Chapter 7 - From DNA to Protein: How Cells Read the Genome

Question 1

What is the main function of the TATA-binding protein?

• to help initiate DNA replication
• to inhibit DNA replication until S phase
• to promote initiation of transcription
• to inhibit transcription until transcriptional activators bind

Answer 1

To promote initiation of transcription.

(TATA-binding protein bends the DNA, which signals assembly of the transcription complex, increasing transcription initiation.)

Question 2

Which of the following events occur when TATA-binding protein binds to the DNA?
Choose all that apply.

• An eight-stranded β-sheet domain of the TATA-binding protein lies on the DNA helix.
• The DNA backbone is kinked nearly 90 degrees.
• Binding leads to assembly of the rest of the transcription complex at the initiation site.
• Four α helices separate the two strands of DNA.

Answer 2

• An eight-stranded β-sheet domain of the TATA-binding protein lies on the DNA helix.
• The DNA backbone is kinked nearly 90 degrees.
• Binding leads to assembly of the rest of the transcription complex at the initiation site.

(The TATA-binding protein β-sheet domain induces a kink in the DNA, leading to assembly of the transcription complex and initiation of transcription.)

Question 3

What structure is responsible for selecting and transporting only properly processed eukaryotic mRNAs into the cytoplasm?

• ribosomes
• snRNPs
• nuclear pore complex
• RNA polymerase
• spliceosome

Answer 3

Nuclear pore complex

(Properly processed mature mRNAs will bind a collection of proteins that aid in their delivery to and through the nuclear pore complex.)

Question 4

The assembly of general transcription factors at a eukaryotic promoter typically begins at what site?

• the sigma site
• the TATA box
• the start codon
• the TFIID sequence

Answer 4

the TATA box

(The TATA box is a key component of many promoters used by RNA polymerase II, and it is typically located about 30 nucleotides upstream from the transcription start site.)

Question 5

At which site on the DNA of a gene does RNA polymerase release its newly made RNA?

• promoter
• TATA box
• stop codon
• poly-A tail
• terminator

Answer 5

Terminator

(RNA polymerase releases its newly made RNA at the terminator. After initiating transcription at the promoter, RNA polymerase continues transcription until it encounters a specific signal in the DNA, the terminator (or stop site), where the polymerase halts and releases both the DNA template and the newly made RNA transcript.)

Question 6

To begin transcription, eukaryotic RNA polymerase recognizes nucleotide sequences in what region of the DNA?

• G-C-rich region
• promoter region
• terminator region
• initiator region
• replication origin

Answer 6

Promotor region

The promoter region is within the 50 or so nucleotides that are before, or upstream of, the transcription start site.

Question 7

An RNA molecule (for example, rRNA or tRNA) within a cell can fold into complex three-dimensional shapes for which reason?

• It contains the sugar ribose rather than deoxyribose.
• It is more primitive than DNA.
• It is double-stranded.
• It is single-stranded.
• It contains the base uracil rather than thymine.

Answer 7

It is single-stranded

The product of transcription is a single-stranded RNA molecule that can form hydrogen bonds with itself.

Question 8

What is the “central dogma”?

• Within the cell, genetic information flows from DNA to RNA to protein.
• For a given individual, the genetic information contained in the DNA of every cell is identical.
• The earliest cells on Earth most likely used RNA to store and copy genetic information.
• The ability of a cell to survive depends on the accurate duplication of genetic information carried in its DNA.
• Much like all viruses, all cells use DNA to encode genetic information.

Answer 8

Within the cell, genetic information flows from DNA to RNA to protein.

(The central dogma states that genetic information flows from DNA to RNA to protein.)

Question 9

Which is not specifically targeted for destruction by the proteasome?

• damaged proteins
• short-lived, regulatory proteins
• misfolded proteins
• phosphorylated proteins
• oxidized proteins

Answer 9

Phosphorylated proteins

(Although phosphorylation can trigger ubiquitin modification of a protein and its subsequent degradation, the phosphorylation itself is not directly recognized by the proteasome. Phosphorylation is regularly used to modify activity of proteins and in some cases can lead to ubiquitination.)

