MULTIPLE CHOICE.

Choose the one alternative that best completes the statement or

answers the question.
1) The functional unit of genetic information is called the 1) _______
A) gene. B) chromosome.
C) nucleotide. D) protein.

2) The process whereby RNA specifies a DNA sequence is known as 2) _______

A) RNA translation.
B) reverse transcription.
C) RNA transcription.
D) the central dogma of molecular biology.

3) Proteins interact predominantly within which portion of a 3) _______

double-stranded DNA helix?
A) telomere B) supercoil
C) minor groove D) major groove

4) AT-rich DNA will denature/melt 4) _______

A) in accordance with the animal or plant from which it was taken.
B) at a higher temperature than GC-rich DNA.
C) at a lower temperature than GC-rich DNA.
D) usually at the same temperature as GC-rich DNA, with some
minor variations.

5) In Bacteria and most Archaea, the enzyme that introduces negative 5) _______
supercoils into DNA is known as
A) supercoiling gyrase. B) prokaryotic gyrase.
C) DNA gyrase. D) prokaryotic supercoilase.

6) Ciprofloxacin, nalidixic acid, and novobiocin are effective antibiotics 6) _______

because they inhibit the activity of
A) DNA gyrase. B) prokaryotic supercoilase.
C) reverse gyrase. D) RNA topoisomerase.

7) Most plasmids are 7) _______

A) replicated in conjunction with the chromosome.
B) double-stranded DNA, though a few are not.
C) found in eukaryotic cells, though a few are found in prokaryotic
cells.
D) linear, though a few are circular.

8) Housekeeping genes are present in 8) _______

A) neither chromosomes nor plasmids.
B) plasmids.
C) chromosomes and plasmids.
D) chromosomes.

9) The precursor of each new nucleotide in a strand of DNA is a 9) _______

A) deoxynucleoside 3'-triphosphate.
B) deoxynucleoside 3'-diphosphate.
C) deoxynucleoside 5'-diphosphate.
 D) deoxynucleoside 5'-triphosphate.

10) DNA replication always proceeds from the ________ of the incoming 10) ______
nucleotide to the ________ of the previously added nucleotide.
A) 3'-hydroxyl /5'-phosphate B) 5'-hydroxyl / 3'-phosphate
C) 5'-phosphate / 3'-hydroxyl D) 3'-phosphate / 5'-hydroxyl

11) During DNA synthesis, the RNA primer is removed by a(n) 11) ______
A) Pol I exonuclease. B) Okazaki fragment.
C) DNA ligase. D) replisome.

12) The template for RNA polymerase is ________, and the RNA chain 12) ______
growth is ________ the chain growth of DNA.
A) DNA / the opposite of
B) DNA / identical to
C) an independent RNA segment / identical to
D) an independent RNA segment / the opposite of

13) Promoters are specific sequences of ________ that are recognized by 13) ______
________.
A) RNA / DNA polymerase B) DNA / RNA polymerase
C) DNA / sigma factor D) RNA / RNA polymerase

14) An example of nucleotide pairing is 14) ______

A) G and U. B) A and T. C) T and U. D) C and U.

15) Stop codons are also called ________ codons. 15) ______
A) degeneracy B) release factor
C) conversion D) nonsense

16) There are about ________ different tRNAs in bacterial cells and about 16) ______
________ in mammalian cells.
A) 40 / 70 B) 100-110 / 140
C) 200 / 200 D) 60 / 100-110

17) tRNA is released from the ribosome at the ________ site. 17) ______
A) E B) A C) R D) P

18) Which statement is generally TRUE regarding protein synthesis? 18) ______
A) The 23S rRNA plays a role in translocation; the 16S rRNA plays a
role in elongation.
B) The 23S rRNA plays a role in termination; the 16S rRNA plays a
role in elongation.
C) The 23S rRNA plays a role in translocation; the 16S rRNA plays a
role in initiation.
D) The 23S rRNA plays a role in elongation; the 16S rRNA plays a
role in translocation.

19) Streptomycin inhibits ________ of protein synthesis, whereas 19) ______

tetracycline inhibits ________ of protein synthesis.
A) maturation / protein folding B) initiation / elongation
C) initiation / maturation D) elongation / protein folding
 20) In all cells, genes are composed of 20) ______
A) proteins. B) nucleic acids.
C) mRNA. D) chaperones.

21) Which of the following is an example of one codon? 21) ______

A) CCGUAA B) CATT
C) CAG D) GCCATT

22) In all cells a gene encodes for 22) ______

A) a tRNA. B) an rRNA.
C) a protein (via mRNA). D) all of the above.

