test 2 questions Flashcards
1) Which of the following amino acids would most likely be found on the surface of a protein? A) Aspartic acid B) Leucine C) Proline D) Valine E) Phenylalanine
A
2) Protein biosynthesis uses only L-amino acids.
Answer: TRUE
3) All amino acids have a chiral α-carbon EXCEPT ________.
Answer: glycine
4) The side chain of ________ has a pKa in the physiological pH range and is therefore often involved in proton transfer during enzymatic catalysis.
Answer: histidine
5) At physiological pH, the carboxylic acid group of an amino acid will be ________, while the amino group will be ________, yielding the zwitterion form.
Answer: deprotonated, protonated
6) At pH=0, the net charge on a polypeptide will be negative.
Answer: FALSE
7) Which of the following modified amino acids is incorporated during translation rather than being modified post-translationally? A) Phosphoserine B) Selenocysteine C) γ-carboxyglutamate D) N-ε-acetyllysine E) 4-hydroxyproline
Answer: B
8) An amide bond between the α-carboxylic acid group of one amino acid and the α-amino group on another is called a ________.
Answer: peptide bond
9) The chemical ________ can cleave amide bonds on the C-terminal side of methionine residues.
Answer: cyanogen bromide
10) Which of the following is FALSE when considering the standard genetic code?
A) Three separate codons encode translation stop signals.
B) There are 64 possible codons to represent 20 common amino acids.
C) AUG serves as the translation start codon in most cases.
D) Apart from methionine, the only other amino acid with a single codon is tryptophan.
E) Each of the three stop codons can also encode rare modified amino acids.
Answer: E
11) Which of the following statements about insulin is INCORRECT?
A) In the active form it has two polypeptide chains joined by disulphide bonds.
B) It is synthesized as a random coil single chain on membrane-bound ribosomes.
C) The leader sequence is cleaved off after membrane transport.
D) The disulphide bonds form after the final proteolytic cleavage to yield mature insulin.
E) It is stored in the pancreas in an inactive form.
Answer: D
12) Most proteins have blocked amino and carboxyl terminals.
Answer: FALSE
13) Conservative amino acid changes never affect stability or function of a protein.
Answer: FALSE
14) When referring to the amino acid sequences of proteins, sequence homology is the same as sequence similarity.
Answer: FALSE
15) Several homologous proteins can be aligned to provide a ________ sequence.
Answer: consensus
Recombinant proteins containing a ________ can be purified using immobilized metal affinity chromatography and eluted by the addition of imidazole, a low pH buffer or a buffer containing EDTA.
Answer: his-tag, or hexahistidine-tag
17) Applications of mass spectrometry include:
A) determination of the mass of a protein.
B) determining the primary structure of proteins.
C) detection of post-translational modifications on proteins.
D) A and B.
E) A, B, and C.
Answer: E
18) In size exclusion chromatography, the smallest proteins are eluted last.
Answer: TRUE
19) ________ chromatography is used to separate proteins based on their surface charge.
Answer: Ion exchange
1) In considering protein secondary structure which of the following is INCORRECT?
A) An α helix repeats after 18 residues and has 3.6 residues per turn.
B) A network of main-chain hydrogen bonds connect β strands in a β sheet.
C) The most common structures are the α helix and the β sheet.
D) The 310 helix is right-handed and often contains proline residues.
E) The β strands can be in either parallel or antiparallel configuration.
Answer: D
2) The amino acid side chain residues in an α helix point outwards away from the center of the helix.
Answer: TRUE
3) ________ between amide protons and carbonyl oxygens is necessary to stabilize a regular folding of protein secondary structure.
Answer: Hydrogen bonding
4) 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.
Answer: Ramachandran
5) Which of the following statements about α-keratins is FALSE?
A) They include a major class of protein that comprises hair, fingernails and animal skin.
B) Individual molecules are α-helical.
C) There is a strip of contiguous hydrophobic surface making a shallow spiral around the helix.
D) They include a small globular regions covalently linked to the surface.
E) Pairs of α-helices twist about each other in a coiled-coil structure held together entirely by hydrophobic interactions.
Answer: E
6) The protein that makes up about a third of the total protein mass in animals is: A) β-keratin. B) collagen. C) hemoglobin. D) myoglobin. E) α-keratin.
Answer: B
7) Fibroin is a β-sheet protein, with a high proportion of glycine.
Answer: TRUE
8) Tropocollagen is a double helix of two left-handed polypeptide chains.