Question 10

Proteasomes act primarily on proteins that have been marked for destruction by the attachment of which small protein?

• termination factor
• ubiquitin
• protease
• histone
• prion

Answer 10

Ubiquitin

(Proteasomes act primarily on proteins that have been marked for destruction by the attachment of ubiquitin. In fact, multiple rounds of ubiquitination must happen before the protein is accepted into the proteasome.)

Question 11

What is a polyribosome?

• a ribosome that is in the process of translating an mRNA into a polypeptide
• a ribosome translating an mRNA molecule that encodes a membrane-embedded protein
• a ribosome translating a polycistronic mRNA molecule
• a cluster of ribosomes simultaneously translating the same mRNA, but positioned at different sites along the mRNA
• a mutant ribosome that contains additional ribosomal subunits

Answer 11

A cluster of ribosomes simultaneously translating the same mRNA, but positioned at different sites along the mRNA

(Multiple ribosomes can bind to an mRNA molecule that is being translated. This increases the efficiency of protein production from the transcript.)

Question 12

Which part of a protein is synthesized by a ribosome first?

• It depends on whether the cell is eukaryotic or prokaryotic.
• It depends on the protein.
• the N-terminus
• the C-terminus
• It depends on where the ribosome binds to the mRNA.

Answer 12

The N-terminus

(The N-terminus is the part of a protein that is synthesized by a ribosome first. The N-terminus corresponds with the 5’, not the 3’, end of the mRNA.)

Question 13

The translation of an mRNA begins at the start codon. What is the sequence of this codon?

• AUG
• UAG
• UGG
• AGU

Answer 13

AUG

(Translation of an mRNA begins at the AUG start codon. In addition to serving as the start translation codon, it also codes for the amino acid methionine.)

Question 14

The genetic code was originally deciphered, in part, by experiments in which synthetic polynucleotides with repeating sequences were used as mRNAs to direct protein synthesis in cell-free extracts. Under these conditions, ribosomes could be made to start translation anywhere within the RNA molecules, with no start codon necessary. What peptide would be made by translation from a synthetic mRNA made entirely of adenine (poly-A)?

• a polymer of lysine: Lys–Lys–Lys…
• the peptide Met–Lys–Lys…
• a polymer of phenylalanine: Phe–Phe–Phe…
• a polymer of methionine: Met–Met–Met…
• a polymer of alanine: Ala–Ala–Ala…

Answer 14

A polymer of lysine: Lys–Lys–Lys…

(The polymer of lysine peptide (Lys–Lys–Lys…) would be made by translation from a synthetic mRNA made entirely of adenine (poly-A). As stated in the question, these experiments with synthetic polynucleotides required no start codon, so translation could start in any reading frame.)

Question 15

What is the best term for an RNA molecule that possesses catalytic activity?

• ribozyme
• ribosomal RNA
• enzyme
• RNase

Answer 15

Ribozyme

(RNA molecules, such as those that compose the ribosome, share features found in protein-based enzymes, including a complex three-dimensional conformation and the ability to recognize specific structures.)

Question 16

Amino acids are attached to their tRNA molecules by which of the following?

• aminoacyl-tRNA synthetases
• RNA ligase
• peptide bonds
• hydrogen bonds

Answer 16

Aminoacyl-tRNA synthetases

(tRNA molecules are molecular adaptors, linking amino acids to codons. For a tRNA molecule to carry out its role as an adaptor, it must be linked—or charged—with the correct amino acid. Recognition and attachment of the correct amino acid depend on enzymes called aminoacyl-tRNA synthetases, which covalently couple each amino acid to the appropriate set of tRNA molecules.)

Question 17

How does the tRNA synthetase enzyme charge a tRNA with the correct amino acid?

