FINAL EXAM FOCUS GUIDE

Define gene and RNA polymerase.

(SEE FOLLOWING)

Define transduction, transformation, conjugation, competence:

(SEE FOLLOWING)

Describe the defining characteristics of Bacterioides, Thiobacillus, Bacillales, Neisseria, Pseudomonas.

(SEE FOLLOWING)

Explain how serological tests and phage typing can be used to identify an unknown organism.

Serological testing can not only differentiate among microbial species, but also among strains within species. Phage typing is a test used for determining which phages a bacterium is susceptible to. DNA fingerprinting analyzes DNA by electrophoresis of restriction enzyme fragments of the DNA.

TYPES OF BIOCHEMICAL TESTS:

(SEE FOLLOWING)

Describe the functions of plasmids and transposons.

PLASMIDS are self-replicating circular molecules of DNA carrying genes that are not usually essential for the cell's survival. There are several types of plasmids, including conjugative plasmids, dissimilation plasmids, plasmids carrying genes for toxins or bacteriocins, and resistance factors. (p. 235)

Differentiate sign, symptoms, and syndrome.

- Symptoms are a subjective characteristic of disease felt only by the patient (pain, mausea, headache, chills, fatigue, itching) - Signs are objective manifestations of disease observed or measured by others (swelling, rash, vomiting, diarrhea, fever, anemia) - Syndomes are a group of symptoms and signs that characterize a disease or abnormal condition

List Koch's Postulates and the exceptions.

-Same pathogen must be present in every case of the disease -Pathogen must be isolated from the host and grown in pure culture -Pathogen from pure culture must cause disease when inoculated into a healthy, susceptile lab animal -Pathogen must be isolated from inoculated animal and must be shown to be the original organism ***List some exceptions to Koch's postulates*** Unique culture requirements; some pathogens can cause several disease conditions; several different pathogens can cause the same signs and symptoms; some pathogens only infect humans

...there are others too, but didn't focus on them in lab...

...

Describe and understand cultural characteristics (appearance of growth) in Petri plates, agar slants, and broth tubes.

?????

Gene

A segment of DNA that encodes a functional product, usually a protein (ORF)

algae

Algae are any eukaryotes, other than plants, that conduct photosynthesis. They range from single-celled organisms to multicellular seaweeds over 180 feet in length with specialized organs. They are found in most environments, especially very wet ones, perhaps most notably the oceans, where they are the dominant producers.

yeasts

Are unicellular fungi which reproduce asexually by blastoconidia formation (budding) or fission

Thiobacillus

Betaprotobacteria Chemoautotrophic; oxidizes sulfur (H2S -> SO4 2-)

Neisseria

Betaprotobacteria Cocci that usually inhabit mucous membranes of mammals Includes pathogens

Describe how DNA serves as genetic information.

DNA is the blueprint for a cell's proteins and is obtained from a parent cell or from another cell; the structure of DNA helps explain two primary features of biological info storage. -first, the linear sequence of bases provides the actual info -genetic info is encoded by the sequence of bases along the strand of DNA, in much the same way as our written language uses linear sequence of letters to form words and sequences

Bacillales

Firmicute Bacillus (endospore-producing rods) Staphylococcus

Describe five ways of getting DNA into a cell.

Electropration: Uses an electrical current to form microscopic pores in the membranes of the cells. The DNA then enters through these pores. Microinjection: DNA introduced directly into an animal cell. Use a glass micropipette to puncture PM, then inject DNA thru it. Protoplasts: Transformation: genes are transfered from one bacterium to another as "naked" DNA in a solution. Protoplast fusion: method of joining two cells by first removing their cells walls, used in genetic engineering Transformation-plasmid must be entered into a cell. They can take up cells from the surrounding environment.

Conjugation

In bacteria, the direct transfer of DNA between two cells that are temporarily joined.

Provide an example of a latent viral infection.

Latent Infection: provirus generally not actively replicating, remains dormant in live host cell, viral DNA permanently part of host DNA Example: HSV1, HIV and chicken pox virus

Describe inhibition of protein synthesis of antibiotics.

Inhibiting Protein Synthesis When you hear the word 'protein,' you might think of a juicy steak or the protein powder that bodybuilders put into their milkshakes. But anyone who's learned a little bit about cell biology knows that proteins are the workhorses of cells, carrying out tons of essential functions like catalyzing enzymatic reactions, sensing and passing on signals and making important physical structures. Without making proteins, most cells wouldn't be able to carry out their day-to-day functions at all. Many types of antibiotics make use of this fact of life by attempting to prevent bacteria from making proteins. In this lesson, we will take a closer look at how these antibiotics work on a molecular level. Target: Bacterial 70S Ribosome All of the antibiotics that target bacterial protein synthesis do so by interacting with the bacterial ribosome and inhibiting its function. The ribosome might not seem like a very good target for selective toxicity, because all cells, including our own, use ribosomes for protein synthesis. The good thing is that bacteria and eukaryotes have ribosomes that are structurally different. Bacteria have so-called 70S ribosomes and eukaryotes have 80S ribosomes. No, not '70s and '80s ribosomes, although that would be pretty entertaining. The S stands for 'Svedberg unit,' and it refers to the rate at which particles sediment down into the tube during high-speed ultracentrifugation. Basically, it tells us about the ribosome's molecular weight and shape. 70S and 80S ribosomes are different enough that antibiotics can specifically target one and not the other. Let's take a closer look at the bacterial 70S ribosome and see where some different kinds of antibiotics act on it. Remember that ribosomes are made of RNA and protein and that they have two subunits, one large and one small. The bacterial 70S ribosome's subunits are the 50S subunit and the 30S subunit. Yes, I know, 50 + 30 = 80, not 70, but this is not a math mistake. Using the Svedberg unit to measure ribosomes means that things don't always add up perfectly, because rates of sedimentation are not additive like molecular weights are. Before we get into the specifics of how antibiotics inhibit bacterial ribosomes, let's briefly review how ribosomes work. First, a tRNA loaded with a particular amino acid enters the ribosome at the A site. The tRNA's anticodon has to match the codon, or group of three nucleotides on the mRNA. Then, at the P site of the ribosome, a peptide bond forms between the previous amino acid and the new amino acid. Finally, the empty tRNA exits at the E site. This process repeats for the whole length of the mRNA, and the polypeptide chain continues to grow. Antibiotics that Inhibit Ribosomes Okay, let's talk about antibiotics. There are many different antibiotics that all inhibit protein synthesis by interacting with the bacterial 70S ribosome in different ways. We'll go through several examples briefly so that you can get an idea of how these antibiotics really work. Let's start with the tetracyclines. These antibiotics bind to the 30S subunit at the A site and prevent the attachment of tRNAs carrying amino acids. This means that the next bead on the polypeptide string can't be brought into the ribosome. Another antibiotic, chloramphenicol, interacts with the 50S subunit of the ribosome and prevents the formation of peptide bonds. When chloramphenicol is around, the amino acid beads can't be linked together into a polypeptide string. The next class of protein synthesis inhibitors is the aminoglycosides. These seem to have a variety of different mechanisms, but one well-known member of this family is streptomycin, which binds to the 30S subunit and causes the ribosome to misread the genetic code. This could make a well-ordered polypeptide string into a jumbled-up mess that can't carry out its function. The macrolides, such as erythromycin, are thought to inhibit protein synthesis by binding to the 50S subunit and blocking the tunnel where the polypeptide string is supposed to exit. This clogs up the ribosome and stops translation.

