Deck 8: Nucleotides and Nucleic Acids

Question 1

The phosphodiester bonds that link adjacent nucleotides in both RNA and DNA:

A)always link A with T and G with C.
B)are susceptible to alkaline hydrolysis.
C)are uncharged at neutral pH.
D)form between the planar rings of adjacent bases.
E)join the 3' hydroxyl of one nucleotide to the 5' hydroxyl of the next.

Answer 1

join the 3' hydroxyl of one nucleotide to the 5' hydroxyl of the next.

Question 2

Based on Chargaff's rules,which of the following are possible base compositions for double-stranded DNA?

Answer 2

A

Question 3

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.
C)a pyrimidine nucleotide.
D)adenosine monophosphate.
E)adenosine.

Answer 3

adenosine.

Question 4

Which of the following statements concerning the tautomeric forms of bases such as uracil is correct?

A)The double-lactim form contains a ketone group.
B)The lactam form contains an alcohol group.
C)The lactam form predominates at neutral pH.
D)Formation of the lactim from the lactam is irreversible.
E)The lactim and double-lactim forms are stabilized at high pH.

Question 5

Which one of the following is true of the pentoses found in nucleic acids?

A)C-5 and C-1 of the pentose are joined to phosphate groups.
B)The pentoses are in a planar configuration.
C)The bond that joins nitrogenous bases to pentoses is an O-glycosidic bond.
D)The pentoses are always in the $\beta$ -furanose forms.
E)The straight-chain and ring forms undergo constant interconversion.

Question 6

The DNA oligonucleotide abbreviated pATCGAC:

A)has seven phosphate groups.
B)has a hydroxyl at its 3' end.
C)has a phosphate on its 3' end.
D)has an A at its 3' end.
E)violates Chargaff's rules.

Question 7

The alkaline hydrolysis of RNA does not produce:

A)2'- AMP.
B)2',3'-cGMP.
C)2'-CMP.
D)3',5'-cAMP.
E)3'-UMP.

Question 8

For the oligoribonucleotide pACGUAC:

A)the nucleotide at the 3' end has a phosphate at its 3' hydroxyl.
B)the nucleotide at the 3' end is a purine.
C)the nucleotide at the 5' end has a 5' hydroxyl.
D)the nucleotide at the 5' end has a phosphate on its 5' hydroxyl.
E)the nucleotide at the 5' end is a pyrimidine.

Question 9

A major component of RNA but not of DNA is:

A)adenine.
B)cytosine.
C)guanine.
D)thymine.
E)uracil.

Question 10

The difference between a ribonucleotide and a deoxyribonucleotide is:

A)a deoxyribonucleotide has an -H instead of an -OH at C-2.
B)a deoxyribonucleotide has an -H instead of an -OH at C-3.
C)a ribonucleotide has an extra -OH at C-4.
D)a ribonucleotide has more structural flexibility than deoxyribonucleotide.
E)a ribonucleotide is a pyranose,deoxyribonucleotide is a furanose.

Question 11

In the Watson-Crick model for the DNA double helix,which of the following is not true?

A)The two strands run anti-parallel to one another.
B)The base-pairing occurs on the inside of the double helix.
C)The double helix is right-handed.
D)There are two equally sized grooves that run up the sides of the helix.
E)The two strands have complementary sequences.

Question 12

The phosphodiester bond that joins adjacent nucleotides in DNA:

A)associates ionically with metal ions,polyamines,and proteins.
B)is positively charged.
C)is susceptible to alkaline hydrolysis.
D)Links C-2 of one base to C-3 of the next.
E)links C-3 of deoxyribose to N-1 of thymine or cytosine.

Question 13

In a double-stranded nucleic acid,cytosine typically base-pairs with:

A)adenosine.
B)guanine.
C)inosine.
D)thymine.
E)uracil.

Question 14

The experiment of Avery,MacLeod,and McCarty in which nonvirulent bacteria were made virulent by transformation was significant because it showed that:

A)bacteria can undergo transformation.
B)genes are composed of DNA only.
C)mice are more susceptible to pneumonia than are humans.
D)pneumonia can be cured by transformation.
E)virulence is determine genetically.

Question 15

Chargaff's rules state that in typical DNA:

A)A = G.
B)A = C.
C)A = U.
D)A + T = G + C.
E)A + G = T + C.

Question 16

In the Watson-Crick model for the DNA double helix (B form)the A-T and G-C base pairs share which one of the following properties?

A)The distance between the two glycosidic (base-sugar)bonds is the same in both base pairs,within a few tenths of an angstrom.
B)The molecular weights of the two base pairs are identical.
C)The number of hydrogen bonds formed between the two bases of the base pair is the same.
D)The plane of neither base pair is perpendicular to the axis of the helix.
E)The proton-binding groups in both base pairs are in their charged or ionized form.

Question 17

The nucleic acid bases:

A)absorb ultraviolet light maximally at 280 nm.
B)are all about the same size.
C)are relatively hydrophilic.
D)are roughly planar.
E)can all stably base-pair with one another.

