Exam 3 Study Guide

What is meant by in silico analysis and annotation 19) The process that locates genes in the genome map and identifies ORF is called A) Genome Annotation B) Comparative genomics C) Southern blot D) RFLP E) __teomics

Biotechnology allows researchers to make conclusions about the function of a gene product exclusively through the use of IN SILICO analysis, or analysis carried out by a COMPUTER. Computers are also used in a process called annotation to determine where genes start and end, which allows them to locate genes on the genome. A) Genome Annotation

What does cloning mean? Compare and contrast the common cloning vectors used in creating Recombinant DNA. What is the significance of Ti plasmid? cold/salt resistance 40) Ti plasmids are used to introduce genes into __________ cells.

Cloning is the process by which a DNA sequence is isolated and replicated using a cloning vector. The following are some of the most common cloning vectors: PLASMIDS - by far, the most commonly used type of cloning vector is a plasmid. It is a self-replicating piece of extrachromosomal DNA found in PROKARYOTES. Plasmids are popular because they can be easily transferred from one organism to another via conjugation or transformation. Plasmids can typically carry inserted sequences in the mid-size range 20,000 base pairs or fewer. Two examples of commercially available plasmids are p322 and pUC19. Often, genes are inserted into PLANT genomes using the tumor-inducing (Ti) plasmid found in Agrobacterium tumefaciens, a type of bacterium. This bacterium induces the formation of tumors in hundreds of plant species. However, scientists have found a way to take out the tumor inducing genes and other-non-essential regions. The plasmid can then be used as a cloning vector that carries the DNA of interest and a selectable marker. The vector can then be incorporated into the plant genome, creating recombinant plants with desirable characteristics, such as SALT resistance or COLD resistance. This is an example of a cloning vector that can be used to transfer a gene from PROKARYOTES to EUKARYOTES. Can also go the other way, eukaryotes can transfer to prokaryotes. PLANT cells

Name three anaerobic environments where methanogens are found and are rich in organics.

Methanogens are strict anaerobes, so they are only found in places without oxygen. Three anaerobic environments where they are found include: 1. ANIMAL RUMENS 2. in ANAEROBIC SLUDGE DIGESTERS 3. within ANAEROBIC PROTOZOA.

Define selective toxicity. It is a term used to describe the actions of _________________.

Selective toxicity is the ability of chemotherapeutic agents to exploit differences in the structures of metabolisms of microbes and the host cells and, consequently, inhibit or kill the pathogens without harming the host cells. This is a key characteristic of a useful microbial agent, and this term is specifically used to describe the action of ANTIBIOTICS.

How do semisynthetic antibiotics differ from their parent molecules?

Semisynthetic antibiotics are often MORE EFFECTIVE than their parent molecules. For example, semisynthetic penicillin is modified to have a broader range than natural penicillins.

List factors contributing to viral pathogenicity (PGFD)

Several factors contributing to viral pathogeneicity are as follows: -The ability to PENETRATE host cells -The ability to GROW within the cell -The ability to FIGHT against the host cell's defense mechanisms -The ability to DAMAGE the host

Explain why there are far fewer antiviral agents than there are antibacterial agents.

There are fewer antiviral agents than antibacterial agents because VIRUSES are NOT METABOLICALLY ACTIVE and CANNOT REPRODUCE on their OWN, so drugs that fight against viruses must have unique targets.

What is the genetic material for viruses? DNA or RNA, single stranded or double stranded?

Viruses can have genomes that consist of DNA or RNA, and these molecules can be either single-stranded or double-stranded. Can not be both.

Define the term provirus/prophage. What is the role of reverse transcriptase in formation of provirus? a. Define virulent phage, temperate phage, and lysogenic conversion During ______________, environmental conditions cause a provirus to initiate synthesis of new virus particles. A. release B. attachment C. induction D. synctia E. viremia

A PROVIRUS refers to viral DNA that has been integrated into a host's chromosome. (A PROPHAGE is specifically a virus that has infected a bacterial host.) Reverse transcriptase is an enzyme that converts single-stranded RNA to double-stranded DNA. This enzyme is necessary for retroviruses to integrate into the host chromosome. Single stranded RNA-> double stranded DNA. Virulent phage: bacterial viruses Temperate phage: phages able to establish lysogeny. Prophage: Integrated phage genome Lysogenic conversion: the ability of some phages to survive in a bacterium as a result of the integration of their DNA into the host chromosome. C. induction

What is meant by temperate phage? What is their role in pathogenic microbes? Which of the following best describes a temperate phage? a. a virus that is capable of undergoing the lytic cycle inside a bacterial host. b. a virus that infects a fungus. c. a virus that is capable of establishing lysogeny inside a bacterial host. d. a virus that is capable of picking up "naked" DNA from the environment. e. None of these is correct.

A TEMPERATE PHAGE is a phage that is capable of establishing LYSOGENY and integrating into the bacterial host. A lysogen is a bacterium that contains a virus. Lysogeny can actually help bacteria as long as the virus does not undergo induction. For example, viruses can carry virulence genes that convey pathogenicity and help bacteria spread. c. a virus that is capable of establishing lysogeny inside a bacterial host.

Name few categories of products made by microbes in industrial scale (industrial microbiology)

A few categories of products made by microbes in industrial scale include primary and secondary metabolites, plant hormones, food additives, biopesticides, and genetically modified plants. -antibiotics -biofuels

Define: therapeutic dose, therapeutic index, and spectrum of activity?

A therapeutic dose is the MINIMUM drug level required for clinical treatment. It is the minimum dose that is effective to achieve the desired results. A drug's therapeutic index is the ratio of the TOXIC DOSE to the THERAPEUTIC DOSE. Therapeutic Index = (Toxic dose) / (Therapeutic dose) Higher=safer the drug It is better for a drug to have a HIGH therapeutic index because it means that overdosing is less likely to have negative consequences. Spectrum of activity: The range of targets against which a drug is biologically active, particularly in terms of clinical effectiveness.

How viruses enter, spread, and exit from the body? 2 major routes of a virus entering the human body 1: respiratory tract, alimentary tract, genital tract, or conjunctiva 2: scratches, insect bites Define the following spreading: Neuroptic virus Lymphotrophic virus Viremia Pregnancy Virus shedding --Remember that the point of exit for viruses DOES NOT necessarily have to be the same as the point of entry.--

A virus can enter the human body through two major routes: 1. The mucous membranes -- The mucous membranes include the respiratory tract, alimentary tract, genital tract, or conjunctiva (which covers the lining of the eyelid and the white part of the eye). By far, the RESPIRATORY TRACT is the most COMMON route of entry for all diseases. 2. The SKIN -- A virus can penetrate the skin via a wound, scratches from animals, or insect bites. -------------------------------------------- Viruses can spread through the body in a number of ways, including the following: -Viruses can spread LOCALLY, over EPITHELIA surfaces -NEUROTROPIC VIRUSES spread through cells in the NERVOUS SYSTEM. For example, the rabies virus spreads this way. -LYMPHOTROPHIC VIRUSES spread through the LYMPHATIC SYSTEM. -Viruses can spread in the BLOOD STREAM. VIREMIA occurs when viruses are present in the blood stream. -In pregnant women, viruses can pass from the mother to the fetus via the placenta, causing congenital diseases. VIRUS SHEDDING (exiting): refers to the many ways that the virus can leave the body. Sometimes, viruses remain within the host organism and do not shed at all. In other cases, viruses are shed through the skin, feces, respiratory secretions, oropharyngeal secretions, or other routes.

