SW Questions Exam 2

B. 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.

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 Choose one: A. heavy metal addition. B. isomorphous replacment. C. isotopic addition. D. molecular replacement.

C. 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.

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. B C. C D. D

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

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)

A. Ligand Z Since both Ligand X and Ligand Y are at the same concentration with equal amounts of Protein X, we can directly compare the concentration of the protein-ligand complex to determine which has the greater affinity for Protein X. Ligand Z associates with Protein X to give 0.09 microM of protein-ligand complex at equilibrium, which is more than the 0.02 microM of Ligand Y. Therefore, Ligand Z has the greater affinity for Protein X. C. 0.031 The Kd for Ligand Z associating with Protein X is 0.031. The Kd equation is Kd = [P][L]/[PL], where P represents protein concentration in M at equilibrium, L represents ligand concentration in M at equilibrium, and PL represents the protein-ligand concentration in M at equilibrium. Be sure to use the protein concentration at equilibrium, not at the beginning of the reaction, to calculate the correct Kd.

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? Choose one: A. Ligand Z B. It is not possible to determine with the given information. C. Ligands Y and Z have equal affinity for Protein X. D. Ligand Y In the question above, what is the Kd for Ligand Z and Protein X? Choose one: A. 19.56 B. .0511 C. 0.031 D. 32.14

It is usually derived from vitamins. A cofactor that has an organic component, but no amino acids

Coenzyme-

D. substrate concentration Experiments are performed to determine the initial reaction velocity of an enzyme-catalyzed reaction. The initial velocities can be used to plot the Michaelis-Menten graph. The substrate concentration is NOT held constant. The substrate concentration is varied as this is plotted against the initial velocity of the reactions to create the Michaelis-Menten plot. Temperature, enzyme concentration, and the volume of the reaction are all held constant in these reactions, however.

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?Choose one: A. enzyme concentration B. volume of reaction C. temperature D. substrate concentration

Lower, more, higher Fetal hemoglobin has a lower affinity for 2,3-BPG than maternal hemoglobin due to its altered subunit. As a result, more hemoglobin molecules are in the R state in fetal hemoglobin, and fetal hemoglobin has a higher affinity for O2 than maternal hemoglobin. This enables the mother to transfer oxygen to the developing fetus via her hemoglobin.

Fetal hemoglobin has a ____________ affinity for 2,3-BPG than maternal hemoglobin due to its altered subunit. As a result, __________ hemoglobin molecules are in the R state in fetal hemoglobin, and fetal hemoglobin has a _________________ affinity for O2 than maternal hemoglobin. This enables the mother to transfer oxygen to the developing fetus via her hemoglobin.

Lysine Fmoc is used to block the amino terminal of a growing peptide. The N-termini of amino acid monomers are proteced by Fmoc and added onto a deprotected amino acid chain. This permits covalent linkage to an activated carboxyl group on the incoming Fmoc-blocked amino acid. Amino acids with amino side groups provide a unique problem for this type of synthesis. The amino acid lysine has an R-NH3+ group on its side chain that will react with Fmoc and thus also needs blocking. Other chemical steps must be taken when lysine is an amino acid to be added in order to avoid a peptide bond forming on this side chain.

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 Choose one: A. lysine B. glycine C. glutamate D. arginine

DNA maintenance: DNA repair proteins, RecA protein, Topoisomerase, Involved in replication and repair of DNA Gene expression control: RNA polymerase enzymes, Involved in gene transcription, Involved in chromatic remodeling There are two types of genomic caretaker proteins: those that maintain the integrity of DNA during replication and repair errors in the DNA code, and those that regulate the expression of genes by controlling transcription and access to DNA via chromatin remodeling. DNA polymerases, topoisomerases, DNA repair proteins, and RecA protein are all examples of genomic caretaker proteins involved in DNA maintenance. RNA polymerases, and other proteins, are involved in gene transcription and chromatin remodeling, which represent the gene expression control type of genomic caretaker proteins.

