Chapter 13

Learning Objectives

  1. Describe and explain the way that promoters operate to orientate the beginning of mRNA or hnRNA synthesis.
  2. Identify and describe the function of termination sites in a prokaryote.
  3. Describe the distinguishing features of the genetic code for amino acids.
  4. Describe how frame shift mutations and their suppressor mutations operate.
  5. Diagram the basic "cloverleaf"structure of tRNA's and identify the anticodon and the 3' ends; discuss the function of the basic structure of the tRNA molecule in binding to the ribosome.
  6. Explain how the ribosome, tRNAs and mRNA function to produce a polypeptide; decode a DNA sequence and mRNA sequence into a sequence of amino acids, identifying the initiation codon and termination codon.
  7. Describe the "Christmas tree" configuration of mRNA with the structural gene, and explain how you can tell the initiation and termination ends of the genes, and how you can demonstrate that either strand of DNA can serve as a template strand in different loci.
  8. Describe how hnRNA is processed into eukaryotic mRNA, and orientate the processes from transcription to translation in the cell.
  9. Describe how the existence of introns and exons can be observed by using molecular hybrids and electron microscopy.
  10. Describe the snRNP and explain their function.
  11. What is exon shuffling, and how does it create more than a single polypeptide from a single locus?
  12. Identify a cistron in a prokaryote and in an eukaryote.
  13. What does polycistronic and monocistronic mean?
  14. Describe the colinearity of DNA, RNA, and protein, including the corresponding "building blocks" of bases or amino acids.
  15. Explain how the "half life" of various parts of the "Central Dogma" of molecular genetics are time and space sensitive, illustrating the organizational parameters of What, When, Where and How much.

Note: Many of the topics in this chapter I consider review at their elementary level, since you must have had them in earlier classes. Please let me know where this is not the case. We will consider them in greater detail, and emphasize the aspects that are most important in eukaryotic organisms.

Note: The 6th edition of Griffiths et al. problem 18, p. 422, omits the double stranded DNA molecule central to the question. It should be located across the bottom of the page, but, instead, it is here.

DEFINE or DESCRIBE:

  1. Transcription: DNA-> RNA In E. coli it is possible to see the strands of RNA transcripts under the electron microscope. Relate the image seen under an electron microscope with the drawing in your book in Figure 13-3. Why do you not see any protein strands coming from the mRNA in the electron microscope image?
  2. Translation: RNA-> protein In E. coli and other prokaryotes, the translation is carried out simultaneously with the transcription. However, in eukaryotes the translation is in the cytoplasm.
  3. Replication: synthesis of DNA; be sure to understand functionality of Fig. 11-30 and the series of 5 drawings for Chapter 11.
  4. Promoters: sequences in the DNA that signal the initiation of transcription
  5. RNA polymerase: enzyme that makes mRNA; involved in transcription; binds to the promoters with sigma factor (subunit that allows binding), released at termination sequence; release may involve the protein rho . (Note: this is prokaryotic system, relate to eukaryotic system where possible, even if imaginary!) There is more than one polymerase.
  6. Initiation site of transcription: The first base transcribed, preceeds the first codon by several to many bases. There is a "consensus sequence" of several bases, for example the TATA-box region at a position of -10 bases ("upstream" on the DNA, before transcription begins) in prokaryotes, but about 100 bases upstream in eukaryotes (represented by yeast).
  7. Initiation of translation codon: AUG codes for N-formylmethionine in prokaryotes. The two ribosome parts, the tRNA and the mRNA form a functional complex before initiation of translation can occur.
  8. Termination codons : UAA, UAG, UGA; do not code for an AA
  9. Amino-acyl-tRNA synthetase: enzyme that hooks AA to tRNA, specific for each AA.
  10. Peptidyl transferase: enzyme that forms the peptide bonds of the nascent protein.
  11. Codon: three base sequence on the mRNA that codes for an AA
  12. Anticodon: complimentary base sequence on the tRNA
  13. Degenerate code: individual AA's are coded for by more that one triplet
  14. Suppressor mutation: a mutation that counteracts or suppresses the affect of another mutation. EX: insertion after a deletion to restore reading frame
  15. Frameshift mutation: a mutation that causes a frame shift in the reading of the genetic code; usually a deletion or insertion
  16. Wobble: sloppy base pairing, primarily in the 3rd base of the codon /anticodon; a single tRNA can recognize more than 1 codon, allows some conservation in the number of tRNA molecules required
  17. Missense mutation: a change in the genetic code that produces a single AA substitution in the polypeptide
  18. Nonsense mutation: change of the codon to read stop; premature termination of translation.

