chapter 5 - 7 study questions
Which of the following modified amino acids is incorporated during translation rather than being modified post-translationally?
Selenocysteine
Human and sperm whale myoglobin have very similar primary structures. Which of the following statements are correct? 1 The two proteins are very likely related evolutionarily. 2 The differences in the sequences in many instances represent a conservative change (such as L for I). 3 The differences in the sequences in many instances represent a nonconservative change (such as D for A). 4 There is no correlation between the two proteins, since they originate from very different species.
Statements 1 and 2 are correct.
Which statements about β turns are correct? 1 Their purpose is to reverse the direction of the polypeptide chain. 2 There are two types, I and II, which differ mainly in the conformation about the i+1 and i+2 residue amide bond. 3 They typically contain large, hydrophobic residues. 4 Their conformation is held in place through H bonds.
Statements 1, 2, and 4 are correct
Loops and turns in proteins are _____
Stretches of non-repeating three dimensional structures in proteins
Proteins can be modified by adding ________ to protein residues.
Sugars, phosphate, hydroxyl, and formyl groups
If apamine does not react with iodoacetate, then how many disulfide bonds are present
two
Which of the following definitions are correct? 1 An antigen is the substance that elicits an immune response. 2 An epitope is a portion on the surface of an invading particle to which specific antibodies bind. 3 An antibody is a specific immunoglobulin that binds to an antigen
All of the listed definitions are correct.
Which of the following statements about protein quaternary structure are correct? 1 It involves a complex of two or more proteins interacting with each other. 2 The subunits of the structure can be either identical or different. 3 The interactions between subunits can give rise to indefinite growth of polymeric complexes. 4 Most assemblies of protein subunits have one or more defined axis of rotation.
All of the listed statements are correct.
Which of the following statements regarding the folding of proteins are true? 1 The burying of hydrophobic groups within a folded protein molecule away from water leads to a stabilizing entropy increase known as the hydrophobic effect. 2 Internal hydrogen bonds stabilize the fold. 3 Salt bridges stabilize the fold. 4 Van der Waals interactions have a stabilizing, cumulative effect.
All statements are correct
What feature does a Ramachandran plot display?
Allowed angles of phi and psi for a polypeptide backbone
A change from one conformation of a molecule to another, involves _______
Rotation about bonds only
To what level of structure do α-helices belong?
Secondary
Proteins structure is broken down into separate levels of organization. The secondary structure of a protein is best described by which statement
Secondary structure of a protein is the adoption of a locally repeating structure.
Which statement is TRUE about the side chains of residues in an α-helix?
They extend radially outward from the helix axis.
Thus, biological reactions that are highly _______tend to also be highly regulated since they are not easily reversed.
spontaneous
The reaction is _______ when the value of ΔG is _______
spontaneous; negative
Which statement(s) is/are true about amyloid fibrils? 1 Amyloid fibrils are characterized by highly organized arrays of β sheet structure. 2 Amyloidogenic proteins are associated with human disease states like Alzheimer's disease, Parkinson's disease, Cataracts 3 Fibrils are formed from a left-handed helix of four "protofibrils". 4 Amyloid disease is not correlated with inherited genetic mutations.
1, 2, and 3
Which statements about immunoconjugates are true? 1 Immunoconjugates are hybrid drugs that link a cytotoxic agent to an antibody. 2 The cytotoxic agent is usually attached to the constant region of the antibody. 3 The antibody has a high affinity to its target. 4 Immunoconjugates are in clinical trials, but none has been approved yet.
1, 2, and 3
Which statement(s) about collagen is/are true? 1 Collagen is the most abundant single protein in most vertebrates. 2 Tropocollagen is a double helix of two polypeptide chains. 3 Tropocollagen is the basic unit of a collagen fiber. 4 The individual chains are left-handed helices, with ∼3.3 residues/turn.
1, 3, and 4
How many monomers are there in an oligomeric protein designated αβ2γ2
5
Which statement correctly describes amphipathic (or amphiphilic) helices and sheets
Amphipathic helices and sheets have predominantly hydrophilic residues on one face and predominantly hydrophobic residues on an opposite face.
The phosphofructokinase tetramer displays which symmetry?
D2 symmetry
Protein folding is a random process, whereby a vast number of possible conformations are tested to find the desired most stable state.
False
Proteins cannot self-assemble into a functional conformation after they have been denatured.
False
The interactions that stabilize multi-subunit complexes are different to those that stabilize tertiary structure.
