Unit 4
A 90-residue peptide is found to be encoded by a 600 nucleotide gene that contains no introns. A) What are possible explanations for the small size of the peptide, relative to the gene? B) The mRNA transcribed from the gene is 680 nucleotides long. The RNA contains 30% adenine, a much higher proportion that predicted from the gene. What explains the large size of the mRNA relative to the gene?
A) If there are no introns, we ave to consider explanations that involve other steps in gene expression. One possibility is that the mRNA has a long 5'UTR or 3'UTR. Another possible explanation is that after translation many polypeptides still have proteolytic cleavage to be done before they are functional. Possibly the pre-processed peptide is much longer than 90 residues. B) The large size of the mRNA is because of the polyA tail, which include over 100 adenine added to the 3' end of the transcript.
In question 12.9 is a cartoon schematic of a eukaryotic gene. A) How many different mRNA products are indicated as being produced by the process of alternate splicing? B) Draw an additional potential splicing pattern for this gene. C) Why is alternate splicing not seen in bacterial genes?
A) Two mRNAs — one that includes exons 1-2-3-4 and one that includes exons 1-3-4. B) Connect exon 1 to exon 2, but skip exon 3 and connect exon 2 directly to exon 4. C) Prokaryotes like bacteria have no introns, and therefore cannot have alternative splicing patterns.
In the translations below the sequence, dashes represent stop codons. Which codons code for the first two leucines (L) of the 2nd reading frame? (see image) A. CTG CTT B. ACT GCA C. AGC CTG D. CAG TGC
A. CTG CTT
The strand shown is the template strand of a gene. What is the sequence of the mRNA transcript? 5' GCAATGCCAT 3' A. 5' UACCGUAACG 3' B. 5' GCAAUGCCAU 3' C. 3' GCUUTGCCUT 5' D. 3' CGUUACGGUA 5'
B. 5' GCAAUGCCAU 3'
Which one of the following is a property that contributes to the promising outlook for vaccine development for CoV-2? A. CoV-2 shows high antigenic drift compared to influenza. B. CoV-2 shows low antigenic drift compared to influenza. C. CoV-2 replication depends on RNA polymerase rather than DNA polymerase. D. It is unknown how long after CoV-2 infection a person produces protective antibodies.
B. CoV-2 shows low antigenic drift compared to influenza.
6. Which is TRUE of furin site of CoV-2? A. It is known to make viruses less pathogenic. B. It is known to make viruses more pathogenic. C. It is found in all coronaviruses. D. It is located within the polymerase gene.
B. It is known to make viruses more pathogenic.
Which one of the following statements is TRUE of eukaryotic transcription? A. It occurs simultaneously with translation B. It produces pre-mRNA molecules that contain introns C. It occurs in the cell's cytoplasm D. It requires the action of sigma factors
B. It produces pre-mRNA molecules that contain introns
5. What is the ACE2 gene and how does it relate to the current pandemic? A. It is one of the 10 genes encoded by coronaviruses and is a key enzyme in the formation of the membrane (M) of the virus. B. It codes for the viral spike (S) glycoprotein, and mutations in this gene can disable the ability of SARS-CoV-2 to bind receptors on host cells. C. It encodes angiotensin-converting enzyme-2, which has been shown to be responsible for cleavage of the spike (S) protein. D. It encodes angiotensin-converting enzyme-2, which has been shown to act as a receptor for binding of the spike protein of SARS-CoV and SARS-CoV-2.
D. It encodes angiotensin-converting enzyme-2, which has been shown to act as a receptor for binding of the spike protein of SARS-CoV and SARS-CoV-2.
Which feature, if mutated, would destroy the ability of an insertion element to be transposed? A. Its transposase gene B. Its target site duplication C. Its reverse transcriptase gene D. Its inverted repeats
D. Its inverted repeats Lecture 2 Slide 9, 10, 11, and 13 "IRs are important for allowing transposase to recognize members of its own family, IR is necessary for transposition because the transposases of various families of TEs recognize specific IRs"
See Question 12.2
Labeling
What are the similarities and differences between the processes of translation as it occurs in bacteria and eukaryotes?