Give examples of anti-fungal and anti-viral drugs a. What is the mechanism of action of: Tamiflu, Amantadine, Polyenes, and Azoles. Also metronidazole b. What are the specific use for the following antimicrobial agents: i. Chloroquine ii. Isoniazid iii. Amphotericin B iv. Acyclovir v. Ribavirin -----Polyenes . . . a. are antibiotics b. are a component of vancomycin c. inhibit protein synthesis d. are anti-fungal drugs. e. inhibit the synthesis of murein -----3) Which class(es) of drugs target(s) cell wall of fungi A) Polyenes B) Azoles C) Quinolones D) Two of these ------27) Drug used to treat infections caused by anaerobic microorganisms A) Amphotensin B) Metronidazol C) Amantadine D) Chloroquine

Acyclovir: inhibits herpes Ribovirin: inhibits hepatitis Amatadine and Tamiflu: inhibits influenza Azoles: Block ergosterol synthesis: inhibits cell membrane synthesis. Polyenes: Binds to sterol, disrupts cell membrane function (amphotericin B) Chloroquine: Anti-protozoa drug, Malaria Metronidazole - entramoeba infections Isoniazid: inhibit lipid synthesis (especially mycolic acid); Isoniazid; treats Tuberculosis These are all anti-viral drugs. Examples of anti-fungal drugs are azoles and polyenes. d. are anti-fungal drugs. A) Polyenes B) Azoles D) Two of these B) Metronidazol

Explain the history/origin of antibiotics. Who discovered penicillin in the 1920s? What produces antibiotics? Why some microorganisms in nature produce antibiotics

Antibiotics are antimicrobial agents that kill or neutralize bacteria. They were discovered by ALEXANDER FLEMING, who discovered PENICILLIN in the 1920s. Antibiotics saved many thousands of lives during the World War II. Antibiotics are produced by bacteria and fungi as a natural defense mechanism against other bacteria. For example, Bacillus is a genus of bacteria that produces antibiotics, and Penicillium is a genus of fungi that produce antibiotics.

Know properties of viruses given in slide 60. -Obligate intracellular parasites -number of viral particles 10^____ -Found in ____ -Size -Living vs non living -structure -DNA or RNA or both? -double, single, or both? -attachment -multiplying -enzymes? Give examples of viral syndrome

As a review, here are some KEY PROPERTIES OF VIRUSES: -They are obligate intracellular parasites of bacteria, protozoa, fungi, algae, plants, and animals. -There are an estimated 10^31 virus particles on earth - approximately 10x the number of prokaryotes. -They are found in nature and have had a major impact on the development of biological life. - They are ultramicroscopic in size, ranging from 40 nm up to 450 nm (diameter). -They are acellular, and their structure is very compact and economical. -They do not independently fulfill the characteristics of life. -Their basic structure consists of protein shell (capsid) surrounding nucleic acid core. -Their nucleic acid can be either DNA or RNA, but NOT BOTH. -Their nucleic acid can be double-stranded DNA, single-stranded DNA, single-stranded RNA, or double-stranded RNA. -Molecules on virus surface impart high specificity for attachment to host cell. -They multiply by taking control of host cell's genetic material and regulating the synthesis and assembly of new viruses. -They lack enzymes for most metabolic processes, and they lack the machinery for synthesizing proteins. A viral syndrome is a collection of signs (objective manifestations) and symptoms (internal manifestations). Examples included oral infections, respiratory tract infections, skin rashes, eye infections, hemorrhagic fevers, flu-like systemic symptoms, gastroenteritis, hepatitis, CNS infection, STDs, and congenital, perinatal, and neonatal diseases.

Define Bio-Conversion, Biosensors, Biopolymers, Bio-Surfactants, biocatalysts, bio-pesticides, GMOs and Biofuels

BIOCONVERSION (or biotransformation) is the use of live organisms (microorganisms, plants, or animals) to facilitate a chemical reaction that converts a substance to a chemically modified form. A microbial BIOSENSOR uses microorganisms, enzymes, or organelles and physical transducer to detect the presence of a substance. BIOPOLYMERS, such as dextran and polyhydroxybutryate (PHB), serve as gelling agents and modify the flow of liquids. Adding biopolymers to a fluid slows its movement through a system, which can be useful in many industrial applications. BIOSURFACTANTS emulsify other substances, such as oil. This makes it particularly useful in oil recovery efforts, dispersing oil spills, and in bioremidiation - using organisms to remove pollutants from a contaminated site. BIOCATALYSTS is an organism used for metabolic activity such as yeast where it reduces ketones. BIOPESTICIDES are certain types of pesticides derived from such natural materials as animals, plants, bacteria, and certain minerals. GMO is an organism whose genome has been altered by the techniques of genetic engineering so that its DNA contains one or more genes not normally found there. BIOFUELS are fuels derived directly from living matter. Microbial fermentation of crop residues consisting of cellulose and hemicellulose produces ethanol, a biofuel that is widely used to power cars and other motor vehicles. Microbes are also involved in the production of methane gas and hydrogen, which can be used as biofuels.

Mechanisms by which bacteria develop resistance to different anti-microbial drugs

Bacteria can become resistant to an anti-microbial drug by developing ways to: prevent its ENTRANCE into the cell, PUMP the DRUG OUT of the cell, MODIFY the DRUG so that is is ineffective, MODIFY the STRUCTURE that the drug acts on, or use an ALTERNATIVE PATHWAY that the one the drug acts on.

Define Bacteriophages Cosmids (PP) Artificial chromosomes -Benefit?

Bacteriophages - a VIRUS that infects Bacteria. These vectors carry smaller fragments of between 9,000 and 25,000 base pairs. Cosmids - a hybrid between a PLASMID and a PHAGE. These can carry larger fragments of between 30,000 and 47,000 base pairs. Artificial chromosomes - synthetic chromosomes that contain fragments of DNA integrated into a host chromosome. Categories of artificial chromosomes include P1 artificial chromosomes (PACs), bacterial artificial chromosomes (BACs), and yeast artificial chromosomes (YACs). The major advantage of artificial chromosomes is that they can carry LARGER fragments. Yeast artificial chromosomes, for example, can carry fragments of up to 1 million base pairs. These vectors were used in the Human Genome Project.

Define bioinformatics. What branches of science are involved in bioinformatics?

Bioinformatics is the study of the genome using COMPUTERS. Bioinformatics integrates computer science, biology, statistics, and math.

How are bacteria used as bio-pesticides? Give an example. (Bt Bacillus thuringiensis) Bacillus thuringiensis is gram positive and it produces parasporal body that kills insects.

Biopesticides are naturally produced agents that kill pests. For example, bacillus thuringiensis (Bt) is a gram-positive bacterium that produces an intracellular protein toxin crystal called the parasporal body during sporulation. This parasporal body kills specific groups of insects. Bt toxin has been used as a biopesticide for more than 40 years. It is generally considered safe because it specifically targets certain pests. In addition, it does not accumulate in the environment like many artificial, chemical insecticides. Scientists have successfully inserted the Bt genes that produce certain biological insecticides into some plant genomes, resulting in genetically modified plants. For example, Bt genes were inserted into the maize plant in 1996 to specifically kill a harmful pest called the European corn borer. There are Bt cotton and Bt potato plants as well.

What is composting? Do microbes have any role in this process?

COMPOSTING is the process of decomposing organic matter and recycling it as fertilizer. Organic matter is placed in the compost, and soil is added. The purpose of adding the soil is to add microorganisms, including bacteria, which will help to break the organic matter down.) The partially decomposed matter can then be used as fertilizer in your home garden. When composting is done on a large scale, it can reduce the garbage going into a landfill.

What are chemotherapeutic agents? (these are just antibiotics and synthetic drugs that control the spread of microbes) how? How metabolic antagonists (antimetabolites) work? List four categories of antimicrobial drugs based on their mechanisms of action.