• Different tRNA synthetases recognize specific sequences in the final three nucleotides on the 3’ end of the tRNA and attach the matching amino acid.
• A single tRNA synthetase in the cell is responsible for recognizing specific anticodon sequences and adding the correct amino acid to each tRNA.
• Each different tRNA synthetase has one region that recognizes the tRNA anticodon and a second region that attaches the matching amino acid to the CCA at the 3’ end of the tRNA.
• Different tRNA synthetases recognize specific sequences in the D and T loops of the tRNA and attach the matching amino acid.

Answer 17

Each different tRNA synthetase has one region that recognizes the tRNA anticodon and a second region that attaches the matching amino acid to the CCA at the 3’ end of the tRNA.

(Specific aminoacyl-tRNA synthetases use multiple contacts to recognize the anticodon triplet and add the matching amino acid.)

Question 18

What is the function of the anticodon?

Answer 18

It forms complementary base pairs with the mRNA, resulting in the proper amino acid being brought into the ribosome.

Question 19

Where are D and T loops found?

Answer 19

In the middle of the tRNA

Question 20

What sequence is found at the 3’ end of the tRNA?

Answer 20

A CCA sequence is found at the 3’ end of the tRNA and this is where the amino acid is attached.

Question 21

Which sugar is not readily made from formaldehyde in experiments simulating conditions on primitive Earth?

• ribose
• glucose
• fructose
• deoxyribose

Answer 21

Deoxyribose

(From this list of carbohydrates, deoxyribose is not readily made from formaldehyde in experiments simulating conditions on primitive Earth.)

Question 22

Which biochemical reaction is catalyzed by a ribozyme?

• RNA polymerization during transcription in prokaryotes
• RNA polymerization during transcription in eukaryotes
• DNA polymerization during DNA replication
• peptide bond formation in protein synthesis
• peptide bond hydrolysis by proteases

Answer 22

Peptide bond formation in protein synthesis.

(Peptide bond formation in protein synthesis is catalyzed by a ribozyme. The ribosome, along with its rRNA that composes the subunits, catalyzes the synthesis of the peptide bond in proteins.)

Question 23

Which type of molecule has the potential to perform the catalytic act of reproducing itself?

• RNA
• DNA
• polysaccharides
• proteins

Answer 23

RNA

(RNA is believed to be an ancient molecule because it possesses several features that allow it to carry out functions needed for life, including autocatalysis.)

Question 24

Which enzyme catalyzes transcription?

Answer 24

RNA polymerase

Question 25

Does transcription occur early or later in gene expression?

Answer 25

Early

(Transcription happens much earlier in the genetic expression cascade because to translate an mRNA to make protein, the mRNA must be created first.)

Question 26

Researchers often want to isolate a certain type of RNA. For some RNA species, this can be accomplished via affinity chromatography, using beads coated with chains of poly-deoxythymidine (poly-dT). The desired RNA will stick to the beads while unwanted RNAs will flow through the column. The retained RNA can then be eluted.

What RNA species can be purified using this method?

• bacterial rRNA
• eukaryotic rRNA
• bacterial mRNA
• eukaryotic mRNA

Answer 26

Eukaryotic mRNA

(Eukaryotic mRNAs end with a long series of adenine residues, which will bind via complementary base-pairing to the thymidine oligomer.)

Question 27

Which of the following statements is supported by the information in this image and is consistent with your knowledge regarding genomic architecture in prokaryotes and eukaryotes?

• The prokaryotic cell must have a cytoplasmic spliceosome to remove introns from RNA.
• The prokaryotic cell must have a nuclear spliceosome to remove introns from DNA.
• The eukaryotic cell must have a nuclear spliceosome to remove introns from RNA.
• The eukaryotic cell must have a nuclear spliceosome to remove introns from DNA.
• The eukaryotic cell must have a cytoplasmic spliceosome to remove introns from RNA.

Answer 27

The eukaryotic cell must have a nuclear spliceosome to remove introns from RNA.

(Eukaryotic genes contain introns, which must be removed from the RNA transcript in the nucleus before translation can occur in the cytosol. Bacterial genes lack introns, so their RNA transcripts do not need splicing.)

