Answers to chapter 7 questions
Mastering Concepts
7.1
1. How did Griffith’s research, coupled with the work of Avery and his colleagues,
demonstrate that DNA, not protein, is the genetic material?
Griffith’s research established that a lethal strain of bacteria (type S) could transfer
a then-unknown molecule to nonlethal bacteria (type R) and confer the ability to kill
mice. Avery and his colleagues added enzymes that destroyed either proteins or
DNA to the mixtures that Griffith used in his experiments. These experiments
showed that DNA, not protein, changed type R bacteria from nonlethal to lethal.
2. How did the Hershey–Chase “blender experiments” confirm Griffith’s results?
The Hershey-Chase “blender experiments” used radioactive sulfur to label the
protein coats of one batch of bacteriophages and used radioactive phosphorus to
label the DNA of another batch of bacteriophages. Both batches of viruses were
allowed to infect bacteria. Then the solutions were separately blended at high
speeds to separate viral protein coats from bacterial cells. Radioactively labeled
bacteria were found only in the batches that had been infected by phages with
radioactively labeled DNA. The protein-labeled phages did not transmit
radioactivity to the bacteria they had infected. These experiments confirmed
Griffith’s conclusion that DNA, not protein, is the genetic material.
7.2
1. What are the components of DNA and its three-dimensional structure?
A DNA molecule is composed of subunits called nucleotides. Each nucleotide is
composed of a deoxyribose sugar bonded to a phosphate group and a nucleotide
base (adenine, thymine, cytosine, or guanine). The three-dimensional structure of
DNA is a double helix, which resembles a twisted ladder.
2. What evidence enabled Watson and Crick to decipher the structure of DNA?
The evidence included Rosalind Franklin’s X-ray diffraction photo of a crystal of
DNA, plus Erwin Chargaff’s work that showed that DNA contains equal amounts of
adenine and thymine and equal amounts of cytosine and guanine.
3. Identify the 3′ and 5′ ends of a DNA strand.
The 3’ and 5’ designators refer to opposite ends of a single DNA strand. The 5’ end
has a phosphate group attached to the 5’ carbon atom, whereas the 3’ end has the
sugar’s -OH (hydroxyl group) attached to the 3’ carbon atom.
7.3
1. What is the relationship between a gene and a protein?
A gene is a strand of DNA that encodes a protein.
2. What are the two main stages in protein synthesis?
Transcription and translation are the two main stages in protein synthesis.
3. What are the three types of RNA, and how does each contribute to protein
synthesis?
Messenger RNA (mRNA) carries the instructions for building the protein; transfer
RNA (tRNA) carries the appropriate amino acid to the ribosome; and ribosomal RNA
(rRNA) is the major component of a ribosome, which is the structure where amino
acids are assembled into polypeptides.
7.4
1. What happens during each stage of transcription?
The steps of transcription are initiation, elongation, and termination. During
initiation, enzymes unzip the DNA, and RNA polymerase binds to the promoter.
During elongation, RNA polymerase uses the DNA template strand to add
complementary nucleotides to the 3’ end of the growing RNA strand. During
termination, synthesis of the RNA molecule ends and the DNA molecule is “zipped”
back into its double helix form.
2. Where in the cell does transcription occur?
Transcription occurs in the nucleus of a eukaryotic cell.
3. What is the role of RNA polymerase in transcription?
RNA polymerase is an enzyme that uses the DNA template to bind additional
nucleotides to the 3’ end of the growing chain of RNA.
4. What are the roles of the promoter and terminator sequences in transcription?
The promoter signals the start of a gene, and the terminator signals the end of a
gene. RNA polymerase recognizes the promoter and terminator, so it starts and
stops transcription at the correct positions along the DNA template strand.
5. How is mRNA modified before it leaves the nucleus of a eukaryotic cell?
Before it leaves the nucleus of a eukaryotic cell, mRNA is altered in the following
ways: a cap is added to the 5’ end of the mRNA molecule; a poly A tail is added to the
3’ end; introns are removed and exons are spliced together.