Chemotherapeutic agents include antibiotics and synthetic drugs that control the spread of microbes, either by killing them or preventing their proliferation. They are used to fight diseases. Antimetabolite: Chemicals that target metabolic pathways. Metabolic antagonists. Antagonize or block functioning of metabolic pathways by competitively inhibiting the use of metabolites by key enzymes. We can categorize antibiotics (and other antimicrobial drugs) based on their mechanism of action, or the way they either kill microbes or prevent them from spreading. -Inhibitors of CELL WALL SYNTHESIS prevent cells from proliferating by preventing the synthesis of cell walls. This is the most important target for antibiotics, but this target is obviously useless to fight against bacteria that do not have cell walls. -PROTEIN SYNTHESIS inhibitors disturb the process of protein synthesis, often by targeting ribosomes. (Recall that the size and composition of prokaryotic and eukaryotic ribosomes differ slightly.) -NUCLEIC ACID SYNTHESIS inhibitors prevent the synthesis of DNA or RNA. -Inhibitors of CELL MEMBRANE FUNCTION somehow impact the assembly or proper functioning of the cell membrane.

What is the rationale behind the combination drug therapy for HIV infections? Combination of RT inhibitors and Protease inhibitors. Give examples of how anti-HIV drugs block HIV replication (Figure 9.16) Don't expect us to know examples however he talked about them.

Combinations of multiple drugs create multiple obstacles to HIV replication. This is why the standard treatment for HIV usually involves a combination of at least 3 drugs from two different classes. -First convert RNA to DNA, reverse transcriptase (RNA dependent DNA polymerase), converts ssRNA into dsDNA, virus then enters host, now called a provirus (if a bacteria, call it a bacteriophage), make more RNA virus, virus exits via budding. Extra: Fusion inhibitors block HIV fusion. RT inhibitors block HIV from uncoating and reverse transcriptase from converting DNA to viral RNA. Protease inhibitors block viral DNA from being transcribed and translated into linear polypeptide that is cut to release viral proteins. Integrase inhibitors block viral DNA from being added to the host DNA by action of a viral integrase.

What is the medical significance of comparative genomics analysis? RFLP?

Comparative Genomics is the study of the DIFFERENCES among the GENOMES of different organisms. This field of study has provided important information about what makes a pathogen virulent, and it has given researchers insights into what kinds of vaccines or therapies may be useful to fight against virulent pathogens. The restriction fragment length polymorphism (RFLP) technique is a tool for genetic fingerprinting, genome mapping, localization of genes, paternity testing, and microbial classification. It takes advantage of the fact that highly conserved and repetitive DNA sequences are present in nearly every genome, including genomes of humans, gram-negative bacteria, and gram-positive bacteria. This technique relies on the premise that every organism's restriction sites will be located at slightly different locations on the genome, so the specific pattern of restriction fragments on the electrophoretic gel will be different from person to person. Therefore, each individual has a unique DNA fingerprint that can be used as forensic evidence or evidence of paternity.

Describe the role of viruses in horizontal gene transfer (HGT); generalized vs specialized transduction Define conjugation, transformation, and transduction first. 21) Bacteria may become resistant to antibiotics by acquiring resistant gene from other bacteria via A. Transformation B. Conjugation C. Transduction D. All of these 23. Temperate phages are used in horizontal gene transfer to establish lysogeny via A. Transposons B. Conjugation C. Transformation D. Transduction

Conjugation: Genetic exchange through pili plasmids Transformation: Genetic exchange from environment like dead bacteria. TRANSDUCTION is a type of horizontal gene transfer that involves the transfer of genetic information from one bacterium to another via a virus (phage). GENERALIZED TRANSDUCTION can involve the transfer of any bacterial gene to a recipient bacterium using a phage. SPECIALIZED TRANSDUCTION involves the transfer of a restricted set of only a few, specific bacterial genes to another bacterium via a phage. The phage genome's location on the chromosome determines which genes are transferred. (Only genes located adjacent to the phage genome are transferred.) D. All of these D. Transduction

Describe DNA MICROarray system. What is its purpose? Where does the sample come from for this analysis? 28) DNA microarray technology is used to measure the (someone double check this one) A. All of these B Levels of specific proteins expressed by cells C. DNA content of cells D. Levels of Specific RNA's expressed by cells

DNA microarray analysis is a tool that allows scientists to OBSERVE the pattern of DNA expression for thousands of genes at a time. DNA microarrays are chips with a collection of tiny DNA spots attached to a solid surface. They are created by robotic machines that arrange hundreds or thousands of genes onto a single chip. The basic process of DNA microarray analysis is as follows: 1. The researcher collects the mRNA molecules present in a cell. 2. The researcher uses reverse transcriptase to convert the mRNA into complementary DNA (cDNA), and the researcher labels the cDNA with a fluorescent dye. 3. The researcher places the cDNA onto the microarray chip. 4. The cDNAs then bind to (or hybridize with) the complementary DNA sequences already on the microarray chip. 5. A special computer scanner is used to measure the intensity of the fluorescence in each area on the slide. The brightest areas represent the genes with the most mRNA. Therefore, these are the most "active" genes in the cell. D. Levels of Specific RNA's expressed by cells

Name different components of a virus. Must have 2 things but can also have 2 other things. Name the two components that every virus must have

Every virus must have a NUCLEIC ACID and a CAPSID. In addition, some viruses may have an ENVELOPE and SPIKES.

What is the scope of functional genomics

Functional genomics is the study of the function of genomes - that is, it is the study of HOW A GENOME WORKS. Paralogs: 2 or more genes found alike in the same genome that likely arose from gene duplication. Orthologs: 2 or more genes very similar in different organisms that are predicted to have same function. Can look at conformation: 3D structure of proteins. Gives structure to proteins. Can predict which organism has a specific function and which one doesn't. Motif: act as active site of an enzyme. Often phylogenetically conserved.

Why are immunosuppressed individuals given antifungal agent?

Fungal infections in immunocompromised patients are difficult to diagnose and a significant cause of mortality. Therefore, immunocompromised individuals are given anti-fungal agents to PROTECT AGAINST fungal infections.

Describe, Explain, Define: Gel Electrophoresis, Vectors, Restriction enzymes, Blotting, Blotting techniques used for detecting. . . Southern: _________ -Often uses radioactive DNA hybridization probes. -Autoradiography Western: __________ Northern: _________

Gel electrophoresis: a technique that separates NUCLEIC ACIDS and PROTEINS on the basis of their SIZE and ELECTRICAL CHARGE, using a gel that is a polymer (typically, either agarose or polyacrylamide). -Wells in the gel, DNA has a charge (acidic), travels to other side of the gel and fragments move. -DNA cut by enzymes, various sizes, smaller=faster, larger=slower Cloning vector: provides a means for transferring a gene of interest to a host organism during the cloning process. Vectors can be inserted into host cells in many ways. For example, bacteria can be made competent to take up naked DNA from the environment through the treatment of calcium chloride and heat shock. -Has an origin of replication -Selectable marker. Restriction Enzymes: endonucleases that cut double-stranded DNA at specific recognition sequences. They are NATURALLY PRODUCED by BACTERIA as a defense against viral infection, but they are commonly used to create recombinant DNA, or DNA that comes from two or more sources. Blotting: a technique that combines ELECTROPHORESIS and HYBRIDIZATION to detect specific DNA fragments. Blotting techniques Southern: DNA -Often uses radioactive DNA hybridization probes. -Autoradiography: method for detecting radioactively labeled molecules. Western: Protein Northern: RNA

What is meant by genetic manipulation

Genetic manipulation involves changing the genome of an organism in order to produce desired traits. Genetic engineering is one form of genetic manipulation.

Define genomics and list the three area of genomics

Genomics is the study of the organization of genomes, the information they store, and the gene products that they code for. The field of genomics can be broken down into three subfields: 1. Structural genomics is the study of the PHYSICAL nature of genomes. 2. Functional genomics is the study of the FUNCTION of genomes. 3. Comparative genomics is the study of the DIFFERENCES among the GENOMES of different ORGANISMS.

