BioChemistry

1. 1Complete hydrolysis of nucleic acids liberates all of the following EXCEPT

   1. A2-deoxyribose from DNA
   2. Bnitrogenous bases.
   3. Camino acids.
   4. Dphosphoric acid.
   5. Eribose from RNA.
2. 2Which is a six-membered heterocyclic aromatic ring

   1. Apyrimidine
   2. Bpurine
   3. Canose
   4. Dsugar portion of DNA
   5. Eribonucleotide
3. 3____ is the most oxidized state for a purine derivative and is ____ found in nucleic acids

   1. AGuanine; always
   2. BAdenine; always
   3. CHypoxanthine; never
   4. DXanthine; always
   5. EUric acid; never
4. 4All are important functional groups participating in H-bond formation EXCEPT

   1. Aamino group of the cytosine, adenine and guanine
   2. Bthe ring nitrogens at position 3 of pyrimidines and 1 of purines
   3. Cthe electronegative oxygen atoms.
   4. Dthe electron density in the double bonds of the bases.
   5. Ethe carbonyl group at position 4 of uracil and thymine, position 2 of cytosine, and position 6 of guanine.
5. 5All are characteristics of pyrimidines EXCEPT

   1. Asix membered ring.
   2. Bheterocyclic.
   3. Cconjugated.
   4. Dfused five membered rings.
   5. Etwo nitrogens separated by a carbonyl.
6. 6Which of the following properties describe both purines and pyrimidines?

   1. Athey are aromatic
   2. Bthey are composed of 6-membered rings
   3. Cthey exhibit strong absorption of UV light
   4. Dthey always contain a carbonyl group
   5. Eboth A and C are correct
7. 7Nucleotides have a nitrogenous base linked to a sugar by a:

   1. Aalpha-anhydride bond
   2. Bbeta-ester bond.
   3. Calpha-N-amide bond
   4. Dbeta-N-acetal (glycosidic) bond.
   5. Ealpha-N-hemiacetal bond.
8. 8Nucleosides are relatively stable to ____ hydrolysis, and pyrimidine nucleotides are stable to ____ hydrolysis, but purine nucleotides are unstable to ____ hydrolysis

   1. Abase; acid; acid
   2. Bbase; base; acid
   3. Cacid; base; base
   4. Dacid; acid; base
   5. Enone are true
9. 9The net charge on nucleotide monophosphates is:

   1. A+1
   2. B0
   3. C-1
   4. D-2
   5. E-3
10. 10cAMP and cGMP are ____ with phosphate esterified as a cyclic ____ and are important as ____ of cellular metabolism

    1. Anucleotides; phosphodiester; inhibitors
    2. Bnucleotides; phosphomonoesters, regulators
    3. Cnucleotides; phosphodiesters, regulators
    4. Dnucleosides; phosphomonoesters, stimulators
       all of the above
    5. Eall of the above

11. 11Which molecule contains an phosphoanhydride bond?

    1. ADNA
    2. BAMP
    3. CUDP
    4. DRNA
    5. EcAMP
12. 12All of the following are examples of nucleotide functions EXCEPT:
    

    1. ACTP in phospholipid synthesis.
    2. BUTP in complex carbohydrate synthesis.
    3. CATP in energy for the cell.
    4. DGTP in protein synthesis.
    5. ETTP in phosphoryl group transfers.
13. 13Nucleotide triphosphates and nucleotide diphosphates often form stable complexes with:
    

    1. ANa+
    2. BFe+3
    3. CK+
    4. DMg+2
    5. ENone of the above.
14. 14In phosphoryl group transfer reactions, the ____ of the nucleotide serves as an information symbol, channeling the nucleotide to appropriate metabolic activities.
    

    1. Asugar
    2. Bdiphosphate anhydride
    3. Csugar-phosphate ester
    4. Dbase
    5. Enone are true
15. 15Which of the following statements regarding the structure of DNA is correct?

    1. Athe two strands are parallel.
    2. Bthe two strands are held together by intrachain hydrogen bonds.
    3. Cthe two strands have complementary base pairing.
    4. Dthe hydrogen bonding that holds the helix together is always between two purines or between two pyrimidines.
    5. Ethe ratio of adenine to guanine is the same in all organisms.
16. 16In a double-stranded nucleic acid, guanine typically base-pairs with:

    1. Aadenosine.
    2. Buracil.
    3. Cinosine.
    4. Dthymine
    5. Ecytosine.
17. 17In a sample of double-stranded DNA containing 32% cytosine, the percentage of adenine would be:

    1. A32%
    2. B68%
    3. C18%
    4. D0%
    5. Einsufficient information to answer question
18. 18The convention in all notations of nucleic acid structure is to read the polynucleotide chain from the ____ of the polymer to the ____.

    1. Apoly U head; poly A tail
    2. B3'-end; 5'-tail
    3. C5'-end; 3'-end
    4. Dpoly-p head; 5'-end
    5. Enone are true
19. 19All of the following are important characteristics of DNA EXCEPT:

    1. Aa 1:1 ratio between pyrimidine residues and purine residues
    2. Badenine base pairs with uracil.
    3. Chydrogen bonding between base pairs.
    4. Dinformation contained in the sequence of one strand conserved in the sequence of other strand.
    5. Einformation is accessed through transcription of the information into RNA.
20. 20In eukaryotic cells, DNA is found principally in the nucleus, but it also occurs in ____ and in ____.

    1. Aribosomes; mitochondria
    2. Bmitochondria; chloroplasts
    3. Cchloroplasts; peroxisomes
    4. Dperoxisomes; vacuoles
    5. Evacuoles; mitochondria
21. 21In eukaryotic cells, a class of ____- and ____-rich proteins called ____ interact ionically with the anionic phosphate groups in the DNA backbone to form ____.
    

    1. Alysine; leucine; prions; ribosomes
    2. Barginine; lysine; histones; nucleosomes
    3. Carginine; alanine; histones; nucleosomes
    4. Darginine; lysine; prions; ribosomes
    5. Enone are true.
22. 22Prokaryotic chromosomes are typically ____, while eukaryotic chromosomes are ____

    1. Acircular; linear and richly protein-associated
    2. Bcircular and richly protein-associated; linear
    3. Clinear and richly protein-associated; circular
    4. Dlinear; circular and richly protein-associated
    5. Enone are true
23. 23Eukaryotic mRNAs are synthesized in the nucleus, are called ____, and contain noncoding regions called ____ because they intervene between coding regions called ____.
    

    1. Apoly A RNAs; noncodons; codons
    2. Bpoly A RNAs; intervening sequences; codons
    3. Cheterogeneous nuclear RNAs; intervening sequences (introns); codons
    4. Dheterogeneous nuclear RNAs; intervening sequences (introns); exons
    5. Enone of the above.
24. 24____ are attached to hnRNAs and mRNAs after transcription has been completed and is essential for efficient translation and stability of the mRNAs.
    

    1. Aexons
    2. Bentrons
    3. Cpoly(A) tails
    4. Dpoly(U) tails
    5. EAll are true
25. 2530S rRNA is a designation of the ____ of the RNA molecule.

    1. Anumber of sugars
    2. Bsedimentation coefficient
    3. Csplicing coefficient
    4. Dsequence repeats
    5. Esplicing number
26. 26Which of the following correctly describes tRNA molecules?

    1. Aeach amino acid in proteins has at least three unique tRNA species dedicated to chauffeuring its delivery to ribosomes for insertion into growing polypeptides.
    2. Bthey are small molecules containing 73 or 74 bases.
    3. Cthey often contain bases such as inosine or pseudouridine
    4. Dthe 5’ end of the molecule is the site of attachment for the amino acid
    5. Enone of the above is correct
27. 27____ are important in the processing of eukaryotic gene transcripts into mature messenger RNAs for export from the nucleus into cytoplasm.

    1. AsnRNAs as snRNPs
    2. BtRNAs
    3. CrRNAs
    4. DsiRNAs
    5. EstRNAs
28. 28RNA is ____ stable to alkaline hydrolysis than DNA because RNA's vicinal ____ group makes the 3'-phosphodiester bond susceptible to ____ cleavage.

    1. Aless; 3'-OH; nucleophilic
    2. Bless; 2'-OH; nucleophilic
    3. Cmore; 2'-OH; electrophilic
    4. Dmore; 2'-OH; nucleophilic
    5. Emore; 3'-OH; electrophilic
29. 29All are true for enzymes that cleave nucleic acids EXCEPT:

    1. AThey are of the lyase class of enzymes.
    2. BThey are called nucleases.
    3. CThey belong to the sub-class of phosphodiesterases.
    4. DThey are found in all cells for "house keeping", and secreted by the pancreas for digestion.
    5. EThey are found in fungi and snake venoms
30. 30Which of the following statements correctly identifies a type II restriction endonuclease?