False
Structural proteins that typically assemble into large cables or threads, to provide mechanical support to cells or organisms are classified as ________ proteins
Fibrous
________ between amide protons and carbonyl oxygens is necessary to stabilize a regular folding of protein secondary structure.
Hydrogen bonding
Protein subunits in a multi-subunit protein are held to each other primarily by _______
Hydrophobic and other weak interactions
The principle force holding the subunits of an oligomeric protein to each other are ______
Hydrophobic interactions
Which of the following is CORRECT when considering the tertiary structure of globular proteins?
Hydrophobic residues are normally on the inside and hydrophilic residues are on the outside.
Scurvy results in weakness in collagen fibers because the enzymes that catalyze ________ of proline and lysine residues in collagen require Vitamin C.
Hydroxylation
The Tm of a protein is temperature at which it ______
Is half denatured
Keratin, a protein comprising hair, can form a helix with ϕ=−60∘ϕ=−60∘ , ψ=−50∘ψ=−50∘. From the Ramachandran plot (see the figure on the left), describe this helix with respect to handedness.
It could have a right-handed αα helix structure.
Which statement is NOT true about an α-helix?
It frequently contains proline residues
Choose the correct equilibrium expression for the following reaction: Gly-Ala(aq)+H2O(l)⇌Gly(aq)+Ala(aq)
Keq=[Gly][Ala]/[Gly-Ala]
Proline is NOT often found in α-helices of proteins because it _______
Lacks a hydrogen atom on its amide nitrogen
Super secondary structures that contain recognizable combinations of α-helices, β-strands and loops (e.g. the Greek Key) are called _______
Motifs
the estimate obtained in Part A is surely too large. Give one reason why.
Not all of these conformations will be sterically possible.
Each residue in a polypeptide chain has two backbone bonds:______, about which rotation is permitted. The angle of rotation about the _____ bond is referred to as ϕ (phi) and that about the ______ bond is called ψ (psi).
N−Cα−C; N−Cα; Cα−C
Protein folding is a thermodynamically favorable process under physiological conditions because ________.
Of the large negative enthalpy change associated with many noncovalent interactions
The amino acid side chain residues in an α helix point ________ away from the center of the helix
Outward
Proteins with alpha helix regions called leucine zippers are ________
Part of pairs of helices that are wrapped around each other
Which statement is TRUE about disulfide bonds and protein folding?
Proteins occasionally adopt non-native conformations and form improper disulfide bonds that can be reversed by the enzyme protein disulfide isomerase.
Which of the following statements about globular proteins are true? 1 The protein folds to make itself as compact as possible. 2 The packing of the protein is such that hydrophilic residues appear on the surface where they can interact with an aqueous environment. 3 β sheets are usually twisted, or wrapped into barrel structures. 4 All parts of a globular protein can be classified as helix, β sheet, or turns.
Statements 1, 2, and 3 are correct.
Ramachandran determined the "allowed" values of the phi and psi angles primarily by considering _______
Steric hindrance
What does it mean when it is said that a protein is oligomeric?
The active protein involves the association of two or more polypeptide chains.
A helical wheel can be used to show ________.
The amphipathic nature of a helix
What is TRUE about the rotation of bonds in a protein backbone?
The bond between the carbonyl carbon and nitrogen is restricted. Other bonds are free to rotate depending only on steric hindrance or the presence of proline residues.
Which of these statements is NOT true about β-sheets?
The side-chains of all amino acids point to the same side of the sheet.
A short 8-residue sequence of a polypeptide is determined to have φ angles ranging from -65 degrees to -80 degrees and ψ angles ranging from -40 degrees to -50 degrees. What conclusion can be drawn from this data?
This segment has helical content.
A β-sandwich forms when ________.
Two hydrophobic sides of β-sheets interact
These entropic and enthalpic effects make Δ G F → U more unfavorable for _______vs. _______ (i.e., the _______is more stable to unfolding than _______).
WT; the mutant; WT; the mutant
Based on the information in the table, which protein do you predict buries the greater hydrophobic surface area upon folding? Assume 2-state folding (i.e., no intermediates), and that the Unfolded state for both proteins is 100%% solvent-exposed.
adaH2 is predicted to bury more hydrophobic surface area upon folding that Top7.