Differentiate among persistent viral infections, slow viral infections, latent viral infections.

Persistent viral= infection occurs gradually over a long period, typically they are fatal; Slow viral infection= A slow virus is a virus, or a viruslike agent, etiologically associated with a disease, having a long incubation period of months to years and then a gradual onset of symptoms which progress slowly but irreversibly and terminate in a severe compromised state or, more commonly, death. A slow virus disease is a disease that, after an extended period of latency, follows a slow, progressive course spanning months to years, frequently involving the central nervous system and ultimately leading to death. Examples include the Visna-Maedi virus, in the genus Lentivirus (family Retroviridae), that causes encephalitis and chronic pneumonitis in sheep, and subacute sclerosing panencephalitis which is apparently caused by the measles virus,[1] as well as Pagets Disease of Bone (Osteitis Deformans) which is associated with paramyxoviridae, especially RSV and Rubeola (Measles). Latent infection= is when a virus remains in equilibrium with the host and not actually produce disease for a long period;

Categorize disease according to frequency of occurrence.

Sporadic - only occasionally Endemic - constantly present in a population Epidemic - many people acquire a disease in a in a relatively short period Pandemic - Worldwide epidemic

Describe general characteristics of picornaviruses.

The Picornaviridae family (picornaviruses) causes a wider range of illnesses than most other, if not all, virus families. Infection with various picornaviruses may be asymptomatic or may cause clinical syndromes such as aseptic meningitis (the most common acute viral disease of the CNS), encephalitis, the common cold, febrile rash illnesses (hand-foot-and-mouth disease), conjunctivitis, herpangina, myositis and myocarditis, and hepatitis. The term Picornaviridae is derived from pico, which means small (typically, 18-30 nm), and RNA, referring to the single-stranded positive-sense RNA common to all members of the Picornaviridae family.[3] All members of this family, whose RNA molecules range from 7.2-8.5 kilobases (kb) in size, lack a lipid envelope and are therefore resistant to ether, chloroform, and alcohol. However, ionizing radiation, phenol, and formaldehyde readily inactivate picornaviruses. What are the Picornaviruses? I. Enteroviruses 1. Poliovirus 2. Coxsackie virus A 3. Coxsackie virus B 4. Echovirus 5. Enterovirus (EV-68,-71) II. Rhinovirus 1. 100 different serotypes III. Heprnavirus 1. Hep A Describe the general characteristics of Picornaviruses. (+)ssRNA non-enveloped transmission: • fecal-oral • contaminated food/water

MacConkey agar

This medium is both selective and differential. The selective ingredients are the bile salts and the dye, crystal violet which inhibit the growth of Gram-positive bacteria. The differential ingredient is lactose. Fermentation of this sugar results in an acidic pH and causes the pH indicator, neutral red, to turn a bright pinky-red color. Thus organisms capable of lactose fermentation such as Escherichia coli, form bright pinky-red colonies (plate pictured on the left here). MacConkey agar is commonly used to differentiate between the Enterobacteriaceae.

Differentiate between virus, viroid, and prion.

Virus= Tiny infectious acellular agent having either DNA or RNA (Does not have a cell, but has a genome.) Viroid= Naked RNA molecule which infects plants Prion= Proteinaceous infectious particle that lacks nucleic acids and replicates by converting similar normal proteins into new prions. (mutation caused protein to have different folding properties)

Differentiate between Western blotting and Southern blotting.

Western blot detects protein. Southern detects DNA. Northern detects RNA.

Differentiate between a tick and a mosquito, and name a disease transmitted by each.

a. A tick is in the phylum arthropod, class Arachnida (meaning it has 8 legs). It is not an insect. The Ixodes tick carries Lyme disease. b. Mosquitos is in the phylum arthropod, class insecta (meaning they have sig legs). Mosquitos transmit the West Nile virus.

Differentiate between cDNA and synthetic DNA.

cDNA: complementary DNA; cDNA is what you get from reverse transcription of RNA (mRNA) while genomic DNA is the natural genetic material

Transformation

modification of a cell or bacterium by the uptake and incorporation of extracellular DNA

Define plaque, lawn of bacteria.

plaques on the bacterial lawn= clear areas on a agar plate where bacteria has been infected with phages lyse

Differentiate among eukaryotic, prokaryotic, and viral species.

prokaryotic species: population of cells with similar characteristics eukaryotic species: group of closely related organisms that breed among themselves viral species: population of viruses with similar characteristics that occupies a particular ecological niche

Explain the purpose of Bergey's Manual and differentiate the types.

purpose is to provide phylogenetic [relationship] information on bacteria and archaea; Bergey's Manual of Systematic Bacteriology is the standard reference on bacterial classification and Bergey' s Manual of Determinative Bacteriology is the standard reference for laboratory identification of bacteria; (SEE IMAGE)

Transduction

the process of transfering genetic material from one cell to another by a plasmid or bacteriophage

Describe the defining characteristics of cyanobacteria, fungi, platyhelminths, cestodes, houseflies, algae, archaezoa, microspore, yeasts, helminthes, protozoa.

(SEE FOLLOWING)

Discuss the relationship of DNA- and RNA-containing viruses to cancer.

*~ 10% of cancers are caused by viruses Several DNA viruses are retroviruses and oncogenic. The genetic material of oncogenic viruses become integrated into the host cells DNA. DNA viruses include HPV and Hep. B. Among the RNA viruses only the retroviruses seem to oncogenic. HTLV-1&2 have been found to cause cancer. *Activated oncogenes transform normal cells into cancerous cells *Transformed cells have increased growth, loss of contact inhibition, tumor-specific transplant antigens, and T antigens *The genetic material of oncogenic viruses becomes integrated into the host cell's DNA

Methyl Red (MR)Test:

+Positive methyl red test are indicated by the development of red color after the addition of methyl red reagent. -A negative methyl red test is indicated by no color change after the addition of methyl red reagent

Voges-Proskauer (VP) test:

-Negative test is indicated by lack of color change after the addition of Barritt's A and Barritt's B reagents. +A positive Voges-Proskauer test is indicated by the development of red-brown color after the addition of Barritt's A and Barritt's B reagents.

Understand and explain the streak plate method.