QUESTIONS:

  1. One of the most important aspects of both transcription and translation is that a multiplicity of processes control them. List the control steps in both translation and transcription of prokaryotes and give an example of those that are given in the textbook. Note that in eukaryotes most of the control is in translation. The rapidity with which a protein synthesis may be "stopped" is thereby a function of how long the mRNA may last. The "half life" of mRNA's vary with the kind, and species. The shorter the half life, the faster it must be replaced, and thereby the quicker the response to a control change in the nucleus.
  2. Explain how it is an absolute necessity of a living system (as illustrated in transcription and translation) that there exist both epistatis (a better name is now non-allelic gene interaction) and pleiotropy. Hint: Where do the enzymes and other proteins involved in transcription and translation originate?
  3. Draw the structure of deoxyribose and ribose sugars (just to the detail we have done in class). Show where the nucleotide is attached, where the phosphate group is attached, and the polarity of the molecule.
  4. What is different about the locations of transcription and translation in prokaryotes vs. eukaryotes?

    eukaryotes: transcription in the nucleus, translation in the cytoplasm, processing of hnRNA -> mRNA in nucleus

    prokaryotic: no physical separation of transcription and translation.

  5. Describe and draw the process of Transcription in the cell. Please include the following in your discussion: promoter regions (Pribnow or TATA boxes), RNA polymerase, initiation site, nonsense and sense strands, polarity of all the strands (DNA and RNA and polypeptide), mRNA, and the possible structure of the termination site.
  6. Describe and draw the process of Translation in the cell. Please include the following: mRNA; tRNA; ribosomes; amino acids; polypeptide; polarity of the codon, anti-codon and the peptide; direction of ribosomal movement; initiation and termination codons; site of amino acid attachment on the tRNA; the P and A site of the ribosome and polarity of addition to AA chain.
  7. What are five properties of the genetic code?
    1. code is non over-lapping
    2.  
    3. three bases code for an AA, these are termed codons
    4.  
    5. code is read from a fixed starting point, continues to the termination sequence
    6. code is degenerate- some AA's are specified by more than 1 codon
    7. some codons do not code for an AA, but are stop codons
  8. Diagram the processing of the primary transcript of eukaryotes (hnRNA) into mRNA, and give an example of alternative splicing pathways to produce more than one polypeptide from a single gene (locus). There is a growing list of examples.
  9. Explain how the snRNA's might participate in the alternative splicing. Comment on their possible origin from other loci that are simultaneously active in transcription and hnRNA processing. Note questions in the figure linked to snRNA's. What are the snRNP's ("snurps") and how do they relate to snRNA's?
  10. How does the cistron relate to the process of transcription and it's control?
  11. Thought question: In the context of alternative splicing in eukaryotes, what are the possible effects on the cis-trans test of Benzer? How is the concept of a cistron affected?

Questions from the end of the chapter : Chapter Integration Problem, Solved problems -- 1, 2; Exercises -- 4, 11, 12, 14, 16, & 18 (This chapter in a previous edition had some mistakes in the answer book. Anytime your answer doesn't agree with the solution's manual, please check with your TA or Instructor. This gives us a better chance to catch errors otherwise we might miss.)

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Last updated 09/01/97