Question 28

Based on the figure, which of these statements is/are correct?

• RNA is always polymerized in the 5’-to-3’ direction.
• The gene promoter is always downstream of the transcription start site.
• The template strand is always read by RNA polymerase in the 5’-to-3’ direction.
• For different genes, opposite strands of DNA can serve as a template.

Answer 28

RNA is always polymerized in the 5’-to-3’ direction.
AND
For different genes, opposite strands of DNA can serve as a template.

(All nucleic acid, RNA included, is always polymerized in the 5’-to-3’ direction, and for different genes, opposite strands of DNA can serve as the template. That is, if one strand is the template for one gene, the other strand can be the template strand for a completely different gene.)

Question 29

The sequence of the coding strand of a DNA molecule (that is, the DNA strand that contains the codons specifying the protein sequence) is 5’-CGGATGCTTA-3’. What is the sequence of the RNA made from this DNA?

• 5’-CGGAUGCUUA-3’
• 5’-UAAGCAUCCG-3’
• 5’-GCCUACGAAU-3’
• 5’-AUUCGUAGGC-3’
• 5’-TAAGCATCCG-3’

Answer 29

5’-CGGAUGCUUA-3’

(If the sequence of the coding strand of a DNA molecule (that is, the DNA strand that contains the codons specifying the protein sequence) is 5’-CGGATGCTTA-3’, then the sequence of the RNA made from this DNA would be 5’-CGGAUGCUUA-3’. The difference between the coding strand sequence and the transcribed RNA sequence is simply uracils in RNA in place of the thymines in DNA.)

Question 30

The sequence of the template strand of a DNA molecule is 5’-ACTGGCAATG-3’. What is the sequence of the RNA transcribed from this DNA?

• 5’-GUAACGGUCA-3’
• 5’-TGACCGTTAC-3’
• 5’-ACUGGCUUAC-3’
• 5’-UGACCGUUAC-3’
• 5’-CAUUGCCAGU-3’

Answer 30

5’-CAUUGCCAGU-3’

(If the sequence of the template strand of a DNA molecule is 5’-ACTGGCAATG-3’, then 5’-CAUUGCCAGU-3’ must be the sequence of the RNA transcribed from this DNA. Transcription generates an antiparallel and complementary strand of nucleic acid.)

Question 31

Suppose the 3’ splice site is mutated from AGG to ACG. Predict the consequence of this mutation.

• Splicing would occur as normal but there would be a point mutation in the mRNA and final protein sequences.
• Splicing would not begin if the 3’ splice site is altered.
• Splicing would begin but not be properly completed if the 3’ splice site is altered.
• Splicing would occur as normal because this splice site is less important than the 5’ splice site.

Answer 31

Splicing would begin but not be properly completed if the 3’ splice site is altered.

(Splicing would still begin with cleavage of the 5’ splice site by the branch-point adenine. The final steps of splicing at the mutated 3’ splice site will be altered.)

Question 32

A primary transcript (immature, non-processed) single-stranded RNA molecule has the following nucleotide composition: 30% A, 20% G, 24% C, and 26% U. What is the nucleotide composition of the double-stranded DNA molecule from which it was transcribed?

• 30% A, 20% G, 24% C, and 26% T
• 26% A, 24% G, 20% C, and 30% U
• 20% A, 30% G, 26% C, and 24% T
• 28% A, 22% G, 22% C, and 28% T
• 26% A, 24% G, 20% C, and 30% T

Answer 32

28% A, 22% G, 22% C, 28% T

(Because the DNA molecule is double-stranded, the nucleotide composition of both strands must be taken into account. The template DNA strand that encodes this RNA molecule would contain: 30% T, 20% C, 24% G, and 26% A. The nontemplate strand, sometimes called the “sense strand” of the DNA, which is complementary to the template strand, would contain: 30% A, 20% G, 24% C, and 26% T. The double helix would thus contain an average of these values: 28% A, 22% G, 22% C, and 28% T.)