-Objective: To obtain isolated microbial colonies from an inoculum by creating areas of increasing dilution on an agar petriplate. -Principle: The streak plate method is a rapid qualitative isolation method. The techniques commonly used for isolation of discrete colonies initially require that the number of organisms in the inoculums be reduced. It is essentially a dilution technique that involves spreading a loopful of culture over the surface of an agar plate. The resulting diminution of the population size ensures that, following inoculation, individual cells will be sufficiently far apart on the surface of the agar medium to effect a separation of the different species present. Although many type of procedures are performed, the four ways or quadrant streak is mostly done. Procedure (Four Quadrant Streak): 1. Loosen the cap of the bottle containing the inoculum. 2. Hold an inoculation loop in your right hand. 3. Flame the loop and allow it to cool. 4. Lift the test tube containing the inoculum with your left hand. 5. Remove the cap/ cotton wool plug of the test tube with the little finger of your right hand. 6. Flame the neck of the test tube. 7. Insert the loop into the culture broth and withdraw. At all times hold the loop as still as possible. 8. Flame the neck of the test tube again. 9. Replace the cap/ cotton wool plug of the test tube using the little finger of your right hand. 10. Place the test tube in a rack. For a liquid culture, dip the loop into the broth, or for solid media, lightly touch a colony with the loop. 11. Partially lift the lid of the Petri dish containing the solid medium. 12. Place a loopful of the culture on the agar surface on the area 13. Flame the loop and cool it for 5 seconds by touching an unused part of the agar surface close to the periphery of the plate, and then drag it rapidly several times across the surface of area1. 14. Remove the loop and close the Petri dish. 15. Reflame and cool the loop, and turn the petri dish 90°C then touch the loop to a corner of the culture in area1 and drag it several times across the agar in area 2, hitting the original streak a few times. The loop should never enter area 1 again. 16. Remove the loop and close the Petri dish. Reflame and cool the loop and again turn the dish 90°C anticlockwise. streak area 3 in the same manner as area 2, hitting last area several times. 17. Remove the loop and close the Petri dish. 18. Flame the loop, again turn the dish 90°C and then drag the culture from a corner of a area3 across area 4, contacting area 3 several times and drag out the culture as illustrated. Using a wider streak. Do not let the loop touch any of the previously streaked areas. The flaming of the loop at the points indicated is to effect the dilution of the culture so that fewer organisms are streaked in each area, resulting in the final desired separation. 19. Remove the loop and close the Petri dish. 20. Tape the plate closed and incubates the plate in an inverted position in an incubator for 24-48 hours. 21. Flame the loop before putting it aside.

Identify five modes of action of antimicrobial drugs.

1) INHIBITION OF CELL SYNTHESIS ex: penicillin (natural vs semisynthetic) - prevent the synthesis of intact peptidoglycan which makes up the cell wall of bacterium - cell walls becomes weakend and the cell undergoes lysis - only actively growing cells are affected by these antibiotics - since human cells dont have peptidoglycan cell walls, penicillin has very little toxicity for host cells 2) INHIBITION OF PROTEIN SYNTHESIS ex: tetracyclines - broad-spectrum antibiotics produced by streptomyces spp - target 70s prokaryotic ribosome by interfereing w/ attachment of tRNA to mRNA 3) INHIBITION OF NUCLEIC ACID REPLICATION AND TRANSCRIPTION - many antibiotics interfere w/ the processes of DNA replication and transcription in microbes - drugs that can do that have limited usefullness cuz they interfere w/ mammalian DNA and RNA as well 4) INJURY TO PLASMA MEMBRANE ex: polypeptide antibiotics - change the permeability of the plasma membrane that result in the loss of important metabolities from the microbial cell ) COMPETITIVE INHIBITORS OF BACTERIAL ENZYME FXN - some enzymatic activity of a microorganism can be competitively inhibited by a substance that closely resembles the normal substrate for the enzyme ex: sulfonamides (sulfa drug) - bacteriostatic in action - resembles para-aminobenzoic acid (PABA) - Sulfonamides competitively inhibits PABA - PABA is the substrate for an enzymatic reaction that leads to the snthesis of folic acid (in bacteria, not in ppl)

Describe biochemical tests that differentiate staphylococcus aureus from staphylococcus epidermis. ***How do you differentiate S. aureus from S epidermis?*** (what tests would you use -2 )

1) coagulase test 2) sugar fermentation test ***RESULTS OF THESE TESTS WOULD BE:*** What would be the difference between S. aureus and S. epidermidis on the coagulase test? S. aureus - positive S. epidermidis - negative What would be the difference between S. aureus and S. epidermidis on the sugar fermentation test? S. aureus - ferment mannitol S. epidermidis - can not ferment mannitol

microspore

A spore from a heterosporous plant species that develops into a male gametophyte

Describe how a gene library is made.

Gene libraries: can be made by cutting up the entire genome with restriction enzymes and inserting the fragments into bacterial plasmids or phages. They make a colletion of clones large enough to ensure that at least one clone exists for every gene in the organism. a collection of bacterial or phage clones each contains a portion of the genetic material of interest, each clone contains one gene of an organism's genome, may contain all genes of a single chromosome, may contain set of cDNA complentary to mRNA When choosing a gene, it has both exons(stretches of DNA that code for protein) and introns(stretches that do not) Introns are removed because the introns make the gene too large to work with.

Describe the characteristics of antifungal drugs.

An antifungal medication is a pharmaceutical fungicide or fungistatic used to treat and prevent mycoses such as athlete's foot, ringworm, candidiasis (thrush), serious systemic infections such as cryptococcal meningitis, and others. Such drugs are usually obtained by a doctor's prescription, but a few are available OTC Antifungals work by exploiting differences between mammalian and fungal cells to kill the fungal organism with fewer adverse effects to the host. Unlike bacteria, both fungi and humans are eukaryotes. Thus, fungal and human cells are similar at the biological level. This makes it more difficult to discover drugs that target fungi without affecting human cells. As a consequence, many antifungal drugs cause side-effects. Some of these side-effects can be life-threatening if the drugs are not used properly. Target of anti-fungal drugs: Ergosterol Some Types/mechanism of action: Amphotericin B Binding to membrane ergosterol Nystatin Binding to membrane ergosterol Miconazole Inhibiting lanosterol demethylase (inhibiting ergosterol synthesis) Fluconazole Inhibiting lanosterol demethylase (inhibiting ergosterol synthesis) Terbinafine Inhibiting squalene epoxidase (inhibing ergosterol synthesis) Flucytosine Inhibiting thymidylate synthase Griseofulvin Disrupts the mitotic spindle Caspofungin Disrupts the cell wall

Describe the process of DNA replication.

During DNA replication, the two strands of the double helix separate at the replication fork, and each strand is used as a template by DNA polymerases to synthesize two new strands of DNA according to the rules of nitrogenous base pairing. The result of DNA replication is two new strands of DNA, each having a base sequence complementary to one of the original strands. Because each double-stranded DNA molecule contains one original and one new strand, the replication process is called semiconservative. DNA is synthesized in one direction designated 5' -> 3'. At the replication fork, the leading strand is synthesized continuously and the lagging strand discontinuously. DNA polymerase proofreads new molecules of DNA and removes mismatched bases before continuing DNA synthesis. Each daughter bacterium receives a chromosome that is virtually identical to the parent's.

Compare and contrast viral and bacterial multiplication.

Bacteria contain the genetic blueprint (DNA) and all the tools (ribosomes, proteins, etc.) they need to reproduce themselves. Viruses are "moochers." They contain only a limited genetic blueprint and they don't have the necessary building tools. They have to invade other cells and hijack their cellular machinery to reproduce. Viruses invade by attaching to a cell and injecting their genes or by being swallowed up by the cell. Viruses do not contain enzymes for energy production or protein synthesis. For a virus to multiply, it must invade a host cell and direct the host's metabolic machinery to produce viral enzymes and components Viruses must have a living host to multiply, such as a plant or animal. Meanwhile, most bacteria can grow on non-living surfaces.[6] Bacteria have all the "machinery" (cell organelles) needed for their growth and multiplication and usually reproduce asexually. By contrast, viruses generally carry information - for example, DNA or RNA, packaged in a protein and/or membranous coat. They need the host cell's machinery to reproduce. The "legs" of a virus attach onto the surface of the cell and then the genetic material contained inside the virus is injected into the cell. Put differently, viruses are not really "living", but are essentially information (DNA or RNA) that float around until they encounter a sufficient host.

List the characteristics of the Bacteria, Archaea, and Eukarya domains.