The overall processes for elongation and termination are very similar, with only some differences in the associated proteins. Initiation is somewhat different. In bacteria, there is a special tRNA that recognizes the start AUG codon known as the f-met-tRNA (since AUG encodes methionine). In eukaryotes, initiation typically depends on the 5' cap on the mRNA.
Define transformation, transduction, and conjugation. Describe how these are different from one another and how they are similar to one another.
Transformation occurs via the uptake of DNA from the environment. While the DNA may originally be double-stranded, it is often made single-stranded during the transfer. Transduction occurs via the activity of different viruses and it usually involves double-stranded DNA. Conjugation occurs via direct contact between the donor and recipient with transfer mediated by a specific set of genes. While single-stranded DNA is transferred, it is replicated upon transfer to become double-stranded.
Although the drug ribavirin is effective against a wide range of viruses, it does not work well against CoV-2. What is the reason for this? A. Ribavirin leads to a "cytokine storm", or overreaction of the immune system, that can be lethal. B. CoV-2 encodes an RNA polymerase that has proofreading ability. C. CoV-2 mutates at a very high rate. D. Ribavirin only works against DNA viruses.
B. CoV-2 encodes an RNA polymerase that has proofreading ability.
Which one statement is true of long terminal repeats (LTRs) A. they are found at the 5' and 3' ends of all retrotransposons B. the 5' and 3' LTRs are identical upon insertion C. they are generated during insertion when the cut overhang strands are filled in D. they are a type of inverted repeat (IR)
B. the 5' and 3' LTRs are identical upon insertion
Which word or term describes a change in gene expression (phenotype) that can be inherited but does not involve a change to the DNA sequence (genotype)? A. Pleiotropic change B. Epistatic change C. Epigenetic change D. None - any change in expression must involve a change in the DNA sequence.
C. Epigenetic change "Heritable changes in phenotype that are not due to changes in the DNA sequence are known as epigenetic changes"
Which one of the following statements about TEs that use a cut-and-paste mechanism is FALSE? A. They are inactive in the human genome B. They are flanked by target site duplications C. They are known as RNA transposons D. They make up only ~3% of human genomic sequence
C. They are known as RNA transposons
The enzyme ________ is associated with a cut and paste mechanism of transposable elements A. Reverse transcriptase B. RNA polymerase I C. Rho factor D. Transposase
D. Transposase Lecture 2
Which component is associated with all transposable elements? A. inverted repeats B. LTRs C. reverse transcriptase D. target site duplications
D. target site duplications
Transposable elements are found in the genomes of nearly every species. What sequence features can be used to distinguish RNA-based elements or retrotransposons from DNA based elements?
DNA-based elements encode transposase and have inverted repeats at their ends. RNA-based elements are more diverse in structure, but often encode reverse transcriptase (abbreviated pol in Figure 11-23) and include a long termI also repeat at the end that serves as the promoter for transcription.
What is meant by the term 'epigenetic' and give an example of an epigenetic modification to DNA.
Epigenetic are heritable changes in the phenotype of an organism that are not caused by changes in the DNA sequence. An example of epigenetics could be methylation of a set of histone that causes the DNA in a region of the genome to condense, and therefore the expression level of those genes would drop, causing a change to the phenotype of those genes without altering the genes themselves.
How do stop codons stop the polypeptide?
Fundamentally, there is no tRNA with an anticodon that can base-pair with one of the stop codons. Thus, translational elongation ends. There are a termination or release factor proteins as well, one protein in eukaryotes and three proteins in bacteria, but they are not discussed in the chapter.
Define each of the following terms: A) Aminoacyl synthetase B) Anticodon C) Wobble D) Evolutionarily accepted mutation
A) Aminoacyl synthetase - One of the category enzymes that attaches the appropriate amino acid to a tRNA. B) Anticodon - The three base sequence on the tRNA molecule that base-pairs with a codon during translation. C) Wobble - The observation that the third or most 3' position in codons (which corresponds to the most 5' position in the anti codon) is rarely used to specify a particular amino acid, suggesting that this base pair is the less stable. In other words, the codons AAA and AAG specify the same amino acid. D) Evolutionarily accepted mutation - When comparing the amino acid sequences of orthologous proteins from two different species, the amino acid changes that have occurred during evolution that still allow the protein to be functional in both species.
