BIOCHEM AAMC +Orgo
In Reaction 1, what is a possible structure for either R1 or R2 of the reactant?
(C2H)15 CH3 Because PE is a lipid, the R groups must represent the acyl chains.
If a thin thread is placed between a screen and a bright source of light, a pattern of parallel dark and bright fringes appears on the screen. The phenomenon best explaining the formation of this pattern is: A. refraction. B. polarization. C. diffraction. D. reflection.
- refraction: when light passes through the interface between optical media with different indices of refraction. There is no change in optical media when light passes by the thread. - polarization: select a certain oscillation direction of the electric field of light. - The thin thread disrupts the propagation of light by impeding light to pass through it. Diffraction causes the initially plane-parallel wave-fronts of light to change direction and partially enter the shadow region behind the thread due to its narrowness. The overlapping of different wave-fronts on the screen causes the pattern of dark and bright fringes on the screen according to the phase difference between the wave-fronts that interfere there.
cell membrane dynamics
-dynamic changes in the concentrations of various membrane proteins are mediated by gene regulation, endocytotic activity, and protein insertion -many cells (particularly those involved in biosignaling) can up- or downregulate the number of specific cellular receptors on their surface in order to meet cellular requirements
What is the net charge of sT-loop at pH 7.2? KTFCGPEYLA HAL DE E = -1 L= +1
0
Which experimental approach can be used to analyze the metal content of soapy precipitate produced by Reaction 1? Dissolve the solid in a known volume of: NaC17H32CO2 = weak base CO2 is a caroboxylate group (a deprotonated carboxylic acid = being a derivative and a base)
0.1 M Hal then titrate with standardized 0.1 M NaOH(aq) using an indicator The soapy precipitate is the salt of a weak base. Addition of HCl will generate the free fatty acid which can then be neutralized by NaOH. The difference in the number of moles of HCl and NaOH required to reach the endpoint gives the number of moles of RCO2 which can then be used to calculate the mass present in the solid and the percentage of the metal content. create an acid and then react with a base
How many molecules of NADH are produced from six molecules of glucose that undergo glycolysis
1 molecule of glucose = 2 NADH 6 molecules = 12 NADH
The radioactive decay described in the passage results in the formation of which two atoms? P32 C14 A. N and S B. B and Si C. B and S D. N and Si
14 = nitrogen 32 = S
A graph of the hydropathy index versus residue number of a membrane protein is shown.
2 The answer is B because a positive hydropathy index means the amino acids are hydrophobic, and therefore more likely to reside within a plasma membrane. The graph shows two distinct stretches of hydrophobic residues.
Disruption of two disulfide bonds within a protein requires:
2 molecules of NADH because the reduction of a disulfide bond requires two electrons and each molecule of NADH can provide two electrons when reducing another compound
How many stereoisomers of Compound 1 exist?
2^n
Compared to a diunsaturated acyl chain of a lipid, a saturated acyl chain possesses how many more total hydrogen atoms?
4 because each double bond in an acyl chain removes two hydrogen atoms when compared with fully saturated chains. "Structure, function, and reactivity of biologically-relevant molecules."
Compared to treatment with Compound 2 alone, which cell line shows the greatest enhancement of chemotherapeutic activity as a result of sensitization by Compound 1? A. Acute leukemia B. Fibrosarcoma C. Cervical carcinoma D. Noncancerous fibroblast
A to figure out the enhancement or efficacy of drug it will be 44/0.6 = rate efficacy for leukemia and using this method you can find the rate efficacy for the rest as well The ratio of the values of CC95 to CC95 Combination, gives the "fold enhancement" that is produced by using a combination of compounds 1 and 2 instead of just Compound 2 alone. Acute leukemia cells show a 74-fold enhancement in apoptotic activity by using the combination of compounds 1 and 2, while the other cancer cell lines show only a roughly 10-fold enhancement.
Which conclusion can be drawn from the experimental results described in the passage? A. Compound 1 selectively sensitizes cancer cells to chemotherapeutic action by Compound 2. B. Compound 1 sensitizes all cells to chemotherapeutic action. C. Compound 2 induces apoptosis in cancer cells only in conjunction with treatment with Compound 1. D. Compound 2 inhibits the NF-κB signaling pathway, which leads to apoptosis.
A. The results shown in Figure 1 and Table 1 show that treatment of cancerous cell lines with Compound 1 sensitizes cancer cells to chemotherapeutic action as a result of exposure to Compound 2.
ACC1-synthesized malonyl-CoA is a precursor molecule in fatty acid synthesis whereas ACC2-synthesized malonyl-CoA acts as a mixed inhibitor of carnitine palmitoyltransferase 1 (CPT 1). Based on the passage, ACC2 is most likely compartmentalized to: A. the mitochondria. B. the cell membrane. C. the cytosol. D. the lysosome.
A. the mitochondria fatty acids are made in cytoplasm = AAC1 Fatty acids broken in mitochondria= fatty acid oxidation= ACC2
Which type of bond is formed by glycogen synthase upon release of UDP? A. α-1,4-Glycosidic bond B. α-1,6-Glycosidic bond C. β-1,4-Glycosidic bond D. β-1,6-Glycosidic bond
A. α-1,4-Glycosidic bond
The amino acids Asp6, Asn9, Thr10, His11, and Arg27 are found near the ADP binding site of PanK3. Which two amino acids contribute to the stabilization of ADP binding described in the passage? A. Asn9 and Thr10 B. His11 and Arg27 (positive) C. Asp6 and Arg27 ( negative, positive) D. Asp6 and His11 (negative, positive)
ADP = - will be stabilized by + charged amino acid
The source of the phosphate groups that are added to rhodopsin is: A. arrestin. B. rhodopsin kinase. C. ATP. D. all-trans-retinol.
ATP The substrate for rhodopsin kinase that the source of phosphate is ATP.
Based on the data from Table 1, what effects do acid and chloride have on the enzymatic activity of laccases? Both acid and chloride decrease the activity. B. Both acid and chloride increase the activity. C. Acid decreases the activity, whereas chloride increases the activity. D. Acid increases the activity, whereas chloride decreases the activity.
Acid increases the activity, whereas chloride decreases the activity.
