Biochem Final Multiple Choice Questions

The steps listed below are used in the chemical synthesis of DNA. Place them in the correct order First nucleoside is attached to solid support ____A trivalent phosphite is oxidized with iodine to form a phosphotriester ____An "activated" and protected nucleotide is added, which forms a 5'-3' linkage ____Diisopropylamino group is added the next nucleotide ____Oligonucleotide is cleaved from the silica gel support ____The DMT group is removed ffrom 5'OH by washing the column with acid ____Repeat previous steps until all residues are added. Removing excess nucleotides before each cycle

4 3 2 6 1 5

The steps listed below are used in the synthesis of cDNA. Place them in the correct order. Some steps will not be used ___mRNA is degraded with a basic solution ___DNA is degraded with basic solution ___Reverse transcriptase extends a primer by adding dNTPs as it scans the template ___Isolation of mRNA from cells expressing gene of interest ___Isolation of genomic DNA from cells with gene of interest ___A primer is allowed to anneal to 3' end of DNA template ___Amplification by PCR using forward and reverse primers and thermostable DNA polymerase ___Oligo dT primer is allowed to anneal to template ___An oligonucleotide of known sequence is ligated to 3' end

4 x 3 1 x 6 7 2 5

Boat and chair conformations are found a. In pyranose sugars b. Only in alpha-D-glucopyranose c. In furanose sugars d. In any sugar without axial -OH groups e. In any sugar without equitorial -OH groups

A

In a stable, right handed alpha helix, the R groups: a. Tend to contribute to a low PONDR score b. Project into the interior of the helix c. Alternate between the outside and the inside of the helix d. Can form ion pairs if they are at position i and i+2 e. Have a higher tendency to form aggregates than R group in beta sheets f. Are responsible to the helix dipole

A

In glycoproteins, the carbohydrate group is always attached though the amino acid residues a. Asn, Ser, or Thr b. Asp or Glu c. Gln or Asn d. Lys or Arg e. Trp, Tyr, or Phe

A

The aggregation of nonpolar molecules or groups in water is thermodynamically due to the: a. Increased entropy of the water molecules b. Increased entropy of the nonpolar molecules when they associate c. Decreased enthalpy of the system d. Significant attraction between the nonpolar molecules or groups e. Absence of van der Waals attractions between water and the nonpolar molecules

A

Why is glucose not stored in its monomeric form in cells: a. Because monomeric glucose would raise the osmolarity of the cytosol to unsafe levels b. Because the monomeric form of glucose is not very soluble c. Because the monomeric form of glucose cannot be readily utililized as an energy source d. Because glucose monomers spontaneously form polymers in the cell e. Because glucose monomers would aggregate and precipitate

A

Treatment of prion preparations with ionizing and UV-radiation does not reduce transmission of disease, however, treatment with denaturants reduces disease transmission. What can be inferred from these observations? Select all that apply a. Prions are proteins b. Prions are smaller than viruses c. Denaturants may affect the tertiary structure of prions d. Prions must not contain genetic information=nucleic acids e. Denaturants act like irreversible inhibitors on prion catalytic activity

A B C D

Which of the following statements is/are TRUE concerning myoglobin and hemoglobin? Select all that apply a. In both myoglobin and hemoglobin there is a distal histidine that forms an H-bond to the oxygen molecule bound to the heme group b. In both myoglobin and hemoglobin the most prevalent secondary structures are alpha-helices c. In both myoglobin and hemoglobin the iron atom of the heme group ends up bound to nitrogen atoms at five of its six coordination sites. d. A decrease in partial pressure of CO2 in the lungs will increases the affinity of Hb for O2 but will have no effect on the affinity of Mb for O2 e. BPG binds to hemoglobin but not myoglobin

A B C E

When the linear form of D-glucose cyclizes: Select all that apply a. The most favorable ring structure is a pyranose in the chair conformation b. The products will have one carbon directly bonded to the two oxygen atoms c. The product is a hemiketal d. The product can be quantitated using UV/Vis spectroscopy e. The product has an additional chiral carbon f. The oxygen in the carbonyl group ends up as one of the ring members

A B E

Which of the following is FALSE about cellulose and amylose? Select all that apply a. Amylose is highly branched while cellulose is not branched b. Cellulose is used mostly for structural support while amylose is used for chemical energy c. Cellulose is found in plants while amylose is stored in animal liver d. Amylose takes on a helical structure while cellulose takes on a fiber form e. Cellulose is generally not digested by animals, whereas starch is easily digestible