Question 33

To crack the genetic code, researchers introduced synthetic messenger RNAs into in vitro translation systems and determined which proteins were produced from these synthetic mRNAs. mRNAs consisting of poly-UUC led to production of three different proteins: poly-Phe, poly-Ser, and poly-Leu. What best explains this result?

• Each amino acid is specified by several codons.
• The synthetic mRNA was read in all three reading frames.
• Transcription started at three different places.
• Each codon codes for several different amino acids.

Answer 33

The synthetic mRNA was read in all three reading frames.

(In a cell, specific start signals initiate translation from a particular nucleotide. However, in a test tube, ribosomes can be forced to translate any RNA molecule and will translate the message in all three possible reading frames.)

Question 34

Several organisms have a homologous protein (inherited from a common ancestor) that is highly similar at the amino acid level. You are comparing the genes that code for these proteins in the different organisms when you note that one of the codon nucleotide positions shows more nucleotide variation than the other nucleotide positions. In which codon nucleotide position do you expect to see the most variability among species?

• fourth nucleotide position
• third nucleotide position
• first nucleotide position
• second nucleotide position

Answer 34

Third nucleotide position

(Since most redundancy in the genetic code occurs at the third nucleotide position, changes at this position are the least likely to change the amino acid coded for and thus are more likely to accumulate over evolutionary time.)

Question 35

The genetic code was originally deciphered, in part, by experiments in which synthetic polynucleotides with repeating sequences were used as mRNAs to direct protein synthesis in cell-free extracts. Under these conditions, ribosomes could be made to start translation anywhere within the RNA molecules, with no start codon necessary. What peptide would be made by translation from a synthetic mRNA made of the repeating dinucleotide CGCG…?

• a polymer of alanine: Ala–Ala–Ala…
• the peptide Met–Arg–Ala–Arg–Ala…
• a polymer of arginine: Arg–Arg–Arg…
• a polymer of arginine plus a polymer of alanine
• a peptide containing alternating arginines and alanines

Answer 35

A peptide containing alternating arginines and alanines

(Depending on where translation begins, the polynucleotide CGCG… contains two different codons, CGC and GCG, which code for arginine and alanine, respectively. The peptide produced would therefore contain alternating residues of arginine and alanine.)

Question 36

Many antibiotics work by inhibiting bacterial protein synthesis. Investigators have isolated a promising new compound and wish to determine its mechanism of action. Using a cell-free translation system similar to the ones originally used to deduce the genetic code, the researchers incubate their drug with the synthetic polynucleotide 5’-AUGUUUUUUUUU.

In the absence of the drug, this polynucleotide directs the synthesis of the peptide Met–Phe–Phe–Phe. When the drug is added, only the peptide Met–Phe is produced. Based on this observation, which is most likely the mechanism of action of this potential new antibiotic?

• It inhibits the peptidyl transferase activity of the large ribosomal subunit.
• It inhibits peptide bond formation.
• It blocks translocation of the large ribosomal subunit, preventing the movement of peptidyl-tRNA from the A site to the P site of the ribosome.
• It blocks the assembly of the initiation complex, including the initiator tRNA and both the large and small ribosomal subunits.
• It blocks binding of aminoacyl-tRNA to the A site of the ribosome.

Answer 36

It blocks translocation of the large ribosomal subunit, preventing the movement of peptidyl-tRNA from the A site to the P site of the ribosome.

(To have just a two-amino-acid peptide produced, there needs to be no translocation of the ribosome, so a translocation-blocking mechanism of action for this antibiotic is the most logical explanation. The methionine is present because the first codon is positioned in the P site, and the phenylalanine is present because another tRNA will enter at the A site, but then no further tRNAs can enter the ribosome.)

Question 37

Investigators treat cells with a chemical that introduces random mutations into the DNA, including single-nucleotide changes that turn one base into another. They then isolate two mutants: one produces a protein that carries an alanine at a site that normally contains a valine; the other produces a protein that carries a methionine instead of the valine.