A homodimeric protein was found to migrate through SDS polyacrylamide gel electrophoresis (SDS-PAGE) with a mobility that matched that of a 45-kDa standard. What change in the experiment would increase the chances of observing the mobility expected for the 22.5-kDa monomer? A. Increasing the gel running time B. Adding a reducing agent C. Using a higher voltage D. Removing the SDS
Adding a reducing agent because adding a reducing agent would eliminate any disulfide bridges and allow the monomers to run separately-thus leading to a migration expected for the 22.5-kDa protein
Based on the relative energy of the absorbed electromagnetic radiation, which absorber, a peptide bond or an aromatic side chain, exhibits an electronic excited state that is closer in energy to the ground state? A. An aromatic side chain; the absorbed photon energy is higher. B. An aromatic side chain; the absorbed photon energy is lower. C. A peptide bond; the absorbed photon energy is higher. D. A peptide bond; the absorbed photon energy is lower.
An aromatic side chain; the absorbed photon energy is lower.
Which structure represents a phosphorylated subunit of glycogen as described in the passage?
Ans D. According to the passage, glycogen has phosphate monoesters at C2 and C3 in one out of every 600-1500 glucose molecules. This glucose molecule is phosphorylated at C2 and C3.
Which secondary structural changes most likely took place in the peptide as result of adding TFE? The secondary structure of the poly-l-lysine changed from: A. random coil to α-helix. B. α-helix to random coil. C. β-sheet to random coil. D. α-helix to β-sheet.
Ans. D multiple graphs provided and are suppose to just compare the two graphs and should be able to find the answer
Which amino acid has the highest isoelectric focusing point?
Arginie pH = 12 isoelectric point of an amino acid is the highest for basic amino acids, and arginine and lysine are both basic amino acids. However, arginine has a higher isoelectric point because it is more basic. "Structure, function, and reactivity of biologically-relevant molecules."
Which amino acid residues were incorporated into Compound 1 to promote the adhesion of cells on the scaffold surfaces? A. Arg and Gly B. Cys and Gly C. Cys and Asp D. Asp and Arg
Asp and Arg
The graph below shows the relationship between the predominant form of iron as a function of solution pH and applied potential. Based on the graph, which of the following statements is true? At a potential of -0.4 V, as pH increases, Fe2+ is reduced and precipitates as Fe(OH)3. B. At a potential of -0.44 V, the equilibrium between Fe and Fe2+ is independent of solution pH below pH 6. C. At pH = 1, as the potential is changed from -0.2 to +0.8, Fe3+ is reduced to Fe2+. D. At pH = 8 and V = -0.1 V, Fe(OH)2 is the predominant form of iron.
At a potential of -0.44 V, the equilibrium between Fe and Fe2+ is independent of solution pH below pH 6. The Pourbaix diagram for iron is given, but only one statement correctly conveys information presented by the diagram. At an applied potential of -0.44V and pH below 6, there is an equilibrium between Fe(s) and Fe2+(aq), as shown by the line of demarcation. The fact that this line moves horizontally with increasing pH up until pH = 6 means that this equilibrium is unaffected by changing the pH.
Which data suggest that the differences in Compound 1 metabolism between the variant and wild-type CYP2C9 enzymes are NOT due to changes in the binding affinity toward Compound 1? A. Compound 1 is still eliminated from the body of patients expressing the CYP2C9*3 allele. B. The KM values for the variant enzymes do not differ significantly from the wild-type enzyme. C. The amino acid substitutions at positions 144 and 359 do not change the binding pocket of the variant enzymes. D. The side chains of the amino acid residues at positions 144 and 359 are charged at physiological pH.
B. Q---> binding affinity affected by A. does not highlight any relation of binding affinity with c1 elimination B. Km and binding affinity closely related (if Km values differ significantly that may cause the binding affinity to reduce however when they are comparable this would not cause an affect on the binding affinity ) C. Although the amino acid substitution at position 359 (I to L) would not be expected to change binding affinity, the change at position 144 (R to C) charges charge and would be expected to change binding affinity, although this change has no significant effect D. 114 is charged and 359 is not therefore the statement is false
What is the effect produced by the PRK technique designed to correct nearsightedness? A. The density of the cornea is increased. B. The radius of curvature of the cornea is increased. C. The index of refraction of the cornea is increased. D. The thickness of the cornea at the apex is increased. Solution
B. The radius of curvature of the cornea is increased. According to the passage, to correct nearsightedness, the laser beam is directed onto the central part of the cornea, resulting in a flattening (expanding) of the cornea. This means that the radius of curvature of the cornea is increased
Based on the passage, as compared to a wild-type mouse, an Acc2-/-/Cpt1-/- double knockout mouse is most likely to exhibit: A. increased insulin secretion. B. decreased fatty acid oxidation. C. decreased triglyceride synthesis. D. increased malonyl-CoA production.
B. decreased fatty acid oxidation. Acc2 func = fatty acid oxidation CPT1 is an essential enzyme in the carnitine shuttle, transporting fatty acids into the mitochondria for oxidization. The absence of CPT1 would prevent the transport of fatty acids into the mitochondria for oxidization, irrespective of the presence or absence of ACC2.
Compound 3 is prepared from Compound 2 (Figure 2) by: A. reduction of the ketone and lactonization of the gamma-hydroxyester. B. hydrolysis of one ester and formation of an acetal from the ketoacid. C. reduction of one ester and formation of an acetal from the gamma-hydroxyketone. D. reduction of one ester and the ketone followed by dehydration to a ketoether.
