Exam 3 Study Guide Flashcards
List tools used in genetic engineering and recombinant DNA technology
• in silico analysis (bioinformatics), DNA microarray analysis, gel electrophoresis, PCR, blotting, autoradiography, cloning vectors, and RFLP analysis
PCR
(Polymerase Chain Reaction) Rapid amplification of a specific DNA fragment from a complex mixture of DNA and other cellular components
RT
reverse transcriptase; synthesizes double-stranded DNA from an RNA template; used to make cDNA
cDNA
complementary DNA, used when provided an RNA molecule and need the DNA, it is complimentary and not the same because there are posttranscriptional and translation modifications (like the removal of introns)
Gel Electrophoresis
used to separate molecules based on their charge and size; DNA is acidic and wants to go from the negative end of the gel to the positive; the smaller the DNA fragments, the more likely it is able to move
vectors
a DNA molecule that can replicate independently of the host chromosome and maintain a piece of inserted foreign DNA, like a gene, into a recipient cell; they can be a plasmid, phage, cosmid, or artificial chromosome; each vectors has an ORI, selectable marker, and unique restriction sites
restriction enzymes
cut DNA at specific sites, to allow for vectors to insert DNA
blotting
there are three different techniques. Southern, western, and northern. Gel is fragile and can break up, therefore you should transfer the fragments onto paper. This is used to locate specific fragments, southern is used for DNA
What is meant by recombinant DNA?
cloning vectors are used to provide many copies of cloned DNA (via replication in a host organism)
Name the tools used to make a recombinant plasmid, genomic library, or run genomic fingerprinting (RFLP)
• Tools used in recombinant DNA: cloning vector, restriction enzymes, DNA ligase;
- tools in genomic library: vectors and fragments;
- tools in RFLP: restriction enzymes, agarose gel, in silico
What is the purpose (goal) of constructing a genomic library for an organism?
- widely used in DNAsequencing techniques and they have been used in the whole genome sequencing of humans and several model organisms
- used when gene of interest is on a chromosome that has not been sequenced
Define metagenomic and its role in identifying microbes that cannot be cultured (isolated) from the environmental samples such as soil and water samples
- Metagenomic: The study of genomes recovered from environmental samples (including the human body) without first isolating members of the microbial community and growing them in cultures.
- This is an important science because not all bacteria can be cultured in a lab environment
What is meant by autonomous replication? List examples
- Can replicate on their own, have their own ORI
* Examples: plasmids, rolling circle replication
plasmid
replicates independently of microbial chromosome so many copies may be maintained in a single cell (important ones: pBR322 and pUC19)
bacteriphage
packaged into lambda phage particle, single-stranded DNA viruses and can generate either double or single stranded DNA in its host
cosmids
can be packaged into lambda phage particles for efficient introduction into bacteria, then replicates as a plasmid
PAC
(p1 artificial chromosomes) based on bacteriophage P1 packaging mechanism
YAC
(yeast articiial chromosome) Engineered DNA that contains all the elements required to propagate a chromosome in yeast and is used to clone foreign DNA fragments in yeast cells.
BAC
(bacterial artificial chromosome) A cloning vector constructed from the Escherichia coli F-factor plasmid.
what is the significance of the Ti plasmid?
o Used as a cloning vector, all nonessential regions, including tumor-inducing genes have been deleted, it is used as a selectable marker where other site can be added
List the types of genes are carried on plasmids.
bacterial chromosomes
plasmids
transposons
conjugation
The form of gene transfer and recombination in bacteria and archaea that requires direct cell-to-cell contact
transformation
A mode of gene transfer in bacteria and archaea in which a piece of free DNA is taken up by a cell and integrated into its genome.
transduction
The transfer of any part of a bacterial or archaeal genome when the DNA fragment is packaged within a virus’s capsid by mistake
protoplast fusion
Combine two cells by removing cell wall and letting cell membranes of the two cells merge
electroporation
used when the host microbe does not have the capacity to be transformed naturally; The application of an electric field to create temporary pores in the plasma membrane to render a cell temporarily transformation competent; makes them more porous
transformation (lab)
plasmids picked up by laboratory-induced competent bacterial cells
Compare in vivo and in vitro transformation (done in lab vs. done in nature)
• transformation more common in vivo (in lab) than in nature (in vitro)
What is the role of Transposons in genetic exchange?