Bacteria- prokaryotic, cell wall contains peptidoglycan, membrane lipids are composed of straight carbon chains attached to glycerol by ester linkage, first amino acid in protein synthesis-formylmethionine, antibiotic sensitivity, rRNA loop is present, common arm of tRNA is present archaea- prokaryotic, cell wall varies in composition; contains no peptidoglycan, membrane lipids are composed of branched carbon chains attached to glycerol by ether linkage, first amino acid in protein synthesis is methionine, no antibiotic sensitivity, rRNA loop is lacking and common arm of tRNA is lacking eukarya- eukaryotic, cell wall varies in composition; contains carbohydrates, composed of straight carbon chains attached to glycerol by ester linkage, first amino acid in protein synthesis is methionine, no antibiotic resistance, rRNA loop is lacking, Common arm of tRNA is present

Describe protein synthesis, including transcription, RNA processing, and translation.

During TRANSCRIPTION, the enzyme RNA polymerase synthesizes a strand of RNA from one strand of double-stranded DNA, which serves as a template. RNA is synthesized from nucleotides containing the bases A, C, G, and U, which pair with the bases of the DNA strand being transcribed. RNA polymerase binds the promoter; transcription begins at AUG; the region of DNA that is the end point of transcription is the terminator; RNA is synthesized in the 5' -> 3' direction.

Explain how capsules and cell wall components contribute to pathogenicity.

Capsules around cell walls increase the organism's virulence. The capsule protects the pathogen from phagocytosis by resisting the host's defenses. Capsules - can prevent phagocytosis When the body produces antibodies against the capsule then phagocytosis is efficient; Capsules - formed by glycocalyx material, resists hosts defenses and prevents phagocytosis Cell wall components - chemical substances contribute to virulence (M protein is heat and acid-resistant/mediates attachment; waxy lipid resists phagocytosis)

cestodes

Cestoda is a class of parasitic flatworms, of the phylum Platyhelminthes. Biologists informally refer to them as cestodes. The best-known species are commonly called tapeworms. cestodes Cestodes (tapeworms) Taenia- tapeworms - cause intestinal infections in animals. Infections caused by ingestion of infected meat (beef, fish, pork). If meat is improperly prepared (for example undercooked), ingestion of a larval stage embedded in the infected meat can result in a tapeworm infected in the human. Beef and fish tapeworm infections tend to have mild to no symptoms. Pork tapeworm infections can sometime lead to serious infections in humans. See below. Taenia solium - pork tapeworm Larval stage in human host called cysticercus can develop in many human organs other than skeletal muscle - when found in eye and brain can be very serious causing neurocysticercosis resulting in blindness and sometimes death - Endemic to Central and South America

Compare and contrast the multiplication cycle of DNA- and RNA-containing animal viruses.

DNA: 1) Attachment- virion attaches to host cell. 2) Entry and Uncoating- virion enters cell, and its DNA is uncoated. 3) A portion of viral DNA is transcribed, producing mRNA that encodes early viral proteins. 4) Biosynthesis- Viral DNA is replicated, and some viral proteins are made. 5) Late translation: Capside proteins are synthesized. 6) Maturation- virions mature. 7) Release- virions are released. RNA: 1) Attachment 2) Entry and uncoating- ssRNA: + or sense strand, ssRNA: - or antisense strand, dsRNA: + or sense strand with - or antisense strand 3) RNA replication by viral RNA-dependent RNA polymerase. 4) Translation and synthesis of viral proteins 5) Maturation and release.

Coagulase test

Coagulase is an enzyme that clots blood plasma. This test is performed on Gram-positive, catalase positive species to identify the coagulase positive Staphylococcus aureus. Coagulase is a virulence factor of S. aureus. The formation of clot around an infection caused by this bacteria likely protects it from phagocytosis. This test differentiates Staphylococcus aureus from other coagulase negative Staphylococcus species.

Compare commensalism, mutualism, symbiosis, and parasitism, and give an example of each.

Commensalism - Symbiotic relationship in which one organism benefits and the other is unaffected (S. epidermis) Mutualism - Benefits both organisms (E. coli synthesizes vitamins K and B) Parasitism - One organism benefits at the expense of the other (disease-causing)

cyanobacteria

Cyanobacteria all live in aquatic environments and use photosynthesis to make their own food. Additionally, all cyanobacteria belong to the larger class of bacteria, which is one of the largest groups of organisms. Most cyanobacteria are unicellular, and they typically live in large colonies.

Describe how a new bacterium can be classified by the following molecular methods: DNA base composition, rRNA sequencing, DNA fingerprinting, PCR, and nucleic acid hybridization.

DNA base composition-this base composition is usually expressed as the percentage of guanine plus cytosine (G + C). The base composition of a single species is theoretically a fixed property; thus, a comparison of the G + C content in different species can reveal the degree of species relatedness. DNA fingerprinting-used to determine the source of hospital-acquired infections. In one hospital, patients undergoing coronary-bypass surgery developed infections caused by Rhodococcus bronchialis. The DNA fingerprints of the patients' bacteria and the bacteria of one nurse were identical. The hospital was thus able to break the chain of transmission of this infection by encouraging this nurse to use aseptic technique. PCR-(polymerase chain reaction) used to increase the amount of microbial DNA to levels that can be tested by gel electrophoresis nucleic acid hybridization:???

Differentiate between an intermediate host and a definitive host and give an example of what parasite stage is seen in humans as intermediate and definitive hosts.

Definitive (primary) host: The organism in which a parasite reaches reproductive maturity. a primary host or definitive host is a host in which the parasite grows mature; a secondary host or intermediate host is a host that harbors the parasite only for a short transition period. For trypanosomes, the cause of sleeping sickness, humans are the primary host, while the tsetse fly is the secondary host. Intermediate host: An organism infected by a parasite while the parasite is in a developmental form, not sexually mature. an intermediate host is an organism inside which a parasite does not sexually reproduce. It may grow or reproduce asexually, but there is no exchange of genetic material between individuals. The host in which the parasite reproduces sexually is the definitive host. For example, the broad fish tapeworm Diphylobothrium latum develops in fish for part of its life cycle but only reproduces sexually when it is in a mammal digestive tract, so its intermediate host is the fish and its definitive host is the mammal. ***Examples of what parasite stage is seen in humans as intermediate and definitive hosts*** -Adult stage in definitive host. -Each larval stage in specific intermediate host.

Define, and give examples of, zoonosis.

Diseases that spread naturally from their usual animal hosts to humans are called zoonoses or zoonotic diseases The routes of transmission of zoonotic diseases are: 1.Bloodsucking arthropods 2. Contact 3. Eating animals Which one is the main mode of transmission of zoonotic diseases? Ex Blood sucking arthropods. - Lyme disease (deer to tick to human) - West nile disease (birds to mosquito to human) Contact route of transmission of zoonotic diseases involve: Direct contact with infected animal (touching) or, Direct contact with infected animal wastes or mucous (bird flu) Eating animals as a route of transmission of zoonotic diseases involve: Consumption of animals that are infected example: mad cause disease Why are humans considered dead-end hosts for zoonotic pathogens? Because we are not the desired hosts and can not act as a reservoir for further infection If a human is infected the disease will not spread anymore. (dead end) Example: deer, tick, human. end

Discuss how genetic mutation and recombination provide material for natural selection to act on.

Diversity is the precondition for evolution Genetic mutation and recombination provide a diversity of organisms, and the process of natural selection allows the growth of those best adapted to a given environment.

