-terminal and C-terminal residues in the sequences of amino acids.
Glycine is N-terminal and leucine is C-terminal.
A protein with a molecular weight of 75 550 g mol–1 has a mass of:
75,550 Da or 755.5 kDa.
7555 Da or 75.55 kDa.
75,550 Da or 75.55 kDa.
755,500 Da or 7.555 kDa.
7,555,000 Da or 75550 kDa.
75,550 Da or 75.55 kDa.
Knowledge of the amino acid sequences is important for several reasons. What is NOT one of those reasons?
Amino acid sequences determine the three-dimensional structures of proteins.
The sequence of a protein reveals much about its evolutionary history.
Knowledge of the sequence of a protein can help to prevent mutations.
Changes in the amino acid sequence can lead to abnormal protein functioning and disease.
The sequence of a protein is necessary to determine its function.
Knowledge of the sequence of a protein can help to prevent mutations
What is the configuration of peptide bonds in proteins?
Almost all peptide bonds are in the cis configuration.
Almost all peptide bonds are in the trans configuration.
Half of all peptide bonds are in the trans configuration and the other half are in the cis configuration.
Approximately one third are in the trans configuration and rest are in the cis configuration.
Approximately one third are in the cis configuration and rest are in the trans configuration.
Almost all peptide bonds are in the trans configuration
An α helix is a coil stabilized by:
intrachain hydrogen bonds between the carbonyl oxygen of a residue and the amide hydrogen of the fourth residue away.
intrachain nitrogen bonds between the carbonyl nitrogen of a residue and the amide nitrogen of the second residue away.
extrachain oxygen bonds between the carbonyl oxygen of a residue and the amide nitrogen of the fifth residue away.
intrachain nitrogen bonds between the carbonyl nitrogen of a residue and the amide nitrogen of the sixth residue away.
extrachain hydrogen bonds between the carbonyl hydrogen of a residue and the amide oxygen of the third residue away.
intrachain hydrogen bonds between the carbonyl oxygen of a residue and the amide hydrogen of the fourth residue away.
A β sheet is formed by linking two or more β strands lying next to one another through:
nitrogen bonds.
oxygen bonds.
ionic bonds.
disulfide bridges.
hydrogen bonds.
hydrogen bonds.
Why are porins considered to be "inside out" relatives to proteins that function in aqueous solution?
Porins are positively charged while usual proteins are negatively charged.
Porins interact with the neighboring alkane chains while usual proteins interact with alkene chains.
Porins function in outer membranes while usual proteins function in inner membranes.
Porins function only in bacteria while usual proteins function in all organisms.
Porins have a reverse distribution of hydrophobic and hydrophilic amino acids.
Porins have a reverse distribution of hydrophobic and hydrophilic amino acids.
What are the interactions that associate the two helices in α-keratin?
hydrogen bonds and electrostatic forces
van der Waals forces and covalent interactions
electrostatic forces and metallic bonds
van der Waals forces and ionic interactions
metallic bonds and van der Waals forces
van der Waals forces and ionic interactions
What is the simplest sort of quaternary structure?
a monomer
a dimer consisting of two different subunits
a dimer consisting of two identical subunits
a trimer consisting of two identical subunits and one diverse subunit
a tetramer consisting of two identical subunits and diverse subunits
a dimer consisting of two identical subunits
What is a structure of the hemoglobin molecule?
α2 dimer
β2 dimer
α2β1 trimer
α1β2 trimer
α2β2 tetramer
α2β2 tetramer
What disrupts the noncovalent interactions in proteins?
guanidinium sulfide
β-mercaptoethanol
uric acid
urea
ammonia
urea
In the ribonuclease experiments performed by Anfinsen, β-mercaptoethanol reduced:
all incorrectly paired bonds and stabilized the protein structure.
all bonds and destroyed the protein structure.
all charged residues, and the protein was unable to take part in signaling.
all bonds, and the unfolded protein molecules became tangled up with one another to form aggregates.
incorrectly paired disulfide bonds, allowing them to reform with the correct pairing until the most stable conformation of the protein had been obtained.
incorrectly paired disulfide bonds, allowing them to reform with the correct pairing until the most stable conformation of the protein had been obtained.
What is the term for a molecule that contains both positive and negative charges but overall has a neutral charge?
enantiomer
amino acid
racemate
zwitterion
amphipath
zwitterion
Which amino acid forms disulfide bonds?
histidine
methionine
proline
serine
cysteine
cysteine
What amino acid has an ionizable R group with a pKa near neutral pH?
histidine
serine
aspartic acid
lysine
tyrosine
histidine
What plot type allows one to investigate the likely ϕ and ψ angles of the peptide backbone?
Hill
Lineweaver–Burk
Hanes–Woolf
Ramachandran
Michaelis–Menten
Ramachandran
What level of protein structure is composed of α helices, β sheets, and turns?
primary
secondary
tertiary
quaternary
supersecondary
secondary
The overall three-dimensional structure of a single polypeptide is referred to as _____ structure.
primary
secondary
tertiary
quaternary
supersecondary
tertiary
At a pH of 12, what is the charged groups present in glycine?
–NH3+
–COO–
–NH2+
–NH+
–CO–
–COO–
The amino acids Tyr, Asn, and Thr:
have aromatic rings.
are negatively charged at pH = 7.0.
are positively charged at pH = 7.0.
have double bonds in side chains.
are polar.
are polar.
Which individual won a Nobel Prize for his or her landmark work in sequencing the protein insulin?
Pauling
McClintock
Gilbert
Maxam
Sanger
Sanger
The term quaternary with respect to protein structure stands for:
a repeating structure stabilized by intrachain hydrogen bonds.
the ability to form all four kinds of noncovalent bonds.
a multisubunit structure.
a linear sequence of four amino acids.
the only four amino acids that can form hydrogen bonds.
a multisubunit structure.
What pair of amino acids is positively charged at a neutral pH?
Lys, Arg
Tyr, Arg
Cys, Met
Leu, Pro
Asp, Glu
Lys, Arg
What is NOT a modification acquired by proteins?
cleavage and trimming of the protein
addition of carbohydrate groups
phosphorylation of certain groups
hydrolysis of all protein
addition of acetyl groups
hydrolysis of all protein
What amino acid residue would MOST likely be buried in the interior of a water-soluble globular protein?
Asp
Ser
Phe
Lys
Gln
Phe
Note 
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