7.5
1. How did researchers determine that the genetic code is a triplet and learn which
codons specify which amino acids?
Researchers knew that life uses four nucleotides and 20 amino acids. They
reasoned that the genetic code could not reflect 1-base or 2-base “words,” because
neither could encode enough amino acids. A triplet code (3-base “words”) could
potentially encode 64 amino acids, which is more than enough for the 20 amino
acids found in biological proteins.
They deciphered the genetic code by adding synthetic mRNA molecules to test tubes
containing all the ingredients needed for translation. They analyzed the sequences
of the resulting polypeptides to determine which codons correspond to which
amino acids.
2. What happens in each stage of translation?
In initiation, ribosomal subunits bind to mRNA, and a tRNA carrying the first amino
acid (methionine) attaches to the first codon. In elongation, the ribosome moves
along the mRNA, adding new amino acids to the growing polypeptide. In
termination, the ribosome reaches a stop codon and releases the last tRNA and the
polypeptide. The ribosomal subunits then dissociate from the mRNA.
3. Where in the cell does translation occur?
Translation occurs at ribosomes, which are either free in the cytoplasm or attached
to the rough ER.
4. How are polypeptides modified after translation?
Polypeptides must be folded to become functional proteins. In addition, sometimes
amino acids are cut out of the chain, and sometimes multiple polypeptides join
together.
7.6
1. What are some reasons that cells regulate gene expression?
Protein production costs a lot of energy; the regulation of gene expression avoids
the production of unnecessary proteins and therefore saves energy.
2. How do proteins determine whether a bacterial operon is expressed?
A repressor protein binds to an operator and prevents the genes in the operon from
being transcribed.
3. How do enhancers and transcription factors interact to regulate gene expression?
Transcription factors bind to certain DNA sequences to regulate transcription, for
example by preparing a promoter site to bind RNA polymerase. Transcription won’t
occur without these factors. Enhancers are sequences of DNA outside of the
promoter. Transcription factors can bind to the enhancers to help regulate gene
expression.
4. What are some other ways that a cell controls which genes are expressed?
Cells can keep DNA coiled or attach methyl groups that inactivate genes. After
transcription, different combinations of introns can be removed. mRNA can be
confined to the nucleus or rapidly degraded. Proteins can also be degraded or
modified in processing.
7.7
1. What is a mutation?
A mutation is a change in a DNA sequence.
2. What are the types of mutations, and how does each alter the encoded protein?
In a substitution mutation, one DNA base is replaced with another. The mutation
may be have no effect on the resulting protein (silent mutation), change one amino
acid (missense mutations), or create a stop codon in the middle of the mRNA
(nonsense mutation). Insertions and deletions add or remove nucleotides; they
often shift the “reading frame” of a gene. Such a frameshift mutation may alter many
amino acids in the protein, drastically changing its shape and function. An insertion
of three nucleotides adds one amino acid to the encoded protein, and a deletion of
three nucleotides removes one amino acid. Expanding repeat mutations increase the
number of copies of three-or four-nucleotide sequences over several generations.
This causes extra amino acids to be inserted into a protein, deforming it. Large-scale
mutations delete, duplicate, or invert large portions of a chromosome. The effects
depend on whether genes are disrupted.
3. What causes mutations?
Mutations are often caused by DNA replication errors, exposure to chemicals or
radiation, and transposons. Large-scale mutations may result from errors in
meiosis.
4. What is the difference between a germline mutation and a somatic mutation?
A germline mutation is one that occurs in a cell that will give rise to a sperm or an
egg cell. A somatic mutation occurs within a non-germline body cell.
5. How are mutations important?
Some mutations cause diseases. Mutations also produce genetic variability, which is
the raw material of evolution. Scientists induce mutations to learn how genes
normally function and to develop new varieties of crop plants.
