Biochem Exam 2

What is the free energy change for transport of glucose from outside the cell to inside the cell at 37ºC when the glucose concentrations are 5 mM outside and 0.1 mM inside?

-10.1

What is the rate enhancement as a result of the presence of an enzyme if the uncatalyzed rate of the reaction is 1.2 102 mmol/sec and the catalyzed rate is 2.4 104 mmol/sec? -0.005 -2 -2.88x10^6 -200 -20

-200

A transporter protein transports Ca2+ ions across a membrane at 37 °C in a cell in which the membrane potential is 100 mV (inside of the cell is negative relative to the outside) and the Ca2+ ion concentrations are 150 mM inside and 15 mM outside. What is the delta G when transporting 2 Ca2+ from the outside of the cell to the inside of the cell? ?

-26.2

A transporter protein transports Ca2+ ions across a membrane at 37 °C in a cell in which the membrane potential is 100 mV (inside of the cell is negative relative to the outside) and the Ca2+ ion concentrations are 150 mM inside and 15 mM outside. What is the delta G when transporting 2 Ca2+ from the outside of the cell to the inside of the cell? ? -7.2 kJ/mol -9.5 kJ/mol +5.9 kJ/mol -13.1 kJ/mol -26.2 kJ/mol

-26.2 kJ/mol

After centrifugation, there is a 10% decrease in activity and a 75% decrease in total protein. What is purification of the target protein? -1.3-fold -3.6-fold -0.28-fold -7.5-fold

-3.6-fold

Select the one TRUE statement regarding how catalysts increase reaction rates -Catalysts lower the ground state energy of both the -product and reactant. -Catalysts lower the ground state energy of the product, thereby lowering deltaG of the reaction. -Catalysts lower the amount of energy required to reach the transition state. -Catalysts raise the ground state energy of both the product and reactant, thereby lowering the activation energy

-Catalysts lower the amount of energy required to reach the transition state.

A mutation in the subunit of hemoglobin is discovered that reduces the affinity of 2,3-BPG binding. Which of the following mutations is most likely to have this consequence? -Asp99 Glu99 -Lys82 Asp82 -Glu6 Val6 -Val1 Ile1

-Lys82 Asp82

Leghemoglobin is an oxygen-binding protein in root nodules that contain bacteria that fix atmospheric nitrogen. Which ONE of the following is TRUE if leghemoglobin is more like myoglobin than hemoglobin? -The O2 binding curve is sigmoidal -O2 binding changes the heme configuration from T to R. -There are four oxygen binding sites -The O2 binding curve is hyperbolic -There is cooperativity in oxygen binding

-The O2 binding curve is hyperbolic

Which of the TWO following statements about x-ray crystallography are true? -All atoms scatter x-rays equally. -The x-ray beam is scattered by the protein sample. -The basic experimental data are relative intensities and positions of scattered electrons. -X-ray crystallography is the only technique which can determine the three-dimensional structure of a protein. -Only crystallized proteins can be analyzed.

-The x-ray beam is scattered by the protein sample. -Only crystallized proteins can be analyzed.

Why is the process of purifying proteins from cells considered challenging? -There is no way to determine the structure of the protein. -There are 10,000 to 100,000 proteins in one sample. -The process is expensive and time consuming. -Proteins are insoluble.

-There are 10,000 to 100,000 proteins in one sample.

Which one of the findings below would provide support for the transition state theory of enzyme catalysis? -Transition state analogs bind tightly to enzyme active sites -Multiple substrates bind in an ordered fashion (i.e. substrate A binds first, then B, then C) to active sites. -The activation energy of an enzyme catalyzed reaction is increased, indicating tight binding of reaction intermediates. -Products of the reaction slowly dissociate from the enzyme

-Transition state analogs bind tightly to enzyme active sites

Nitrite reductase contains two histidine amino acids that coordinate a Cu2+ ion. When the ion is present in the enzyme, the ion is a __________ and the enzyme is a __________. -coenzyme; holoenzyme -coenzyme; apoenzyme -cofactor; holoenzyme -cofactor; apoenzyme

-cofactor; holoenzyme

What type of transport is depicted in the figure below? -passive transport of molecules down a concentration gradient -active transport of molecules up a concentration gradient -active transport of molecules down a concentration gradient -passive transport of molecules up a concentration gradient -membrane diffusion

-passive transport of molecules down a concentration gradient

Both passive and active transport proteins are needed to transport __________ across membranes. -polar and nonpolar molecules -nonpolar molecules and ions -metals and nonpolar molecules -polar molecules and ions

-polar molecules and ions

A reaction coordinate diagram comparing an uncatalyzed reaction with an enzyme-catalyzed reaction can directly illustrate that the enzyme __________, but will not directly illustrate that the enzyme __________. -stabilizes the transition state; orients the substrates appropriately for the reaction to occur -stabilizes the transition state; provides an alternative path for product formation -provides an alternative path for product formation; stabilizes the transition state -orients the substrates appropriately for the reaction to occur; provides an alternative path for product formation

-stabilizes the transition state; orients the substrates appropriately for the reaction to occur

Which resin should you subject your mixture to get the best separation? Choose the resin with the correct attribute of the resin and protein that will separate the proteins.

. CMC cellulose, because the pH is above two of the contaminating proteins and less than YPOI and contaminant protein 3. These two proteins can then be separated by ionic conditions (salt gradient).

You have a collaborator who thinks she has created a compound to bind and inhibit an enzyme involved in lung cancer metastasis. Which of the following experiments using lysate from a tumor should be considered to test whether or not this drug would bind to the protein?

. Fix the drug compound to a chromatography bead and perform an affinity chromatography on the lysate to detect the protein that binds the drug.

Which of the following is accurate in terms of the relationship between the velocity of a reaction and the rate constant (k) of a reaction?

. In a first-order reaction, the rate constant of a reaction is equal to the velocity of the reaction divided by the concentration of substrate.

The following are critical for enzyme structure and function, EXCEPT

. covalent modification affecting the bioavailability of an enzyme.

Within deoxyhemoglobin, there are a total of beta sheets.

0

In the question above, what is the Kd for Ligand Z and Protein X?

0.031

Identify the three types of enzyme-mediated reactions

1. reversible covalent modification reactions 2. coenzyme-dependent redox reactions 3. metabolite transformation reaction

Shown here is the myoglobin protein. Consider its molecular structure and manipulate the molecule according to the instructions below to answer the following questions. First, view just the heme cofactor of myoglobin and locate the four amine nitrogen atoms that are in close proximity to the iron ion (bright blue color in the center). Next, click the dropdown menu in the upper right corner and click the "Measure Distance" icon. Now use the angstrom measurement tool to determine the approximate distance between any one of the four amine nitrogen atoms and the iron ion.This distance is approximately _____ angstoms

2 angstroms

Consider the reaction above. For the uncatalyzed reaction, kF(uncatalyzed) = 5 X 10-4 s-1 and Keq is 2.5 X 102. For the same reaction in the presence of an enzyme, kF(catalyzed) is 5 X 105 s-1.What is kR(catalyzed)?

2 x 10^3 s^-1

What is the rate enhancement as a result of the presence of an enzyme if the uncatalyzed rae of the reaction is 1.2 x 10^2 mmol/sec and the catalyzed reaction rate is 2.4 x 10^4 mmol/sec? 200 2 2.88x10^6 0.005

200

What is the rate enhancement as a result of the presence of an enzyme if the uncatalyzed rate of the reaction is 1.2 102 mmol/sec and the catalyzed rate is 2.4 104 mmol/sec?

200

What is the rate enhancement as a result of the presence of an enzyme if the uncatalyzed rate of the reaction is 1.2 × 102 mmol/sec and the catalyzed rate is 2.4 × 104 mmol/sec?

200

Which percentage of polyacrylamide would give the best separation for large proteins?

5%

The change in free energy for Solute A concentration across a membrane is calculated to be -10 kJ/mol at 37ºC. If Solute B is transported across the same membrane against its own concentration gradient using a secondary active symporter transport mechanism linked to Solute A, what is the maximum concentration ratio that can be achieved for Solute B?

