Unit 7 1 UNIT 7 PART A: RNA STRUCTURE AND FUNCTION PART B: TRANSCRIPTION PART C: CO- AND POST-TRANSCRIPTIONAL MODIFICATION OF RNA PART D: TRANSCRIPTIONAL CONTROL OF PROTEIN SYNTHESIS PART A: RNA STRUCTURE AND FUNCTION In eukaryotes, DNA is largely confined to the nucleus, whereas protein synthesis occurs on ribosomes in the cytoplasm. In the early 1950's, it was found that the onset of protein synthesis was acompanied by an increase in the amount of RNA in the cytoplasm. RNA caries the genetic information from DNA to the protein biosynthetic machinery of the ribosome in the cytoplasm. Asignment: Nelson & Cox, review pp. 271 - 273, 283 - 287. 1. Describe the function of each of the following (p. 271): a. rRNA b. mRNA c. tRNA Unit 7 2 2. Compare DNA and RNA with respect to: a. Identity of the pentose ring (ribose vs deoxyribose; Fig. 8-1, p. 271). b. Which nitrogen bases (C,A,G,U, and/or T) are found in DNA? In RNA? (Fig. 8-2, p. 272) 3. Distinguish betwen monocistronic and polycistronic mRNA (p. 284). Is eukaryotic mRNA monocistronic or polycistronic? What about prokaryotic mRNA? 4. Secondary structure (pp. 284 - 286) a. Is DNA usualy double or single stranded? b. Is RNA usualy double or single stranded (p. 284)? Does single stranded RNA have any double stranded regions? Using Fig. 8-23 (p. 285) to ilustrate your answer, point out a hairpin loop (sometimes caled a stem and loop). Within double-stranded regions of RNA, define two types of base pairs. Note: The molecule shown in Fig. 8-24 (p. 285) has much more secondary structure than would be found in a typical mesenger RNA. 5. Tertiary Structure: Note what RNA structures actualy look like (Fig. 8-25, p. 286, x-ray structures). Unit 7 3 PART B: TRANSCRIPTION Replication and transcription difer in one important respect. During replication the entire chromosome is copied to yield daughter DNAs identical to the parent DNA. Transcription, in contrast, is selective. Only particular genes or groups of genes are transcribed at any one time. The transcription of DNA can be regulated so that only genetic information needed by the cel at a particular moment is transcribed. Specific regulatory sequences indicate the beginning and end of the segments of DNA to be transcribed, as wel as which DNA strand is to be used as the template. Asignment: Nelson & Cox pp. 1021 - 1031. 1. Use Fig. 26-1 (p. 1023) to give an overview of transcription by RNA polymerase. Distinguish betwen RNA polymerases and DNA polymerase I in terms of : a. Substrates b. Whether a primer is needed c. The direction of synthesis (3' ? 5') or (5' ? 3') d. The nucleophilic atack in bond formation e. The role of pyrophosphate and pyrophosphatase in the overal reaction f. The requirement for a template 2. What is meant by the terms "template" and "non-template" strands (Fig. 26-2, p. 1024). 3. Does the same strand of the chromosome always serve as the template strand (Fig. 26-3, p. 1024)? Unit 7 4 4. Discuss the quaternary structure of RNA polymerase (pp. 1024 - 1025). 5. Does RNA polymerase have 3' to 5' exonuclease activity? Why is it unnecesary (p. 1024)? 6. Discuss the general organization of an E. coli promoter. In doing so, consider the following (p. 1025): a. What is meant by the term "consensus sequence"? Use Fig. 26-5 (p. 1025) to discuss how a consensus sequence is determined? Note that the term "consensus sequence" is a general term. In Fig. 26-5 we are focusing on the consensus found at prokaryotic transcription initiation sites. There are, however, many diferent consensus sequences with many diferent functions. b. Define the numbering system which is used to identify regions such as the -10 and -35 regions. c. What is the significance of the -35 and -10 regions (p. 1025)? d. What is the relationship betwen the "strength" of a promoter (i.e. the frequency at which transcription is initiated at a particular promoter) and the degre of match to a consensus sequence (p. 1025)? e. What is the function of the sigma (?) subunit (p. 1025)? 