Problem Set 2 (ch 7-13) Flashcards
The sequence shown below belongs to a DNA region transcribed by the RNA polymerase from a promoter on the left side to a terminator on the right side. This entire DNA segment is transcribed into RNA.
5′-AGCATGGCAATATCGTAGTA-3′
3′-TCGTACCGTTATAGCATCAT-5′
Asked what is the sequence of the RNA produced from this DNA, Jordan claims that it is:
3′-AGCATGGCAATATCGTAGTA-5′
Give two reasons why Jordan’s answer is incorrect.
First, the RNA molecule should have uracil instead of thymine bases. Second, the polarity of the molecule is incorrectly labeled. The correct RNA molecule produced, using the bottom strand of the DNA duplex as a template, would be:
5′-GGCAUGGCAAUAUUGUAGUA-3′
The length of a particular gene in human DNA, measured from the start site for transcription to the end of the protein-coding region, is 5,000 nucleotides, but the length of the mRNA produced from this gene is 3,000 nucleotides. How is this possible?
The gene contains one or more introns.
The following RNA sequence includes the beginning of the sequence encoding protein X. What would be the result of a mutation that changed a C (bolded and underlined below) into an A?
5′-AGGCUAUGAAUCGACACUGCGAGCCC . . .
The change creates a stop codon (TGA, or UGA in the mRNA) very near the beginning of the protein-coding sequence and in the correct reading frame (the beginning of the coding sequence is indicated by the ATG). Thus, the translation would terminate after only four amino acids had been joined together, and the complete protein would not be made.
One strand of a section of DNA isolated from the bacterium E. coli reads:
5′-GTAGCCTACCCATAGG-3′
A. Suppose that an mRNA is transcribed from this DNA using the complementary strand as a template. What will be the sequence of the mRNA in this region (make sure you label the 5′ and 3′ ends of the mRNA)?
B. How many different peptides could potentially be made from this sequence of RNA, assuming that translation initiates upstream of this sequence?
C. What are these peptides? (Give your answer using the one-letter amino acid code.)
A. 5′-GUAGCCUACCCAUAGG-3′
B. Two. (There are three potential reading frames for each RNA. In this case, they are
GUA GCC UAC CCA UAG . . .
UAG CCU ACC CAU AGG . . .
AGC CUA CCC AUA GG? . . .
The center one cannot be used in this case, because UAG is a stop codon.)
C. VAYP; SLPIG
Note: PTHR will not be a peptide because it is preceded by a stop codon.
In a diploid organism, the DNA encoding one of the tRNAs for the amino acid tyrosine is mutated such that the sequence of the anticodon is now 5′-CTA-3′ instead of 5′-GTA-3′. What kind of aberration in protein synthesis will this tRNA cause? Explain your answer.
If the DNA sequence specifying the anticodon is changed from 5′-GTA-3′ to 5′-CTA-3′, this tRNA will now pair with the 5′-UAG-3′ codon (instead of 5′ -UAC-3′). The UAG codon normally serves as a stop codon. Thus, this change will result in the amino acid tyrosine being incorrectly incorporated where there is a stop codon, resulting in the addition of amino acids at the end of proteins that normally would come to a stop because of the UAG codon in the mRNA. (Note that the tyrosine codons will NOT cause premature termination of translation, as tyrosine should continue to be incorporated into proteins, as there are additional tyrosine-tRNA genes in the cell that will provide a normal supply of tyrosine-tRNAs.)
A neuron and a white blood cell have very different functions. For example, a neuron can receive and respond to electrical signals, while a white blood cell defends the body against infection. This is because
a. all of the proteins found in a neuron are completely different from the proteins found in a white blood cell.
b. the neuron and the white blood cell within an individual have the same genome.
c. the neuron expresses some mRNAs that the white blood cell does not.
d. neurons and white blood cells are differentiated cells and thus no longer need to transcribe and translate genes.
C
Different cell types express different mRNAs, leading to differences in protein expression. There are proteins common to all cells in multicellular organisms. Although it is true that the neuron and white blood cells within an individual have the same genome, this does not explain why these two cells have different functions. Differentiated cells still need to transcribe and translate genes.
You work in a lab that studies the Ucb gene. You already know that the Ucb protein is normally produced when cells are exposed to high levels of both fructose (Fru) and maltose (Mal), two types of carbohydrates. SugX, SugY, and SugZ are proteins that bind to the promoter of the Ucb gene and regulate its transcription. SugX binds to the “X” site in the promoter region, SugY to the “Y” site, and SugZ to the “Z” site. You create binding-site mutations in the X, Y, and Z sites and measure the number of transcripts produced by the Ucb gene. Your results are summarized in the table below.
A) Which of the following proteins are likely to act as gene activators?
B) In the same scenario of the previous question, which of the following proteins are likely to act as gene repressors?
A) Both SugX and SugZ
B) SugY
The figure below shows the phylogenetic tree of a family of plant species. Use the tree to answer the following questions.
A. When did species M and N share their last common ancestor and how much do their genome sequences divergence?
B. Compared to species P and S, are species M and N more or less closely related to each other?
C. If you were trying to discover nucleotide sequences with a very important function in species M, would you rather compare its genome with species N or with species Q?
A. M and N diverged 10 million years ago. There is an average of 2.0% nucleotide substitution in species M compared with species N (follow the path connecting the two species, which is twice the distance between each one and their common ancestor).
B. Neither more nor less. They show roughly the same degree of relatedness. The sequence divergence between species M and N is about 2.0%, the same as that between species P and S. Both pairs of species diverged 10 million years ago.
C. It is more informative to compare species that are separated by a greater evolutionary distance; thus, comparing species M and Q, which diverged 20 million years ago, will be better able to identify sequences that are likely to be important for function. Closely related species share many sequences by chance because there has been insufficient time for neutral mutations to accumulate.