Name the microbes that produce most of the antibiotics.

GRAM + 1) bacillius subtilis 2) paenibacillus polymxa ACTINOMYCETES 1) streptomyces nodosus 2) streptomycems venezuelae 3) streptomycems aureofaciens 4) saccharopalyspora erythrae 5) streptomycems fradiae 6) streptomycems griseus 7) micromonospora purpurea FUNGI 1) cephalosporium spp 2) penicillium griseofulvum 3) penicillium chrysogenum

Identify the IMViC reactions for E. coli.

Each of the letters in "IMViC" stands for one of these tests. "I" is for indole; "M" is for methyl red; "V" is for Voges-Proskauer, and "C" is for citrate, lowercase "i" is added for ease of pronunciation. IMViC is an acronym that stands for four different tests: -Indole test -Methyl red test -Voges-Proskauer test -Citrate utilization test To obtain the results of these four tests, three test tubes are inoculated: tryptone broth (indole test), methyl red - Voges Proskauer broth (MR-VP broth), and citrate. IMViC tests are employed in the identification/differentiation of members of family enterobacteriaceae. Cultures of any members of enterobacteriaceae have to grow for 24 to 48 hours at 37°C and the respective tests can be performed: ***********REACTIONS FOR E. coli:************(see following slides for how things will react) IMViC tests of Escherichia coli Indole: Positive + Methyl-Red: Positive + Voges-Proskauer test: Negative - Citrate test: Negative -

Pseudomonas

Gammaprotobacteria Pseudomonas Opportunistic pathogens Metabolically diverse Polar flagella Soil and nature

Discuss the causes of symptoms in fungal, protozoan, helminthic, and algal disease.

Fungal infections- can be caused by capsules, toxins, and allergic responses. Protozoan and helminths-can be caused by damage to host tissue of by the metabolic waste products of the parasite. some protozoa change their surface antigens while growing in a host, thus avoiding destruction by the hosts antibodies. algae-produce neurotoxins that cause paralysis when ingested by humans.

fungi

Fungi are eukaryotes. They reproduce by means of spores, and they reproduce both sexually and asexually. They are nonvascular, and they are heterotrophic. Fungi store their food as starch. They have a small nucleus. They digest their food before they ingest it. They are nonmotile. They have cell walls composed of chitin.

List the major characteristics used to differentiate the three kingdoms of multicellular Eukarya.

Fungi, plants, and animals make up the three kingdoms of more complex eukaryotic organisms, most of which are multicellular: Fungi: 1. Organism that belongs to Kingdom { }, & eukayortic. 2. Unicellular yeasts, multicellular molds, & macroscopic species such as mushrooms. To obtain raw materials for vital functions, "it" absorbs dissolved organic matter through its plasma membrane. The cells of a multicellular { } are commonly joined to form thin tubes- hyphae- which are usually divided into multinucleated units by cross-walls that have holes, so cytoplasm can flow between the cell-like units. { } develop from spores or from fragments of hyphae. Plantae (plants): (Eukayortic- all multicellular). The Kingdom { } includes some algae and all mosses, ferns, conifers, and flowering plants. To obtain energy, it uses photosynthesis, the process that converts carbon dioxide and water into organic molecules used by the cell. Has cellulose cell walls. Animalia (Animals): (Eukayortic- all multicellular). The Kingdom { } includes sponges, various worms, insects, and animals with backbones (vertebrates). They obtain nutrients and energy by ingesting organic matter through a mouth of some kind. Lacks cell walls. Protista: (***NOT PART OF EUKARYA***) Protists (unicellular eukaryotes and their close relatives.) Unicellular & simple multicellular eukaryotes; usually protozoa & algea. -In 1969, simple eukaryotic organisms, mostly unicellular, were grouped as the Kingdom { }, a catchall kingdom for a varietyof organisms. Historically, eukaryotic organisms that didn't fit into other kingdoms were placed in the { }.

Discuss general characteristics of viruses and general taxonomy of viruses.

General characteristics of viruses: 1) obligatory intracellular parasites 2) filterable: can pass through bacterial filters 3) contain DNA OR RNA 4) contain a protein coat 5) some may be enclosed by an envelope 6) most are tissue specific General taxonomy of viruses: How are viruses classified? They are classified into families. What name do viruses end in? Viridae How many RNA and DNA viruses are there? 14 RNA virus families • 13 ssRNA • 1 dsRNA 8 DNA virus families • 7 dsDNA • 1 ssDNA How are the different classifications named? • Genus - Each family has numerous genera - Ends in virus e.g. Enterovirus • Species - Name of the disease virus causes e.g. poliovirus causes polio - italicized • Types - Each species contains numerous types e.g. Rhinovirus contains 100 types Why are there so many different types of species? They each have different antigens. Like the Rhinovirus

Discuss the advantages of the three-domain system.

bacteria (prok, PG), archea (prok, no PG), eukarya (euk) Classified by cell type, cell wall, rRNA, membrane lipid structure, tRNA, sensitivity to antibiotics; Ribosomes are present in all cells. The three domains provide a method of comparing cells. It also allows us to see the order in life. all organisms evolved from cells that formed over 3 billion years ago, the DNA passed on from ancestors is described as conserved, ribosomes are not the same in all cells-showed they are distinctly different cell groups

protozoa

In some systems of biological classification, the Protozoa are a diverse group of unicellular eukaryotic organisms. Historically, protozoa were defined as single-celled organisms with animal-like behaviors, such as motility and predation.

Define operon.

In bacteria, a group of coordinately regulated structural genes with related metabolic functions, plus the promoter and operator sites that control their transcription In the operon model for an inducible system, a regulatory gene codes for the repressor protein. When the inducer is absent, the repressor binds to the operator, and no mRNA is synthesized. On the other hand, when the inducer is present, it binds to the repressor so that it cannot bind to the operator; thus, mRNA is made, and enzyme synthesis is induced. In repressible systems, the repressor requires a corepressor in order to bind to the operator site; thus, the corepressor controls enzyme synthesis.

Describe the lysogenic cycle of bacteriophage lambda.

In contrast, the lysogenic cycle does not result in immediate lysing of the host cell. Those phages able to undergo lysogeny are known as temperate phages. Their viral genome will integrate with host DNA and replicate along with it fairly harmlessly, or may even become established as a plasmid. The virus remains dormant until host conditions deteriorate, perhaps due to depletion of nutrients; then, the endogenous phages (known as prophages) become active. At this point they initiate the reproductive cycle, resulting in lysis of the host cell. As the lysogenic cycle allows the host cell to continue to survive and reproduce, the virus is reproduced in all of the cell's offspring. An example of a bacteriophage known to follow the lysogenic cycle and the lytic cycle is the phage lambda of E. coli. 1) Phage attaches to host cell and injects DNA 2) Phage DNA circularizes and enters lysogenic cycle. 3) Phage DNA integrates within the bacterial chromosome by recombination, becoming a prophage. 4) Lysogenic bacterium reproduces normally. 5) Many cell divisions. 6) Occasionally, the prophage may excise from the bacterial chromosome by another recombination event, initiating a lytic cycle.

Indole test:

It is performed on sulfide-indole-motility (SIM) medium or in tryptophan broth. Result is read after adding Kovac's reagent. +The positive result is indicated by the red layer at the top of the tube after the addition of Kovács reagent. -A negative result is indicated by the lack of color change at the top of the tube after the addition of Kovács reagent.