Match the following terms as they apply to either of the two different roles of genomic caretaker proteins. Maintenance / repair or gene expression control: DNA repair proteins RecA protein DNA polymerase enzymes Involved in gene transcription RNA polymerase enzymes Topoisomerase Involved in replication and repair of DNA Involved in chromatic remodeling

The heme group of catalase is an example of one of these. A coenzyme that is permanently associated with an enzyme

Prosthetic group-

a, d, c, b

Rank the following molecules from lowest to highest ability to bind molecular oxygen. a hemoglobin with CO bound to it b fetal hemoglobin c adult hemoglobin d hemoglobin with CO2 bound to it

Sample ionization Peptide separation based on m/z Peptide fragmentation to subfragment peptides by collision with helium Separation of subfragments based on m/z Each peptide is attracted to the detector Like an Edman degradation tryptic digest, each fragment can be sequences using a proteomics search algorithm

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

Prilosec: Used to treat ulcers, heartburn, and acid reflux Decreases the amount of H+ pumped into the stomach, thereby increasing the pH of the stomach Is an inhibitor of the gastric proton pump, which is a primary active transporter Zoloft: Reduces the amount of serotonin that is taken back into a neuron Is a legal antidepressant drug Causes psychological changes due to increased neurotransmitter signaling, specifically serotonin Cocaine: Inhibits the dopamine transporter protein Is derived from the coca leaf Causes psychological changes due to increased neurotransmitter signaling, specifically dopamine

Sort the following descriptions of pharmaceutical drugs into the appropriate boxes.

Negative: 2,3-BPG, H+, CO2 Positive: O2 H+, CO2, and 2,3-BPG are negative allosteric effectors that cause hemoglobin to prefer the T state, while O2 is a positive allosteric effector that increases the likelihood of hemoglobin forming the R state. The R state is more likely to bind O2 molecules, so the R state is necessary for effective oxygen transport within the blood.

Sort the following four molecules as to whether they are negative or positive allosteric effectors toward the R state (oxyhemoglobin) of hemoglobin. 2,3-BPG, O2, H+, CO2 Negative : Positive :

Statin drugs reduce cholesterol levels by binding to and inhibiting the enzyme HMG-CoA reductase. HMG-CoA reductase is an essential enzyme in the cholesterol biosynthetic pathway such that if it is not functioning, less cholesterol can be produced by an individual.

Statin drugs are used to reduce cholesterol in patients exhibiting high cholesterol levels. Statin drugs target ________ reductase , reducing the activity of the enzyme. This enzyme helps lower cholesterol levels because it is in the ______________ biosynthetic pathway.

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. B. carbon monoxide binding to the iron in the heme

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. Which of the following situations would likely result in the F helix moving into its oxygen-bound conformation (when heme is planar)? A. no oxygen, or any ligand, binding to the iron in the heme B. carbon monoxide binding to the iron in the heme C. iron within the heme being in the +3 oxidation state D. proximal histidine (HisF8) being mutated to an alanine residue

D. Small, hydrophobic molecules, such as steroid hormones, are able to cross cell membranes via diffusion. Larger molecules and polar molecules require proteins to cross the membrane. Transport through carrier proteins is generally slower as only one or a few biomolecules are moved at a time with high specificity. As there are limited binding sites in the carrier proteins, these transporters can be saturated with substrate. Channels are semiselective pores with increasing transfer rates with high concentrations of substrate.

The figure below shows different ways that biomolecules are able to cross cell membranes. Which of the following statements is correct? Choose one: A. Transport via passive transport channels is slower than through passive transport carriers. B. Small, hydrophilic molecules are able to diffuse across cell membranes. C. Channels are highly selective pores. D. Both passive and active transport carrier proteins can be saturated with substrate.

D. 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. Tryptic fragments are ionized as the laser irradiates the sample, leaving the protein free from solvent and fragmented.

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? Choose one: A. Small peptide fragments are released from a small metallic capillary under high voltage that removes the solvent and ionizes the peptides into the gas phase. B. Liquid chromatography is used for elution into a focused laser beam to fragment each eluted protein." C. Trypsinized fragments can be exposed directly to the first chamber of a tandem mass spectrometry chamber, where collisions with gas particles cause peptide fragmentation. D. 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.

D. covalent modification affecting the bioavailability of an enzyme. Enzyme activity is highly regulated by two main mechanisms. Bioavailability refers to the amount of enzyme present in a cell, so regulation occurs at the level of gene expression or protein turnover. The catalytic efficiency can be controlled by either regulatory molecules or covalent modification, such as phosphorylation. Enzymes commonly bind their substrates with high affinity and specificity and the binding of the substrate to the active site induces changes in protein structure, sometime substantial changes.