Proline is not able to ___________the ideal ϕ and ψ angles for an α helix, owing to the presence of the rigid imidic group as its side chain
adopt
A protein stripped of its cofactor or metal ion is best described as?
apoprotein
These angles describe the ______conformation of any particular residue in any protein, and allow one to predict whether a combination of amino acids in a polypeptide will be able to form and maintain _______
backbone; a stable secondary structure
For an irreversible and spontaneous biological reaction, a different series of reactions and _______is required for this step to go in the opposite direction.
enzymes
Many biological pathways use the same reactions and ______for the forward and reverse directions because the reactions are close enough to equilibrium that small changes in reactant and product concentrations can change the net direction of the pathway.
enzymes
The basic secondary structure of which of these fibrous proteins is a β-sheet structure
fibroin
A tetrameric protein contains _______
four different or four identical subunits only
The folded conformation of proteins can be stabilized by the binding of a ________ or ________
metal ion, cofactor
The formation of favorable ________ionic or __________ interactions in a __________protein replace interactions between solvent (water) and the ionic species (or ________ donors and acceptors) in the _________state. The favorable Δ H obtained by formation of _________ bonds in the _______protein is offset by the energy required to ________many interactions with solvent going from the ___________to the _________state.
intramolecular; h-bonding; folded; h-bond; unfolded; intramolecular bonds; folded; break; unfolded; folded
Chaperones are meant to prevent _______________ which is mediated by the intermolecular association of ________surfaces. A _____protein will minimize solvent-exposed __________surface area. Thus, as proteins unfold, more ________surface area will be exposed, triggering __________by chaperones.
irreversible aggregation of unfolded proteins; hydrophobic; folded; hydrophobic; hydrophobic; recognition
Interactions of _______side chains in the protein sequence lead to the formation of a tightly packed ______core. This core is stabilized by a ______number of __________ contacts. When a mutation occurs, it destabilizes the protein core and weakens _________ contacts leading to misfolding
nonpolar; hydrophobic; large; van der Waals contacts; van der Waals contacts
the reaction favors the _______when the equilibrium constant is _______
products; greater than one
The antibody binds to the specific antigen at the binding site formed by.
the variable domains of the light and heavy chains.
Nearly all peptide bonds are in the trans configuration because _______
trans peptide bonds minimize steric hindrance of R groups
Proteins have an asymmetrical tertiary structure, while multi-subunit proteins can exhibit several types of symmetry.
true
Due to loss of ________interactions in the folded state, ________will be more than________
van der waals; Δ H F → U (WT); Δ H F → U (MUT)
_______ because differences in conformational entropy around ϕ (Phi) and ψ (Psi) angles are _______ for Leu vs. Ala
Δ S protein F → U (WT) ≈ Δ S protein F → U (mut); smaller
Thus, the differences in ΔH and _______ both predict that the mutant will be_______stable to denaturation than the WT protein. stable to denaturation than the WT protein.
ΔSsolvent; less
Furthermore, proline does not have an _______group that acts as a stabilizing ___________ in the middle of the helix. As a consequence, the secondary structure is predicted to be ____________.
α − N H group; H-bond donor; destabalized
The ________ is the single shape that a protein adopts under physiological conditions.
Native conformation
Proteins have what charge on their carboxyl terminals at physiological pH?
Negative
Amino acids which are NOT incorporated into polypeptides are sometimes converted into _______
Neurotransmitters
Histidine has pKa values of 1.8, 6.0 (R-group) and 9.3. At pH 8.0, the net charge on histidine is _______
Neutral (uncharged)
In size exclusion chromatography, which of the following proteins would be eluted last ________
Protein of 8 kD
Which of the following codons serves as stop signal?
UAG
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.
+0.5
What is the net charge on the tripeptide Gly-Arg-Lys at pH 7? The table below gives the pKa's of the ionizable groups on the free amino acids
+2
Which structure below is appropriate for glycine at neutral pH?
+H3NCH2COO-
At the isoelectric pH of an amino acid which has two pKa values the net charge is ______
0
The sequence logo for the alignment of 412 sequences from the cytochrome c family is shown in figure 5.23 on page 128. Which statement(s) is/are true. 1 The amino acid found most frequently at a given position is shown on top. 2 Single letters at a position are amino acids absolutely conserved at these positions. 3 The relative size is correlated with the relative frequency of that amino acid in that position. 4 The amino acid number is displayed along the Y axis.