The sequence of an mRNA is 5'AUGGCUACUUGCAG3'. A) Using the codon table in Figure 13-13, translate this into an amino acid sequence in all three reading frames. B) Is one of these three reading frames more or less likely to be correct for this gene?
A) Beginning with A, the peptide sequence is Met-Gly-Thr-Cys-Ser (AG-pyrimidine) or Arg (AG-purine). Beginning with the U, Trp-Leu-Leu-Ala with the final G as the first base in the next codon. Beginning with the G, Gly-Tyr-Leu-Gln. B) We are not told if this sequence is found at the beginning of a coding region; if so, the frame beginning with AUG is the most likely. If not, none of them has a stop codon, so none is unlikely.
Define the following terms: A) Competent B) F plasmid C) Ti plasmid D) Lytic and lysogenic phage E) Transposable element
A) Competent: cells that are able to incorporate DNA via transformation B) F plasmid: a circular DNA molecule that encodes about 28 genes that are directly needed for conjugation C) Ti plasmid: a circular DNA molecule in Agrobacterium that transfers sequences from the bacterium to the infected plant cell, where it is incorporated into the plant's genome. D) Lytic and lysogenic phage: Phage are viruses that infect bacteria. Lytic phage are those that replicate immediately upon infection and destroy or lyse the host bacteria. Lysogenic phage can incorporate their genome into the bacterial chromosome and remain quiescent with only minimal phage gene expression for some time. At some point, they can switch to a Lytic phase and destroy the host cells. E) Transposable element: A transposable element is a discrete (meaning that it has defined ends and sequence) segment of DNA that can move to other locations within a genome.
The figure in question 12.7 shows DNA wrapped around a set of proteins into a structure known as a nucleosome. A) What are these proteins called and what are the four types of covalent modifications that occur on them that can alter their function? B) Indicate on the figure which are of the protein sis subject to these modifications. C) In your own words describe what is meant by H3K27Ac. D) Briefly explain how modifications to these proteins can alter gene expression levels.
A) H2A, H2B, H3, H4 I. Methylation II. Acetylation III. Ubiquitination IV. Phosphorylation B) The tails of the proteins, which still out from the nucleosome. C) This is a code to describe histone modification. H3 indicates the histone being modified (H3). K27 indicates the amino acid on the histone that is modified lysine (K) which is the 27th amino acid. And Ac indicated the type of modification — and Acetylation. D) Depending on the combinations of these modifications, the DNA wrapped around these nucleosomes can be either "open" or "closed", which affects the levels of transcription of the DNA, thus altering expression levels. Open and closed refers to the accessibility of the chromatin to transcription factors, RNA polymerase, splicing factors, replication, recombination and repair, and so on.
Use OMIM.org and look up the CFTR gene (#602421). Mutations in the CFTR gene are responsible for cystic fibrosis, as discussed in chapter 10. See 'allelic variants' to answer these questions; more than 135 allele variants are listed from patients who have been diagnosed with cystic fibrosis. Of these, the most common is variant 0001, the in-frame three base deletion discussed in chapter 10; this is abbreviated PHE508DEL to indicate the amino acid (PHE), the position (508), and the change in the gene (DEL). Use the codon table in figure 13-13. A) What single nucleotide change could produce variant 0011, SER54ILE? B) What change in the DNA sequence occurred in variant 0050, and how did this affect the amino acid sequence? C) What change in the DNA sequence occurred in variant 0053, and how did this affect the amino acid sequence? D) What change in the DNA sequenced occurred in variant 0008 and how did this affect the function of the gene?