7.8
1. What question about the FOXP2 gene were the researchers trying to answer?
Researchers wanted to know how the human version of the FOXP2 gene differs from
that of other primates. They also wanted to know if human-specific mutations could
be linked to the acquisition of language.
2. What insights could scientists gain by intentionally mutating the FOXP2 gene in a
developing human? Would such an experiment be ethical?
Many answers are possible, but one idea would be to mutate the FOXP2 gene so that
it is nonfunctional at different stages of development to learn whether it is active
through development or just in a critical window. Such an experiment would not be
ethical.
Write It Out
1. Explain how Griffith’s experiment and Avery, MacLeod, and McCarty’s experiment
determined that DNA in bacteria transmits a trait that kills mice.
Some strains of Streptococcus pneumoniae bacteria (type S) cause pneumonia,
whereas others (type R) do not. Griffith’s experiment determined that heat-killed
type S bacteria can transform type R bacteria into pneumonia-causing killers. Avery,
MacLeod, and McCarty’s followup experiment determined that DNA, not proteins,
from the dead type S bacteria altered the type R bacteria. When heat-killed type S
bacteria were treated with a protein-destroying enzyme, the type R bacteria still
became killers. But when type S bacteria were treated with DNA-destroying
enzymes, the type R bacteria remained harmless.
2. Describe the three-dimensional structure of DNA.
DNA is a double helix that resembles a twisted ladder. In this molecule, the “twin
rails” of the ladder are alternating units of deoxyribose and phosphate, and the
ladder’s rungs are A-T and G-C base pairs joined by hydrogen bonds.
3. Explain Chargaff’s observation that a DNA molecule contains equal amounts of A
and T and equal amounts of G and C.
DNA has two complementary strands. Each adenine (A) on one strand pairs with a
thymine (T) on the opposite strand. Likewise, each guanine (G) on one strand pairs
with a cytosine (C) on the other strand. Therefore, DNA has one T for every A and
has one C for every G.
4. Write the complementary DNA sequence of each of the following base sequences:
a.
AGGCATACCTGAGTC
b.
GTTTAATGCCCTACA
c.
AACACTACCGATTCA
The complementary sequences are:
a) TCCGTATGGACTCAG
b) CAAATTACGGGATGT
c) TTGTGATGGCTAAGT
5. Put the following in order from smallest to largest: nucleotide, genome,
nitrogenous base, gene, nucleus, cell, codon, chromosome.
From smallest to largest, the order is nitrogenous base, nucleotide, codon, gene,
chromosome, nucleus, and cell.
6. What is the function of DNA?
The function of much of the DNA in a cell is not known, but some of it encodes the
cell’s RNA and proteins.
7. Use figure 7.9 to describe the structural and functional differences between RNA
and DNA.
RNA nucleotides contain a sugar called ribose; DNA nucleotides contain a similar
sugar called deoxyribose. RNA has the nitrogenous base uracil, which behaves
similarly to the thymine in DNA - that is, both uracil and thymine form
complementary base pairs with adenine. RNA can be single-stranded; DNA is
double-stranded. RNA can catalyze chemical reactions, a role not known for DNA.
8. Explain how information in DNA is transcribed and translated into amino acids.
Transcription copies the information encoded in a DNA base sequence into the
complementary language of mRNA. Once transcription is complete and mRNA is
processed, the cell is ready to translate the mRNA message into a sequence of amino
acids that builds a protein. Transcription occurs in the nucleus, and translation
occurs at ribosomes in the cytoplasm.
9. Some people compare DNA to a blueprint stored in the office of a construction
company. Explain how this analogy would extend to transcription and translation.
Transcription would be the process of scanning or copying the blueprints so that the
contractor would have a set at the construction site. Translation would be the
process of the contractor directing the assembly of all the raw materials at the site
into the finished building.