Question 18

Purines have ____ ring(s), (each)containing _____ nitrogen(s),whereas pyrimidines have _____ ring(s), (each)containing _____ nitrogens.

A)1;1;1;1
B)1;2;1;2
C)2;1;1;2
D)2;2;1;1
E)2;2;1;2

Question 19

The difference between thymine and uracil is:

A)one methylene group on the pyrimidine ring.
B)one methyl group on the pyrimidine ring.
C)one hydroxyl group on the ribose ring.
D)one amine group on the pyrimidine ring.
E)one methyl group on the purine ring.

Question 20

In the Watson-Crick structure of DNA,the:

A)absence of 2'-hydroxyl groups allows bases to lie perpendicular to the helical axis.
B)adenine content of one strand must equal the thymine content of the same strand.
C)nucleotides are arranged in the A-form.
D)purine content (fraction of bases that are purines)must be the same in both strands.
E)two strands are parallel.

Question 21

In the Watson-Crick model of DNA structure:

A)both strands run in the same direction,3' $\rightarrow$ 5';they are parallel.
B)phosphate groups project toward the middle of the helix,where they are protected from interaction with water.
C)T can form three hydrogen bonds with either G or C in the opposite strand.
D)the distance between the sugar backbone of the two strands is just large enough to accommodate either two purines or two pyrimidines.
E)the distance between two adjacent bases in one strand is about 3.4 Å.

Question 22

Which of the following are possible base compositions for single-stranded RNA?

Question 23

For the helix in double-stranded B-form DNA,the majority of the stability can be attributed to:

A)base-pairing interactions via H-bonds.
B)interactions along the phosphate backbone.
C)base-stacking interactions via van-der-Waals interactions.
D)covalent bonds between adjacent bases in one strand.
E)ionic interactions with metal ions.

Question 24

Which of the following is not true of all naturally occurring DNA?

A)Deoxyribose units are connected by 3',5'-phosphodiester bonds.
B)The amount of A always equals the amount of T.
C)The ratio A+T/G+C is constant for all natural DNAs.
D)The two complementary strands are antiparallel.
E)Two hydrogen bonds form between A and T.

Question 25

Triple-helical DNA structures can result from Hoogsteen (non Watson-Crick)interactions.These interactions are primarily:

A)covalent bonds involving deoxyribose.
B)covalent bonds involving the bases.
C)hydrogen bonds involving deoxyribose.
D)hydrogen bonds involving the bases.
E)hydrophobic interactions involving the bases.

Question 26

In DNA sequencing by the Sanger (dideoxy)method:

A)radioactive dideoxy ATP is included in each of four reaction mixtures before enzymatic synthesis of complementary strands.
B)specific enzymes are used to cut the newly synthesized DNA into small pieces,which are then separated by electrophoresis.
C)the dideoxynucleotides must be present at high levels to obtain long stretches of DNA sequence.
D)the role of the dideoxy CTP is to occasionally terminate enzymatic synthesis of DNA where Gs occur in the template strands.
E)the template DNA strand is radioactive.

Question 27

The double helix of DNA in the B-form is stabilized by:

A)covalent bonds between the 3' end of one strand and the 5' end of the other.
B)hydrogen bonding between the phosphate groups of two side-by-side strands.
C)hydrogen bonds between the riboses of each strand.
D)nonspecific base-stacking interaction between two adjacent bases in the same strand.
E)ribose interactions with the planar base pairs.

Question 28

Which of the following is a palindromic sequence?

A)AGGTCC TCCAGG
B)CCTTCC GCAAGG
C)GAATCC CTTAGG
D)GGATCC
E)GTATCC

Question 29

Double-stranded regions of RNA:

A)are less stable than double-stranded regions of DNA.
B)can be observed in the laboratory,but probably have no biological relevance.
C)can form between two self-complementary regions of the same single strand of RNA.
D)do not occur.
E)have the two strands arranged in parallel (unlike those of DNA,which are antiparallel).

Question 30

In the laboratory,several factors are known to cause alteration of the chemical structure of DNA.The factor(s)likely to be important in a living cell is (are):

A)heat.
B)low pH.
C)oxygen.
D)UV light.
E)both C and D.

Question 31

When double-stranded DNA is heated at neutral pH,which change does not occur?

A)The absorption of ultraviolet (260 nm)light increases.
B)The covalent N-glycosidic bond between the base and the pentose breaks.
C)The helical structure unwinds.
D)The hydrogen bonds between A and T break.
E)The viscosity of the solution decreases.

Question 32

Double stranded regions of RNA typically take on a(n):

A)A-form left-handed helix.
B)A-form right-handed helix.
C)B-form left-handed helix.
D)B-form right-handed helix.
E)Z-form left-handed helix.

Question 33

The ribonucleotide polymer (5')GTGATCAAGC(3')could only form a double-stranded structure with:

A)(5')CACTAGTTCG(3').
B)(5')CACUAGUUCG(3').
C)(5')CACUTTCGCCC(3').
D)(5')GCTTGATCAC(3').
E)(5')GCCTAGTTUG(3').

