Biochemistry - Chapter 8: Nucleotides and 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.

C) a pyrimidine nucleotide.

D) adenosine monophosphate.

E) adenosine.

E

A major component of RNA but not of DNA is:

A) adenine.

B) cytosine.

C) guanine.

D) thymine.

E) uracil.

E

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 configuration; ribonucleotide has the configuration at C-1.

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.

A

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) C-5 of the pentose is joined to a nitrogenous base, and C-1 to a phosphate group.

C) The bond that joins nitrogenous bases to pentoses is an O-glycosidic bond.

D) The pentoses are always in the -furanose forms.

E) The straight-chain and ring forms undergo constant interconversion.

D

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.

E

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.

A

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.

D

The DNA oligonucleotide abbreviated pATCGAC:

A) has 7 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.

B

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

D

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.

D

Which of the following 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.

C) The lactam form predominates at neutral pH.

D) They are geometric isomers.

E) They are stereoisomers.

c

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

A) adenosine.

B) guanine.

C) inosine.

D) thymine.

E) uracil.

B

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.

A

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) There are two equally sized grooves that run up the sides of the helix.

C) The base-pairing occurs on the inside of the double helix.

D) The two strands have complementary sequences.

E) The double helix is right handed.

B

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.

B

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.

E

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

%A %G %C %T %U

A) 5 45 45 5 0

B) 20 20 20 20 20

C) 35 15 35 15 0

D) all of the above

E) none of the above

A

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.

A

In the Watson-Crick model of DNA structure:

A) both strands run in the same direction, 3' 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.

E

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.

C

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.

E

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.

D

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.

C

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

D

In double-stranded DNA:

A) only a right-handed helix is possible.

B) sequences rich in A-T base pairs are denatured less readily than those rich in G-C pairs.

C) the sequence of bases has no effect on the overall structure.

D) the two strands are parallel.

E) the two strands have complementary sequences

E

Which of the following is a palindromic sequence?

A) AGGTCC

TCCAGG

B) CCTTCC

GCAAGG

C) GAATCC

CTTAGG

D) GGATCC

CCTAGG

E) GTATCC

CATAGG

D

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.

D

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

%A %G %C %T %U

A) 5 45 45 0 5

B) 25 25 25 0 25

C) 35 10 30 0 25

D) all of the above

E) none of the above

D

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).

C

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.

B

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')

B

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').

D

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.

E

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.

E

Compounds that generate nitrous acid (such as nitrites, nitrates, and nitrosamines) change DNA molecules by:

A) breakage of phosphodiester bonds.

B) deamination of bases.

C) depurination.

D) formation of thymine dimers.

E) transformation of A T.

B

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.

D

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.

D

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.

E

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

A) deoxyribonucleoside triphosphate

B) di-nucleotide

C) peptide

D) ribonucleotide

E) ribonucleoside triphosphate

E

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

E

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.

B

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.

B

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.

F) The two strands have complementary sequences

D

A common mutation that results in the removal of a nucleobase from its nucleotide at the N-glycosidic bond is:

A) depurination

B) deamination of bases

C) breakage of phosphodiester bonds

D) formation of thymine dimers

E) transformation of A → T

A

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

Avery et al. showed that DNA isolated from a virulent (disease-causing) bacterium (Streptococcus pneumoniae), when mixed with living cells of a nonvirulent strain of this bacterium, provided the genetic instructions for transforming the nonvirulent strain to a virulent strain.

Match the type of bond with the role below:

Bond type Role

(a) phosphodiester

(b) N-glycosidic

(c) phosphate ester

(d) hydrogen

Role

____links base to pentose in nucleotide

___ joins adjacent nucleotides in one strand

___ joins complementary nucleotides in two strands

___ difference between a nucleoside and a

nucleotide

b; a; d; c

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

3.4 Å x 10,000 = 34,000 Å = 3.4 µm

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.

(a) nucleotides;

(b) adenine and guanine;

(c) thymidine;

(d) G-C;

(e) A-T

Two molecules of double-stranded DNA, each containing 5,000 base pairs, are the same length but differ in base composition. Molecule 1 contains 54% A+T and Molecule 2 contains 28% A+T. Which molecule has a higher Tm? What percentage of residues are C in the 54% A+T molecule?

A) 2; 46%

B) 1; 46%

C) 1; 23%

D) 2; 23%

E) 2; 72%

D

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

The nucleotide sequences of complementary strands are such that wherever an A occurs in one strand, there is a T in the other strand with which it can form a hydrogen-bonded base pair. Wherever a C occurs in one strand, a G occurs in the other. A is the base complementary to T, and C is the base complementary to G.

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

A-form DNA is a right-handed helix; Z-form DNA is a left-handed helix.

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

Any double-stranded sequence that has the form:

1-2-3-4-5-6-6'-5'-4'-3'-2'-1'

1'-2'-3'-4'-5'-6'-6-5-4-3-2-1

where each number and its prime represent correctly paired bases (A with T, C with G) all along the double-stranded molecule.

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

Hydrogen-bonding in regions of complementarity within an RNA chain can result in regions of double helix that are stabilized by base-stacking. Breaks in complementary regions can result in loops and bulges that together with the helical regions, can generate a precise three-dimensional structure.

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)?

Lower ionic strength reduces the screening of the negative charges on the phosphate groups by positive ions in the medium. The result is stronger charge-charge repulsion between the phosphate, which favors strand separation.

Describe qualitatively how the tm for a double-stranded DNA depends upon its nucleotide composition.

In general, the higher the proportion of G and C, the higher the melting temperature, tm. More thermal energy is required to break the three hydrogen bonds holding GC pairs than to break the two hydrogen bonds holding A=T pairs.

