Questions - Nucleic Acids

The compound that consists of ribose linked by an N-glycosidic bond to N-9 of adenine is:
A) a deoxyribonucleoside.
B) a purine nucleotide.
) a pyrimidine nucleotide.
!) adenosine monophosphate.
") adenosine.
A ma#or component of $NA but not of !NA is:
A) adenine.
B) cytosine.
) guanine.
!) thymine.
") uracil.
%hich one of the follo&ing is true of the pentoses found in nucleic acids'
A) -( and -) of the pentose are #oined to phosphate groups.
B) -( of the pentose is #oined to a nitrogenous base* and -) to a phosphate group.
) The bond that #oins nitrogenous bases to pentoses is an O-glycosidic bond.
!) The pentoses are al&ays in the -furanose forms.
") The straight-chain and ring forms undergo constant intercon+ersion.
The nucleic acid bases:
A) absorb ultra+iolet light maximally at ,-. nm.
B) are all about the same si/e.
) are relati+ely hydrophilic.
!) are roughly planar.
") can all stably base-pair &ith one another.
%hich of the follo&ing statements concerning the tautomeric forms of bases such as uracil is
correct'
A) The all-lactim form contains a ketone group.
B) The lactam form contains an alcohol group.
) The lactam form predominates at neutral p0.
!) They are geometric isomers.
") They are stereoisomers.
1n tissues that do not carry out de no+o synthesis* maintenance of an ade2uate supply of adenine
nucleotides:
A) occurs soley by adenine sal+age using A-3$T.
B) re2uires AT3 uptake from the blood.
) depends upon the action of nucleoside phosphorylase
!) is accomplished entirely by the action of adenylate kinase.
") in+ol+es hypoxanthine sal+age using 04-3$T.
%hat in+ol+e5s) reduction and clea+age of the nitrogen-containing ring
A. atabolism of guanine
B. atabolism of uracil
)) A only
-,) B only
6) Both A and B
7) Neither A or B
8rotic acid is an intermediate of:
A. atabolism of guanine
B. atabolism of uracil
)) A only
,) B only
6) Both A and B
7) Neither A or B
Thioredoxin is important for the:
A) con+ersion of A93 to AT3.
B) con+ersion of d:93 to dT93.
) con+ersion of a ribonucleotide to a deoxyribonucleotide.
!) inhibition of xanthine oxidase as a treatment for gout.
") degradation of nucleoprotein.
The follo&ing en/ymes are part of the catabolism of A93 to uric acid. The order of their use is:
). A deaminase
,. A nucleoside phosphorylase
6. A nucleotidase
7. ;anthine oxidase
A) )* ,* 6* 7
B) )* 6* ,* 7
) )* 7* ,* 6
!) 6* ,* )* 7
") 6* )* ,* 7
The foremost control of de no+o pyrimidine nucleotide synthesis is:
A) feedback inhibition of glutamine-3$33 amidotransferase.
B) feedback inhibition of aspartate transcarbamylase.
) a+ailability of N-acetyl glutamate.
!) substrate a+ailability.
") competiti+e inhibition of carbamoyl phosphate synthetase 11.
1n the degradation of T3:
A) uric acid is an end product.
B) nitrogen &ill be released in the form of ammonia 5ammonium ion ).
) the nitrogen-containing ring &ill be oxidi/ed.
!) the final product &ill ha+e the same type of nitrogen-containing ring as T3.
") hypoxanthine &ill be an intermediate.
The formation of deoxyAT3 5dAT3) for !NA synthesis occurs mostly by:
A) de no+o synthesis beginning &ith d3$33.
B) sal+aging adenine using A-3$T.
) sal+aging adenine using a nucleoside phosphorylase and d$ )-3.
!) con+erting A!3 to dA!3 using thioredoxin.
") con+erting d193 to dA93 using (*).-methylene T0<.
%hich of the follo&ing &ould N8T be expected to contribute to gout 5hyperuricemia)'
A) :nusually high le+els of 3$33.
B) 1nhibition of xanthine oxidase.
) :nusually high turno+er of nucleic acids.
