BBMB 316 All Questions, BBMB 316 Exam 1 Review, BBMB 316 2018 Iowa state university FINAL EXAM, BBMB 316 Final Exam-Ambrosio, BBMB 316 Final Exam previous questions, BBMB 316 Final, BBMB 316 Final Exam

E1 Which carbon atom is part of the aldehyde functional group?

#1

1.3 Prions are similar in size to viruses, but are composed only of protein. All of the following occur during prion infection except:

(except) Prions enzymatically catalyze the production of more prions (correct statements) Normal cellular proteins are converted into abnormal prion proteins Misfolded prion proteins form aggregates that are insoluble, ultimately leading to cell death destruction A portion of a-helical structures from a normal protein is refolded into a b-sheet structure Mad cow disease is caused by infectious prions

E1 Acid precipitation has lowered the pH of a particular lake to 4.0. The hydroxide ion (OH-) concentration in the lake is:

1 x 10 ^-10 M

2.1 For a Lineweaver-Burk plot, the y-intercept

1/Vmax

E2 The y-intercept of a Lineweaver-Burk plot is:

1/Vmax

E1 If an aqueous solution has a hydroxyl ion concentration of 10 ^-8 M, what is the concentration of hydrogen ion?

10 ^-6

1.2 What is the isoelectric point of histidine, based on the titration graph below:

7.5

1.2 The chemical equation that describes the equilibrium between dissolved CO2 and HCO3- in blood is:

A

2.3 Glucose in plants is stored as:

B) amylose, a linear polymer of glucose units joined by α-1,4-glycosidic bonds and C) amylopectin, a branched polymer with glucose molecules joined by α-1,4-glycosidic bonds that are linked at approximately every 30 glucose units with α-1,6-glycosidic bonds.

E2 Identify the diagram that best describes the equilbra associated with an uncompetitive inhibitor (I)?

Diagram (B)

1.1 The loss of a proton (H+) from a water molecule is known as:

Dissociation

E1 Many of the loops on the proteins that have been described are composed of hydrophobic amino acids

False

2.4 A lipid micelle is most likely formed by

Fatty acids

E1 Identify an amino acid that interacts with NaOH:

Glutamate

1.2 A phosphate buffer solution at a pH = pK1 = 2.15 would have equal amounts of phosphate in the H3PO4 form and the:

H2PO4- form

E1 A phosphate buffer solution at a pH = pK1 = 2.15 would have equal amounts of phosphate in the H3PO4 form and the:

H2PO4- form

E1 Identify the predominate form of glycine at pH 7.0.

H3N+CH2COO-

1.2 Interactions between side chains of Aspartate and Arginine at neutral pH would be?

Ionic

1.2 Why is the peptide bond planar?

It exhibits partial double-bond character, preventing rotation.

2.2 For the chymotrypsin enzyme, predict the effect of mutating the active site aspartate residue to a tyrosine.

It is likely that the mutant chymotrypsin enzyme will lose all activity.

E2 For the chymotrypsin enzyme, predict the effect of mutating the active site aspartate residue to a tyrosine.

It is likely that the mutant chymotrypsin enzyme will lose all activity.

1.1 Which class of compounds contains a carbonyl group bonded to two other carbon atoms?

Ketones

E2 Which class of enzymes act to add atoms or functional groups to remove a double bond, as depicted in the enzymatic reaction shown below:

Lyases

E1 Which charged group(s) are present in lysine at pH 2.5? Note: Lysine has three ionizable groups: α-carboxyl group (pKa value = 3.1) α-amino group (pKa value = 8.0) and its R group (pKa value = 10.8)

NH3+

E1 Bends, loops and turns, often without a repeating secondary structure are:

Nonregular, nonrepetitive secondary structures

E1 Which of the following amino acids would most likely be buried in the interior of a water-soluble, globular protein?

Phenylalanine

1.1 Identify the unbranched polymer that, when folded into its three-dimensional shape, performs much of the work of the cell.

Protein

E1 The main function of the plasma membrane is to:

Provide a selectively permeable barrier with the aid of transport proteins.

E2 Reaction-progress curves for two different reactions are shown below. Which of the following statements is true?

Reaction A is exergonic.

1.3 What is the advantage of adding SDS to gel electrophoresis?

SDS allows proteins to be separated on the basis of appropriate mass

E1 What is the advantage of adding SDS to gel electrophoresis?

SDS allows proteins to be separated on the basis of approximate mass

2.3 Which of the five sugars shown in the figure below are the straight chain and hemiketal forms of fructose?

Sugars B and C

E2 In the laboratory, you are attempting to determine the KM of an enzyme by measuring the reaction velocity at different substrate concentrations. You notice that under the experimental conditions chosen to monitor the reaction, the substrate tends to precipitate out of solution. How would this affect your measurement of KM?