    1. AThey work on both DNA and RNA.
    2. BThey recognize a palindromic sequence and cut just before the palindromic sequence.
    3. CThe result of this endonuclease is blunt ends.
    4. DThey degrade DNA by subsequently removing bases from each end.
    5. EThey cut DNA only at sites in specific nucleotide sequences with a two-fold axis of symmetry.
31. 31All are necessary for restriction endonuclease mapping of DNA molecules EXCEPT

    1. ADetermining the 5'- and/or 3'-ends of the molecule.
    2. BElectrophoresis of fragments.
    3. CHydrolysis with two or more endonucleases.
    4. DKnowing where each endonuclease hydrolyzes.
    5. EAll are true.
32. 32If a restriction site of 6 bases starts with 5’-TGG, what are the last three bases in the sequence?

    1. A5’-ACC-3’
    2. B5’-GGT-3’
    3. C5’-CCA-3’
    4. D5’-TGG-3’
    5. Enone of the above
33. 33Inosine, one of the common alternative bases found in RNA, is shown below. How would inosine form hydrogen bonds in a double helical section of RNA?
    

    1. A1 H-bond donor group, 0 H-bond acceptor groups
    2. B0 H-bond donor groups, 1 H-bond acceptor group
    3. C1 H-bond donor group, 1 H-bond acceptor group
    4. D2 H-bond donor groups, 1 H-bond acceptor group
    5. E1 H-bond donor group, 2 H-bond acceptor groups
34. 34Which of the following restriction sites would provide staggered 3’ends? The restriction site in each sequence is shown with an arrow.
    

    1. A5’-T/TCGAA-3’
    2. B5’-GTT/AAC-3’
    3. C5’-CCC/GGG-3’
    4. D5’-CTGCA/G-3’
    5. Enone of the above
35. 35Which of the following explains why it is often easier to sequence a gene rather than sequence the corresponding protein?

    1. ADNA sequencing can be performed on picogram quantities of DNA
    2. BDNA is composed of only 4 different monomers while proteins are composed of 20 different monomers
    3. Crestriction endonucleases can be used to cut DNA at specific sequences to generate DNA fragments that can easily be sequenced
    4. Dall of the above
    5. Eboth B and C are correct
36. 36Which of the following statements correctly describes the process of DNA sequencing by chain termination?
    

    1. Athe enzyme DNA polymerase is used to form a primer that binds to the template DNA
    2. Bin order to effectively sequence the DNA, the dideoxynucleotides must be present at a higher concentration than the deoxynucleotides
    3. Cthe use of 4 unique fluorescent labels attached to the dideoxynucleotides allows for a single reaction to be run
    4. Dthe dideoxynucleotides lack a 5'-OH and therefore can not serve as acceptors in nucleotide addition
    5. Eboth B and C are correct
37. 37How is a fluorescent tag that is unique for each nucleotide incorporated into the newly synthesized DNA using the chain termination protocol for DNA sequencing?
    

    1. AEach of the ddNTPs is labeled with a specific fluorophore
    2. BThe primer strand is labeled with a specific fluorophore
    3. CThe template strand is labeled prior to the experiment with complimentary fluorophores
    4. DThe 5'-end is labeled with a fluorophore.
    5. EAll dNTPs are labeled with a fluorophore
38. 38All are true for DNA polymerase EXCEPT:

    1. Arequires a primer with a free 5'-OH end, but the 3'-end may be phosphorylated.
    2. Bcopies the sequence of nucleotides of one strand to form a new second strand.
    3. Ccopies the sequence of nucleotides of one strand in a complementary fashion.
    4. Dgenerates dsDNA from ssDNA
    5. Esynthesizes new strands by adding successive nucleotides in the 5'3' direction.
39. 39DNA double helix structure is stabilized by all of the following EXCEPT:

    1. Athe sugar-phosphate backbones are oriented in opposite directions.
    2. Bthe glycosidic bonds holding paired bases are directly across the helix from one another.
    3. Ccations such as Mg2+ bind to the anionic phosphates.
    4. Dbases stack together through hydrophobic interactions and van der Waals forces.
    5. Eappropriate base pairing builds a polymer whose external dimensions are uniform.
40. 40All of the following are characteristics for in vitro DNA synthesis EXCEPT:

    1. ADNA polymerase adds nucleotides in a 5'3' direction.
    2. BThe primer strand of DNA determines the nucleotides added.
    3. CCorrect hydrogen bonding is the primary check of the newly synthesized DNA.
    4. DA primer strand must contain a free 3'-OH.
    5. EDNA polymerase copies the complementary strand of DNA.
41. 41Double helical DNA:RNA hybrids and double-stranded regions of RNA chains often assume an:

    1. AA-like conformation.
    2. BB-like conformation.
    3. CZ-like conformation.
    4. Dall of the above.
    5. Enone of the above.
42. 42DNA intercalating agents include all of the following EXCEPT:

    1. Aethidium bromide.
    2. Bactinomycin D.
    3. Cacridine orange.
    4. Dstreptomycin.
    5. Eall are true.
43. 43The hyperchromic shift that occurs when dsDNA is ____ is a(n) ____ in absorption at ____ nm.

    1. Amethylated; increase; 220
    2. Bmethylated; decrease; 260
    3. Cdenatured; decrease; 260
    4. Ddenatured; increase; 260
    5. Emelted; decrease; 280
44. 44The higher the ____ content of a DNA, the ____ the melting temperature, and the ____ the ionic strength, the ____ the melting temperature.

    1. AG:C; higher; higher; lower
    2. BG:C; lower; higher; lower
    3. CG:C; higher; lower; lower
    4. DA:T; higher; higher; lower
    5. EA:T; lower; lower; higher
45. 45Urea and formamide are agents that denature dsDNA by
    

    1. Aintercalating between base pairs and disrupting va
    2. Bforming ionic bonds with the backbone phosphates.
    3. Ccompeting effectively with the H-bonding between the base pairs.
    4. Dchanging the pH to cause hydrolysis.
    5. Enone are true
46. 46ssDNA will renature requiring ____ of the DNA strands into a dsDNA and this is called ____ which occurs best if the temperature is ____ Tm but warm enough to promote diffusion of the DNA molecules.
    

    1. Ahydrolysis; reannealing; below
    2. Breassociation; reannealing; below
    3. Creassociation; melting; above
    4. Dcomplementing; solidifying; below
    5. Enone are true
47. 47Which of the following enzymes introduces negative supercoils into DNA?

    1. ADNA polymerase
    2. BDNA gyrase
    3. CDNA ligase
    4. Dprimase
    5. EDNA photolyase
48. 48B-DNA is characterized by which of the following?
    

    1. A12 base pairs per helix turn
    2. Bhelix axis runs through the minor groove
    3. Ca wide major groove an narrow minor groove
    4. Dright-handed helix
    5. Eboth C and D are correct
49. 49Nucleic acid hybridization is a commonly employed procedure in molecular biology to investigate all EXCEPT:
    

    1. Aevolutionary relationships.
    2. Bspecific genes against a vast background.
    3. Cspecific probe based isolation of genes.
    4. Dquantify gene expression.
    5. Eall are true.
50. 50Naturally occurring, self-replicating, extra-chromosomal DNA molecules found in bacteria that carry genes specifying novel metabolic capacity advantageous to the bacterium are called:
    

    1. Aprobes.
    2. Bcruciform.
    3. Ctoroidal DNA.
    4. Dplasmids.
    5. Eall of the above.
51. 51DNA ____ is analogous to twisting or untwisting a two stranded rope so that it is torsionally stressed.