50:1

An experiment is performed in which the kinetics of an enzyme-catalyzed reaction at different pHs is monitored. It is found that the Km does not change but that the kcat increases as the pH goes above 7. Which of the following is true?

A chemical group within the enzyme that has a pKa of around 7 is likely involved in the catalytic mechanism.

Which of the following is not a critical aspect of enzyme structure and function? (The structural and functional aspects of enzymes vary widely, but for this question, be sure to focus on critical aspects that apply to virtually all enzymes, and not just specific enzymes.)

A covalent bond forms between an enzyme and substrate following substrate binding.

Which of the following is true about sickle cell anemia?

A mutation of residue 6 of hemoglobin from glutamate to aspartic acid would likely not cause sickle cell symptoms. B.An effective method of treatment may include inducing the adult overexpression of the gene that codes for the 𝛾γ subunit of fetal hemoglobin. C.A mutation of residue 6 of hemoglobin from glutamate to isoleucine would likely cause sickle cell symptoms.

Consider five proteins with the properties shown in the table above and answer the following four questions. Record your answers and choose the set of correct answers for questions a --> d. a) Which protein would elute first from a (+) charged anion exchange column in buffer at pH 4.0? b) Which protein would migrate the slowest in an SDS-PAGE gel? c) Which protein would elute last from a gel filtration chromatography column under non-denaturing conditions? d) Which protein would elute last from a (-) charged cation exchange column in buffer at pH 4.0?

A, E, C, A

Which of the following is true regarding apoenzymes and holoenzymes? A. Apoenzymes do not have a non-amino, acid-based cofactor bound, whereas holoenzymes do. B. Holoenzymes do not have a cofactor bound to the center, so they appear "hollow" compared to their apoenzyme counterpart. C. Apoenzymes do not require a cofactor, whereas holoenzymes do. D. Apoenzymes do not have an amino, acid-based cofactor bound, whereas holoenzymes do.

A. Apoenzymes do not have a non-amino, acid-based cofactor bound, whereas holoenzymes do.

Which of the following mutations in the active site of the enzyme enolase is most likely to result in an enzyme that still catalyzes its reaction? A. Glu295→Asp295B. B.Lys396→Ile396 C. Lys396→Glu396 D. Glu295→Lys295

A. Glu295→Asp295

Using ion exchange and affinity chromatography, you have isolated a protein. To check on the size of the protein, you subject the purified protein to gel filtration chromatography and the protein elutes with a molecular mass of 140,000 Daltons. However, to show that the protein is purified, you perform SDS PAGE on the protein, and two bands with molecular masses of 25,000 and 45,000 Daltons are identified. Which answer best explains your results?

The native protein, as seen after gel filtration chromatography, has a molecular mass of 140,000 Daltons. But denatured protein, as seen during SD-PAGE, reveals that the protein is comprised of four subunits: two 25,000-Dalton subunits and two subunits at 45,000 Daltons.

Using immunoprecipitation, you can isolate a protein (protein X) you think is involved in chronic myelogenous leukemia (CML), which is caused, in part, by a hyperactive tyrosine protein kinase called ABL. You think one of the targets of ABL is the protein X that you can purify. In comparing tissues with and without the disease, you subject the samples to isoelectic focusing. Understanding how IEF works, how would you expect the samples with CML to migrate compared to the wild-type, non-diseased sample protein? Use the figure to help you consider your response.

The phosphorylated protein will have a lower isoelectric point and thus migrate further toward the anode.

Oxygen binding is monitored for a solution of hemoglobin. During the experiment, the curve changes from sigmoidal to hyperbolic. Which of the following may be the reason for the change? -The protein dissociated into individual subunits. -A positive allosteric effector was added. -The protein denatured. -None of these answers are correct. -A negative allosteric effector was added.

The protein dissociated into individual subunits.

Which of the following is not an assumption that is made when applying Michaelis-Menten kinetics to an enzyme?

The rate constant of E + P re-associating to form the ES complex must be considered

h of the following is not an assumption that is made when applying Michaelis-Menten kinetics to an enzyme? The reaction must be considered early, before any appreciable amount of product has been generated. B. The rate constant of E + P re-associating to form the ES complex must be considered. C. The product release is a rapid step in the process .D. The concentration of ES is relatively constant after the initial reaction time.

The rate constant of E + P re-associating to form the ES complex must be considered.

Which of the following statements is true regarding the potassium channel protein discussed in the animation?

The selectivity channel of potassium channel proteins functions due to the amino acids in the channel desolvating potassium ions, but not sodium ions.

Which of the following is correct about turnover number (kcat) and the specificity constant for an enzyme?

The specificity constant is defined as kcat/Km.

Trypsin, chymotrypsin, and elastase are all serine proteases that cleave after different amino acids. What is responsible for the substrate specificity?

The substrate binding pockets accommodate different amino acids.

most common catalytic reaction mechanisms

The three most common catalytic reaction mechanisms in an enzyme active site are acid-base catalysis, covalent catalysis, and metal-ion catalysis.

Why is a water molecule always observed between potassium ions in the selectivity filter of a channel like this?

The water molecule provides a spacer between two nearby K+ ions, which would otherwise repel each other and prevent net transport of K+ ions through the channel.

Select the answer that is true regarding Gibbs free energy relationships in active and passive transport.

The ΔΔG of the movement of a molecule into a cell in the absence of a transport protein is +14.4 kcal/mol. Transport of this molecule would require active transport

Which of the following statements are true about the role of calcium ions in muscle contraction?

When Ca2+ binds to the troponin complex, the resulting conformational change allows the myosin head to bind to actin. B.Calcium binding is an essential first step in the actin-myosin reaction cycle. C.Although Ca2+ binding is required for muscle contraction, it does not actually bind to myosin

Which of the following best explains the relationship between the T- and the R- states of this protein? The correct relationship below promotes cooperativity of oxygen binding. Consider the meaning of cooperativity and protein confomation before answering.

When O2(g) is bound to the cofactor, then the protein has adopted the relaxed configuration.

why binding is the strongest in transition state

When an enzyme binds a substrate, it begins to make interactions, which accounts for the specificity seen in enzymes. As the reaction moves toward the transition state, additional weak interactions, as well as exclusion of water, occur, which strengthens the binding between the enzyme and the transition state. These strong interactions have been demonstrated via the use of transition state analogs. After product forms, contacts are lost and the product is released.

Which of the following statements are true regarding hemoglobin?

When hemoglobin shifts from the T-state conformation to the R-state conformation, many noncovalent interactions are broken and reformed. D.The R state of hemoglobin has a higher affinity for oxygen than the T state.

Which of the following is not an assumption made in Michaelis-Menten kinetics?

Working conditions have [E] >> [S].

The binding of molecular oxygen to the iron within the heme of hemoglobin causes the puckered heme to become planar. This alteration in the heme geometry causes a conformational change in the structure of hemoglobin, as illustrated in the figure below. Which of the following situations would likely result in the F helix moving into its oxygen-bound conformation (the conformation shown in the bottom of this figure when heme is planar)?

carbon monoxide binding to the iron in the heme Carbon monoxide can displace oxygen in the oxygen binding site of hemoglobin. Carbon monoxide will bind to the iron in the heme with an even stronger affinity than molecular oxygen, thereby un-puckering the heme into the planar conformation and moving the F helix of hemoglobin into the oxygen-bound conformation.

Select the one TRUE statement regarding how catalysts increase reaction rates

catalysts lower the amount of energy required to reach the transition state

Which of the following is responsible for peptide fragmentation in a tandem mass spectrometer?

collision chamber

Oxygen binds to a single subunit of a multi-subunit hemoglobin protein. As a result, all subunits switch to the R state. This is an example of the ______________ model of allostery (best answer to fill in the blank).

concerted

Thick filaments _______, but thin filaments do/are not

contain myosin

A kinase adds a phosphate group to a target enzyme, altering the catalytic efficiency of the enzyme. This is an example of

covalent modification

Which of the following is/are true regarding observed effects of pH on enzyme activity and rate, and the underlying causes of these effects?

he rate of an enzyme-catalyzed reaction will slow down when outside the optimal pH range of the enzyme. C.The active site of an enzyme can change shape and overall charge when pH is not optimal, possibly reducing the enzyme's activity.

