Biochem Exam 1 Homework
A protein was purified to homogeneity. The determination of the mass by gel-filtration chromatography yields a value of 60 kDa. Chromatography in the presence of urea results in a 30 kDa species. Repeating the chromatography in the presence of both urea and beta-mercaptoethanol, however, results in a single molecular species of 15 kDa. What do the data suggest about the structure of the protein? 1. The 60 kDa protein is composed of two 30 kDa subunits linked by noncovalent interactions. Each 30 kDa subunit is composed of two 15 kDa subunits joined by disulfide bonds. 2. The 60 kDa protein is composed of multiple 15 kDa domains that hydrolyze upon treatment with an oxidizing agent. Some of the domains reassociate in the gel filtration column. 3. The 30 kDa protein is composed of 15 kDa subunits held together by disulfide bonds. Treatment increases the protein's association with the gel-filtration column and increases the apparent protein mass. 4. The 60 kDa protein is composed of two 30 kDa subunits held together by disulfide bonds. Each 30 kDa subunit is composed of two 15 kDa subunits linked by noncovalent interactions.
1
The graph represents the titration of amino acid with NaOH solution. Where does the amino acid have a net charge of +1: pKa1 = 2.34; pI = 6.01; pKa2 = 9.69. 1. below pH 2.34 2. at pH = 2.34 3. at pH = 6.01 4. at pH = 9.69 5. above pH 9.69
1
Which polypeptide is more soluble at pH 7.0? 1. 20 Glu 2. 3 (Phe-Met)
1
Which weak acid would be best to use when preparing a buffer solution with a pH of 8.40? 1. an acid with Ka = 4.2 x 10^(-9) 2. an acid with Ka = 5.0 x 10^(-5) 3. an acid with Ka = 7.9 x 10^(-6) 4. an acid with Ka = 2.5 x 10^(-10) 5. an acid with Ka = 6.3 x 10^(-7) 6. an acid with Ka = 0.00063
1
Which molecules are bound to hemoglobin when hemoglobin is in the R state? 1. oxygen 2. Fe2+ 3. CO2 4. 2,3-biphosphoglycerate 5. Fe3+
1, 2
Identify the true statements regarding disulfide bridges (disulfide bonds). 1. Disulfide bridges can exist between two amino acid residues on different chains. 2. Disulfide bridges have a stabilizing effect on proteins. 3. A disulfide bridge forms between two cysteine residues. 4. Disulfide bridges are formed by an irreversible oxidation reaction. 5. Disulfide bridges are important to primary and tertiary structure, not quaternary.
1, 2, 3
Examine the peptide: TEPIVAPMEYGK. 1. Estimate the net charge on the peptide at pH 7. 2. Estimate the net charge on the peptide at pH 12.
1. -1 2. -4
The graph represents the titration of amino acid with NaOH solution. At what point has enough base been added to react with 1/2 of the COOH groups: pKa1 = 2.34; pI = 6.01; pKa2 = 9.69. 1. 1/2 of COOH reacted = 2. when 1/2 of COOH has reacted, the pH =
1. 0.5 2. 2.34
Classify each amino acid by the chemical properties of its side chain (R group) at pH 7. Select the amino acid that fits best in each category. Each amino acid will be selected only once: arginine, glutamine, glutamate. 1. Which amino acid has a positively charged R group? 2. Which amino acid has a negatively charged R group? 3. Which amino acid has a neutral polar R group?
1. arginine 2. glutamate 3. glutamine
Place each form of alanine under the pH condition where it would be the predominant form: both protonated, carboxyl deprotonated, both deprotonated, carboxyl protonated and amino deprotonated. The pKa values for the carboxyl group and amino group are approximately 2.3 and 9.7, respectively. 1. pH < 1 2. pH = pI 3. pH > 11 4. Does not occur in significant amounts at any pH
1. both protonated 2. carboxyl deprotonated and amino protonated 3. both deprotonated 4. carboxyl protonated and amino deprotonated
Classify the words or phrases as descriptions or examples of fibrous proteins, globular proteins, or both. 1. structure is rod-like, intermediate filaments, insoluble in water, primary function as structural proteins in the cell 2. exhibit secondary protein structure, polymers of amino acids 3. some function as enzymes, structure is somewhat spherical, hemoglobin, soluble in water
1. fibrous proteins 2. both 3. globular proteins
1. The prosthetic group of hemoglobin and myoglobin is _____. 2. The organic ring component of heme is _____. 3. Under normal conditions, the central atom of heme is _____. 4. In _____, the central iron atom is displaced out of the plane of the porphyrin ring system. 5. The central atom has _____ bonds: _____ to nitrogen atoms in the porphyrin, one to a _____ residue, and one to oxygen.
