Biochemistry Ch 9

Explain the mechanism of the action of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) in treating diseases.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are repetitive stretches of DNA found in archaea and bacteria. The sequences interact with CRISPR-associated proteins or Cas proteins. This combination is used by the bacteria as a protective mechanism against foreign DNA. The proteins are guided by a short strand of RNA to a specific DNA sequence to cut the DNA in two pieces. The bacteria take the RNA strand from the invading organism and use it to target the invader's DNA.

The human genome has 3 × 10^9 base pairs (bp) of DNA. If this were one continuous molecule and extended such that each nucleotide was separated from the adjacent nucleotide by 4 Å, as proposed in the Watson and Crick model, what would the end-to-end distance be? a. 1 meter b. 1 centimeter c. 1000 centimeters d. 1014 Å

a. 1 meter

Calculate the length/diameter ratio for the extended E. coli DNA (4 Å between adjacent nucleotides). E. coli DNA has 2 × 106 bp. a. 4 × 105 b. 1 × 105 c. 3 × 108 d. 3 × 106

a. 4 × 105

Which of the following best describes the structure of a nucleosome? a. DNA wrapped around an octomer containing two each of H2A, H2B, H3, and H4 with H1 on the outside. b. DNA wrapped around an octomer of H1 with H2A,B, H3 & H4 on the outside. c. DNA wrapped around a octomer of either H2A/H2B or H3/H4 with H1 on the outside. d. DNA wrapped around a tetramer of either H2A/H2B or H3/H4 with H1 on the outside. e. None of these

a. DNA wrapped around an octomer containing two each of H2A, H2B, H3, and H4 with H1 on the outside.

Which of the following statements concerning the B-form of DNA is false? a. It twists in a left-handed direction. b. The distance between base pairs is 3.4Å. c. The width of a base pair is about 1.1 nm. d. The diameter, including the phosphate, is about 20 Å.

a. It twists in a left-handed direction.

The hydrogen bonding interactions in a Watson-Crick AT base-pair involve what units in the adenine base? a. N-1 and the amino group on C-6 b. N-1 and N-3 c. N-7 and the amino group on C-6 d. N-7 and C-8

a. N-1 and the amino group on C-6

What distinguishes nucleotides from nucleosides? a. Nucleosides lack the phosphate group. b. Nucleosides lack the sugar group. c. Nucleosides lack a nitrogenous base. d. The two words are synonymous

a. Nucleosides lack the phosphate group.

Which of the following groups is not found in nucleosides? a. Phosphates b. Purines c. Pyrimidines d. Sugars e. All of these are found in nucleosides

a. Phosphates

Protein synthesis can occur while the mRNA molecule is being synthesized in: a. Prokaryotes only. b. Eukaryotes only. c. Unicellular organisms only. d. Multicellular organisms only. e. Plants but not animals

a. Prokaryotes only.

Which of the following statements is true for double-stranded DNA? a. The amount of A is the same as the amount of T, and the amount of G is the same as the amount of C. b. The amount of A is the same as the amount of G, and the amount of T is the same as the amount of C. c. The amount of A is the same as the amount of C, and the amount of G is the same as the amount of T. d. More than one of the above is true.

a. The amount of A is the same as the amount of T, and the amount of G is the same as the amount of C.

Transfer RNA molecules are characterized by all the following, except: a. They are one of the largest of the RNAs. b. Cloverleaf shape. c. Many modified bases. d. Extensive secondary and tertiary structure. e. All of these characterize transfer RNA molecules.

a. They are one of the largest of the RNAs.

Comparison of DNA sequences between widely diverse organisms indicates that all organisms have genetic similarity. a. True b. False

a. True

Which of the following is the most common modification of nucleic acid bases? a. addition of a methyl group b. addition of a carboxylic acid c. addition of a fluorine d. reduction of a carbonyl to an alcohol

a. addition of a methyl group

Which of the following nucleobases is a purine? a. adenine b. cytosine c. thymine d. uracil

a. adenine

The oligonucleotide AGGUCCAUUGAAp, is best described as a. an RNA oligonucleotide with a 3'phosphate b. an RNA oligonucleotide with a 5'phosphate c. a DNA oligonucleotide with a 3'phosphate d. a DNA oligonucleotide with a 5'phosphate

a. an RNA oligonucleotide with a 3'phosphate

Histones are proteins that a. are frequently associated with eukaryotic DNA b. are frequently associated with prokaryotic DNA c. are never found in association with DNA d. contain a high percentage of residues with carboxylic acid side chains e. None of these

a. are frequently associated with eukaryotic DNA

In DNA structure, hydrophobic bonding via pi-clouds is referred to as a. base stacking. b. propeller twist. c. hyperchromicity. d. supercoiling. e. denaturation

a. base stacking.