Answer: FALSE
9) Scurvy results in weakness in collagen fibres because the enzymes that catalyze ________ of proline and lysine residues in collagen require Vitamin C.
Answer: hydroxylation
10) Which of the following is CORRECT when considering the tertiary structure of globular proteins?
A) β sheets are usually twisted or wrapped into barrel structures.
B) Hydrophobic residues are normally on the inside and hydrophilic residues are on the outside.
C) The amino acid proline never occurs in a region where the polypeptide chain bends or turns.
D) All parts of the proteins can be classified as helix, β sheet or turns.
E) None of the above.
Answer: B
11) Proteins cannot self-assemble into a functional conformation after they have been denatured.
Answer: FALSE
12) Protein folding is a random process, whereby a vast number of possible conformations are tested to find the desired most stable state.
Answer: FALSE
13) The folded conformation of proteins can be stabilized by the binding of a metal ion or cofactor.
Answer: TRUE
14) The interactions that stabilize multisubunit complexes are different to those that stabilize tertiary structure.
Answer: FALSE
15) Protein folding is a thermodynamically favorable process under physiological conditions because:
A) there is an increase in entropy associated with protein folding.
B) there is a decrease in entropy of the solvent by burying hydrophobic groups within the molecule.
C) of the large negative enthalpy change associated with many noncovalent interactions.
D) no intermediate stage disulphide bonds form during the folding process.
E) all of the above.
Answer: C
16) The cavity in the GroEL-GroES complex from E. coli provides a favorable environment that prevents ________ and mis-folding.
Answer: aggregation
17) Bovine spongiform encephalopathy is an infectious disease caused by a prion protein, which undergoes a ________ change to become pathogenic.
Answer: conformational
18) Proteins have an asymmetrical tertiary structure, while multisubunit proteins can exhibit several types of symmetry.
Answer: TRUE
19) The functional organization of proteins where specific complexes of two or more polypeptides are formed is called ________ structure.
Answer: quaternary
20) Which technique is able to investigate secondary structural features of proteins? A) Infrared spectroscopy B) Ultraviolet spectroscopy C) Fluorescence spectroscopy D) Circular dichroism E) All of the above
Answer: E
21) ________ spectroscopy can be used to study dynamic processes in solution.
Answer: Nuclear magnetic resonance
22) SDS gel electrophoresis can be used to determine:
A) whether subunits in a protein complex are identical or not.
B) the molecular mass of a native protein complex.
C) the overall charge on a polypeptide.
D) the molecular mass of denatured protein subunits.
E) none of the above.
Answer: D
1) Which of the following is NOT true of immunoglobulin molecules?
A) They consist of four polypeptide chains held together by disulphide bridges.
B) They have two identical heavy chains and two identical light chains.
C) Antigenic determinants reside only in the variable region of the light chains.
D) Proteolytic cleavage can generate fragments containing the antigen-binding site.
E) Some are membrane bound.
Answer: C
2) The immunoglobulin domain is a stable scaffold containing two antiparallel β- sheets upon which to display hypervariable loops.
Answer: TRUE
3) The specific interaction between an antibody and antigen occurs by virtue of both shape and ________ complementarity.
Answer: charge
4) Which of the following statements is FALSE?
A) Myoglobin is a single polypeptide chain folded about a heme prosthetic group.
B) Hemoglobin is a tetramer, each of which binds a heme group.
C) In both hemoglobin and myoglobin, iron is chelated by a tetrapyrole ring system.
D) The iron in both hemoglobin and myoglobin has two coordination sites that bind to oxygen.
E) Hydrogen bonding to a histidine residue assists stabilization of the Fe2+ -O2 complex in both hemoglobin and myoglobin.
Answer: D
5) Both myoglobin and hemoglobin exhibit cooperative binding to oxygen.
Answer: FALSE
6) The conserved residues in the hemoglobins and myoglobins include the ________ proximal and distal to the heme iron.
Answer: histidines
7) The ________ binding of oxygen to hemoglobin is facilitated by changes in protein conformation upon oxygen binding to one subunit that affect the binding of oxygen to another subunit.
Answer: cooperative
8) Which of the following observations helps to explain the conformational changes that occur in hemoglobin upon binding to oxygen?
A) The four heme groups are positioned close to the surface of the molecule.
B) An αβ dimer rotates and slides with respect to the other dimer upon binding oxygen.
C) Neither the heme nor the iron ion in the deoxy conformation is in a planar conformation.
