BIOL 201

What is the catalytic triad of chymotrypsin, a type of serine protease? the amino acids serine, histidine, and aspartate the amino acids serine, histidine, and glutamate the enzyme−cofactor−substrate complex the amino acids cysteine, histidine, and aspartate the enzyme−cofactor−intermediate complex

the amino acids serine, histidine, and aspartate

What is the ratio [A−]/[HA] at pH 3.75? The pKa of formic acid (methanoic acid, H−COOH) is 3.75.

1

What is the hydroxide ion concentration, [OH−], in an aqueous solution with a hydrogen ion concentration of [H+]=6.8×10−5 M?

1.5 x 10^-10 M

A monoprotic weak acid, HA, dissociates in water according to the reaction HA(aq)−⇀↽−H+(aq)+A−(aq) The equilibrium concentrations of the reactants and products are [HA]=0.120 M, [H+]=2.00×10−4 M, and [A−]=2.00 ×10−4 M. Calculate the Ka value for the acid HA.

3.3 x 10^-7

What is the pH of an aqueous solution with a hydrogen ion concentration of [H+]=6.8×10−5 M?

4.2

RNase is an enzyme that cleaves the P-O5′ bond in RNA. It has two His residues in the active site. Suggest a plausible explanation why the enzyme activity changes when pH is increased or decreased from pH 6.0, as shown in the graph. Choose all of the true statements. A. Both His residues are deprotonated at pH higher than than 6.5. B. The RNase reaction is an example of metal ion catalysis with a positively charged metal. C. The substrate is affected by the change in pH and is inactive (postively charged) when pH is above 6.0. D. RNAse is an acid‑base catalyst. E. There are two His residues and both are deprotonated below pH 4.2.

A. Both His residues are deprotonated at pH higher than than 6.5. D. RNAse is an acid‑base catalyst.

Which of the following statements about enzymes are true (choose all that apply)? A. Catalysis occurs at the active site, which usually consists of a crevice on the surface of the enzyme. B. A substrate must bind to the active site before catalysis can occur. C. An enzyme yields a specific product, whereas a nonbiological catalyst may produce more than one product with the occurence of side reactions. D. Nonbiological catalysts and enzymes tend to have a similar degree of reaction specificity. E. Generally, an enzyme is specific for a particular substrate. For example, thrombin catalyzes the hydrolysis of the peptide bond between Arg and Gly.

A. Catalysis occurs at the active site, which usually consists of a crevice on the surface of the enzyme. B. A substrate must bind to the active site before catalysis can occur. C. An enzyme yields a specific product, whereas a nonbiological catalyst may produce more than one product with the occurence of side reactions. E. Generally, an enzyme is specific for a particular substrate. For example, thrombin catalyzes the hydrolysis of the peptide bond between Arg and Gly.

Which three statements about amino acids are true? Use this chart of amino acid structures for reference. A. Isoleucine has more than one stereocenter (chiral center). B. The Ala side chain does not form hydrogen bonds with other amino acids. C. Methionine is a thiol. D. The form of glycine used by the human body is D‑glycine. E. Proline has an overall charge at physiological pH (7.4). F. Gln and Ser are polar amino acids.

A. Isoleucine has more than one stereocenter (chiral center). B. The Ala side chain does not form hydrogen bonds with other amino acids. F. Gln and Ser are polar amino acids.

Consider the reaction. Sk1⇌k2P What effects are produced by an enzyme on the general reaction? A. The activation energy for the reaction is lowered. B. ΔG for the reaction decreases. C. The formation of the transition state is promoted. D. The reaction equilibrium is shifted toward the products. E. The concentration of the reactants is decreased. F. The rate constant for the forward reaction (k1) increases.

A. The activation energy for the reaction is lowered. C. The formation of the transition state is promoted. F. The rate constant for the forward reaction (k1) increases. (and for backwards too)

The α‑helix is.....(choose the true statement) A. formed by repeated H-bonds between peptide bond groups. B. stabilized primarily by the hydrophobic effect. C. a left‑handed helix with 3.6 amino acids per turn. D. formed by R‑group interactions.

A. formed by repeated H-bonds between peptide bond groups.

The concept of induced fit refers to the fact that A. substrate binding may induce a conformational change in the enzyme, which then brings catalytic groups into proper orientation. B. when a substrate binds to an enzyme, the enzyme induces a loss of water (desolvation) from the substrate. C. enzyme specificity is induced by enzyme-substrate binding. D. enzyme-substrate binding induces movement along the reaction coordinate to the transition state. E. enzyme-substrate binding induces an increase in the reaction entropy, thereby catalyzing the reaction.

