Answer To: Biology 260 Biology 260 Model Building Exercise 02 (Version 05) Stage 02 – Antimicrobials:...
Preeti answered on Mar 05 2022
Biology 260
Biology 260 Model Building Exercise 02 (Version 05)
Stage 02 – Antimicrobials: Susceptibility & Resistance
Building a model to explain a natural phenomenon
Natural Phenomenon: Antimicrobial drug resistance is an enormous global health problem. Many bacteria and viruses were once susceptible to many different antimicrobials, but now they are becoming resistant. How does antimicrobial drug resistance happen??
BACTERIA: ANTIMICROBIAL SUSCEPTIBILITY
Our back story: Now that a pathogenic bacterium has been transmitted to our patient by getting past our microbial control methods, has made it past the patient’s normal microbiota, has found the right environment and nutrients, has harvested energy, and has grown through binary fission, and we’ve gone from one bacterium to a population of millions of bacteria causing tissue damage and disease, our patient is given an antimicrobial.
1. Explain what a biofilm is (p.94), how it forms, and how it can protect a population of bacteria from the environment (which includes antimicrobial drugs, microbial control methods, and the immune system).
Biofilm refers to the immobile communities of microbes that are attached to the surface or found as aggregates in extracellular matrix. It composed of extracellular protein, DNA etc. that helps the bacteria to tolerate harsh conditions and provides resistant against the antibacterial drugs. The common examples where biofilms can be reported are Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus epidermidis etc.
The synthesis of Biofilm requires three different stages:
a. Cell attachment to the substrate or surface
b. Adhesion
c. Growth
Bacteria lives in these biofilms that are built on abiotic surfaces as well as biotic surfaces such as roots. It is difficult to kill those bacteria which lives inside the biofilms.
Glycocalyx is an integral part of the biofilms and it prevents the antibiotics from reaching to their respective targets [1]. It also helps in the protection of immune system. Enzyme-mediated resistance, metabolic reactions that are occurring inside biofilms, etc. increases antibiotic resistance of biofilm [2].
2. What does it mean for a population of bacteria to be susceptible to a drug?
Susceptible to a drug means that the antibiotic is effective against the bacteria, means the bacteria can’t grow in the presence of that drug.
Table 1. List of antibacterial drug classes
i. Beta-lactam drugs (penicillins, cephalosporins, carbapenems, monobactams)
ii. Glycopeptide drugs
iii. Bacitracin
iv. Protein synthesis inhibitors (aminoglycosides, tetracyclines, glycylcyclines, macrolides, chloramphenicol, lincosamides, oxazolidonones, pleuromutilins, streptogramins)
v. Fluoroquinolones
vi. Rifamycins
vii. Metronidazole
viii. Trimethoprims + Sulfonamides
a. For each class of antimicrobial above, describe
i. the cell synthesis process that it inhibits (cell wall synthesis, protein synthesis, nucleic acid synthesis, biosynthesis)
There are mainly three targets that is targeted by antibiotics:
1. Cell wall
2. Nucleic acid and,
3. the machinery that is involved in protein synthesis
The first three classes of drugs i.e., Beta-lactam drugs, Glycopeptide drugs and Bacitracin inhibit the cell wall synthesis of bacteria. The protein inhibiting drugs mainly targets the 70s ribosomes by targeting the formation of 30s initiation complex, elongation of ribosomes. Fluoroquinolones and Rifamycin target nucleic acid synthesis. Metronidazole targets the double helical structure of DNA and breaks the strand ultimately targeting the protein synthesis and hence causing the death of the microbe. Trimethoprims and Sulfonamides targets the folic acid synthesis.
ii. the target of the class of drugs (what protein or molecule does it bind to?),
Beta-lactam drugs (penicillins, cephalosporins, carbapenems, monobactams)
Inhibits peptidoglycan synthesis by inhibiting glycan chains cross-linking
Glycopeptide drugs
Peptidoglycan synthesis, by binding to the chain of NAM which blocks cross-linking
Bacitracin
Peptidoglycan synthesis
Protein synthesis inhibitors (aminoglycosides, tetracyclines, glycylcyclines, macrolides, chloramphenicol, lincosamides, oxazolidonones, pleuromutilins, streptogramins)
Formation of 30s complex, Ribosome elongation,
Fluoroquinolones
DNA
Rifamycins
RNA
Metronidazole
DNA double helix
Trimethoprims + Sulfonamides
Folic acid synthesis
iii. where in the cell you would find that target?