D) All of the above
E) B and C
Answer: E
9) Fetal hemoglobin has a higher affinity for oxygen than does maternal hemoglobin because it has a higher affinity for the allosteric regulator 2,3-bisphosphoglycerate.
Answer: FALSE
10) The production of carbon dioxide during respiration in aerobic tissues lowers the pH in erythrocytes, which in turn ________ the affinity of oxygen binding to hemoglobin.
Answer: decreases
11) Comparison of globin sequences from many different species suggests that myoglobin and hemoglobin have evolved from a single myoglobin-like protein.
Answer: TRUE
12) The sickle cell mutation causes oxyhemoglobin molecules to ________ due to hydrophobic interactions because a glutamate residue is replaced with a valine.
Answer: aggregate
13) Which of the following statements about muscle contraction is TRUE?
A) ATP hydrolysis releases myosin from actin.
B) ATP hydrolysis results in strong binding of myosin to actin.
C) ATP hydrolysis causes a conformational change in the myosin head.
D) Muscle contraction occurs as ATP is hydrolyzed.
E) ATP hydrolysis must occur before the actin-binding site closes.
Answer: C
14) The heavy chain of the muscle form of myosin:
A) forms a coiled-coil structure with a globular head domain.
B) contains the motor domain within the C-terminal region.
C) is a complex of 540 kDa.
D) binds ATP near the C-termini.
E) has two covalently bound light chains.
Answer: A
15) F-actin is a polymer of G-actin monomers and exhibits symmetry.
Answer: FALSE
16) The A band of skeletal muscle is formed by noncovalent cross-bridges between the thin filaments that are mainly ________ and the thick filaments that are mainly ________.
Answer: actin, myosin
17) The most critical substance in stimulating muscle contraction is: A) ATP. B) Ca2+. C) tropomyosin. D) troponin C. E) troponin T.
Answer: B
18) Calcium regulates muscle contraction by binding to: A) actin. B) myosin. C) tropomyosin. D) troponin C. E) troponin T.
Answer: D
19) The greatest conformational change in the neck piece of myosin occurs during ATP hydrolysis.
Answer: FALSE
20) The concentration of Ca2+ in the myoplasm can increase as much as 10,000 fold in response to a motor nerve impulse.
Answer: TRUE
21) Antibodies cannot be used to purify proteins because the antibody-antigen interaction is too strong.
Answer: FALSE
22) Enzyme-linked immunosorbent assay, western blotting and immunofluorescent light microscopy all make use of the specific interaction between an antigen and an ________.
Answer: antibody
1) Which of the following statement is FALSE?
A) The free energy barrier in a chemical reaction must be overcome in order for products to form.
B) An increase in temperature can result in an increased reaction rate.
C) Lowering the free energy of the transition state can increase a reaction rate.
D) At a given temperature and time all molecules in a solution or a sample will have the same energy.
E) An enzyme can increase a reaction rate by lowering the activation energy.
Answer: D
2) In a favorable reaction the free energy of the products is ________ than the free energy of the reactants.
Answer: less
3) Catalysts affect the thermodynamic f of a chemical reaction.
Answer: FALSE
4) Pyruvate carboxylase is an example of the ligase class of enzymes.
Answer: TRUE
5) In an enzyme-catalyzed reaction, the lifetime of the transition state is similar to the vibrational frequencies of covalent bonds.
Answer: TRUE
6) Non-catalyzed biochemical reactions always occur at physiological useful timescales.
Answer: FALSE
7) Electrostatic catalysis proceeds via covalent bonding interactions.
Answer: FALSE
8) A second-order reaction:
A) occurs when one substrate is converted into one product.
B) is characterized by two molecules coming together to form a product.
C) is the rate-limiting step of a reaction.
D) has a rate constant with units of (time)-1.
E) only occurs in multistep processes.
Answer: B
9) The equilibrium constant for a first-order ________ reaction is equivalent to the ratio of the rate constant for the forward and reverse reactions.
Answer: reversible
10) Enzymes can accelerate reactions by:
A) binding a substrate or substrates.
B) promoting the removal or addition of protons.
C) correctly positioning a metal ion for catalysis.
D) lowering the energy for activation.
E) all of the above.
Answer: E
11) The equilibrium state of a biochemical reaction is approached ________ in the presence of a catalyst.
Answer: more rapidly
12) The lock and key model of substrate binding and enzymatic catalysis explains:
A) the release of product.
B) substrate specificity.
C) formation of a transition state.