23) Which of the following is NOT correct regarding DNA and RNA 23) ______
synthesis?
A) DNA is the template for both DNA and RNA synthesis.
B) The template strand is antiparallel to the newly synthesized strand.
C) The overall direction of chain growth is from the 5' to 3' end.
D) Both processes require an RNA primer to begin.

24) Termination of RNA synthesis is ultimately determined by 24) ______

A) special protein factors.
B) CG-rich sequences followed by AT-rich sequences.
C) specific nucleotide sequences on the template strand.
D) exhaustion of RNA polymerase activity.

25) GTP provides energy for 25) ______

A) protein folding. B) translation.
C) DNA replication. D) transcription.

26) Transcription of chaperonins is greatly accelerated when a cell is 26) ______

stressed by
A) excessive heat. B) extremes in pH value.
C) excessive osmotic pressure. D) lack of oxygen.

27) The flow of biological information begins with 27) ______

A) mRNA translation. B) DNA replication.
C) RNA transcription. D) transcriptional regulation.

TRUE/FALSE. Write 'T' if the statement is true and 'F' if the statement is false.
28) Most prokaryotic genomes are double-stranded circular DNA. 28) ______

29) Inverted repeats can lead to stem-loop structures in the DNA molecule. 29) ______

30) In nature, the predominant form of DNA is supercoiled in a negative 30) ______
direction.

31) A polymerase chain reaction (PCR) amplifies a specific DNA sequence 31) ______
up to a billion-fold.

32) The genetic material in a virus is technically called a plasmid. 32) ______
 33) DNA replication is bidirectional in prokaryotes with circular 33) ______
chromosomes.

34) RNA acts at both the genetic and the functional levels. 34) ______

35) Sometimes it appears that bases in tRNA loops are actually paired with 35) ______
bases in other tRNA loops, which is not the case because pairing occurs
exclusively within a given loop.

36) Aminoacyl-tRNA synthetase catalyzes the reaction between the 36) ______
appropriate amino acid and ATP to form an activated amino acid:
amino acid + ATP ↔ aminoacyl-AMP + P-P

37) One high-energy phosphate bond is required for the activation of an 37) ______
aminoacyl-tRNA.

38) rRNA has a functional role in all stages of protein synthesis. 38) ______

39) Proteins known as chaperones are found only in Bacteria, and their 39) ______
sequences vary from organism to organism.

40) Throughout the living world, the genetic code is generally universal; 40) ______
however, there are some slight variations.

41) DNA replication involves the synthesis of an RNA primer on one strand 41) ______
of the DNA.

SHORT ANSWER. Write the word or phrase that best completes each statement or answers
the question.
42) DNA participates in protein synthesis through a(n) ________. 42) _____________

43) A DNA double helix occurs when ________. 43) _____________

44) The artificial construction of a double-stranded nucleic acid by 44) _____________

complementary base pairing of two single-stranded nucleic
acids is known as ________.

45) In Bacteria, a chromosome can be distinguished from a plasmid, 45) _____________

because by definition a chromosome is a genetic element whose
genes encode for ________.

46) A transposable element is the general term for ________. 46) _____________

47) In complementary base pairing of DNA, adenine pairs with 47) _____________
________ (or ________ in RNA) and cytosine always pairs with
________.

48) The function of the DNA polymerase is to ________. 48) _____________

49) DNA replication is started with a(n) ________, which, in most 49) _____________
cases, in vivo is a short stretch of ________.
 50) The function of RNA polymerase is to ________. 50) _____________

51) If a transcription unit contains two or more genes, these genes 51) _____________
are then ________, giving a single RNA molecule.

52) A group of genes that are transcribed together is called a(n) 52) _____________
________, which synthesizes a(n) ________.

53) Bacterial proteins that kill closely related strains or species are 53) _____________
collectively called ________, and the genes that encode for them
are usually present on ________.

54) The genetic code is conventionally written as ________ rather 54) _____________
than ________, because that is the molecule with which the
translation process occurs.

55) The universal start codon is ________, and it codes for ________ 55) _____________
in Bacteria.

56) The structure and function of a protein are determined by its 56) _____________
________ sequence.

57) The sequence of three to nine nucleotides upstream of the start 57) _____________
codon that helps bind the mRNA to the ribosome is known as
the ________.

58) When several ribosomes are simultaneously translating a single 58) _____________
mRNA molecule, the complex is called a(n) ________.

59) To fold properly or to assemble into larger complexes, many 59) _____________
proteins require assistance from other proteins called ________.

60) The twenty-first and twenty-second genetically encoded amino 60) _____________
acids are ________ and ________.

61) ________ is an enzyme that adds phosphodiester bonds 61) _____________

between nicked regions of DNA.

