Network Firewall Visualization File Options Help Network Traffic: DNS Database traffic Email VOIP Web traffic Chat Traffic Workstation traffic Active Attacks: OS Exploits Virus Trojan Syn Scan Ack Scan Web Attacks Trojan Reply System Scanned Successful Attack 192.168.1.* 192.168.2.* Speed: Congestion: Firewall Log: -FW1: Cloud to Chat:5222 TCP -FW1: Cloud to Chat:31337 TCP -FW1: Cloud to VOIP:38287 TCP -FW1: Cloud to DNS:53 UDP -FW1: Cloud to DNS:53 UDP -FW1: Work1 to Cloud:80 TCP -FW1: DNS to Cloud:53 UDP -FW1: VOIP to Cloud:38287 TCP -FW1: DNS to Cloud:53 UDP -FW1: Cloud to Database:3306 TCP -FW1: Cloud to Chat:31337 TCP -FW1: Cloud to DNS:53 UDP -FW1: DNS to Cloud:53 UDP -FW1: Cloud to VOIP:38287 TCP -FW1: Cloud to Web:31337 TCP -FW1: DNS to Cloud:53 UDP -FW1: DNS to Cloud:53 UDP -FW1: DNS to Cloud:53 UDP -FW1: Mail to Cloud:25 TCP Malicious Traffic Allowed 0 Legitimate Traffic Denied: 94
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Class 6: Viruses (and Cells, continued) Making connections: viruses and microbes Match the cell biology concept with an important application of that concept. Then answer the follow-up questions. Cell Biology concepts 1. Bacteria that cannot construct new cell wall material become fragile and break down. 2. During influenza infection, the viral enzyme neuraminidase is required to release new viruses from the host cell in which they were made. Once released, the new viruses can infect many additional cells. 3. Thermus aquaticus is a bacterium found in hot springs and can live at temperatures up to ~80°C (175°F). It has adapted so that its enzymes are most functional at the elevated temperatures, compared with many organisms’ enzymes that function best at ~37°C (98°F). 4. Until the isolation and investigation of retroviruses, scientists thought that RNA could be copied from DNA, but DNA could not be copied from RNA. Research on this class of viruses led to an update to this “Central Dogma” of biology. 5. Some bacteria have adapted, so that the enzymes involved in making cell wall materials have a slightly different shape and can no longer be bound by certain drugs. 6. Rhizobia are bacteria that colonize the roots of certain plants (legumes, including beans and peas). The host plant benefits from the prokaryotes’ ability to “fix” nitrogen, converting N2 from the atmosphere into a form that is usable by the plant. 7. Many species of bacteria contain the enzyme cellulase. More than 10 billion such bacteria and other symbiotic microbes may be found in a single milliliter of material from inside the digestive system of ruminant mammals. 8. Fungi, including those that cause athlete’s foot, use ergosterol to maintain healthy membranes. Animal cells do not make ergosterol, they use a similar lipid – cholesterol. 9. During retrovirus infection, a DNA copy is made of the virus’s RNA genome. A cut is made in the host cell’s DNA and the DNA copy of the viral genome is pasted into the host chromosome by a viral enzyme called integrase. 10. Prokaryotic cells contain smaller ribosomes (“70S” ribosomes) than eukaryotic cells (“80S” ribosomes). Both types of ribosomes synthesize proteins, but the macromolecules they use to do it are somewhat different. Applications _______ Oseltamivir, also called Tamiflu, binds and inhibits the viral protein neuraminidase. _______ Clotrimazole is a drug that is used to treat certain infections. It interferes with synthesis of ergosterol, a lipid involved in phospholipid membranes. _______ Penicillin is a drug that interferes with synthesis of peptidoglycans (these are biological molecules that are part protein and part carbohydrate) that are present in certain cell walls. _______ HIV is often treated with several drugs that inhibit different parts of the viral replicative cycle. Raltegravir is an example of a drug that interferes with the integration of viral genes into the host cell’s chromosome. _______ Cows, like other vertebrates, lack the ability to break down cellulose. Yet they are able to live on a diet of grass and other vegetation high in cellulose. _______ Enzymes isolated from extremophiles have been very useful in laboratory research. For example, Taq polymerase facilitates PCR, a revolutionary technique for production of DNAs of particular sequences, which requires cycling reactions through high temperatures. _______ Plants and animals require nitrogen to make biological macromolecules, however they’re unable to convert atmospheric nitrogen (N2) into a biologically useful form. _______ Azithromycin is a drug that binds to 70S ribosomes and blocks synthesis of any new proteins. _______ Methicillin-Resistant Staphylococcus aureus (MRSA) can cause life-threatening infections of the skin and bloodstream. One of the reasons MRSA infections are so serious is that they are resistant to treatment by many antibiotics, including methicillin and penicillin. _______ The enzyme reverse transcriptase, isolated from retroviruses, is an important tool in molecular biology research. Scientists interested in learning what genes are turned on in particular cells use it to make DNA copies of RNAs they are studying (The DNA copies are useful because they are more stable). Follow-up questions: • What types of infections can be treated with the following drugs? o Penicillin o Clotrimazole o Azithromycin o Tamiflu o Raltegravir • Why are these drugs (above) safe for you to take? That is, why don’t they kill your cells? • Cancer cells are your own human cells that have become deregulated so that they divide and pile up in an uncontrolled way. Many chemotherapy drugs treat cancer by interfering with cell division and other cell processes. o Why are there so many more side effects for individuals undergoing chemotherapy than for individuals taking antibiotics?