- Transposons are jumping genes; they can be used in transmitting drug resistance; these genes can jump from one part of the chromosome to another while also taking genes from other organisms with it
- A mobile genetic element that encodes recombinase, which is needed for transposition, and contains other genes that are not required for transposition.
insertion sequences
A transposable element that contains genes only for those enzymes, such as transposase, that are required for transposition.
transposable elements
A small DNA molecule that carries the genes for transposition and thus can move around the genome.
transposition
The movement of a piece of DNA around the chromosome
List some of the Human peptide and proteins synthesized by genetic engineering
• insulin, blood clotting factors, calcitonin, epidermal growth factor, interleukins, growth hormone, relaxin, and tumor necrosis factor
What does metabolic engineering mean?
• Genetic manipulation of enzymes, changing industrially important product; cut off one pathway to make another
How industrial microbiology defines fermentation? Compare Chemostat vs batch for large scale industrial growth
- Mass culture of microorganisms; regular fermentation is the metabolism of sugars
- A chemostat can continuously make new products and a batch culture can only make products at once; a chemostat is more beneficial in industrial microbiology
How does reverse vaccinology work?
- Search for appropriate molecules that could be used as a vaccine; looking for genes whose products can be used as a vaccine. Proteins are antigenic compounds, which means your body responds to them more than any other molecule
- Subunit vaccine: piece of a virus made in a lab, like a protein or polypeptide, the body thinks you have been infected by that virus and produces antibodies
- Have to pick which protein would have the best response against a virus
Name few categories of products made by microbes in industrial scale (industrial microbiology)
• Industrial products, agricultural products, food additives, medical products, primary and secondary metabolites, plant horomones, GMOs, and biofuels
bioconversion
microbial transformations or biotransformations, minor changes in molecules carried out by nongrowing microbes, microbes act directly or indirectly as biocatalysts, can be carried out by free enzymes or cells or by immobilized enzymes or cells – advantages • produce appropriate stereoisomer • very specific • done using mild conditions
biosensors
living microbes, enzymes, or organelles are linked to electrode to detect specific substance, detection is done by converting biological reaction products into electrical currents
biopolymers
used to modify flow characteristics of liquids and to serve as gelling agents; dextran
bio-surfactants
used for emulsification, solubilization, important in bioremediation, oil spill dispersion, and enhancing oil recovery
biocatalyst
enzymes used in the industrial production of chemicals and pharmaceuticals
bio-pesticides
biological agent, microbes or their components, to kill susceptible insects
GMO
genetically modified organism
biofuel
ethanol is produced by microbial fermentation of crop residues that consist of cellulose and hemicellulose
How bacteria may be used as bio-pesticides? Give an example.
- Bacteria can be genetically modified so that the plant has this bacteria within its cells; when an insect eats the plant it dies
- These added cells makes the plant resistant to pests
- One example of this is Bacillus thuringiensis (Bt)
Define genomics and list the three area of genomics
• Genomics: study of molecular organization of genomes< their information content and gene products they encode
structural genomics: physical nature of genomes
functional genomics: how genomes function
comparative genomics: compares genomes of different organisms
What does whole genome shotgun sequencing mean?
• Genome sequencing in which random fragments of a complete genome are individually sequenced. The nucelotide sequences of the fragments are placed in the proper order based on overlapping identical sequences. Looking at a lot of DNA at once; automated sequencing
Define bioinformatics. What branch of science is involved in bioinformatics?
- Define: The interdisciplinary field that manages and analyzes large biological data sets, including genome and protein sequences. In silico
- All branches of science, it is a tool that should be used by all scientists. Specifically, the fields of biology, mathematics, computer science, and statistics
What is meant by in silico analysis and annotation?
• In silico means analyzed by a computer, bioinformatics utilizes this
o The study of biology through the examination of nucleic acid and amino acid sequence
• Annotation: if you know the open reading frame, you can predict the three dimensional shape of the protein and can tell what the function is
o The process of determining the location and potential function of specific genes and genetic elements in a genome sequence.
What is the scope of functional genomics?