62) A triplet of bases on an mRNA molecule is known as a(n) 62) _____________

________.

63) Each adenine-thymine base pair has ________ hydrogen bonds, 63) _____________
while each guanine-cytosine base pair has ________ hydrogen
bonds.

64) DNA synthesis occurs continuously on the ________ strand, 64) _____________
while on the ________ strand DNA synthesis occurs
discontinuously.

ESSAY. Write your answer in the space provided or on a separate sheet of paper.
65) Name and give one characteristic feature of each of the three major types of
transposable elements.
66) Define genome in terms of the various DNA components of the cell or virus.

67) Explain why DNA, RNA, and proteins are often called informational
macromolecules.

68) Explain the difference between transcription and translation.

69) Explain the concept of semiconservative replication.

70) Discuss the initiation of DNA synthesis in Bacteria using the terms origin of
replication, replication fork, and theta structures.

71) Explain the function of the helicases.

72) In DNA replication, relate the leading strand to the lagging strand.

73) Explain the role of sigma factors in RNA synthesis.

74) Explain the process of RNA transcription using the terms upstream, Pribnow box, and
consensus sequence.

75) Explain the difference between an intrinsic terminator and a Rho-dependent

termination site.

76) How can an open reading frame (ORF) be used to determine the location of a
protein-encoding gene?

77) Describe protein synthesis in terms of initiation, elongation, and termination/release.

78) Explain the A site, the P site, and the E site in terms of the ribosomal subunits.

79) Explain the role of the signal recognition particle (SRP) in protein secretion
compared to SecA.

80) Explain how Escherichia coli can grow with a doubling time of 20 minutes when
chromosome replication takes 40 minutes.

81) Speculate on why the half-life of mRNA is short, while the half-lives of rRNA and
tRNA are long.

82) Speculate on why it may be problematic to clone a gene from a prokaryote into a
eukaryote.

83) Explain why GC-rich DNA requires a higher temperature to denture or melt than
AT-rich DNA.

84) Explain why a cell needs both type I and type II topoisomerases.

85) Explain the differences between viruses and plasmids.