A) Isoleucine is encoded by AU-pyr (or AUA), while serine can be encoded AG-pyr. So I'd a trans version replaced the G at the second position with a U, isoleucine would replace serine. B) This is a two base deletion at nucleotide position 1221 (which the description tells us is exon 7), which created a far shift mutation. C) Glutamic acid at position 827 is replaced by a stop codon. Glutamic acid codons are GAA and GAG, while stop codons (in the DNA) are TAA and TAG , so this was a transversion from G at the first position in the codon to a T. D) This is a G to A transition that affected the splice site for the tenth intron (IVS 10 means intervening sequence of intron 10) so the mRNA is not spliced correctly and the proper protein is not made.
The expression patterns of two genes, Gene 1 and Gene 2, are being monitored using reporter genes in an animal. The structures of the genes and the reporter gene constructs in the figure shown in question 12.18. For Gene 1, one reporter construct (1A) is made in which the coding region of the gene is replaced by the reporter gene mCherry. For Gene 2, two reporter constructs (2A and 2B) are made. In reporter 2A, the coding region of the region is replaced with GFP, while in reporter 2B, GFP is placed downstream of the coding region of the gene but the coding region of the gene is left in place. In each case, the core promoter regions and the upstream cis regulatory module for each gene is used to drive the expression of the reporter. A) What aspect of gene expression is being monitored by the reporter constructs, 1A or 2A? B) What aspect of gene expression is being monitored by 2B?
A) The transcription of the gene. These reporters remove most of the regular coding sequence of the gene, so none of the proper modifications can be made. These constructs will identify where and when the gene is transcribed. B) This reporter is looking at the translation of the gene and where the protein made by this gene will go. By adding the reporter to the DNA of the gene it is still possible for the correct protein to be made, which also makes it possible to track that protein to its final location, unlike in a transcriptional reporter.
Which statement is TRUE of the ChIP-seq technique? A. It shows where transcription factors bind DNA under particular conditions B. It involves crosslinking of RNA transcripts to DNA C. It is a method for sequencing transcription factors D. It is a method to measure transcript levels of genes
A. It shows where transcription factors bind DNA under particular conditions
Which gene product determines which cells the virus can enter (its "tropism")? A. Spike glycoprotein B. Nucleoprotein C. Membrane protein D. Envelope small membrane protein
A. Spike glycoprotein
How do cAMP and CAP interact in their regulation of the lac operon? A. cAMP enables CAP to bind to the operon, activating transcription B. cAMP causes CAP to release from the operon, de-repressing transcription C. CAP enables cAMP to bind to the operon, repressing transcription D. cAMP enables CAP to bind to the operon, blocking RNA polymerase
A. cAMP enables CAP to bind to the operon, activating transcription
Which event is most likely to produce a human sperm cell that carries an X and a Y chromosome? A. nondisjunction during meiosis I B. nondisjunction during meiosis II C. nondisjunction during mitosis D. nonhomologous recombination
A. nondisjunction during meiosis I
Describe what happens at the A, the P, and the E sites of the ribosomes.
According to Figure 13-7, the codon appears at the A site and the tRNA with the amino acid "charged" to it base-pairs with it. The P site has the previous codon and the corresponding tRNA with the peptide formed so far. The E site is where the uncharged tRNA is ejected after the peptide has been moved to the next amino acid. Amino acid, peptide, exit.