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Use of Modern Molecular Techniques to Determine the Synthetic Pathway of a Novel Amino Acid Most of the biosynthetic pathways described in this chapter were determined before the development of recombinant DNA technology and genomics, so the techniques were quite different from those that researchers would use today. Here we explore an example of the use of modern molecular techniques to investigate the pathway of synthesis of a novel amino acid, $(2 S)-4$ -amino- 2 -hydroxybutyrate (AHBA). The techniques mentioned here are described in various places in the book; this problem is designed to show how they can be integrated in a comprehensive study. AHBA is a $y$ -amino acid that is a component of some aminoglycoside antibiotics, including the antibiotic butirosin. Antibiotics modified by the addition of an AHBA residue are often more resistant to inactivation by bacterial antibiotic-resistance enzymes. As a result, understanding how AHBA is synthesized and added to antibiotics is useful in the design of pharmaceuticals. In an article published in $2005,$ Li and coworkers describe how they determined the synthetic pathway of AHBA from glutamate. (EQUATION CANNOT COPY) (a) Briefly describe the chemical transformations needed to convert glutamate to AHBA. At this point, don't be concerned about the order of the reactions. Li and colleagues began by cloning the butirosin biosynthetic gene cluster from the bacterium Bacillus circulans, which makes large quantities of butirosin. They identificd five genes that are essential for the pathway: $b t r I, b t r J, b t r K, b t r O,$ and $b t r V$. They cloned these genes into $E .$ coli plasmids that allow overexpression of the genes, producing proteins with "histidine tags" fused to their amino termini to facilitate purification (see p. 332). The predicted amino acid sequence of the BtrI protein showed strong homology to known acyl carrier proteins (see Fig. $21-5$ ). Using mass spectrometry, Li and colleagues found a molecular mass of 11,812 for the purificd BtrI protein (including the His tag). When the purificd BtrI was incubated with coenzyme A and an enzyme known to attach CoA to other acyl carrier proteins, the majority molecular species had an $M_{\mathrm{r}}$ of $12,153 .$ (b) How would you use these data to argue that BtrI can function as an acyl carrier protein with a CoA prosthetic group? Using standard terminology, Li and coauthors called the form of the protein lacking CoA apo-BtrI and the form with CoA (linked as in Fig. $21-5$ ) holo-BtrI. When holo-BtrI was incubated with glutamine, ATP, and purificd BtrJ protein, the holo-BtrI species of $M_{\mathrm{r}}$ 12,153 was replaced with a species of $M_{\mathrm{r}} 12,281,$ corresponding to the thioester of glutamate and holo-Btri. Based on these data, the authors proposed the following structure for the $M_{\mathrm{r}} 12,281$ species, $\gamma$ -glutamyl-S-BtrI: (FIGURE CANNOT COPY) (c) What other structure(s) is (are) consistent with the data above? (d) Li and coauthors argued that the structure shown here ( $\gamma$ -glutamyl-S-BtrI) is likely to be correct because the $\alpha$ -carboxyl group must be removed at some point in the synthetic process. Explain the chemical basis of this argument. (Hint: See Fig. $18-6,$ reaction C.) The BtrK protein showed significant homology to PLP-dependent amino acid decarboxylases, and BtrK isolated from $E$. coli was found to contain tightly bound PLP. When $\gamma$ -glutamyl-S-BtrI was incubated with purificd BtrK, a molecular species of $M_{\mathrm{r}}$ 12,240 was produced. (c) What is the most likely structure of this species? (f) When the investigators incubated glutamate and ATP with purified BtrI, BtrJ, and BtrK, they found a molecular species of $M_{\mathrm{r}} 12,370 .$ What is the most likely structure of this species? Hint: Remember that BtrJ can use ATP to $\gamma$ -glutamylate nucleophilic groups. Li and colleagues found that BtrO is homologous to monooxygenase enzymes (see Box 21-1) that hydroxylate alkanes, using FMN as a cofactor, and BtrV is homologous to an NAD(P)H oxidoreductase. Two other genes in the cluster, btr $G$ and $b t r H,$ probably encode enzymes that remove the $\gamma$ -glutamyl group and attach AHBA to the target antibiotic molecule. (g) Based on these data, propose a plausible pathway for the synthesis of AHBA and its addition to the target antibiotic. Include the enzymes that catalyze each step and any other substrates or cofactors needed (ATP, NAD, ctc.).