What is the significance of transforming infections? -The virus affects the host's _______ ______, causing some kind of mutation in the host chromosome. List Viruses that cause cancer. -Human papillomavirus Virus (HPV) -Hepatitis B and C (HBV and HCV) Oncogenic Viruses? -HBV -HCV -HHV8 47) Viral infections may result in cancer. Which of these statements of induced cancer is not correct? a. Virus may insert a promoter or enhancer next to cellular oncogene b. HPV can cause cancer c. All of these are correct d. Viruses may carry oncogene into cell and insert it into the host genome e. Both HBV and HPV infections can cause cancer

In a TRANSFORMING INFECTION, the virus affects the host's genetic makeup, causing some kind of mutation in the host chromosome. Often, a transforming infection involves the integration of a viral genome at a point of the host's genome called the ONCOGENE, which has the capacity to cause cancer. For example, integration of the viral genome in a part of the host chromosome responsible for proper cell division might cause cells to never cease growing, leading to the formation of a tumor. c. All of these are correct a. Virus may insert of promoter or enhancer next to cellular oncogene (true) b. HPV can cause cancer (true) d. Viruses may carry oncogene into cell and insert it into the host genome (true)

How industrial microbiology defines fermentation? Compare Chemostat vs batch for large scale industrial growth

In industrial microbiology, fermentation refers to the MASS CULTURE of microorganisms. A chemostat is a BIOREACTOR in which the VOLUME is kept CONSTANT by continuously adding fresh medium while REMOVING the culture LIQUID. In this way, the GROWTH RATE of the microorganism can be easily CONTROLLED. A batch culture, on the other hand, is a technique to grow bacteria in which bacteria grow until the LIMITED SUPPLY of BACTERIA is USED UP.

List steps in virus replication. (6) What is the importance of un-coating step in viral infection

In order, the steps in viral replication are: 1. attachment/absorption 2. Penetration (enter) 3. Uncoating (release of DNA/RNA inside the cell) 4. Synthesis/replication (more virus components) 5. Assembly (maturation, packaging) 6. Release (of virus particles) If the viral capsid penetrates the cell, it must be shed inside the cell so as to expose the nucleic acid. After coating, the virus fuses with the endosome and the nucleic acid is released into the cell.

What is meant by protoplast fusion? Electroporation? Transformation (plasmids picked up by laboratory-induced competent bacterial cells). Compare in vivo and in vitro transformation (done in lab vs. done in nature) a. What is the role of Transposons in genetic variation, mutation, and genetic exchange b. Define: Transposons, Transposition, Insertion Sequences (IS), Transposable Elements Protoplast fusion is most commonly observed in . . . a. fungi b. bacteria c. animals d. viruses e. protozoans 31) One can use protoplast fusion to insert genes into the fungal cell A True B False

In protoplast fusion, scientists use enzymes (such as cellulose) or other means to REMOVE the CELL WALLS of multiple cells, creating protoplasts. -Combine two cells by removing cell wall and letting cell membranes of the two cells merge. They then put the protoplasts together in solution and apply an electric shock (ELECTROPORATION), causing them to FUSE TOGETHER, forming a somatic hybrid. This method is most commonly USED WITH FUNGI. Competent: Pick up the DNA from the outside. Transformation involves the direct uptake of genetic material from a bacterium's surroundings. Transformation is very rare in nature, but it is commonly used in the laboratory. Transposon: a chromosomal segment that can undergo transposition, especially a segment of bacterial DNA that can be TRANSLOCATED as a whole between chromosomal, phage, and plasmid DNA in the absence of a complementary sequence in the host DNA. Transposition: the transfer of genetic material between organisms other than a vertical gene transfer. (horizontal gene transfer) Insertion sequences: part of the transposon that uses insertion sequences to insert itself into another part of the genome. Transposable elements: also known as transposons, are sequences of DNA that move or jump from one location in the genome to another. a. fungi True

Why is protein synthesis (translation) an excellent target against some infectious diseases, but not others? Antibiotics harm bacterial cells and not human cells because . . . a. bacteria have RNA but humans (as eukaryotes) have DNA. b. bacterial proteins are more susceptible to the negative impacts of antibiotics. c. bacteria divide via binary fission, and antibiotics target this process specifically. d. humans and bacteria have different ribosomes. e. all bacteria have cell walls but eukaryotic cells do not.

Many antibiotics work by specifically binding to the small (30S) or large (50S) subunits of the prokaryotic ribosomes, preventing them from assembling or carrying out their proper functions. The size and composition of prokaryotic and eukaryotic ribosomes differ, so antibiotics can effectively prevent protein synthesis in prokaryotic ribosomes while leaving the eukaryotic host's ribosomes unaffected. d. humans and bacteria have different ribosomes.

Which part of cells could be used as a target for antimicrobial agents a. Define metabolic antagonism (antimetabolites) -disrupt key steps in metabolic pathways. b. Compare the action of Sulfa drugs and Trimethoprim c. Give an example and describe the mechanism of antibiotics affecting DNA replication and RNA transcription (one for each)

Metabolic antagonists disrupt steps in key metabolic pathways. These drugs are typically structural analogs that resemble an actual molecule in the metabolic pathway and does not function like that molecule. -Sulfonamides (Sulfa Drugs): a p-aminobenzoic acid (PABA) analog. PABA is precursor for the synthesis of folic acid. Act as antimetabolite Structural analogue. -Trimethoprim: a synthetic antibiotic that also interferes with folic acid production at a different level. Quinolones act on DNA replication. Rifamycin acts on RNA transcription.

What does metabolic engineering mean? Explain DNA shuffling and whole genome shuffling. Which one is used to propagate mutations? Which one is involves the use of protoplast fusion?

Metabolic engineering is the practice of optimizing genetic processes in order to INCREASE the PRODUCTION of a certain SUBSTANCE. Two evolutionary tools used in metabolic engineering include DNA shuffling and whole-genome shuffling, which are used directed evolution, or a process that mimics the process of natural selection to evolve proteins toward a user-defined goal. DNA shuffling is a technique used to propagate beneficial MUTATIONS and increase the size of a DNA library by randomly fragmenting a pool of related genes and reassembling those fragments. Whole genome shuffling involves the use of PROTOPLAST FUSION to introduce recombination throughout the entire genome. After these techniques have been applied, organisms with the desired phenotype can be selected.

What are methanogens and what are their ecological and/or environmental impact -------10) Do all of these match? A) Halophiles-requires sodium to grow B) Bioremediation- use of microbes to remove pollutants C) All of these do not match D) Methanogens- generate methane gas E) Methanotrophs- use methane gas as a carbon source F) All of these do match -------True or false: Methanogens are obligate aerobes. -------36) Identify the FALSE statement A. Adding dirt to the compost heap introduces the necessary microorganisms to the mix B. Secondary sewage treatment uses microbes to remove most of the organics and reduce the BOD C. Anaerobic sludge treatment uses Archaea to break down organics and produce methane gas D. Septic tank resemble anaerobic sludge digester in sewage treatment plants

Methanogens produce METHANE as a metabolic byproduct. They live in anaerobic environments and are commonly found in the RUMENS of COWS alongside grass. They are used by humans in sewage plants to digest sludge. F) All of these do match True or false: Methanogens are obligate aerobes. FALSE: Methanogens are obligate ANaerobes. 36) Identify the FALSE statement Septic tank resemble anaerobic sludge digester in sewage treatment plants

What is the difference between methanogens and methanotrophs?

Methanotrophs are able to METABOLIZE METHANE as their main source of carbon and energy. Methanogens, on the other hand, PRODUCE METHANE as a metabolic byproduct.

Describe the role of microbes in biogeochemical cycling. Their roles in C, N, S, and P cycles. Which cycle does not involve microbes?

Microbes play an important role in each of the biogeochemical cycles. -Microbes and the carbon cycle Microbial decomposition releases carbon dioxide into the atmosphere. Methanotrophs consume methane, and methanogens produce methane. -Microbes and the nitrogen cycle Microbes convert one form of nitrogen into another. Examples include denitrifying bacteria, nitrifying bacteria, nitrogen-fixing bacteria, and bacteria that assist in the decay of organic waste. -Sulfur Bacteria engage in a number of redox reactions the reduction of sulfur oxides (SO2, SO3, and SO4) to hydrogen sulfide (H2S). -Microbes play NO MAJOR ROLE in the phosphorus cycle.