Which of the following is best described as a prosthetic group?

heme

If an enzyme carries out acid-base catalysis, which of the following amino acids could act as general acid? - his -gly -alanine -phenylalanine

hisitidine

If an enzyme carries out acid-base catalysis, which of the following amino acids could act as general acid?

histidine

Isolate any one subunit of deoxyhemoglobin along with the heme cofactor. Observe the amino acid sequence of residues that likely interact with the heme cofactor, and determine how the cofactor interacts with the protein. The most logical means of interaction are both the hydrophobic interaction and also ________ bonding.

hydrogen

The selectivity of aquaporin for H2O relies on which of the following? Choose the correct 3.

hydrogen bonding to ASN, inverted alpha helix dipoles, a 2.8 A constriction point within the protein

Sickle cell anemia

is thought to provide heterozygous individuals protections from malaria.

When using tandem mass spectrometry for peptide sequence determination, what is the input into the second mass spectrometer from the collision chamber?

isolated and fragmented peptides

Which answer correctly pairs the enzyme class with the type of reaction catalyzed?

isomerase, intramolecular rearrangements

There are three primary types of reactions used in metabolite transformation, listed in the bins. Sort the statements into the correct bins, depending on the type of reaction to which they are most applicable.

isomerization, condensation, hydrolysis and dehydration pic

Often times, two X-ray defraction patterns are needed to make phase determinations that are required to determine a protein's structure. When the procedure for calculating phase determinations uses a second pattern from a crystal made with an electron-dense atom such as mercury or selenium, the procedure is called

isomorphous replacment Isomorphous replacement is a method to solve a structure where the diffraction spots are difficult to assign. It compares the diffraction pattern of the native crystal with a second pattern in which an electron dense atom, like selenium or mercury, is included in the crystal. This enables the phases of the diffracted X-rays to be determined, which is essential for figuring out the protein's structure.

The K+ channel protein does not allow Na+ ions to pass through because

it is unfavorable for the Na+ ions to lose their associated water molecules, which makes the solvated Na+ ions to large to fit through the channel.

Sort the following statements into the appropriate bins based on the classes of enzymes they belong to or describe.

ligase, lyase, transferase pic

An enzyme can increase the rate of a reaction inside a cell by ____________ the energy of the ____________.

lowering, transition state

An enzyme can increase the rate of a reaction inside the cell by _________ the energy of the ________.

lowering; transition state

Generally, the chemistry of Fmoc blocking is straightforward for most amino acids during solid state peptide synthesis. There is one amino acid, however, that presents a problem for Fmoc blocking during solid state peptide synthesis. That amino acid is

lysine

The five major protein classes are _____________, structural proteins, _____________, genomic caretaker proteins, and _______________.

metabolic enzymes, transport proteins, cell signaling proteins

Identify the three types of enzyme-mediated reactions from the list below.

metabolite transformation reaction coenzyme-dependent redox rxn reversible covalent modification reactions

Identify the three types of enzyme-mediated reactions from the list below.

metabolite transformation reactions, reversible covalent modification reactions, coenzyme-dependent redox reactions

In isoelectric focusing, a protein with a pH below the pI would

migrate toward the cathode

The primary function of myoglobin and hemoglobin are best described by

myoglobin stores oxygen whereas hemoglobin transports oxygen

Consider a system where a passive transport channel is available for a neutral molecule X. If RTln(C2/C1) is zero, then

no net transport will occur

A kinase adds a phosphate group to a target enzyme, altering the catalytic efficiency of the enzyme. This is an example of A. none of these answers are correct. B. feedback inhibition. C.proteolytic processing. D. noncovalent modification. E. binding of regulatory molecules.

none of these are correct

Identify the location within myoglobin where O2 interacts. Which best describes where and how O2 interacts in myoglobin?

on one side of the heme cofactor and associated with the iron ion

If the histidine on the F helix (His F8) that coordinates the O2 that binds to the heme iron in hemoglobin is mutated to an alanine, what effect would be most likely? Choose the ONE most correct answer.

oxygen binding would not cause movement of the F helix, since the alanine at F8 cannot coordinate oxygen

What type of transport is depicted in the figure below (Figure 1) -- only round molecules

passive transport of molecules down a concentration gradient

Match each characteristic to the appropriate chromatography technique.

pic

Match each phrase with its step within the five-step actin-myosin reaction cycle.

pic

Review the image and list in order each step of tandem mass spectroscopy analysis for a peptide.

pic

Both passive and active transport proteins are needed to transport __________ across membranes.

polar molecules and ions FEEDBACK: Because the cell membrane is nonpolar, neither polar molecules nor ions can diffuse across the membrane. Transport proteins provide a way for these molecules to be exchanged between the cell and the environment.

Based on how data is collected in the techniques of X-ray crystallography compared to NMR, the technique of NMR is the only choice for studying

protein unfolding

What protein feature will cause the protein to bind to a metal in chelation affinity chromatography—specifically, a resin with immobilized Ni2+?

recombinant proteins engineered to have six or more histidines at the N or C terminus of the protein A metal chelating chromatography uses metal like nickel to bind recombinant proteins with six or more histidines. These histidine tags are placed on either the N or C terminus of the protein. Elution is achieved by adding imidazole, the functional side group of histidine.

Which of the following may result from a His143 Ala143 mutation in adult hemoglobin?

reduced affinity for 2,3-BPG

A conformational change in troponin that opens the myosin-binding sites on actin is triggered by the

release of calcium by the sarcoplasmic reticulum Hide Feedback FEEDBACK: In relaxed muscle, the myosin-binding sites on actin are blocked by tropomyosin and troponin. When Ca2+ is released from the sarcoplasmic reticulum, troponin undergoes a conformational change that causes the myosin-binding sites to be accessible.

The transport system shown below in (Figure 2) -- square molecules

secondary active symporter

The mass-to-charge ratios of denatured proteins are equivalent for different mass proteins. However, the cross-linked nature of the acrylamide media can limit migration through the polymer matrix. Gels with less cross-linked acrylamide (low % SDS gels) will do which of the following?

separate larger proteins at the expense of smaller proteins, which will not resolve well

A reaction coordinate diagram comparing an uncatalyzed reaction with an enzyme-catalyzed reaction can directly illustrate that the enzyme __________, but will not directly illustrate that the enzyme __________.

stablizes the transition state ; orients the substrates appropriately for the reaction to occur

Experiments are performed to determine the initial reaction velocity of an enzyme-catalyzed reaction. What is NOT held constant so that the initial velocities can be used to plot the Michaelis-Menten graph?

substrate concentration

Which of the following statements applies to hemoglobin but not to myoglobin?

subunit interactions are critical for function

which of the following is FALSE when isolating proteins from whole cells?

the amount of protein in each fraction isolated during centrifugation increases

A mixture of enzyme and inhibitor is run through a size-exclusion chromatography column. The activity of the enzyme is assessed before and after the chromatography. The enzyme has more activity after the chromatography step. Which of the following is true?

the inhibitor is a reversible inhibitor

For reversible binding between a protein and a ligand,

the larger the Ka, the higher the affinity between the protein and ligand.