- Genomic analysis concerned with determining the way a genome functions
- For example, if you know the motif of a protein, then you know the function of that protein
- If one protein in an organism has a specific motif, then another organism with that same motif will also have a protein with that same function
- This can help determine the protein, RNA, and DNA
- Can help determine: metabolic pathways, transport systems, and potential regulatory and signal transduction mechanisms
Describe DNA microarray system. What is its purpose? Where does the sample come from for this analysis
- Looks for the expression of RNA at each point; looking for RNA, reverse transcription to DNA, then you can perform PCR
- Solid supports that have DNA attached in organized arrays and are used to evaluate gene expression
What is proteomics?
- Grow cells in a tube, extract protein content, run in two dimensional electrophoresis, can come up with both beta and alpha sheets
- Both structural and functional proteomics
Describe how two-dimensional gel electrophoresis works. What is it used for?
- Very similar to regular gel electrophoresis
- 2D is only for proteins
- First take a tube of gel, different regions of the tube have different pH values
- Then you run the proteins through it; at an isoelectric point, this is where the protein will stop moving (stops at pH 6, that is where the isoelectric point is)
- Then you put the gel into another gel and run again in the vertical direction
- It runs again, and is very similar to 1D electrophoresis; the smaller the molecule the more it will move down the gel
- This process is used to compare proteins and DNA and where they overlap
Define the human microbiome and explain the role metagenomics plays in its investigation.
- Human microbiome: The sum of all the microorganisms that live on and in the human body.
- Metagenomics are used to determine what an unknown microbe is
- In this process, you collect a large sample with different microbes, then extract DNA, using a cloning vector with restriction enzymes, each vector has one fragment and one plasmid. Then sequence the fragment to find the function
bioprospecting
looking for different products that can be developed from using different microbes; predicting how a microbe will interact in an environment and how it can help in real life; such as oil eating bacteria
high-throughout screening
A system that combines liquid handling devices, robotics, computers, data processing, and a sensitive detection system to screen thousands of compounds for a single capability; shotgun sequencing
Explain the role of RNA in origin of life.
- Life began with a prebiotic soup with lipid molecules and RNA; RNA caused enzymatic reactions, eventually leading to life as we know it
- The first organism on the phylogenetic tree is based on SSU of RNA and is compared with all other organisms
- has the ability to replicate and act as a catalyst for chemical reasons
- it could have been the nucleic acid used in Earth’s earliest life forms
- it could have eventually given rise to DNA
what are the methanogens?
Strictly anaerobic archaea that derive energy by converting CO2, H2, formate, acetate, and other compounds to either methane or methane and CO2.
what is the environmental impact of the methanogens?
Methanogenic archaea are estimated to produce about 1 billion tons of methane annually. In freshwater ecosystems, rates of methane production can be so great that bubbles of methane sometimes rise to the surface of lakes and ponds. Rumen methanogens are so active that a cow can belch 200 to 400 liters of methane a day. Methanogenesis is also an environmental problem. Methane absorbs infrared radiation and is a more potent greenhouse gas than CO2. Atmospheric methane concentrations have been rising over the last 200 years.
what is the ecological impact of the methanogens?
Methanogenic archaea are potentially of great practical importance, as discussed in the chapter opening story. Anaerobic digesters use fermentative bacteria to degrade particulate wastes Page 478such as sewage sludge to H2, CO2, and acetate (see figure 43.7). CO2-reducing methanogens then form CH4 from CO2 and H2, while acetoclastic methanogens cleave acetate to CO2 and CH4.
How terms such as sub-microscopic, obligate intracellular parasite, and host specificity characterize viruses.
- Viruses are infectious agents
- Sub-microscopic: cannot see with a light microscope, needs an electron microscope
- Obligate intracellular parasite: always need a host, goes into a host, uses host genetics, metabolism, and components to multiply
- Host specific: an animal virus will effect an animal, with very few crossovers
- Size: measured in nanometers
Name different components of a virus. Name the two components that every virus must have
- Nucleic acid, capsid, envelope, spike
* All viruses must have some form of a nucleic acid and a capsid
List steps in virus replication. What is the importance of un-coating step in viral infection?