A. substrate binding may induce a conformational change in the enzyme, which then brings catalytic groups into proper orientation.

When α helices and β sheets are described as being amphipathic, it means that: A. they have one side or face that is predominantly polar, with the other side being predominantly hydrophobic. B. they have polar residues in the N‑terminal part and charged residues in the C‑terminal part. C. they have large R groups on one side and small R groups on the other, because small groups are easier to pack in the interior of the protein. D. they have positive charges on one side and negative charges on the other.

A. they have one side or face that is predominantly polar, with the other side being predominantly hydrophobic.

Select the true statements about protein secondary structure. Peptide bonds stabilize secondary structure. A. In a β‑pleated sheet, the side chains are located between adjacent segments. B. In an α‑helix, the side chains are located on the outside of the helix. C. The secondary level of protein structure refers to the spatial arrangement of short segments of the protein. D. The α‑helix is held together by hydrogen bonds between the amide N−H and C=O groups.

B. In an α‑helix, the side chains are located on the outside of the helix. C. The secondary level of protein structure refers to the spatial arrangement of short segments of the protein. D. The α‑helix is held together by hydrogen bonds between the amide N−H and C=O groups.

The β‑sheet.....(choose the true statement) A. has strands in which the R groups of the amino acids are all on the same side of the sheet. B. is formed and primarily stabilized by hydrogen bonds. C. can be either parallel or perpendicular. D. with parallel beta-strand arrangement are more stable than those with anti-parallel strand arrangements. E. is composed of amino acid residues all very near each other in the primary structure.

B. is formed and primarily stabilized by hydrogen bonds.

Which one of the following statements is true of enzyme catalysts? A. They increase the stability of the product of a desired reaction by allowing ionizations, resonance, and isomerizations not normally available to substrates. B. They bind to substrates but are never covalently attached to substrate or product. C. They lower the activation energy for the conversion of substrate to product. D. They increase the equilibrium constant for a reaction, thus favoring product formation. E. To be effective, they must be present at the same concentration as their substrates.

C. They lower the activation energy for the conversion of substrate to product.

During the 1st step in two-dimensional gel electrophoresis (2D-GE), a series of protein bands are generated on a pH gradient strip by isoelctric focusing (IEF). During the 2nd step, the IEF strip is turned 90 degrees and placed on another gel containing SDS, for a 2nd round of electrophoresis. In the 2nd step ___________________. (choose the best answer) A. the individual bands on the IEF strip will break up into separate spots on the second gel as a result of being subjected to another round of electric field. B. the IEF bands become stained so that the isoelectric focus pattern can be visualized. C. proteins with similar isoelectric points (pI) become further separated based on their molecular weights. D. the proteins in the bands separate more completely as the 2nd electric field is in the opposite polarity to the first round of electrophoresis.

C. proteins with similar isoelectric points (pI) become further separated based on their molecular weights.

By adding SDS (sodium dodecyl sulfate) during electrophoresis of proteins in SDS-PAGE, it is possible to ______________. (choose the best answer) A. determine the protein's isoelectric point (pI). B. determine the protein's enzymatic function. C. separate proteins exclusively on the basis of their molecular weight. D. preserve a protein's native structure and biological activity. determine the amino acid composition of the proteins.

C. separate proteins exclusively on the basis of their molecular weight.

During isoelectric focusing (IEF) of proteins, they stop moving at specific points along the pH gradient, because ______________. (Choose the best answer) A. the proteins have a net negative charge at that pH on the gradient strip. B. the proteins ahead of them slow down and prevent their migration along the gradient strip. C. the proteins have a net charge of zero at that pH on the gradient strip. D. the proteins have a net positive charge at that pH on the gradient strip. E. the proteins are no longer ionized at that pH on the gradient strip.

C. the proteins have a net charge of zero at that pH on the gradient strip.

Which of the statements about peptide bonds are true? A. A tetrapeptide contains five amino acid residues. B. Peptide bonds are ester linkages. C. The formation of a peptide bond involves a dehydration reaction. D. Peptide bonds form from nucleophilic attack by an electron pair on an α‑amino nitrogen atom on an α‑carboxyl carbon atom of another amino acid. E. Peptides are polymers of proteins.