B. hydrolysis of one ester and formation of an acetal from the ketoacid.
Which of the following functional groups is present in pyrrolizidine (Figure 1)? A. An amide B. An amine C. An imine D. A carbamate
B. amide (carbonyl +NH2 ) amine NH3 or NR3 Imine R2C=NR (there is a double bond btwn Carbon and amine. Carbamate (like amide except there is no hydroxyl group) R1O(C=O)NR2R3, R1 = C
Assume that cellular uptake rates and drug delivery rates of compounds 1 and 2 are identical. If the proposed mechanism of sensitization by Compound 1 is correct, what cancer cell treatment protocol is most likely to produce the most apoptosis 20 h after treatment? A. Administration of both Compound 1 and Compound 2 simultaneously B. Administration of Compound 1 followed by Compound 2 after 0.5 h C. Administration of Compound 2 followed by Compound 1 after 0.5 h D. Administration of Compound 2 followed by Compound 1 after 1 d
B. Administration of Compound 1 followed by Compound 2 after 0.5 h Whenever 2 dress are used in combination there needs to be some amount of the that needs to ease before the administration of the 2nd drug The NF-κB signaling pathway is anti-apoptotic and is initiated by degradation and release of the inhibitor binding protein IκB. Once started, this process is not easily reversed. If the chemotherapeutic agent is administered at the same time as the sensitization agent, there is good reason to believe that some cells will be exposed to Compound 2 prior to Compound 1 as a result of random probability. The researchers found that administration of Compound 1 prior to Compound 2 by 0.5 h provided benefit.
Assuming the amino acid transport protein complex examined in Figure 1 follows standard Michaelis-Menten kinetics, Kt is equal to: A. two times the maximal transport capacity. B. the substrate concentration at one-half the maximal transport capacity. C. the transport capacity at one-half the substrate concentration. D. the substrate concentration at one-third the overall transport rate.
B. the substrate concentration at one-half the maximal transport capacity.
Which statement about the cooperativity of RIα/C activation and RIα protein folding is supported by the data in figures 2 and 3?
Both activation and folding are cooperative. because both have a sigmoidal curve
Why is the velocity of blood flow slower in capillaries than in arteries? A. Capillary walls are more elastic than arterial walls. B. Capillaries have less resistance to blood flow than arteries. C. The total cross-sectional area of capillaries exceeds that of arteries. D. Blood pressure is higher in the capillaries than in arteries.
C. The total cross-sectional area of capillaries exceeds that of arteries.
The Na2CO3 used in Step 5 of Figure 3 is necessary to: A. dissolve the bromoester. B. remove an α-hydrogen from the bromoester. C. convert the ammonium salt in Compound 4 to the amine. D. replace the chloride ion in Compound 4 with the carbonate ion
C. convert the ammonium salt in Compound 4 to the amine.
Which of the following compounds is most likely the intermediate product formed in Step 4 of Figure 2 if four equivalents of base are used?
C. When four equivalents of base (-OH) are used, one -OH will saponify the lactone to form the secondary alcohol and carboxylate, a second -OH will hydrolyze the carbamate, with the remaining -OH as excess.
The hardness ions described in the passage are:
Derived from atoms upon loss of two electrons All the ions described in the passage have a +2 charge, meaning they lost two electrons.
Researchers noted that in the absence of a reducing agent the elution time of a certain protein from a size-exclusion column decreased considerably relative to the elution time when the buffer contained a reducing agent. Which type of molecular interaction was responsible for this observation?
Disulfide bonding because the presence of a disulfide bond between two subunits of a protein would cause the protein to have a different elution time on a size-exclusion column. The fact that reducing agents eliminate this interaction is more evidence that a disulfide bond was present. "Structure, function, and reactivity of biologically-relevant molecules."
Absorption of ultraviolet light by organic molecules always results in what process? A. Bond breaking B. Excitation of bound electrons C. Vibration of atoms in polar bonds D. Ejection of bound electrons
Excitation of bound electrons The absorption of ultraviolet light by organic molecules always results in electronic excitation. Bond breaking can subsequently result, as can ionization or bond vibration, but none of these processes are guaranteed to result from the absorption of ultraviolet light
When used in place of spHM, which peptide would be most likely to achieve the same experimental results? original FLGFTY A. FLGFAY B. FLGFQY C. FLGFGY D. FLGFEY
FLGFEY STY = phosphate = negative charge = acidic amino
Addition of which disaccharide to a solution of Ag2O in NH3(aq) will NOT result in the deposition of shiny silver mirror on the walls of the reaction vessel?
For a sugar to be able to reduce another sugar it needs to be able to get oxidized therefore it must have an OH group on the anomeric carbon formally regarded as the hemiacetal group
The side chain of which amino acid is most likely to form a hydrogen bond with the side chain of glutamate?
Gln hydrogen bond with glutamate, an amino acid side chain must contain a hydrogen bond donor group to match with the glutamate acceptor. Glutamine has an NH2 group that can act in this way. "Structure, function, and reactivity of biologically-relevant molecules."
Each of the following equations shows the dissociation of an acid in water. Which of the reactions occurs to the LEAST extent? A. HCl + H2O → H3O+ + Cl− B. HPO42− + H2O → H3O+ + PO43− C. H2SO4 + H2O → H3O+ + HSO4− D. H3PO4 + H2O → H3O+ + H2PO4−
HPO42− + H2O → H3O+ + PO43−
a polysaccharide of glucose
Has numerous hydroxyl groups that can hydrogen bond to the polar side chains that are typically exposed on a protein surface.
Which reaction is catalyzed by LipA? LYSOSOMAL lipase A. ATP hydrolysis B. Peptide bond cleavage C. Hydrolysis of triacylglycerides D. Transfer of carboxyl groups
Hydrolysis of triacylglycerides
Based on the passage, what is the primary type of interaction that RT makes with Compound 2? A. Covalent B. Hydrogen bonds C. Ionic D. Hydrophobic
Hydrophobic The passage states that the strongest RT interactions with the inhibitors come from the side chains of valine and phenylalanine. These side chains are hydrophobic, so they would make hydrophobic interactions with the inhibitor
Based on the information in the passage, PDK1 catalyzes the addition of phosphate to what functional group? A. Hydroxyl B. Amine C. Carboxyl D. Phenyl
Hydroxyl phosphate is added to STY and STY have the hydroxyl group in common
What causes duplex DNA with a certain (A + T):(G + C) ratio to melt at a higher temperature than comparable length duplex DNA with a greater (A + T):(G + C) ratio? A. Stronger van der Waals forces of pyrimidines B. Stronger van der Waals forces of purines C. Increased π- stacking strength D. Reduced electrostatic repulsion of phosphates
Increased π- stacking strength G-C base pairs form stronger π-stacking interactions than A-T base pairs, thereby creating the most thermal stability. This disparity has often been used to explain the increased melting temperature of DNA rich in GC content.