    1. Abuoyant density
    2. Bhairpin turn
    3. Ccloverleaf
    4. Dsupercoiling
    5. Eall of the above
52. 52All are true for linking number EXCEPT:

    1. AIt is a basic parameter characterizing supercoiled DNA.
    2. BL = T + W.
    3. CIt is the number of times that two strands are intertwined providing both strands remain covalently intact.
    4. DL = 40 in a relaxed circular DNA duplex of 400 bp.
    5. EAll are true.
53. 53The function of DNA topoisomerases is:
    

    1. Apackaging DNA into nucleosomes.
    2. Bforming cruciform DNA.
    3. Cunwinding G:C rich areas in DNA.
    4. Dbreaking one or more strands of DNA, winding them tighter or looser, and rejoining the ends.
    5. Epromoting DNA hybridization.
54. 54All are characteristics of DNA gyrase in E.coli EXCEPT:
    

    1. AIt hydrolyzes ATP during its reaction mechanism.
    2. BIt cuts both strands of a dsDNA.
    3. CIt works to induce negative supercoiling in DNA.
    4. DIt is classified as a topoisomerase.
    5. EAll are true.
55. 55DNA sequences that are inverted repeats, or ____, have the potential to form a ____ structure known as a ____ if the normal ____ base pairing is replaced by ____ pairing

    1. Aprobes; secondary; cruciform; interstrand; intrastrand
    2. Bpalindromes; tertiary; cruciform; interstrand; intrastrand
    3. Ccruciforms; secondary; palindrome; intrastrand; interstrand
    4. Dpalindromes; tertiary; cruciform; intrastrand; interstrand
    5. Enone are true.
56. 56All are properties of nucleosomes EXCEPT:

    1. Aprotein spools neatly wrapped with DNA.
    2. Bfundamental structural unit in chromatin.
    3. Cprotein spools made up of pairs of histones H2A, H2B, H3 and H4 octameric aggregates.
    4. DDNA binds histones by ionic bonds of positively charged amino acids and the negative charged phosphate groups.
    5. Eall are true.
57. 57Histones are rich in the amino acids ____, and interact with DNA via ____.

    1. Aalanine and glycine; covalent bonds
    2. Bglutamic acid and aspartic acid; hydrogen bonds
    3. Cglutamic acid and aspartic acid; ionic bonds
    4. Dlysine and arginine; hydrogen bonds
    5. Elysine and arginine; ionic bonds
58. 58Individual amino acids are attached to their corresponding tRNAs:

    1. Athrough an ester linkage to the 3'-OH in the acceptor stem.
    2. Bthrough an amide linkage to the anticodon loop.
    3. Cthrough an amide linkage to the adenine ring at the 3'end of the tRNA.
    4. Dthrough a phosphoester linkage to the 5' end of the tRNA.
    5. ENone of the above.
59. 59All are secondary structure components of tRNA EXCEPT:

    1. Aacceptor stem.
    2. BD loop.
    3. CAnticodon loop.
    4. DAll are true.
60. 60The major interactions that fold components of the secondary structure of tRNA together and bend the cloverleaf into a stable L-shaped tertiary form are:

    1. Ahydrophobic interactions.
    2. Bbase-pairing interactions.
    3. Cionic interactions.
    4. Delectrostatic interactions.
    5. Eboth a and b.
61. 61rRNA strands exhibit which of the following:
    

    1. Ainstrastrand sequence complementarity
    2. Bhighly folded patterns including many stem-loop structures
    3. Can anticodon loop
    4. Dboth a and b
    5. Ea, b and c
62. 62Phylogenetic comparisons of secondary structures of rRNAs from a variety of species revels ____ structures and ____ nucleotide sequences of the rRNAs themselves.
    

    1. Astrikingly similar; high degree of similarity
    2. Bstrikingly similar; low degree of similarity
    3. Cdissimilar; high degree of similarity
    4. Ddissimilar; low degree of similarity
    5. Enone of the above
63. 63Which of the following histone proteins has only one copy per nucleosome?

    1. AH1
    2. BH2A
    3. CH2B
    4. DH3
    5. EH4
64. 64The dimethoxytrityl (DMTr) group protects which functional group during synthetic DNA synthesis?

    1. Athe primary amine group of adenine and guanine
    2. Bthe primary amine group of cytosine
    3. Cthe 5' hydroxyl of the deoxyribose
    4. Dboth A and B are correct
65. 65All are characteristic of plasmids EXCEPT:
    

    1. Anaturally occurring, circular extrachromosomal DNA.
    2. Bable to perpetuate themselves without a host organism.
    3. Cartificial plasmids can be constructed by restriction endonuclease digestion, insertion, and ligation.
    4. Dharbor genes for novel metabolic activities.
    5. Ean origin of replication must be included in the plasmid to facilitate propagation.
66. 66All are features of a plasmid useful for cloning EXCEPT:

    1. Aexpressed sequence tag.
    2. Ba cloning site.
    3. Ca replicator (origin of replication).
    4. Da selectable marker.
    5. Eall are features.
67. 67If the pBR322 were treated with PstI in order to insert a gene into the plasmid, which of the following would be correct regarding cells that were transformed with the resulting vector?

    1. Acells that contained the desired vector would be resistant to ampicillin but sensitive to tetracycline
    2. Bcells that contained the desired vector would be resistant to tetracycline but sensitive to ampicillin
    3. Ccells that contained the desired vector would be resistant to both ampicillin and tetracycline
    4. Dcells that contained the desired vector would be sensitive to both ampicillin and tetracycline
    5. Enone of the above
68. 68To position a gene in an expression vector downstream from a promoter (i.e., perform directional cloning), it is best to:

    1. Ause the largest plasmid available.
    2. Btreat the gene with DNase I.
    3. Crestrict both the gene and the plasmid with one restriction endonuclease and then screen all colonies for those that express the gene.
    4. Drestrict each end of the DNA fragment (gene) with a different restriction endonuclease and do likewise for the plasmid.
    5. Euse a vector with two sites for the same restriction endonuclease.
69. 69A method used to insert or transform cells with a plasmid is to:
    

    1. Aadd the DNA to bacterial cells that have been lightly treated with lysozyme to produce "holes" in the cell wall.
    2. Badd the DNA to a heated suspension of cells at 42C.
    3. Ctreat the bacteria with Ca2+, add the DNA, and briefly heat to 42C.
    4. Dincubate the DNA with the cells overnight at 4C.
    5. Emixing plasmids with an extract of broken cells.
70. 70If DNA fragments of about 4 kb are to be cloned, which vector would be most useful?

    1. Aplasmid
    2. Bcosmid
    3. CYACs (yeast artificial chromosomes)
    4. Dbacteriophage lambda
    5. EE. coli chromosome
71. 71All are steps in the sequence for construction of a chimeric plasmid EXCEPT:

    1. Aannealing the ends of the vector and foreign DNA.
    2. Bcutting the source of the foreign DNA with a restriction endonuclease.
    3. Creannealing the ends of the vector back together.
    4. Dcutting the vector plasmid with the same restriction endonuclease.
    5. Enone of the above.
72. 72One of the problems with plasmids like pUR278 is that there is no true marker for determining whether or not the plasmid contains the inserted gene since the cloning site does not lie within any specific gene. Which of the following would be an extremely useful tool for rapid selection of those bacteria that have taken up a plasmid with the desired DNA insert?
    

    1. Alook for the production of the lacZ gene by adding X-gal to the growth medium
    2. Binclude the gene for a fluorescent protein such as GFP in the inserted DNA
    3. Cafter ligating the DNA insert and plasmid, separate the mixture of DNA molecules by agarose gel electrophoresis to isolate the DNA molecule that corresponds to the size of the plasmid+insert
    4. Dlook for ampicillin resistance in the transformed cells
    5. Enone of the above would be effective
73. 73The advantages of using the pET plasmid system include ____.

    1. Agenes to be expressed are under the control of a T7 promoter
    2. Bthe T7 polymerase is slower than a typical E coli polymerase
    3. Cthe expressed protein never accounts for more than 5% of the total cell protein
    4. Dthe T7 polymerase is under the control of the lac operon and is thus only active when induced by an agent such as IPTG
    5. Eboth a and d are correct
74. 74Shuttle vectors have the property that they:

    1. Acontain promoters for the expression of the gene.
    2. Bhave origins of replication for two different cell types, usually bacteria and yeast.
    3. Care capable of incorporating very large DNA fragments.
    4. Dcontain more than one antibiotic resistant gene.
    5. Enone of the above
75. 75All are characteristic of YACs (yeast artificial chromosomes) EXCEPT:

    1. AYACs can successfully propagate DNA molecules of 2 megabase pairs in length.
    2. BYACs have been transferred into animals.
    3. CYACs must include a centromere.
    4. DYACs must include telomers.
    5. EAll are true.
76. 76A genomic DNA library is:

    1. Aa collection of short fragments from nuclear DNA digestion.
    2. Barrays of synthetic oligonucleotides used to select for a specific DNA.
    3. Ca set of cloned fragments that collectively represent the genes of a particular organism.
    4. Da short segment of DNA whose sequence is complementary to a portion of the DNA of interest.
    5. Ea circular DNA molecule of 1 kb to 200 kb found in bacteria and yeast cells.
77. 77A genomic DNA library is:

    1. Aa collection of short fragments from nuclear DNA digestion.
    2. Barrays of synthetic oligonucleotides used to select for a specific DNA.
    3. Ca set of cloned fragments that collectively represent the genes of a particular organism.
    4. Da short segment of DNA whose sequence is complementary to a portion of the DNA of interest.
    5. Ea circular DNA molecule of 1 kb to 200 kb found in bacteria and yeast cells.
78. 78The correct sequence for colony hybridization experiments is:
    
    A.
    A replica of the bacterial colonies is obtained on an absorbent disc.
    B.
    Autoradiography of the disc reveals probe complementary DNA.
    C.
    Host bacteria with plasmid are plated and allowed to grow overnight.
    D.
    The disc is treated with alkali.
    E.
    The disc is reacted with labeled probe.
    