1, 2, and 3
Aromatic amino acids absorb light in the near-ultraviolet region of the electromagnetic spectrum. Which of the following statements about absorption of proteins are true? 1 The absorption of light at 280 nm is often used for the detection and/or quantification of proteins. 2 Phenylalanine does not absorb at 280 nm, and it absorbs only weakly at 258 nm. 3 Amino acids absorb as strongly as nucleic acids 4 Tryptophan and tyrosine account for most of the UV absorbance by proteins in the region around 280 nm.
1, 2, and 4
Which of the following statement(s) about amino acids is/are true? 1 Arginine has a guanidinyl group. 2 The side chain of histidine has a pKa value of 6.0. 3 Histidine forms a covalent bond with the α-amino group. 4 The side chain of cysteine has a pKa of 8.3.
1, 2, and 4
Which statements about the "energy landscape" model of protein folding are true? 1 The depth of the funnel corresponds to free energy, and the width of the funnel corresponds to the number of conformational states at a given value of free energy. 2 This model averts Levinthal's paradox. 3 The classical pathway model and the folding funnel are not compatible. 4 The trajectory of protein folding is "downhill". It proceeds with a decrease in free energy.
1, 2, and 4
The stability of the folded structure of a globular protein depends on the interplay of which of these factors: 1 ΔH generally favors the folded state and is associated with changes in noncovalent bonding interactions. 2 ΔH of the surrounding medium, which generally favors the folded state of the protein. 3 ΔSconformation of the protein favors the unfolded state. 4 ΔSsolvent is favorable due to the release of water from clathrates. This occurs when solvent exposed hydrophobic groups become buried within the molecule.
1, 3, and 4
Which statements about the primary structure of a specific protein are true? 1 The primary structure is a unique and defined amino acid sequence. 2 The primary structure is different from one organism to the next organism of the same species. 3 The primary structure determines the secondary and tertiary structure. 4 The amino acids are connected through peptide bonds.
1, 3, and 4
The pKa of arginine's α-Carboxyl group, α-Amino group and side chain are 1.8, 9.0 and 12.5, respectively. Calculate the isoelectric point.
10.8
The pKa of a certain weak acid is 4.0. Calculate the ratio of proton acceptor to proton donor at pH 7.0
1000:1
Match the appropriate cells with the correct immune response. 1) T lymphocytes a) humoral immune response 2) B lymphocytes b) cellular immune response 3) macrophages 4) immunoglobulins
1:B; 2:A; 3:A; 4:A
Match the amino acid (AA) with its right side chain category: 1) methionine A) negatively charged polar AA 2) histidine B) nonpolar aromatic AA 3) alanine C) positively charged polar AA 4) threonine D) nonpolar AA 5) tryptophan E) polar AA 6) aspartic acid F) nonpolar aliphatic AA
1:D; 2:C; 3:F; 4:E; 5:B; 6:A
Match the codon with the amino acid it encodes: 1) UCA A) Stop 2) CUA B) Lys 3) AAG C) Start/Met 4) GUA D) Leu 5) AUG E) Val 6) UAG F) Ser
1:F; 2:D; 3:B; 4:E; 5:C; 6:A
Which of the following proteins assist/help in protein folding? 1 Proteasome 2 Protein disulfide isomerase 3 Prolyl isomerase 4 Molecular chaperones like GroEL-GroES complex
2, 3, and 4
Which statements about the binding of oxygen to heme are true? 1 The iron ion bound to the porphyrin group is +3. 2 In deoxyhemoglobin, the porphyrin nitrogens make up four of its six ligands, the nitrogen of His F8 makes up the fifth ligand, and the last remaining coordination site is empty. 3 When O2 is bound to the iron cation, His E7 makes a key H-bonding interaction with this ligand. 4 Heme is capable of binding other ligands, such as CO and NO, but it is the key interactions of oxygen with protein side chain residues that enhance the specificity for oxygen.
2, 3, and 4
It depends on the occurrence of polar and nonpolar residues in a sequence. Peptide #1 has every ______ residue _______, so it has more chance to be helical. On the other hand, peptide #2 has a higher appearance of _______ residues in its sequence, approximately every __________. This means Peptide #2 is likely to form a hairpin.
3-4; nonpolar, nonpolar, second one
Which of the statements fit the description of α helices best.
5.4Å/turn, extensive hydrogen bonding network, large dipole moment
The pKa of isoleucine's α-Carboxyl group and α-Amino group are 2.3 and 9.8, respectively. Calculate the isoelectric point.
6.0
If the reduced unfolded protein were oxidized prior to the removal of the urea, what fraction of the resulting mixture would you expect to possess native disulfide bonds?