The apparent KM would be greater than the true KM. The actual experimental substrate concentration would be less than expected, because some of the substrate has precipitated out of solution during the reaction.

E2 The enzyme phosphofructokinase-1 is an allosteric enzyme and demonstrates a sigmoidal curve when V0 is plotted against [S]. If a positive allosteric effector like AMP is added, then:

The concentration of substrate necessary to reach half maximal velocity will decrease.

1.3 How a protein folds is FUNDAMENTALLY determined by

The order of the amino acids found in the sequence

E2 Succinylcholine is a fast acting, short duration muscle relaxant that is used when a tube (bronchoscope) is inserted into a patient's trachea and bronchi to look for signs of cancer. Within seconds of the administration of succinylcholine, the patient experiences muscle paralysis and is placed on a respirator while the examination proceeds. Succinylcholine is a competitive inhibitor of acetylcholinesterase, and this inhibition causes paralysis. However, succinylcholine is hydrolyzed by blood-serum cholinesterase, thus, paralysis lasts until the succinylcholine is hydrolyzed by the serum cholinesterase, usually several minutes later. Some patients have a mutant form of the serum cholinesterase that displays a KM of 10 mM, rather than the normal 1.4 mM. What will be the effect of this mutation on the patient?

The patient will clear the drug at a much slower rate, and paralysis time will be extended.

2.1 What is Vmax?

The rate at which product is formed when an enzyme is completely saturated with substrate.

E2 Which of the following best describes the term Vmax?

The rate at which product is formed when an enzyme is completely saturated with substrate.

E1 Which of the following statements best describes the tertiary structure of a protein?

The total 3-D conformation of an entire polypeptide chain including α-helices, β-sheets, and any other loops or bends.

1.3 Which of the following statements best describes the tertiary structure of a protein?

The total 3D conformation of an entire polypeptide chain including a-helicies, b-sheets, and any loops or bends

E2 You find that your patient has a blood alcohol concentration of 1 mM. Assume that the VMax of cytosolic and mitochondrial alcohol dehydrogenase enzymes are equivalent and that the KM values are 0.04 mM and 11 mM, respectively. Which of the following statements is correct:

The velocity of the cytosolic alcohol dehydrogenase will be at ~ Vmax.

2.3 At equilibrium, D-glucose consists of a mixture of its anomers, such a solution will be composed of:

The β-anomer is more stable and predominates over the α-anomer by a ratio of approximately 2:1.

2.4 The notation of 12:2 indicates which of the following about a fatty acid?

There are 12 carbons in the chain with 2 double bonds

E1 The polyprotic molecule aspartic acid, with three ionizable acidic-side chains, has _______ potential buffering regions?

Three

1.1 A molecule of water (H2O) contains a permanent dipole.

True

1.1 An oxygen nucleus attracts electrons more strongly than the single proton in the hydrogen nucleus.

True

E1 An oxygen nucleus attracts electrons more strongly than the single proton in the hydrogen nucleus.

True

E1 The SDS gel below demonstrates the effectiveness of this purification scheme as the band for the protein of interest becomes more prominent relative to other bands

True

E1 The amino acid sequence completely determines the three-dimensional structure and all other properties of a protein.

True

E2 Data recorded for a kinetic analysis of the MEK5 kinase and its substrate ERK5 is shown in the table below. Based on this data, determine the VMAX and KM for the MEK5 enzyme:

VMAX = 61 μM/minute and KM = 5 μM

2.2 A compound that reduces the concentration of enzyme available for substrate binding is called:

a competitive inhibitor

E2 An enzyme will bind its substrate with high specificity due to:

a large number of weak interactions at the active site.

2.3 The structure of normal hemoglobin can be best described as:

a tetramer composed of two αβ dimers.

E1 Why are electronegative atoms important in biochemistry?

after assuming a partial negative charge, hydrogen bond formation can occur.

E1 Below is a titration curve of an unknown amino acid in water.

alanine

E1 Choose the amino acid that contains an alkyl side chain:

alanine

E2 What is the physiological significance of cooperativity in sigmoidal kinetics?

allosteric enzymes are mostly either ON (R state) or OFF (T state) below a certain substrate concentration there is very little enzyme activity for allosteric enzymes allosteric enzymes display a threshold effect

E1 In liquid water, each molecule is hydrogen bonded to approximately 3.4 molecules of water. What effect would freezing water have on the number of hydrogen bonds?

allows formation of more hydrogen bonds

E1 What is an electronegative atom?

an atom that has a high affinity for electrons

E1 The psi (ψ) angle:

angle of rotation between the LaTeX: \alpha α -carbon atom and the carbonyl carbon atom.