    1. AA, C, E, B, D
    2. BC, A, E, D, B
    3. CC, E, A, B, D
    4. DC, A, E, B, D
    5. EC, A, D, E, B
79. 79In the Southern hybridization procedure, the gel after electrophoresis is treated with NaOH and then neutralized before blotting. What is the primary function of the alkaline treatment?
    

    1. AIt neutralizes any acid soluble impurities in the gel.
    2. BIt cleaves the DNA into smaller fragments to permit greater efficiency of transfer.
    3. CIt inactivates any restriction endonucleases that may be in the gel.
    4. DIt neutralizes any acidic phosphate groups that might prevent hybridization.
    5. EIt denatures the duplex DNA to single-stranded DNA (ssDNA).
80. 80All are true for cDNA libraries EXCEPT:
    

    1. Areverse transcriptase synthesizes a DNA strand complement of the mRNA templates.
    2. BmRNA templates are isolated using oligo (dA)-cellulose chromatography.
    3. Clinkers are added and the cDNA is cloned into suitable vectors.
    4. Dthe cDNA are copies from mRNA templates.
    5. Eall are true.
81. 81The correct sequence of procedures in the Southern blotting (hybridization) technique is:
    
    A.
    hybridization with radioactive probe.
    B.
    agarose gel electrophoresis and visualize bands.
    C.
    transfer (blot) to nitrocellulose filter.
    D.
    digest DNA with restriction nucleases.
    E.
    expose filter to X-ray film, develop and observe.
    

    1. AB, A, C, E, D
    2. BD, C, B, A, E
    3. CC, D, B, E, A
    4. DD, B, C, A, E
    5. EA, B, C, D, E
82. 82Looking at all of the genes that are activated during a major metabolic shift or during embryogenesis and development of organisms is called:

    1. Afractional expression.
    2. Bgenetic fractionation.
    3. Cfunctional genomics.
    4. Dmutagenesis.
    5. Enone of the above.
83. 83The study of all of the proteins expressed by a certain cell or tissue under specific conditions is called:
    

    1. Agenetics.
    2. Bproteomics.
    3. Cembryogenesis.
    4. Dmutagenesis.
    5. Eall of the above.
84. 84To express a eukaryotic protein in E. coli, the eukaryotic cDNA must be cloned in a(n) ____ that contains ____ and ____.
    

    1. Aexpression vector; promoter; ribosomal-binding site
    2. Bhybridization complex; promoter; transition start site
    3. CmRNA; ribosomal-binding site; promoter
    4. DmRNA; introns; exons
    5. Enone of the above
85. 85Hybrid proteins or fusion proteins are produced by:
    

    1. Aincubation of two proteins with a protease.
    2. Bexpression of genes coding for multiple proteins.
    3. Ctranslation of mRNAs without removing exons.
    4. Dtranslation of recombinant sequences from expression vectors carrying cDNA inserts cloned directly into the coding sequence of a vector-born protein-coding gene.
    5. Eall of the above.
86. 86Reporter genes such as those for green fluorescent protein (GFP) are found on many commercial plasmids. These genes are useful to determine:
    

    1. Aif the plasmid is in the host.
    2. Bif a gene is present in a library.
    3. Cif a foreign protein is being expressed on a vector.
    4. Dthe relative strength of a promoter sequence.
    5. Eall of the above.
87. 87Each cycle of amplification in PCR involves all of the steps EXCEPT:

    1. Athe addition of fresh dNTPs to the reaction mixture.
    2. Bannealing of oligodeoxyribonucleotide primers to DNA.
    3. Cthermal denaturation of the target duplex DNA.
    4. Dreaction with DNA polymerase at approximately 70C.
    5. Enone of the above.
88. 88RT-PCR differs from basic PCR in that:

    1. Areverse temperatures are used for annealing and transcription.
    2. Btranscription is reversed from 5' to 3' ends.
    3. Creverse transcriptase is used to synthesize a cDNA strand complementary to an RNA strand.
    4. Dreverse transcripase is used to synthesize an RNA strand from the DNA strand.
    5. Enone of the above.
89. 89In vitro ____ makes it possible to alter the nucleotide sequence of a cloned gene systematically.

    1. Aprotein synthesis
    2. BmRNA synthesis
    3. Chybridization
    4. Dmutagenesis
    5. Eall are true
90. 90Which of the following is the appropriate source of the DNA polymerase included in the PCR reaction mixture?

    1. AE. coli
    2. Bbacteriophage T4
    3. CThermus aquaticus
    4. DDrosophila melanogaster
    5. EHuman
91. 91What would be the 9-residue primer used to amplify:
    5'-ATCGACGTTACGCTACATAGCATAAGGCTT-3'
    

    1. A5'-TAGCTGCAA-3'
    2. B5'-AAGCCTTAT-3'
    3. C5'-UAGCUGCAA-3'
    4. D5'-AAGCCUUAU-3'
    5. E5'-TGCGATGTA-3'
92. 92PCR-based mutagenesis is used to create

    1. Amutant strains of an eukaryotic organism.
    2. Bgenerally modified plasmid vectors.
    3. Cmutant bacterial strains.
    4. Dmutant DNA libraries.
    5. Especifically altered proteins.
93. 93How does RNA interference function?
    

    1. AsiRNA binds to genes and prevents transcription
    2. Ba single strand of the siRNA binds to the gene transcript, preventing translation
    3. Cthe double stranded siRNA binds to mRNA to prevent ribosomal association
    4. DsiRNA binds to RNA polymerase preventing mRNA production
    5. Enone of the above
94. 94The most promising vector for human gene therapy is ____.
    

    1. Ayeast
    2. BE coli
    3. Chuman papilloma virus
    4. Dadenovirus
    5. Ebacteriophage 
95. 95All are strategies for human gene therapy EXCEPT:
    

    1. Ause of expression cassettes.
    2. Bincorporation into expression vectors.
    3. Ctransfer into patient cells.
    4. Dintroduction of transformed stem cells.
    5. Eall are true.
96. 96The original development of PCR did not use the Taq polymerase. What is the reason that the Taq polymerase is currently used?
    

    1. Athe DNA melting step at 95°C would cause denaturation of most DNA polymerases from other organisms
    2. Bthe Taq polymerase is one of the most rapid DNA polymerase enzymes known and is therefore extremely useful for PCR
    3. Cthe original method of PCR required that DNA polymerase be added prior to each round of elongation, something that is not conducive to automation
    4. Dthe Taq polymerase is the only DNA polymerase that will allow production of 2n amounts of DNA (where n=number of cycles)
    5. Eboth A and C are corect
97. 97In a DNA microarray, how many different oligonucleotides can be produced if each oligonucleotide is 20 nucleotides long?

    1. A4^20
    2. B20^4
    3. C80
    4. D20
    5. Enone of the above
98. 98Which of the following describes the major utility of a eukaryotic cDNA library if one is trying to express a protein present in a eukaryotic cell?
    

    1. Athe library represents all genes that were actively expressed at a specific time
    2. Bthe genes lack introns and thus can be expressed by bacterial expression systems
    3. CcDNA libraries are readily available
    4. Dall of the above are correct
    5. Eboth A and B are correct
99. 99All are distinctive features of enzymes EXCEPT:

    1. Aregulation.
    2. Bcatalytic activity.
    3. Cability to change G.
    4. Dspecificity.
    5. Enone is true.
100. 100Enzymes work by:
     

     1. Aproviding an alternate reaction pathway
     2. Bincreasing the spontaneity (G) of the reaction
     3. Clowering the activation energy of the reaction
     4. Daltering the concentration of the reactants to achieve a favorable G
     5. Eproceeding in only one direction, from reactants to products
101. 101Which of the following statements is true regarding enzyme pathways?
     

     1. Athe most effective way to control a pathway is to regulate every enzyme in the pathway
     2. Ban enzyme pathway always proceeds in only one direction, never in reverse
     3. Ca regulatory enzyme is regulated only by molecules within the given pathway
     4. Dmetabolic pathways are necessary since enzymes usually catalyze only one specific reaction
     5. Enone of the above are true
102. 102If the rate constant for the enzyme catalyzed reaction is 2  105/sec and the rate constant for the uncatalyzed reaction is 2  106/sec, the catalytic power of the enzyme is:
     

     1. A10^11
     2. B2x10^11
     3. C10
     4. D2x10
103. 103An enzyme's specificity can be due to:

     1. Athe ratio of catalyzed rate to the uncatalyzed rate of reaction.
     2. Bmolecular recognition based on structural complementarity.
     3. Camount of enzyme produced by the cell.
     4. Damount of substrate available.
     5. Emetabolic activators.
104. 104The specific site on the enzyme where ____ binds and catalysis occurs is called the ____ site.
     