10. List the three major types of RNA and their functions.
Messenger RNA (mRNA) carries the information that specifies a protein. Ribosomal
RNA (rRNA) combines with proteins to form a ribosome, the physical location of
protein synthesis. Transfer RNA (tRNA) molecules are “connectors” that bind
mRNA codons at one end and specific amino acids at the other. Their role is to carry
each amino acid to the ribosome at the correct spot along the mRNA molecule.
11. List the sequences of the mRNA molecules transcribed from the following
template DNA sequences:
a.
TGAACTACGGTACCATAC
b.
GCACTAAAGATC
The complementary sequences are:
a) ACUUGAUGCCAUGGUAUG
b) CGUGAUUUCUAG
12. How many codons are in each of the mRNA molecules that you wrote for
question 11?
a. 6 codons
b. 4 codons
13. Refer to the figure to answer these questions:
a. Add labels for mRNA (including the 5’ and 3’ ends) and tRNA. In addition, draw
the RNA polymerase enzyme and the ribosomes, including arrows indicating the
direction of movement for each.
b. What are the next three amino acids to be added to polypeptide b?
c. Fill in the nucleotides in the mRNA complementary to the template DNA strand.
d. What is the sequence of the DNA complementary to the template strand (as much
as can be determined from the figure)?
e. Does this figure show the entire polypeptide that this gene encodes? How can you
tell?
f. What might happen to polypeptide b after its release from the ribosome?
g. Does this figure depict a prokaryotic or a eukaryotic cell? How can you tell?
a. Refer to figures 7.10 (Transcription Creates mRNA) and 7.15 (Translation
Creates the Protein).
b. Lys-Gly-Ser
c. The remaining mRNA nucleotides are (from left to right): CUUAGGACACC
d. The complementary DNA sequence is (from left to right): CTTAGGACACC
e. No, because the last codon would be a stop codon (UAA, UAG, or UGA)
f. The peptide would fold into its proper shape and then either begin performing
its function in the cell or be exported to the cell’s exterior.
g. The figure depicts a prokaryotic cell. In eukaryotes, the mRNA is fully
synthesized in the nucleus, undergoes processing, and then is transcribed in
the cytoplasm. The figure shows translation occurring simultaneously with
transcription, which only occurs in prokaryotes.
14. Is changing the first nucleotide in a codon more likely or less likely to change the
encoded amino acid than changing the third nucleotide in a codon?
Consult the dictionary of the genetic code. Changing the first nucleotide in a codon
typically changes the encoded amino acid. In contrast, changing the third nucleotide
of a codon often does not change the encoded amino acid (e.g., look at the codons for
serine, proline, and alanine).
15. Titin is a muscle protein whose gene has the largest known coding sequence—
80,781 DNA bases. How many amino acids long is titin?
The titan protein is 26,927 amino acids (80,781 nucleotides divided by 3
nucleotides per amino acid).
16. If a protein is 1259 amino acids long, what is the minimum size of the gene that
encodes the protein? Why might the gene be longer than the minimum?
1259 x 3 = 3,777 bases plus three bases for stop codon = 3,780 bases. The gene
would have bases for the leader sequence on the mRNA and might include any
number of introns.
17. How did researchers reason that a combination of at least three RNA bases must
specify each amino acid?
Since RNA has four types of bases and proteins have 20 types of amino acids, one
RNA base could not specify each amino acid. If a combination of two RNA bases
specified one amino acid, then only 16 amino acids could be encoded (four
possibilities for position 1 of the codon multiplied by four possibilities for position 2
equals 16 combinations of RNA bases). Therefore, at least three RNA bases must
specify each amino acid (4x4x4=64). Later studies confirmed that each codon
contains three RNA bases.
18. The roundworm C. elegans has 556 cells when it hatches. Each cell contains the
entire genome but expresses only a subset of the genes. Therefore, the cells
“specialize” in particular functions. List all of the ways that a roundworm cell might
silence the unneeded genes.