A C

Which of the following is/are TRUE of the structure of nucleic acids? Select all that apply a. The nucleic acids are relatively hydrophobic b. All four bases absorb ultraviolet light maximally at 620nm c. The bonds of RNA are more susceptible to hydrolysis by base d. The bond that joins nitrogenous bases to pentoses is an O-glycosidic bond e. C-5 of the pentose is joined to a nitrogenous base, and C1 to a phosphate bond

A C

A PCR reaction includes: Select all that apply a. All four deoxynucleoside triphosphates b. Heat stable DNA ligase c. Oligonucleotide primers that hybridize to sequence that flank target sequence d. Heat stable DNA polymerase e. DNA template containing target sequence to be amplified f. One type of dideoxynucleotides g. Thermocycler

A C D E G

Which of the following are needed to build a cDNA library? Select all that applly a. All four deoxynucleoside tripshophates b. Genomic DNA from lysed cells c. mRNA from lysed cells d. Reverse transcriptase e. RNA polymerase f. poly (dA) primers g. poly (dT) primers

A C D G

Which of the following statements are TRUE about allosteric enzymes? Select all that apply a. Allosteric enzymes generally have more than one subunit b. Phosphorylation of cysteine residues is a common way to regulate enzyme activity c. In the case of homotropic enzyme, a plot of v0 vs. [S] would show a hyperbolic curve d. K0.5 represents the modulator concentration that increases the catalytic rate by 50% e. Allosteric enzymes have binding sites for regulatory molecules that are separate from the active sites

A E

Compounds that generate nitrous acid (such as nitrites, nitrates, and nitrosamines) change DNA molecules by: a. breakage of phosphodiester bonds b. Deamination of bases c. Depurination d. Formation of thymine dimers e. Hydrolysis of glycosyl bond between base and sugar groups

B

The enzyme glucose oxidase catalyzes the oxidation of beta-D-glucose to D-glucono-delta-lactone. Yet, blood glucose contains both the alpha and the beta forms of glucose. How is it possible that this enzyme reaction is used to quantitate the total amount of glucose in a blood sample? a. The glucose oxidase reaction is first used to calculate the beta form and then the amount in alpha form is easily calculated by doubling the amount since the ratio is 1:1 b. As the enzyme oxidases the beta form, more of the alpha form is spontaneously converted to beta form c. The amount of alpha-glucose in blood is so small so it can be ignored d. The glucose oxidase method is being replaced by other methods (ie. Benedict's test) due to this source of error e. Blood samples are pre-treated with a different enzyme that converts all the alpha-glucose to beta-glucose

B

Which of the following describes the correct order of enzyme activities involved in Nucleotide Excision Repair (NER)? a. DNA helicase-->DNA polymerase e-->Exinuclease-->DNA ligase b. Exinuclease-->DNA helicase-->DNA polymerase e-->DNA ligase c. DNA glycosylase-->AP endonuclease-->DNA polymerase I-->DNA ligase d. AP endonuclease-->DNA glycosylase-->DNA polymerase I-->DNA ligase e. None of the above

B

Which of the following gases is the most soluble in water: a. Nitrogen gas b. Dihydrogen sulfide c. Carbon dioxide d. Oxygen gas e. Methane gas

B

Which of the following is a class of protein that are known for the ability to bind to specific oligosaccharides a. dextrans b. lectins c. lactones d. antibodies e. peptidoglycans

B

Which of the following qPCR dyes or probes does not involve a fluorophore and a quencher? a. Molecular beacon b. SYBR green c. TaqMan probe

B

Which of the following statements about hemoglobin and myoglobin structure are TRUE. Select all that apply: a. Molecular oxygen binds irreversibly to Fe2+ in heme b. Both Hb and Mb contain a presthetic group called a heme, that contains an iron atom c. By itself, heme is not a good oxygen carrier. It must be part of a larger protein to prevent oxidation of the iron atom d. Hb and Mb are heterotetramers e. Each iron atom can form six coordination bonds: one of these bonds is formed between iron and molecular oxygen f. Mb can bind to only one oxygen molecule while Hb can bind to four oxygen molecules

B C E F

A cyanobacterium is able to use CO2, light, H2O, and O2 to synthesize biomolecules-it is therefore a? a. Chemoautotroph b. Chemoheterotroph c. Photoautotroph d. Photoheterotroph e. Lithotroph