7. Use Fig. 26-6 (p. 1027) to discuss the events in transcription initiation. 8. Is transcription usualy regulated at the level of initiation, elongation, or termination (p. 1028). Is it ever regulated at the other levels? 9. Discuss two distinguishing features of the termination signal in the mRNA in rho independent termination of transcription in prokaryotes (Fig. 26-8, p. 1029). Unit 7 5 10. Transcription in eukaryotes (pp. 1030 - 1031) a. Using Fig. 26-9 (p. 1030), describe the sequences typicaly found at a eukaryotic promoter. How do these sequences compare to those found at a prokaryotic promoter? b. What is a transcription factor (p. 1030)? PART C: CO-TRANSCRIPTIONAL AND POST-RANSCRIPTIONAL MODIFICATION OF RNA RNA is often procesed (i.e. cut and pasted) or modified. These alterations are made either while the RNA is being synthesized (co-transcriptionaly) or after it is synthesized (post-transcriptionaly). It is not easy to distinguish experimentaly betwen the two. We don't expect you to make this distinction in your answers, but rather to focus on the nature of the modifications themselves. Asignment: Nelson & Cox, pp. 1033 - 1041, 1050 - 1061. 1. Use Fig. 26-12 (p. 1034) to discuss the formation of an mRNA primary transcript and its procesing during maturation. 2. During the procesing of eucaryotic mRNA a "5' cap" is added (Fig. 26-13, p. 1035). Describe and list two functions of the cap (p. 1034). 3. Splicing of the primary transcript (pp. 1035 - 1039): a. Distinguish betwen "exons" and "introns" (p. 1035). b. Do al eukaryotic genes contain introns (p. 1035)? Do most? c. Does splicing take place at the level of DNA or RNA? Unit 7 6 d. Discuss the splicing mechanism in mRNA shown in Fig. 26-17 (p. 1038). 1) Point out features at exon-intron junctions that provide signals for correct splicing. What are the consequences of imprecise splicing? 2) What is a spliceosome? What is an snRNP (also caled a snurp)? 3) How do individual snRNAs locate the consensus sequences that flank introns (p. 1037)? 4) Point out the location and identity of the nucleotide that wil make the initial atack on the 3' end of the exon. 5) What is the "lariat structure"? 4. Another modification of eukaryotic mRNA is addition of a 3' poly (A) tail (pp. 1039 - 1040). a What is the function of the poly (A) tail (p. 1039)? b. Discuss the key steps in the addition of a poly (A) tail (Fig. 26-18, p. 1039). 1) Is the tail encoded in the gene? 2) Name the enzyme involved in making the poly (A) tail. 3) Does this enzyme add residues in a template directed manner like DNA polymerase? 5. Clearly distinguish betwen the proceses shown in Fig. 26-19 and "RNA editing" described briefly in the text (p. 1040) and covered more fully in Unit 8? 6. Use Fig. 26-20 (p. 1041) to distinguish betwen poly A site choice and alternative splicing. Discuss the role of each of these mechanisms in generating protein diversity from a single gene. Note that because there are substantialy fewer genes in the human genome (~25,000) than the number Unit 7 7 of diferent proteins made (>50,000), it is believed that many genes can actualy encode more than one protein through these types of mechanisms. 7. RNA-dependent synthesis of RNA and DNA (pp. 1050 - 1061) a. Use Fig. 26-33 (p. 1050) to discuss how retroviruses (like HIV) infect host cels. What is the role of reverse transcriptase? b. AZT is a common component in the triple cocktail used to treat HIV positive patients. Discuss why AZT interferes with viral replication (Box 26-2, p. 1053). c. What is meant by "RNA world". What evidence is used in support of the hypothesis (pp. 1056 - 1059)? 8. What percentage of the human genome is believed to encode protein (Box 26-4, pp. 1060 - 1061)? How much of our genome is currently believed to be transcribed into RNA? What is a "TUF"? PART D: TRANSCRIPTIONAL CONTROL OF PROTEIN SYNTHESIS Asignment: Nelson & Cox, pp. 1115 - 1127, 1136 - 1141, 1045 - 1046, 1132-1134, 1145 - 1146. 