!) 0igh acti+ity of adenosine deaminase.
") !eficiency of 04-3$T.
=ources of purine ring atoms in the de no+o synthesis of 193 include:
). glutamine.
,. a component of the tetrahydrofolate one-carbon pool.
6. aspartate.
7. glycine.
A) )* , and 6
B) ) and 6
) , and 7
!) 7 only
-") All four
A nucleoside phosphorylase:
). clea+es a nucleoside &ith the production of ribose )-phosphate.
,. is necessary for the ma#or sal+age path&ay for pyrimidines.
6. is used in the degradation of purine nucleotides.
7. is responsible for the e2uilibration of nucleoside monophosphates and nucleoside
diphosphate.
A) )* , and 6
B) ) and 6
) , and 7
!) 7 only
9ethotrexate is an inhibitor of the dihydrofolate reductase en/yme. Administration of
methotrexate &ould inhibit:
). de no+o synthesis of :93.
,. con+ersion of d:93 to dT93.
6. con+ersion of 193 to 493.
7. de no+o synthesis of 193.
A) )* , and 6
B) ) and 6
) , and 7
!) 7 only
") All four
Assume a cell has an ade2uate supply of adenine nucleotides but re2uires more guanine
nucleotides for protein synthesis:
). 4lutamine-3$33 amidotransferase &ill not be fully inhibited.
,. A93 &ill be a feedback inhibitor of the condensation of 193 &ith aspartate.
6. AT3 &ill stimulate the production of 493 from 193.
7. AT3 &ill inhibit nucleoside diphosphate reductase.
A) )* , and 6
B) ) and 6
) , and 7
!. 7 only
". All four
<oremost controls of de no+o A93 synthesis include:
). allosteric inhibition by 493.
,. allosteric inhibition by A93.
6. a+ailability of 3$33.
7. stimulation by 4T3.
A) )* , and 6
B) ) and 6
) , and 7
!) 7 only
") All four
Aspartate is in+ol+ed in all of the follo&ing ";"3T:
A) con+ersion of :T3 to T3.
B) de no+o synthesis of A93.
) de no+o synthesis of orotic acid.
!) maintenance of the adenine nucleotide pool by a sal+age mechanism.
") synthesis of most proteins.
Allopurinol is an inhibitor of the xanthine oxidase en/yme. :sing allopurinol &ith a patient &ith
gout and normal 04-3$T le+els &ould be expected to lead to all of the follo&ing ";"3T:
A) decreased de no+o synthesis of 193.
B) decreased urate in the urine.
) an increase in hypoxanthine in the blood.
!) increased le+els of 3$33.
") increased xanthine in the blood.
9atch the type of bond &ith the role belo&:
Bond>type $ole
5a) phosphodiester >>> links base to pentose in nucleotide
5b) N-glycosidic >>> #oins ad#acent nucleotides in one strand
5c) phosphate ester >>> #oins complementary nucleotides in t&o
strands
5d) hydrogen >>> difference bet&een a nucleoside and a
nucleotide
!ra& the chemical structure of (-methyl cytosine
The follo&ing 2uestions a-d refer to the nucleic acid oligomer sho&n belo&:
a. ?abel the bases and the (@ and the 6@ ends.
b. 1s this oligomer $NA or !NA'
c. :sing the single letter code* indicate the
se2uence of the$NA molecular
complementary to the oligomer.
d. Any mistakes'
0o& are a nucleoside and a nucleotide similar and
ho& are they different'
To incorporate radiolabeled nucleotides into ne&ly synthesi/ed !NA* researchers use -
phosphorus
6,
-labeled nucleotides* in a !NA synthesis reaction* &here the denotes the
position of the radioacti+e phosphate moiety. "xplain &hy the position and not the or
position is the best position for the radioacti+e group in these experiments.
The phosphodiester bonds that link ad#acent nucleotides in both $NA and !NA:
A) al&ays link A &ith T and 4 &ith .
B) are susceptible to alkaline hydrolysis.
) are uncharged at neutral p0.
!) form bet&een the planar rings of ad#acent bases.
") #oin the 6' hydroxyl of one nucleotide to the (' hydroxyl of the next.