The following are critical for enzyme structure and function, EXCEPT Choose one: A. that the catalytic efficiency of an enzyme can be controlled by regulatory molecules. B. enzymes commonly binding substrates with high affinity. C. binding of a substrate inducing changes in protein structure. D. covalent modification affecting the bioavailability of an enzyme.

C. separate larger proteins at the expense of smaller proteins, which will not resolve well A low-percentage gel means that there is less overall cross-linked acrylamide and the matrix has larger "gaps" for the larger proteins to enter and begin to be separated. The rate of migration of smaller proteins is NOT as affected, and thus they are not well separated. Therefore, a low percentage-gel separates larger-mass proteins at the expense of lower-molecular weight proteins.

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? Choose one: A. separate the smaller proteins based on the percentage gel at the expense of larger proteins B. separate proteins as in size-exclusion chromatography, with the smaller proteins migrating most slowly and the larger proteins migrating farther through the gel C. separate larger proteins at the expense of smaller proteins, which will not resolve well D. allow the negative charge contributed by the smaller SDS molecules to more easily migrate through a low-percent acrylamide because of the increase in negative charge

ESI: Degrades and charges the peptide with high voltage Sample becomes ionized due to high voltage. Ionization evaporates solvent, leaving peptide in gas phase to travel through the separating mass spectrometer. MALDI: Laser will be absorbed by the peptide containing material releasing the peptide into the gas phase. Proteins or peptides are mixed in a solid matrix rather than a solution. Peptides become fragmented and charged due to laser exposure. BOTH: Uses mass-to-charge (m/z) ratio to determine molecular mass Can be used for proteins or peptides that have been treated with proteases like trypsin Is based on the mass and acceleration though a chamber ending in a detector

There are two main methods to get proteins into a gas phase for mass spectroscopy: electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). Place the appropriate description of each ionization method in the appropriate space.

A. gel filtration chromatography conditions enable a protein to retain its quaternary structure. In this case, the protein is a heterotetramer made of two 25,000-Dalton subunits and two subunits of 45,000 Daltons each. These four subunits are separated from one another under the denaturing conditions used in SDS polyacrylaminde gel electrophoresis.

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? A. 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. B. The protein is not actually purified. You have four proteins, two of 25,000 Daltons and two of 45,000 Daltons, that form a tetrameric complex when exposed to the buffer used in gel filtration chromatography. This gives the appearance of a single 140,000 Dalton protein. C. During gel filtration chromatography, as the protein moves through and around the beads, the protein denatures into two 25,000-Dalton subunits and two subunits of 45,000 Daltons. As the protein exits the gel, it renatures into a single 140,000 Dalton protein.

D. a ligand is used to capture the specific protein that binds the ligand.

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

A. Isolated and fragmented peptides Tryptic fragments are introduced into mass spectrometer 1 via electrospray ionization. These fragments are separated by size and a narrow range of masses is selected to enter the collision chamber, where the peptides are fragmented into smaller pieces. These fragmented peptides then enter mass spectrometer 2. The resulting fragments are detected, analyzed, and compared to peptide masses in databases to determine the peptide sequence.

When using tandem mass spectrometry for peptide sequence determination, what is the input into the second mass spectrometer from the collision chamber?Choose one: A. Isolated and fragmented peptides B. Whole protein C. Tryptic fragments of the protein of interest D. Peptides from a select range of masses

E. 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.

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

A, B, C, D

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

A, B, C, D Enzymes do function primarily by lowering the activation energy of a given reaction. Oftentimes, multiple protein subunits must come together in order to form a functional enzyme, which is usually designated with an "-ase" suffix in the protein name. The amino acids in an enzyme's active site play a direct role in the way the enzyme lowers the activation energy in its appropriate reaction. For this question, all options are therefore true.

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

B 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.

Which of the following is FALSE when isolating proteins from whole cells? Choose one: A. Cells can be homogenized using a French press. B. The amount of protein in each fraction isolated during centrifugation separation increases. C. Salting out separates proteins based on their solubility. D. The amount of protein in a fraction is measured by reading the sample absorbance at 280 nm.

Heme 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 is best described as a prosthetic group? Choose one: A. Thiamine pyrophosphate B. Heme C. Zn2+ D. NAD+

Pepsinogen is the inactive precursor of pepsin. When in an acidic environment, like the pH of the stomach, pepsinogen self cleaves to form the active pepsin protein. Pepsin is a protease that hydrolyzes peptide bonds, aiding in digestion of food.