An individual roundworm cell can keep some of its DNA coiled or attach methyl
groups to inactivate genes. Transcription factors and enhancers needed for
transcription might not be available. After transcription, different combinations of
introns can be removed. mRNA can be confined to the nucleus or rapidly degraded.
The proteins can also be degraded.
19. The genome of the human immunodeficiency virus (HIV) includes nine genes.
Two of the genes encode four different proteins each. How is this possible?
The genes each contain several introns. To make each protein, a different
combination of introns is removed with the remaining mRNA spliced together.
20. The shape of a finch’s beak reflects the expression of a gene that encodes a
protein called calmodulin. A cactus finch has a long, pointy beak; its cells express the
gene more than a ground finch, which has a short, deep beak. When researchers
boosted gene expression in a ground finch embryo, the bird’s upper beak was longer
than normal. Develop a hypothesis that explains this finding.
One possibility is that the calmodulin gene influences the length of the upper beak.
Boosting calmodulin expression in the ground finch would therefore promote
additional growth in the bird’s upper beak. Perhaps the ground finch’s lower beak
was unaffected because other genes influence its size.
21. If a gene is like a cake recipe, then a mutation is like a cake recipe containing an
error. List the major types of mutations, and describe an analogous error in a cake
recipe.
Missense: instead of baking powder, the recipe lists baking soda. Nonsense: the
recipe cuts off after a partial list of ingredients. Insertion (3 nucleotides): the recipe
lists one extra ingredient. Deletion (three nucleotides): the recipe leaves out one
ingredient. Frameshift: the word spacing is altered, e.g., flour, wate, regg, ssuga,
rsalt etc. Expanding repeat: the recipe lists an ingredient repeatedly.
22. A protein-encoding region of a gene has the following DNA sequence:
TTTCATCAGGATGCAACT
Determine how each of the following mutations alters the amino acid sequence:
a.
substitution of an A for the T in the first position
b.
substitution of a G for the C in the 17th position
c.
insertion of a T between the fourth and fifth DNA bases
d.
insertion of a GTA between the 12th and 13th DNA bases
e.
deletion of the first DNA nucleotide
a. Nonsense mutation; instead of encoding the amino acid lysine, the codon would
recruit a release factor protein.
b. Missense mutation; instead of incorporating the amino acid cysteine, the protein
would incorporate serine.
c. Frameshift mutation; valine is replaced by aspartic acid, and the remainder of the
protein is disrupted.
d. Insertion mutation; the amino acid histidine is added within the protein.
e. Frameshift mutation; the entire protein is disrupted.
23. Explain how a mutation in a protein-encoding gene, an enhancer, or a gene
encoding a transcription factor can all have the same effect on an organism.
A mutation in the gene can lead to a polypeptide that is too short or has the wrong
amino acids; in either case it will not fold properly, and therefore will not function
properly. This means that the organism will not express the effects of that protein.
A mutation to either an enhancer or a gene encoding a transcription factor can leave
the transcription factor unable to bind to the gene, blocking transcription.
24. How can a mutation alter the sequence of DNA bases in a gene but not produce a
noticeable change in the gene’s polypeptide product? How can a mutation alter the
amino acid sequence of a polypeptide yet not alter the organism?
A mutation may alter the sequence of a gene but not produce a noticeable change in
the gene’s polypeptide sequence because several different codons encode most
amino acids. A mutation may alter the amino acid sequence but not alter the
phenotype because the protein’s shape may not change, other proteins may take
over the altered protein’s function, or the protein may not be essential.
25. Describe the mutation shown in figure 7.26 and explain how the mutation affects
the amino acid sequence encoded by the gene.
Figure 7.26 shows a deletion mutation. Since exactly three nucleotides are deleted,
the reading frame of the gene remains the same. One amino acid is deleted from the
protein.