The !NA oligonucleotide abbre+iated pAT4A:
A) has A phosphate groups.
B) has a hydroxyl at its 6' end.
) has a phosphate on its 6' end.
!) has an A at its 6' end.
") +iolates hargaff@s rules.
<or the oligoribonucleotide pA4:A:
A) the nucleotide at the 6' end has a phosphate at its 6' hydroxyl.
B) the nucleotide at the 6' end is a purine.
) the nucleotide at the (' end has a (' hydroxyl.
!) the nucleotide at the (' end has a phosphate on its (' hydroxyl.
") the nucleotide at the (' end is a pyrimidine.
!ouble stranded !NA has a helical conformation. 1s the helix right or left handed in most cases'
!ra& the structure of either an adenine-thymine or a guanine-cytosine base pair as found in the
%atson-rick double-helical structure of !NA. 1nclude all hydrogen bonds.
The composition 5mole fraction) of one of the strands of a double-helical !NA is BAC D ..6* and
B4C D ..,7. alculate the follo&ing* if possible. 1f impossible* &rite E1.E
<or the same strand:
BTC D 5a) >>>>
BC D 5b) >>>>
BTC F BC D 5c) >>>>
<or the other strand:
BAC D 5d) >>>>
BTC D 5e) >>>>
BAC F BTC D 5f) >>>>
B4C D 5g) >>>>
BC D 5h) >>>>
B4C F BC D 5i) >>>>
1n the %atson-rick model for the !NA double helix 5B form) the AGT and 4G base pairs share
&hich one of the follo&ing properties'
A) The distance bet&een the t&o glycosidic 5base-sugar) bonds is the same in both base
pairs* &ithin a fe& tenths of an angstrom.
B) The molecular &eights of the t&o base pairs are identical.
) The number of hydrogen bonds formed bet&een the t&o bases of the base pair is the
same.
!) The plane of neither base pair is perpendicular to the axis of the helix.
") The proton-binding groups in both base pairs are in their charged or ioni/ed form.
1n double-stranded !NA:
A) only a right-handed helix is possible.
B) se2uences rich in AGT base pairs are denatured less readily than those rich in 4G pairs.
) the se2uence of bases has no effect on the o+erall structure.
!) the t&o strands are parallel.
") the t&o strands ha+e complementary se2uences.
1n the %atson-rick model of !NA structure 5no& called B-form !NA):
A) a purine in one strand al&ays hydrogen bonds &ith a purine in the other strand.
B) AGT pairs share three hydrogen bonds.
) 4G pairs share t&o hydrogen bonds.
!) the (' ends of both strands are at one end of the helix.
") the bases occupy the interior of the helix.
1n the %atson-rick structure of !NA* the:
A) absence of ,'-hydroxyl groups allo&s bases to lie perpendicular to the helical axis.
B) adenine content of one strand must e2ual the thymine content of the same strand.
) nucleotides are arranged in the A-form.
!) purine content 5fraction of bases that are purines) must be the same in both strands.
") t&o strands are parallel.
1n the %atson-rick model of !NA structure:
A) both strands run in the same direction* 6' ('H they are parallel.
B) phosphate groups pro#ect to&ard the middle of the helix* &here they are protected from
interaction &ith &ater.
) T can form three hydrogen bonds &ith either 4 or in the opposite strand.
!) the distance bet&een the sugar backbone of the t&o strands is #ust large enough to
accommodate either t&o purines or t&o pyrimidines.
") the distance bet&een t&o ad#acent bases in one strand is about 6.7 I.
%hich of the follo&ing is not true of all naturally occurring !NA'
A) !eoxyribose units are connected by 6'*('-phosphodiester bonds.
B) The amount of A al&ays e2uals the amount of T.
) The ratio AFTJ4F is constant for all natural !NAs.
!) The t&o complementary strands are antiparallel.
") T&o hydrogen bonds form bet&een A and T.
The double helix of !NA in the B-form is stabili/ed by:
A) co+alent bonds bet&een the 6' end of one strand and the (' end of the other.
B) hydrogen bonding bet&een the phosphate groups of t&o side-by-side strands.