6.67% (5 possible random disulfides) × (3 possible random disulfides) × (1 possible disulfide) = 15 possible random combinations of disulfides → 1 native combination/15 possible = 6.67%% (1 in 15) native disulfides would form randomly.
When incorporated into a protein, the side chain of histidine has a typical pKa value in the range of 6.5-7.4. The pKa value is dependent on the electrostatic environment surrounding the histidine residue. However, when analyzing the pKa values in a particular protein, scientists determined that one particular His residue has an unusually low pKa value of 4.8. Which answer is a possible explanation for this observation?
A negatively charged amino acid could be in close proximity to this residue
Which of the following statements characterize an α helix (A) or antiparallel β strand (B)? 1 The rise per residue is 1.5 Å. 2 The side chains are located on opposite faces of the secondary structure element. 3 There are 2 residues per turn. 4 9The pitch is 5.4 Å.
A-1,4; B-2,3
The cavity in the GroEL-GroES complex from E. coli provides a favorable environment that prevents ________ and misfolding
Aggregation
If the R group of an amino acid is -CH3, then the name of this compound is _______
Alanine
Glycine is NOT a stereoisomer because ________
All of the above
The R group of an amino acid determines if it is _______
All of the above
The chemical ________ can cleave amide bonds on the C-terminal side of methionine residue
Cyanogen bromide
Which statement(s) about the peptide bond is/are true? 1 The peptide bond has a substantial fraction of double-bond character. 2 Two α-carbon atoms on either side of a peptide bond can be in either cis or trans configurations. 3 The peptide bond is metastable (meaning that it will hydrolyze in an aqueous solution when a catalyst is present). 4 Peptide bonds hydrolyze in aqueous solution in the presence of proteases, strong mineral acids or cyanogen bromide.
All statements are true.
Conservative amino acid changes never affect stability or function of a protein.
Always false
When referring to the amino acid sequences of proteins, sequence homology is the same as sequence similarity.
Always false
the overall shape of a protein is greatly influenced by _______
Amino acid R group properties
Which substance is used to fractionate proteins based on differences in their solubility as a function of salt concentration
Ammonium sulfate
The peptide bond is which of the following?
An amide bond
Alanine, valine, leucine and isoleucine are important in three dimensional structure because they _______
Are highly hydrophobic
Which of the following amino acids would most likely be found on the surface of a protein?
Aspartic acid
Which of the following statement is true about a protein in aqueous solution that has a pH equal to the isoelectric point (pI) of the protein?
At pH = pI, there is no net charge on the protein.
Amino acids with non-ionizable side chains are zwitterions when they are _______
At physiological pH, pH = 7.4
At PO2 = 40 mm Hg, which statement about the saturation of either myoglobin (Mb) or hemoglobin (Hb) is true?
At this partial pressure of oxygen, Mb would be almost completely saturated but Hb would not.
iodoacetate
Cysteine
The amino acids in polypeptide chains which contain sulfur (S) are _______
Cysteine and methionine
Which is NOT an example of an oligomeric protein?
Cytochrome c
Although the hydroxyl groups in serine and threonine are uncharged, they can react within active sites of some enzymes ________
Because the hydroxyl group is polar
A sequence of amino acids with a relatively high hydropathy is very likely to function by ______
Being embedded in a cell membrane
Disulfide bridges can form in proteins ________.
Between cysteine residues that are close in three-dimensional space, but not necessarily close in the primary structure
The trans configuration of most peptide groups is adopted in cells because it ______
Both minimizes steric hindrance of R groups and is favored in protein synthesis
In peptide bonds, the bonds between ________.
C and N are shorter than typical C-N bonds
An amino acid with two chiral carbon atoms _______
Can form four possible stereoisomers
Which biochemical technique is used to determine the approximate content of α-helix, β-strand, and random coil in a protein. This method is not considered high resolution
Circular dichroism (CD)
The protein that makes up about a third of the total protein mass in animals is ______
Collagen
Bovine spongiform encephalopathy is an infectious disease caused by a prion protein, which undergoes a ________ change to become pathogenic
Conformational
Several homologous proteins can be aligned to provide a ________ sequence
Consensus
The formation of insulin from preproinsulin follows 4 steps. Organize them into the correct order. A) Disulfide bonds form B) The connecting sequence is cleaved to form the mature insulin molecule C) After membrane transport, the leader sequence is cleaved and the resulting proinsulin folds into a stable conformation D) Preproinsulin is synthesized as a random coil on membrane-associated ribosomes
D-C-A-B
Applications of mass spectrometry include _______
Determination of the mass of a protein
Which of the following is FALSE when considering the standard genetic code?