Discuss biosynthesis of bacteriophage.

Once the bacteriophage DNA has reached the cytoplasm of the host cell, the biosynthesis of viral nucleic acid and protein occurs. Host protein synthesis is stopped by virus-induced degradation of the host DNA, viral proteins that interfere with transcription, or the repression of translation. ***(SEE PG. 397)***

Define normal and transient microbiota.

Normal - Microorganisms that colonize but do not produce disease Transient - Appear for several days, weeks, or months and then disappear

platyhelminths

Platyhelminthes are small worms with flattened body plans and simple organs of seemingly ancient origin. Individual species in this group are called flatworms or tapeworms, indicating their distinct body shape.

Outline the PCR process and provide an example of its use.

Polymerase chain reaction (PCR) used to make multiple copies of a desired piece of DNA enzymatically. 1. denaturation: DNA incubated at high temp (94c) which breaks hydrogen bonds of DNA 2. Priming: DNA incubated at relatively low temp allows primerers to attach to single stranded target DNA 3. extension: DNA incubated at intermediate temp, DNA polymerase rapidly replicates DNA 4. DNA present doubles after each round. After 30 rounds, amplified by more than a billion times. PCR used to increase the amounts of DNA in samples to detectable levels.

Define restriction enzymes, and outline how they are used to make recombinant DNA.

Restriction enzymes cut specific sequences of DNA; destroy bacteriophage DNA in bacterial cells; cannot digest (host) DNA with methylated cytosines. if phages were used to infect bacteria other than their usual hosts, restriction enzymes in the new host deserted almost all phage DNA. restriction enzymes protect a bacterial cell by hydrolyzing phage DNA. the bacterial DNA is protected from digestion because the cell methylates some of the cytosines in its DNA.

Compare selection and mutation.

SELECTION: culture a naturally occurring microbe that produces the desired product VS. MUTATION: mutagens cause mutations that might result in a microbe with a desirable trait; site-directed mutagenesis: change a specific DNA code to change a protein

archaezoa

Summary The taxon Archezoa was proposed to unite a group of very odd eukaryotes that lack many of the characteristics classically associated with nucleated cells, in particular the mitochondrion. The hypothesis was that these cells diverged from other eukaryotes before these characters ever evolved, and therefore they repre- sent ancient and primitive eukaryotic lineages. The kingdom comprised four groups: Metamonada, Microsporidia, Parabasalia, and Archamoebae. Until re- cently, molecular work supported their primitive status, as they consistently branched deeply in eukaryotic phylogenetic trees. However, evidence has now emerged that many Archezoa contain genes derived from the mitochondrial symbiont, revealing that they actually evolved after the mitochondrial symbiosis. In addition, some Archezoa have now been shown to have evolved more recently than previously believed, especially the Microsporidia for which considerable evidence now indicates a relationship with fungi. In summary, the mitochondrial symbiosis now appears to predate all Archezoa and perhaps all presently known eukaryotes.

Compare the mechanisms of genetic, recombination in bacteria.

TRANSFORMATION: During this process, genes are transferred from one bacterium to another as "naked" DNA in solution. This process occurs naturally among a few genera of bacteria. CONJUGATION: process where one bacterium transfers genetic material to another; requires contact between living cells. One type of genetic donor cell is an F+; recipient cells are F-. F cells contain plasmids called F factors; these are transferred to the F- cells during conjugation. When the plasmid becomes incorporated into the chromosome, the cell is called an Hfr (high frequency of recombination) cell. Now, during conjugation, an Hfr cell can transfer chromosomal DNA to an F- cell. Usually, the Hfr chromosome breaks before it is fully transferred. TRANSDUCTION: In this process, DNA is passed from one bacterium to another in a bacteriophage and is then incorporated into the recipient's DNA. In generalized transduction, any bacterial genes can be transferred.

Oxidase Test

This test is used to identify microorganisms containing the enzyme cytochrome oxidase (important in the electron transport chain). It is commonly used to distinguish between oxidase negative Enterobacteriaceae and oxidase positive Pseudomadaceae. Cytochrome oxidase transfers electrons from the electron transport chain to oxygen (the final electron acceptor) and reduces it to water. In the oxidase test, artificial electron donors and acceptors are provided. When the electron donor is oxidized by cytochrome oxidase it turns a dark purple. This is considered a positive result. In the picture below the organism on the right (Pseudomonas aeruginosa) is oxidase positive.

Catalase Test

This test is used to identify organisms that produce the enzyme, catalase. This enzyme detoxifies hydrogen peroxide by breaking it down into water and oxygen gas. The bubbles resulting from production of oxygen gas clearly indicate a catalase positive result. The sample on the right below is catalase positive. The Staphylococcus spp. and the Micrococcus spp. are catalase positive. The Streptococcus and Enterococcus spp. are catalase negative.

Explain the regulation of gene expression in bacteria by induction, repression, feedback inhibition, and catabolic repression, using the lac operon as an example.

The Regulation of Bacterial Gene Expression 1. Regulating protein synthesis at the gene level is energy-efficient because proteins are synthesized only as they are needed. 2. Constitutive enzymes produce products at a fixed rate. Examples are genes for the enzymes in glycolysis. 3. For these gene regulatory mechanisms, the control is aimed at mRNA synthesis. REPRESSION: controls the synthesis of one or several (repressible) enzymes. When cells are exposed to a particular end-product, the synthesis of enzymes related to that product decreases. INDUCTION: In the presence of certain chemicals (inducers), cells synthesize more enzymes. Ex of Induction: the production of B-galactosidase by E. coli in the presence of lactose; lactose can then be metabolized. CATABOLITE REPRESSION: Transcription of structural genes for catabolic enzymes (such as B-galactosidase) is induced by the absence of glucose. Cyclic AMP and CRP must bind to a promoter in the presence of an alternative carbohydrate. Note: The presence of glucose inhibits the metabolism of alternative carbon sources by catabolite repression.

Diagram the Southern blot procedure and provide an example of its use.

The Southern Blot procedure breaks DNA into fragments using a restriction enzyme, runs the fragments on a gel, and then uses a specific labeled sequence as a probe. The DNA sequences are spaced out on the gel by length. The shortest sequence travels the furthest distance and the longest sequence travels the shortest distance. The pattern of bands is thus entirely due to the number and location of the restriction sites where the DNA is cut. The addition or loss of a single restriction site can place the target sequence in a new band on the gel even when the rest of the DNA is unchanged. Example animation: https://highered.mheducation.com/sites/9834092339/student_view0/chapter17/southern_blot.html

Mannitol Salt Agar (MSA)

This type of medium is both selective and differential. The MSA will select for organisms such as Staphylococcus species which can live in areas of high salt concentration (plate on the left in the picture below). This is in contrast to Streptococcus species, whose growth is selected against by this high salt agar (plate on the right in the picture below). The differential ingredient in MSA is the sugar mannitol. Organisms capable of using mannitol as a food source will produce acidic byproducts of fermentation that will lower the pH of the media. The acidity of the media will cause the pH indicator, phenol red, to turn yellow. Staphylococcus aureus is capable of fermenting mannitol (left side of left plate) while Staphylococcus epidermidis is not (right side of left plate).

Describe the spectrum of antibiotic activity.