- Attachment/adsorption
- Nucleic acid gets in through the capsid
- Virus becomes circular (rolling circle replication)
- Protein synthesis in the cytoplasm
- Membranes from Golgi apparatus
- The organism stops making their own components and starts to only make the components for the virus
- Uncoating is important because if the virus enters into a cell with a capsid on, the capsid needs to be degraded before it can start to replicate the nucleic acid
List the damages inflicted on host cells by viruses
- Cell lysis/transformation
- Alter host structure; Nuclear and or Cytoplasmic
- Take control of genetic and metabolism by;
- Altering host gene expression
- Inhibiting host RNA/protein synthesis
- Transcribing viral RNA
- Encouraging host cell apoptosis (programmed cell death
Define CPE and give examples.
- Cytoplasmic effects, visual damages on the host
- Plaque formation, cell fusion, inclusion bodies, attachment and detachment, nuclear enlargement or becomes smaller, and changes in the membrane (from budding)
What are icosahedra and helical structures?
- Icosahedra and helical structures are capsids
- Helical = spiral around the nucleic acid, made of the same protein, so only one gene to produce one protein
- Icosahedra are unique to viruses
How do viruses enter into the body?
viruses enter through endocytosis
o The envelope fuses with the cell membrane of the host
o The capsid with the nucleic acid goes in and uncoating may or may not occur
o Viruses releases the nucleic acid
o Receptor mediated endocytosis may occur
how do viruses exit the body?
virion release
o Nucleic acid is packaged as it exits (enveloped)
o Sometimes the cell will lyse other times it will not so it can continue to make more viruses
lytic
normal viral cycle; kills the host and releases more viruses
latent
apart of the viral life cycle; during which no virions are released, followed by a rise period where virions are released. Early in the latent period is an eclipse period, in which no virus particles are present in infected cells.
transforming
virus alters DNA of host, causes mutation and can cause cancer
chronic
viruses are reproduced slowly and are released by the cell slowly, some hosts die, can become long term
What is the significance of transforming infections?
because it alters the DNA of the host, it can cause cancer
list viruses that cause cancer
Herpes, Epstein-Barr, Hepatitis B and C, HPV, Human T-cell lymphotropic virus (HTLV)
oncogenic viruses
oncogenes are used as regulatory genes that control cell division; oncogenic viruses can cause cancer by manipulating these genes to cause growth or they can come from the virus itself;
Define One-Step growth cycle? What is the meaning of eclipse period?
- Only performed by viruses
- When a virus attaches to a host, it is undeteable at first, which is the eclipse period
- The viruses are in the form of nucleic acid in the host
- You can only see the virus once is has assembled
- The eclipse period is the time before maturation
- Steps of one-step growth: attachment, penetration, (uncoating), synthesis, assembly – (maturation or assembly), and exit
What is meant by temperate phage? What is their role in pathogenic microbe?
- Temperate phage: phages able to establish lysogeny
- Eventually will become prophage, which is when it is integrated in the host viral DNA
- In pathogenic bacteria, it can lead to increased virulent factors, and when a phage wants to leave the host, they will take some of the DNA from the old host and bring it into a new host through transduction
- An example of this is endotoxin production, like sore throat in diphtheria
compare and contrast the lytic an lysogenic cycle
- Lytic: normal viral cycle; kills the host and releases more viruses
- Lysogenic: virus enters the cell, doesn’t kill the host, and stays for a long time; the nucleic acid becomes apart of the host and can stay indefinitely
- One advantage of having a lysogenic stage is being able to stay long and produce even more viruses with the host machinery
Describe the role of viruses in horizontal gene transfer (HGT)
- Viruses contribute to transduction through lysogeny
- Either generalized (take any piece of DNA from a host and bring to another) or specialized (virus takes a specific DNA piece from an old host and brings it to a specific sequence on a new host)
How does viral multiplication differs from growing bacteria.
• Bacteria participate in binary fission, while viruses participate in one-step growth cycle
What is the role of monolayer in virus multiplication? List other culturing methods used to propagate viruses in laboratory
- The monolayer is important because you add a virus into the flask, the virus lyse the bacteria and you can centrifuge to have a clear solution of just your virus – called passing the virus
- Embryonic eggs, plaque assay, grown in a plant,
Explain how one quantifies viruses in laboratory?
