Prescott’s Microbiology, 9th Edition
Chapter 13 – Bacterial Genome Replication and Expression
GUIDELINES FOR ANSWERING THE MICRO INQUIRY QUESTIONS
Figure 13.1 Based on what we now know about proteins, why can we conclude from this experiment that genetic information was unlikely to be carried by proteins?
Now we know (and they did not back then) that the genetic code is degenerate, thus there are 2-6 nucleotide triplet codons that code for each amino acid. Thus, you cannot go backwards from the amino acid to the codon, because you don’t know what one it is. In Griffith’s experiment above, heat-killing the smooth strain denatures the proteins, but the DNA survives (including the genes that code for the capsule synthesis). This is an example of transformation.
Figure 13.4To which carbon of ribose (deoxyribose) is each of the following bonded: adenine and the hydroxyls of adenosine and deoxyadenosine?
In a nucleotide, the purine (including adenine) or pyrimidine base is always covalently attached to the 1’ (one prime) carbon of the ribose sugar. Adenosine (part of RNA) has two hydroxyl groups attached to the 2’ and 3’ ribose carbons. Deoxyadenosine (part of DNA) has only on hydroxyl group, attached to the 3’ carbon. So, one difference between RNA and DNA is ribose versus deoxyribose, with RNA have a 2’ hydroxyl and DNA having a 2’ hydrogen.
Figure 13.5How many H bonds are there between adenine and thymine, and between guanine and cytosine?
There are 2 hydrogen bonds between adenine and thymine and 3 hydrogen bonds between guanine and cytosine. This is why GC-rich DNA has a slightly higher melting temperature than AT-rich DNA of the same length.
Figure 13.7Identify the two other peptide bonds of the tetrapeptide chain.
Shown in yellow are the two other peptide bonds.
Figure 13.10 What provides the energy to fuel this reaction?
Reaction coupling is used to make this reaction favorable. The reaction shown above is coupled with hydrolysis of the pyrophosphate (PPi) into inorganic phosphate (2 Pi), thus the overall reaction pair is favorable.
Figure 13.12 What is the difference between helicase and gyrase? Which is a topoisomerase?
Helicase is an enzyme that unwinds or separates the DNA double helix during replication whereas DNA gyrase is a topoisomerase that nicks and seals the DNA and relieves supercoiling that can occur by rapid unwinding.
Figure 13.15 Why can’t DNA polymerase perform this reaction?
During the polymerization reaction, an incoming nucleotide triphosphate is added to the 3’ OH of a DNA strand (figure 13.10), and a pyrophosphate is cleaved from it. With a nick, there is no incoming nucleotide triphosphate, nor any phosphate to be removed. The ligase enzyme that performs this reaction has to have another mechanism to make the reaction favorable, and so utilized NAD+ or ATP as an energy source.
Figure 13.20 Why is the nontemplate strand called the “coding strand”?
The coding strand, in blue above, is identical in sequence to the mRNA (except Ts are replaced with Us). The template strand, in purple, is complementary to the coding stand and to the mRNA.
Figure 13.25 Are the -35 and -10 regions considered “upstream” or “downstream” of the +1 nucleotide?
RNA polymerase is considered to move “down the stream.” So, according to the direction of transcription (shown as black arrow), any negatively numbered nucleotides (including the -35 and -10 boxes in the sigma factor-binding region of the promoter) are upstream of the +1 site. The +1 site is the first nucleotide in DNA that is mirrored in the mRNA, so the remainder of the gene is downstream from the +1 start site. Important note: the +1 start site for transcription is NOT the first codon (the start site of translation).
Table 13.4 For each of the above codons, determine what is normally encodes. Choose one of the variants and suggest how it might have evolved.
Looking at Table 13.3, students can determine the common coding for a codon. For example, AGA commonly codes for Arg. It may be evolutionarily-related to the common stop codon, UGA.
Figure 13.33 Why is simultaneous transcription and translation impossible in eukaryotes?
Transcription occurs in the nucleus in eukaryotes, while translation occurs in the cytoplasm. Thus compartmentalization prevents this.
Figure 13.35 What would be the outcome if an aminoacyl-tRNA synthetase added the wrong amino acid to a tRNA (i.e., the anticodon specified a different amino acid than that added to the 3’ end of the tRNA)?
This question points out the fact that the ribosome does not have any proofreading activity. Error control is at the level of the synthetase enzymes, which is why they are very specific in charged tRNAs with certain amino acids. If a tRNA was charged with the incorrect amino acid, the ribosome would simply incorporate it, thus the protein would have a single amino acid mutation (not coded in the gene). This has been done in E. coli.
Figure 13.37 Why would it be impossible for fMet-tRNA to initiate peptide bond formation with another amino acid? (Hint: Examine figure 13.40 closely.)
The front end of a protein is the amino, or N-terminus, while the back end and last part synthesized is the carboxy or C-terminus. FMet is the first amino acid, and can form a peptide bond using its carboxyl end with the second amino acid in the protein. However, another amino acid cannot be added in front of the fMet because the amino group is not free, it is covered with the formyl group. Thus all internal Met residues do not have the formyl group.
Figure 13.40 What provides the energy to fuel this reaction?
No extra energy source is required for peptide bond formation because the bond linking an amino acid to tRNA is high in energy. This high energy was put in during the charging reaction catalyzed by the amino acyl tRNA synthetase enzymes (figure 13.35), in which ATP is hydrolyzed.
Figure 13.45 What are two distinguishing features of protein translocation via the Tat system was compared to that using the Sec system?
The Sec pathway translocates unfolded proteins whereas the Tat pathway translocates folded proteins. Furthermore, the Tat pathway only translocates proteins that feature twin arginine residues in their signal sequence.
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