Question 34

In comparison with DNA-DNA double helices,the stability of DNA-RNA and RNA-RNA helices is:

A)DNA-DNA > DNA-RNA > RNA-RNA.
B)DNA-DNA > RNA-RNA > DNA-RNA.
C)RNA-DNA > RNA-RNA > DNA-DNA.
D)RNA-RNA > DNA-DNA > DNA-RNA.
E)RNA-RNA > DNA-RNA > DNA-DNA.

Question 35

In the chemical synthesis of DNA:

A)the dimethoxytrityl (DMT)group catalyzes formation of the phosphodiester bond.
B)the direction of synthesis is 5' to 3'.
C)the maximum length of oligonucleotide that can be synthesized is 8-10 nucleotides.
D)the nucleotide initially attached to the silica gel support will become the 3' end of the finished product.
E)the protecting cyanoethyl groups are removed after each step.

Question 36

In nucleotides and nucleic acids,syn and anti conformations relate to:

A)base stereoisomers.
B)rotation around the phosphodiester bond.
C)rotation around the sugar-base bond.
D)sugar pucker.
E)sugar stereoisomers.

Question 37

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)transformation of A $\rightarrow$ T.

Question 38

In the Watson-Crick model of DNA structure (now called B-form DNA):

A)a purine in one strand always hydrogen bonds with a purine in the other strand.
B)A-T pairs share three hydrogen bonds.
C)G-C pairs share two hydrogen bonds.
D)the 5' ends of both strands are at one end of the helix.
E)the bases occupy the interior of the helix.

Question 39

Which of the following deoxyoligonucleotides will hybridize with a DNA containing the sequence (5')AGACTGGTC(3')?

A)(5')CTCATTGAG(3')
B)(5')GACCAGTCT(3')
C)(5')GAGTCAACT(3')
D)(5')TCTGACCAG(3')
E)(5')TCTGGATCT(3')

Question 40

B-form DNA in vivo is a ________-handed helix,_____ Å in diameter,with a rise of ____ Å per base pair.

A)left;20;3.9
B)right;18;3.4
C)right;18;3.6
D)right;20;3.4
E)right;23;2.6

Question 41

Briefly describe the experimental evidence of Avery,MacLeod,and McCarty that DNA is the genetic material.

Question 42

Describe briefly what is meant by saying that two DNA strands are complementary.

Question 43

Describe qualitatively how the t_m for a double-stranded DNA depends on its nucleotide composition.

Question 44

The composition (mole fraction)of one of the strands of a double-helical DNA is [A] = 0.3,and [G] = 0.24.Calculate the following,if possible.If impossible,write "I."
For the same strand:
[T] = (a)____
[C] = (b)____
[T] + [C] = (c)____
For the other strand:
[A] = (d)____
[T] = (e)____
[A] + [T] = (f)____
[G] = (g)____
[C] = (h)____
[G] + [C] = (i)____

Question 45

What is the principal effect of ultraviolet radiation on DNA?

Question 46

Write a double-stranded DNA sequence containing a six-nucleotide palindrome.

Question 47

Compounds that contain a nitrogenous base,a sugar,and a phosphate group are called (a)________.
Two purines found in DNA are (b)______________ and __________________.
A pyrimidine found in all DNA but in only some RNA is (c)_________________.
In DNA,the base pair (d)___ -___ is held together by three hydrogen bonds;
the base pair (e)___ -___ has only two such bonds.

Question 48

Match the type of bond with the role below:

Question 49

What is the approximate length of a DNA molecule (in the B form)containing 10,000 base pairs?

Question 50

The "energy carrier" ATP is an example of a(n):

A)deoxyribonucleoside triphosphate
B)di-nucleotide
C)peptide
D)ribonucleotide
E)ribonucleoside triphosphate

Question 51

In living cells,nucleotides and their derivatives can serve as:

A)carriers of metabolic energy.
B)enzyme cofactors.
C)intracellular signals.
D)precursors for nucleic acid synthesis.
E)all of the above.

Question 52

Based on the spontaneous deamination of cytosine,explain why it is advantageous for DNA to contain thymine,not uracil.

Question 53

Why does lowering the ionic strength of a solution of double-stranded DNA permit the DNA to denature more readily (for example,to denature at a lower temperature than at a higher ionic strength)?

Question 54

Explain how nucleoside triphosphates (such as ATP)act as carriers of chemical energy.

Question 55

A solution of DNA is heated slowly until the t_m is reached.What is the likely structure of the DNA molecules at this temperature?

Question 56

Describe briefly how noncovalent interactions contribute to the three-dimensional shapes of RNA molecules.

Question 57

In one sentence,identify the most obvious structural difference between A-form (Watson-Crick)DNA and Z-form DNA.

Question 58

Mouse DNA hybridizes more extensively with human DNA than with yeast DNA.Explain by describing the factor or factors that determine extent of hybridization.

Question 59

How are a nucleoside and a nucleotide similar and how are they different?

Question 60

What happens in automated Sanger DNA sequencing reaction if you forget to add
a)all fluorescent ddNTPs?
b)fluorescent ddGTP?
c)all dNTPs?
d)dGTP?