 1) A
2) B
3) D
4) C
5) C
6) A
7) B
8) D
9) D
10) C
11) A
12) B
13) C
14) A
15) D
16) D
17) A
18) C
19) B
20) B
21) C
22) D
23) D
24) C
25) B
26) A
27) B
28) TRUE
29) TRUE
30) TRUE
31) TRUE
32) FALSE
33) TRUE
34) TRUE
35) FALSE
36) TRUE
37) FALSE
38) TRUE
39) FALSE
40) TRUE
41) TRUE
42) RNA intermediate
43) two long antiparallel polynucleotide chains whose purine and pyrimidine bases are held
together by hydrogen bonds
44) hybridization
45) products necessary for essential cellular functions
46) a molecule of DNA that can move from one site on a DNA molecule to another site on the
same molecule or on a different DNA molecule
47) thymine / uracil / guanine
48) catalyze the addition of deoxynucleotides
49) primer / RNA
50) catalyze the formation of phosphodiester bonds between ribonucleotides
51) cotranscribed
52) operon / polycistronic mRNA
53) bacteriocins / plasmids
54) mRNA / DNA
55) AUG / N-formylmethionine
56) amino acid
57) Shine-Dalgarno sequence
58) polysome
59) chaperones (or chaperonins)
60) selenocysteine / pyrrolysine
61) DNA ligase
62) codon
63) two / three
64) leading / lagging
65) Insertion sequences are the smallest, and no additional genetic information is carried other
than what is required to move about the chromosome. Transposons are larger with
additional genes being potentially transposable. Certain viruses such as Mu are also
bacteriophages.
66) Answers will vary but should include a statement that the genome includes the entire
complement of genes in a cell or virus, and that it includes the chromosome as well as
other genetic elements.
67) Answers will vary but should focus on the central dogma of molecular biology and how
each of these three macromolecules holds discrete information in its amino acid (protein)
or nucleotide (DNA and RNA) sequences.
68) Transcription is the process in which mRNA (transcripts) is synthesized from DNA,
whereas translation uses RNA as a template to synthesize peptides (or proteins).
69) During replication, only one of the two strands is used as a template (called the parental
strand) to form a complementary strand called the progeny (or daughter) strand. Therefore,
because only one of the two parental strands is needed for replication, it is considered
partially (or semi-) conservative.
70) The initiation protein DnaA binds to the origin of replication (oriC gene) where DnaB and
DnaC proteins help unwind the DNA. This unwound and accessible region of DNA, called
the replication fork, is where DNA synthesis occurs. Theta structures are used to describe
the appearance of the DNA replication during bidirectional circular DNA replication.
71) Helicase enzymes require energy from ATP to unwind double-stranded DNA into
single-stranded (ss) DNA. Its function is necessary during the initiation of DNA synthesis,
because the polymerase can operate only on ssDNA as the template.
72) Figure 6.16 in the textbook illustrates these two strands during DNA replication. The
leading strand always has a 3'-hydroxyl group nearest to the replication fork, where a new
nucleotide can be added continuously. The other strand lags during replication because the
3'-hydroxy group is at the opposite end of the replication fork, and therefore primase must
make new RNA primers to add on new nucleotides to the growing strand of DNA.
73) A sigma factor is one of five subunits within an RNA polymerase involved exclusively in
transcription of DNA to RNA. It identifies and binds to a promoter (initiation) site, notably
the highly conservative -10 and -35 sites, which creates an RNA polymerase-DNA template
complex that facilitates transcription initiation. A sigma factor then dissociates from the
template after a short stretch of RNA is synthesized. They are also subject to regulation by
anti-sigma factor proteins that temporarily inactivate a sigma factor and thus halt RNA
synthesis.
74) RNA polymerase holoenzyme initiates transcription without the need for a primer. The
sigma factor component of RNA polymerase easily dissociates from the holoenzyme to
first nize the promoter region by specifically binding to the Pribnow box and consensus
recog sequence, which are both upstream of the transcriptional start site.
75) Intrinsic terminators occur at the nucleotide (DNA) level and require no additional protein
involvement. They can develop into secondary structures such as loops, which freely form
through base pairing with itself to ultimately halt transcription of RNA. Rho-dependent
termination also stops RNA transcription but requires the protein Rho, which interacts
with the DNA template-RNA polymerase complex to dissociate the complex at specific
nucleotide sequences.
76) Answers will vary, but an ORF is often predicted by identifying a start codon, followed by
a nucleotide sequence, and a terminating nonsense codon in the same reading frame. Once
an ORF is predicted using computational (i.e., bioinformatics) methods, it then is possible
for a geneticist to identify the mRNA transcript to confirm the ORF is a gene. From the
ORF sequence, the amino acid sequence can be predicted, which aids in the biochemical
characterization of the translated protein.
77) Answers should describe Figure 6.35b in the textbook where initiation involves a complex
formation of the ribosome, initiation proteins, formylmethionine-tRNA, GTP, and mRNA.
Elongation uses elongation factors, GTP, and tRNAs to extend a peptide, and termination
occurs when release factors are recruited to a nonsense codon that breaks apart the tRNA
and polypeptide to release the newly synthesized protein.
78) A theme to this answer should be how a ribosome can interact with and translocate several
molecules (e.g., tRNAs) all at once by having structurally distinct subunits (A, P, and E).
During translation, an incoming tRNA attaches to the A site of the ribosome in the
presence of elongation factor (EF)-Tu. The P site of the ribosome binds the previous tRNA
used with the growing polypeptide chain, and the E site serves as an exit/release point for
the previously used tRNA.
79) SecA and SRP both carry proteins to the membrane secretion system. A protein to be
transported contains a signal sequence, which allows for the binding of either SecA or SRF
depending on the sequence. SRP carries proteins to remain in the cell membrane, and SecA
binds proteins that are to be secreted out of the membrane.
80) Answers will vary, but the principle idea is that essential genes are made earlier during the
replication of its chromosome. When E. coli is placed in a nutrient rich medium, many
pathways, such as amino acid biosynthesis, are not evoked.
81) An important feature present in rRNA and tRNA yet lacking in mRNA is the secondary
structures that make them more difficult to degrade by ribonucleases. These additional
bonds also require more energy input to degrade them.
82) Answers will vary, but one issue is that the universal genetic code does have exceptions.
This means some mRNA could be translated into different proteins in different cells or not
terminated at the correct location. Codon bias is another problem that can influence
translational efficiency. The machinery and methods of post-translational modification are
also very different and can therefore make interdomain cloning difficult.
83) The overall increase in stability of G-C pairing should be emphasized over A-T binding. A
DNA strand with high GC content (low AT) has more triple H bonds compared to an AT
rich (low GC) strand of the same length contains mostly double H bonds. More energy is
therefore required to break more H bonds, and thus GC rich DNA is more heat resistant to
denaturation.
84) Prokaryotes use topoisomerase II (DNA gyrase) to negatively supercoil DNA, which is
critical for packaging large quantities of DNA into a small volume. DNA gyrase also can
work in the opposite way to unwind a supercoil by breaking both strands for DNA
replication. Topoisomerase I instead makes only a break on one of the two DNA strands,
and this nicking process unwinds a coiled region of DNA.
85) A major difference between a plasmid and a virus is that viruses infect other cells to
propagate, and plasmids do not. Viruses also can lyse and kill its host, and plasmids
cann
ot.