The Elements of Life In biology, the elements of life are the essential building blocks that make up living things. They are carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. The first four of these are the most important, as they are used to construct the molecules that are necessary to make up living cells. These elements form the basic building blocks of the major macromolecules of life, including carbohydrates, lipids, nucleic acids and proteins. Carbon is an important element for all living organisms, as it is used to construct the basic building blocks of life, such as carbohydrates, lipids, and nucleic acids. Even the cell membranes are made of proteins. Carbon is also used to construct the energy-rich molecules adenosine triphosphate (ATP) and guanosine triphosphate (GTP). Hydrogen is used to construct the molecules water and organic compounds with carbon. Hydrogen is also used to construct ATP and GTP. Nitrogen is used to construct the basic building blocks of life, such as amino acids, nucleic acids, and proteins. It is also used to construct ATP and GTP. Oxygen is used to construct the basic building blocks of life, such as carbohydrates, lipids, and nucleic acids. It is also used to construct ATP and GTP. Phosphorus is used to construct the basic building blocks of life, such as carbohydrates, lipids, and nucleic acids. Show
Nucleosomes inhibit... A) activators B) RNA polymerase C) translation D) assembly of transcription factors D) assembly of transcription factors Feedback:
Nucleosomes inhibit the formation of transcription factor complexes but not activators or RNA polymerase. Unlike prokaryotes, the control of transcription by eukaryotes is designed to react to change by... A) changing B) ignoring change C) remaining constant D) changing the environment C) remaining constant Feedback: Eukaryotes seek to maintain homeostasis, remaining stable in the face of changing environments. A form of binding motif containing a nearly identical sequence of 60 amino acids in many eukaryotes is the... A) homeodomain motif B) zinc finger motif C) leucine zipper motif D)
universal motif A) homeodomain motif Feedback: The homeodomain motif, common to many eukaryotes, contains a nearly identical sequence of 60 amino acids. Which of the following does not occur in the function of the catabolite activator protein (CAP) of E. coli? A)
Cyclic-AMP binds to the CAP protein. B) The protein changes shape. C) Space is increased by the binding of tryptophan. D) Helix-turn-helix motifs are enabled to bind to the DNA. C) Space is increased by the binding of tryptophan. Feedback: The binding of cAMP to the CAP protein causes the protein to change shape, allowing helix-turn-helix motifs to bind to
the DNA. All of the following can be found in a human transcription complex except... A) activator B) RNA C) enhancer D) silencer B) RNA Feedback: The human transcription complex is highly complex, containing activators, enhancers, TATA binding
proteins, silencers, basal factors, and coactivators. Enhancers are... A) proteins located adjacent to promoters B) distant sites where regulatory proteins bind C) expediters of RNA polymerase capture D) proteins that bind with repressors, deactivating them E) a bacterial form of promoters B) distant sites where regulatory proteins bind Feedback: In genetics, an enhancer is a short (50-1500 bp) region of DNA that can be bound with proteins (activators) to activate transcription of a gene or genes. These proteins are usually referred to as transcription factors. Enhancers are generally cis-acting, located up to 1 Mbp (1,000,000 bp) away from the gene and can be upstream or downstream from the start site, and either in
the forward or backward direction. When tryptophan is present in the medium, the transcription of tryptophan producing genes in E. coli is stopped by a helix-turn-helix regulator binding to the... A) trp repressor B) trp operon C) trp promoter D) trp operator E) trp polymerase When a homeodomain binds to DNA, the actual binding portion of the homeodomain is... A) a leucine zipper B) the operon C) zinc fingers D) the histine E) a helix-turn-helix motif E) a helix-turn-helix motif Feedback: In proteins, the helix-turn-helix (HTH) is a major structural motif (a supersecondary structure in a chain-like molecule) capable of binding DNA. It is composed of two α helices joined by a short strand of amino acids and is found in many proteins that regulate gene expression. It should not be confused with the helix-loop-helix domain The assembly of transcription factors on a promoter begins some 25 nucleotides upstream where it binds to a start _______________ sequence. A) ATAT B) AATT C) TTAA D) TAAT E) TATA E) TATA Feedback: The TATA box is a DNA sequence (cis-regulatory element) found in the promoter region of genes in archaea and eukaryotes. Considered to be the core promoter sequence, it is the binding site of either general transcription factors or histones (the binding of a transcription factor blocks the binding of a histone and vice versa) and is involved in the process of transcription by RNA polymerase. When tryptophan is present in the environment of E. coli, the tryptophan binds to the... A) trp operon B) trp promoter C) trp operator D) trp repressor E) trp polymerase D) trp repressor Feedback: In the bacterium E. Coli, a group of five genes code for enzymes required to synthesise the amino acid tryptophan. All five genes are transcribed together as a unit called an operon. An operon is a group of genes that is under the control of a single operator site. A regulatory protein called a repressor can bind to the operator site and prevent transcription. When typrophan is lacking in the environment, the repressor is inactive. RNA polymerase binds to the promoter site and then proceeds down the DNA, transcribing the genes for the tryptophan biosynthesis enzymes. When tryptophan is present in the environment, the organism no longer needs to make tryptophan. Tryptophan binds to the repressor and activates it. The activated repressor now binds to the operator, located withing the tryptophan promoter and blocks transcription. The tryptophan repressor is a helix-turn-helix regulatory protein. When tryptophan is absent from the environment, the repressor is in an inactive conformation and cannot bind to the DNA to prevent transcription. When tryptophan is abundant, two molecules of tryptophan bind to the repressor. This alters the orientation of the helix-turn-helix motifs in the repressor and causes their recognition helices to fit into adjacent major grooves of the DNA. Thus the synthesis of tryptophan occurs when it is needed, but is repressed when tryptophan is available. Transcription factors appear to be unable to bind to a nucleosome because... A) activators are inhibited by the configuration B) of inhibition of RNA polymerase C) of histones positioned over promoters D) nucleosomes are especially vulnerable to repressors E) operators are placed in an inaccessible position C) of histones positioned over promoters In the zinc fingers motif, the spacing of the helical segments is performed by... A) beta sheets B) helical clusters C) zinc atoms D) gamma helices E) an alpha helix Translation repressor proteins may shut down translation of processed mRNA transcripts by... A) binding with the poly-A tail B) resetting the reading frame C) reinserting introns into the transcript D) excising a short sequence of nucleotides D) excising a short sequence of nucleotides In many animals, the genes that regulate the development of stem cells are activated... A) once B) only twice C) up to 10 times D) over a hundred times E) not at all The leucine zipper motif involves the cooperation of two _______________ subunits. A) leucine B) protein C) RNA D) polymerase E) histone Regulatory domains of most activators interact with A) the transcription factor complex B) RNA polymerase C) repressors D) the regulatory factor complex E) the DNA binding domain A) the transcription factor complex The operon that controls tryptophan producing genes in E. coli consists of _______________ . A) only one gene B) two genes C) three genes D) four genes E) five genes In order for a gene to be transcribed, RNA polymerase must have access to the DNA helix and be able to bind to the genes A) activator B) regulator C) promoter D) operator E) repressor In the function of the lac operon in E. coli, the lac genes are transcribed in the presence of lactose because A) RNA polymerase binds to the operator B) the repressor cannot bind to the promoter C) an isomer of lactose binds to the repressor D) CAP does not bind to the operator E) of the absence of cAMP C) an isomer of lactose binds to the repressor The role of methylation of DNA is now viewed as... A) interfering with DNA transcription by blocking base pairing between cytosine and guanine B) complexing with enhancers to prevent transcription C) prevention of mutation D) insuring that genes that are turned off, stay off E) irrelevant to gene transcription D) insuring that genes that are turned off, stay off. In order for the helix-turn-helix motif to bind to DNA, the _______________ must fit into the major groove of the DNA. A) homeotic switches B) zinc fingers C) operator D) recognition helix E) protein link The most common form of gene expression regulation in both bacteria and eukaryotes is... A) translational control B) transcriptional control C) post-transcriptional control D) post-translational control E) control of passage from the nucleus B) transcriptional control. In eukaryotes, many genes may have to interact with each other, requiring more interacting elements than can fit around a single promoter. This physical limitation is overcome by... A) alternating promoters and operators B) placing promoters on both sides of each gene C) the use of very long promoters D) distant sites in a chromosome controlling transcription