If SERCA (calcium transporter) is not functioning in a myoblast, which of the following may occur?

the myofibrils can shorten but not lengthen

Which of the following accounts for some of the specificity of the K+ channel?

the orientation of backbone carbonyl oxygen atoms in the channel

Choose the most correct statement below regarding the function of the two histidine residues in globin proteins that are responsible for oxygen binding

the proximal histidine moves toward the heme group in response to oxygen binding

Identify three proteins below that are considered to be genomic caretaker proteins

toposiomerase dna polymerase rna polymerase

looking at the figure below, to which of the following does an enzyme bind the strongest?

transition state

Which of the following is not one of the three most common catalytic reaction mechanisms in an enzyme active site?

using the histidine side chain to form covalent bonds with the substrate

Within the selectivity channel, which component of the protein do these ions interact with? Note that in the molecular structure, two potassium ions and a water molecule are shown in the selectivity channel.

with loops between alpha helices Within the selectivity channel, potassium ions interact with loops between alpha helices within the channel protein. Although the overall structure of this protein involved considerable spans of alpha helices, there is no ion-helix interaction within the selectivity channel. There are no instances of beta sheet secondary structures within the potassium channel.

Within this molecular structure, the polyatomic ion sulfate (SO42-) is observed. Which of the following best describes the interaction between myoglobin and this polyatomic ion? A. Sulfate was used during precipitation of myoglobin and is seen in this molecular structure interacting with amino acids. B. Sulfate is part of the normal cellular physiology of myoglobin and is seen in this molecular structure interacting with amino acids. C. Sulfate is part of the normal cellular physiology of myoglobin and is seen in this molecular structure interacting with the heme cofactor. D. Sulfate was used during precipitation of myoglobin and is seen in this molecular structure interacting with the heme cofactor.

A. Sulfate was used during precipitation of myoglobin and is seen in this molecular structure interacting with amino acids.

Evaluate which of the following statements is/are true about enzymes and the transition from reactants to products.

An enzyme does not change the energy of the reactants or product, nor does it change the equilibrium constant of a reaction. B.An enzyme lowers the activation energy of a reaction, which means the transition state is not as energetically unfavorable as it would be without the presence of an enzyme.

Which of the following is true regarding apoenzymes and holoenzymes?

Apoenzymes do not have a non-amino, acid-based cofactor bound, whereas holoenzymes do. Cofactors are non-amino, acid-based groups (such as metals and coenzymes) that bind to proteins to make a fully functional enzyme. Enzymes that require a cofactor to perform their functions, but do not have one bound, are called apoenzymes, while enzymes with their required cofactor bound are termed holoenzymes.

Which of these is not an amino acid that allows for the selectivity of its listed transporter protein?

Asp75 (aspartic acid at position 75) within the Omp32 porin protein

Considering the fractional saturation binding curve of hemoglobin as shown below, as well as the definition of fractional saturation, which of the following statements are true about hemoglobin's oxygen binding profile?

At partial pressures of oxygen of more than 12 kPa, hemoglobin is as saturated with oxygen as it can be, indicating that in the vast majority of hemoglobin proteins, all four oxygen binding sites are occupied .C.The sigmoidal curve is indicative of cooperative binding.

Which of the following is/are true regarding initial and maximal velocity of enzyme-mediated reactions?

At very low substrate concentrations, the initial velocity of an enzyme reaction will be lower than the maximal velocity of the enzyme reaction. C.The initial velocity is determined by the slope of the line at the beginning of a reaction when one plots the experimental results of reaction time versus product formed. Maximal velocity is then determined by when the initial velocity no longer significantly changes with increasing substrate concentration. D.When an enzyme behaves with Michaelis-Menten kinetics, the initial velocity of that enzyme reaction changes with substrate concentration, but the maximal velocity of that particular enzyme remains the same at a constant enzyme concentration and identical reaction conditions.

The change in the activation energy of the reaction because of the presence of an enzyme is illustrated by the energy of _______ minus the energy of ________.

B - C

Which of the following is not a property or characteristic of both hemoglobin and myoglobin? A. a protein that contains heme as a prosthetic group B. a protein composed of four polypeptide chains C. a protein that contains iron as a metal cofactor D. a protein that binds O2

B. a protein composed of four polypeptide chains

Which of these statements about transport across cell membranes is false?

Both active and passive transport require the addition of external energy, usually in the form of ATP.

Which of the following mutations would most likely keep the transitions of T state to R state in hemoglobin unchanged, or similar to the transitions that occur in the native molecule? The three-letter codes for amino acids are used, and the numbers following the amino acids designate the amino acid position in the protein. By convention, the original, native amino acid is listed first, followed by the mutational change.

Correct; the Asp94→Glu94 mutation would both maintain the negative charge on position 94 at physiological pH, and allow that position (94) to still hydrogen bond with Asn102. This hydrogen bonding between Asp94 and Asn102 is essential to moving from the T state to the R state in native hemoglobin.

In the figure below, Km is indicated at

D

Bird hemoglobins are tetrameric and very similar in structure and function to mammalian hemoglobins. However, in some bird species, O2 binding affinity to hemoglobin is not regulated by 2,3-bisphosphoglycerate (BPG), but rather by a different compound that functions as a BPG analog. Considering the chemical and physical properties of the following compounds, which is the most likely candidate for the BPG analog in bird red blood cells?

D- inositol hexaphosphate

Which of the following statements about the concerted and sequential models of allostery is false? A. In the sequential model, it is believed that the binding of one ligand to one unit of the tetramer causes a conformational change in other units in the tetramer. This conformational change makes nearby subunits more likely to bind ligands and shift to the R state. B. In the concerted model, it is proposed that the T and R states are in equilibrium. The T state is favored when there is no, or very little, ligand bound. As more ligands (oxygen) bind to the tetramer, the equilibrium shifts toward the R state. C. Both the concerted and the sequential model have experimental support. As such, it is likely that the actual mechanism of cooperative binding of hemoglobin is a mixture of these two models. D. Both models are "symmetrical" in that all complexes have symmetry since they do not contain mixtures of subunits in the T and R states.

D. Both models are "symmetrical" in that all complexes have symmetry since they do not contain mixtures of subunits in the T and R states.

Which of the following reactions directly alters DNA and affects gene expression? A. Metabolite transformation reactions B. Reversible covalent modification involving phosphorylation C. Coenzyme-dependent redox reactions D. Reversible covalent modification involving methylation

D. Reversible covalent modification involving methylation

Which of the following is correct about turnover number (kcat) and the specificity constant for an enzyme? A. kcat = vmax/[ES] B. The specificity constant is defined as (kcat)(Km). C. The kcat reveals how well an enzyme works. D. The specificity constant is defined as kcat/Km.

D. The specificity constant is defined as kcat/Km.

Select the answer that is true regarding Gibbs free energy relationships in active and passive transport. A. The ΔΔG of the movement of a molecule into a cell in the absence of a transport protein is +14.4 kcal/mol. Transport of this molecule would require either active or passive transport. B. The ΔΔG of the movement of a molecule into a cell in the absence of a transport protein is +14.4 kcal/mol. Transport of this molecule would require passive transport. C. The ΔΔG of the movement of a molecule into a cell in the absence of a transport protein is +14.4 kcal/mol. Transport of this molecule would require diffusion-based transport. D. The ΔΔG of the movement of a molecule into a cell in the absence of a transport protein is +14.4 kcal/mol. Transport of this molecule would require active transport.

D. The ΔΔG of the movement of a molecule into a cell in the absence of a transport protein is +14.4 kcal/mol. Transport of this molecule would require active transport.

What is the method used to purify a protein by exploiting the specific binding of the protein to its ligand called? A. high binding interaction chromatography B. Ni2+ chelating chromatography C. ion exchange chromatography D. affinity chromatography

D. affinity chromatography

Shown here is the potassium channel. Consider its molecular structure and manipulate the molecule according to the instructions below to answer the following questions. How many of the four subunits of the potassium channel contain membrane-spanning helices? (Note that the initial view contains the ribbon structure of all four subunits visible.) ] A. one B. two C. three D. four

D. four

Identify the location within myoglobin where O2 interacts. Which best describes where and how O2 interacts in myoglobin? A. on both sides of the heme cofactor and associated with amine nitrogen atoms B. with the negatively charged carboxy terminus of the polypeptide C. with an amino acid sequence within a beta sheet of the protein D. on one side of the heme cofactor and associated with the iron ion

D. on one side of the heme cofactor and associated with the iron ion

Match the following terms as they apply to either of the two different roles of genomic caretaker proteins.