C

Carbon monoxide a. binds to Hb irreversibly and cannot be removed even in high O2 pressure b. Competes with BPG for binding to Hb c. Binds more tightly than O2 to heme and to hemoglobin d. Binds to Hb and alters its structure so that it is similar to the structure of HbS e. Poisoning in a patient can only be detected by laboratory analysis because it is a colorless and odorless gas

C

Osmosis is water movement across a semi-permeable membrane. Which of the following is TRUE about water movement across a membrane? a. In an isotonic solution, cells will shrink b. Water cannot penetrate the plasma membrane because it is polar c. In a hypotonic solution, cells will swell d. In a hypotonic solution, cells will neither swell nor shrink e. None of the above are TRUE statements

C

Oxygen affinity is altered during exercise due to the Bohr effect. The molecular mechanism and result of the Bohr effect is: a. The protonation of histidine residues increases the affinity or O2 b. The small molecule 2,3 BPG binds and increases the affinity for O2 c. The protonation of histidine residues stabilizing the T-state d. A point mutation causing the aggregation of Hb leading to sickle shaped red blood cells e. None of the above

C

Proline has a limited number of allowed conformations compared to other amino acids because a. It has a relatively bulky side chain compare to others b. It is an aliphatic amino acid chain that avoids water contact c. Its side chain is linked to the alpha amino group d. Its side chain has a chiral carbon e. The alpha amino group is charged along the peptide backbone

C

The Yeast Two Hybrid System a. Relies on the fact that Protein A has high affinity for the Fc portion of IgG b. Is a technique used to mutate the DNA at a very specific sites to study the effects of amino acid substitutions on protein structure and function c. Relies on the fact that the Gal4 binding domain and DNA binding domain must end up close to each other in vivo to activate a reporter gene d. Is used to measure the relative expression of a target gene inside a transgenic yeast strain e. Is used to amplify the sequences of short tandem repeats in yeast cells

C

The technique of DNA genotyping based on short tandem repeats (STR) a. Relies on DNA sequencing of short tandem repeats b. Involves loading of PCR products on ion exchange chromatography c. Involves dye-labeled PCR primers that hybridize to unique sequences flanking a series of short tandem repeats d. Relies on molecular beacons that recognize short DNA repeats e. Involves the use of fluorescently labeled nucleotides (dNTPs) each tagged to a different fluorescent color

C

When an enzymatic activity is purified from a complex mixture of proteins what usually happens to the total amount of protein and the specific activity during the purification process? a. The total amount of protein and the specific activity both decrease b. The total amount of protein and the specific activity both increase c. The total amount of protein decreases and the specific activity increases d. The total amount of protein increases and the specific activity decreases e. The total amount of protein decreases and the specific activity remains constant

C

Which of the following is FALSE? a. Cu2+ can oxidize D-glucose to D-gluconate b. Salivary amylase hydrolyzes alpha1--->4 glycosidic linkages between glucose-glucose residues c. Lysozyme hydrolyzes alpha1--->4 glycosidic linkages between MurNAc-GlcNAc residues d. Lactase hydrolyzes beta1--->4 glycosidic linkages between galactose-glucose residues e. Cellulase hydrolyzes beta1--->4 glycosidic linkages between glucose-glucose residues

C

Which of the following is NOT a factor that helps explains how enzymes increase reaction rates: a. The effective concentration of the substrate is increased when it is bound to the enzyme b. The binding energy makes up for the distortion of the substrate during the reaction c. The entropy of enzyme and substrate increase when the substrate binds the enzyme d. The enzyme binds to the substrate so as to orient the substrate in a position that favors the reaction e. The enzyme decreases the free rotation of reacting groups

C

Which of the following is a heteropolysaccharide? a. cellulose b. chitin c. agarose d. amylopectin e. glycogen

C

Which of the following is true about the titration curves of solutions of weak acids? a. The pKa of a weak acid is the pH at which 1.0 equivalent of OH moles has been added b. The pH for optimal buffering power of a weak acid is 7.0 c. At a pH above the pKa of a weak acid, its conjugate base will predominate d. To calculate the pKa of an acid, all that is needed is the concentration of the weak acid e. None of the above are true statements

C

Amyloid fibrils are associated are associated with many fatal degenerative diseases of humans and livestock. Which of the following descriptions are TRUE statements. Select all that apply: a. Amyloid fibrils have a high amount of alpha-helical structure b. Proteins that convert to an amyloid structure form soluble fibrils c. Some amyloid fibrils are formed from proteolytic fragments that self-assemble into extended beta-sheet structures d. Proteins that form amyloid fibrils are normally soluble e. Most newly synthesized proteins fold correctly, but the accumlation of misfolded proteins tends to occur slowly and this explains the late onset of disease.