     1. Acoenzyme; substrate
     2. Bsubstrate; active
     3. Ccoenzyme; regulatory
     4. Dregulatory; active
     5. Enone of the above
105. 105The trivial term for an enzyme that moves a functional group from one place to another on the substrate is ___________,
     

     1. Aisomerase
     2. Boxidoreductase
     3. Cprotease
     4. Dkinase
     5. Ecatalase
106. 106All of the following are properties of a coenzyme EXCEPT:

     1. AThey are usually actively involved in the catalytic reaction of the enzyme.
     2. BThey tend to be stable to heat.
     3. CThey can serve as intermediate carriers of functional groups.
     4. DThey are protein components.
     5. EThey may contain vitamins as part of their structure.
107. 107The catalytically active complex of an apoenzyme and its prosthetic group is referred to a(n) ____.

     1. Acatalytic duo
     2. Bholoenzyme
     3. Cprosthetic enzyme
     4. Ddimeric enzyme
     5. Enone of the above
108. 108What reaction would NOT proceed via bimolecular elementary steps?

     1. AC + D ->  T + U
     2. BA reaction with a rate constant in the units of s1.
     3. C2A ->  D + E
     4. DA reaction with a molecularity of 2.
     5. EA reaction with a rate constant in the units of M1s1.
109. 109The free energy of activation, G, is defined as:

     1. AThe average free energy of the product formed.
     2. BThe rate of a chemical reaction in relationship to the concentration of reactant molecules.
     3. CThe energy required to raise the average energy of one mole of reactant to the transition state energy.
     4. DThe amount of energy released by a spontaneous reaction.
     5. EThe lowest point on a free energy diagram.
110. 110All of the following are true statements about the transition state of a reaction EXCEPT:

     1. AThe transition state is not an appropriate indication of the rate of a reaction.
     2. BThe transition state is located at the height of a free energy diagram.
     3. CThe energy required to raise the average energy of one mole of reactant to the transition state is the free energy of activation.
     4. DReaching the transition state indicates that there is a high probability that the reaction will occur.
     5. EThe transition state energy level is the sum of the energy levels of the reactants and products.
111. 111How do catalysts work to accelerate a chemical reaction?
     

     1. AThey raise the average energy of the reactants.
     2. BThey provide a means of acceleration by being completely consumed in the reaction.
     3. CThey lower the energy of activation.
     4. DThey lower the overall free energy change of the reaction.
     5. EThey raise the overall free energy change of the reaction.
112. 112All are true for catalysts EXCEPT:
     

     1. AThey work by lowering the energy of activation.
     2. BThe average energy of the reaction is unchanged.
     3. CThey combine transiently with the reactants promoting a reactive transition state condition.
     4. DThey are regenerated after each reaction cycle.
     5. EAll are true.
113. 113When every enzyme molecule in the reaction mixture has its substrate-binding site occupied by substrate, the kinetics become ____-order, and the velocity is ____.
     

     1. Azero; Vmax
     2. Bfirst; Vmax
     3. Csecond; Vmax/2
     4. Dzero; Vmax/2
     5. Efirst; Vmax/2
114. 114Which of the following is true regarding the Briggs and Haldane steady state assumption?
     

     1. AThe concentration of the enzyme-substrate complex reaches a constant value even in a dynamic system.
     2. BThe enzyme-substrate complex will always dissociate to form E + P.
115. 115Which statement is correct about the Michaelis-Menten constant, Km, for the kinetic mechanism below?

     1. AIt is numerically equal to the substrate concentration required to achieve one half the maximum velocity.
     2. BIts defined as Km = k1/(k1 + k2).
     3. CIt is approximately equal to the dissociation constant for the enzyme-substrate complex to E + P.
     4. DThe value of Km is constant for an enzyme regardless of the specific substrate molecule used to determine it.
     5. EIts numeric value has the units of moles1.
116. 116All of the following statements are true about the relationships between [S], Km and Vmax EXCEPT:
     

     1. AAs the [S] is increased, v approaches the limiting value, Vmax.
     2. BKm = Vmax/2.
     3. CThe rate of the reaction, v, follows a first order rate equation
        v = K'[A] and K' = Vmax/Km.
     4. DThe rate of product formed, v, is at Vmax when [S] >> Km.
     5. EKm and Vmax assist in finding the rate of the enzyme catalyzed reaction only if the reaction is irreversible.
117. 117If an enzyme has a Vmax of 15 mM/min, what is the velocity if the substrate is present at 1/5 of the Km?
     

     1. A12 mM/min
     2. B6 mM/min
     3. C3 mM/min
     4. D2.5 mM/min
     5. Ecannot be determined from given information
118. 118For an enzyme-catalyzed reaction, the initial velocity was determined at two different concentrations of the substrate. Which of the following would be closest to the value of Km?
     

     1. A0.17 mM
     2. B5.7 mM
     3. C2.7 mM
     4. D0.60 mM
     5. E1.7mM
119. 119For an enzyme-catalyzed reaction, the initial velocity was determined at two different concentrations of the substrate. Which of the following would be closest to the value of Vmax?
     

     1. A4.7 mM/min
     2. B0.67 mM/min
     3. C3.19 mM/min
     4. D1.5 mM/min
     5. E0.32 mM/min
120. 120All are true for kcat EXCEPT

     1. Areferred to as the molecular activity of the enzyme.
     2. Bcalled the turnover number of the enzyme.
     3. Cmeasures the maximal catalytic activity or kinetic efficiency of an enzyme.
     4. Ddefines the number of substrate molecules converted into product/enzyme molecule/unit of time when the enzyme is saturated with substrate.
     5. Eall are true
121. 121Which of the following statements is NOT characteristic of kcat/Km

     1. AIt corresponds to a second-order rate constant.
     2. BIt provides an excellent parameter for comparison of the catalytic efficiency of enzymes.
     3. CIt reflects the property of the enzyme when substrate concentration is at saturation.
     4. DThe upper limit for the kcat/Km value is fixed by the diffusion-controlled limit for reactions, which is 109 M1 s1.
     5. EIt is also referred to as the turnover number.
122. 122The International Units of an enzyme are based on the:

     1. Aratio of enzyme to other proteins.
     2. Bmicromoles of product formed per minute.
     3. Cmoles of substrate reacted.
     4. Dmicromoles of product produced at Vmax/2.
     5. Enone of the above.
123. 123In transforming the Michaelis-Menten equation into a straight line equation, y = mx + b, the Lineweaver-Burk double reciprocal plot, which of the following is NOT a true representation?
     

     1. Aslope = Km/Vmax
     2. By-intercept is 1/Vmax
     3. Cx-intercept is 1/Km
     4. Dy = 1/V
     5. Ex = 1/[S]
124. 124The pH optimum of an enzyme is:
     

     1. Aalways between pH 6-8.
     2. Bnearly the same for all enzymes.
     3. Coften dependent upon the amino acids that form the active site
     4. Doccurs when there is optimum secondary and tertiary structure in the active site of the enzyme.
     5. Eboth C and D are correct
125. 125All are true for inhibitor I if it is a competitive inhibitor EXCEPT:

     1. AIt binds a site other than the active site.
     2. BIt is structurally similar to the substrate.
     3. CEI does not give rise to E + P.
     4. DFor a given [I], v decreases.
     5. EAt some point, S can displace all of I on E.
126. 126 All of the following statements about competitive inhibition are correct EXCEPT:

     1. ACompetitive inhibitors are often chemical analogs of the substrate.
     2. BFor a group-specific enzyme, one substrate would be a competitive inhibitor of reactions of the other possible substrate.
     3. CSometimes a product of an enzyme-catalyzed reaction is a competitive inhibitor of its own production.
     4. DIn the presence of a competitive inhibitor, the apparent Km would be altered and Vmax would be decreased.
     5. ECompetitive inhibitors usually interact with the enzyme at the binding site for a substrate.
127. 127Malonate inhibition of succinate dehydrogenase is an example of:
     

     1. Anoncompetitive inhibition.
     2. Bcompetitive inhibition.
     3. Cmixed noncompetitive inhibition.
     4. Dirreversible inhibition.
     5. Euncompetitive inhibition.
128. 128All of the following statements about noncompetitive inhibition are true EXCEPT:

     1. AThey interact with the enzyme as well as the enzyme-substrate complex.
     2. BIncreasing the concentration of [S] can overcome the inhibition.
     3. CThe Vmax value does not remain the same as for a reaction that is not inhibited.
     4. DThe inhibitor can cause a conformational change in the enzyme.
     5. EThe inhibitor binds to a different site than does the substrate.
129. 129Identify the type of reaction that would give the following graph:
     

     1. Adouble displacement bisubstrate reaction.
     2. Bcompetitively inhibited reaction.
     3. Csingle displacement bisubstrate reaction.
     4. Dmixed noncompetitively inhibited reaction.
     5. Epure noncompetitively inhibited reaction.
130. 130A plot of 1/V vs. 1/[S] for an enzyme catalyzed reaction gave a line with an equation of y = 0.5x + 0.2. The same enzyme with an inhibitor present gave a line with an equation of y = 1.1x + 0.2. Which of the following statements is true?
     