Which of the following RNAs is the least abundant in a typical cell? a. mRNA b. rRNA c. snRNA d. tRNA

a. mRNA

Cytosine is a(n) _____ nitrogenous aromatic compound. a. one-ring b. two-ring c. four-ring d. six-ring

a. one-ring

The nucleotide sequence of DNA is which level of structure? a. primary b. secondary c. tertiary d. quaternary

a. primary

The outside diameter of a piece of DNA is closest to a. 2 Å. b. 20 Å. c. 200 Å. d. 2000 Å

b. 20 Å.

The human genome is though to have about how many genes? a. 10,000 b. 25,000 c. 50,000 d. 100,000 e. None of these is close to the estimate

b. 25,000

Which piece of DNA will have the higher Tm, one with a cytosine plus guanine content of 30% or one with a cytosine plus guanine content of 50% if both are heated under the same experimental conditions? a. 30% cytosine plus guanine will have the higher Tm. b. 50% cytosine plus guanine will have the higher Tm. c. Their Tm's will be the same. d. There's no way to predict for this information.

b. 50% cytosine plus guanine will have the higher Tm.

Which is the dominant form of DNA found in the cell? a. A b. B c. Z d. H e. All forms of DNA are found in equal amounts

b. B

The most recent discoveries in RNA research are: a. mRNA and tRNA b. MiRNA and SiRNA c. snRNA and snurps d. tRNA and MiRNA

b. MiRNA and SiRNA

Which of the following is not true? a. The amount of UV absorbance increases, but the wavelength does not change as DNA nears its melting point b. Once DNA is denatured, it cannot renature c. The melting temperature partially depends on the GC content d. The nature of the solvent the DNA is in can affect the melting temperature

b. Once DNA is denatured, it cannot renature

The Tm for melting the double helix is: a. The temperature at which the helix starts to open. b. The midpoint of the range over which the helix denatures. c. The temperature at which the helix is completely open. d. The energy needed to melt the DNA. e. None of these is correct.

b. The midpoint of the range over which the helix denatures.

Which best describes the relationship between the nucleobases in a piece of DNA? a. They are parallel to the helical axis. b. They are perpendicular to the helical axis. c. They are randomly oriented with respect to the helical axis. d. They are covalently bonded between the nucleobases across from one anothr in the two DNA strands e. The four nucleobases are present in equal quanitites in a piece of DNA

b. They are perpendicular to the helical axis.

The backbone of nucleic acids consists of a. a phosphodiester bond between the 2' and 5' hydroxyl groups of neighboring sugars b. a phosphodiester bond between the 3' and 5' hydroxyl groups of neighboring sugars c. a glycosidic bond between a pyrimidine and a sugar d. a glycosidic bond between a purine and a sugar

b. a phosphodiester bond between the 3' and 5' hydroxyl groups of neighboring sugars

In the DNA in chromatin, substitution mutations: a. are at a maximum in the linker regions b. are at a maximum in the nucleosomes c. occur maximally in the same places as deletion mutations d. are rarely seen, but deletion mutations are common

b. are at a maximum in the nucleosomes

In a melting profile for DNA, the absorbance at 260 nm increases as result of the disruption of the DNA structure. What is the fundamental physical basis for the absorbance increase? a. the effective concentration of DNA changes b. denatured DNA absorbs light more strongly than native DNA because the bases have become unstacked c. native DNA absorbs light more strongly than denatured DNA because the bases are stacked d. the absorbance of DNA is highly sensitive to temperature

b. denatured DNA absorbs light more strongly than native DNA because the bases have become unstacked

Base pairs with a propeller-twist a. are found only in Z-DNA b. have optimum base stacking c. bind water in the minor groove d. have stronger hydrogen bonds than base pairs without a propeller twist

b. have optimum base stacking

The strands in the double helix a. both run in the same 3' → 5' direction, i.e., they are parallel. b. have their 3' → 5' directions opposed, i.e., they are anti-parallel. c. can be either parallel or anti-parallel. d. are perpendicular to one another. e. None of these

b. have their 3' → 5' directions opposed, i.e., they are anti-parallel.