DNA Maintenance: -DNA repair proteins -RecA protein -DNA polymerase enzymes -Topoisomerase Involved in replication and repair of DNA Gene Expression Control: -Involved in chromatic remodeling -RNA polymerase enzymes -Involved in gene transcription

Which three of the following allosteric effectors characterize the Bohr effect and contribute to shifting the equilibrium for hemoglobin from the R state conformation to the T state conformation?

H+ 2,3-biophosphoglycrate CO2

One explanation for the prevalence of the sickle cell anemia trait in the human population in Africa is

Heterozygous individuals carrying the Val-6 mutation are less susceptible to malaria because their red blood cells are resistant to infection by the malarial parasite

Which amino acid acts as a general acid and a general base in the mechanism of chymotrypsin?

His 57

Which amino acid acts as a general acid and a general base in the mechanism of chymotrypsin?

His57

Which of these mutations is the most likely to eliminate the ability of chymotrypsin to perform its function? (Amino acids are represented by their three-letter code, with the residue number immediately following the name of the amino acid. The amino acid listed before the arrow is the original amino acid, and the amino acid listed after the arrow is the amino acid into which it has been mutated.)

His57→Tyr

Which of these mutations is the most likely to eliminate the ability of chymotrypsin to perform its function? (Amino acids are represented by their three-letter code, with the residue number immediately following the name of the amino acid. The amino acid listed before the arrow is the original amino acid, and the amino acid listed after the arrow is the amino acid into which it has been mutated.

His57→Tyr Although any of the four amino acid changes listed in the catalytic triad very well may eliminate the function of chymotrypsin, mutating histidine to tyrosine is the most likely to do so. Even though this mutation maintains a ring structure and a functional group, the hydrogen-bonding capability of histidine will be partially lost. In the triad, histidine at position 57 serves as both a hydrogen-bond donor to Asp102 and a hydrogen-bond acceptor to Ser195. The hydrogen-bonding network between the three amino acids in the triad is essential for catalytic function. Tyrosine is only capable of one hydrogen bond, being a hydrogen-bond donor, whereas the native histidine forms two hydrogen bonds with neighboring amino acid R groups.

2D gel

In 2-D gels, proteins are first separated based on their isoelectric points (pI) in an isoelectric focusing experiment. The pI-separated proteins are then separated again on the basis of mass in a standard SDS-PAGE gel. Thus, low pI proteins are on the left and high pI proteins are on the right, while high mass proteins are at the top and low mass proteins are at the bottom of the gel.

A polypeptide was digested by trypsin and chymotrypsin. Use the following information to determine the polypeptide sequence. Trypsin DigestLMYK MGFCE WDER Chymotrypsin Digest CE LMYKW DERMGF

LMYKWDERMGFCE

Which of the following statements is true?

Ligand X and Ligand Y both bind to Protein Z. The interaction of Ligand X with Protein Z has a Kd = 0.2 mM, while the interaction of Ligand Y with Protein Z has a Kd = 0.6 mM. Ligand X therefore has a higher affinity for Protein Z than Ligand Y.

Rank the following molecules from lowest to highest ability to bind molecular oxygen.

Lowest ability to bind to oxygen: -Hemoglobin with CO bound to it -Hemoglobin with CO2 bound to it -Adult hemoglobin -Fetal hemoglobin

Which component of a tandem mass spectrometer determines the mass of subfragments?

Mass spectrometer 2 Tandem mass spectrometry uses two chambers to separate peptides. The first separates peptides that have been fragmented by digestive enzymes such as trypsin. The second chamber separates like-sized fragments that have been further fragmented to separate into much smaller peptides.

When analyzing the amino acid sequences of the globin proteins shown in this figure, which of the following statements are true?

Mutating the glycine immediately to the right of the E7 position shown in human myoglobin to a tyrosine amino acid would likely reduce, or eliminate, the correct function of human myoglobin .B.Histidines at positions E7 and F8 are conserved in all three proteins because they are the amino acids required to coordinate the oxygen binding in the heme cofactor of the given globin molecules.

myoglobin

Myoglobin is an oxygen storage protein and its binding behavior indicates that role. Myoglobin is saturated with oxygen at pO2 at and above values found in resting muscle. Even when the pO2 decreases, as is the case in active muscle, only a rather small fraction (approximately 20 percent) of the oxygen is released. Most of the binding sites remain filled with O2. If myoglobin was acting as a transporter, like hemoglobin, it would be more efficient to release more bound oxygen in response to lower pO2.

You have discovered a small organic compound that you think will cause a significant shift in the peptide loop covering the active site of the enzyme, inhibiting the protein's function. Which approach(es) would be most appropriate to test for this hypothesis?

NMR spectroscopy D.X-ray crystallography

AA and channels

Not only is there no Asp75 in Omp32 porin protein, but if there were, it would reduce the specificity since aspartic acid has a negative charge. That negative charge would repel the negative charges of chloride and malate, instead of encouraging their transport through the membrane. The arginine residues within the Omp32 porin, on the other hand, do allow for selectivity because their positive charge attracts the overall negative charge of anions and malate molecules. Likewise, the phosphorylation of Asp351 is required for the import of calcium into the cell membrane in the SERCA protein, and asparagine residues at positions 69 and 185 select for water over protons and other small, polar species in human aquaporin 5.

The figure below shows the coordination of heme, O2, and two critical histidine residues in globin proteins. Which of the following steps happens first in the oxygen binding process?

O2 binds to the iron of heme.

Which of the following statements are true about the poison ouabain?

Ouabain inhibits the Na+-K+ ATPase protein, and this particular inhibition stops muscles such as the heart and lungs from relaxing after contracting. Ouabain is a poison found in the seeds of the climbing oleander plant, and is used by African tribesmen in poison arrows. However, in small doses, it can be used to treat patients with heart problems

Which of the following is false regarding the protein pepsin? Pepsinogen is the active form of pepsin. B. Pepsin hydrolyzes peptide bonds. C. Pepsinogen self-cleaves at the pH found in the stomach. D. Pepsin is a type of protease.

Pepsinogen is the active form of pepsin.

Which of the following peptides would be eluted last when separated using gel filtration chromatography? A, 360, -2 B, 1080, -1 C, 1800, 0 D, 1440, +1

Peptide A

The following peptides are separated using an anion exchange resin in ion-exchange chromatography. Which peptide is eluted first? A, 360, -2 B, 1080, -1 C, 1800, 0 D, 1440, +1

Peptide D

Protein phosphorylation is carried out by which of the following signaling proteins?

Phosphorylation is catalyzed by protein kinases and Src kinase is a signaling protein that phosphorylates tyrosine on target proteins. Adrenergic receptors are membrane receptors and are coupled to G proteins. G proteins are intracellular signaling proteins that activate protein targets. Estrogen receptors are soluble nuclear receptor proteins that regulate gene expression.

The first step of protein mass spectrometry is to get the protein (usually peptide fragments) into a gas phase as an ion. Which of the following describes matrix-assisted laser desorption/ionization (MALDI) ionization?

Protein fragments are embedded in a solid mixture that absorbs light, and then a laser flashes on this mixture, leaving fragmented and ionized peptides in the gas phase.

What is responsible for the "power stroke" of the actin-myosin cycle?

Release of Pi from the myosin head Ca2+ binding to troponin reveals the myosin binding site on actin. Release of Pi from the myosin head induces conformation changes that leads to the power stroke and pulls actin. Release of ADP from the myosin head frees the nucleotide binding site in myosin so ATP can bind. ATP binding releases myosin from actin and allows for recovery of the system so the cycle can start again.

Which of the following reactions directly alters DNA and affects gene expression?

Reversible covalent modification involving methylation

Sodium dodecylsulfate (SDS) plays an important role in SDS PAGE. Select each correct description of what SDS does in denatured electrophoresis.