Which statement describes an "insertionally polymorphic" endogenous retrovirus? A. An ERV sequence is found at a particular genomic locus in both Kaitlyn and Mary but differs at some nucleotide positions between the two copies B. An ERV sequence is found at a particular genomic locus in Mary, but is absent from the same locus in Kaitlyn C. An ERV sequence that disrupts a gene-coding region D. An ERV sequence at a particular genomic locus in Mary copies itself to many other loci
B. An ERV sequence is found at a particular genomic locus in Mary, but is absent from the same locus in Kaitlyn
Bacterial plasmids that carry multiple antibiotic resistance genes are known as: A. Transposons B. R factors C. Insertion sequences D. Syncytins
B. R Factors
There are seven members of the Coronaviridae virus family that can infect humans. What three cause severe disease? A. SARS CoV-1, SARS-CoV-2, and OC42 B. SARS CoV-1, SARS-CoV-2, and MERS C. HKU1, SARS CoV-1, SARS-CoV-2 D. HKU1, MERS, OC43
B. SARS CoV-1, SARS-CoV-2, and MERS
What is the official name of the coronavirus AND the disease that it causes (respectively)? A. CoV-19; SARS B. SARS-CoV-2; COVID-19 C. COVID-19; SARS-CoV-2 D. COVID-19; nCoV-2
B. SARS-CoV-2; COVID-19
The genome of CoV2 is a single strand of RNA. An infected cells treats the CoV-2 viral genome as if it were its own mRNA, translating it into proteins. Given this information, how would we term the viral genome? A. negative-sense B. positive-sense C. segmented D. dsDNA
B. positive-sense
How did CoV-2 most likely acquire a cleavage site for furin proteases (RRAR motif)? A. Meiotic nondisjunction B. Random single base pair mutations C. Recombination with other similar coronaviruses D. Insertion of RNA transposons
C. Recombination with other similar coronaviruses
What would be the expected outcome if the Mediator complex does not function? A. TFs cannot bind to their binding sites in the CRM B. The wrong RNA polymerase will be recruited to the promoter C. The CRM cannot be brought into contact with the promoter region D. Transcription will not terminate properly
C. The CRM cannot be brought into contact with the promoter region Lecture 3a slide 11, The mediator complex brings TFs at CRM into contact with RNAP II at the promoter.
In the past few years, CRISPR has become a widely used method to "edit" the genomes of any organism. Very briefly describe how CRISPR is done.
CRISPR technology currently uses the Cas9 enzyme that can cleave DNA and a small RNA that is complementary to the region of the genome to be edited. Cas9 also requires a tracrRNA to guide the cellular ribonuclease to make a cut in the DNA. The simplest edit to make is a small deletion in part of the gene of interest. A small RNA of approximately 25 nucleotides is synthesized in vitro to be complementary to the region in which the edit is made. (Since Cas9 cuts both strands, the small RNA will be complementary to one strand and identical to the other, except for the replacement of T with U in the RNA). The tracrRNA required by Cas9 is also synthesized so the RNA molecule includes both the small RNA sequence and the tracrRNA sequence as one longer RNA molecule. This is introduced into the cell along with the Cas9 protein or gene; it is common to have the Cas9 gene encoded on a plasmid, which is then transcribed and translated by the cell into an active enzyme. This combination of Cas9 and the guide RNA will make a double-stranded cut at the region targeted by the guide RNA. This double-stranded cut is repaired by the cell, usually by the process of non-homologous end-joining. Small deletions or insertions usually occur at the junction site where NHEJ has worked, which results in the small deletion at that site that knocks out the gene.
What mRNA codon binds to the anticodon 5'-CGU-3'? A. 5'-GCA-3' B. 5'-UGC-3' C. 5'-TCG-3' D. 5'-ACG-3'
D. 5'-ACG-3'
What is techniques are applied in the swab test for presence of the new coronavirus? A. mRNA is converted into cDNA B. sample is analyzed on a microarray chip C. PCR is performed with primers to a virus sequence D. A and C
D. A and C
Which retroelement in humans has been most successful in terms of number of copies in the genome? A. LINE1 B. ERV C. IS elements D. Alu
D. Alu
Which is an expected direct result of deletion of the TATA box in a eukaryotic gene? A. Nothing — TATA boxes are a feature of prokaryotes, and not eukaryotes B. Incorrect splicing C. Failure of transcription to terminate D. Failure of transcription to initiate
D. Failure of transcription to initiate Lecture 3a Slide 5 and 10, TBP binds to TATA box and this is an initiator element
In eukaryotic cells, mRNA is transcribed by A. RNA polymerase I B. Ribosomes C. tRNA D. RNA polymerase II
D. RNA polymerase II Lecture 3a Slide 5, Different RNA polymerase produce different types of txts and RNA pol II produces mRNA
Which statement about microRNAs is true? A. They block transcription initiation B. They hybridize to the DNA downstream of a gene C. They are short stretches of double-stranded RNA D. They base pair with the 3' UTR of an mRNA transcript
D. They base pair with the 3' UTR of an mRNA transcript Lecture 4 Slide 5, "Their target sequences are usually in 3' UTR"
Why do human genomes have such a high load of transposable element sequences, which can be somewhat harmful? A. We have a relatively high Ne, so natural selection is weak. B. We have a relatively high Ne, so natural selection is strong. C. We have a relatively low Ne, so natural selection is strong. D. We have a relatively low Ne, so natural selection is weak