D. Peptide bonds form from nucleophilic attack by an electron pair on an α‑amino nitrogen atom on an α‑carboxyl carbon atom of another amino acid. C. The formation of a peptide bond involves a dehydration reaction.

Biochemists have routinely denatured proteins to understand protein folding. In this biochemical context, protein denaturation refers to: A. Disruption of all bonds in the protein. B. Breaking of covalent bonds and degradation of the protein. C. Breaking of disulfide bonds. D. a loss of functional confirmation due to disruption of non-covalent interactions. E. Complete unfolding of the protein to its primary sturcture.

D. a loss of functional confirmation due to disruption of non-covalent interactions.

In an aqueous environment, protein folding (and thereby protein conformation) is determined by a combination of many interactions and factors. Two major factors however, are considered to be the drivers of protein folding - one is the formation of maximum number of hydrogen bonds possible, and the other is the ________: (choose the best answer) A. placement of polar amino acide residues around the extrerior of the protein to increase the entropy of water. B. minimization of entropy of the system by formation of a water solvent shell around the protein. C. formation of maximum number of hydrophilic interactions possible. maximization of ionic interactions of charged groups. D. placement of the hydrophobic amino-acyl residues within the interior of the protein.

D. placement of the hydrophobic amino-acyl residues within the interior of the protein.

Anfinsen's experiments on denaturation and renaturation, after the reduction and reoxidation of the S=S bonds in the enzyme ribonuclease (RNAse A), have shown that: A. folding of the denatured RNAse into its native conformation requires the input of energy. B. the completely unfolded and denatured protein, with all its S=S bonds broken, is still enzymatically active. C. denaturation process degraded the protein irreversibly - meaning, it could not become functional again. D. the primary sequence of RNAse contains the necessary information to accomplish folding to its functional structure. E. the functional conformation of RNAase is independent of its amino acid sequence.

D. the primary sequence of RNAse contains the necessary information to accomplish folding to its functional structure.

Isoelctric focusing (IEF) is a method used in laboratory to determine the isoelctric point (pI) of a protein. During IEF, the pH gradient strip _________. (choose the best answer) A. neutralizes all ionic groups on a protein by titrating them with strong bases. B. is made of a series of antibodies specific to the protein of interest. C. relates the unknown protein to a series of protein markers with known molecular weights, Mr. D. contains a denaturing detergent that can distribute uniform negative charges over the protein's surface. E. exhibits a stable pH gradient when ampholytes become distributed in an electric field.

E. exhibits a stable pH gradient when ampholytes become distributed in an electric field.

The role of an enzyme in an enzyme‑catalyzed reaction is to A. bind a transition state intermediate, such that it cannot be converted back to substrate. B. ensure that the product is more stable than the substrate. C. ensure that all of the substrate is converted to product. D. make the free‑energy change for the reaction more favorable. E. increase the rate at which substrate is converted into product.

E. increase the rate at which substrate is converted into product.

Write the balanced chemical equation for the reaction of the weak acid HCN with water. Include the phase of each species. chemical equation: Ka expression?

HCN(aq)+H2O(l)−⇀↽−CN−(aq)+H3O+(aq) Ka: (H3O+)(CN-)/(HCN)

Protein A has a mass of 15,400 Daltons and a pI of 8.2, while Protein B has a mass of 7,500 Daltons and a pI of 8.3. Based on this information alone, which method would best separate the two proteins from each other; and which protein would elute first? Ion-exchange chromatography; Protein B. Affinity Chromatography; Protein A. Ion-exchange chromatography; Protein A. Size-exclusion chromatography; Protein A. Size-exclusion chromatography; Protein B. Affinity Chromatography; Protein B.

Size-exclusion chromatography; Protein A.

In a partion experiment conducted with an amino acid analogue (AA analogue) carrying amino acid side chain X, the AA analogue in the water phase to octanol phase was documented as 1:10. Based on these results, this AA analogue is: amphipathic hydrophillic ambivalent hydrophobic hydroelectric

hydrophobic

Which interactions can contribute to the intrinsic binding energy during enzymatic catalysis? van der Waals interactions electrostatic interactions permanent covalent bonding nucleophilic attack by serine hydrogen bonding

van der Waals interactions electrostatic interactions hydrogen bonding

Protein folding occurs spontaneously. This means the folded state is more stable. Which of the options below correctly fits with this observation? ΔGoFOLD=−50 kJ/mol ΔGoFOLD=50 kJ/mol ΔGoFOLD=0 kJ/mol

ΔGoFOLD=−50 kJ/mol