When these mutant cells are subjected to the same mutagenic treatment, they both produce proteins that contain a threonine at the site of the original valine. Assuming that the mutations causing these alterations are single-nucleotide changes, what were the codons that specified each of the amino acids discussed?

• Val, GUG; Ala, GCG; Met, AUG; Thr, ACG
• Val, GAU; Ala, GCU; Met, AUG; Thr, ACG
• Val, GUC; Ala, GCC; Met, UAC; Thr, ACU

Answer 37

Val, GUG; Ala, GCG; Met, AUG; Thr, ACG

(The codon specifying valine must have been GUG (the mutation having changed the initial G to an A) from methionine AUG. If that is the case, the codon specifying alanine must be GCG (the mutation having changed the U in GUG to a C in GCG). Finally, the codon specifying threonine must be ACG (one mutation changing AUG to ACG, the other changing GCG to ACG).)

Question 38

The genetic code was originally deciphered, in part, by experiments in which synthetic polynucleotides with repeating sequences were used as mRNAs to direct protein synthesis in cell-free extracts. Under these conditions, ribosomes could be made to start translation anywhere within the RNA molecules, with no start codon necessary. What peptide would be made by translation from a synthetic mRNA made of the repeating trinucleotide UCGUCG…?

• a polymer of only serine: Ser–Ser–Ser…
• a polymer of Ser–Arg–Ser… and a polymer of Arg–Val–Arg…
• a peptide containing serines, arginines, and valines: …Ser–Arg–Val–-a polymer of serine (Ser–Ser–Ser…), a polymer of arginine (Arg–Arg–Arg…), and a polymer of valine (Val–Val–Val…)

Answer 38

a polymer of serine (Ser–Ser–Ser…), a polymer of arginine (Arg–Arg–Arg…), and a polymer of valine (Val–Val–Val…)

(For the peptides produced by translation from a synthetic mRNA made of the repeating trinucleotide UCGUCG…, a polymer of serine (Ser–Ser–Ser…) plus a polymer of arginine (Arg–Arg–Arg…) plus a polymer of valine (Val–Val–Val…) are expected. This is because each of the three reading frames will be read, but each will generate a distinct polypeptide.)

Question 39

Which macromolecule(s) is/are critical in the active site of the ribosome for catalysis of peptide bond formation?

• ribosomal RNA, protein, and carbohydrate
• ribosomal protein
• ribosomal carbohydrate
• ribosomal RNA
• ribosomal RNA and protein

Answer 39

Ribosomal RNA

(The ribosomal RNA is the critical component in the active site. Protein helps support the RNA but does not participate in the catalysis of peptide bond formation.)

Question 40

Translation proceeds in a series of steps in the active site of the ribosome. Which of the following are important steps in polypeptide formation?

• The RNA in the P site makes hydrogen bonds with the 3’ end of the aminoacyl-tRNA.
• The incoming aminoacyl-tRNA forms a covalent bond with the RNA in the A site.
• The hydrogen bonds formed between ribosomal RNA and tRNAs position the aminoacyl-tRNAs to catalyze peptide bond formation.
• The tRNA holding the growing polypeptide moves from the P site to the A site after peptide bond formation.

Answer 40

The RNA in the P site makes hydrogen bonds with the 3’ end of the aminoacyl-tRNA.
AND
The hydrogen bonds formed between ribosomal RNA and tRNAs position the aminoacyl-tRNAs to catalyze peptide bond formation.

(Hydrogen bonds with the ribosomal RNA are used to position both the A site and P site tRNAs and to position the amino acids for catalysis of peptide bond formation.)

Question 41

It has been proposed that the first cells used RNA for both information storage and catalysis and that DNA and proteins evolved later. Which modern macromolecules may be relics of the hypothesized RNA world?

• spliceosome
• sigma factor
• ribosome
• RNA polymerase

Answer 41

Ribosome and Spliceosome

(Both the spliceosome and the ribosome contain catalytic RNAs and hence may be holdovers of ribozymes present in the hypothetical RNA world.)