Which enzymatic kinetic parameter is NOT affected by the presence of an uncompetitive inhibitor?
KM/Vmax uncompetitive inhibitors affect both the kcat and KM of an enzymatically catalyzed reaction in a way that does not change the slope of the Lineweaver-Burk plot, which means the KM/Vmax is not changed. "Principles of chemical thermodynamics and kinetics."
The concentration of enzyme for each experiment was 5.0 μM. What is kcat for the reaction at pH 4.5 with NO chloride added when Compound 3 is the substrate? A. 2.5 × 10-2 s-1 B. 1.3 × 102 s-1 C. 5.3 × 103 s-1 D. 7.0 × 105 s-1
Kcat = Vmax / Et Kcat = 5x10^-6 / 125 x 10^-9 = 1/ 25 x 10^3
From the data presented in Figure 3, which RIα variant is the most stable? A. L203A B. I204A C. Y229A D. R241A
L203A stability = high melt or boil temp more stable version will melt at high temp
Compound 1 remains mainly confined to the central phase during the experiments because it is: Researchers demonstrated that Compound 1 (Figure 1) allowed control of the relative rate of cation transport in vitro. Compound 1 mimicked competitive Ca2+/K+ transport coupled to H+ antiport in a pH gradient as shown schematically in Figure 2 With only one binding site, it extracted and transported either monovalent or divalent cations from the "IN" phase to the "OUT" phase one at a time. (no mention going against gradient and req ATP therefore symport)
Lipophilic, with both polar and non polar groups Since transporter of ions must be in membrane and since it says is "confined to the central phase" means in the middle of membrane = in hydrophobic part of membrane Compound 1 mimics a membrane symport. Thus, it is lipophilic. The structure has both polar (X: carboxyl group) and nonpolar (18-crown-6 itself and Y: amide and ether) groups.
The side chain of which amino acid is used by transaminases to bind to pyridoxal phosphate in the enzyme's resting state?
Lys The side chain depicted in Figure 2, is -(CH2)4NH2 which corresponds to lysine, or Lys.
A scientist proposed that the 32P label was entering PE molecules by direct exchange (swapping phosphate groups with those found in solution) and NOT through synthesis of new PE by bacterial cells. What experimental modification can show this is NOT the case?
Measure the rate of incorporation of 32PO4 3- into acellular PE The rates of bacterial PE(lipid) synthesis and any potential phosphate exchange should be different. Also, it is unlikely that phosphate would exchange from a phospholipid.
Phosphoenolpyruvate (PEP) transfers a phosphate group to ADP in a spontaneous reaction, and ATP transfers a phosphate group to glucose in a spontaneous reaction, both under standard conditions. Based on this information, what is the relationship between the absolute values of the standard free energies of hydrolysis of PEP, ATP, and glucose 6-phosphate (G6P)?
PEP> ATP > G6P the molecule with the most negative standard free energy of hydrolysis is also the molecule that is able to spontaneously transfer a phosphate group to create phosphorylated compounds of lower free energy Therefore, if ATP can spontaneously transfer phosphate to glucose and PEP can spontaneously transfer phosphate to ADP, then PEP has the most negative standard free energy of hydrolysis followed by ATP. The absolute value of the most negative number is the largest value. "Principles of bioenergetics and fuel molecule metabolism."
The transition of which amino acid from the interior of a soluble globular protein to the surface is associated with the largest positive ΔGº?
Phe Phe is a hydrophobic amino acid that makes favorable interactions within a protein interior but does not make favorable interactions with solvent. This means that any transition to solvent would involve an unfavorable, or positive, ΔGº. "Structure, function, and reactivity of biologically-relevant molecules."
Consider the dissociation constant data Kd for four proteins and their respective ligands. Which protein has the highest affinity for its ligand?
Protein 2 because the protein with the lowest binding dissociation constant has the highest affinity for its ligand. The dissociation constant represents the ligand concentration that is necessary to achieve 50% binding. "Structure, function, and reactivity of biologically-relevant molecules."
What are the configurations (R or S) of the chiral centers bonded to substituents X and Y, respectively, in Compound 1?
R,R draw it out For the carbon atoms bonded to the Y groups, the lowest priority group is already in the back and so the ranking of the remaining groups, which occurs in a clockwise manner, gives the Rconfiguration. For the carbon atoms bonded to X, the X group is in the back, and the relative rank of the remaining groups occurs in a counter-clockwise manner. When H is placed in the back, however, this would also be clockwise, or R.
In addition to glucose, what other monosaccharide is part of the UDP-glucose structure? A. Xylose B. Fructose C. Ribose D. Arabinose
Ribose= furanose
What stereochemical designation can be assigned to naturally occurring aspartic acid?
S The correct stereochemical designation can be made by using either the Fischer projection of Compound 8 (with R = CH2CO2H) or the perspective drawing of Compound 1. For the Fischer projection, the priorities of the remaining three groups are NH2 > CO2H > R. This occurs in a clockwise fashion. Since the H is pointing towards the viewer in this drawing, however, the priorities would reverse to counterclockwise, or S when viewed with H (the lowest priority group) in the back.
The physical properties for two proteins are shown Protein 1 disulfide bond Protein 2 no disulfide bond Based on the information in the table, which technique would be best suited to separate the two proteins from one another?
