Genetics Chapter 13 and 14 HW
RNA interference (RNAi) is a mechanism of gene silencing that is mediated by the presence of double‑stranded RNA. Arrange the steps involved in gene silencing by RNAi.
-Double‑stranded RNA (dsRNA) is introduced into a cell. -Long dsRNA is cleaved into short dsRNA. -RNA‑induced silencing complex (RISC) binds to short dsRNA. -The sense strand is separated from the antisense strand and degraded. -Antisense RNA pairs with the target RNA. -Target RNA is not translated but degraded. -A gene's expression is silenced.
Identify the statements that are features of a promoter.
-In eukaryotes, the promoter often contains a TATA box, which is where the TATA‑binding protein binds. -In both prokaryotes and eukaryotes, the promoter is located in the 5′5′ direction, upstream from the transcription start site. -In prokaryotes, the promoter contains a -35 and -10 region upstream of the transcription start site.
Which of the following statements describes the function of the sigma factor in prokaryotic transcription?
-It facilitates the binding of RNA polymerase to the promoter to initiate transcription
What problem is solved by the requirement that a PAM sequence be adjacent to a protospacer in order to be recognized by CRISPR‑Cas systems?
A PAM sequence allows for the recognition and cleavage of foreign DNA without destroying the spacer DNA within the CRISPR array.
What happens during the initiation step of DNA transcription?
A portion of the DNA unwinds and RNA polymerase attaches to the DNA within transcription bubble.
Select the description of a poly‑A tail.
Poly A tail is added to the RNA at the end of transcription (added to the end of pre-mRNA) sequence of adenine nucleotide added on to the end of pre mRNA.Due to this poly A tail it can not degrade due to enzyme present in cytoplasm and also helps in transcription.
At least three types of RNA are required for protein synthesis. Compare and contrast mRNA, rRNA, and tRNA by moving the descriptions of their structure and function to the appropriate categories. Some phrases may describe all three types of RNA.
mRNA Read in codons, three base sequences for specific amino acids. rRNA Joins amino acids by peptide bonds (acts as an enzyme for peptide synthesis) tRNA Delivers amino acid to the site of protein synthesis mRNA tRNA rRNA Composed of ribo nucleic acid In eukaryotes, can present outside the nucleus.
A strain of bacteria possesses a temperature‑sensitive mutation in the gene that encodes the sigma factor. The mutant bacteria produce a sigma factor that is unable to bind to RNA polymerase at elevated temperatures. -What effect will this mutation have on the process of transcription when the bacteria are raised at elevated temperatures?
-The sigma factor is essential for bacterial RNA Polymerase because sigma factors confers the specificity of binding of RNA Pol to the promoter region in the DNA strand. -In the absence of the sigma factor the RNA Pol will be able to bind the DNA strand non-specifically and the transcription will take place INEFFICIENTLY -Transcription will not be initiated in the specific promoter regions but initiation will start from single-stranded regions, nicks or duplex ends. -So at elevated temperatures the process of transcription will be initiated at nonspecific regions in the DNA strand. ANSWERS: -Transcription that begins prior to the temperature shift will be completed. -Transcription initiation will not occur normally at the elevated temperature.
In which scenarios would the clustered regularly interspaced short palindromic repeats (CRISPR) system provide valuable information to test a hypothesis?
-inserting a gene or DNA sequence to assay altered expression phenotype -precisely knocking out a specific gene or gene region to test its function
Match each function to the appropriate type of RNA. How many codons could be formed if each codon was two bases long?
1. hydrogen bonds with codon - tRNA2. contains the codon for the polypeptide sequence = mRNA3. catalyzes peptides bond formation - rRNA4. transports amino acids to the ribosome -tRNA How many codons could be formed if each codon was two bases long? -Answer: total no. of codon if each codon is two bases long = 42 =16 codons
How do cells regulate gene expression using alternative RNA splicing?
Alternate RNA splicing determines which proteins are produced from each gene. -Gene expression involves transcription of a gene into a messenger (mRNA) and translation of an mRNA into a protein. Eukaryotic genes contain coding regions, called exons, and noncoding regions, called introns. When eukaryotic genes are transcribed to pre‑mRNA, the pre‑mRNA contains both exons and introns. During mRNA splicing, introns are removed and the exons are joined together to generate a mature mRNA. Exons can be joined together in different combinations, or particular exons can be left out of the mature mRNA. This process is highly controlled and is referred to as alternative RNA splicing. Alternative RNA splicing can result in many different mRNAs with different nucleotide sequences to be generated from a single gene. Because the mRNAs have different nucleotide sequences, when they are translated they result in proteins that have a different amino acid sequence. Thus, alternative RNA splicing determines which proteins are produced from each gene. Alternative splicing is one way that gene expression is regulated within the cell. There are many ways besides alternative RNA splicing for regulating gene expression within the cell. For example, there are a number of proteins that interact with DNA that help determine which genes are transcribed to mRNA. Proteins that bind to regions of DNA can also help under‑ or overexpress particular genes in certain cell types. Other mechanisms exist to control how fast certain proteins are degraded within a cell and to regulate how much of a particular protein is translated.