• Counts the clear zones around bacteria, the plaque forming units (PFU); indirect ways to count them
plaque assay
A method used to determine the number of infectious virions; bacterial lawn, the number of clear zones in the sample is how many viral colonies there are
Hem-agglutination assay
A testing procedure based on a hemagglutination reaction; any animal virus particles bind to the surface of red blood cells. If the ratio of virions to cells is large enough, virions will join the red blood cells together; that is, they agglutinate, forming a network that keeps the red blood cells in suspension.
virion
A complete virus particle; at the simplest, it consists of a protein capsid surrounding a single nucleic acid molecule.
viriod
An infectious agent that is a single-stranded RNA not associated with any protein; the RNA does not code for any proteins and is not translated.
prions
An infectious agent consisting only of protein
satellites
subviral infectious agents composed of DNA or RNA encapsulated with the aid of an unrelated helper virus.
phages
Viruses that lyse their host cells at the end of the viral life cycle.
Define the term provirus/prophage. What is the role of reverse transcriptase in formation of some proviruses?
- Provirus and prophage are the stages of viruses and bacteria that once the infection has reached the nucleic acid and the viral or bacterial genome is in the host machinery
- Reverse transcriptase is RNA dependent DNA polymerase that recognizes RNA as a template and converts ssRNA to dsDNA so that it can integrated into the host cell
virulent phage
a bacteriophage that has to begin multiplying immediately upon entering its bacterial host, followed by release from the host by lysis.
temperate phage
bacteriophages that have two options: upon entry into the host, they can multiply like virulent phages and lyse the host cell, or they can remain within the host without destroying it
lysogenic conversion
A change in the phenotype of a bacterium due to the presence of a prophage
What is the genetic material for viruses, DNA or RNA, single stranded or double stranded?
- The genetic material for viruses ranges greatly, they can be both ds or ss DNA and ds or ss RNA
- This is one of the reasons that viruses are not considered to be living organisms because their form of nucleic acid varies and is not always dsDNA, which is a principle in the definition of life
List factors contributing to viral pathogenicity
• Enter into the host (penetration), growing within the cell, overcoming host cell defense mechanisms, and damaging the host cells
how many viral particles are there on earth?
10^31 virus particles on earth approximately 10 times the number of prokaryotes
what is the range for viral sizes?
20 nm to 450 nm in diameter
what do the molecules on the viral surface do?
Molecules on virus surface impart high specific for attachment to host cell
what do viruses lack?
- Lack enzymes for most metabolic processes
* Lack machinery for synthesizing proteins
give some examples of viral syndromes
- Oral and respiratory tract infections
- Flu-like and systemic symptoms
- Exanthems and skin rashes
- Infections of the eye
- Hemorrhagic fevers
- Gastroenteritis
- Hepatitis
- Infections of the central nervous system
- Sexually transmitted viral diseases
- Congenital, neonatal and perinatal viruses
List three basic principles of antimicrobial therapy
- Selective toxicity - to exploit differences in structure and metabolism of pathogens and host cells (to kill organisms not man)
- Reach the site of infection at inhibitory concentrations
- Penetrate and bind to target, avoiding inactivation and extrusion
Explain the history/origin of antibiotics? Why some microorganisms in nature produce antibiotics?
- They were first discovered by Alexander Flemming
* Some organisms like fungi use it to prevent bacterial growth, and some bacteria use it to kill the competition
chemotherapeutic agents
chemicals that treat all diseases
List four categories of antimicrobial drugs based on their mechanisms of action.
Four categories: peptidoglycan synthesis, translation, metabolic activity, and replication/transcription
metabolic antagonist
stop metabolic function; will prevent certain pathways from forming or will slow them down
Compare the action of Sulfa drugs and Trimethoprim
• Sulfa drugs and trimethoprim both stop the production of folic acid, except they both target at different areas in the pathway
Give an example and describe the mechanism of antibiotics affecting DNA replication and RNA transcription (one for each)
- Used to block DNA replication and transcription
- DNA replication: Ciprofloxacin, stops DNA gyrase from opening up DNA or supercoiling, used with anthrax
- Transcription: Rifampicin, inhibits RNA transcriptase, used against TB
What is Beta-Lactam ring? Which group of antibiotics contain beta lactam ring?