SDS is an amphipathic compound that binds to the hydrophobic portion of the protein, coating the mixture and giving the protein an overall negative charge proportional to the size of the protein. Because SDS is a detergent, it plays a role in denaturing the protein.

sickle cell anemia

Since the mutation takes place on the 𝛽β subunit of hemoglobin, which does not replace the fetal 𝛾γ subunit until about 6 months of age, the symptoms of the disease are not present in newborns. Additionally, overexpressing the gene for the 𝛾γ subunit in adults is an effective treatment option. Mutating residue 6 to aspartic acid would maintain a negative charge and polarity at this position, making it unlikely to polymerize due to hydrophobic effects. However, mutating the residue 6 to another nonpolar amino acid such as isoleucine would likely lead to polymerization.

cofactors

Small molecules that aid the catalytic mechanism of enzymes are called cofactors. These can include metal ions, such as Zn2+. Enzyme cofactors with an organic component are called coenzymes. NAD+ and thiamine pyrophosphate are examples of important coenzymes. When a coenzyme is permanently associated with enzymes, the coenzyme is referred to as a prosthetic group. Heme is a key example of a prosthetic group.

Which of the following correctly describe a feature of how enzymes function as reaction catalysts?

Some of the amino acids in an enzyme's active site play a direct role in lowering the activation energy of the given reaction. B.Enzymes function primarily by lowering the activation energy of a reaction in order to speed up the rate of the reaction. C.Adding the suffix "-ase" to the end of a protein's name denotes that the protein is an enzyme. D.Most enzymes contain multiple protein subunits.

Which of the following describes how thyroid diseases are diagnosed using radioactive iodine?

Some thyroid hormones, thyroxine and triiodothyronine, will incorporate radioactive iodine, which leads to cell death as a useful diagnosis of and treatment for hyperthyroidism or thyroid diseases .D.Radioactive iodine is transported into thyroid gland cells by the Na+-I- symporter protein, a secondary active transporter.

Within this molecular structure, the polyatomic ion sulfate (SO42-) is observed. Which of the following best describes the interaction between myoglobin and this polyatomic ion?

Sulfate was used during precipitation of myoglobin and is seen in this molecular structure interacting with amino acids.

water and selectivity filter

The H2O molecule provides a spacer between two nearby K+ ions, which would otherwise repel each other and prevent net transport of K+ ions through the channel. This allows for bulk ion movement very quickly. The water molecule is much smaller than the potassium ion; water is only 18.02 amu whereas potassium is 39.10 amu. Moreover, oxygen is in Period 2 and potassium is in Period 4 on the periodic table of elements. Upon close examination of the amino acid residues that line the interior of the potassium ion selectivity channel, there are multiple tyrosine (Y) and threonine (T) residues. Thus, the channel is not solely comprised of only nonpolar residues. For the residues that are nonpolar, the carbonyl oxygen atoms of the polypeptide backbone are positioned towards the interior of the channel.

Which of the following statements about oxygen binding to hemoglobin is NOT correct?

The T state refers to oxyhemoglobin and the R state refers to deoxyhemoglobin. For hemoglobin, the T state refers to the deoxygenated, tense configuration while the R state is the relaxed, oxygenated configuration. The sigmoidal curve observed indicates cooperative binding of oxygen, although two models have been proposed to explain the binding process. In the concerted model, binding of oxygen to the R state stabilizes those protein molecules in the R state and increases the population of R state proteins. All four subunits are in the same state. In the sequential model, binding of oxygen to one subunit affects adjacent subunits so they are more likely to bind oxygen.

Which of the following is FALSE when isolating proteins from whole cells?

The amount of protein in each fraction isolated during centrifugation separation increases.

constriction point

The constriction point within the water channel of aquaporin proteins is formed by two short α helices, each of which contains a conserved asparagine residue. Reorientation of H2O molecules as they pass through the constriction point disrupts the proton wire by breaking hydrogen bonds between adjacent H2O molecules. Both hydrogen bonding to the amino group of the Asn residues and charge repulsion aided by α helix dipoles contribute to reorientation of the H2O molecules. Of the list of options, asparagine is the only amide side chain that is consistent with the molecular structure, and adenosine is a nucleoside and therefore not part of protein structure.

Which of the following is an assumption made when using Michaelis-Menten kinetics?

The conversion of EP E + P is rapid.

ATCase

The enzyme ATCase is regulated by allosteric mechanisms. The binding of ATP to ATCase upregulates the activity of ATCase, while the binding of CTP downregulates the activity of ATCase. When ATP binds to ATCase, the R state conformation of ATCase forms, causing the catalytic site to become activated .

association constant

The equilibrium constant for the binding of a protein and a ligand is called the association constant or Ka. The dissociation constant, or Kd, is the equilibrium constant for the opposite process, or dissociation of the protein and ligand. The units on Ka are M-1, while Kd is expressed in units of M. A large Ka value means high affinity, while a high Kd value means low affinity.

here are nine lysine residues within pea gylcine carboxylase. Why would a specific lysine attachment site for lipoamide be conserved among orthologous decarboxylase proteins?

The lipoamide needs to be precisely located near the enzyme active site.

Rank the steps in the sequential order in which they occur as hemoglobin binds oxygen, with the first step/conformation at the top and the last step/conformation at the bottom.

First: Fe2+ is coordinated in the heme, and the heme is in a puckered conformation Iron moves into the same plane as the heme, moving the F helix toward distal histidine Asp94 hydrogen bonds with Asn102, while Tyr42 breaks its hydrogen bond with Asp99

Hemoglobin is composed of ______ individual polypeptide chain(s). Each of these individual polypeptide chains contains ____ heme cofactor(s) with _______ iron atom(s). Therefore, one hemoglobin molecule can potentially bind ______ O2 molecule(s).

Four, one, one, four

Which of the following mutations in the active site of the enzyme enolase is most likely to result in an enzyme that still catalyzes its reaction?

Glu295→Asp295

For chymotrypsin, which amino acid is involved in forming the oxyanion hole, but is not part of the catalytic triad?

Gly 193

One step in the reaction mechanism of aldolase is represented in this molecular structure. Which of the following best describes the stage of the aldolase mechanism that is captured here?You may need to rotate the ball-and-stick or the space-filling model of the atomic representation so that you can observe the amino acid side chain. The ribbon structure will provide the least amount of help. Additionally, be sure to view the amino acid sequence and observe that the side chain of interest is flanked by a leucine residue and a proline residue. A. The dihydroxyacetone phosphate is covalently bound to a lysine side chain. B. The glyceraldehyde-3-phosphate is covalently bound to a lysine side chain. C. The glyceraldehyde-3-phosphate is noncovalently associated to a lysine side chain. D. The dihydroxyacetone phosphate is noncovalently associated to a lysine side chain.

A. The dihydroxyacetone phosphate is covalently bound to a lysine side chain.

Which of the following is not an assumption made in Michaelis-Menten kinetics? A. Working conditions have [E] >> [S]. B. Product release is a rapid step. C. The formation of ES from EP is negligible. D. The concentration of ES remains relatively constant.

A. Working conditions have [E] >> [S].

Within the selectivity channel, which component of the protein do these ions interact with? Note that in the molecular structure, two potassium ions and a water molecule are shown in the selectivity channel. A. with loops between alpha helices B. with only beta sheet structure C. with loops between beta sheets D. with only alpha helix structure

A. with loops between alpha helices

An enzyme has a single active site at which it can bind and hydrolyze either X or Y; however, the enzyme cannot bind X and Y at the same time. Answer the following questions regarding the Km and vmax of this enzyme. A) Will the apparent Km for X be affected if Y is present in the reaction mixture? B) Will vmax for X be affected if Y is present in the reaction mixture?

A. yes B. No

Considering that the Na+-K+ ATPase membrane protein is essential for maintaining an electrochemical gradient across cell membranes, which of the following is likely not a component of an electrolyte solution for treating dehydration?

ATP

What distinguishes P-type transporters from ABC transporters?