SDS PAGE under reducing conditions because the two proteins have the same molecular mass and pI, which means they will not be well-resolved on either native PAGE or isoelectric focusing Also, the presence of a disulfide bond in the dimer means that the proteins would not resolve as well on SDS-PAGE under nonreducing conditions. Only SDS-PAGE under reducing conditions would show two bands for Protein 1 at distinctly different molecular weights than the single band for Protein 2
Which amino acid was incorporated into Compound 1 as a future site of covalent attachment to HA prior to mineralization? A. Ser B. Ala C. Tyr D. Thr
Ser is the residue that was phosphorylated at its primary alcohol side chain for future attachment of nanocrystals of HA
Compound 1 was designed to exhibit pH-dependent self-assembly. What feature(s) of the molecule is(are) responsible for the pH dependence of aggregation (Equation 1)? A. Thiol side chains that can hydrogen bond B. Long alkyl tail that exhibits predominantly London forces C. Side chains whose net charge responds to pH D. Covalent linkages that reversibly hydrolyze
Side chains whose net charge responds to pH
SDS-PAGE electrophoresis
Sodium dodecyl sulfide separates based on mass SDS binds to proteins and creates large chains with net negative charges, thereby neutralizing the protein's original charge and denaturing the protein The only variable affecting their velocity is f, the frictional coefficient, which depends on mass SDS page can not reduce disulfide bonds (covalent bonds) requires a stronger reducing agent
Cyanogen bromide cleaves peptide bonds by first undergoing nucleophilic attack by the side chain of a methionine residue. Which atom is the nucleophile in this reaction?
Sulfur The answer is A because sulfur is the only atom in the methionine side chain that has lone pairs of electrons available, which makes it a better nucleophile.
Substituting the residue at position 54 of BvgA with which amino acid will LEAST likely prevent the expression of the PTx operon? A. Glycine B. Asparagine C. Glutamate D. Alanine
The PTx operon is activated in response to binding of an inducer protein (BvgA) to the promoter region. Two lines of evidence suggest that the D54 residue in BvgA and its phosphorylation are essential for promoter binding. D= Aspartic Acid or -ate = same thing ate-ic = rep same thing B and C - all have in -ine except glutamate
A pump is used to force an aqueous solution through a pipe at high temperature according to Poiseuille's Law: where ΔP is the pressure difference applied by the pump, r is the radius of the pipe, L is the length of the pipe, and η is the viscosity of the solution. Which graph depicts the rate of energy consumed over time in order to maintain constant flow through a pipe subject to boiler scale?
The energy consumed by the pump is used to create the pressure difference that maintains the viscous flow through the pipe. For a constant flow to occur while the pipe's diameter decreases, the pressure difference should increase in time. According to Poisseuille's Law, at constant flow rate, the pressure difference is inversely proportional to the radius of the pipe to the fourth power. The energy used is equal to the work done in moving the fluid, hence is proportional to the pressure difference. In other words, energy is inversely proportional to the radius of the pipe to the fourth power. As the radius decreases in time, the energy used increases more due to the fourth power dependence of the radius. In other words, more power (energy per unit time) is required to maintain the same flow through a pipe with decreased radius. Hence, the only choice that depicts such a power increase that is getting larger in time is shown in graph D. GRAPH= energy inc exponentially r^4 = radius is dec to maintain the same flow pressure must inc exponententially since radius exponentially. Energy = Work (mgh) = P (mgh) will inc exponentially
What factor explains how a single stereoisomer is formed in Reaction 2? A. One of the reactants is chiral. B. Both reactants are chiral. C. The solvent medium is chiral. D. The enzyme is chiral.
The enzyme is chiral. the products or reactant were not chiral An enzyme is a chiral catalyst capable of preferentially forming one enantiomer because a lower energy chiral transition state leads to the preferred product.
What is the [H3O+] in the solution used in the experiment done at the lowest pH? A. 0.01 μM B. 0.1 μM C. 1.0 μM D. 100 μM
The lowest pH is 6. Because pH = -log([H3O+]), [H3O+] = 1.0 × 10-6 M or 1.0 μM.
What happens to the pH of a soapy solution as a result of the introduction of hardness ions? M2+(aq) + 2HCO3-(aq) → H2O(l) + CO2(g) + MCO3(s) H2CO3 = acid HCO3- =base Going from Base to neutral = therefore dec pH
The pH dec as OH- dec Removal of weak bases such as RCO2-results in a decrease in pH, and a decrease in [OH - ].
What event will most likely occur if Protein X is inserted into the inner membrane of mitochondria? A. The citric acid cycle will cease to function. B. The electron transport chain will cease to function. C. The proton gradient across the inner membrane will dissipate. D. The pH of the intermembrane space will decrease.
The proton gradient across the inner membrane will dissipate.
What are the structural features possessed by storage lipids? A. Two fatty acids ester-linked to a single glycerol plus a charged head group B. Three fatty acids ester-linked to a single glycerol C. Two fatty acids ester-linked to a single sphingosine plus a charged head group D. Three fatty acids ester-linked to a single sphingosine
Three fatty acids ester-linked to a single glycerol
Why must the person either lean forward or slide their feet under the chair in order to stand up? A. To increase the force required to stand up B. To use the friction with the ground C. To reduce the energy required to stand up D. To keep the body in equilibrium while rising
To keep the body in equilibrium while rising The person is in equilibrium only when the center of mass is directly above their feet. Otherwise, if the person did not lean forward or slide the feet under the chair, the person would fall backward due to the large torque created by the combination of the weight of the body (applied at the person's center of mass) and the distance along the horizontal between the center of mass and the support point.
A heterotrimeric protein consists of three subunits with molecular weights of 10 kDa, 40 kDa, and 100 kDa. The protein is denatured with 3 M urea and subjected to size-exclusion chromatography. Which solute is the last compound to elute from the column?
Urea because a size-exclusion column allows larger molecules to pass more freely through the column matrix and hinders the passage of smaller molecules. Urea is this smallest solute and would be the last to elute "Separation and purification methods."
A researcher measures the initial rate (V0 = Δ[P]/Δt) of an enzymatically catalyzed reaction at a variety of substrate concentrations [S]0. Which graph best represents the observed relationship between [S]0 versus V0?
V0 (y-axis) vs. [S] (x-axis) inc linear and then level off For enzymatically catalyzed processes, the reaction rate will level off with increasing concentration of substrate as the enzyme becomes the bottleneck for the reaction. This is called saturation kinetics.
Compared to the wild-type LipA, what is the change in net charge in variant XI at pH 7? A. +4 B. +3 C. −3 D. −4
Variant XI has a change of -1 charge with R33G (+1 to 0), -2 charge with K112D (+1 to -1), and -1 charge with M134D (0 to -1) for a net change of -4.
The pressure and volume changes that occur during a cycle of breathing are illustrated graphically in the figure shown.