Name two groups of Archaea and describe their unique characteristics

None of archaea cause diseases. Two groups of archaea include: METHANOGENIC ARCHAEA (strict anaerobes that produce methane as a byproduct of metabolism) and EXTREMELY HALOPHILLIC ARCHAEA (primarily chemoorganoheterotrophs that require a sodium chloride concentration of less than or equal to 1.5 M.

List the common reasons for increasing drug resistance and emergence of superbugs. How one may prevent the emergence of drug resistant microbes?

OVER-PRESCRIPTION of antibiotics has selected against bacteria that lack resistance to drugs, leaving only drug-resistant bacteria in the population. As a result, a greater share of remaining bacteria is resistant to antibacterial drugs, leaving humans without an effective way of treating bacterial infections. Humans can take a number of steps to prevent drug resistance. -Doctors can prescribe antibiotics in high enough concentrations and in the correct combination to kill all of the bacteria. As we have discussed, giving two or more drugs at a time often has synergistic effects. -Doctors can prescribe fewer antibiotics. Doctors should only prescribe antibiotics when necessary. -Researchers can develop new drugs and treatments. For example, researchers are always trying to modify drugs to make them more effective. In some cases, the use of novel techniques - such as the use of bacteriophages to treat disease -- may be appropriate.

Compare and contrast lysogenic vs lytic cycle. A virus could do either, why it chooses one over the other LYTIC CYCLE FIRST The type of infection caused by influenza and polio viruses is (a) . . . a. latent infection b. transforming infection. c. lytic infection d. persistent infection e. syncytia

Phage viruses can reproduce by two mechanisms 1. The lytic cycle 2. The lysogenic cycle The lytic cycle - A type of phage replication cycle resulting in the release of new phages by lysis (and death) of the host cell. The mechanism by which this occurs is as follows: 1. The phage binds to a surface receptor on a host and injects its DNA into the cell. 2. The DNA of the host is degraded through HYDROLYSIS. 3. The host's metabolic machinery is used to make the DNA and protein of the phage from the host's own nucleotides. 4. The phage encodes the production of lysozymes, which causes the cell to lyse and be destroyed. As a result, new phages are released. As a consequence of the lytic cycle, the host ultimately dies and new phages are produced c. lytic infection

Define/explain how do bioprospecting and high-throughput screening (HTS) work?

Pharmaceutical companies regularly send researchers to collect soil samples in remote places (such as oil fields, rainforests, volcanoes, copper mines, and hot springs). They do so in the context of bioprospecting, or the search for species that have medical and commercial uses for humans. Researchers bring environmental samples back to the lab, extract the DNA of the organisms found in the soil, put it into a vector (such as a plasmid), and then put the recombinant DNA into a bacterial cell, such as an E. coli cell. This metagenomic library can then be used in genomic sequence analysis (to determine the sequence of the genes) or in a function-driven analysis (to analyze the proteins that the genes produce). High-throughput sequencing technology allows researchers to RAPIDLY and CHEAPLY sequence and analyze a large amount of DNA; this is critical in the field of metagenomics.

Question 4 What are plasmids? What is meant by autonomous replication?

Plasmids are circular, double-stranded, extrachromosomal bits of DNA. Plasmids are capable of autonomous replication, meaning that they replicate INDEPENDENTLY of the bacterial chromosome. A segment of a DNA molecule necessary for the initiation of its replication; generally a site recognized and bound by the proteins of the replication system.

List the type of genes carried on plasmids. How are plasmids transferred between bacteria cells?

Plasmids can carry genes that cause DISEASES or convey ANTIBIOTIC RESISTANCE. The genetic material contained within a circular plasmid is directly transferred from one cell to another via a bridge-like structure called a PILUS during CONJUGATION.

Describe, Explain, Define: PCR, RT, and cDNA,

Polymerase Chain reaction (PCR): a technique for quickly and easily making many copies of even a very small amount of DNA. Used to amplify DNA Needs a PRIMER, new DNA synthesized, 1-2-4-8-16 etc. Needs a DNA polymerase such as Taq polymerase (withstand high temperature) Needs a thermocycler is the instrument used here Reverse transcriptase: as enzyme that turns single-stranded RNA into double-stranded DNA. RNA dependent DNA polymerase Complementary DNA (cDNA) is DNA produced from an RNA template using reverse transcriptase. It is often used to clone eukaryotic genes in prokaryotes. Basic process for constructing cDNA As you can see, this technique creates a double-stranded DNA molecule from a single-stranded RNA template. The double-stranded DNA molecule can then be inserted into vectors and used in traditional cloning techniques, or it can be amplified using PCR. The basic process for constructing cDNA is as follows: 1. Beginning with a single-stranded RNA molecule, apply a short poly-T primer. This is important because, like DNA polymerase III, reverse transcriptase can only add nucleotides to an existing 3' hydroxyl group. Therefore, it requires a primer. 2. Add reverse transcriptase and the four nucleotides (A, C, G, and T). The enzyme will begin to synthesize a complementary strand of DNA from the RNA template. This will produce a DNA-RNA hybrid. 3. Add an enzyme called RNaseH to cut up the rNA and regenerate the RNA primers. If you're interested in having a double-stranded DNA molecule, you need to get rid of the existing RNA molecule. 4. Add DNA polymerase and DNA ligase to synthesize a new strand. DNA polymerase will fill in the gaps between the primers, which will eventually be replaced with DNA. DNA ligase will seal the fragments together, producing a new complementary strand.

What is the significance of primers and Taq polymerase in PCR? What is the advantage of RT-PCR (qPCR) over traditional technique?

Primers: nucleic acid sequences that start DNA synthesis. Taq polymerase: First heat stable DNA polymerase for PCR. Transformed DNA amplification, making the process rapid and efficient. The combination of Taq polymerase, primers and nucleotide triphosphates creates new DNA strands, and the helix forms. qPCR is used to detect, characterize and quantify nucleic acids for numerous applications. Use of dyes helps to measure fluorescence to quantify the DNA. PCR amplifies the DNA.

What is proteomics?

Proteomics is the study of proteomes, or entire collections of PROTEINS produced by an organism.

Explain the role of RNA in origin of life. Ability to do what 2 things?

RNA played a major role in life's early beginnings because it has the ability to REPLICATE and act as a CATALYST for chemical reactions. RNA could have been the nucleic acid used in Earth's earliest life forms, and RNA could have eventually given rise to DNA.

Name one mechanism by which resistance may spread through a bacterial population. a. Describe the Role of R-plasmids, viruses, transposons, and Integron in spread of antibiotic resistant gene from one cell to another R plasmids carry . . . A. virulence genes B. marker genes that introduce a premature "stop" codon C. marker genes that carry a promoter sequence that can be used in biotechnology. D. antibiotic resistance genes. E. none of these are correct.

Resistance may spread through a bacterial population as R plasmids are transferred between bacteria. R-plasmids: Plasmids bearing one or more drug-RESISTANCE GENE. -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. Viruses can carry antibiotic resistant genes in their genetic makeup. Integron: A genetic element with an attachment site for site-specific recombination and an integrase gene. It can capture genes and gene cassettes. D. antibiotic resistance genes.

How does reverse vaccinology work?

Reverse vaccinology involves the use of bioinformatics to screen the ENTIRE genome of a pathogen in order to identify genes that are good vaccine targets.

Name some of the industrial and medical products produced via biotechnology

Scientists have engineered bacteria to produce INSULIN, a-, b-, and gamma interferons, and many other useful proteins such alpha1-antitrypsin (used to treat emphysema), BLOOD-CLOTTING factors (used to hemophilia), and CALCITONIN (used to treat osteomalacia), among many others. Industrial microbiology often focuses on producing primary and secondary metabolites for use of food, amino acids, antibiotics, and other purposes.