D) the catalytic mechanism.
E) structural changes that occur on substrate binding.
Answer: B
13) Which of the following amino acid residues are often involved in proton transfers in enzyme-catalyzed reactions?
A) Histidine, aspartate, serine, and cysteine
B) Serine, tyrosine, arginine, and cysteine
C) Glutamine, asparagine, lysine, and tyrosine
D) Histidine, aspartate, lysine, and serine
E) Histidine, aspartate, glutamate, arginine, and lysine
Answer: E
4) The ________ hypothesis suggests that an enzyme can induce distortion of the substrate or the substrate can induce conformational changes in the enzyme that stabilize the transition state.
Answer: induced fit
15) The formation of an enzyme-substrate complex tends to be thermodynamically favorable due to ________ interactions between the substrate and enzyme.
Answer: noncovalent
16) Which of the following statements about the proposed mechanisms of action for hen egg white lysozyme does NOT support either model?
A) Glycosidic bond cleavage occurs by general acid/base catalysis.
B) A covalent intermediate is formed between an active site aspartate and C1 of the substrate.
C) A water molecule is deprotonated, which then attacks C1 of the substrate.
D) The active site aspartic acid changes between being protonated and deprotonated.
E) The active site glutamic acid changes between being protonated and deprotonated.
Answer: D
17) A Lineweaver-Burk plot for a first order enzyme-catalyzed reaction gives values of 1/KM = 2.5 × 104 (M)-1 and 1/Vmax of 1.25 × 10-2 (µmolL-1 sec-1)-1. Calculate the rate constant k.
Answer: 2 sec-1
18) Serine proteases make use of covalent catalysis as well as electrostatic stability of the transition state to achieve rate enhancement.
Answer: TRUE
19) A common feature of serine proteases is the catalytic triad consisting of a nucleophile, a general base and an acid. In chymotrypsin these amino acid residues are ________, ________, and ________ respectively.
Answer: serine, histidine, aspartic acid
20) The cofactor NAD+ is:
A) a reductant.
B) an oxidant.
C) oxidized to NADH/H+ in dehydrogenase reactions.
D) able to accept 2 electrons and 2 protons.
E) covalently linked to enzymes in whose catalytic activity it assists.
Answer: B
21) Coenzymes or cofactors are irreversibly changed during catalysis.
Answer: FALSE
22) Which of the following statements applies to metalloenzymes?
A) Some metal ions assist in ATP binding.
B) Amino acid residues in the enzyme are never covalently linked to the metal ion.
C) The metal does not bind at the catalytic site.
D) Many are oxido-reductases.
E) A and D
Answer: E
23) Metal ions are often required for catalytic efficiency but they may not remain permanently bound to the protein or take part in the catalytic process.
Answer: TRUE
24) Which of the following statements BEST describes the Michaelis-Menton constant KM?
A) It is numerically equal to the affinity between the enzyme and its substrate.
B) It is numerically equal to the substrate concentration required to reach half maximal velocity for an enzyme-catalyzed reaction.
C) It is a measure of the rate of a catalytic process.
D) It is a measure of enzyme efficiency.
E) It has units of concentration.
Answer: B
25) A mutation causing an amino acid change in an enzyme that affects the turnover number kcat will always affect the KM as well.
Answer: FALSE
26) A Lineweaver-Burk plot can be used to determine KM using initial-rate data for an enzyme-catalyzed reaction.
Answer: TRUE
27) A graph of initial velocity vs substrate concentration will be ________ for an enzyme that obeys Michaelis-Menton kinetics.
Answer: hyperbolic
28) Random substrate binding, ordered substrate binding and the ping-pong mechanism are all features of ________ enzyme-catalyzed reactions.
Answer: multisubstrate
29) Which of the following statements about inhibitors of enzyme-catalyzed reactions is TRUE?
A) An uncompetitive inhibitor typically affects KM but not kcat.
B) A competitive inhibitor does not affect Vmax.
C) An uncompetitive inhibitor will always bind at the active site.
D) A competitive inhibitor binds irreversibly to the enzyme at the active site.
E) Reversible inhibitors bind to either free enzyme or the enzyme-substrate complex but not both.
Answer: B
30) A reversible ________ inhibitor is one that binds to the active site of an enzyme but cannot undergo the chemical conversion step of the reaction.
Answer: competitive
31) Which of the following is NOT a feature of substrate-level enzyme regulation?
A) A high substrate concentration will speed up the rate of reaction.