The range of bacteria that an antibiotic affects can be divided into narrow spectrum and broad spectrum: -Narrow spectrum antibiotics act against a limited group of bacteria, either gram positive or gram negative, for example sodium fusidate only acts against staphylococcal bacteria. USES OF NARROW SPECTRUM ANTIBIOTICS:2 Narrow spectrum antibiotics are used for the specific infection when the causative organism is known. ADVANTAGES OF NARROW SPECTRUM ANTIBIOTICS:2 The narrow-spectrum antibiotic will not kill as many of the normal microorganisms in the body as the broad spectrum antibiotics. So, It has less ability to cause superinfection. The narrow spectrum antibiotic will cause less resistance of the bacteria as it will deal with only specific bacteria. DISADVANTAGES OF NARROW SPECTRUM ANTIBIOTICS: Narrow spectrum antibiotics can be used only if the causative organism is identified. If you don't choose the drug very carefully, the drug may not actually kill the microorganism causing the infection. NARROW SPECTRUM ANTIBIOTICS: Azithromycin Clarithromycin Clindamycin Erythromycin Vancomycin -Broad spectrum—antibiotics act against gram positive and gram negative bacteria, for example amoxicillin; A broad-spectrum antibiotic acts against both Gram-positive and Gram-negative bacteria, in contrast to a narrow-spectrum antibiotic, which is effective against specific families of bacteria. An example of a commonly used broad-spectrum antibiotic is ampicillin.

Citrate utilization test:

The test is performed on Simmons citrate agar: Negative citrate utilization test is indicated by the lack of growth and color change in the tube A positive citrate result as indicated by growth and a blue color change.

Blood Agar Plates (BAP)

This is a differential medium. It is a rich, complex medium that contains 5% sheep red blood cells. BAP tests the ability of an organism to produce hemolysins, enzymes that damage/lyse red blood cells (erythrocytes). The degree of hemolysis by these hemolysins is helpful in differentiating members of the genera Staphylococcus, Streptococcus and Enterococcus. Beta-hemolysis is complete hemolysis. It is characterized by a clear (transparent) zone surrounding the colonies. Staphylococcus aureus, Streptococcus pyogenes and Streptococcus agalactiae are b-hemolytic (the picture on the left below shows the beta-hemolysis of S. pyogenes). Partial hemolysis is termed alpha-hemolysis. Colonies typically are surrounded by a green, opaque zone. Streptococcus pneumoniae and Streptococcus mitis are a-hemolytic (the picture on the right below shows the a-hemolysis of S. mitis). If no hemolysis occurs, this is termed gamma-hemolysis. There are no notable zones around the colonies. Staphylococcus epidermidis is gamma-hemolytic.

Glucose broth with Durham tubes

This is a differential medium. It tests an organism's ability to ferment the sugar glucose as well as its ability to convert the end product of glycolysis, pyruvic acid into gaseous byproducts. This is a test commonly used when trying to identify Gram-negative enteric bacteria, all of which are glucose fermenters but only some of which produce gas. Like MSA, this medium also contains the pH indicator, phenol red. If an organism is capable of fermenting the sugar glucose, then acidic byproducts are formed and the pH indicator turns yellow. Escherichia coli is capable of fermenting glucose as are Proteus mirabilis (far right) and Shigella dysenteriae (far left). Pseudomonas aeruginosa (center) is a nonfermenter. The end product of glycolysis is pyruvate. Organisms that are capable of converting pyruvate to formic acid and formic acid to H2 (g) and CO2 (g), via the action of the enzyme formic hydrogen lyase, emit gas. This gas is trapped in the Durham tube and appears as a bubble at the top of the tube. Escherichia coli and Proteus mirabilis (far right) are both gas producers. Notice that Shigella dysenteriae (far left) ferments glucose but does not produce gas. *Note - broth tubes can be made containing sugars other than glucose (e.g. lactose and mannitol). Because the same pH indicator (phenol red) is also used in these fermentation tubes, the same results are considered positive (e.g. a lactose broth tube that turns yellow after incubation has been inoculated with an organism that can ferment lactose).

Methyl Red / Voges-Proskauer (MR/VP)

This test is used to determine which fermentation pathway is used to utilize glucose. In the mixed acid fermentation pathway, glucose is fermented and produces several organic acids (lactic, acetic, succinic, and formic acids). The stable production of enough acid to overcome the phosphate buffer will result in a pH of below 4.4. If the pH indicator (methyl red) is added to an aliquot of the culture broth and the pH is below 4.4, a red color will appear (first picture, tube on the left). If the MR turns yellow, the pH is above 6.0 and the mixed acid fermentation pathway has not been utilized (first picture, tube on the right). The 2,3 butanediol fermentation pathway will ferment glucose and produce a 2,3 butanediol end product instead of organic acids. In order to test this pathway, an aliquot of the MR/VP culture is removed and a-naphthol and KOH are added. They are shaken together vigorously and set aside for about one hour until the results can be read. The Voges-Proskauer test detects the presence of acetoin, a precursor of 2,3 butanediol. If the culture is positive for acetoin, it will turn "brownish-red to pink" (tube on the left in the second picture). If the culture is negative for acetoin, it will turn "brownish-green to yellow" (tube on the left in the second picture). Note: A culture will usually only be positive for one pathway: either MR+ or VP+. Escherichia coli is MR+ and VP-. In contrast, Enterobacter aerogenes and Klebsiella pneumoniae are MR- and VP+. Pseudomonas aeruginosa is a glucose nonfermenter and is thus MR- and VP-.

Bacterioides

a genus of gram-negative, obligate anaerobic bacteria. Bacteroides species are non-endospore-forming bacilli, and may be either motile or non-motile, depending on the species.[1] The DNA base composition is 40-48% GC. Unusual in bacterial organisms, Bacteroides membranes contain sphingolipids. They also contain meso-diaminopimelic acid in their peptidoglycan layer.

Discuss characteristics of viral host range.

What is a virus's host range determined by? The specific attachment site on the host cell's surface and the availability of host cellular factors; Define host range. the amount of host cells where a virus can multiply. Most viruses infect only specific types of cells in one host species.

Describe the primary characteristics of microbial antagonism.

What is microbial antagonism? Why is it important? -defend against pathogens the normal microbiota can benefit the host by preventing the overgrowth of harmful microorganisms. Microbial antagonism involves competition among microbes. One consequence of this competition is that the normal microbiota protect the host against colonization by potentially pathogenic microbes by competing for nutrients, pro- ducing substances harmful to the invading microbes, and affect- ing conditions such as pH and available oxygen. When this balance between normal microbiota and pathogenic microbes is upset, disease can result. Give examples of microbial antagonism. For example, the normal bacterial microbiota of the adult human vagina maintains a local pH of about 4. The presence of normal microbiota inhibits the overgrowth of the yeast Candida albicans, which can grow when the balance be- tween normal microbiota and pathogens is upset and when pH is altered. If the bacterial population is eliminated by antibiotics, excessive douching, or deodorants, the pH of the vagina reverts to nearly neutral, and C. albicans can flourish and become the dom- inant microorganism there. This condition can lead to a form of vaginitis (vaginal infection). Another example of microbial antagonism occurs in the large intestine. E. coli cells produce bacteriocins, proteins that inhibit the growth of other bacteria of the same or closely re- lated species, such as pathogenic Salmonella and Shigella. A bac- terium that makes a particular bacteriocin is not killed by that bacteriocin but may be killed by other ones. Bacteriocins are used in medical microbiology to help identify different strains of bacteria. Such identification helps determine whether severaloutbreaks of an infectious disease are caused by one or more strains of a bacterium. A final example involves another bacterium, Clostridium difficile (difʹfi-sē-il), also in the large intestine. The normal microbiota of the large intestine effectively inhibit C. difficile, possibly by making host receptors unavailable, competing for available nutrients, or producing bacteriocins. However, if the normal microbiota are eliminated (for example, by antibiotics), C. difficile can become a problem. This microbe is responsible for nearly all gastrointestinal infections that follow antibiotic therapy, from mild diarrhea to severe or even fatal colitis (in- flammation of the colon). How does microbial antagonism help or hurt the host? -Microbial antagonism involves competition among microbes. One consequence of this competition is that the normal microbiota protect the host against colonization by potentially pathogenic microbes by competing for nutrients, pro- ducing substances harmful to the invading microbes, and affect- ing conditions such as pH and available oxygen. When this balance between normal microbiota and pathogenic microbes is upset, disease can result.