Each of the three stop codons can also encode rare modified amino acids.
Cysteine is likely to be isolated from proteins that are _______
Extracellular
Ferrous iron (Fe2+) is octahedrally coordinated. This means it should have six ligands. Which are the coordination sites in hemoglobin?
Four ligands are provided by the nitrogen atoms of the porphyrin ring. The fifth ligand is the ε-nitrogen from histidine residue 93. The sixth coordination site is the binding site for oxygen.
The first treatment of a crude protein extract usually involves _______
Fractionation with varying salt concentrations and centrifugation
Name the N-terminal and C-terminal residues for the following peptide sequence.Peptide sequence: EASY
Glutamic acid is the N-terminal residue; tyrosine is the C-terminal residue.
All amino acids have a chiral α-carbon EXCEPT ________.
Glycine
The amino acid that destabilizes alpha-helical structures and is usually found at the ends of alpha helices is ________
Glycine
Knowing the chemical properties and bulkiness (molecular weight) of amino acids indicates often the functionality of amino acids in protein structure. Sort glycine, tryptophan, phenylalanine, cysteine, and lysine by their molecular weight. Sort from lowest to highest molecular weight.
Glycine - cysteine - lysine - phenylalanine - tryptophan
Glycine, alanine, valine, leucine, isoleucine, and proline are considered amino acids with nonpolar aliphatic side chains. Which of these amino acids are often observed on the surface of protein?
Glycine and proline
What would be expected for the formation of an α-helix, for a segment of a protein chain that contains lysine approximately every fourth residue with all other residues being mostly hydrophobic
Helix formation would be favored at high pH.
Recombinant proteins containing a ________ can be purified using immobilized metal affinity chromatography and eluted by the addition of imidazole in increasing concentrations
Hexahistidine-tag
The side chain of ________ has a pKa in the physiological pH range and is therefore often involved in proton transfer during enzymatic catalysis.
His
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
Histidine
A protein that contains more isoleucine, phenylalanine and leucine than asparagine, lysine and arginine is most likely ________
Hydrophobic
Hydropathy is an important determination of protein-chain folding because ______
Hydrophobic R groups tend to cluster in the interior of proteins
CO2 and 2,3-BPG effect the ability of hemoglobin to bind oxygen. Which statement is true?
If stripped Hb is treated with 2,3-BPG and CO2, the O2-binding curve for Hb will mirror that of fully intact Hb.
Protein X can bind to either protein A or protein B to form a complex. The association constants are 108.0M-1 (X with A) and 106.0M-1 (X with B). Which statement is TRUE?
In the presence of excess X, it takes fewer molecules of A than B to generate a given amount of complex.
Insulin is a peptide therapeutic used to manage Type 1 diabetes, which affects more than 20 million people worldwide according to the International Diabetes Federation. A significant limitation to the broad distribution and use of insulin to treat Type 1 diabetes is the fact that it must be administered by injection rather than orally. Why is insulin administered by injection and not orally?
Insulin would not survive transit through the stomach and gut environments.
________ chromatography is used to separate proteins based on their surface charge
Ion exchange
What chromatographic method should make it possible to isolate pure AA and BB chains?
Ion exchange chromatography. The A chain contains no basic residues in comparison with the B chain, so ion-exchange chromatography should work well.
Amino acids are named that because each one ________.
Is an amino derivative of a carboxylic acid
Protein biosynthesis uses only _______
L-amino acids
The primary structure of a protein specifically describes the _____
Linear sequence of amino acids
Concentrations of some proteins cannot be estimated by UV spectrophotometry because they are _______
Low in tryptophan and tyrosine
The ionic charges associated with a protein molecule are _______
Mostly contributed by the side chains of constituent amino acids
The conformation of the backbone of a polypeptide is described completely by the angle(s) of rotation about which bond(s)?
N-Cα and Cα-C bonds only
acetic anhydride
N-terminal amine
APFLLIGDWY is chain of amino acids, which can also be referred to as a(n).
Oligopeptide
Which of the following statements about the Bohr effect are true? 1 This is the effect of pH on the binding of O2 to Hb. 2 As blood travels from lung to tissue, there is a drop in pH, causing Hb to unload more oxygen than if there were no change in pH. 3 As blood travels from lung to tissue, there is an increase in pH, causing Hb to unload more oxygen than if there were no change in pH. 4 Myoglobin and Hb exhibit similar pH profiles.