     1. Athe type of inhibition is competitive
     2. Bthe type of inhibition is noncompetitive
     3. Cthe type of inhibition is uncompetitive
     4. Dthe Vmax with the inhibitor present has decreased
     5. Ethe Km with the inhibitor present has decreased
131. 131In uncompetitive inhibition:

     1. AI combines only with ES.
     2. BI combines only with E.
     3. CI combines with E and ES.
     4. DI combines with EP.
     5. Enone of the above.
132. 132Penicillin is an example of a mechanism-based enzyme inactivator and is a(n):

     1. Acompetitive inhibitor.
     2. Bnoncompetitive inhibitor.
     3. Csuicide substrate.
     4. Duncompetitive inhibitor.
     5. Enone of the above.
133. 133Penicillin and other -lactam antibiotics form a covalent bond to the enzyme glycoprotein transpeptidase. What type of bond is formed?
     

     1. Aester
     2. Bthioester
     3. Camide
     4. Dphosphate
     5. Enone of the above
134. 134Sildenafil citrate (Viagra) was developed as an inhibitor of:

     1. Aacid phosphatases.
     2. BcAMP phosphodiesterases.
     3. Cglycogen phosphorylase.
     4. DcGMP phosphodiesterases.
     5. Etestosterone reductase.
135. 135In the enzyme catalyzed reaction sequence below, can the E-PO4 intermediate be predicted and why?
     

     1. AYes, the mechanism is a double-displacement reaction.
     2. BYes, the reaction fits the ping-pong model.
     3. CNo, the reaction is random single-displacement.
     4. DNo, the reaction is double-displacement.
     5. ENone of the above.
136. 136In the reaction mechanism below, ____ are competitive for binding to free enzyme E.

     1. AP & A
     2. BA & B
     3. CB & Q
     4. DQ & A
     5. EALL OF THE ABOVE
137. 137In the glutamate:aspartate aminotransferase catalyzed reaction mechanism, glutamate would react with ____ to form alpha -ketoglutarate.
     

     1. AE-pyridoxal phosphate complex
     2. BE-pyridoxamine phosphate complex
     3. Caspartate
     4. Doxaloacetate
     5. Enone of the above
138. 138All are characteristics of ordered single-displacement reactions EXCEPT:
     

     1. ALineweaver-Burk plots with lines that intersect to the left of the 1/v axis.
     2. Ba chemically modified enzyme-intermediate.
     3. Cthe lack of any exchange reaction activity.
     4. Dthe lack of competitive substrate effects.
     5. Esingle substrate initial binding activity.
139. 139All are characteristics of ribozymes EXCEPT:
     

     1. AThey are critical for removal of introns from mRNA
     2. BThey are substrate specific.
     3. CThey enhance the reaction rate.
     4. DOn the ribosome, they catalyze the peptidyl transferase reaction
     5. EAll are true.
140. 140Catalytic antibodies, also called ____, are generated against an antigen that is:
     

     1. Aabzymes; an analog of the transition-state intermediate in the reaction.
     2. Babzymes; the substrate of the reaction.
     3. Czymogens; an analog of the product of the reaction.
     4. Dholoenzyme; an analog of the transition-state intermediate in the reaction.
     5. Enone of the above.
141. 141All are characteristics of the enzyme hexokinase EXCEPT:
     

     1. AIt is not highly specific and will catalyze phosphorylation of a number of hexoses at the six position.
     2. BHexoses bind the active site and induce a solvent inaccessible fit to the hexose.
     3. CGlycerol may fit into the active site, but it does not bind to induce a conformational change necessary for catalysis.
     4. DWhen a hexose binds the active site, the active site is modified to promote changes in the substrate to a transitional-state intermediate.
     5. EAll are true.
142. 142An enzymatic reaction has a Vmax of 30x10^-6 M/min and a Km of 50 M. If the concentration of the substrate is 25 M, which of the following is true?

     1. Athe velocity will be 7.5 x10^-6M/min
     2. Bthe velocity will be 20 x10^-6 M/min
     3. Cthe velocity will be 10 x10^-6M/min
     4. Dthe velocity will be 25 x10^-6 M/min
     5. Ethe velocity will be 15 x10^-6 M/min
143. 143Which of the following statements regarding inhibitors is correct?

     1. Aa transition state analog binds covalently to the enzyme
     2. Ba non-competitive inhibitor causes an increase in the Vmax
     3. Cthe presence of a competitive inhibitor can be overcome by addition of more inhibitor
     4. Da competitive inhibitor results in a higher apparent Km value
     5. Enone of the above are correct
144. 144Carbonic anhydrase has two substrates, carbon dioxide and bicarbonate, which are both converted to carbonic acid. Kinetic data for each is given below. While determining the kinetics of HCO3- as a substrate, how would the addition of CO2 effect the reaction if the rate were measured by the disappearance of bicarbonate?

     1. ACO2 would increase the activity of the enzyme
     2. BCO2 would cause an apparent decrease in the Km for HCO3-
     3. CCO2 would act as a noncompetitive inhibitor
     4. DCO2 would act as a competitive inhibitor
     5. Enone of the above
145. 145Carbonic anhydrase has two substrates, carbon dioxide and bicarbonate, which are both converted to carbonic acid. Kinetic data for each is given below. Typical values for Kcat/Km range from less than 1 mM-1sec-1 to as high as 2.8105 mM-1sec-1. What can be said about the Kcat/Km for CO2?
     

     1. Acarbonic anhydrase binds CO2 well but poorly converts it to carbonic acid
     2. Bcarbonic anhydrase binds CO2 poorly but effectively converts it to carbonic acid
     3. Ccarbonic anhydrase binds CO2 well and converts it to carbonic acid very well
     4. Dcarbonic anhydrase binds CO2 poorly and poorly converts it to carbonic acid
     5. Ethe data above is useless for this question
146. 146Enzymes have active sites which have the greatest complementarity to the

     1. Asubstrate.
     2. Btransition state.
     3. Cproduct.
     4. Dboth substrate and product.
     5. Enone of the above.
147. 147All are true for the enzyme-transition state complex EXCEPT:

     1. AIt is designated as EX.
     2. BThe enzyme stabilizes the transition-state complex more than it stabilizes the substrate complex.
     3. CThe enzyme is "designed" to bind the transition-state structure more tightly than the substrate or product.
     4. DThe energy barrier between ES and EX is less than the energy barrier between S and X.
     5. EAll are true
148. 148All are catalytic mechanisms or factors that contribute to the performance of enzymes EXCEPT

     1. Aentropy gain in ES formation.
     2. Bcovalent catalysis.
     3. Cgeneral acid or base catalysis.
     4. Dproximity and orientation.
     5. Eall are true.
149. 149Which of the following statements regarding enzymes and transition states is true?

     1. Astabilization of the transition state must be less than stabilization of ES for catalysis to occur
     2. Bbinding of substrate to an enzyme often causes strain, thus promoting transition state formation
     3. Cthe transition state conformation of an enzyme catalyzed reaction is identical to the conformation seen in the uncatalyzed transition state
     4. Dformation of the transition state always assures that the reaction will proceed to product
     5. Enone of the above are true
150. 150Because the enzymatic reaction rate is determined by the difference in energy between ES and ____, the tighter binding of the substrate, the ____ the rate of reaction.
     

     1. AS; higher
     2. BP; lower
     3. CEX; lower
     4. DEX; higher
     5. ES; lower
151. 151An enzyme-catalyzed reaction rate will be increased if the energy level of ES can be increased. Which of the following will not increase the energy level of ES?
     

