BIOCHEM CH 8
Draw the structure of either an adenine-thymine or a guanine-cytosine base pair as found in the Watson-Crick double-helical structure of DNA. Include all hydrogen bonds.
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Draw the structures of hydrogen-bonded adenine and thymine.
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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. (See p. 338.)
A major component of RNA but not of DNA is: A) adenine. B) cytosine. C) guanine. D) thymine. E) uracil.
A major component of RNA but not of DNA is: E) uracil.
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. (See Fig. 10-19, page 338.)
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.
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.
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
B-form DNA in vivo is a ________-handed helix, _____ Å in diameter, with a rise of ____ Å per base pair. D) right; 20; 3.4
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
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
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.
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.
Chargaff's rules state that in typical DNA: E) A + G = T + C. (Chargaff's rule states that the amount of adenine is equal to thymine while the amount of guanine is equal to cytosine; 1:1 ratio of purine and pyrimidine bases.)
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.
Compounds that contain a nitrogenous base, a sugar, and a phosphate group are called (a) nucleotides. Two purines found in DNA are (b)adenine and guanine. A pyrimidine found in all DNA but in only some RNA is (c)thymidine. In DNA, the base pair (d)G-C is held together by three hydrogen bonds; the base pair (e)A-T has only two such bonds.
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.
Compounds that generate nitrous acid (such as nitrites, nitrates, and nitrosamines) change DNA molecules by: B) deamination of bases.
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).
Double-stranded regions of RNA: C) can form between two self-complementary regions of the same single strand of RNA.
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.
For the oligoribonucleotide pACGUAC: D) the nucleotide at the 5' end has a phosphate on its 5' hydroxyl.
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.
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.
In DNA sequencing by the Sanger (dideoxy) method: D) the role of the dideoxy CTP is to occasionally terminate enzymatic synthesis of DNA where Gs occur in the template strands.
In a double-stranded nucleic acid, cytosine typically base-pairs with: A) adenosine. B) guanine. C) inosine. D) thymine. E) uracil.
In a double-stranded nucleic acid, cytosine typically base-pairs with: B) guanine.
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.
In comparison with DNA-DNA double helices, the stability of DNA-RNA and RNA-RNA helices is: E) RNA-RNA > DNA-RNA > DNA-DNA.
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.
In double-stranded DNA: E) the two strands have complementary sequences.
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 G---C pairs than to break the two hydrogen bonds holding A=T 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.
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.
In living cells, nucleotides and their derivatives can serve as: E) all of the above.
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.
In nucleotides and nucleic acids, syn and anti conformations relate to: C) rotation around the sugar-base bond.
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.
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.
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.
In the Watson-Crick model of DNA structure (now called B-form DNA): E) the bases occupy the interior of the helix.
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.
In the Watson-Crick model of DNA structure: E) the distance between two adjacent bases in one strand is about 3.4 Å.
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.
In the Watson-Crick structure of DNA, the: A) absence of 2'-hydroxyl groups allows bases to lie perpendicular to the helical axis.
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.
In the chemical synthesis of DNA: D) the nucleotide initially attached to the silica gel support will become the 3' end of the finished product.
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.
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): E) both C and D.
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.
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.
Match the type of bond with the role below: ___ 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 (a) phosphodiester (b) N-glycosidic (c) phosphate ester (d) hydrogen
Match the type of bond with the role below: b) N-glycosidic- links base to pentose in nucleotide a) phosphodiester- joins adjacent nucleotides in one strand d) hydrogen- joins complementary nucleotides in two strands c) phosphate ester- difference between a nucleoside and a nucleotide
The "energy carrier" ATP is an example of a(n): A) deoxyribonucleoside triphosphate B) di-nucleotide C) peptide D) ribonucleotide E) ribonucleoside triphosphate
The "energy carrier" ATP is an example of a(n): E) ribonucleoside triphosphate
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.
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.
The DNA oligonucleotide abbreviated pATCGAC: B) has a hydroxyl at its 3' end.
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.
The alkaline hydrolysis of RNA does not produce: D) 3',5'-cAMP.
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) ____
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) 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
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.
The compound that consists of ribose linked by an N-glycosidic bond to N-9 of adenine is: E) adenosine.
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 β configuration; ribonucleotide has the β 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.
The difference between a ribonucleotide and a deoxyribonucleotide is: A) a deoxyribonucleotide has an —H instead of an —OH at C-2.
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.
The double helix of DNA in the B-form is stabilized by: D) nonspecific base-stacking interaction between two adjacent bases in the same strand.
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.
The experiment of Avery, MacLeod, and McCarty in which nonvirulent bacteria were made virulent by transformation was significant because it showed that: B) genes are composed of DNA only.
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.
The nucleic acid bases: D) are roughly planar.
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.
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
The phosphodiester bond that joins adjacent nucleotides in DNA: A) associates ionically with metal ions, polyamines, and proteins.
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.
The phosphodiester bonds that link adjacent nucleotides in both RNA and DNA: E) join the 3' hydroxyl of one nucleotide to the 5' hydroxyl of the next.
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').
The ribonucleotide polymer (5')GTGATCAAGC(3') could only form a double-stranded structure with: D) (5')GCTTGATCAC(3').
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.
Triple-helical DNA structures can result from Hoogsteen (non Watson-Crick) interactions. These interactions are primarily: D) hydrogen bonds involving the bases.
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.
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.
When double-stranded DNA is heated at neutral pH, which change does not occur? B) The covalent N-glycosidic bond between the base and the pentose breaks.
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
Which of the following are possible base compositions for single-stranded RNA? D) all of the above
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')
Which of the following deoxyoligonucleotides will hybridize with a DNA containing the sequence (5')AGACTGGTC(3')? B) (5')GACCAGTCT(3')
Which of the following is a palindromic sequence? A) AGGTCC TCCAGG B) CCTTCC GCAAGG C) GAATCC CTTAGG D) GGATCC CCTAGG E) GTATCC CATAGG
Which of the following is a palindromic sequence? D) GGATCC CCTAGG
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.
Which of the following is not true of all naturally occurring DNA? C) The ratio A+T/G+C is constant for all natural DNAs.
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.
Which of the following statements concerning the tautomeric forms of bases such as uracil is correct? C) The lactam form predominates at neutral pH.
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 β-furanose forms. E) The straight-chain and ring forms undergo constant interconversion.
Which one of the following is true of the pentoses found in nucleic acids? D) The pentoses are always in the β-furanose forms.