Only statements 1 and 2 are correct.
Which of the following characteristics are true about a typical peptide (amide) bond? 1 The bond is planar. 2 There is free rotation about the carbonyl carbon and nitrogen bond. 3 There is substantial double-bond character to this bond. 4 There is a net negative charge on nitrogen and net positive charge on oxygen.
Only statements 1 and 3 are correct.
Hemoglobin (Hb) can be viewed as having two quaternary states, a low oxygen affinity state (T), and a high oxygen affinity state (R). Which of the following statements about the binding of O2 by Hb are true? 1 Upon binding a molecule of oxygen, Hb undergoes a conformational change that makes the binding of subsequent O2 molecules more favored. 2 The conformational change induced in Hb upon binding oxygen is the result of a small movement (0.2 Å) of the iron cation into the center of heme. 3 Site-directed mutagenesis studies have indicated that the cooperativity of O2 binding in Hb is attributable to the movement of the F helix in Hb. 4 Site-directed mutagenesis studies in which the proximal His residues of the F helix have been replaced by glycines have indicated the mutant protein still shows cooperativity of O2 binding.
Only statements 1, 2, and 3 are true.
Which statements regarding shape and charge complementarity are true? 1 Charge complementarity occurs when specific noncovalent binding interactions occur between two contacting surfaces. 2 The charge complementarity refers to noncovalent bonding interactions such as charge-charge, hydrogen-bonding, or van der Waals interactions. 3 Shape complementarity refers to the intimate contact made between an antibody and its target antigen. 4 Shape and charge complementarity explain exclusively the interactions between an antibody and its target antigen.
Only statements 1, 2, and 3 are true.
Which of the following statements regarding Anfinsen's denaturing experiments with ribonuclease A (RNAse A) are valid? 1 Exposing the denatured protein to air oxidation and then dialysis to remove urea restored the protein to its original functionality. 2 Removing urea by dialysis and then allowing air oxidation of the denatured protein restored the protein to its original functionality. 3 Denaturing the protein with both urea and β-mercaptoethanol yielded an inactive protein. 4 Anfinsen concluded that protein folding is determined by its primary sequence.
Only statements 2, 3, and 4 are valid.
An amide bond between the α-carboxylic acid group of one amino acid and the α-amino group on another is called a ________
Peptide bond
Many of the D-amino acids found in nature have been discovered in bacterially produced peptides that have antibiotic properties. Bacteria secrete these peptides into their environments to kill competitor bacteria and thereby gain a selective advantage. Given your answer to part (a) of this question, what potential advantages might D-amino acids confer to a secreted peptide toxin?
Peptides containing DD-amino acids are less likely to be recognized as substrates by proteolytic enzymes in the gut
Which amino acids are linked in phenylalanylglycine
Phenylalanine and glycine
Tyrosine and tryptophan are less hydrophobic than phenylalanine because ________.
Phenylalanine has no polar group in the side chain
The distance along a helix axis for one complete turn is called the ______
Pitch
Which of the following secondary structure element is left-handed
Polypeptide II helix
Primary structure of proteins is dictated by its ______
Polypeptide sequence
At pH=0, the net charge on a polypeptide will be ________
Positive
Basic amino acids are ________ (positive, negative) at pH 7 and acidic R group amino acids are ________ (positive, negative) at pH 7.
Positive; negative
Ammonium sulfate is often used as a first step in protein purification because it ______
Precipitates all proteins
A polypeptide chain may have abrupt changes in direction and restriction in geometry because of the presence of _______
Proline
Which statement demonstrates that the primary structure of a protein determines its tertiary structure?
Proteins refold when the amino acid sequence is the same as in the native conformation.
Arginine is the most basic of the 20 amino acids because its side chain is ________ under most cell conditions
Protonated
The functional organization of proteins where specific complexes of two or more polypeptides are formed is called ________ structure.
Quaternary
A ________ plot describes which structures in a polypeptide are sterically possible and which are not based on the angles of rotation about the backbone Namide -Cα and Cα-Ccarbonyl bonds.
Ramachandran
Dialysis during protein purification is a process to _______
Remove low molecular weight solutes such as salts
Which represents the backbone of a protein?Note: R = amino acid side chainN = nitrogenCα = alpha carbonC = carbonyl carbon
Repeating units of N-Cα-C
In considering protein secondary structure which of the following is INCORRECT?