) hydrogen bonds bet&een the riboses of each strand.
!) nonspecific base-stacking interaction bet&een t&o ad#acent bases in the same strand.
") ribose interactions &ith the planar base pairs.
1n nucleotides and nucleic acids* syn and anti conformations relate to:
A) base stereoisomers.
B) rotation around the phosphodiester bond.
) rotation around the sugar-base bond.
!) sugar pucker.
") sugar stereoisomers.
B-form !NA in +i+o is a >>>>>>>>-handed helix* >>>>> I in diameter* &ith a rise of >>>> I per
base pair 5non examinable detailK).
A) leftH ,.H 6.9
B) rightH )-H 6.7
) rightH )-H 6.L
!) rightH ,.H 6.7
") rightH ,6H ,.L
1n double-stranded !NA:
A) only a right-handed helix is possible.
B) se2uences rich in AGT base pairs are denatured less readily than those rich in 4G pairs.
) the se2uence of bases has no effect on the o+erall structure.
!) the t&o strands are parallel.
") the t&o strands ha+e complementary se2uences.
The !NA in a eukaryotic chromosome is best described as:
A) a single circular double-helical molecule.
B) a single linear double-helical molecule.
) a single linear single-stranded molecule.
!) multiple linear double-helical molecules.
") multiple linear single-stranded molecules.
!escribe the reaction cataly/ed by topoisomerase 1
!ouble stranded !NA has a helical conformation. 1s the helix right or left handed in most cases'
3lasmid !NAs are circular. These molecules are isolated as Mclosed circularN or MnickedN
structures. %hat do these t&o terms mean'
=ingle stranded polynucleotides fre2uently ha+e secondary structures. !ra& an example of such a
structure &ith indi+idual nucleotides identified by the single letter code.
$ank the follo&ing double stranded !NA molecules in terms of their thermal stability:
4T4A 4T44A 4TATA 4TA4TA
A4T4 A44T4 A4AT ATAT
%hat are histones and &hat is their principal role in chromatin structure'
!escribe the composition and structure of a nucleosome.
%hen histones bind to closed circular !NA molecules they cause the formation of super helical
&rithe. %hat effect &ould this ha+e on the !NAOs t&ist' %hat effect &ould this ha+e on the
!NAOs linking number' 5Not expected from course)
The !NA in a bacterial 5prokaryotic) chromosome is best described as:
A) a single circular double-helical molecule.
B) a single linear double-helical molecule.
) a single linear single-stranded molecule.
!) multiple linear double-helical molecules.
") multiple linear single-stranded molecules
The !NA in a eukaryotic chromosome is best described as:
A) a single circular double-helical molecule.
B) a single linear double-helical molecule.
) a single linear single-stranded molecule.
!) multiple linear double-helical molecules.
") multiple linear single-stranded molecules
!NA in a closed-circular* double-stranded molecule &ith no net bending of the !NA axis on
itself is:
A) a left-handed helix.
B) a mixed right- and left-handed helix.
) relaxed.
!) supercoiled.
") under&ound.
0istones are >>>>>>> that are usually associated &ith >>>>>>>>>.
A) acidic proteinsH !NA
B) acidic proteinsH $NA
) basic proteinsH !NA
!) basic proteinsH $NA
") coen/ymes deri+ed from histidineH en/ymes
The fundamental repeating unit of organi/ation in a eukaryotic chromosome is:
A) the centrosome
B) the lysosome.
) the microsome.
!) the nucleosome
") the polysome.
%hich of the follo&ing contributes to the structure of nucleosomes' 5not expected from the
course)
A) 3lectonemic supercoiled !NA
B) $elaxed closed-circular !NA
) =olenoidal supercoiled !NA
!) =pacer !NA
") P 5left-handed) !NA
Nucleosomes:
A) are important features of chromosome organi/ation in eukaryotes and bacteria.
B) are composed of proteins rich in acidic amino acids* such as Asp and 4lu.
) are composed of protein and $NA.
!) bind !NA and alter its supercoiling.
") occur in chromatin at irregular inter+als along the !NA molecule.