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

The DNA molecules are partially denatured; in each molecule approximately 50% of the DNA is single-stranded and 50% is double-helical. The single-stranded regions, which appear as "bubbles" within the molecules, are those which denatured at lower temperatures because of their higher content of A-T base pairs.

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

In general, the more similar the sequences in two DNA molecules are, the more readily they will hybridize. Because the evolutionary distance between mouse and yeast is greater than that between mouse and human, mouse and human DNA sequences are more similar than those of mouse and yeast.

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) ____

For the same strand:

[T] = (a) I

[C] = (b) I

[T] + [C] = (c) 0.46

For the other strand:

[A] = (d) I

[T] = (e) 0.3

[A] + [T] = (f) I

[G] = (g) I

[C] = (h) 0.24

[G] + [C] = (i) I

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

Both have a nitrogenous base and a pentose; nucleotides also have a phosphate group, which nucleosides lack.

What is the principal effect of ultraviolet radiation on DNA?

UV radiation causes the formation of a dimer between adjacent thymine bases on the same DNA strand. This results in a kink in the double helix at that site.

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

In these molecules, there is a phosphoric anhydride linkage between the phosphates. Hydrolysis of this linkage (i.e., of ATP to ADP and phosphate) is a highly exergonic reaction that results in the release of a large amount of free energy. Conversely, the input of a large amount of free energy is required for the synthesis of the linkage; i.e., for the phosphorylation of ADP to form ATP. Thus, synthesis of ATP results in the storage of energy that can be released upon hydrolysis.

Briefly describe the experimental evidence of Avery, MacLeod, and McCarty that DNA is the geneticmaterial

Avery et al. showed that DNA isolated from a virulent (disease-causing) bacterium (Streptococcus pneumoniae), when mixed with living cells of a nonvirulent strain of this bacterium,provided the genetic instructions for transforming the nonvirulent strain to a virulent strain

Briefly describe the Hershey-Chase experiment, which showed that DNA is the genetic material

Hershey and Chase showed that when the bacteriophage (virus) T2 infected the bacterium E.coli, new genetic instructions appeared in the infected cells. Because only the DNA and not theproteins of T2 entered the infected cell, DNA must carry the new genetic instructions

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

The nucleotide sequences of complementary strands are such that wherever an A occurs in onestrand, there is a T in the other strand with which it can form a hydrogen-bonded base pair. Wherevera C occurs in one strand, a G occurs in the other. A is the base complementary to T, and C is the basecomplementary to G.

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

A-form DNA is a right-handed helix; Z-form DNA is a left-handed helix

Describe briefly how noncovalent interactions contribute to the three-dimensional shapes of RNAmolecules

Hydrogen-bonding in regions of complementarity within an RNA chain can result in regions of double helix that are stabilized by base-stacking. Breaks in complementary regions can result in loops and bulges that together with the helical regions, can generate a precise three-dimensional structure.

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

The DNA molecules are partially denatured; in each molecule approximately 50% of the DNAis single-stranded and 50% is double-helical. The single-stranded regions, which appear as "bubbles"within the molecules, are those which denatured at lower temperatures because of their higher contentof A-T base pairs

How is a nucleotide and a nucleoside similar?

They both have a nitrogenous base linked to ribosyl pentose via an N-glycosidic bond.

How is a nucleotide and a nucleoside different?

Nucleotides have a 5' phosphate, whereas nucleosides have a 5' hydroxyl.

What are the two ways that nucleotides in DNA are different from nucleotides in RNA?

1. DNA has U, an RNA has T.

2. DNA molecules have a 2'H and RNA have a 2'OH.

Is the following true for DNA, RNA, BOTH or NEITHER? :

The secondary structure is primarily a double helix.

DNA

What are three functions of nucleotides?

1. energize metabolism (ex. ATP)

2. enzyme cofactors (ex. NAD+)

3. signal transmission (ex. cAMP)

What are four functions of nucleic acids?

1. storage of genetic information (DNA)

2. transmission of genetic information (mRNA)

3. processing genetic information (ribozymes)

4. protein synthesis (tRNA and rRNA)

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

In general, the higher the proportion of G and C, the higher the melting temperature, tm. More thermal energy is required to break the three hydrogen bonds holding GC pairs than to break the two hydrogen bonds holding A=T pairs. Also, GC pairs stack better than A=T pairs, thereby stabilizing the double helix better.

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

Cytosine undergoes spontaneous deamination to form uracil. If uracil were normally present in DNA, a deamination event could not be recognized as "damaged goods." Thus, CU changes would not be repaired by normal cellular processes (see Chapter 25), and these "new" U's would end up pairing with A, leading to a point mutation. The extra methyl group in thymine is sufficient for differentiating U and T.

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?

a) The polymerase will synthesize the whole strand without any breaks, but you will not detect any product at all because there are no short fragments and there is no detectable molecule.

b) The polymerase will never "stop" at a complementary C when incorporating a G. All other bases will work normally. Thus, you will interpret that your sequence does not contain any C. However, if you look carefully, there should be an extra space (gap) in the sequence, where a normal non-terminatin dGTP was incorporated.

c) Essentially, no reaction will occur, with the exception of incorporating the first ddNTP. Thus, you will see nothing.

d) The polymerase reaction will proceed up to the first complementary C in the sequence and then terminate. Thus, you will see at best a very short strand of DNA sequence.

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

In these molecules, there is a phosphoric anhydride linkage between the phosphates. Hydrolysis of this linkage (i.e., of ATP to ADP and phosphate) is a highly exergonic reaction that results in the release of a large amount of free energy. Conversely, the input of a large amount of free energy is required for the synthesis of the linkage; that is, for the phosphorylation of ADP to form ATP. Thus, synthesis of ATP results in the storage of energy that can be released upon hydrolysis.