C D E

A Ramachandran plot describes, for a particular amino acid, the sterically permitted angles for: a. Rotation about the Calpha-C bond b. Roation about the N-Calpha bond c. Rotation about the C-N bond d. Both a and b e. Both a and c f. Both b and c g. All three: a, b, and c

D

A metabolic pathway proceeds according to the scheme R-->S-->T-->U-->V-->W. A regulatory enzyme, E, catalyzes the first reaction in the pathway. Which of the following is most likely correct for this pathway? a. Either metabolite U or V is likely to be a positive modulator, increasing the activity of E b. The last product W, is likely to be a positive modulator, increasing the activity of E c. The first product S, is probably the primary negative modulator of E, leading to feedback inhibition d. The last product W, is likely to be negative modulator of E, leading to feedback inhibition e. The last reaction will be catalyzed by a second regulatory enzyme

D

All of the following are true statements about collagen, EXCEPT: a. Its tertiary structure is stabilized by interstrand hydrogen bonds between backbone (N-H and C=O) b. Its primary structure is rich in glycine residues (~1 out of 3) c. Its structure does not include beta sheets d. Its tertiary structure consists of two helices that wind around each other e. It's a strong protein found in connective tissue, bone, and the extracellular matrix

D

Assume that a fusion gene has been introduced into E.Coli. The 5' end codes for beta hemoglobin subunit and the 3' end codes for a tail of histidines (His6). What type of column chromatography would be useful to isolate the fusion protein from the rest of the proteins in the cell extract? a. Maltose column b. Gel exclusion chromatography column (Sephadex 10,000) c. Glutathione column d. Nickel column e. Ion exchange chromatography (DEAE) column

D

Consider the binding reaction shown below. This hypothetical protein will display NO cooperativity if: P+L<--->PL+L<--->PL2 a. nH>1 b. Kd1<Kd2 c. Kd1>Kd2 d. Kd1=Kd2 e. None of the above

D

The Hill Coefficient (nH) for myoglobin is _____; whereas the nH for Hb is about _______. a. 1.0; 2.0 b. 3.0; 1.0 c. 4.0; 1.0 d. 1.0; 3.0 e. 3.0; 4.0

D

The pKa values of phosphoric acid are 2.2, 7.2, and 12.7. A phosphate buffer of pH 8.0 can be prepared using: a. H3PO4 + HCl + water b. H2PO4 + HCl + water c. H3PO4 + H2PO4 + water d. H2PO4 + NaOH + water e. PO4 + NaOH + water

D

What is the most likely effect of substituting His57 in chymotrypsin with alanine: a. The Km would increase and kcat would remain about the same b. The Km would decrease and kcat would remain about the same c. The Km would remain about the same and kcat would increase d. The Km would remain about the same and kcat would decrease e. Both the Km and kcat would decrease f. Both the Km and kcat would remain about the same

D

Which ligand binds tightest to its protein? a. Ligand A, with a Kd= 10^-3M b. Ligand B, with a Kd=10^-8M c. Ligand C, with a percent occupancy of 50% at 1uM d. Ligand d, with a percent occupancy of 60% at 1nM e. Ligand E, with a percent occupancy of 90% at 1mM

D

Which of the following is NOT needed for pyrosequencing of DNA: a. All four deoxynucleoside triphosphates (dNTPs) b. Sulfurylase c. Luciferase d. Dideoxynucleotides (ddNTPs) e. Apyrase f. DNA polymerase

D

Which of the following statements is FALSE? a. Both carbon and silicon combine with oxygen to form a dioxide: CO2 and SiO2, respectively. b. Both carbon and silicon have 4 valence electrons c. Both carbon and silicon can form single bonds with H: CH4 and SiH4 d. Carbon is more abundant than silicon on the Earth's crust e. The length of a C-H bond is shorter compared to a Si-H bond