1. In this unit you wil learn one of the methods by which the amount of an enzyme present in a cel can be controlled. Thinking back to Unit 4, recount briefly thre mechanisms which control the activity of enzymes in the cel. 2. Distinguish betwen constitutive and regulated gene expresion. (p. 1116). Unit 7 8 3. Define each of the following (pp. 1117 - 1118): a. specificity factor b. represor c. activator d. operator e. negative regulation f. positive regulation 4. Use Fig. 28-5 (p. 1119) to describe the key features of an "operon". Are operons found in prokaryotes or eukaryotes (p. 1118)? Do they encode monocistronic or polycistronic mRNA (p. 1118)? 5. Using words or structures, write an equation representing the hydrolysis of lactose to its component monosacharides. What is the name of the enzyme which catalyzes this reaction (Fig. 28-6, p. 1119)? 6. The lac operon consists of thre tandem genes that encode enzymes involved in lactose utilization controlled transcriptionaly by a single promoter and regulatory region (pp. 1119 - 1121). a. Draw a diagram of the lac operon (Fig. 28-7, p. 1120). b. Label each of the following: operon, promoter site, operator sites, structural genes. c. Name each of the thre structural genes and describe the function of each (p. 1119). d. Describe how the lac operon can be negatively regulated. What protein is involved? Name the gene that encodes this protein? What molecule acts as the inducer (pp. 1119 - 1121)? Unit 7 9 e. How do proteins interact at specific DNA sequences? What type of interaction is most often involved (Fig. 28-9, p. 1121)? ithin the DNA double helix, where does this interaction occur (Fig. 28-8, p. 1121)? Use Figs. 28-11, 28-12, 28-13, and 28-14 (pp. 1123 - 1124) to distinguish betwen the following DNA-binding motifs: Helix- turn-helix, zinc finger, homeodomain, and leucine zippers. 7. Describe the phenomonon caled catabolite represion (p. 1126). 8. Discuss the role of the following in the positive regulation of the lac operon (pp. 1126 - 1127). a. cAMP receptor protein (CRP) b. cAMP 9. Transcription of the lac operon is controlled by the binding of protein factors at the promoter and operator regions (Fig. 28-18, p. 1127). a. Which of the following proteins - Represor protein, and / or CRP is / are efectively bound to the lac operon under each of the following conditions of cel growth. For each energy source, state whether transcription occurs or not. Energy source Represor CRP Transcription +/- +/- +/- Lactose Glucose Glucose + Lactose 10. What is a regulon (p. 1127). Unit 7 10 11. Regulation of gene expresion in eukaryotes (pp. 1136 - 1141). a. List four important features that distinguish regulation of gene expresion in eukaryotes from prokaryotes (p. 1136). b. Distinguish betwen heterochromatin and euchromatin (p. 1136). c. Discuss the structural features of active chromatin (open or condensed; p. 1136). d. Is DNA methylation more or les common in transcriptionaly active areas (p. 1137)? e. What is meant by "chromatin remodeling" (p. 1137)? f. What is an enhancer (pp. 1138 - 1139)? g. Use Fig. 28-29 (p. 1139) to discuss the role of each of the following in transcriptional activation: 1) basal transcription factors 2) transcription activators 3) chromatin modification and remodeling proteins 4) coactivators h. Gene expresion in higher eukaryotes is also controlled by a new mechanism of micro-RNA's (miRNA) (pp. 1045 - 1046, 1145-1146) that target mRNA's for hydrolysis. Discuss the synthesis and procesing of miRNAs as shown in Figs. 26-28 (p. 1046) and 28-36 (p. 1146). What is RNAi (p. 1145)? i. Use Fig. 28-25 (p. 1133) to show how the sRNAs DsrA promote while OxyS blocks translation of bacterial mRNAs. Are these examples of cis or trans regulation? j. Use Fig. 28-26 (1133) to discuss how riboswitches can terminate transcription, block translation, or interfere with splicing, Are riboswitches an example of cis or trans regulation? Jim Blankenship Microsoft Word - U07_F08.doc
Want to see the other 10 page(s) in U07F08.pdf?JOIN TODAY FOR FREE!