ATP hydrolysis by P-type transporters results in a phosphorylated intermediate while ATP hydrolysis causes ABC transporters to convert from an outward facing transporter to an inward facing transporter. P-type and ABC transporters are both primary active transporters that use ATP to move molecules against their chemical gradients. Hydrolysis of ATP by P-type transporters results in a phosphorylated intermediate that results in conformational changes for transport of molecules across the membrane. ABC transporters undergo conformational changes to bind ATP. Hydrolysis of ATP causes a large conformation change that flips the transporter from outward facing to inward facing.

Which of the following sample preparation steps is used for both native PAGE and SDS-PAGE?

Addition of glycerol to the sample loading buffer SDS-PAGE uses denaturing conditions to separate polypeptides on the basis of size. Native PAGE uses non-denaturing conditions to maintain protein structure and allows for characterization of protein complexes. Sodium dodecyl sulfate, or SDS, is a detergent that denatures proteins and gives the protein an overall negative charge. β-mercaptoethanol reduces disulfide bonds. Heating the sample facilitates denaturation. Glycerol in the sample loading buffer gives density to the sample so it sinks to the bottom of the gel well when loading.

Which of the following correctly describe a feature of how enzymes function as reaction catalysts? A.Some of the amino acids in an enzyme's active site play a direct role in lowering the activation energy of the given reaction. B.Most enzymes contain multiple protein subunits. C.Adding the suffix "-ase" to the end of a protein's name denotes that the protein is an enzyme. D.Enzymes function primarily by lowering the activation energy of a reaction in order to speed up the rate of the reaction.

All of the options are correct

When analyzing the amino acid sequences of the globin proteins shown in this figure, which of the following statements are true? A.It is equally reasonable to assume that changing amino acids at either conservative or nonconservative substitution sites will yield similar results in terms of the structure and function of a globin protein. B.Histidines at positions E7 and F8 are conserved in all three proteins because they are the amino acids required to coordinate the oxygen binding in the heme cofactor of the given globin molecules. C.Mutating the glycine immediately to the right of the E7 position shown in human myoglobin to a tyrosine amino acid would likely reduce, or eliminate, the correct function of human myoglobin. D.Mutating the threonine just to the right of the F8 amino acid in human myoglobin to an aspartic acid would almost certainly reduce or eliminate the correct functionality of the protein.

B and C are correct

Which of the following statements are true about the poison ouabain? A.Ouabain is a small molecule that contains 35 carbon atoms and multiple hydroxyl groups decorating a fused ring system. B.Ouabain is a poison found in the seeds of the climbing oleander plant, and is used by African tribesmen in poison arrows. However, in small doses, it can be used to treat patients with heart problems. C.Ouabain inhibits the Na+-K+ ATPase protein, and this particular inhibition stops muscles such as the heart and lungs from relaxing after contracting. D.Ouabain inhibits the Na+-K+ ATPase membrane transport protein, which is used to passively transport sodium and potassium ions through the cell membrane.

B and C are correct

Refer to the reaction coordinate diagram below. The change in the activation energy of the reaction because of the presence of an enzyme is illustrated by the energy of ____________minus the energy of ____________ .

B, C

Which of the following sample preparation steps is used for both native PAGE and SDS-PAGE? A. Addition of β-mercaptoethanol B. Addition of glycerol to the sample loading buffer C. Heating sample in boiling water bath D. Addition of sodium dodecyl sulfate

B. Addition of glycerol to the sample loading buffer

Protein secondary structure is important to the function of proteins and consists of three main types: alpha helix, beta strand, and beta turn. What type of protein secondary structure is highlighted? A. Beta turn B. Alpha helix C. Beta strand

B. Alpha helix

On the 2-D gel shown in the figure below, where would a protein with a high pI and a high mass be found? A. A B. C C. D D. B

B. C

Which of the following is accurate in terms of the relationship between the velocity of a reaction and the rate constant (k) of a reaction?A. In a second-order reaction, the rate constant is equal to the velocity of the reaction multiplied by the concentration of both substrates. B. In a first-order reaction, the rate constant of a reaction is equal to the velocity of the reaction divided by the concentration of substrate. C. For both first-order and second-order reactions, the concentration of substrate is equal to the product of the velocity of the reaction and the rate constant of the reaction. D. For a first-order reaction, the rate constant of a reaction is equal to the product of the substrate concentration and the velocity of the reaction.

B. In a first-order reaction, the rate constant of a reaction is equal to the velocity of the reaction divided by the concentration of substrate.

Lipoamide is a covalently attached coenzyme that plays a key role in several decarboxylase reactions, including glycine decarboxylase, and is attached to a lysine residue in the enzyme.Review the molecule again. Manipulate it in order to identify the specific lysine residue that serves as the attachment site for lipoamide in the enzyme glycine decarboxylase. You may want to view the hint if you need help. A. Lysine 17 B. Lysine 63 C. Lysine 8 D. Lysine 118

B. Lysine 63

Which component of a tandem mass spectrometer determines the mass of subfragments? A. Collision chamber B. Mass spectrometer 2 C. Mass spectrometer 1 D. Ionization chamber E. Detector

B. Mass spectrometer 2

What is responsible for the "power stroke" of the actin-myosin cycle? A. Binding of ATP to the myosin head B. Release of Pi from the myosin head C. Release of ADP from the myosin head D. Ca2+ binding to troponin

B. Release of Pi from the myosin head

Using immunoprecipitation, you can isolate a protein (protein X) you think is involved in chronic myelogenous leukemia (CML), which is caused, in part, by a hyperactive tyrosine protein kinase called ABL. You think one of the targets of ABL is the protein X that you can purify. In comparing tissues with and without the disease, you subject the samples to isoelectic focusing. Understanding how IEF works, how would you expect the samples with CML to migrate compared to the wild-type, non-diseased sample protein? Use the figure to help you consider your response. A. Non-diseased proteins will migrate with a lower pI than those from diseased tissues and thus the samples from the non-diseased samples will migrate more to the anode than diseased protein. B. The phosphorylated protein will have a lower isoelectric point and thus migrate further toward the anode. C. The non-phosphorylated proteins from the non-diseased samples will move further to the anode without the bulky phosphate group attached to a tyrosine. D. The phosphorylated protein will be more attracted to the negative charge on the anode.

B. The phosphorylated protein will have a lower isoelectric point and thus migrate further toward the anode.

Why is a water molecule always observed between potassium ions in the selectivity filter of a channel like this? A. The water molecule is much larger than the potassium ion and its presence allows the channel to dilate to accomodate the ions. B. The water molecule provides a spacer between two nearby K+ ions, which would otherwise repel each other and prevent net transport of K+ ions through the channel. C. All amino acids that line the channel are completely nonpolar and the presence of the water provides the polar environment for the ion to move within. D. All of these answers address the reason why water is observed within the channel.

B. The water molecule provides a spacer between two nearby K+ ions, which would otherwise repel each other and prevent net transport of K+ ions through the channel

Which of the following statements about the concerted and sequential models of allostery is false?

Both models are "symmetrical" in that all complexes have symmetry since they do not contain mixtures of subunits in the T and R states. The concerted model and the sequential model are both used to explain the fact that the more oxygen molecules that a hemoglobin binds, the easier it is for the remaining empty hemes in the hemoglobin to bind additional oxygens. This cooperativity is allosteric in nature, and there is experimental evidence supporting both models. The concerted model postulates that as more ligands bind to the subunits of hemoglobin, the equilibrium of the whole hemoglobin shifts more toward the R state. "Concerted" means that all subunits in a single hemoglobin are in either the T or R state. The sequential model, on the other hand, states that the binding of additional ligands causes conformational changes to the whole complex, which ends up pushing certain subunits more toward the T state. However, in the sequential model, a single hemoglobin molecule can have subunits in either the T or R state.