of a gene E) having factors on one chromosome control genes on another gene D) distant sites in a chromosome controlling transcription of a gene E. coli is able to use foods other than glucose in the absence of available glucose, because falling levels of glucose cause an increase of... A) cAMP B) CAP C) lactase D) glu operons E) tRNA In the absence of glucose, E. coli can import lactose to change into glucose and galactose because CAP binds to the... A) cAMP B) DNA C) lac operon D) operator E) repressor Which is not part of the lac operon? A) repressor B) activator protein C) operator D) promotor E) structural gene In an operon the location of the regulatory region occurs ________ the structural genes. A) after B) within C) before In eukaryotic gene regulation, the location of the promoter is always before and the location of the enhancer always after the gene being regulated. A) True B) False Proteins that block the passage of RNA polymerase are called: A) operons B) activators C) repressors D) enhancers E) promoters Which of the following is part of an operon? A) structural genes B) an operator C) a promoter D) a CAP binding site E) all of the above Which of the following are not matched correctly? A) exon splicing-occurs in nucleus B) post-translational modifications-phosphorylation C) snRNA-splice out exons from transcript D) activated enhancers-trigger transcription E) all are matched correctly C) snRNA-splice out exons from transcript A single gene may use a regulatory site to control the expression of that gene, but genes rarely have multiple regulatory sites. A) True B) False If the genetic code consisted of four bases per codon rather than three, the maximum number of unique amino acids that could be encoded would be... A) 16 An RNA-dependent RNA polymerase is likely to be present in the virion of a... A) DNA virus that multiplies in the cytoplasm B) DNA virus that multiplies in the nucleus C) minus-strand RNA virus D) plus-strand RNA virus E) transforming virus C) minus-strand RNA virus In E. coli, the inability of the lac repressor to bind an inducer would result in... A) no substantial synthesis of ß-galactosidase B) constitutive synthesis of ß-galactosidase (C) inducible synthesis of ß-galactosidase (D) synthesis of inactive  ß-galactosidase (E) synthesis of ß-galactosidase only in the absence of lactose A) no substantial synthesis of ß-galactosidase Which of the following statements about retrotransposons is correct? A) They transpose via an RNA intermediate. B) They contain genes for ribosomal proteins. C) They possess a gene for RNA-dependent RNA polymerase. D) They possess genes that encode proteins that integrate RNA into chromosomes. E) They are found only in bacteria. A) They transpose via an RNA intermediate. A mutation deleting an upstream activating sequence for a single gene would be expected to be... A) polar B) trans-dominant C) cis-dominant D) silent E) revertible C) cis-dominant Feedback: cis dominant- mutations (eg of an operator) that alter the functioning of genes on that same piece of DNA. Proline disrupts α-helical structure in proteins because it is... A) an acidic amino acid B) an aromatic amino acid C) an imino acid D) a basic amino acid E) a sulfur-containing amino acid C) an imino acid Feedback: Proline is unique in that it is the only amino acid where the side chain is connected to the protein backbone twice, forming a five-membered nitrogen-containing ring. Strictly speaking, this makes Proline an imino acid. Proline is unable to occupy many of the main chain conformations easily adopted by all other amino acids. Proline can introduce kinks into alpha helices, since it is unable to adopt a normal helical conformation. All of the following are proteins within the core nucleosome particle EXCEPT A) H1 B) H2A C) H2B D) H3 E) H4 A) H1 Feedback: The nucleosome core particle consists of approximately 147 base pairs of DNA wrapped in 1.67 left-handed superhelical turns around a histone octamer consisting of 2 copies each of the core histones H2A, H2B, H3, and H4 Linker histones such as H1 and its isoforms are involved in chromatin compaction and sit at the base of the nucleosome near the DNA entry and exit binding to the linker region of the DNA. In the context of prokaryotic gene expression, which of the following is the most appropriate definition of an operator? A) A cluster of genes that are regulated by a single promoter. B) A DNA-binding protein that regulates gene expression. C) A non-coding, regulatory DNA sequence that is bound by RNA polymerase. D) A non-coding, regulatory DNA sequence that is bound by a repressor protein. D) A non-coding, regulatory DNA sequence that is bound by a repressor protein. Feedback: In terms of lac operon regulation, what happens when E. coli is grown in medium containing both glucose and lactose? A) Both CAP and the lac repressor are bound to the DNA. B) CAP is bound to the DNA but the lac repressor is not. C) Lac repressor is bound to the DNA but CAP is not. D) Neither CAP nor the lac repressor are bound to the DNA. D) Neither CAP nor the lac repressor are bound to the DNA. Feedback: Which of the following can be described as 'a sequence that can be several thousand base pairs upstream or downstream of a eukaryotic promoter and which increases gene expression as much as 200-fold.'