SYNTHETIC STRATEGIES Part of the skill in planning a synthesis is deciding in what order to carry out the reactions. Let us suppose, for example, that we want to synthcsize $\theta$ bromonitrobenzenc. We can see very quickly that we should introduce the bromine into the ring first because it is an ortho-para director: (FIGURE CANNOT COPY) O-Bromonitro- benzene $p$ -Bromonitrobenzene The ortho and para products can be scparated by various methods because they have different physical propertics. However, had we introduced the nitro group first, we would have obtained $m$ -bromonitrobenzene as the major product. Other examples in which choosing the proper order for the reactions is important are the syntheses of the ortho-, meta-, and para-nitrobenzoic acids. Because the methyl group of toluene is an electron-donating group (shown in red below), we can synthesize the ortbo- and para-nitrobenzoic acids from toluene by nitrating it, separating the ortbo-and para-nitrotoluenes, and then oxidizing the methyl groups to carboxyl groups: (FIGURE CANNOT COPY) We can synthesize $m$ nitrobenzoic acid by reversing the order of the reactions. We oxidize the methyl group to a carboxylic acid, then use the carboxyl as an electron-withdrawing group (shown in blue) to direct nitration to the meta position. (FIGURE CANNOT COPY) B Use of Protecting and Blocking Groups Very powerful activating groups such as amino groups and hydroxyl groups cause the benzene ring to be so reactive that undesirable reactions may take place. Some reagents used for electrophilic substitution reactions, such as nitric acid, are also strong oxidizing agents. Both clectrophiles and oxidizing agents seek electrons. Thus, amino groups and hydroxyl groups not only activate the ring toward electrophilic substitution but also activate it toward oxidation. Nitration of aniline, for example, results in considerable destruction of the benzene ring because it is oxidized by the nitric acid. Direct nitration of aniline, consequently, is not a satisfactory method for the preparation of $o$ -and $p$ nitroaniline. Treating aniline with acetyl chloride, $\mathrm{CH}_{3} \mathrm{COCl},$ or acetic anhydride, $\left(\mathrm{CH}_{3} \mathrm{CO}\right)_{2} \mathrm{O},$ converts the amino group of aniline to an amide (specifically an acctamido group, $-\mathrm{NHCOCH}_{3}$ ), forming acctanilide. An amide group is only moderately activating, and it docs not make the ring highly susceptible to oxidation during nitration. Thus, with the amino group of aniline blocked in acetanilide, direct nitration becomes possible: (FIGURE CANNOT COPY) Aniline Acetanilide $p-$ Nitroacetanilide $(90 \%)$ o-Nitro- acetanilide (trace). (FIGURE CANNOT COPY) Nitration of acetanilide gives $p$ -nitroacctanilide in excellent yield with only a trace of the ortho isomer. Acidic hydrolysis of $p$ -nitroacetanilide (Section $17.8 \mathrm{F}$ ) removes the acetyl group and gives $p$ -nitroaniline, also in good yield. Suppose, however, that we need $o$ -nitroaniline. The synthesis that we just outlined would obviously not be a satisfactory method, for only a trace of $o$ -nitroacetanilide is obtained in the nitration reaction. (The acetamido group is purely a para director in many reactions. Bromination of acetanilide, for example, gives $p$ -bromoacetanilide almost exclusively.) We can synthesize $o$ -nitroaniline, however, through the reactions below. (FIGURE CANNOT COPY) Acetanilide o-Nitroaniline $(56 \%)$ Here we see how a sulfonic acid group can be used as a blocking group. We can remove the sulfonic acid group by desulfonation at a later stage. In this example, the reagent used for desulfonation (dilute $\mathrm{H}_{2} \mathrm{SO}_{4}$ ) also conveniently removes the acetyl group that we employed to "protect" the benzene ring from oxidation by nitric acid.
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