Beta-lactam ring is essential for bioactivity in penicillin
What do penicillin, cephalosporin, cyloserine, bacitracin, and vancomycin have in common
Inhibitors of bacterial cell wall formation
What is the role of beta-lactamase in bacteria resistance to antibiotics?
o There has now become MRSA that are able to fight off the antibiotic; an enzyme that inactivates antibiotics by hydrolyzing a bond in the beta-lactam ring
Why protein synthesis (translation) is an excellent target against some infectious diseases, but not others?
many antibiotics work by binding to the small (30S) or alrge (50S) subunits of the prokaryotic ribosomes, preventing them from assembling or carrying out their proper functions
size and composition of prok/euk ribosomes differ, so antibiotics can effectively prevent protein synthesis in prok ribosomes while leaving the euk host’s ribosomes unaffected
therapeutic dose
drug level required for clinical treatment
therapeutic index
ratio of toxic dose to therapeutic dose; the higher this number is, the safer the drug is to take because it is less toxic
spectrum of activity
narrow spectrum will kill a specific type of bacteria while a broad spectrum kills a whole wide range of bacteria; better to use narrow to prevent microbial antibiotic resistance
Define selective toxicity. It is a term used to describe action of_____
- Selective toxicity: ability of drug to kill or inhibit pathogen while damaging host as little as possible
- antibiotics
Describe the Mechanisms by which bacteria develop resistance to different anti-microbial drugs
• Prevent drug entrance, efflux pumps, drug inactivation, modification of drug target, alternative pathway
Name one mechanism by which resistance may spread through a bacterial population.
• By genes, chromosome, plasmids, R-plasmids, viruses, transposons
How do semisynthetic antibiotics differ from their parent molecules?
- Semisynthetic molecules typically keep a main part of molecule and only differ in an R group
- For example, natural penicillin has a beta-lactam ring with an R group attached; all other forms of penicillin have that ring, but differ slightly by their R group
Briefly describe the Kirby-Bauer test and its purpose.
- Used test the effectiveness of antibiotics
- Paper disks with the bacteria are used and if there is a clear zone in a ring around the disk then the antibiotic was effective. If there is no growth then the bacteria has resistance against antibiotics or that particular antibiotic is not effective against bacteria
Disk dilution test
Small paper disks, each impregnated with a different antibiotic, are placed on the inoculated agar. When the antibiotic diffuses radially outward through the agar, it produces a concentration gradient. The antibiotic is present at high concentrations near the disk and affects even minimally susceptible microorganisms. On the other hand, resistant organisms will grow close to the disk.
E-test
used in sensitivity testing; MIC determined; In general, each bacterial isolate to be tested for antimicrobial sensitivities is inoculated on the surface of an agar medium and then Etest® strips are placed on the surface (figure 9.4). Each strip contains a gradient of an antibiotic and is labeled with a scale of MIC values. After 24 to 48 hours of incubation, an elliptical zone of inhibition appears. As shown in figure 9.4, MICs are determined from the point of intersection between the inhibition zone and the strip’s scale of MIC values.
Describe techniques used to detect the presence of Drug resistant gene in microorganisms.
• There are two types of drug resistance: intrinsic and acquired
o Intrinsic means they naturally do not have the drug targets (like not having a cell wall)
o Acquired means the bacteria receive the resistance occurs when there is a change in the genome of a bacterium that converts it from one that is sensitive to an antibiotic to one that is resistant. There is also drug tolerance;
• you can test for drug resistance by testing the gene or gene products, and can observe a color change if the bacteria has a target modifying enzyme or a beta-lactamase reacts with a chromophore, and can identify through PCR
How one can overcome Drug Resistance?
o tighter control over antibiotic prescriptions and in animal feed
o patients must finish their prescriptions or properly dispose of them
o avoid broad spectrums
Give an example of how synergistic drug interaction between two drugs work
- Synergistic: target 2 parts of a pathway
- It is used to further stop infection and at a faster rate
- One example of this is Sulfonamides and Trimethoprim to stop the production of folic acid at two different steps of the metabolic pathway
Why are immunosuppressed individuals given antifungal agents?