Describe the purpose of the catalase and coagulase tests and give examples.

What is the purpose of the catalase test? It determines the ability of some microorganisms to degrade hydrogen peroxide by producing the enzyme catalase; This test demonstrate the presence of catalase, an enzyme that catalyses the release of oxygen from hydrogen peroxide (H2O2). It is used to differentiate those bacteria that produces an enzyme catalase, such as staphylococci, from non-catalase producing bacteria such as streptococci. Normally 3% H2O2 is used for the routine culture while 15% H2O2 is used for detection of catalase in anaerobes. Examples: Positive: Copious bubbles produced, active bubbling Examples: Staphylococci, Micrococci, Listeria, Corynebacterium diphtheriae, Burkholderia cepacia, Nocardia, the family Enterobacteriaceae (Citrobacter, E. coli, Enterobacter, Klebsiella, Shigella, Yersinia, Proteus, Salmonella, Serratia), Pseudomonas, Mycobacterium tuberculosis, Aspergillus, Cryptococcus, and Rhodococcus equi. Negative: No or very few bubbles produced. Examples: Streptococcus and Enterococcus spp What is the purpose of the coagulase test? Coagulase test is used to differentiate Staphylococcus aureus (positive) which produce the enzyme coagulase, from S. epidermis and S. saprophyticus (negative) which do not produce coagulase. i.e Coagulase Negative Staphylococcus (CONS).Coagulase Positive Organisms: Staphylococcus aureus and other animal host bacteria like S. pseudintermedius, S. intermedius, S. schleiferi, S. delphini, S. hyicus, S. lutrae, S. hyicus Examples: Coagulase Negative Organisms: Staphylococcus epidermidis, S. saprophyticus, S. warneri, S. hominis, S. caprae, etc.

Describe the lytic cycle of T-even bacteriophages.

With lytic phages, bacterial cells are broken open (lysed) and destroyed after immediate replication of the virion. As soon as the cell is destroyed, the phage progeny can find new hosts to infect. An example of a lytic bacteriophage is T4, which infects E. coli found in the human intestinal tract. Lytic phages are more suitable for phage therapy. Some lytic phages undergo a phenomenon known as lysis inhibition, where completed phage progeny will not immediately lyse out of the cell if extracellular phage concentrations are high. 1) Attachment: Phage attaches to host cell 2) Penetration: Phage penetrates host cell and injects its DNA 3) Biosynthesis: Phage DNA directs synthesis of viral components by the host cell 4) Maturation: Viral components are assembled into virions 5) Release: Host cell lyses and new visions are released.

Explain how each of the following antibiotics interferes with protein synthesis:

[ Chloramphenicol] • Chloramphenicol- inihibits the formation of peptide bonds in the growing polypeptide chain by reacting with the 50S portion of the 70s prokaryotic ribosome. Its structure allows it to be less expensive for the pharmaceutical industry to synthesize it. [Tetracycline] Tetracycline- interfere with the attachment of the tRNA carrying the amino acids to the ribosome at the 30S portion of the 70S ribosome, preventing the addition of amino acids to the growing polypeptide chain. [Streptomycin] Streptomycin- type of aminoglycoside, it interferes with the initial steps of protein synthesis by changing the shape of the 30S portion of the 70S prokaryotic ribosome, this causes the genetic code of the mRNA to be read incorrectly, especially effective against gram-negative bacteria. Streptomycin is used as an alternative drug in the treatment of tuberculosis.

Competence

cells that can take up DNA from their surrounding environment and integrate it into their own chromosomes by recombination.

RNA polymerase

complex enzyme that carries out transcription by making RNA copies (called transcripts) of a DNA template strand RNA polymerase Holoenzyme in bacteria: >Composed of: -Core polymerase: alpha2, beta, beta' (required for elongation) -Sigma factor: proteins that guide RNA polymerase to genes; required ONLY for initiation of RNA synthesis

Describe how staining and biochemical tests are used to identify bacteria.

morphological characteristics: useful for identifying eukaryotes differential staining: gram staining, acid-fast staining biochemical tests: determines presence of bacterial enzymes; what enzymes they have and how they use them; for ex. rapid ID tests: add bacteria to all points in tube and see which one of these substances it can use to grow and put together results to determine

helminthes

worm, Helminths are animals Helminths, also commonly known as parasitic worms, are large multicellular organisms, which when mature can generally be seen with the naked eye. 3 types: 1) Trematoda - flukes 2) Cestoda - tapeworms 3) Nematoda - roundworm

Identify the principal ports of entry, know which is the preferred.

portals of entry Pathogens can gain entrance to the human body and other hosts through several avenues, which are called WHAT? This for pathogens are mucous membranes, skin, and direct deposition beneath the skin or membranes. Many bacteria and viruses gain access to the body by penetrating mucous membranes lining the respiratory tract, gastrointestinal tract, genitourinary tract, and conjunctiva (membrane over eyeballs) respiratory tract (portals of entry) WHAT is the easiest and most frequently traveled portal of entry for infectious microorganisms. Microbes are inhaled into the nose or mouth in drops of moisture and dust particles. Diseases include common cold, pneumonia, tuberculosis, influenza, measles, and smallpox. gastrointestinal tract (portals of entry) Microorganisms can gain access to WHAT in food and water via contaminated fingers. Most microbes that enter the body in these ways are destroyed by hydrochloric acid (HCl) and enzymes in the stomach. Those that survive can cause disease. Microbes in this tract can cause poliomyelitis, hepatitis A, typhoid fever, amoebic dysentery, giardiasis, shigellosis. These pathogens are then eliminated with feces and can be transmitted to other hosts via contaminated water, food, or fingers. genitourinary tract (portals of entry) WHAT is a portal of entry for pathogens that are contracted sexually. Some microbes that cause STDs may penetrate an unbroken mucuous membrane. Examples of STDs are HIV infection, genital warts, chlamydia, herpes, syphilis, and gonorrhea. skin (portals of entry) WHAT is one of the largest organs of the body in terms of surface area and is an important defense against disease. Unbroken skin is impenetrable by most microorganisms. Some microbes gain access to the body through openings such as hair follicles and sweat gland ducts. parenteral route (portals of entry) Other microorganisms gain access to the body when they are deposited directly into the tissues beneath the skin or into mucous membranes when these barriers are penetrated or injured. This route is called WHAT? Punctures, injections, bites, cuts, wounds, surgery, and splitting due to swelling or drying can all establish parenteral routes. (Blood, biting arthropods, needles/syringes)