Which of the following mutations has the lowest chances of being selectively neutral?
a. A mutation that deletes 50% of a pseudogene.
b. A mutation that changes the CCC codon to the CCT codon in a protein-coding gene.
c. A mutation that changes the TCC codon to the AGT codon in a protein-coding gene.
d. A mutation that changes the TAT codon to the TAG codon in a protein-coding gene.
D
TAT codes for tryptophan, while TAG codes for a stop codon. This substitution is most likely to be detrimental to gene function. Although TCC and AGT look very different at the nucleotide level, both codons code for serine. Similarly, CCC and CCT will both code for proline. Pseudogenes do not make functional proteins, and thus removal of 50% of a pseudogene is likely to be neutral.
Which of the following statements about the human genome is FALSE?
a. About 50% of the human genome is made up of mobile genetic elements.
b. More of the human genome comprises intron sequences than exon sequences.
c. About 1.5% of the human genome codes for exons.
d. Only the exons are conserved between the genomes of humans and other mammals.
D
About 5% of the human genome is highly conserved with other mammalian genomes, yet only about 1.5% of the human genome codes for exons.
Consider the hypothetical protein Lng that can carry oxygen through the bloodstream. Mutation A and mutation B each cause Lng to be a very ineffective oxygen carrier, yet a Lng gene containing both mutations X and Y encodes a protein that carries oxygen even better than the original Lng protein. The chances that a single mutational event will generate both mutations X and Y are almost negligible. However, you discover an organism with a mutant Lng gene containing both mutations X and Y. Explain a simple way how that double-mutant Lng gene could have arisen during evolution.
The simplest way to evolve the new gene is by duplication and divergence. If the gene is duplicated, then the cell or lineage can maintain one functional, intact old copy of the original gene and can thus tolerate the disabling mutations in the other copy. The other copy can first be modified by the X or Y mutation that impairs its function; second, at some later time, the gene with the single mutation can acquire the additional mutation to yield the doubly mutant X + Y gene with the new or improved function.
Cameron wants to amplify the DNA between the two double-stranded sequences shown in the figure below. Of the 8 primers listed below, which two primers should Cameron choose to amplify the DNA by PCR?
The appropriate PCR primers are primer 1 (5′-GACCTGTGGAAGC-3′) and primer 8 (5′-TCAATCCCGTATG-3′). The first primer will hybridize to the bottom strand and prime synthesis in the rightward direction. The second primer will hybridize to the top strand and prime synthesis in the leftward direction. (Remember that strands pair antiparallel.)
The middle two primers in each list (primers 2, 3, 6, and 7) would not hybridize to either strand. The remaining pair of primers (4 and 5) would hybridize, but would prime synthesis in the wrong direction—that is, outward, away from the central segment of DNA.
How does the Cas9 system target where it produces a double-strand break in the DNA?
a. A guide RNA molecule is associated with Cas9 and will direct Cas9 to bind at sequences complementary to the guide RNA.
b. The Cas9 protein contains amino acids that can interact with specific sequences in the DNA, targeting Cas9 to those specific sites.
c. The Cas9 protein binds to a recombinase, allowing it to disable the gene of interest.
d. A guide RNA molecule associated with Cas9 provides the catalytic activity to cleave the DNA where Cas9 binds.
a
The guide RNA associated with Cas9 directs it to a segment of DNA with a complementary sequence. Researchers take advantage of this property by supplying an appropriate guide RNA to target Cas9 to wherever in the genome researchers may wish to make a cut to alter a gene.
While many prokaryotic cells have a single membrane bilayer, all eukaryotic cells have a complex system of internal membrane-bound compartments. How might it be advantageous for the cell to have these additional compartments?
Compartmentalization using intracellular membranes allows eukaryotic cells to separate a variety of cell processes. Although this requires a higher degree of coordination, the cell also gains more control over these processes (examples include: the separation of transcription and translation; the separation of enzymes involved in protein modifications for secreted versus cytosolic substrates; the separation of proteolytic events in the lysosomes versus the cytosol; the separation of anaerobic metabolism in the cytosol and aerobic metabolism in the mitochondria).
Explain the importance of glycolipids in the plasma membrane, identify where they are produced inside the cell, and describe the mechanism by which they are transported to the plasma membrane and presented to the extracellular environment.
Glycolipids are found on the surface of healthy cells and contribute to the cell’s defense against chemical damage and infectious agents. Glycolipids are produced by enzymes inside the Golgi apparatus. They are then transported to the plasma membrane through a process of vesicle budding. These secretory vesicles then fuse with the plasma membrane. The glycolipids that were facing the lumen of the Golgi apparatus will now face the extracellular environment.
What chemical principles explain the observation that a protein-free lipid bilayer is a billion times more permeable to water than to a sodium ion?
Water is a small, uncharged molecule that diffuses directly across the membrane, despite needing to pass through a hydrophobic lipid core. In cells, ions pass through lipid bilayers via ion channels or transporters. Because ions carry a charge, they have strong electrostatic interactions with water molecules. There are no compensating interactions in the hydrophobic lipid core of the bilayer, which prevents ions from entering.
True or False. If a statement is false, explain why it is false.
Facilitated diffusion can be described as the favorable movement of one solute down its concentration gradient being coupled with the unfavorable movement of a second solute up its concentration gradient.
False. This describes coupled transport, which is one type of active transport. Facilitated diffusion can also be called passive transport, in which a solute always moves down its concentration gradient.
TRUE or FALSE. If a statement is false, explain why it is false.
Transporters undergo transitions between different conformations, depending on whether the substrate-binding pocket is empty or occupied.
True