• Many anti-fungal treatments have adverse affects on the patient, therefore immunosuppressed individuals are given fluconazole as treatment to prevent fungal infections because adverse effects of fluconazole are relatively uncommon, it is used prophylactically to prevent life-threatening fungal infections
Explain why there are far fewer antiviral drugs than there are antibacterial drugs.
- There are fewer antiviral drugs purely because there are no mechanisms of actions that can be inhibited like antibiotics do to bacteria.
- For example, viruses are intracellular parasites, they live in the host machinery, so a drug could potentially harm the patient
- Only supportive therapy and vaccination are the best options for viruses
What is the rationale behind the combination drug therapy for HIV infections?
• If you use a combination of different drugs then multiple pathways can be stopped, making the drugs more effective together than apart; a cocktail could be used by using two RT and one protease
o RT inhibitors block RNA from becoming DNA and Protease inhibitors helps to stop viral protein from being synthesized by the host
Name two groups of Archaea and describe their unique characteristics
- Extreme halophiles: A group of archaea that depend on high NaCl concentrations for growth and do not survive at a concentration below about 1.5 M NaCl.
- Methanogens: Strictly anaerobic archaea that derive energy by converting CO2, H2, formate, acetate, and other compounds to either methane or methane and CO2.
- Thermophiles: A microbe that has its growth optimum between 85° and about 120°C. Hyperthermophiles usually do not grow well below 55°C.
What is the difference between methanogens and methanotrophs?
- Methanogens: Strictly anaerobic archaea that derive energy by converting CO2, H2, formate, acetate, and other compounds to either methane or methane and CO2.
- Methanotroph: A microbe that has the ability to grow on methane as its sole carbon and energy source
Name three anaerobic environments (organic-rich) where methanogens are found.
animal rumens
anaerobic sludge digesters
anaerobic protozoa
Describe the role of microbes in biogeochemical carbon cycling
o Can convert to all types of carbon into CH4, CO2, and organics
o Involved in producing GHG: CO2 and CH4
This is involved in controlling the amount of infared radiation, which controls the warming and cooling of the earth
o The carbon cycle begins with carbon fixing, which is turning CO2 into organics, and half of all carbon fixing is performed by microbes
o Only archaea can produce methane
Describe the role of microbes in biogeochemical phosphorous cycling.
o not really involved into this cycle; turns insoluble into usable materials
Describe the role of microbes in biogeochemical nitrogen cycling
o Nitrogen needs to become soluble, which is performed by microbes
o 80% of it is in the air
o Nitrogen fixation: converting inorganic N2 into organics, performed only by bacteria and archaea
o Nitrification: The oxidation of ammonia to nitrate. (NH4 – NO2- - NO3-)
o Denitrification: The reduction of nitrate to gaseous products, primarily nitrogen gas, during anaerobic respiration.
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Describe the role of microbes in biogeochemical sulfur cycling
o reduced by plants and microbes for use in amino acid and protein biosynthesis
o DMSP, bacterioplankton (floating bacteria) use it as a sulfur and carbon source. In the process, it is metabolized to dimethylsulfide (DMS) and released into the atmosphere. There DMS is rapidly converted into a variety of sulfur compounds that serve as nuclei for water droplet formation, contributing to the formation of clouds. Because clouds help keep the Earth’s surface cool, it is hypothesized that increased DMS production could help mitigate the effects of global climate change.
What is the overall purpose of sewage treatment process? `
• Waste water needs to be treated or else the organics released would take up all the oxygen in water, called BOD (biological oxygen demand), so it needs to be processed
List three stages of sewage treatment process
Primary: physical; separates sediments from the water
Secondary: biological; separtes microbes, organics, and BOD from the water
Tertiary: chemical; no microbe removal, but it removes inorganic chemicals
Which stage of sewage treatment process removes most of the BOD?
Secondary – removes organics and microbes
What is BOD?
Biological oxygen demand
The amount of oxygen used by organisms in water under standard conditions; it provides an index of the amount of microbially oxidizable organic matter present.
What is the role of microbes in the sewage treatment process?
Leftover solid waste is moved into an anaerobic digester, where microbes will break down the sediments and turn it into methane
This methane can then be converted into energy
What is the purpose of anaerobic sludge digestion?
