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. A G G C A T A C C T G A G T C
b. G T T T A A T G C C C T A C A
c. A A C A C T A C C G A T T C A
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. T G A A C T A C G G T A C C A T A C
b. G C A C T A A A G A T C
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