List and give examples of antibiotics effective against protein synthesis and nucleic acid synthesis. Describe their modes of action for: a. Aminoglycosides b. Tetracycline c. Macrolides d. Chloramphenicol 2) Aminoglycoside antibiotics such as streptomycin and gertamycin interfere with A) Cellular metabolic pathways B) Translation in prokaryotes ("disrupts the process of correctly reading mRNA") C) Peptidoglycan synthesis D) Replication in prokaryotes

Several classes of drugs that affect protein synthesis are as follows: a. AMINOGLYCOSIDE antibiotics bind to the 30S RIBOSOMAL SUBUNIT, directly inhibiting protein synthesis and causing misreading errors. Translation in prokaryotes ("disrupts the process of correctly reading mRNA") b. TETRACYCLINES bind to the 30S RIBOSOMAL SUBUNIT, inhibiting tRNA from binding to the ribosome at the A site. c. MACROLIDE ANTIBIOTICS bind to the 50S RIBOSOMAL SUBUNIT and inhibit elongation or peptides. d. CHLORAMPHENICOL binds to the 50S RIBOSOMAL SUBUNIT and interferes with the peptidyl transferase reaction. Two classes of drugs that affect nucleic acid synthesis are as follows: QUINOLONES are broad-spectrum, synthetic drugs that inhibit DNA gyrase and DNA topoisomerase, which are molecules involved in making the DNA supercoiled. Against replication RIFAMPICIN is a drug that is part of the common treatment for tuberculosis. It works by inhibiting RNA polymerase. Against RNA synthesis. RNA dependent RNA polymerase: makes RNA out of RNA. B) Translation in prokaryotes ("disrupts the process of correctly reading mRNA")

List factors influencing effectiveness of antimicrobial drugs. What is a parenteral route?

Several factors influencing the effectiveness of antimicrobial drugs include: -the amount that is administered -the speed of uptake -the rate of clearance from the body -the susceptibility of the pathogen -and other hurdles such as necrotic tissue or blood clots that might prevent the drug from reaching its target. Parenteral routes: unconventional routes of administration by passing the skin. (mosquito bites, cuts, bruises, etc.) MIC: minimal inhibitory concentration

List and describe types of virus-host cell interactions for animal viruses...lytic (acute), abortive, persistent, latent, transforming, chronic

Several possible virus-host cell interactions are as follows: LYTIC INFECTIONS -(also sometimes called a permissive infection or productive infection) is the "STANDARD" kind of viral infection, in which the VIRUS infects the HOST, "hijacks" the host's cellular machinery to make more copies of itself, and then DESTROYS the HOST by causing lysis. Only occurs for a short period of time. ABORTIVE INFECTION -(also sometimes called a non-productive infection) is one which the virus is UNABLE to successfully complete the process of REPLICATION. PERSISTENT INFECTION -occurs when viruses reproduce SLOWLY and are released by the cell slowly over a long period of time. These infections do not abruptly kill the host as in a lytic infection. TRANSFORMING INFECTION -the virus affects the host's genetic makeup, causing some kind of MUTATION in the host chromosome. LATENT INFECTION -the virus remains in the host cell in a DORMANT state until a trigger activates it and causes it to make more copies of itself. Latency happens with HERPES, becomes part of some of your cells. CHRONIC INFECTION -long lasting like herpes.

List the differences between bacteria and viruses. 1. size 2. life 3. cell walls 4. ribosomes 5. cellular 6. replication method Compare different forms of acellular structures: Virion, Viroid, Prions, satellites, and phages. Side note: Bacteria: 0.5 - 2.0 micro meters Viruses: 50 nm to 800 nm Extremely small

Some difference between bacteria and viruses are as follows: -Viruses are SMALLER than bacteria -Bacteria are LIVING; viruses are NONLIVING -Bacteria have CELL WALLS; viruses do NOT -Bacteria have RIBOSOMES; viruses do NOT -Bacteria are CELLULAR; viruses are ACELLULAR -Bacteria can REPLICATE ON THEIR OWN; viruses require a HOST Virion: Virus particles Viroids: infections RNA, plant pathogens Prion: infectious proteins Satellites: A satellite is a sub viral agent composed of nucleic acid that depends on the co- infection of a host cell with a helper or master virus for its multiplication. Phage: something that eats or consumes something else.

List some of the human peptide and proteins synthesized by genetic engineering

Some human peptides and proteins synthesized by genetic engineering include: insulin (for diabetics), alpha1-antitrypsin (used to treat emphysema), blood-clotting factors (used to treat hemophilia), calcitonin (used to trat osteomalacia), epidermal growth factor (used to treat wounds), crythropoietin (used to treat anemia), growth hormone (which promotes growth), interleukins (which treat tumors and immune disorders), macrophage colony stimulating factor (used to treat cancer), relaxin (used to aid in childbirth), serum albumin (a plasma supplement), somatostatin (used to treat acromelagy), streptokinase and tissue plasminogen activator (anticoagulants), and tumor necrosis factor (used to treat cancer).

List tools used in genetic engineering and recombinant DNA technology

Some important tools used in biotechnology and genetic engineering are in silico analysis, DNA microarray analysis, gel electrophoresis, PCR, and RFLP analysis, among others.

What is Beta-Lactam ring and which group of antibiotics contain beta lactam ring? a. What do penicillin, cephalosporin, cyloserine, bacitracin, and vancomycin have in common b. What is the role of beta-lactamase in bacteria resistance to antibiotics 22) Vancomycin and penicillin use different mechanisms to inhibit bacterial cell wall synthesis. True or False

The BETA-LACTAM RING is a crucial feature of PENICILLIN, Beta-lactam binds to and inhibits enzymes responsible for the final step of bacterial CELL WALL SYNTHESIS (transpeptidation). All have beta-lactam ring and all are affective against transpeptidation of the cell wall. Cycloserine: affects synthesis inside Bacitracin: prevents transportation Vancomycin: similar to penicillin, just different site. They act like secondary metabolites. Cephalosporin: Structurally and functionally similar to penicillin broad-spectram antibiotics given to those who are allergic to penicillin. Vancomycin: Glycopeptide antibiotics, inhibit cell wall synthesis by blocking transpeptidation at a different site than penicillin. Last resort for MRSA. Beta-lactamase: Breaks down penicillin breaks down the beta lactam ring. TRUE

Briefly describe the Kirby-Bauer test and its purpose. Describe disk dilution tests, ETest? (Page 192-194) a. Describe techniques used to detect the presence of Drug resistant gene in microorganisms. (Page 192-194)

The Kirby-Bauer method is the standardized method for carrying out DISK DIFFUSION TESTS. This method for determining the sensitivity of a bacterium to a particular antibiotic. The bacterium is allowed to grow on an agar plate until it completely fills the plate. A disk soaked with the antibiotic is then placed on the plate. If the bacterium is insensitive to the antibiotic, the bacteria will simply grow over the disc. However, if the bacterium is sensitive to the antibiotic, growth will be inhibited in a "clear zone" called a zone of inhibition or zone of no growth around the disc. The diameter of the zone of inhibition can be quantified and compared against existing tables to determine whether the drug will be sufficiently effective in the body. ETest is a manual in vitro diagnostic device used by laboratories to determine the MIC, or Minimum inhibitory Concentration, and whether or not a specific strain of fungus or bacterium is susceptible to a particular antimicrobial agent. Spread bacteria on plate, if growth grows around them, antibiotic didn't work on it.

Define One-Step growth cycle? What is the meaning of eclipse period? -No detectable _______ ______ in the cell, although the virus is using the cell's internal machinery to produce the components needed to produce more viruses.

The ONE-STEP GROWTH CYCLE was a technique developed in the 1930s by bacteriophage virologists. It involves exposing bacteria to viruses then diluting the sample enough that no additional host cells will be infected by new viruses. Viruses can then be measured in the sample via plaque assay. The typical one-step vial growth curve is as follows: -Attach or adsorb to cell -Entry Penetration by fusion or endocytosis -Eclipse - infectious virus NOT detectable -Rise - infectious particles detectable During the attachment and penetration period, the virus binds to receptors on the host's cell membrane. During the ECLIPSE PERIOD, there are no detectable infectious viruses in the cell, although the virus is using the cell's internal machinery to produce the components needed to produce more viruses. During the yield period the number of observable infectious viruses in the cell increases as the viruses begin to assemble. During the release period, the number of particles remains high. Eventually, the viruses are liberated from the cell.