Work done W= PV
Based on the data presented in figures 2 and 3, what is the most likely role of Y229 in protein stability and cAMP activation? Y229 is important for protein stability but not critical for cAMP activation. B. Y229 is important for cAMP activation but not critical for protein stability. C. Y229 is important for protein stability and critical for cAMP activation. D. Y229 is not important for protein stability and not critical for cAMP activation.
Y229 is not important for protein stability and not critical for cAMP activation. looking at the first graph which tells about cAMP activation % the Y229 strain is not present at all thus indicating it is not crucial for cAMP activation and in the other graph it has relatively low melt temp therefore being very unstable
Addition of laforin to the reaction mixtures used to generate the data in Figure 2 will result in: A. a decrease in the intensity of the band representing WT without glucosidase when visualized with 14C decay. B. an increase in the intensity of the band representing WT without glucosidase when visualized with 14C decay. C. a decrease in the intensity of the band representing WT without glucosidase when visualized with 32P decay. D. an increase in the intensity of the band representing WT without glucosidase when visualized with 32P decay.
a decrease in the intensity of the band representing WT without glucosidase when visualized with 32P decay. Laforin has a lot of P32 but wild type doesn't has enough phosphate therefore WT band pattern will be less intense
porphyrin pyrole ring
a five-sided heterocycle containing one nitrogen atom with one double bond in the ring cofactor = heme = pyrole ring basic unit of a porphyrin is the pyrrole ring
What is the general structure of a hydroxamic acid? hydroxyl amine acetylation of the nitrogen in Compound 2 produces a hydroxamic acid
acetylation = addition of RC=O
Cytochrome P450
acts as monooxygenases, where an oxygen atom is inserted into a substrate (the drug of interest), thereby resulting in the oxidation of the substrate.
The 32P label was generated from naturally occurring phosphorous by:
adding a neutron to the nucleus This question requires you to apply knowledge of the nuclear structure of the naturally occurring 31P nucleus, and of nuclear radioactivity through the process of beta decay. The 32P isotope contains an additional neutron in the nucleus compared to the naturally occurring 31P nucleus, which does not change the identity of the atom. The extra neutron emits a beta particle via beta-minus decay.
Which amino acid will contribute to the CD signal in the far UV region, but NOT the near UV region, when part of a fully folded protein? A. Trp B. Phe C. Ala D. Tyr
ala all chiral + nonaromatic amino acids = will contribute solely to the CD signal in the far UV region
Uracil is produced from cytosine as a result of a conversion of:
an amine group to a carbonyl group because in the deamination of cytosine, the amine group of cytosine is replaced with a carbonyl group, resulting in the structure of uracil. "Structure, function, and reactivity of biologically-relevant molecules."
Compound 1 is used to treat HIV infection based on its ability to act as: A. an agonist. B. an antagonist. C. a placebo. D. a catalyst.
an antagonist Descb in passage One such molecule is Compound 1, shown in Figure 2, which is a potent HIV protease inhibitor.
aldol addition
an elongate attacks a carbonyl carbon leading to a new carbon-carbon bond occurs if there is no dehydration in an aldol condensation. The product must be a b-hydroxyketone. (ketone and b
Protein secondary structure is characterized by the pattern of hydrogen bonds between: A. backbone amide protons and carbonyl oxygens. B. backbone amide protons and side chain carbonyl oxygens. C. side chain hydroxyl groups and backbone carbonyl oxygens. D. side chain amide protons and backbone carbonyl oxygens. Solution
backbone amide protons and carbonyl oxygens. econdary structure is represented by repeated patterns of hydrogen bonds between the backbone amide protons and carbonyl oxygen atoms.
The side chain of tryptophan will give rise to the largest CD signal in the near UV region when: A. present as a free amino acid. B. part of an α-helix. C. part of a β-sheet. D. part of a fully folded protein.
because tryptophan has an aromatic side chain that will give rise to a significant CD signal in the near UV region if it is found in a fully folded protein. has aromatic side chain and if the protein is fully folded that ensures that the side chain will be intact and allow for absorption near the UV region
Which statement correctly describes both PO43- and TNBS?
both are hydrophilic The structure of TNBS shows that it contains three polar substituents on a benzene ring, which makes the molecule hydrophilic. Also, it does not cross the hydrophobic membrane. Phosphate is a negatively charged hydrophilic ion.
Soaps are chemically modified natural products that can be derived from all of the following EXCEPT: soaps are made of fatty acids fatty acids are RCO2H which can easily be converted to soaps RCO2Na by the addition of NaOH.
cholesterol
What is the structure of the product formed when Compound 3 is the substrate of laccase-catalyzed reaction?
compound 3 will become more conjugated and in the conjugated form it will have the hydrogens of the OH dissolved as the oxygen double bond with carbon Based on Reaction 1 and the fact that the product of oxidation absorbs strongly in the visible region, the most likely structure of the product is the highly conjugated quinone
Which event is LEAST likely to occur during apoptosis? cytochrome c release from the mitochondria cell shrinkage and blebbing caspase (a family of protease enzymes that provide critical links in cell regulatory networks controlling inflammation and cell death) activation damage to nearby cells caused by lysis
damage to nearby cells caused by lysis The answer is D because damage to nearby cells caused by lysis is a characteristic of necrosis, not apoptosis "Processes of cell division, differentiation, and specialization."
What modification of Compound 1 will favor transport of Na+ relative to K+? Preodic table K to Na = size dec The central portion of this molecule, known as a crown ether, selectively binds to cations based on their ionic radii.
dec the ring size by removing one -CH2CH2O- From the passage, it was stated that K+is transported within the central portion of Compound 1. Since Na+ is chemically similar to K+ it is reasonable to assume that there might be a way to favor its transport over K+ by changing the size of the ring. The change necessary would be to decrease the ring size since Na+ is smaller than K+.