The 310 helix is right-handed and often contains proline residues
For an amino acid such as aspartic acid, what impact would you expect a neighboring carboxylic acid to have on the apparent pKa value of the side chain?
The apparent pKa value for aspartic acid increases.
Which of the following statements about insulin is INCORRECT?
The disulfide bonds form after the final proteolytic cleavage to yield mature insulin.
Proline is distinct among the 20 commonly found amino acids because ______
The nitrogen of the amino group is cyclized in a ring
How does the pKa values of an ionizable side chain compare when the amino acid is free versus when it is in a polypeptide chain
The pKa of the side chain may be lower or higher in a polypeptide chain due to weaker inductive effects and differences in their microenvironments.
Which statement is NOT true about a peptide bond?
The peptide bond is longer than the typical carbon-nitrogen bond.
An enzyme works well as a catalyst at a pH of 7.2. It is found that catalytic activity is significantly less at a pH of 8.4. What could likely cause the decrease in enzyme activity?
The protein has changed shape due to a change in charge
Proteomics is _____
The study of large sets of proteins, such as the entire complement of proteins produced by a cell
Which factor does NOT help to explain why many proteins exhibit quaternary structure?
The subunits always are able to maintain the same three-dimensional structure whether they are associated into an oligomer or not.
The isoelectric point of alanine is pH = 6.15. It is mixed with proline (pHCOOH = 2.0; pHNH2 = 10.6), and the mixture is placed in an electric field at pH 6.15. Which statement is TRUE?
The two amino acids will be separated.
Do you predict that the αα helix and ββ sheet are amphiphilic or not? Briefly explain.
The α helix and β sheet are amphiphilic because the folding of the helix next to the sheet requires the formation of a hydrophobic core. Here, hydrophobic surfaces of both structures face each other, while their outer hydrophilic surfaces are exposed to the solvent.
The pH inside cells is normally near pH 7. At pH 7 which statement is TRUE about the charges (ionization state) of the α-Carboxyl and α-Amino groups of an amino acid?
The α-Carboxyl group is 1- and the α-Amino group is 1+.
The pKa 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
The α-carboxyl group is closer to the α-amino group than the side chain is.
For the amino acid lysine, the Henderson-Hasselbalch equation can be applied to ________ ionization group(s)
Three
Ultraviolet (UV) light can be used to estimate protein solution concentrations because ________
Tryptophan and tyrosine absorb at 280 nm
kinase + ATP
Tyrosine
What is the N-terminal for the pentapeptide Val-Ile-Glu-Arg-Tyr?
Valine
At neutral pH, the net charge of serine is _______
Zero
The protein data bank (PDB) is...
a repository of protein and nucleic acid structures.
Peptides typically carry ______ that reduce transport across the ______core of the membrane bilayer
charged groups (i.e., N- or C-termini and some side chains); hydrophobic
At physiological pH, the carboxylic acid group of an amino acid will be ________, while the amino group will be ________, yielding the zwitterion form
deprotonated, protonated
A spontaneous irreversible reaction has a Δ G value that is _______ in magnitude and _______in sign in one direction. The reverse reaction is then nonspontaneous and has a Δ G value that is _______in magnitude and _______in sign.
large; negative; large; positive
Δ S solvent is likely to be ______unfavorable for the mutant because the _____Ala side chain is predicted to have _____ clathrate structure in the unfolded state than the WT Leu side chain. Thus,________ will be less than ________
less; smaller; less; Δ S s o l v e n t F → U ( W T ); Δ S s o l v e n t F → U ( m u t )
What is the net charge on the following peptide at pH = 0?Peptide sequence: DSVK
net charge = +2
According to the Henderson-Hasselbalch equation, when the concentrations of proton acceptor and proton donor are the same, then ________.
pH = pKa
Modification of the N- and C-termini (by, respectively, acetylation and amidation) will ______the charge density on peptides. This would make them ______likely to cross membranes
reduce; more
The hydrophobic residues in this sequence tend to recur roughly every 3-4 amino acids, suggesting that the protein sequence shown is in the form of an _________ comprising __________ residues. Such a sequence would result in a ___________ structure which has opposing _______________ faces. Thus, this sequence is that of an amphipathic (or amphiphilic) ______.
α helix; hydrophobic and hydrophilic; secondary; hydrophobin and hydrophilic; α helix