? A) CAAT box B) Enhancer C) Insulator D) TATA box B) Enhancer Feedback: Nuclear receptors belong to which class of transcription factor? A) Helix-loop-helix proteins B) Helix-turn-helix proteins C) Leucine zipper proteins D) Zinc finger proteins D) Zinc finger proteins Feedback: A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions in order to stabilize the fold. What best describes the mechanism by which the coactivator CREB-binding protein (CBP) activates transcription? A) CBP has DNA methyltransferase activity. B) CBP has histone acetyl transferase activity. C) CBP interacts with the basal transcription complex. D) CBP interacts with the basal transcription complex and also has histone acetyl transferase activity. C) CBP interacts with the basal transcription complex. Feedback: Which of the following statements, concerning regulation of trp operon expression by attenuation, is correct? A) The leader peptide sequence encodes enzymes required for tryptophan synthesis. B) The leader peptide sequence contains no tryptophan residues. C) Rapid translation of the leader peptide allows completion of the mRNA transcript. D) Rapid translation of the leader peptide prevents completion of the mRNA transcript. D) Rapid translation of the leader peptide prevents completion of the mRNA transcript. Feedback: Which of the following statements regarding regulation of transferrin-receptor protein synthesis is correct? A) The iron-responsive element is an iron-binding sequence in the mRNA that encodes transferrin-receptor protein. B) The iron-responsive element is in the 5' untranslated region of the mRNA that encodes transferrin-receptor protein. C) When iron is abundant the IRE-binding protein binds to and stabilizes the mRNA that encodes transferrin-receptor protein. D) When iron is scarce the IRE-binding protein binds to and stabilizes the mRNA that encodes transferrin-receptor protein. D) When iron is scarce the IRE-binding protein binds to and stabilizes the mRNA that encodes transferrin-receptor protein. Feedback: 'RNAi' stands for which of the following? A) RNA inducer. B) RNA insertion. C) RNA interference. D) RNA intron. C) RNA interference. Feedback: Suppose a
certain gene contains the double-stranded sequence: A) 5'-AUGUUUAGCGCC-3' B) 5'-CCGCGAUUUGUA-3' C) 5'-GGCGCUAAACAU-3' D) 5'-UACAAAUCGCGG-3' C) 5'-GGCGCUAAACAU-3' Feedback: The effectors of gene silencing are short double-stranded RNA molecules produced by the action of the enzyme dicer. Approximately what size are these molecules? A) 11 bp B) 22 bp C) 75 bp D) 100 bp B) 22 bp Feedback: Which of the following is true of the lac operon in E. coli? A) The operon is only switched on in the absence of lactose in the growth medium. B) The lac operon messenger RNA is a polycistronic mRNA (it carries information for synthesis of several proteins) C) The enzyme β-galactosidase is only produced in large quantities when the lac repressor is bound to the operator. D) The promoter is the binding site for the lac repressor. B) The lac operon messenger RNA is a polycistronic mRNA (it carries information for synthesis of several proteins) Feedback: Which of the following statements about mRNA stability is correct? Please select all that apply. A) Prokaryotic mRNAs have a half-life of only a few minutes. B) Regulation of mRNA stability is a way of regulating gene expression. C) It is thought that polyA tails stabilise eukaryotic mRNAs. D) Histone mRNAs have especially long polyA tails and are especially stable. A) Prokaryotic mRNAs have a half-life of only a few minutes. B) Regulation of mRNA stability is a way of regulating gene expression. C) It is thought that polyA tails stabilise eukaryotic mRNAs. Feedback: An epigenetic change in gene expression is an inherited change that does not involve any change in the nucleotide sequence of the gene. True or false? A) True B) False A) True Feedback: Which of the following statements is true of RNA interference? A) RNA interference is a normal way for organisms to regulate gene expression. B) RNA interference is a mechanism for combating virus infection in plants. C) RNA interference occurs only in vertebrates. D) RNA interference is already used therapeutically for many disorders. A) RNA interference is a normal way for organisms to regulate gene expression. B) RNA interference is a mechanism for combating virus infection in plants. Feedback:
Which of the following is true of RNA synthesis (transcription)? A) RNA synthesis is always in the 5' - 3' direction. B) RNA polymerase needs a primer to initiate transcription. C) In transcription, U is inserted opposite T. D) New nucleotides are added on to the 2' OH of the ribose sugar. A) RNA synthesis is always in the 5' - 3' direction. Feedback: In bacterial promoters, which of the following describes the 'Pribnow box'? A) The 5' untranslated region B) The -10 box C) The -35 box D) The termination sequence B) The -10 box Feedback: The role of the sigma factor in bacterial RNA polymerase is: A) to catalyse RNA synthesis: B) to position RNA polymerase correctly on the template DNA. C) to terminate RNA synthesis. D) to unwind the DNA template. B) to position RNA polymerase correctly on the template DNA. Feedback: Which of the following statements regarding termination of transcription in prokaryotes is correct? A) In Rho dependent termination the Rho factor moves along the DNA template ahead of the RNA polymerase. B) Rho factor has topoisomerase activity for relieving supercoiling. C) Termination often involves a stem-loop structure forming in the RNA transcript. D) Termination often involves a stem-loop structure forming in the DNA template. C) Termination often involves a stem-loop structure forming in the RNA transcript. Feedback: What is the role of eukaryotic RNA polymerase I? A) Transcription of mRNA only. B) Transcription of mRNA, rRNA and tRNA. C) Transcription of 'small' RNAs including TRNAs, 5S RNAs and snRNAs. D) Transcription of the major rRNA transcript. D) Transcription of the major rRNA transcript. Feedback: Which of the following does the abbreviation TBP stand for? A) TATA-box binding protein B) Transcription associated factor C) Transcription factor binding protein D) TATA box polymerase A) TATA-box binding protein Feedback: Which of the following best describes the 'cap' modification of eukaryotic mRNA? A) A modified guanine nucleotide added to the 3' end of the transcript. B) A modified guanine nucleotide added to the 5' end of the transcript. C) A string of adenine nucleotides added to the 3' end of the transcript. D) A string of adenine nucleotides added to the 5' end of the transcript. B) A modified guanine nucleotide added to the 5' end of the transcript. Feedback: Which of the following statements regarding splicing of eukaryotic mRNA transcripts is correct? A) Exons are spliced out and introns are retained in the mature mRNA transcript. B) Several reactions in the splicing process involve hydrolysis of ATP. C) Small nuclear RNAs are retained in the mature mRNA transcript. D) Splicing takes place in the cytosol. B) Several reactions in the splicing process involve hydrolysis of ATP. Feedback: Which of the following statements about mRNA splicing is true? A) The existence of split genes has no advantage B) Self-splicing introns do not require the help of any protein for splicing to occur accurately. C) β-thalassaemia results from a genetic defect in the spliceosome. D) Splicing occurs in the cytosol. B) Self-splicing introns do not require the help of any protein for splicing to occur accurately. Feedback: Is the following statement true or false? 'Eukaryotic mRNA is transcribed by RNA polymerase II.' A) True B) False A) True Feedback: The polyA tail on eukaryotic mRNA is encoded by a long string of Ts at the end of the gene. Is this statement true or false? A) True B) False B) False Feedback: Which of the following occur in both eukaryotic and bacterial transcription? Please select all that apply. A) 5' cap. B) polyA tail. C) Promoter. D) DNA-dependent RNA polymerase. C) Promoter. D) DNA-dependent RNA polymerase. What is the natural function of restriction enzymes? A) Protecting bacteria by cleaving the DNA of infecting viruses. B) Protecting bacteria by cleaving their own DNA. C) Protecting bacteria by methylating their own DNA. D) Protecting bacteria by methylating the DNA of infecting viruses. A) Protecting bacteria by cleaving the DNA of infecting viruses. Feedback: What is the correct sequence of events in Southern blotting? A) Hybridization of DNA fragments with a labelled probe sequence followed by separation by electrophoresis and then transfer to a membrane. B) Separation of DNA fragments by electrophoresis followed by hybridization with a labelled probe sequence and then transfer to a membrane. C) Separation of DNA fragments by electrophoresis followed by transfer to a membrane and then hybridization with a labelled probe sequence. D) Transfer of DNA fragments to a membrane followed by separation by electrophoresis and then hybridization with a labelled probe sequence. C) Separation of DNA fragments by electrophoresis followed by transfer to a membrane and then hybridization with a labelled probe sequence. Feedback: Dideoxynucleoside triphosphates (ddNTPs) are used in sequencing DNA because: A) ddNTPs are fluorescent. B) ddNTPs are incorporated very efficiently into DNA by DNA polymerase. C) ddNTPs cannot be incorporated into DNA by DNA polymerase. D) ddNTPs prevent further DNA synthesis once they are incorporated into the DNA