Select the description of a 5′ cap.
Ans: Modified form of guanine nucleotides added onto the front of pre-mRNA Eukaryotic mRNA have a Peculiar enzymatically appended cap structure, Present in the 5' end consisting of 7 methyl guanosine Residue that is joined via 5'--5' triphosphate bridge. It protects the m RNA from degradation and helps in the transfer of m RNA from nucleus to cytoplasm.
Select the description of an intron
Answer: non coding portion of a DNA sequence that is removed from pre-mRNA Introns are noncoding sections of RNA transcript or DNA encoding it. They are sliced out before RNA is translated into a protein. The coding sections are called exon
Identify the true statements about CRISPR‑Cas9.
CRISPR sequences are only found within the genomes of prokaryotes. CRISPR spacer sequences are derived from viral DNA fragments. Cas9 cleaves target DNA adjacent to a PAM (protospacer adjacent motif) sequence.
Which is not found in a spliceosome that is actively splicing?
DNA -Spliceosome are involved in splicing of pre - mRNA by using small nuclear RNA , small nuclear riboproteins and other acessory proteins. U1,U2,U4,U5 and U6 are small nuclear RNA which associate with small nuclear riboproteins and formed spliceosomes.
How are siRNAs and miRNAs made?
Dicer processes and cleaves double‑stranded RNA to produce 21‑ to 25‑nucleotide‑long sequences.
According to the central dogma, double-stranded DNA serves as the template for the production of RNA during transcription. -Which of the two DNA strands serves as the template for transcription?
Either DNA strand may be used as a template, by RNA polymerase but a single DNA strand oriented in the 3-5' direction is used as template each time transcription occurs.
DNA encodes the cell's genetic instructions for making proteins. The process of making proteins from DNA is divided into two stages called transcription and translation. Transcription is further divided into three steps called initiation, elongation, and termination. Classify the statements about transcription according to the step in which each occurs.
Initiation: -RNA polymerase binds to the group of transcription factors at the promoter. -The DNA double helix unwinds and RNA synthesis begins. Elongation: -The newly transcribed RNA transcript is proofread for errors. -The RNA polymerase traverses the DNA template, adding complementary base pairs in the 5' to 3' direction Termination: -The RNA polymerase stops adding base pairs when it reaches a certain DNA sequence that signals the end of the gene. -The RNA polymerase detaches from the DNA. -The RNA transcript is released
Suppose a mutation occurs in the gene encoding eukaryotic RNA polymerase I, II, or III that renders that polymerase non-functional. Match each RNA polymerase mutation with all of the cellular processes that it would disrupt.
Mutation in eukaryotic RNA polymerase I: -rRNA processing -mRNA translation Mutation in eukaryotic RNA polymerase II: -rRNA processing -Pre mRNA synthesis -pre- mRNA processing (as most of the snRNA will not produced, that pla processing in splicing). -RNAi- mediated gene regulation (as miRNA will not produced) Mutation in eukaryotic RNA polymerase III: -tRNA synthesis -rRNA synthesis --pre- mRNA processing (also disrupt because no production of U6 snRNA(need in splicing process). -RNAi- mediated gene regulation
Which description applies to alternative mRNA splicing?
Processing of exons in mRNA that results in a single gene coding for multiple proteins - Alternative mRNA splicing
Place the steps of eukaryotic transcription in order of occurrence.
RNA polymerase II binds DNA promoter element. RNA polymerase unwinds DNA Ribonucleotides align with complementary DNA nucleotides RNA polymerase links triphosphate ribonucleotides together Guanylyl transferase adds a guanine cap to this 5" end of th emRNA RNA polymerase is released from DNA Splicing and polyadenylation events modify the mRNA Processed mRNA leaves the nucleus.
Why is a cap added to mRNA, but not to tRNA or rRNA?
RNA polymerase II transcribes mRNA, whereas RNA polymerase I transcribes rRNA and RNA polymease III transcribes tRNA. The domain that assists other enzymes in adding the cap is found in RNA polymease II only.
What happens during the elongation step of DNA transcription?
RNA polymerase moves along the template strand of the DNA creating an mRNA strand. -There are four steps in Transcription of DNA. 1)Initiation 2)Elongation 3)Termination 4)Processing During elongation RNA polymerase moves along the template strand and uses base pairing complimentary with the DNA template to create an RNA copy .If the template strand runs from 3' --> 5' the produced RNA copy runs in opposite direction ie from 5' --->3'.(except that thymines are replaced with uracils )
In Arabidopsis thaliana, the Flowering Locus C (FLC) gene codes for a regulatory protein that suppresses flowering. FLC is expressed in seedlings to prevent premature flowering. In mature plants, FLC expression decreases with cooler temperatures, and flowering occurs once sufficiently cool temperatures are reached. If small‑interfering RNA (siRNA) that is complementary to FLC mRNA is introduced, how would RNA interference (RNAi) affect flowering?