D

L-Dopa is an oral medication used to treat Parkinson's disease, the symptoms which result from a lack of dopamine in the brain. L-Dopa relies on L-type, or leucine-preferring, transport proteins to cross the blood-brain barrier, and it is converted to dopamine in the brain by the enzyme aromatic-L-amino acid decarboxylase. Identify the properties of its enantiomer D-Dopa. Select ALL that apply: a. Highly soluble in water b. Reduces symptoms of Parkinson's disease c. Rotates plan-polarized light counterclockwise d. Solid at room temperature e. Aromatic-L-amino acid decarboxylase has a different affinity for D-Dopa f. Density is less than that of L-Dopa

D E

An enzyme follows Micahelis-Menten kinetics. Indicate the effect of adding the following compounds to the enzyme reaction. Indicate increase, decrease, or no effect: Adding an uncompetitive inhibitor Km= Vmax=

Decrease Decrease

Hemoglobin glycation is a process where ____________ is ___________ attached to hemoglobin a. glycerol; enzymatically b. glucose; enzymatically c. galactose; non-enzymatically d. glycerol; non-enzymatically e. glucose; non-enzymatically f. None of the above

E

Select the one FALSE statement regarding antibody (specifically immunoglobulin G) structure: a. The antigen-binding site is located on the Fab fragment b. The antigen-binding site is formed as a combination of variable domains from one heavy and one light chain c. Only the Fab fragment has variable domains d. The heavy and light chains are linked by noncovalent and disulfide bonds e. Only the Fc fragment has constant domains

E

Treatment of gram-positive bacteria with penicillin will have what effect? a. Inhibition of cell wall synthesis by hydrolyzing the beta1-4 bonds between carbohydrate residues of the cell wall b. It will inhibit the linkage between MurNAc and GlcNAc subunits in bacterial cell walls c. It will activate lysozyme, an enzyme which helps fight bacterial infections d. It will inhibit synthesis of liposaccharides in the outer membrane e. It will inhibit cell wall synthesis by preventing the synthesis of peptide cross-links in the cell wall peptidoglycans

E

Two proteins that have the same MW but differ in their pI are best separated by: a. SDS PAGE b. Dialysis c. Gel Exclusion Chromotography d. MALDI MS e. Carboxymethyl Cation Exchange Chromotography

E

Which of the following is TRUE about the differences between ELISA and Western Immunoblot assays? a. Only Western blots allow for detection of protein antigens b. Only Western Immunoblots are used to measure amount of antigen present c. Only ELISA assays require a nitrocellulose membrane d. A secondary antibody is only used on ELISA assays e. Only Western blots enable an approximation of an antigen's molecular weight

E

An enzyme follows Micahelis-Menten kinetics. Indicate the effect of adding the following compounds to the enzyme reaction. Indicate increase, decrease, or no effect: Adding 6M Urea Km= Vmax=

Increase Decrease

An enzyme follows Micahelis-Menten kinetics. Indicate the effect of adding the following compounds to the enzyme reaction. Indicate increase, decrease, or no effect: Adding a mixed inhibitor Km= Vmax=

Increase Decrease

An enzyme follows Micahelis-Menten kinetics. Indicate the effect of adding the following compounds to the enzyme reaction. Indicate increase, decrease, or no effect: Adding a competitive inhibitor Km= Vmax=

Increase No effect

For each of the following statements determine if it is describing an intermediate, a transition state analogue, or a transition state Examples include ES and EP

Intermediate

For each of the following statements determine if it is describing an intermediate, a transition state analogue, or a transition state Some are stable enough to be detected and structurally characterized

Intermediate

An enzyme follows Micahelis-Menten kinetics. Indicate the effect of adding the following compounds to the enzyme reaction. Indicate increase, decrease, or no effect: Double the substrate Km= Vmax=

No effect No effect

Synthetic polypeptides can assume an alpha-helical structure under appropriate conditions. Indicate which of the following will form an alpha-helix at the indicated pH values. Circle all that apply: Polylysine at pH 2 Polylysine at pH 7 Polylysine at pH 13

Polylysine at pH 13

For each of the following statements determine if it is describing an intermediate, a transition state analogue, or a transition state Contains partially formed and partially broken bonds

Transition state

For each of the following statements determine if it is describing an intermediate, a transition state analogue, or a transition state Hypothetical maximum energy species of a reaction pathway without a finite lifetime

Transition state

For each of the following statements determine if it is describing an intermediate, a transition state analogue, or a transition state Often serves as a potent enzyme inhibitor

Transition state analogue