sequence. D) ddNTPs prevent further DNA synthesis once they are incorporated into the DNA sequence. Feedback: A PCR reaction that continues for 30 cycles will produce approximately how many PCR products from a single template DNA molecule? A) 64 B) 128,000 C) Approximately 1 million D) Approximately 1 billion D) Approximately 1 billion Feedback: Which of the following is NOT required for a PCR reaction? A) A thermostable DNA polymerase B) Dideoxy-dNTPs (ddNTPs) C) Primers D) Template DNA B) Dideoxy-dNTPs (ddNTPs) Feedback: Plasmid vectors used in cloning often contain a gene for the N-terminal 146 amino acids of the enzyme β-galactosidase. What is the purpose of including this gene in the vector? A) It allows selection of E. coli host cells that contain the plasmid. B) It allows selection of E. coli host cells that contain plasmid in which the insert has been ligated. C) It cleaves the insert to allow it to be ligated into the vector. D) It enables the plasmid vector to replicate in E. coli host cells. B) It allows selection of E. coli host cells that contain plasmid in which the insert has been ligated. Feedback: RT-PCR is a method that is used for: A) forensic analysis of DNA. B) amplification of genomic DNA sequences. C) amplification of mRNA sequences. D) analysis of mRNA expression. D) analysis of mRNA expression. Feedback: Which of the following statements about forensic analysis of DNA is correct? A) DNA profile using short tandem repeats is unique to an individual. B) Forensic analysis makes use of SNPs in coding sequences to distinguish between individuals. C) PCR is used for DNA profiling (DNA fingerprinting). D) DNA fingerprinting cannot be used for paternity testing. C) PCR is used for DNA profiling (DNA fingerprinting). Feedback: In the creation of a knockout mouse using homologous recombination, a viral thymidine kinase gene is often included in the vector outside of the region of homology between the vector and targeted chromosome. What is the purpose of this? A) To allow negative selection of cells in which integration of the targeting sequence has occurred by homologous recombination. B) To allow negative selection of cells in which integration of the targeting sequence has occurred by random insertion into the genome. C) To allow positive selection of cells in which integration of the targeting sequence has occurred by homologous recombination. D) To allow positive selection of cells in which integration of the targeting sequence has occurred by random insertion into the genome. B) To allow negative selection of cells in which integration of the targeting sequence has occurred by random insertion into the genome. Feedback: Which of the following methods for introducing DNA into cells is used only for plants? A) A gene 'gun' B) Electroporation C) Microinjection D) Transformation of competent cells A) A gene 'gun' Feedback: The first gene therapy clinical trial took place in 1990, on patients with SCID (severe combined immunodeficiency syndrome). True or false? A) True B) False A) True Feedback: Which of the following is true of restriction enzymes? Please select all that apply. A) Restriction enzymes are exonucleases. B) Restriction enzymes are endonucleases. C) Restriction enzymes always cut to leave DNA 'sticky' ends. D) Restriction enzymes are part of the defence system of bacteria against attack by bacteriophages. B) Restriction enzymes are endonucleases. D) Restriction enzymes are part of the defence system of bacteria against attack by bacteriophages. Feedback: Which of the following therapies have been developed using recombinant DNA techniques? Please select all that apply. A) Hepatitis B vaccine. B) Human insulin for treatment of diabetes. C) Human growth hormone. D) Tissue plasminogen activator, used for blood clot removal. A) Hepatitis B vaccine. B) Human insulin for treatment of diabetes. C) Human growth hormone. D) Tissue plasminogen activator, used for blood clot removal. Feedback: Which enzymes remove supercoiling in replicating DNA ahead of the replication fork? A) helicases B) DNA polymerases C) primases D) topoisomerases D) topoisomerases Feedback: Which reaction in DNA replication is catalysed by DNA ligase? A) Addition of new nucleotides to the lagging strand. B) Addition of new nucleotides to the leading strand. C) Base pairing of the template and the newly formed DNA strand. D) Formation of a phosphodiester bond between the 3'-OH of one Okazaki fragment and the 5'-phosphate of the next on the lagging strand. D) Formation of a phosphodiester bond between the 3'-OH of one Okazaki fragment and the 5'-phosphate of the next on the lagging strand. Feedback: In which of the following would you find telomeres? A) Human mitochondrial DNA B) Human chromosomes C) Bacterial chromosomes D) The influenza virus genome B) Human chromosomes Feedback: Which of the following reactions is required for proofreading (i.e. correcting replication errors) during DNA replication