1. heme 2. porphyrin 3. Fe2+ 4. deoxyhemoglobin 5. 6; 4; histidine
1. ______ molecules are polar and can form either ion-dipolar interactions or hydrogen bonds with water. 2. _____ molecules are nonpolar and do not form hydrogen bonds. 3. _____ molecules contain both hydrophilic and hydrophobic reactions (cholesterol).
1. hydrophilic 2. hydrophobic 3. amphipathic
1. _____ are molecules that are generally insoluble in water. For example, glycerophospholipid contains few polar functional groups compared to the number of carbon atoms. 2. _____ have the general formula (CH2O)n. They can be draw in an open chain form (erythrulose) or in a ring form (ribose). 3. _____ consist of a five-membered carbohydrate ring, one or two rings that include nitrogen, and one or more phosphate groups, which consist of phosphate and oxygen. 4. ______ have an amino group and a carboxyl group. These groups are ionized at physiological pH.
1. lipids 2. carbohydrates 3. nucleotides 4. amino acids
Determine which statements apply to hemoglobin, myoglobin, or neither. 1. Oxygen binds irreversibly to this molecule, carbon monoxide binds at an allosteric site, lowering oxygen binding affinity 2. The oxygen dissociation curve is sigmoidal in shape; as oxygen binds to this molecule the shape of the molecule changes, enhancing further oxygen binding; the binding pattern for this molecule is considered cooperative; this molecule delivers oxygen more efficiently to tissues 3. The oxygen dissociation curve is hyperbolic in shape, this molecule has a greater affinity for oxygen
1. neither 2. hemoglobin 3. myoglobin
1. Nucleic acids are polymers of _____. 2. Proteins are polymers of _____. 3. Polysaccharides are polymers of _____. 4. A polypeptide is a polymer of _____. 5. Cellulose is a polymer of ______.
1. nucleotides 2. amino acids 3. monosaccharides 4. amino acids 5. monosaccharides
Determine the highest level of protein structure described by each item: order of amino acids, beta-pleated sheet, overall macromolecule structure containing more than one polypeptide chain, alpha-helix, overall shape of a single polypeptide unit. 1. Primary structure 2. Secondary structure 3. Tertiary structure 4. Quaternary structure
1. order of amino acids 2. alpha-helix, beta-pleated sheet 3. overall shape of a single polypeptide unit 4. overall macromolecule structure containing more than one polypeptide chain
Select which represent a hydrogen bond. 1. H - H 2. - N -- H - O - 3. - C -- H - F - 4. - O -- H - C -
2
The graph shows a titration curve for the amino acid histidine. Several parts of the titration curve are labeled by OH- equivalents: 0, 0.5, 1.0, 1.5, 2.0, 2.5. Which statement describes the curve at 1.5 OH equivalents? 1. histidine has zero net charge 2. pH is equal to the pKa of the imidazole group 3. the average net charge of histidine is -0.5 4. pH is equal to the pKa of the carboxyl group
2
Which polypeptide is more soluble at pH 3.0? 1. 5 (Ala-Asp-Gly) 2. 5 (Asn-Ser-His)
2
Which polypeptide is more soluble at pH 6.0? 1. 5 (Ala-Ser-Gly) 2. 5 (Asn-Ser-His)
2
Which polypeptide is more soluble at pH 7.0? 1. 20 Gly 2. 3 (Lys-Ala)
2
Select the three true statements. 1. Nonpolar molecules that have no polar groups can readily form micelles. 2. The tendency of hydrophobic molecules to aggregate in water is called the hydrophobic effect. 3. Placing a hydrophobic molecule into water disrupts some of the water-water bonds. 4. The bilayer of a cellular membrane is primarily composed of amphipathic (amphiphilic) lipids. 5. Forming an ordered network of water around hydrophobic molecules increases the entropy of water.
2, 3, 4
Why does oil not dissolve in water? 1. Hydrogen bonds form between oil molecules, causing them to aggregate. 2. Water molecules form stronger associations with other polar molecules than with oil. 3. Oil is less dense than water, which causes it to separate form water instead of dissolving. 4. Water molecules form hydrogen bonds with each other and exclude oil molecules.