What factor can account for the relative rate of Ca2+transport across the membrane as a function of pH? A. deprotonation of the X groups ( acid has COOH) B. deprotonation of the Y groups ( basic bcz has N group) C. Protonation of the cental O atom D. change in the ring size of macrocycle
deprotonation of the X groups at high pH Ca2+ transport inc and at high pH acid is deprotonated: therefore the acidic group (X) is deprotonated The overall rate of ion transport does not change much (consider the sum of the two rates in Table 1), but the rate of Ca2+ increases at the expense of K+ at high pH This can only be due to deprotonation of the X groups. The overall entity maintains electrical neutrality by preferentially binding to a divalent cation. B. The Y groups will not change protonation state under the conditions of the experiment (bcz only if the experiment condition was extremely basic then Y would be deprotonated) C. The central O atoms of the ring are not sufficiently basic to be protonated under these conditions. (to be more basic the O needs to have extra electron pairs on them) D. The macrocyclic ring will be unaffected by pH changes in the range 2-9.
Specific activity is a measure of:
enzyme units per milligram of total protein in a solution because the activity is a measure of the amount of enzyme per milligram of total protein. This provides a measure of the purity of an enzymatic mixture. "Separation and purification methods."
If sounds produced by the human vocal cords are approximated as waves on a string fixed at both ends, and the average length of a vocal cord is 15 mm, what is the fundamental frequency of the sound? (Note: Use 3 m/s for the speed of sound through the vocal cord.)
f = v/(2L) = (3 m/s)/(30 × 10-3 m) = 1/10-2 H = 100 Hz
The scientists who developed the experimental protocol described in the passage chose TNBS over many potential candidates to label PE molecules. What characteristic about the rate of reaction between TNBS and outer envelope PE molecules allowed the experiment to provide useful data? The rate of TNBS reaction with outer envelope PE molecules is:
faster than the rate of exchange between inner and outer envelope PE molecules In order for TNBS treatment to accurately determine the state of membrane phospholipids at any given time interval, the rate of the reaction must be faster than the time it takes to establish a new membrane state. Reaction with TNBS must be very fast in order to freeze the state of the membrane so that it may be analyzed.
Which amino acid is found in greatest abundance in the active site of a laccase? Phe B. Tyr C. His D. Cys
histidine
A common column material used in size-exclusion chromatography is dextran, a polysaccharide of glucose. Which type of interaction most likely occurs between proteins and the dextran column material? A. Aromatic B. Hydrophobic C. Salt bridge D. Hydrogen bonding Solution
hydrogen bonding because a polysaccharide of glucose has numerous hydroxyl groups that can hydrogen bond to the polar side chains that are typically exposed on a protein surface.
Which of the following compounds is most likely to be a major product in Step 2 if the aldol condensation is NOT followed by a dehydration reaction?
in the dehydrated product there is no OH group and has a double bond in the new ring therefore if no dehydration will see a OH group and always make sure that all the carbons in the compound have only 4 bonds
What is the dependent variable in an experiment that determines the Michaelis-Menten kinetic parameters of an enzyme?
initial velocity (rate of reaction V0) the independent variable in the experiment is the substrate conc The answer to the question is A because enzymatic assays should be conducted in this way to generate a curve of velocity versus substrate concentration, which can then be used to determine the Vmax and KM of the reaction.
Sites I and II are most likely lined with the side chains of which amino acids? A. R and L B. E and Y C. D and E D. D and H Solution
ligands are to be anionic and hydrophobic anioin(acid) pair with cation(base) hydrophobic binds with hydrophobic (LDF)
Which combination of lipid type and temperature results in the most disordered membrane?
lipids with unsaturated acyl chains at high temp The key is D because lipids with unsaturated acyl chains do not pack well against one another, increasing the level of disorder. Increased temperature also increases the level of disorder in the membrane because there is more movement at higher temperatures
The passage states that compounds 1-3 can bind to RT both before and after the substrate has bound. Also, the compounds do not exclude substrate binding. What type of inhibitor is used
mixed inhibition is most likely
Four organic compounds: 2-butanone, n-pentane, propanoic acid, and n-butanol, present as a mixture, are separated by column chromatography using silica gel with benzene as the eluent. What is the expected order of elution of these four organic compounds from first to last?
n-Pentane → 2-butanone → n-butanol → propanoic acid ( has OH group and the negative charge) The four compounds have comparable molecular weights, so the order of elution will depend on the polarity of the molecule. Since silica gel serves as the stationary phase for the experiment, increasing the polarity of the eluting molecule will increase its affinity for the stationary phase and increase the elution time (decreased Rf).
phosphatadylethanolamine (PE (lipid))
name of a phospholipid (found in biological membrane) has acyl Phospholipid = fatty acid acyl chains ( only has CH non polar)
Compared to normal glycogen, the amount of what type of bond is decreased in Lafora bodies? A. Phosphomonoester B. Phosphodiester C. α-1,4-Glycosidic bond D. α-1,6-Glycosidic bond
normal glycogen has α-1,6-Glycosidic bond
Which biological molecule can react with Compound 11 so that pyridoxal phosphate (Compound 5) is regenerated?
oxaloacetate Respondents need to connect the dots and appreciate that the sequence shown in Figure 2 accomplishes only half the net reaction shown in Figure 1. Compound 5 is regenerated from Compound 11 and a molecule of α-keto acid (such as oxaloacetate) and the cycle can continue. This was alluded to in the passage as well, when it was stated that "pyridoxal phosphate acts as a carrier of the amino acid NH2 group during the reaction."
fatty acids similar structures (-RCO2H)
phospholipid RCO2- Phospholipids also contain RCO2- groups that can be released by hydrolysis and precipitated as soap. triacylglycerol (glycerol) RCO2- RCO2- groups that can be released by hydrolysis and precipitated as soap.
Based on the data in Table 1, the binding site of CPFX on BSA was determined to be: A. primarily at Site II. (ibruopfen) B. equally partitioned between Site I and Site II. C. primarily at Site I. (warfarin) D. at a site distinct from either Site I or Site II.
primarily at Site I. Ka/K0 < 1 = so decrease in binding Warfrin < Ibruopfen < 1 0.46< 0.87 < 1 so the CPFx is competing for binding with first Warfrin and then Ibruopfen because of the decrease in binding indicated by Ka/K0 being less than 1 therefore since CPFx primarily competing with Warfrin it is binding there firstly
By what factor is the proton concentration increased in the experiments shown in Figure 1B from those shown in Figure 1A? A. 2 B. 10 C. 200 D. 1000
proton concentration = pH shift from 7 to 4 = 3 folds = 1000
Which compound is NOT a component of the citric acid cycle?
pyruvate pyruvate is converted to acetyl-CoA prior to entering the citric acid cycle. "Principles of bioenergetics and fuel molecule metabolism."