B) A high product concentration will slow the rate of reaction.
C) The product can be a competitor.
D) It is sufficient for regulation of most enzyme-catalyzed reactions.
E) Sometimes products can be competitive or uncompetitive.
Answer: D
32) Almost all irreversible enzyme inhibitors bind noncovalently to the enzyme.
Answer: FALSE
33) Feedback regulation of a metabolic pathway can either be activation or inhibition.
Answer: TRUE
34) Which of the following is a feature of allosteric regulation of enzyme activity?
A) Ligand binding causes a conformation change in the enzyme.
B) Allosteric enzymes often have multiple active sites.
C) Cooperativity in substrate binding.
D) There is often a range of different effectors for a single enzyme.
E) All of the above
Answer: E
35) Covalent modification can either activate or inhibit enzymes.
Answer: TRUE
36) Protein kinases add a phosphoryl group to the —OH group of a ________, ________, or ________ residue of the target protein.
Answer: serine, tyrosine, threonine
37) Proteolytic cleavage is an example of an ________ post-translational modification.
Answer: irreversible
38) Catalytically inactive enzyme precursors are called ________.
Answer: zymogens
39) A ribonucleic acid that can act as a biological catalyst is called a ________.
Answer: ribozyme
40) A stopped-flow apparatus is used to measure rates of pre-steady state slow enzymatic reactions.
Answer: FALSE
which of the following statements about muscle contraction is true?
a) ATP hydrolysis releases myosin from actin
b) ATP hydrolysis results in strong binding of myosin to actin
c) ATP hydrolysis causes a conformational change in the myosin head
d) muscle contraction occurs as ATP is hydrolyzed
c
calcium regulates muscle contraction by binding to
a) troponin C
b) myosin
c) tropomyosin
d) actin
a
which of the following is NOT a catalytic strategy used by enzymes to process/turnover substrate?
a) metal ion catalysis
b) allosteric activation
c) general acid base catalysis
d) covalent catalysis
b
in the presence of an uncompetitive and noncompetitive inhibitor, vmax is lowered. what happens to Kmapp in the presence of an uncompetitive and noncompetitive inhibitor respectively?
a) Kmapp is increased:increased
b) Kmapp is reduced:reduced
c) Kmapp is not changed:increased
d) Kmapp is reduced:increased
D
The most critical substance in stimulating muscle contraction is: A) ATP B) tropomyosin C) calcium D) troponin T
C
An enzyme has a KM for substrate, S, of 10mM and a Vmax of 5μmol L-1 sec-1 at a total enzyme concentration of 1nM. At [S]=10mM, kcat is
a) 2500 per sec
b) 5000 per M per sec
c) 2500 per M per sec
d) 5000 per sec
D
Molecular chaperones are required for proteins that spontaneously fold.
false
Tropocollagen is a double helix of two left-handed polypeptide chains
false
Which of the following amino acid side chains can form hydrogen bonds with each other, ultimately contributing to tertiary structure? Assume physiological pH
a)Leu and Arg
b) Tyr and Gln
c) Ala and Pro
d) Asn and Val
e) Asp and Ile
f) Phe and Tyr
Tyr and Gln
Which of the following amino acid side chains can have ion-dipole interactions with each other, ultimately contributing to tertiary structure? Assume physiological pH.
Ser and Thr
Lys and Asn
Asp and Lys
Val and Pro
Gln and Gln
Phe and Trp
Lys and Asn
Which of the following interactions contribute to stabilizing the tertiary structure of a protein?
Ionic (Salt bridge)
Covalent bond
London forces (van der Waals)
Ion-dipole
All of the listed interactions contribute to stabilizing the tertiary structure of a protein
Hydrogen bond
all of the above
Hydrogen bonding patterns stabilize secondary structure. Which atom is the hydrogen bond acceptor?
Apha-carbon hydrogen
Carbonyl oxygen of the backbone amide
Amide hydrogen of an amide side chain
Carbonyl oxygen of an amide side chain
Amide hydrogen of the backbone amide
carbonyl oxygen of the backbone amide
Which level of protein structure ultimately dictates the final, three-dimensional fold of a protein?
Tertiary structure
Secondary structure
Quaternary structure
Primary structure
primary
Which of the following amino acid side chains can have ionic, salt bridge interactions with each other, ultimately contributing to tertiary structure? Assume physiological pH.
Asp and Glu
Pro and Asp
Arg and Asp
Asn and Ala
Val and Ile
Tyr and Ser
arg and asp