2, 4
Select the true statements about SDS-PAGE, a method of separating proteins. Assume that SDS-PAGE is performed under reducing conditions. 1. Proteins are visualized. using a dye that binds to the gel matrix, but not to proteins. 2. A protein binds roughly 1.4 times its mass of SDS, resulting in a large overall negative charge. 3. SDS-PAGE utilizes agarose gel to separate proteins. 4. Protein-SDS complexes migrate toward the positive electrode. 5. Smaller proteins migrate faster through the polyacrylamide gel. 6. Sodium dodecyl suflate binds proteins, resulting in protein-SDS complexes that are similar in size.
2, 4, 5
All of the cells in the body need oxygen. Hemoglobin molecules in red blood cells transport oxygen through the bloodstream. Oxygen is loaded onto hemoglobin molecules in the lungs and unloaded from the hemoglobin molecules in the tissues. What drives the unloading of oxygen from hemoglobin molecules in the tissues? 1. the high partial pressure of carbon dioxide in the tissues 2. the low partial pressure of carbon dioxide in the tissues 3. the low partial pressure of oxygen in the tissues 4. the high partial pressure of oxygen in the tissues
3
Choose the major force controlling tertiary protein structure. 1. hydrogen bonding 2. inorganic ions 3. hydrophobic effect 4. disulfide bonds 5. ion pairs
3
How does hemoglobin function as a pH buffer? 1. Hemoglobin releases hydrogen ions after carbon dioxide enters the red blood cell. 2. Hemoglobin releases hydrogen ions when oxygen exits the red blood cell. 3. Hemoglobin binds hydrogen ions after carbon dioxide enters the red blood cell. 4. Hemoglobin binds hydrogen ions when carbon dioxide exits the red blood cell.
3
How does hyperventilation affect blood pH? 1. It decreases CO2 and increases H+ in the blood, increasing pH 2. It increases CO2 and decreases H+ in the blood, increasing pH 3. It decreases CO2 and H+ in the blood, increasing pH 4. It increases CO2 and H+ in the blood, decreasing pH
3
The graph shows a titration curve for the amino acid histidine. Several parts of the titration curve are labeled by OH- equivalents: 0, 0.5, 1.0, 1.5, 2.0, 2.5. Which statement describes the curve at 0 OH equivalents? 1. histidine is completely titrated by OH- 2. histidine is fully deprotonated 3. the predominant form of histidine has a +2 charge 4. histidine's buffering power is the greatest at this pH
3
The graph shows a titration curve for the amino acid histidine. Several parts of the titration curve are labeled by OH- equivalents: 0, 0.5, 1.0, 1.5, 2.0, 2.5. Which statement describes the curve at 0.5 OH equivalents? 1. pH is equivalent to histidine's isoelectric point 2. histidine's carboxyl group completely titrated 3. the average net charge of histidine is +1.5 4. histidine's buffering capacity is the lowest
3
The graph shows a titration curve for the amino acid histidine. Several parts of the titration curve are labeled by OH- equivalents: 0, 0.5, 1.0, 1.5, 2.0, 2.5. Which statement describes the curve at 2.0 equivalents: 1. histidine moves toward cathode in an electric field 2. pH is equal to pKa of imidazole ring 3. histidine has zero net charge 4. average net charge of histidine is -2
3
What effect will hemoglobin have on the bicarbonate reaction in active muscle? 1. It will increase the amount of O2 unloaded 2. It will increase CO2 production 3. It will increase HCO3- production 4. It will decrease the pH level
3
Select the true statements about protein secondary structure. 1. In a beta-pleated sheet, the side chains are located between adjacent segments. 2. Disulfide bonds stabilize secondary structure. 3. The secondary level of protein structure refers to the spatial arrangements of short segments of the protein. 4. In an alpha-helix, the side chains are located on the outside of the helix. 5. The beta-pleated sheet is held together by hydrogen bonds between adjacent segments.
3, 4, 5
Which statements accurately describe the polarity and electronegativity of water? 1. Water molecules have slight charges and are attracted to each other by ionic bonds. 2. Water has polar bonds and a linear symmetrical shape, so it is polar. 3. Water molecules are polar and thus associate with each other through hydrogen bonds. 4. The oxygen atom in a water molecule is strongly electronegative. 5. The atoms of the water molecule are held together by covalent bonds.