     1. Adestabilization of ES by strain caused by non-covalent interactions between E and S.
     2. Bloss of entropy due to binding of E and S.
     3. Cdestabilization of ES by distortion.
     4. Ddestabilization of ES by solvation.
     5. Edestabilization of ES by electrostatic effects.
152. 152The transition state has an estimated life-time of about:

     1. Amicroseconds (10^6 s).
     2. Bnanoseconds (10^9 s).
     3. C(10^2 s).
     4. D(10^14 to 10^13 s).
     5. Emilliseconds (10^3 s).
153. 153The good transition state analog is one which would serve also as an extremely effective:

     1. Acompetitive inhibitor.
     2. Bnoncompetitive inhibitor.
     3. Callosteric inhibitor.
     4. Dmixed-noncompetitive inhibitor.
     5. Eirreversible inhibitor.
154. 154 Transition-state analogs are:
     

     1. Aapproximations of the transition state that bind more tightly than the substrate.
     2. Bcompounds that compete for the active site, but are not necessarily very similar to the substrate.
     3. Cstable molecules that can not be expected to resemble the true transition state too closely.
     4. Dstable chemically and structurally similar molecules to the transition state.
     5. Eall of the above.
155. 155Most covalent catalysis is carried out by enzymes using a:
     

     1. Aping-pong kinetic mechanism.
     2. Bsequential bisubstrate kinetic mechanism.
     3. Crandom bisubstrate kinetic mechanism.
     4. Dsimple unimolecular kinetic mechanism.
     5. Enone of the above.
156. 156Since enzymes are not rigid molecules but rather flexible proteins, which of the following may be attributed to this fact?
     

     1. Aactive sites are able to conform to the shape of the substrate
     2. Bcatalytic residues are oriented in such as way to aid in bond breakage and bond formation
     3. Cstrain is placed upon the substrate while it binds to the enzyme
     4. Dnear-attack conformations are achieved during formation of the transition state during an enzyme catalyzed reaction
     5. Eall of the above are correct
157. 157Which of the following amino acids would NOT provide a nucleophilic center for covalent catalysis?
     

     1. Aalanine
     2. Blysine
     3. Cglutamic acid
     4. Dserine
     5. Ecysteine
158. 158Because the pKa is near 7, ____ side-chains are often involved in general acid-base catalysis.

     1. Acysteine
     2. Baspartate
     3. Cglutamate
     4. Dlysine
     5. Ehistidine
159. 159All are true for low-barrier hydrogen bonds EXCEPT:

     1. AThe hydrogen is centered between the two heteroatoms.
     2. BThe interactions are more covalent.
     3. CThe bond order approaches 0.5 for both OH interactions.
     4. DThe barrier that the hydrogen atom must surmount to exchange oxygens becomes lower.
     5. EAll are true.
160. 160The catalytic mechanism below is an example of:

     1. Acovalent nucleophilic catalysis.
     2. Bcovalent electrophilic catalysis.
     3. Cspecific base catalysis.
     4. Dgeneral base catalysis.
     5. Elow barrier hydrogen bond catalysis.
161. 161Metal ion catalysis include all EXCEPT:

     1. Aincreased acidity of a nucleophile with an ionizable proton.
     2. Bmetal ion requirement to maintain the stable, native state of the enzyme.
     3. Cmetal binding weakly, perhaps only during the catalytic cycle.
     4. Delectrophilic catalysis, stabilizing the increased electron density or negative charge that can develop during a reaction.
     5. Eall are true.
162. 162The mechanism of chymotrypsin involves which of the following elements?

     1. Adeprotonation of an active site Asp residue by His to start the reaction
     2. Bformation of an acyl-enzyme intermediate that must be hydrolyzed to complete the reaction
     3. Cstabilization of the positively charged His by a Gln residue
     4. Ddirect deprotonation of water by His to generate a hydroxide ion for initiation of the reaction
     5. Eboth a and b occur
163. 163In the catalytic triad common to many serine proteases, _____ increases the basicity of _____, thus allowing deprotonation of _____ to serve as a nucleophile.

     1. ASer-His-Asp
     2. BHis-Ser-Asp
     3. CSer-His-His
     4. DAsp-His-Ser
     5. ECys-His-Ser
164. 164In the hydrolysis of p-nitrophenylacetate by chymotrypsin all of the following are correct EXCEPT:

     1. Athe first product is acetic acid.
     2. Ban acetyl-enzyme intermediate forms during the mechanism.
     3. Cattack of a water molecule on the acyl-enzyme intermediate yields the second product.
     4. Dthe active site contains a serine residue, an unprotonated histidine, and an unprotonated aspartate residue at pH 7.0 prior to binding the substrate.
     5. Enone of the above.
165. 165Organic fluorophosphates are ____ inhibitors of serine proteases such as chymotrypsin.

     1. Acompetitive
     2. Buncompetitive
     3. Cnoncompetitive
     4. Dirreversible
     5. Emixed noncompetitive
166. 166The initial bond formation in the covalent intermediate in the chymotrypsin catalyzed reaction is between:

     1. Aserine and the carbonyl carbon in the peptide backbone.
     2. Bserine and the nitrogen in the peptide backbone.
     3. Chistidine and the carbonyl carbon in the peptide backbone.
     4. Dhistidine and the nitrogen in the peptide backbone.
     5. Easpartate and the carbonyl carbon in the peptide backbone.
167. 167In the chymotrypsin reaction mechanism there is a low-barrier hydrogen bond (LBHB) formed between:

     1. AAsp102 and Ser195.
     2. BAsp102 and His57.
     3. CHis57 and Ser195.
     4. DSer195 and carbonyl oxygen in the peptide bond.
     5. ENone of the above.
168. 168Aspartate proteases display a variety of substrate specificities, but normally they are most active in cleavage of peptide bonds:
     

     1. Aon the carboxyl side of the basic amino acids.
     2. Bon the carboxyl side of aromatic amino acids.
     3. Con the carboxyl side of small, neutral residues.
     4. Dbetween two hydrophobic amino acid residues.
     5. Enone of the above.
169. 169The mechanism of aspartate protease catalysis is proposed to be:
     

     1. Acovalent nucleophilic catalysis.
     2. Bcovalent electrophilic catalysis.
     3. Cspecific base catalysis.
     4. Dgeneral base-general acid catalysis facilitated by a low barrier hydrogen bond.
     5. Eall of the above.
170. 170 HIV-1 protease is different from most mammalian aspartic acid proteases in that it has:
     

     1. Atwo subunits each with a two-aspartate active site.
     2. Btwo subunits each contributing an aspartate to the active site.
     3. Ctwo active sites on one protein.
     4. Dtwo subunits, one with an active site, and the other with a regulatory activity.
     5. Enone of the above.
171. 171Effective HIV-1 protease inhibitors should have all of the following characteristics EXCEPT:

     1. Aeffective delivery in sufficient quantities to the desired site(s) of action in the organism.
     2. Brelative specificity for the HIV-1 protease.
     3. Ca backbone OH group that forms a weak association with the two active-site carboxyl groups of the protease.
     4. Dresults in inhibiting the production of new virus particles in cells of infected patients.
     5. Ebroad spectrum enough to be effective against mutant viral forms.
172. 172Which of the following are relevant to the reaction catalyzed by chorismate mutase?

     1. Athe reaction involves a concerted intramolecular rearrangement of chorismate to prephenate during the synthesis of phenylalanine.
     2. Bthe enzyme catalyzed and uncatalyzed reactions follow almost identical routes
     3. Cthe enzymatic reaction is thought to involve transition state stabilization by 12 electrostatic and hydrogen bond interactions
     4. Dthe geometry of the enzyme active site is such that the difference in energy between ES and the near attack conformation is less than 1 kJ/mol
     5. Eall of the above are true
173. 173 Which of the following statements regarding enzymes is true?
     

     1. Astabilization of the transition state must be less than stabilization of ES for catalysis to occur
     2. Ban enzyme mechanism is vastly different from the uncatalyzed reaction
     3. Cbinding of substrate to an enzyme often causes strain, thus promoting transition state formation
     4. Da random single displacement mechanisms requires that substrates bind to the enzyme in a specific order
     5. Enone of the above
174. 174If the transition state of an enzyme catalyzed reaction contained a positive charge, which of the following amino acids would most likely be present in the active site to aid in transition state formation?
     

     1. ALys
     2. BVal
     3. CAsn
     4. DGlu
     5. ECys
175. 175If the substrate for an enzyme catalyzed reaction contained a negative charge, which of the following amino acids would most likely be present in the active site to provide electrostatic destabilization of the ES complex?
     