Eukaryotic mRNA requires a. less processing after synthesis than prokaryotic mRNA. b. more processing after synthesis than prokaryotic mRNA. c. about the same amount of processing after synthesis as prokaryotic mRNA.

b. more processing after synthesis than prokaryotic mRNA.

Supercoiling of DNA a. is not observed in prokaryotes b. requires the action of topoisomerase enzymes c. does not require ATP d. is not observed in eukaryotes

b. requires the action of topoisomerase enzymes

The double helix of DNA is which level of structure? a. primary b. secondary c. tertiary d. quaternary e. None of these

b. secondary

Which of the following sequences of DNA is most likely to form Z-DNA? a. 5'-ATCTACATCTACATAGATAT-3' 3'-TAGATGTAGATGTATCTATA-5' b. 5'-AAAAAAAAAAAAAAAAAAAA-3' 3'-TTTTTTTTTTTTTTTTTTTT-5' c. 5'-GCGCGCGCGCGCCGCGCGCG-3' 3'-CGCGCGCGCGCGCGCGCGCG-5' d. 5'-GGGGGGGGGGGGGGGGGGGG-3' 3'-CCCCCCCCCCCCCCCCCCCC-5'

c. 5'-GCGCGCGCGCGCCGCGCGCG-3' 3'-CGCGCGCGCGCGCGCGCGCG-5'

Which contains a phosphoanhydride bond? a. DNA b. RNA c. ATP d. AMP e. None of these

c. ATP

Eukaryotic and prokaryotic ribosomes can be compared in all these ways, except: a. Both have large and small subunits. b. Eukaryotic ribosomes are larger. c. Both contain the same number of RNA molecules. d. Eukaryotic ribosomes contain more proteins. e. All of these statements are accurate comparisons.

c. Both contain the same number of RNA molecules.

The helix can be untwisted by the action of which type of topoisomerase? a. Type I only b. Type II only c. Both types I and II d. Topoisomerases cannot untwist the helix

c. Both types I and II

RNA is hydrolyzed in basic solution, but DNA is not. This occurs because a. thymine is found in DNA, and uracil is not b. DNA is double stranded, and RNA is single stranded c. DNA contains 2'-deoxyribose, but RNA does not d. RNA has modified bases, but DNA does not

c. DNA contains 2'-deoxyribose, but RNA does not

Where can drugs or polypeptides bind to DNA? a. The minor groove only. b. The major groove only. c. Either the minor or major groove. d. Neither the minor or major groove.

c. Either the minor or major groove.

The study of DNA changes that are not reflected in the base sequence is called: a. Molecular biology b. Histology c. Epigenetics d. Physical genetics

c. Epigenetics

Which of the following statements concerning transfer RNA is true? a. It has the highest molecular weight of the commonly occurring forms of RNA. b. It has no internal hydrogen bonding. c. It bonds to amino acids in the course of protein synthesis. d. It is the smallest of the RNA types e. All of these are true

c. It bonds to amino acids in the course of protein synthesis.

How does the enzyme ATP(CTP):tRNA nucleotidyletransferase aid in quality control of formation of tRNA? a. It puts a CCA on the 5' end b. It puts a CCA on the 3' end c. It puts a CCACCA on the 3' end of defective tRNA molecules or tRNA-like molelcules that are not true tRNA d. None of these

c. It puts a CCACCA on the 3' end of defective tRNA molecules or tRNA-like molelcules that are not true tRNA

Which conclusion can be drawn from the experimental observation that a single strand of DNA contains 2100 dA residues and 1800 dT residues? a. There must have been some loss of material in the extraction because the number of dA and dT residues must be the same. b. This is a palindromic sequence. c. There must be 2100 dT and 1800 dA residues on the complementary strand. d. This must be prokaryotic DNA e. None of these

c. There must be 2100 dT and 1800 dA residues on the complementary strand.

Propeller twists occur in B-DNA so that a. Z-DNA can form b. base pairing distances are optimized c. base stacking can better occur d. none of these

c. base stacking can better occur

Micro RNA technology is used in the treatment of _____. a. osteoporosis b. migraine c. hepatitis C d. anaemia

c. hepatitis C

Histones contain large amounts of which of the following amino acids? a. histidine b. glutamic acid c. lysine d. leucine e. tryptophan

c. lysine

Deoxythymidylate (dT) is a: a. purine base b. pyrimidine base c. pyrimidine based nucleotide d. purine based nucleotide e. nucleoside

c. pyrimidine based nucleotide

The following types of RNA are common to all organisms, except: a. mRNA b. rRNA c. snRNA d. tRNA e. All types are found in all organisms

c. snRNA

Topoisomerases are associated with a. production of RNA from DNA. b. joining of nucleotide monomers to make polynucleotides. c. supercoiling of DNA. d. ribosomes. e. All of these

c. supercoiling of DNA.