26. Parkinson disease causes rigidity, tremors, and other motor symptoms. Only 2%
of cases are inherited, and these tend to have an early onset of symptoms. Some
inherited cases result from mutations in a gene that encodes the protein parkin,
which has 12 exons. Indicate whether each of the following mutations in the parkin
gene would result in a smaller protein, a larger protein, or no change in the size of
the protein.
a. deletion of exon 3
b. deletion of six consecutive nucleotides in exon 1
c. duplication of exon 5
d. disruption of the splice site between exon 8 and intron 8
e. deletion of intron 2
a) Smaller protein. b) Smaller protein. c) Larger protein. d) No change. e) No
change.
27. Consult the genetic code to write codon changes that could account for the
following changes in amino acid sequence.
a. tryptophan to arginine
b. glycine to valine
c. tyrosine to histidine
Multiple answers are possible; these are examples. a) UGG to CGG. b) GGU to GUU. c)
UAC to CAC.
28. Researchers use computer algorithms that search DNA sequences for indications
of specialized functions. Explain the significance of detecting the following
sequences:
a. a promoter
b. a sequence of 75 to 80 nucleotides that folds into a backwards letter L
c. RNAs with poly A tails
a) A promoter signals the start of a gene. b) These nucleotides compose a tRNA
molecule. c) The poly A tails signal an mRNA.
29. In a disorder called gyrate atrophy, cells in the retina begin to degenerate in late
adolescence, causing night blindness that progresses to blindness. The cause is a
mutation in the gene that encodes an enzyme, ornithine aminotransferase (OAT).
Researchers sequenced the OAT gene for five patients with the following results:
• Patient A: A change in codon 209 of UAU to UAA
• Patient B: A change in codon 299 of UAC to UAG
• Patient C: A change in codon 426 of CGA to UGA
• Patient D: A two-nucleotide deletion at codons 64 and 65 that results in a
UGA codon at position 79
• Patient E: Exon 6, including 1071 nucleotides, is entirely deleted.
a. Which patient(s) have a frameshift mutation?
b. How many amino acids is patient E missing?
c. Which patient(s) will produce a shortened protein?
a) Patient D. b) 357 amino acids. c) All will produce a shortened protein.
Pull It Together
1. Why is protein production essential to cell function?
Cell structure and function depend on proteins. Enzymes are proteins and are
required for almost all chemical reactions to occur within a cell. Without enzymes,
the cell could not synthesize ATP, which the cell uses for energy. In addition,
proteins embedded within cell membranes have several important functions such as
adhesion, cell recognition, and transport of water-soluble molecules; without
protein production, new cell membrane proteins could not be produced when the
cell divides.
2. Where do promoters, terminators, stop codons, transcription factors, RNA
polymerase, and enhancers fit into this concept map?
Both “Transcription factors” and “RNA polymerase” can connect with the phrase
“bind to” to “Promoters.” Both “Promoters” and “Terminators” can connect with the
phrase “are non-coding sequences of” to “DNA.” “Promoters” can also connect with
the phrase “signals the starting point for ” to “Transcription.” “Terminators” can also
connect with the phrase “signals the end point for” to “Transcription.” “Stop codons”
can connect with the phrase “ends the process of” to “Translation.” “Transcription
factors” can connect with the phrase “bind to” to “Enhancers.”
3. Use the concept map to explain how DNA nucleotides are related to amino acids.
DNA nucleotides are transcribed to RNA nucleotides. An mRNA molecule is divided
into three-nucleotide codons, each of which corresponds to one amino acid.
4. Use the concept map to explain why a mutation in DNA sometimes causes protein
function to change.
A mutation is a change in a DNA sequence. If the mutation leads to a change in the
encoded amino acid sequence, the protein’s shape could be altered or destroyed.
Therefore, mutations could lead to changes in protein function. (A gene that
undergoes a neutral mutation, however, encodes the same amino acid sequence. The
protein’s function therefore does not change.)