by DNA polymerase III? A) 3' - 5' exonuclease activity B) 5' - 3' exonuclease activity C) 3' - 5' endonuclease activity D) 5' - 3' endonuclease activity A) 3' - 5' exonuclease activity Feedback: How does the mismatch repair system distinguish between the parental (i.e. correct) DNA strand and the newly synthesised strand containing the mismatched base? A) Thymine in the parental strand of the helix is methylated at GATC. B) Thymine in the new strand of the helix is methylated at GATC. C) Guanine in the parental strand of the helix is methylated at GATC. D) Guanine in the new strand of the helix is methylated at GATC. D) Guanine in the new strand of the helix is methylated at GATC. Feedback: What is the name of the DNA repair system in E. coli in which dual incisions are made in the damaged part of the double helix, and a 12-13 base segment is removed and replaced with new DNA? A) Mismatch repair B) Base excision repair C) Nucleotide excision repair D) AP site repair C) Nucleotide excision repair Feedback: Which of the following is the name of the human genetic disorder resulting from defects in nucleotide excision repair? A) Hereditary nonpolyposis colorectal cancer (HNPCC) B) Xeroderma pigmentosum (XP) C) Lynch syndrome D) Diabetes B) Xeroderma pigmentosum (XP) Feedback: During which phase of the cell cycle is DNA replicated? A) G1 phase. B) S phase. C) G2 phase. D) M phase. B) S phase. Feedback: The supercoils are produced in front of a growing DNA chain during DNA replication are positive supercoils, resulting from overwinding of the helix. True or False? A) True B) False A) True Feedback: During DNA replication, nucleotides are added on to the 5' end of the growing DNA strand. True or False? A) True B) False B) False Feedback: Which of the following statements about the E. coli chromosome is correct? Please select all that apply. A) The E. coli chromosome is a single replicon. B) Replication begins at oriC. C) Replication can start at any point in the chromosome. D) A single replication fork moves around the molecule until the chromosome is completely replicated. A) The E. coli chromosome is a single replicon. B) Replication begins at oriC. Feedback: Which of the following statements is correct? Please select all that apply. A) Telomeres become shorter as cells age. B) Somatic cells have very little telomerase. C) Immortal cancer cell lines always have high levels of telomerase. D) Telomeres become longer as cells age. A) Telomeres become shorter as cells age. B) Somatic cells have very little telomerase. Feedback: Practical RNA interference can be used to? a. Inhibit expression of a specific gene product. a. Inhibit expression of a specific gene product. Practical In which one of the following organisms are morpholinos NOT commonly used? a. Yeast Practical You want to clone a cDNA fragment into a pEGFP expression vector, that contains a kanamycin resistance marker, and have digested the plasmid DNA with SalI and ApaI and have isolated the SalI-ApaI cDNA fragment from an agarose gel. After the ligation reaction, you set up the following transformations: a: pEGFP (SalI-ApaI) + cDNA fragment (SalI-ApaI) + ligase Assuming that all 4 transformations contained the same amount of plasmid DNA, which transformation is likely to give you the highest number of bacterial colonies when plated on kanamycin containing agar plates? Practical Which one of the following is a major trigger for co-suppression in plants? a. Double strand DNA breaks. b. The production of double stranded RNA. Practical Dicer is an enzyme involved in generating siRNAs, what type of enzyme is it? a. A reverse transcriptase. c. A nuclease. Feedback: The Dicer enzyme is able to snip a double-stranded form of RNA into segments that can attach themselves to genes and block their activity. Dicer cleaves dsRNA into smaller fragments called short interfering RNAs (siRNAs) and microRNAs (miRNAs). Dicer then helps load these fragments into a large multiprotein complex called RISC. Dicer is an endoribonuclease. Practical Which one of the following contains an AGO sub-unit? a. The RISC complex. a. The RISC complex. Feedback: The RNA-induced silencing complex, or RISC, is a multiprotein complex that incorporates one strand of a small interfering RNA (siRNA) or microRNA (miRNA). RISC uses the siRNA or miRNA as a template for recognizing complementary mRNA. Ago, Argonaute protein family plays a central role in RNA silencing processes, as essential catalytic components of the RISC. RISC complex is responsible for the gene silencing phenomenon known as RNA interference (RNAi). AGO proteins bind different classes of small non-coding RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). Small RNAs guide Argonaute proteins to their specific targets through sequence complementarity (base pairing), which then leads to mRNA cleavage or translation inhibition. Practical Which of the following statements relating to DNA sequencing using a