The _____ structure in DNA refers to the supercoiling of the DNA molecule. a. primary b. secondary c. tertiary d. quaternary

c. tertiary

Which of the following characteristics is associated with the B form of DNA? a. the sugars are located in the interior of the double helix b. the distance between base pairs along the axis of the helix is 8 Å c. the major and minor grooves are readily apparent d. the planes of the bases make about a 20 degree angle with the helix axis

c. the major and minor grooves are readily apparent

Which of the following modifications is likely to happen to the mRNA in a eukaryotic cell? a. capping of the 5' end b. addition of a poly-A tail to the 3' end c. removal of intervening sequences (introns) d. All of the above occur in eukaryotic cells.

d. All of the above occur in eukaryotic cells.

Quaternary structure refers to the non-covalent interaction(s) between polymeric units, such as two or more monomer protein units that noncovalently interact. Which of the following scenarios for nucleic acids most closely resembles quaternary structure? a. self-assembly of subunits in the tobacco mosaic virus b. interaction of DNA with proteins c. RNA and protein association in ribosomes d. All of these e. None of these

d. All of these

Which of the following can be an epigenetic change to chromatin? a. methylation b. acetylation c. phosphorylation d. All of these e. None of these

d. All of these

Which of the following statements concerning ribosomes is true? a. They consist of two RNA subunits, one of which is larger than the other. b. They contain both RNA and protein. c. They can be dissociated and reassembled by controlling the Mg2+ concentration of the medium. d. All of these are true

d. All of these are true

The glyosidic linkage in a nucleoside forms from the C-1' carbon of the sugar to the _____. a. N-9 nitrogen of pyrimidines b. N-6 nitrogen of purines c. N-2 nitrogen of purines d. N-1 nitrogen of pyrimidines

d. N-1 nitrogen of pyrimidines

Which of the following bases is not found in RNA? a. A b. C c. G d. T e. All of these are found in RNA.

d. T

The A and B forms of DNA a. both have 10 base pairs per turn of the helix b. both have 11 base pairs per turn of the helix c. are both left-handed helices d. are both right-handed helices

d. are both right-handed helices

The fundamental differences between RNA and DNA are a. the organic bases only b. bases, ribose units, and the phosphodiester linkage c. bases, ribose units, and the glycosidic bond type d. bases and the ribose units only

d. bases and the ribose units only

The melting profile for a DNA is found to differ in two different salt solutions. In 0.001 M NaCl, Tm = 55° C, and in 0.01 M NaCl, Tm = 65° C. The fundamental reason for this change is a. higher salt concentration increases the electrostatic repulsions between phosphates b. the base stacking is more effective in high salt c. hydrogen bonding between complementary bases in enhanced at high salt d. higher salt concentration decreases the electrostatic repulsions between phosphates

d. higher salt concentration decreases the electrostatic repulsions between phosphates

Deoxyadenylate (dA) is a: a. purine base b. pyrimidine base c. purine based nucleoside d. purine based nucleotide e. pyrimidine based nucleotide

d. purine based nucleotide

The three dimensional structure of nucleic acids can include all except: a. Supercoiling b. Base stacking c. Hairpin loops d. Circular molecules e. All of these can be included in the three dimensional structure

e. All of these can be included in the three dimensional structure

Which of the following statements concerning small nuclear RNA is true? a. This RNA is usually found in snurps. b. This RNA is involved in removing exons from the RNA. c. This RNA was the first RNA shown to have catalytic activity. d. This RNA is small in size. e. All of these describe small nuclear RNA.

e. All of these describe small nuclear RNA.

Which of the following is the most distinguishing difference between a purine and a pyrymidine a. purines are found in DNA while pyrimidines are found in RNA b. purines have nitrogens in the rings while pyrimidines do not c. pyrimidines have nitrogens in the rings while purines do not d. purines are found in RNA while pyrimidines are found in DNA e. purines are double ring structures while pyrimidines have a single ring

e. purines are double ring structures while pyrimidines have a single ring

The Z-form of DNA a. does not exist in nature. b. is right-handed. c. tends to occur in purine-only sequences. d. tends to occur in pyrimidine-only sequences. e. tends to occur in alternating purine-pyrimidine sequences.

e. tends to occur in alternating purine-pyrimidine sequences.