Name the tools used to run genomic fingerprinting (RFLP)

The Restriction Fragment Length Polymorphism (RFLP) technique is a tool for genetic fingerprinting, genome mapping, localization of genes, paternity testing, and microbial classification. It takes advantage of the fact that highly conserved and repetitive DNA sequences are present in nearly every genome, including genomes of humans, gram-negative bacteria, and gram-positive bacteria. Basic technique is as follows: 1. Isolate the DNA of interest 2. Amplify the DNA using PCR techniques 3. Cut the DNA up with restriction enzymes, producing restriction fragments. 4. Use gel electrophoresis to separate the restriction fragments according to their lengths on an agarose gel. 5. Use computers to analyze the result.

Define CPE (ctyopathic effects can see visual damage) and give examples. -Viral plaque -Enlargement of either the cell, nucleus, or both. What is syncytia? Paramyxovirus causes the formation of _____________, or single, large cells with multiple nuclei. a. PCRs b. holoblast c. syncytia d. RFLPs e. none of these is correct. 49) Virus host cell interaction results in cytopathic effects (CPE). Examples of CPE includes all of these except: a. Syncytia formation b. Plaque formation c. Alteration of nuclear structure d. Enlargement of cytoplasm e. All of these could be manifestation of CPE

The cytopathic effects (CPE) of a virus on an infected cell specifically refer to the effects of a viral infection that can be VISUALIZED with a microscope. Several cytopathic effects are as follows: -The formation of VIRAL PLAQUE; or a visible area where the virus has destroyed infected cells in a cell culture. -The enlargement of either the CELL (and its cytoplasm), the NUCLEUS, or BOTH. -MEMBRANE changes, such a greater ELASTICITY. (More elastic membranes better allow viruses to exit the cell through budding) -The FUSION of cells, producing a multinucleate cell called a SYNCYTIUM. This essentially produces a more efficient "virus production machine" with more polymerases and ribosomes to be used for the expression of the viral genome. (Dr. Asghari linked this to removing the fences between houses and turning an entire neighborhood into one gigantic compound.) Syncytia are a common cytopathic effect caused by paramyxovirus. c. syncytia e. All of these could be manifestation of CPE -"Leaky" internal organs, such as inclusion bodies, vacuoles, and lysosomes. This can cause damage to the host cell.

Define the human microbiome and explain the role metagenomics plays in its investigation.

The human microbiome is the aggregation of ALL of the microorganisms that reside ON or IN the human body. Metagenomics is the study of metagenomes, or genetic material recovered from environmental samples. Metagenomics can be used to study the composition of the human gut genome through analysis of fecal samples.

Compare and contrast lysogenic vs lytic cycle. A virus could do either, why it chooses one over the other LYSOGENIC CYCLE

The lysogenic cycle (lysogeny) - A phage replication cycle in which the viral genome becomes incorporated in the bacterial host chromosome as a prophage and oes not kill the host. The mechanism by which this occurs is as follows: 1. The phage binds to a surface receptor on the host and injects its DNA into the cell. 2. The DNA of the phage takes a round shape and integrates into the chromosome of the bacteria by crossing over. (Note that an integrated phage is called a prophage. Prophages can stay integrated in the host's DNA for many generations). 3. Occasionally, a biological cue tells the bacterial cell to excise the prophage from the genome. Induction is the process in which the environmental cue causes the prophage to being synthesizing new phage particles. The new phages will eventually enter the lysogenic cycle and kill the host. A virus might by lytic in order to QUICKLY replicate and spread in the population. The problem with this strategy is that the virus could eventually kill all the host cells and effectively be without a host. THEREFORE, a virus might opt for a lysogenic cycle so that the host can survive and the virus can remain integrated in the host. The virus can then begin the process of induction when the environmental conditions are right.

What is the overall purpose of sewage treatment process? a. Why treating sewage is necessary before releasing it in the environment? i. Compare the three stages of sewage treatment process. Which stage removes most of the BOD? What is BOD? ii. What is the role of microbes in this process? iii. What is the purpose of anaerobic sludge digestion? iv. Where in Sewage treatment process methane gas is produced? What do they use methane gas for? v. How septic tank is compared to industrial sewage treatment process?

The overall purpose of water treatment is to reduce the BIOLOGICAL OXYGEN DEMAND (BOD), a measure of the amount of dissolved oxygen required by aerobic biological organisms in a body of water to break down the organic material in the water. The more organic material in the water, the greater the biological oxygen demand and the more stress is put on marine life. Reducing the BOD means that hte sewage will support the growth of less bacteria. Microbes are involved in processing sewage in water treatment plants. Raw sewage goes though the following major rounds of treatment: 1. PRIMARY TREATMENT Physically removing solid organic material. Once this has been done, the sludge is transferred to a large tank called an anaerobic digester, where ANAEROBIC METHANOGENS degrade the organic molecules, producing METHANE as a byproduct. Methane gas burns very clean, and many plants use this gas as an energy source to generate electricity . The liquid portion of the sewage is passed on to secondary treatment. 2. SECONDARY TREATMENT Uses microbes to remove organic material from the liquid portion of the sewage. Three major options for secondary treatment include trickling filtration, activated sludge processing, and the use of large lagoons. (The details of these processes are beyond the scope of this class; just remember that secondary treatment involves the use of microbes to remove organic material from the water.) 3. TERTIARY TREATMENT Involves the removal of inorganic materials. This is achieved through chemical means and not with microbes. 4. DISINFECTION The final step is to disinfect the water to remove all microbes. This can be done, for example, through chlorination. Removal of organic material in the primary and secondary treatment steps of the sewage treatment process reduces the biological oxygen demand. (Primary treatment removes approximately 20% to 30% of the BOD in the particles, and secondary treatment removes about 90% to 95% of the BOD in the dissolved organic matter.) A SEPTIC TANK is simply a holding tank for waste water; it is not really a water treatment system. Solid organic material falls to the bottom of the tank and settle, and the tank has to be periodically emptied after a few years. Microbes do not play a major role in this process. (Septic tanks are somewhat effective, but the overflow still has high biological oxygen demand; this is why areas around a septic tank tend to have extremely green grass.)

Compare three domains of microorganisms. Compare viruses with all other living things Viruses rely on? What does obligate intracellular parasite mean? Organelles? Nuclei? single vs multicellular?

The three domains of life are Archaea, Bacteria, and Eukarya. Research shows that members of these three domains are related. Archaea and Bacteria include PROKARYOTES - single-celled organisms that lack a membrane-enclosed nuclei and membranous organelles. Eukaryotes have membrane-enclosed nuclei and membranous organelles. Eukaryotes also have DIFFERENT RIBOSOMES than prokaryotes and they lack gas vesicles. Moreover, eukaryotic mRNA contains INTRONS and has to be further processed after transcription, while prokaryotic mRNA does not. Viruses, on the other hand, are ACELLULAR and considered NONLIVING, as they rely on the machinery and ENERGY of their HOSTS' cells to live and reproduce. -Sub microscopic -Obligate intracellular parasites with host specificity (rely on the host) -Animals, plants, bacteria, etc...