Which of the following is/are true regarding observed effects of pH on enzyme activity and rate, and the underlying causes of these effects? A.All enzymes exhibit their fastest rate of reaction at an approximate physiological pH of 7.4, as all organisms maintain a pH range very close to this in order to avoid alkalosis or acidosis. B.Most enzymes will display the same reaction rate across a broad range of pH levels due to the flexibility of the active site. C.The active site of an enzyme can change shape and overall charge when pH is not optimal, possibly reducing the enzyme's activity. D.The rate of an enzyme-catalyzed reaction will slow down when outside the optimal pH range of the enzyme.

C and D are correct

Place the following HMG-CoA reductase steps in the correct order: A. Reduction of aldehyde B. Breakdown of hemithioacetal C. Reduction of thioester D. Cofactor exchange

C, D,B,A

Which of the following statements is false, considering Michaelis-Menten enzyme behavior and plots? A. High substrate concentrations corresponds to the "plateau" area in the Michaelis-Menten graph. B. kcat is the turnover number of an enzyme-catalyzed reaction. C. Decreasing the concentration of enzyme will result in a decrease of Vmax and a decrease of Km. D. The turnover number is the catalytic rate for an enzyme-catalyzed reaction, but does not by itself signal how specific the enzyme is to its particular substrate.

C. Decreasing the concentration of enzyme will result in a decrease of Vmax and a decrease of Km.

A particular genomic caretaker protein, Protein X, has an affinity for both Ligand Y and Ligand Z. When you have 0.23 microM of Protein X in a solution and mix it with 0.11 microM of Ligand Y, the resulting solution contains 0.20 microM of free Protein X, 0.09 microM of free Ligand Y, and 0.02 microM of the protein-ligand complex, after equilibrium has been reached. However, when you have 0.23 microM of Protein X in a solution and mix it with 0.11 microM of Ligand Z, the resulting solution contains 0.14 microM of free Protein X, 0.02 microM of free Ligand Z, and 0.09 microM of the protein-ligand complex, after equilibrium has been reached. Which ligand has a greater affinity for Protein X?

C. Ligand Z

There are nine lysine residues within pea gylcine carboxylase. Why would a specific lysine attachment site for lipoamide be conserved among orthologous decarboxylase proteins? A. Allosteric regulators prevent lipoamide from attaching at the other lysine residues. B. Lysine residues in alpha helices have side chains that are sequestered from being able to bind cofactors. C. The lipoamide needs to be precisely located near the enzyme active site. D. Glycine decarboxylase is not subject to selective pressure and is unlikely to undergo mutation.

C. The lipoamide needs to be precisely located near the enzyme active site.

Generally, the chemistry of Fmoc blocking is straightforward for most amino acids during solid state peptide synthesis. There is one amino acid, however, that presents a problem for Fmoc blocking during solid state peptide synthesis. That amino acid is A. arginine B. glutamate C. lysine D. glycine

C. lysine

Experiments are performed to determine the initial reaction velocity of an enzyme-catalyzed reaction. What is NOT held constant so that the initial velocities can be used to plot the Michaelis-Menten graph? A. volume of reaction B. enzyme concentration C. substrate concentration D. temperature

C. substrate concentration

shearing

Cells can be homogenized using a variety of techniques, including sonication, shearing (as is the case with a French press), or detergents. When processing the cell extract and separating proteins into fractions via different methods, including centrifugation, the amount of protein decreases in each fraction. However, the activity of the fraction containing the protein of interest increases. Salting out is useful for separating proteins based on their solubility. Due to the presence of aromatic amino acids, the A280 nm readings can provide information about the amount of total protein in a fraction.

Within the aquaporin, each subunit contains a channel that allows H2O passage. Through which of the following views would you expect water to travel? Assume water is represented by the red dot.

Circular shaped

Which of the following statements is false, considering Michaelis-Menten enzyme behavior and plots?

Decreasing the concentration of enzyme will result in a decrease of Vmax and a decrease of Km.

The lysine residue that is integral to the reaction mechanism of aldolase is positioned between a leucine residue and a proline residue. Which of the following is true about this lysine? A. It is one of the residues connecting one β sheet to another β sheet. B. It is part of an α helix. C. It is one of the residues connecting one α helix to another α helix. D. It is part of a β sheet. E. It is one of the residues connecting a β sheet to an α helix.

E. It is one of the residues connecting a β sheet to an α helix.

actin and myosin cycle steps

In the actin-myosin reaction cycle, calcium binds to troponin and causes a conformational change that uncovers the myosin binding sites of actin filaments (step 1). Next, inorganic phosphate is released from the myosin head, which causes a change in the conformation of myosin such that the actin filament (now bound to myosin) is pulled toward the myosin tail. This is the power stroke (step 2). After this power stroke, ADP is released from the myosin head (step 3). This release leaves an empty nucleotide binding site on the myosin head, which is then occupied by ATP (step 4). This ATP is hydrolyzed, and an inorganic phosphate then occupies the phosphate site on the myosin head. This causes the myosin to return to its original conformation prior to the power stroke (step 5) so that the cycle can repeat with a new influx of calcium.

puckered heme

In the deoxygenated state, heme is puckered and the iron is not in the plane due to its size. O2 binding to iron reduces the size of the iron and allows the iron to move into the plane of heme. This movement pulls the proximal histidine and the F helix toward the heme. The movement of the F helix is important for overall structural changes in the protein.

Proteins can be separated from each other based on a number of different characteristics. Match each separating characteristic with the appropriate technique.

Ion Exchange: Eluting of proteins by changing pH or changing salt concentration Gel Filtration: Separation based on the likelihood that a protein can diffuse in and out of a porous bead Affinity Chromatography: Immobilizing a protein's ligand to capture the protein of interest Salting Out: Adding a strong salt and making the protein precipitate

The lysine residue that is integral to the reaction mechanism of aldolase is positioned between a leucine residue and a proline residue. Which of the following is true about this lysine?

It is one of the residues connecting a β sheet to an α helix.

A genetic mutation that causes which of the following substitutions would be the least likely to destroy the catalytic mechanism that relies upon the lysine residue discussed in Parts 1 and 2 regarding the aldolase enzyme?

K to R

A genetic mutation that causes which of the following substitutions would be the least likely to destroy the catalytic mechanism that relies upon the lysine residue discussed in Parts 1 and 2 regarding the aldolase enzyme? K to R K to E K to G K to Y K to D

K to R

The glutamate side chain in the active site of HMG-CoA reductase acts as a general base only after

a conformational change triggers the exchange for NADP+ for NADPH

The glutamate side chain in the active site of HMG-CoA reductase acts a general base only after

a conformational change triggers the exchange of NADP+ for NADPH

The glutamate side chain in the active site of HMG-CoA reductase acts as a general base only after

a conformational change triggers the exchange of NADP+ for NADPH

Sometimes after an intense exercise routine, an individual will have sore muscles 1 to 2 days following the exercise; this is called delayed onset muscle soreness. Although not completely understood, it is believed that one cause of this is damage that occurs to the Z disks and contractile filaments in the muscles. When the body attempts to repair this damage, an inflammatory response occurs that causes soreness a couple of days after the exercise has taken place. Which of these situations would likely lead to less delayed onset muscle soreness in an individual?

a mutation in the Z-disk protein that caused the attachment of the Z disk to the titin protein to be stronger

Which of the following is not a property or characteristic of both hemoglobin and myoglobin?

a protein composed of four polypeptide chains

Primary active ABC transporters and P-type transporters both require

a protein conformational change to function

In secondary active transporters

a proton gradient is used to transport molecules across the membrane.

What is the method used to purify a protein by exploiting the specific binding of the protein to its ligand called?

affinity chromatography

The constriction point within the water channel of aquaporin proteins is formed by two short α helices, each of which contains a conserved __________ residue that interacts with translocating water molecules.

asparagine

Consider the reaction coordinate diagram shown below. X is ____________ ; Y is ____________.

delta G of uncatalyzed reaction; transition state

Consider the reaction diagram below. X is ________; Y is _________.

delta G+ of uncatalyzed reaction; transition state

After some discussion, you feel that your protein is a tetramer and that the SDS and reducing agent have:

denatured the protein, which is made of equally sized monomers.

Extracting a protein bound to a column is called which of the following

elution