There are mainly three targets that is targeted by antibiotics, cell wall, nucleic acid and the machinery that is involved in the protein synthesis. Hence the target can be the outer layer of the bacteria or can be found in the cytoplasm of the bacteria.
iv. how this class of antimicrobials kill or inhibit bacteria, and
Beta-lactam drugs, Glycopeptide drugs and Bacitracin inhibit the cell wall synthesis of bacteria. The protein inhibiting drugs mainly targets the 70s ribosomes by targeting the formation of 30s initiation complex, elongation of ribosomes. Fluoroquinolones and Rifamycin target nucleic acid synthesis. Metronidazole targets the double helical structure of DNA and breaks the strand ultimately targeting the protein synthesis and hence causing the death of the microbe. Trimethoprims and Sulfonamides targets the folic acid synthesis.
v. how this class of antimicrobials exhibits selective toxicity.
The selective toxicity of the drug can be found by targeting only those targets which are solely found in the bacteria and won’t cause any harm to the animal or human host.
b. Many of these antimicrobials work through competitive or noncompetitive inhibition of the specific enzyme or molecule (a target) that is required for these synthesis pathways. Describe how competitive and non-competitive inhibition work (review from Bio160).
The main difference between the competitive and non-competitive inhibitor is the binding site of the inhibitor. The competitive inhibitor binds to the active site of the enzyme and hence, inhibits its activity while the non-competitive inhibits the enzymatic activity by binding at the site which is not the active site of the enzyme.
c. Draw or copy and paste a Gram-positive and a Gram-negative cell wall and cytoplasmic membrane (See Figure 3.32 and 3.33). Make sure to include all the structures and label each structure.
i. On those pictures:
1. Name, draw, and label the targets of the antimicrobials in Table 2 below
Shirly Berezin et al [3]
2. Draw and explain how these drugs (Table 2) gain access to their targets.
Table 2. List of antimicrobials
ertapenem
azithromycin
co-trimoxazole
Table 2. List of antimicrobials
Target
ertapenem
Cell wall synthesis
azithromycin
Protein synthesis
co-trimoxazole
Folic acid metabolism
Ertapenem binds with the penicillin binding protein of the cell wall and inhibits its synthesis.
Azithromycin inhibits the translation of mRNA (refer to above mentioned figure)
Co-trimoxazole blocks the folic acid enzymes in the synthesis pathway.
ANIMAL VIRUSES: ANTIMICROBIAL SUSCEPTIBILITY
How do animal viruses replicate? How can we use this information to explain how antiviral drugs work? In your answer explain how the following two viruses replicate:
The animal viruses first get attached to the cell membrane of the animal cell and then injects its genetic material (DNA or RNA) inside the cytoplasm of the animal cell. There by using the host cell machinery the genome of virus replicates and make multiple copies of itself. They use host machinery for packaging of the virion. Then, by killing the cell (lytic phase) or budding off the cell membrane (lysogeny), the newly synthesised viruses released outside the cell.
The antiviral drugs can target the attachment of the virus to the cell membrane of the animal cell or they can also target the viral enzymes such as protease, methyltransferase or RNA-dependent RNA polymerase of the virus, which can ultimately stop its replication. For example, methyltransferase enzyme provides stability to the mRNA of positive-stranded RNA viruses by capping its mRNA. Hence, if a drug targets the methyltransferase enzyme, then the viral RNA won’t be stable and the uncapped RNA will be destroyed by host immune system.
Replication cycle of HIV:
HIV enters the hos body and gets fused with T-cells and uses the host machinery. The reverse transcriptase enzyme of the virus helps to produce complementary DNA of the virus using RNA genome of the virus as template. The host machinery will help to produce more viral RNA copies by transcribing the HIV cDNA. The new viral RNA and proteins forms immature HIV and this immature HIV gets released from the cell. The HIV protease protein is used in the polyprotein processing to form a mature HIV virus.
Replication cycle of Influenza virus:
After entering the host body, Influenza virus binds with the host cell using hemagglutinin (HA) protein. After cleavage of HA, the virus is transferred into the host cell using endocytosis. The viral genome and proteins is then released into the cytoplasm of the cell. The influenza virus is a negative-stranded RNA virus hence, first the negative strand is first used as a template to produce a positive-stranded RNA, which is then translated into the viral proteins. It is used as a template to create more copies of viral genome and then the viral genome and proteins is assembled into the virions and released out of the cell.
Table 3. List of viruses
Special...