     1. AVal
     2. BAsp
     3. CArg
     4. DSer
     5. EGln
176. 176All of the following are correct statements about enzyme regulation EXCEPT:

     1. AEnzymes can be inhibited by the products they produce.
     2. BEnzymes can be inactivated by the addition of a functional group.
     3. CCoenzyme and substrate availability can regulate enzyme reaction rate.
     4. DThe reaction rate slows as equilibrium is approached.
     5. EThe activity of an enzyme is covalently affected by allosteric regulators.
177. 177All of the following are examples of a zymogen and its activating protease EXCEPT:

     1. Achymotrypsinogen and chymotrypsin.
     2. Bprocarboxypeptidase and elastase.
     3. Cproelastase and elastase.
     4. Dpepsinogen and pepsin.
     5. Etrypsinogen and trypsin.
178. 178Proinsulin is converted into insulin by:
     

     1. Aproteolytic excision of a specific peptide.
     2. Ballosteric binding of glucose.
     3. Cphosphorylation to the active form.
     4. Dremoval of phosphate by converter enzymes.
     5. Enone of the above.
179. 179Regulation of metabolism by activation of the gene encoding a particular enzyme is called ____.

     1. Acovalent modification
     2. Brepression
     3. Cinduction
     4. Dallosteric activation
     5. Enone of the above
180. 180Usually the quickest method of influencing an enzymatic activity is by:

     1. Aallosteric regulation.
     2. Bcovalent modification.
     3. Cenzyme induction.
     4. Dactivation of a zymogen.
     5. Eenzyme destruction.
181. 181Which of the following statements is correct regarding isozymes?

     1. Athey catalyze the same reaction but have vastly different structures
     2. Bthey are always monomeric proteins
     3. Ctheir differences are based upon the type of tissue in which they are present
     4. Dthey often respond to different inhibitors and activators
     5. Eboth c and d are correct
182. 182All are true about isozymes of lactate dehydrogenase (LDH) that are present in a number of different tissues EXCEPT:
     

     1. AThey have differing Km values for lactate.
     2. BThe amount of subunit phosphorylation differs.
     3. CThey have differing Km values for pyruvate.
     4. DThe ratios of A and B subunits differ depending upon the tissue type
     5. EThey have different kinetic parameters.
183. 183All are characteristic of allosteric enzymes EXCEPT:
     

     1. AEffectors may show stimulatory or inhibitory activity.
     2. BThey have multiple subunits.
     3. CThey obey Michaelis-Menten kinetics.
     4. DThe regulatory effect is by altering conformation and interaction of subunits.
     5. EBinding one subunit impacts binding of substrate to other subunits.
184. 184All are properties of regulatory enzymes EXCEPT:
     

     1. Apathway end-products may act as allosteric inhibitors.
     2. Bv vs [S] plots are sigmoid- or S-shaped.
     3. Csubstrate binding is cooperative.
     4. Dmonomeric enzymes with a single regulated active site.
     5. Emay be stimulated by allosteric activators.
185. 185Which of the following statements regarding enzyme regulation is true?

     1. Aaddition of an inhibitor to a V system results in kinetics similar to addition of a competitive inhibitor to a typical hyperbolic system
     2. Ballosteric effectors are always more powerful than covalent modification
     3. Caddition of an allosteric activator to a K system changes the plot of V vs. [S] from a sigmoidal curve to a more hyperbolic curve
     4. Dthe T state of an enzyme generally has more activity than the R state
     5. Enone of the above are true
186. 186When binding one equivalent of S to an allosteric protein enhances the binding of additional equivalents of S to the same protein molecule, it is termed a(n):

     1. Apositive heterotropic effector.
     2. Bpositive homotropic effector.
     3. Cnegative heterotropic effector.
     4. Dnegative homotropic effector.
     5. Enone of the above.
187. 187The presence of a negative allosteric effector on an allosteric protein would:
     

     1. Acause a shift to the left in the sigmoidal curve.
     2. Bincrease the number of R conformations.
     3. Cdecrease the cooperativity of the substrate.
     4. Draise the apparent value of the equilibrium constant, L.
     5. Eincrease the likelihood of the binding of S.
188. 188An enzyme that displays negative cooperativity has ____ activity when the substrate is present at concentrations ____ than the value of K0.5 when compared with enzymes that display no cooperativity.
     

     1. Aincreased; greater
     2. Bincreased; less
     3. Cdecreased; greater
     4. Ddecreased; less
     5. Eboth b and c are correct
189. 189The addition of an effector to an enzyme that acts as a K system of the MWC model causes the half-maximum velocity (K0.5) to ____ and Vmax to ____.
     

     1. Aremain constant; remain constant
     2. Bremain constant; change
     3. Cchange; remain constant
     4. Dchange; change
     5. Enone of the above
190. 190The function of glycogen phosphorylase is:

     1. Athe conversion of glucose-1-phosphate to glucose-6-phosphate.
     2. Bto break down ATP.
     3. Cto catalyze the phosphorolysis of glucose-1-phosphate from glycogen molecules.
     4. Dto inhibit the production of glucose-1-phosphate.
     5. Eto stimulate the build up of glycogen.
191. 191Characteristics of glycogen phosphorylase include all EXCEP

     1. Acovalently linked pyridoxal phosphate.
     2. Ban active site at the center of each of two identical subunits.
     3. Cregulatory phosphorylation site on a Ser residue.
     4. Dallosteric effector sites for ATP and glucose-6-phosphate.
     5. Eall are true.
192. 192For muscle glycogen phosphorylase, Pi (inorganic phosphate) is a:

     1. Apositive homotropic effector.
     2. Bnegative homotropic effector.
     3. Cpositive heterotropic effector.
     4. Dnegative heterotropic effector.
     5. Enone of the above.
193. 193The correct sequence for the hormone-activated enzymatic cascade that leads to activation of glycogen phosphorylase is:
     
     A.
     Phosphorylation to activate phosphorylase kinase
     B.
     Activation of G-protein
     C.
     Activation of adenylyl cyclase to produce cAMP
     D.
     Phosphorylation of glycogen phosphorylase
     E.
     cAMP activation of protein kinase A (PKA)
     

     1. AA, B, C, D, E
     2. BB, C, E, A, D
     3. CC, B, A, D, E
     4. DB, D, E, A, C
     5. EE, A, D, C, B
194. 194The G subunit of GTP-binding protein (G protein) has all of the following characteristics EXCEPT:

     1. Aactivates adenylyl cyclase.
     2. Bhormone-receptor complex promotes G release from G.
     3. Chas a very active GTPase activity.
     4. Dbinds GDP in the G complex.
     5. EGTP hydrolysis leads to G-adenylyl cyclase dissociation.
195. 195All are true for cAMP-dependent protein kinase EXCEPT:
     

     1. Aalso known as PKA.
     2. Bphosphorylase kinase is a substrate.
     3. Cconsists of a pair of catalytic subunits.
     4. Dtwo regulatory subunits block catalytic activity without cAMP binding.
     5. Ephosphorylates glycogen phosphorylase.
196. 196Glycogen phosphorylase displays allosteric activation and inhibition by multiple modes. Which of the following is a correct relation?
     

     1. Aphosphate: positive heterotropic effector
     2. BAMP: negative heterotropic effector
     3. CATP: positive heterotropic effector
     4. Dglucose-6-phosphate: negative heterotropic effector
     5. Ephosphorylation: covalent inhibitor
197. 197Adenylyl cyclase catalyzes the synthesis of cAMP, and cAMP hydrolysis is catalyzed by a 5'-phosphodiesterase. If caffeine inhibits 5'-phosphodiesterases, drinking a caffeinated beverage would ____ cAMP levels and ____ glycogen phosphorylase activity.
     

     1. Aincrease; decrease
     2. Bincrease; increase
     3. Cdecrease; decrease
     4. Ddecrease; increase
     5. Ehave no effect; have no effect
198. 198The polypeptide of myoglobin serves all of the following functions EXCEPT:

     1. Aprotects the heme iron from oxidation.
     2. Bcradles the heme group.
     3. Cprovides a pocket for O2 to fit.
     4. Dkeeps the heme iron in the ferric form.
     5. Enone of the above.
199. 199Which statement below about contrasting Hb and Mb is FALSE?

     1. AHb shows sigmoidal, whereas Mb shows hyperbolic oxygen saturation curves.
     2. BHb shows cooperativity, whereas Mb does not.
     3. CHb binds O2 more tightly than Mb.
     4. DOxygen binds to a ferrous ion in both proteins.
     5. EHb-oxygen binding is dependent on physiological changes in pH, whereas Mb-oxygen binding is not.
200. 200When O2 binds to heme in hemoglobin, the ____ ion is drawn into the plane of the ____ causing a conformational change that is transmitted to adjacent subunits enhancing the ____ for additional O2 binding.
     

     1. AMg2+; globin; planarity
     2. BFe3+; heme; folding
     3. CMg2+; globin; attraction
     4. DFe3+; porphyrin; affinity
     5. EFe2+; porphyrin; affinity

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Chemistry Test sobre BioChemistry, creado por Tiffany Nguyen el 17/10/2016.

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