3, 4, 5
Identify the buffer solution that can be used for eluting a transcription factor bound to a DNA affinity column. 1. high sugar concentration 2. high imidazole concentration 3. a mixture of free DNA nucleotides 4. high salt concentration
4
The graph shows a titration curve for the amino acid histidine. Several parts of the titration curve are labeled by OH- equivalents: 0, 0.5, 1.0, 1.5, 2.0, 2.5. Which statement describes the curve at 1.0 OH equivalents? 1. half of histidine's amino groups are protonated 2. the average net charge of histidine is -1 3. histidine's buffering power is the greatest at this pH 4. histidine's carboxyl group is completely titrated
4
The graph shows a titration curve for the amino acid histidine. Several parts of the titration curve are labeled by OH- equivalents: 0, 0.5, 1.0, 1.5, 2.0, 2.5. Which statement describes the curve at 2.5 OH equivalents? 1. pH is equivalent to histidine's isoelectric point 2. histidine is completely titrated by OH- 3. average net charge of histidine is +1.5 4. pH is equal to the pKa of the amino group
4
Consider a mixture of four proteins with various molecular weights. Arrange the molecules in order of their elution from a gel filtration column. 1. histone (15 kDa) 2. p53 (53 kDa) 3. actin (42 kDa) 4. IgG (150 kDa)
4, 2, 3, 1
Which statements about peptide bonds are true? 1. Peptide bonds are ester linkages. 2. Peptide bond formation is a hydrolysis reaction. 3. A tetrapeptide contains five amino acid residues. 4. Peptides are polymers of amino acids. 5. A tripeptide contains three amino acid residues.
4, 5
The graph represents the titration of amino acid with NaOH solution. What is the pI: pKa1 = 2.34; pI = 6.01; pKa2 = 9.69.
6.01
The graph represents the titration of amino acid with NaOH solution. At what pH are about 1/2 the amino groups ionized: pKa1 = 2.34; pI = 6.01; pKa2 = 9.69.
9.69
The graph represents the titration of amino acid with NaOH solution. At which pH value does the amino group of the amino acid have the best buffering capacity: pKa1 = 2.34; pI = 6.01; pKa2 = 9.69.
9.69
The illustration shows several oxygen-dissociation curves. Assume curve 3 corresponds to hemoglobin with physiological concentrations of CO2 and 2,3-biphosphoglycerate at pH 7. 1. loss of quaternary structure 2. increase in 2,3-BP 3. decrease in CO2 4. no perturbation 5. an increase in pH
Curve 1: 1 Curve 2: 3, 5 Curve 3: 4 Curve 4: 2
The change in hemoglobin's oxygen affinity due to a change in pH is known as the Bohr effect. Physiological pH levels in tissues typically vary little, but these changes have a noticeable effect on the oxygen affinity of hemoglobin. The graph contains three oxygen dissociation curves for hemoglobin, each curve representing a different pH level. Identify the pH for each oxygen dissociation curve in the graph. 1. pH 7.2 2. pH 7.4 3. pH 7.6
Curve 1: 3 Curve 2: 2 Curve 3: 1
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] = 0.240 M, [H+] = 3.0 x 10^(-4) M, and [A-] = 3.00 x 10^-4 M. Calculate the Ka value for the acid HA.
Ka = [H+][A-] / [HA] = (3.00 x 10^(-4))(3.00 x 10^(-4)) / 0.240 = 3.75 x 10^(-7)
What is the hydroxide ion concentration, [OH-], in an aqueous solution with a hydrogen ion concentration of [H+] = 3.0 x 10^(-5)
Keq = [H+][OH-] 1.0 x 10^(-14) = (3.0 x 10^(-5)) [OH-] [OH-] = (1.0 x 10 ^(-14)) / (3.0 x 10^(-5)) = 3.3 x 10^(-10) M
What is the pH of an aqueous solution with a hydrogen ion concentration of [H+] = 3.0 x 10^(-5)
pH = -log [H+] = -log (3.0 x 10^(-5)) = 4.52
The dissociation of lactic acid to lactate is shown in the reaction. Lactic acid has a pKa of 3.86. A solution containing a mixture of lactic acid and lactate was found to have a pH of 4.12. Calculate the ratio of the lactate concentration to the lactic acid concentration in this solution.
pH = pKa + log [lactate]/[lactic acid] [lactate]/[lactic acid] = 10 ^ (4.12 - 3.86) = 1.8
Calculate the pI of glycine using the given values: pKa of carboxyl = 2.72; pKa of amino = 9.60.
pI = (pKa1 + pKa2) / 2 = (2.72 + 9.60) / 2 = 6.16
Anfinsen started with purified ribonuclease A in its native state. To begin, he _____ it with beta-mercaptoethanol and 8M urea. This process resulted in denatured ribonuclease A protein. Next, he _____ the urea and beta-mercaptoethanol resulting in oxidation of S-H bonds, which allowed ribonuclease a to return to its native state.
treated; removed