thermocycler is FALSE? a. A heat stable DNA polymerase is used. d. The template DNA is amplified in an exponential manner as the reaction proceeds. In a plasmid vector designed to express a recombinant protein in E. coli, which would be the correct order for the following elements? a. -35 sequence, -10 sequence, RBS, ATG. a. -35 sequence, -10 sequence, RBS, ATG. Practical Proteomics is the study of: a. gene-transcribing proteins b. all proteins in an organism Feedback: The proteome is the entire set of proteins, produced or modified by an organism or system. Proteomics is the large-scale study of proteins, particularly their structures and functions. Practical The sequence 5’ ATG 3’ in a DNA molecule is: a. A sequence where transcription must initiate. d. A sequence that could encode methionine. Practical Western blotting allows the detection of a specific protein. a. A short oligonucleotide d. An antibody Feedback: The Western blot is a widely used to detect specific proteins in a sample of tissue homogenate or extract. It uses gel electrophoresis to separate native proteins by 3-D structure or denatured proteins by the length of the polypeptide. The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are stained with antibodies specific to the target protein. The gel electrophoresis step is included in Western blot analysis to resolve the issue of the cross-reactivity of antibodies. Practical Which marker gene is commonly used to select mammalian cells that have taken up an expression vector in G418? a. ampicillin (amp)
resistance c. neomycin (neo) resistance Practical Which enzyme can add template-independent nucleotides to the 3’end of double- stranded DNA? a. Reverse
transcriptase b. Terminal transferase Feedback: Terminal transferase (TdT) is a template independent polymerase that catalyzes the addition of deoxynucleotides to the 3' hydroxyl terminus of DNA molecules. Protruding, recessed or blunt-ended double or single-stranded DNA molecules serve as a substrate for TdT. Practical Retroviral expression vectors are plasmid-based shuttle vectors that contain a deleted version of the viral genome. Which of the following has to be provided by the helper cell in trans in order to produce non-replicating recombinant retroviral stock? a. long terminal repeats (LTRs) b. reverse transcriptase (RT) Practical When were methods for sequencing DNA molecules first developed? a. The 1950s. Practical In 2008 the whole genome sequence of James Watson, the co-discoverer of the structure of DNA, was published. Approximately how long did it take to generate this sequence? a. 2 years Practical Which part of the adeno-associated viral genome is sufficient for replication, transcription, proviral integration and rescue? a. inverted
terminal repeat (ITR) a. inverted terminal repeat (ITR) Practical What type of enzyme is DpnI? a. A heat stable DNA polymerase. b. A restriction endonuclease. Feedback: Type IIM restriction endonucleases, such as DpnI, are able to recognize and cut methylated DNA Practical Which one of the following is an affinity tag? a. The Ala tag d. The His tag Feedback: Affinity tags are peptide sequences genetically grafted onto a recombinant protein. Often these tags are removable by chemical agents or by enzymatic means, such as proteolysis or intein splicing. Tags are attached to proteins for various purposes. The ideal affinity tag should be small in size and as inert as possible to limit any potential interaction with the recombinant protein or proteins that might be present in culture media. The poly(His) tag is a widely used protein tag; it binds to metal matrices. Which of the following statement regarding termination of transcription in prokaryotes is correct?Correct answer:
Rho-mediated termination and hairpin loop formation are both common ways to terminate prokaryotic transcription.
What occurs during the termination phase of transcription in a prokaryote?Termination in Prokaryotes
Near the end of the gene, the polymerase encounters a run of G nucleotides on the DNA template and it stalls. As a result, the rho protein collides with the polymerase. The interaction with rho releases the mRNA from the transcription bubble.
How is transcription terminated in prokaryotic cells quizlet?- RNA sequences called terminators signal the end of transcription. -In intrinsic terminators (above) hairpin loops form within the RNA. -RNA polymerase and the mRNA are then released from the DNA. -In extrinsic terminators, the rho protein is required to terminate transcription.
Which is correct for the termination of transcription in eukaryotes?The termination of transcription is different for the different polymerases. Unlike in prokaryotes, elongation by RNA polymerase II in eukaryotes takes place 1,000–2,000 nucleotides beyond the end of the gene being transcribed. This pre-mRNA tail is subsequently removed by cleavage during mRNA processing.
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