D. We have a relatively low Ne, so natural selection is weak.
Which phrase describes a retrogene? A. the product of alternative splicing B. an inactive, retrotransposed copy of a gene C. a type of regulatory RNA D. a functional gene that arose from retrotransposition
D. a functional gene that arose from retrotransposition
What is a poly-A tail? A. the termination signal of bacterial translation B. the region where the ribosome initiates translation C. a complementary base-pairing region that forms stem-loop structures D. a modification of the 3' end of eukaryotic transcripts
D. a modification of the 3' end of eukaryotic transcripts
All of the following statements are true of retroviruses EXCEPT: A. they can be transmitted both horizontally(infection) and vertically(inherited) B. a DNA copy of the retrovirus genome inserts into the host genome C. they encode their own reverse transcriptase enzyme D. after initial insertion, only actively replicating retroviruses survive in germ cells
D. after initial insertion, only actively replicating retroviruses survive in germ cells
List the basic steps involved in transcription in bacteria. What are some of the other steps found in eukaryotes that are not present in bacteria?
Initiation of transcription in bacteria starts with the binding of the sigma factor to the promoter, unlike eukaryotic transcription which starts with the binding of transcription factors. The sigma factor then recruits the rest of the bacterial RNA polymerase (which is made of 5 subunits instead of the 12 like eukaryotic RNAP) and then the sigma factor begins to unwind the DNA upstream of the TSS. After initiation, there is a transcriptional pause and then transcription elongation begins with bases being added to the 3' end. Transcriptional termination happens using either Rho-independent (happens after the formation of a hairpin structure) or Rho-dependent (happens after a specific motif is found) termination, similar processes take place in eukaryotes, but are less well understood. Bacteria do not have the eukaryotic 5' cap added to them, and only a few bacterial transcripts are given a polyA tail.
What is meant by the term "genomic island"?
Since horizontal gene transfer typically involves a contiguous block or segment of DNA, the sequence of the acquired DNA often has features that distinguish it from the surrounding parts of the genome. This defines it as a genomic island - a region of the genome that has been acquired via horizontal gene transfer.
When the influenza virus genome enters the nucleus of a human host cell, it cleaves off the 5' end of host RNAs as they are being made. These 'snatched caps' are then attached to the 5' ends of viral RNAs. Why might 'cap-snatching' be necessary for this RNA virus to complete its lifecycle in a human cell?
The 5' on mRNA is critical because it allows the mRNA to leave the nucleus, protects it from degradation, and allows it to interact with the ribosome during translation. By stealing the cap, the virus gives its own RNA the ability to do all these things in the host cell and also weakens the host cell by destroying RNA that the cell needs to produce more proteins.
In sickle cell anemia , a glutamic acid in β-globin is replaced by a valine. What is the minimal number of base changes that is required to produce this change and what are they?
The codon for glutamic acid is GA-purine. The codon for Valine is GU_ with any base in the third position. So this substitution could occur by a single base change at the second position of the codon, a trans version from A to U.
Restriction enzymes are very widely used tools in molecular biology research. B) What is the natural role of restriction enzymes and how do bacteria protect themselves from this natural role?
The natural role of restriction enzymes is to detect and cut foreign or invading DNA by recognizing a specific sequence within the invading molecule. Bacteria protect themselves against this activity by methylating the recognition site or target sequence when it occurs within their own genomes.
In what way do CRISPR regions of bacterial genomes provide insights into the history of that bacterial strain?
When foreign DNA (such as from a virus) invades a bacterium, some of its DNA will be included as a spacer and incorporated into the genome of the bacteria as part of the CRISPR array. Thus, the spacer sequences in the CRISPR array record the history of which viruses have invaded the bacteria in the past.