E1 The molecular structure of the porin protein is shown in green below:

antiparallel β-sheets, reverse turns and loops, α-helix

1.3 Nonregular, nonrepetitive secondary structures:

are bends, loops, and turns that do not have a repeating element

1.2 Amino acids with charged side chains include:

aspartate, glutamate, lysine and arginine

E2 Most carbon dioxide is transported to the lungs from red blood cells in the form of:

bicarbonate (HCO3—)

E2 Penicillin:

binds covalently to its target enzyme and inactivates it.

E1 For the following molecules, which has the best buffering potential in living organisms?

carbonic acid, Ka = 4.3 × 10 ^-7 and pka = 6.37

2.2 An inhibitor that binds to the active site of an Michaelis-Menten enzyme and resembles the substrate:

competitive inhibitor

E1 Unpaired valence electrons equally shared between atoms:

covalent bond

E2 The active site of acetylcholine esterase contains a powerful nucleophile reactive group that becomes temporarily covalently modified in the course of catalysis. Which catalytic strategy does acetylcholine esterase employ?

covalent catalysis

E1 Which of the following is the strongest evidence that protein structure and function are correlated?

denatured (unfolded) proteins do not function normally.

1.2 At a pH above its pKR, the β-carboxylate group of Asp is:

deprotonated and charged

E1 What is the function of secretory granules in the cell?

destined for fusion with the plasma membrane

E1 What would be the effect of an organic solvent on electrostatic interactions, when compared with a polar solvent?

electrostatic interactions would be stronger

2.1 Definition: No net change in the concentration of substrate or product:

equilibrium.

E1 At pH 12, glutamate would be:

fully deprotonated, with a negative charge of - 2

E2 Elastase, a protease that breaks down elastin, preferentially cleaves a peptide bonds on the carboxyl site of glycine, alanine and valine. This is because the specificity pocket of elastase:

has a small hydrophobic pocket, containing the amino acid residues valine and threonine.

E1 The addition of a proton (H+) to a water molecule results in:

hydronium ion

E2 The imadazole side chain of histidine can function in an enzyme active site as either a general acid catalyst or a general base. Which of the following is a correct statement?

in the physiological pH range, the nitrogen in the ring can be easily protonated/deprotonated.

E1 The best experimental design:

includes a large sample size and a control, and alters only one condition between the controls and the experimental condition.

E1 Which class of compounds contains a carbonyl group bonded to two other carbon atoms?

ketones

2.1 How do enzymes accelerate the rate of a chemical reaction ?

lowering the free energy of activation of the reaction.

E2 How do enzymes accelerate the rate of a chemical reaction?

lowering the free energy of activation of the reaction.

E1 Why are weak bonds important in biochemistry?

many weak bonds allow for highly specific yet transient interactions

E1 Examine the peptide below: Thr-Glu-Pro-Ile-Val-Pro-Met-Glu-Tyr-Gly-Lys estimate the net charge at pH 12

minus 4

E1 Identify the atom(s) commonly found in biological molecules that are often hydrogen-bond acceptors:

oxygen and nitrogen

E2 The effect of pH on the activity of an enzyme was examined. At its active site, the enzyme has an ionizable group that must be negatively charged in order for substrate binding and catalysis to take place. The ionizable group has a pKa of 6.0. The substrate is positively charged throughout the pH range of the experiment. At which pH will the velocity equal one-half of the maximal velocity attainable under these conditions?

pH 6

1.2 Identify the Henderson-Hasselbalch equation:

pH = pKa + log10 [A-]/[HA]

E1 Identify the Henderson-Hasselbalch equation:

pH = pKa + log10 [A-]/[HA]

E1 Fully extended peptide chain:

primary structure

E1 This amino acid residue disrupts the α-helix because its side chain contains a unique ring structure that restricts bond rotations.

proline

E1 The hydrophobic effect depends on:

sequestration away from water molecules in aqueous solutions.

2.2 Choose the term from those presented below to place between the brackets to correctly complete this sentence. The mechanism of chymotrypsin involves the formation of an unstable [ ] -shaped intermediate that is stabilized by the oxyanion hole.

tetrahedral

E2 Cleland representations are used to graphically depict:

the binding order of substrates and the release order of products in a multi-substrate reaction

E1 In our discussion of the oxidation states of carbon, carbon is reduced by:

the gain of electrons by the addition of hydrogen

1.1 How a protein folds is fundamentally determined by:

the order of the amino acids found in the sequence.

E1 Definition of pKa:

the pH at which the concentration of the acid equals the concentration of conjugate base.

2.3 Define the Bohr effect:

the regulation of hemoglobin binding by hydrogen ions and carbon dioxide.

2.1 The molecular structure that is short lived in an enzymatic reaction:

transition state

1.2 Porin is a transmembrane protein, which of the following amino acids is most likely to be found on the membrane-contacting surface of the protein?

tryptophan

E2 For a Michaelis-Menten enzymes, this type of inhibitor binds only to the ES (enzyme-substrate) complex:

uncompetitive inhibitor