Generation of Compound 3 is the result of Compound 2 undergoing: A. oxidation. B. reduction. C. hydrolysis. D. carboxylation.
reduction
Which example of movement across a cell membrane is an example of active transport?
sodium and potassium moving through the Na+K+ atpase "Assemblies of molecules, cells, and groups of cells within single cellular and multicellular organisms."
What are the hybridization states of the carbon atoms involved in the conversion of trans to cis retinal? A. sp B. sp2 C. sp3 D. sp3d
sp2
Squalene is produced in the human body as a precursor to which important class of compounds? A. Triacyl glycerols B. Phospholipids C. Steroid hormones D. Prostaglandins Solution
steroid 4 fused rings 6665 Squalene is a precursor of the fused four-ring system common to cholesterol and all of the steroid hormones.
Consider four DNA strands. Which strand, when Watson-Crick paired to its complementary strand, has the highest melting temperature?
strand 3 because it is rich in GC bonds that req 2 OH bond and thus have high melt temp The answer is C because the melting temperature of double stranded DNA is a function of how many GC base pairs it contains. There is also a positive effect if the GC pairs occur at the ends of the DNA. hydrogen bonding in base pairs to make a claim about melting temperature.
Human speech is generated in the vocal cords as the lungs push air past them. What property of the vocal cords is changed so that the frequency of sound can be altered?
tension The frequency of the sound produced in vibrating cords and strings (such as vocal cords) of fixed length is proportional to the propagation speed of the sound through the cord. In turn, the propagation speed of a transverse wave (such as the sound wave in the vocal cords) is directly proportional to the tension applied along the cord.
Ethanol may be metabolized to acetic acid, then condensed with a coenzyme to form acetyl coenzyme A. Acetyl coenzyme A may then participate in: A. the Krebs (citric acid) cycle. B. glycolysis. C. electron transport. D. oxidative phosphorylation.
the Krebs (citric acid) cycle.
Which event occurs when a G protein-coupled receptor is activated?
the alpha subunit binds GTP the exchange of GDP for GTP in the α subunit is what accompanies G protein-coupled receptor activation. inactivated form = alpha subunit bond to GDP "Structure and functions of the nervous and endocrine systems and ways in which these systems coordinate the organ systems."
The most rapid rate of gluconeogenesis will most likely occur in the body when: A. blood glucose levels are high. B. cortisol release is inhibited. C. the body's stores of carbohydrates are low. D. the body's stores of proteins are low.
the body's stores of carbohydrates are low. Gluconeogenesis is the pathway for the synthesis of glucose (a carbohydrate) from other metabolic compounds such as lipids and amino acids. Therefore, this pathway is activated when the body's stores of carbohydrates are low.
Which forms of guanine and thymine are favored under physiological conditions? A. The keto form of guanine and the keto form of thymine B. The keto form of guanine and the enol form of thymine C. The enol form of guanine and the keto form of thymine D. The enol form of guanine and the enol form of thymine
the keto form is more favorable under physiological conditions
Researchers collected the following data for an enzyme-catalyzed reaction. What is the approximate numerical value of the slope of the Lineweaver-Burk plot of these kinetic data?
the slope of a Lineweaver-Burk plot is equivalent to KM/Vmax. From the data it is apparent that the Vmax is 200 μM/min, and the KM is therefore the substrate concentration at a V0 of 100 μM/min, or 10 μM. The numerical value of the slope is then 10/200 or 0.05. "Principles of chemical thermodynamics and kinetics."
he half-life of a radioactive material is: A. half the time it takes for all of the radioactive nuclei to decay into radioactive nuclei. B. half the time it takes for all of the radioactive nuclei to decay into their daughter nuclei. C. the time it takes for half of all the radioactive nuclei to decay into radioactive nuclei. D. the time it takes for half of all the radioactive nuclei to decay into their daughter nuclei.
the time it takes for half of all the radioactive nuclei to decay into their daughter nuclei. - which may or may not also be radioactive.( daughter nuclei
PAGE gel electrophoresis
used to separate and analyze a sample of DNA containing strands of possibly different lengths by pushing the negative dna down a gel. Shorter strands move further because they have greater acceleration.
Suppose that, under the experimental conditions employed, Compound 1 is "saturated" with cations. What graph depicts the expected change in rate of K+transport from the "IN" to the "OUT" phases at pH 2 (Trial 1 conditions) as a function of increasing K+ ion concentration in the "IN" phase? Researchers demonstrated that Compound 1 (Figure 1) allowed control of the relative rate of cation transport in vitro.
v (K+) y-axis vs. [K+] constant graph Compound 1 acts like a catalyst for cation transport across the organic phase. If Compound 1 is saturated with substrate, increasing the substrate concentration will not increase the rate. In a plot of velocity V versus [S] (classic Michaelis-Menten kinetic treatment) the rate of cation transport is at the limiting value, called Vmax.
The data in Figure 1 show that: A. the unfolding of LipA proteins is a non-reversible process. B. exposure to high temperature eliminates any variant protein activity. C. variation in the flexible regions of LipA decreases the temperature sensitivity of activity. D. wild-type LipA loses all activity when first heated to 50°C
variation in the flexible regions of LipA decreases the temperature sensitivity of activity.
The Michaelis-Menten kinetic data for an enzyme in the presence and absence of an inhibitor is shown. Which statement about the mechanism for inhibitor binding is supported by the data in the Table? The inhibitor binds:
within the active site instead of the substrate V max constant Km inc --------------------- properties of competitive inhibitor therefore must interact with the active site Competitive inhibitors bind in the enzyme active site to the exclusion of the substrate.
In designing the experiment, the researchers used which type of 32P labeled ATP? A. α32P-ATP B. β32P-ATP C. γ32P-ATP D. δ32P-ATP
γ32P-ATP he phosphoryl transfer from kinases comes from the γ-phosphate of ATP.