RNAi would degrade FLC mRNA and stimulate flowering. -RNA interference (RNAi), also called RNA silencing or post‑transcriptional gene silencing, combats foreign genes, most frequently from viruses, and modulates overexpression of native genes. When double‑stranded RNA is present, Dicer protein activates and cleaves it into small‑interfering RNA (siRNA) or microRNA (miRNA). One class of siRNA combines with the RNA‑Induced Silencing Complex (RISC) and acts as a template for the RISC protein complex to identify and degrade other copies of the RNA. A second class of siRNA binds to complementary sequences in DNA and attracts enzymes that inhibit transcription via demethylation of DNA and histones. If Dicer cleaves the double‑stranded RNA into miRNA, the miRNA combines with the RISC protein complex, which imperfectly pairs with and remains attached to other copies of the RNA, thereby inhibiting translation. Because the siRNA in the question is complementary to FLC mRNA, it would combine with the RISC protein complex, which would cleave and degrade FLC mRNA. Without FLC mRNA, the regulatory protein that represses flowering is not translated and flowering will occur.
Complete the table by matching each RNA type and abbreviation with the appropriate function.
Small Nuclear RNA (snRNA): involved in the splicing process when mRNA is formed Ribosomal RNA (rRNA): combines with proteins to form ribosomes Transfer RNA (tRNA): brings amino acids to sites of mRNA during protein synthesis Small interfering RNA (siRNA): eliminates the expression of an undesirable gene Messenger RNA (mRNA): carries genetic information to ribosomes for protein synthesis Micro RNA (miRNA): inhibits the translation of mRNA into protein
Place the following components of CRISPR‑Cas systems in the order in which they function during generation of CRISPR‑Cas immunity.
Spacer are incorporated in to CRISPR array The CRISPR array is transcribed into a long CRISPR pre RNA CRISPR precursor RNA is cleaved and processed into CRISPR RNA CRISPR RNA combines with a cas protein to form a effector complex The effector complex binds to the foreign DNA The cas protein in the effector complex cleaves the foreign DNA
What are the three stages by which CRISPR‑Cas immunity occurs, and what takes place during each stage?
Step-1 Adaptation - Foreign DNA is cleaved and incorporated into the CRISPR - Cas array as spacers. Step -2 Expression - The CRISPR array is transcribed and proceed to produce CRISPR RNA that combines with a Cas protein to form an effector complex. Step-3 Interference - .The effector complex binds to foreign DNA,and the Cas proteins cleave the foreign DNA, which is then degraded.
What happens during the termination step of DNA transcription?
The mRNA detaches from the RNA polymerase as the RNA polymerase leaves the DNA strand.
What is the role of the eukaryotic promoter in transcription?
The site where transcription factors (RNA Polymerase) bind (to initiate transcription) and function. -The promoter is defined as the region containing binding sites that can support transcription at normal efficiency and with proper control. The major feature defining the promoter for an eukaryotic mRNA is the location of binding site for transcription factors. Each promoter contains characteristics set of short conserved sequences that are recognized by appropriate class of factors
What is the function of the spliceosome?
The spliceosome produces a mature mRNA by connecting two exons and releasing the intron. -A spliceosome consists of five small ribonucleoproteins. Each of these ribonucleoproteins consists of a small nuclear RNA molecule.The pre-mRNA nuclear introns are spliced within the spliceosome and exons are joined together by transesterification reaction.
Which statement is not correct about how siRNAs and miRNAs function?
They can integrate into DNA sequences of specific genes.
An RNA molecule has the following percentages of bases: A=23%,23%, U=42%,42%, C=21%,21%, and G=14%.14%. Is this RNA single‑stranded or double‑stranded? How can you tell? What would be the percentage of bases in the template strand of the DNA that contains the gene for this RNA?
This is a single stranded RNA because if it was double-stranded, the percentage of A's and U's would have to equal since they base pair together when it's double stranded, as would the percentages of G and C. -B. For the template DNA, you would have:23% T (because A bonds with T), 42% A (because U bonds with A, 21% G (because C bonds with G), 14% C (because G bonds with C)
Classify each description to the appropriate category.
Transcription: -Catalyzed by RNA polymerase -Acts only on one strand Replication: -Catalyzed by DNA polymerase -RNA primase is required Both: -Localized in the cytoplasm in prokaryotic cells
Gene transcription occurs from right to left for gene A and gene B, whereas transcription occurs from left to right for gene C, as in the diagram.
Whats the template strand for the genes: Gene A: Top, Gene B: Top, Gene C: Bottom During gene transcription, RNA polymerase reads the template strand in the 3' to 5'direction, but the mRNA is formed in the 5' to 3' direction.