The microbiological treatment of sewage wastes under anoxic conditions to produce methane
To get rid of recalcitrant organics
Where in Sewage treatment process methane gas is produced? What do they use methane gas for?
Methane gas is produced during the anaerobic sludge digestion
The gas is vented and often burned for heat and electricity production
How septic tank is compared to industrial sewage treatment process?
Septic tanks don’t employ a similar process to sewage treatment, instead it only focuses on primary processes
No microbe involvement
Removes the sediment and the water is put back into the soil
What is composting? What is the role of microbes in this process?
- Composting reduces waste by 2/3 in a few months, and can be used for fertilizers or mulch
- Microbes are involved in breaking down the organic material in the compost piles so that it can used in the soil and be recycled
R-plasmids
resistance plasmids
– the plasmid can be transferred to other cells by conjugation, transduction, and transformation
– can carry multiple resistance genes
composite transposons
contain genes for antibiotic resistance – some
have multiple resistance genes
• can move rapidly between plasmids and through
a bacterial population
List the common reasons for increasing drug resistance and emergence of superbugs.
1) over prescription of antibiotics
2) lack of regulation of antibiotic sales
3) not completing course of antibiotics
4) inc. use of antibiotics for animals produced for consumption
5) taking too small a dose of antibiotics
How one may prevent the emergence of drug resistant microbes.
- Use high concentrations/ Use two or more drugs at same time/Minimize use
- possible future solutions
- continued development of next generation of drugs or new drugs
- use of bacteriophages to treat bacterial disease
Give examples of anti-fungal drugs
- polymixin B - used against cell membrane - toxicity
- amphotericin B - makes the cell leaky, a type of this is nystatin
- azoles - Block ergosterol synthesis-inhibits cell membrane synthesis, Miconazole
Give examples of anti-viral drugs
- amantadine
- tamiflu
- acyclovir
mechanism of action for amantadine
- anti-viral drug
- used to prevent some types of influenza infections
– blocks penetration and uncoating of influenza virus
mechanism of action for tamiflu
- anti-viral drug
- a neuraminidase inhibitor
– though not a cure for influenza, has been shown to shorten course of illness
mechanism of action for polyenes
- anti-fungal
- Bind to sterol, disrupts cell membrane function
– Amphotericin B
– Nystatin
mechanism of action for azoles
Block ergosterol synthesis-inhibits cell membrane synthesis
– Miconazole
chloroquine
- also can use mefloquine
used to treat malaria, take before going to a country where this disease is prevalent
Isoniazid
- antimetabolite
- MOA: inhibit lipid synthesis
- used to treat mycobacteria, mostly TB
Amphotericin B
- anti-fungal
- type of polyenes
- Bind to sterol, disrupts cell membrane function
Acyclovir
- anti-viral drugs
- Inhibit herpes replication
Mechanism of action for Aminoglycosides
- antibiotics
Bind to 30S ribosomal subunit, interfere with protein synthesis by
directly inhibiting the process and by causing misreading of the
messenger RNA
• Resistance and toxicity
mechanism of action for Tetracycline
- antibiotic
- chlortetracycline and doxycycline
all have a four-ring structure to which a variety of side chains
are attached
• are broad-spectrum, bacteriostatic
• combine with 30S ribosomal subunit
– inhibits bind of aminoacyl-tRNA molecules to the A site of the
ribosome
• sometimes used to treat acne
mechanism of action for Macrolides
- anti-biotics
- contain 12- to 22-carbon lactone rings linked to one or more
sugars
• e.g., erythromycin
– broad spectrum, usually bacteriostatic
– binds to 23S rRNA of 50S ribosomal subunit
• inhibits peptide chain elongation
• used for patients allergic to penicillin
mechanism of action for Chloramphenicol
- anti-biotic
- now is chemically synthesized
• binds to 23s rRNA on 50S ribosomal subunit and
inhibits peptidyl transferase reaction
• toxic with numerous side effects so only used in life-
threatening situations
Give examples of how anti-HIV drugs block HIV replication
o Block entry/penetration (fusion), block reverse transcriptase (block RNA from becoming DNA), block the integration of provirus, and translation modification (protease inhibition)