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

C. Working conditions have [E] >> [S]. There are three assumptions made in Michaelis-Menten kinetics. The formation of ES from EP is negligible, thus eliminating the rate constant for that conversion from the equation. Product release is also considered rapid, so the conversion of EP to E + P is not considered. The concentration of ES remains relatively constant and this occurs when working under conditions where [S] >> [E].

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

D. The rate constant of E + P re-associating to form the ES complex must be considered. Three simplifying assumptions are made about reaction conditions when applying Michaelis-Menten kinetics to an enzyme reaction: (1) no appreciable product has yet been formed, (2) product release is a rapid step in the reaction, and (3) steady-state conditions are reached quickly. The rate constant of the reverse reaction, in which E + P re-associates to form the ES complex, is assumed to be zero, and need not be considered.

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

C, using the histidine side chain to form covelant bonds with the substrate The three most common catalytic reaction mechanisms in an enzyme active site are acid-base catalysis, covalent catalysis, and metal-ion catalysis.

Which of the following is not one of the three most common catalytic reaction mechanisms in an enzyme active site? Choose one: A. protonation or deprotonation of an amino acid, or water, on the enzyme B. temporarily sharing electrons between two atoms C. using the histidine side chain to form covalent bonds with the substrate D. utilizing positively charged metal ions to correctly orient the substrate, or to mediate redox reactions

D. Isomerization reaction Condensation reactions combine substrates into a larger product with the loss of a smaller molecule, such as water. A substrate can be cleaved to generate products with the addition (i.e., hydrolysis) or removal (dehydration) of water. Isomerization reactions change the connectivity of atoms in a substrate, but do not change the molecular formula.

Which of the following metabolite transformation reactions produces the same molecular formula for the product and the substrate? Choose one: A. Hydrolysis reaction B. Dehydration reaction C. Condensation reaction D. Isomerization reaction

C. Reversible covalent modification involving methylation Enzyme reactions can be grouped into three general categories. Reversible covalent modification reactions are important for regulation. The reversible methylation of cytosine in DNA is important for regulating gene expression.

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

Glycerol in the sample loading buffer gives density to the sample so it sinks to the bottom of the gel well when loading. 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.

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

A, B Ouabain inhibits the active transport protein Na+-K+ ATPase, which inhibits the flow of sodium and potassium ions in and out of the cell. Such inhibition prevents muscles such as the heart and lungs from relaxing after contraction, leading to death. African tribesmen used plant extracts containing ouabain to poison the tips of their arrows for hunting; however, in very small doses, ouabain can also be used to help a patient's heart contract.

Which of the following statements are true about the poison ouabain? Choose one or more: A.Ouabain inhibits the Na+-K+ ATPase protein, and this particular inhibition stops muscles such as the heart and lungs from relaxing after contracting. 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 is a small molecule that contains 35 carbon atoms and multiple hydroxyl groups decorating a fused ring system. D.Ouabain inhibits the Na+-K+ ATPase membrane transport protein, which is used to passively transport sodium and potassium ions through the cell membrane.

A. Decreasing the concentration of enzyme will result in a decrease of Vmax and a decrease of Km. Decreasing the concentration of an enzyme will result in a decrease of Vmax, but will not change the Km value of that reaction. The Michaelis-Menten constant is a constant that is specific for a particular enzyme.

Which of the following statements is false, considering Michaelis-Menten enzyme behavior and plots? Choose one: A. Decreasing the concentration of enzyme will result in a decrease of Vmax and a decrease of Km. B. 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. High substrate concentrations corresponds to the "plateau" area in the Michaelis-Menten graph. D. kcat is the turnover number of an enzyme-catalyzed reaction.

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.

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.) Choose one: A. Ser195→His B. Asp102→Glu C. His57→Tyr D. Ser195→Thr

B, D Both X-ray crystallization and NMR spectroscopy will identify changes in the shape of a protein before and after drug binding.

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? Choose one or more: A. ELISA B. X-ray crystallography C. Affinity chromatography D. NMR spectroscopy

A small molecule that an enzyme requires to function; can be a metal or an organic compound A metal, such as iron, that is not permanently associated with an enzyme may be an example of one of these.

cofactor -