What is meant by recombinant DNA? Name the tools used to make a recombinant plasmids and genomic libraries. (3 tools) a. What is the purpose (goal) of constructing a genomic library for an organism b. Define metagenomic and its role in identifying microbes that cannot be cultured (isolated) from the environmental samples such as soil and water samples

The tools used to make recombinant plasmids include RESTRICTION ENZYMES, CLONING VECTORS (such as plasmids), and DNA LIGASE. Restriction enzymes cut the DNA of interest and the bacterial plasmid at specific restriction sites, leaving fragments with sticky ends. These sticky ends can base pair with one another, allowing DNA from different sources to be combined. DNA ligase then seals the strands together by catalyzing phosphodiester bonds between the single-strand breaks. The result is recombinant DNA. A genomic library is a collection of an organism's entire genomic DNA, which is stored in a population of identical vectors, each of which has a fragment of the DNA. Just as a library contains multiple books, a genomic library contains multiple vectors, each which contains a fragment of DNA. 1. Extract the DNA from the cell of interest. 2. Use restriction enzymes to cut the DNA into fragments of a specific size. 3. Insert the fragments into a vector. 4. Insert the vector into a host organism, such as E. Coli. 5. Once the vector is inside the host cell, it can be easily amplified or retrieved for analysis. Metagenomics is the study of the collective genomes of the members of a microbial community. It involves cloning and analyzing the genomes without culturing the organisms in the community, thereby offering the opportunity to describe the planet's diverse microbial inhabitants, many of which cannot yet be cultured. -Go to environment, take sample -Have sample with a ton of different organisms. -Grow genes into different plasmids, put them into a cloning vector, then into new host, -one plasmid, one fragment, sequence the fragment, look for function. -trap mosquitos, sequence them, look for virus, look at alot of things through this testing.

List three basic principles of antimicrobial therapy 1. ST 2. ART 3. ABPC 38) The selective toxicity of Sulfa drugs is based on A. The ability of bacteria to synthesize folic acids B. Differences in translation process between eukaryotes and prokaryotes C. None of these explain in the selective toxicity of Sulfa drugs D. Differences in replication process between eukaryotes and prokaryotes Selective toxicity describes one of the characteristics of . . . A. exotoxins B. murein C. ribozymes D. antibodies E. antibiotics

Three general principles of antimicrobial therapy are as follows: -The antimicrobial drug MUST HAVE SELECTIVE TOXICITY for the target microbe. -The antimicrobial drug has to be ABLE to REACH the TARGET at the right concentration. -Once the antimicrobial drug reaches the target cell, it must be ABLE to BIND to and PENETRATE the CELL, avoiding inactivation and extrusion. A. The ability of bacteria to synthesize folic acids E. antibiotics

Give an example of how synergistic drug interaction between two drugs work (Slide 14)

Timetheroprim and sulfonamides (two metabolic antagonists) are often prescribed and used together to make the treatment more efficient. (Septra is the name of the drug that combines the two.) This is an example of a SYNERGISTIC EFFECT in which two drugs working together accomplish more than the additive effect of the two drugs working separately. (You can think of synergy as "2+2=5," rather than the normal additive effects of "2 +2=4.") Another example of synergy occurs in Augmentin, which is an antibiotic that is a combination of amoxicillin and beta-lactamase inhibitor called clavulanate potassium. Yet another example of synergy occurs when Isoniazid (an antimetabolite) is prescribed along the Rifampin (a nucleic acid inhibitor). This combination of drugs is the standard prescription for treatment of tuberculosis (TB).

Explain how one quantifies viruses in laboratory through the following two methods: 1. Plaque assay 2. Hemagglutination assay -HA and NA are spikes on flu virus, enters through endocytosis, RNA comes in, and synthesizes more viruses, released.

Two tools used in virus quantification, or counting the number of viruses in a specific volume to determine the concentration of viruses, are as follows: First is PLAQUE ASSAY - 1. Place a few drops of the host cells (such as bacterial cells) on a plate with soft agar. (The soft agar holds the bacterial cells in place. It is less concentrated than the standard agar you might have used in lab.) 2. Allow the host cells to grow to fill the entire plate. 3. Infect the bacteria with the virus. 4. Count the number of viral plaques, or clear areas where the virus has killed a group of cells through lysis. This techinique allows researchers to count the number of viruses in a known volume of a sample. Second is HEMAGGLUTINATION ASSAY - takes advantage of the fact that hemagglutinin (a surface protein of influenza viruses) causes red blood cells to agglutinate, or clump up. By exposing a solution containing viruses to red blood cells and observing how much they clump up, researchers can QUANTIFY the red blood cells in the sample.

Describe how two-dimensional gel electrophoresis works. What is it used for? Which of the following specifically refers to a technique for detecting radioactively labeled molecules?

Two-dimensional gel electrophoresis uses an electrophoretic gel to separate proteins based on two dimensions: CHARGE and MOLECULAR MASS. (Note that this technique can be used to analyze DNA and RNA fragments in a similar way.) A pH gradient separates proteins by charge using isoelectric focusing, and gravity is used to separate proteins based on molecular mass. A mixture of proteins is first loaded into an isoelectric focusing tube gel, which consists of a pH gradient that separates proteins by charge. The proteins move in the gel until they reach the point where their net charge is ZERO. The isoelectric focusing tube gel is then laid on its side, and the proteins are allowed to migrate from the top of the gel to the bottom of the gel based on their molecular mass. (Smaller proteins will migrate farther down into the gel) The final product of two-dimensional gel electrophoresis is an AUTORADIOGRAPH that has a specific pattern reflecting the charge and molecular mass of the proteins being analyzed. AUTORADIOGRAPHY

How does virus multiplication differ from growing bacteria? (requirements for viral growth vs bacterial growth) What is the role of monolayer in virus multiplication? List other culturing methods used to propagate viruses in laboratory 16) Which of the following is culturing and propagating viruses? A) Embryoted chicken eggs B) Labratory animals C) All of these can be used to propagate viruses D) Monolayer

Viral multiplication differs from bacterial growth in that VIRUSES require a HOST to multiply, whereas BACTERIA have the machinery to MULTIPLY on their OWN. Researchers can propagate viruses in the laboratory by growing them in bacterial cells or in animal cells. A monolayer is a layer of homogenized cells growing side by side. If they are exposed to cancer cells, they will become 'immortal", and can be used to propagate viruses. This idea of growing forever is called hybridoma. Other techniques for propagating viruses include growing viruses in entire organisms or in embryonated chicken eggs. C) All of these can be used to propagate viruses

List the damages inflicted on host cells by viruses What is apoptosis?

Viruses damage or change their host organisms in a number of ways, including the following: -Inducing lysis, which KILLS the cell. -TRANSFORMING the cell's genome -Altering the nuclear or cytoplasmic STRUCTURE of the host, such as by making the nucleus larger, making the cell larger, or causing the cell membrane to become more elastic -Altering gene EXPRESSION in the host, such as by shutting down expression of the host's genes or causing the host to produce gene products from the viral genome -INHIBITING RNA synthesis or the synthesis of proteins -Using the product of transcription (RNA molecules) to construct new viruses rather than in normal gene expression for the host. -Encouraging programmed cell death, or APOPTOSIS, in the host cell

What are icosahedra and helical structures?

Viruses have a number of shapes, but one of the most distinctive shapes that is unique to virus is the icosahedron shape, a polyhedron with 20 triangular faces, 30 edges, and 12 vertices. Another common shape is the helical shape, which consists of a helical array of proteins wrapped around the nucleic acid.

How terms such as sub-microscopic, obligate intracellular parasite, and host specificity characterize viruses.

Viruses have the following characteristics: -They are SUB-MICROSCOPIC. This means that you CANNOT SEE viruses with a microscope because they are so SMALL. -They are OBLIGATE INTRACELLULAR PARASITES. This means that they CANNOT GROW or PRODUCE ENERGY on their OWN; they REQUIRE a HOST to replicate and pass their genetic information on to future generations. -They exhibit HOST SPECIFICITY. This means that specific viruses only attack a SPECIFIC range of ORGANISMS.

What does whole genome shotgun sequencing mean?

Whole genome shotgun sequencing is a method used for sequencing long DNA strands. In shotgun sequencing, DNA is randomly broken up into numerous small segments and is then reassembled by computer programs by looking for regions of overlap. This was the method of genome sequencing that was used to map the human genome.