What Is The Importance Of The 2', 3', And 5' Carbons Of RNA (And/Or DNA)? PDF

1. 2. 3. What is the importance of the2’, 3’, and 5’ carbons of RNA (and/or DNA)? What do we mean when we say the genetic code is “universal”? and “degenerate”? Given that there are 20 amino acids, explain why the genetic code cannot consist of two nucleotides per codon, and why it would be overkil...

1. 2. 3. What is the importance of the2’, 3’, and 5’ carbons of RNA (and/or DNA)? What do we mean when we say the genetic code is “universal”? and “degenerate”? Given that there are 20 amino acids, explain why the genetic code cannot consist of two nucleotides per codon, and why it would be overkilled to use four nucleotides per codon. 4. Distinguish between the terms DNA, gene, codon, exon, and chromosome. 5. If the template strand is used as template to produce RNA, why do we call the nontemplate strand the “coding strand”? 6. What is the role of the sigma factor in prokaryotic transcription initiation? 7. In both prokaryotes and eukaryotes, the initiation of transcription is tightly controlled with respect to where transcription is initiated. Why is this important? 8. During mRNA synthesis, where does the energy come from to create bonds between nucleotides? 9. Compare and contrast transcription in prokaryotes and eukaryotes. 10. Where in the eukaryotic cell do transcription, mRNA processing, and translation occur? What makes this different than prokaryotes? 11. What is the role of tRNA? How are tRNAs “charged”? 12. Which direc)on does DNA run in gel electrophoresis? 13. What enzyme is used in PCR? What enzymatic activity does it have? 14. PCR is sort of like the replication fork in a test tube. What components of the replication fork are not present in PCR, and why are they not needed? 15. Recombinant DNA often includes putting the DNA of one species, like humans, into other species, like bacteria. Why does this work, even though humans are very different than bacteria? 5. How is DNA ligase used in molecular cloning? 16. Transcription and translation occur simultaneously in prokaryotes, but not eukaryotes. Why must eukaryotes wait until transcription is complete before beginning translation? 17. If a strain of E. coli has a mutation in the operator of the trp operon that prevents binding by a repressor, will the operon be transcribed in the presence of tryptophan? Will the operon by transcribed in the absence of tryptophan? 18. If a strain of E. coli has a mutation in the operator of the trp operon that results in the repressor binding all the time even in the absence of tryptophan, explain what will happen in the presence and absence of tryptophan. 19. If a strain of E. coli has a mutation so that no repressor protein is made. Will transcription occur in the presence of lactose if glucose levels are high? Will transcription occur in the presence of lactose if glucose levels are low? Will transcription occur in the absence of lactose if glucose levels are low? 20. In our E. coli examples, the trp operon is on by default, while the lac operon is off by default. Why do you think that is? 21. How are histone modifications used to alter the transcription of a gene? 22. What is the difference between a general transcription factor and a specific transcription factor? 23. Explain why alternative splicing can never change the order of exons in an mRNA transcript. 24. Any given mRNA in a eukaryote can be translated many times. What prevents an mRNA from existing in the cell forever and therefore being translated forever? 25. How can a microRNA stop translation of a specific mRNA, but not all mRNAs in the cell? 26. What are the advantages or disadvantages for a eukaryote to regulate the amount or activity of a protein in a cell via transcriptional control vs. post-translational control? That is, why might a cell want to regulate production of a protein early in the transcription/translation process vs. late in the process? Words to know Gel electrophoresis, PCR, primer, denaturation, annealing, Southern blotting, northern blotting, cloning, restriction enzyme/endonuclease, ligase, recombinant DNA, recombinant protein, transgenic, genetically modified organism (GMO), gene therapy, Purine, pyrimidine, nucleotide, 5’, 3’, Central Dogma, genetic code, degenerate, codon, anticodon, amino acid, reading frame, start codon, stop codon (nonsense codon), RNA polymerase, template strand, nontemplate strand (coding strand), initiation, elongation, termination, promoter, sigma factor, -35 region, -10 region, TATA box, primary RNA transcript, mature mRNA, splicing, intron, exon, 5’ cap, poly-A tail, tRNA, ribosome, aminoacyl tRNA synthetase, Kozak sequence, Shine-Delgarno sequence, the A, P, and E sites in the ribosome, operon, activator, repressor, operator, promoter, positive regulation, negative regulation, epigenetic, histone, chromatin, X- chromosomal inactivation, histone modification, CpG island, general transcription factor, specific transcription factor, enhancer, alternative splicing, untranslated region, 5’ UTR, 3’ UTR, microRNA, kinase