Microbio - Review Exam 2

7/31/2019 Microbio - Review Exam 2

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Kevin Kelleher, MTC

Biology 225 Study Notes Exam 21

Biology 225Study Notes Exam 2

Chapter 8: Microbial Genetics

Genetics science of heredityGenome: all the DNA in a cell

- DNA chains in cell are organized into chromosomes- DNA in nucleus is organized into chromatin (DNA in chromosomes + complex of

proteins)

DNA chains (strands) pair to form a double helix

- each strand in double helix has a sugar-phosphate backbone, with a nitrogenous baseattached to each sugar

- base pairs form in the center of the double helix by complementary base pairing ofnitrogenous bases- Adenine hydrogen bonds to Thymine; Cytosine hydrogen bonds to Guanine

Thegenetic code in a gene is translated to the amino acidsequence in a polypeptide

Genotype: the genetic makeup or genetic information that codes for characteristics of anorganismPhenotype: the traits specified (expressed) by an organisms genotype

Bacteria generally have a single circular chromosome attached at one or more points tothe plasma membrane

- The E. coli genome is about 4 million bases (base pairs) & ~ 1 mm in length- Chromosome is packaged to take up only ~ 10% of cell- Genes can be (& have been) roughly mapped to specific regions of the

chromosome by conjugation experiments

- Genomics the sequencing & characterization of genomes can be (& has been)used to determine the sequence of the entire genome

DNA Replication:

DNA replication is carried out by the enzymeDNA Polymerase, as well as someadditional protein factors

- the double helix is unwound (hydrogen bonds between complementary bases arebroken) in preparation for replication

- Replication is unidirectional (5 to 3). One strand (the leading strand) issynthesized continuously, while the other strand (the lagging strandwhich is in the 3to 5 direction) is synthesized discontinuously in short fragments in the 5 to 3direction the fragments are sealed together byDNA ligase

- DNA Polymerase has a proofreading activity to correct replication errors (adding thewrong base). The corrected error rate (after proofreading) is about 1 in 1 billion bases

- DNA replication is semiconservative:


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- each newly replicated DNA molecule consists of 1 old strand from the originaldouble- stranded DNA molecule, and 1 newly synthesized strand

- DNA replication is endergonic (requires energy) the energy required is supplied bythe nucleotides

- cleavage of phosphates in a nucleotide triphosphate releases energy (high energyphosphate bonds, as in ATP (an RNA nucleotide)

Transcription:

Transcription is carried out by a5 to 3 RNA Polymerase, as well as additional proteinfactors

- a strand ofmRNA is synthesized by complementary base pairing with the sensestrand of the DNA within a gene (producing a short term copy of the gene that thecell can use to synthesize the gene product (polypeptide) for that gene

- RNA polymerase binds to the promoter region of the gene to begin transcription- RNA polymerase moves along the DNA within the gene, synthesizing the

corresponding strand of RNA, until the terminator region is reached at which

point RNA polymerase & the new mRNA are released- In eukaryotes, the RNA synthesized by RNA polymerase must be modified to

produce the mature RNA sent to the ribosome for translation (5 cap & poly-A tail areadded, & exons are spliced together)

Translation:

Translation occurs at the ribosomes

- rRNA along with proteins comprise the structure of the 2 subunits of the ribosome- mRNA moves to the ribosome to begin translation- Ribosome subunits associate immediately prior to translation, and dissociate

following translation

- Ribosomes generally begin translation at the first AUG (start) codon- The AUG start codon specifies formylmethionine in bacterial cells (elsewhere

AUG specifies methionine) & methionine in eukaryotic cells

- The ribosome moves along the mRNA in the 5 to 3 direction as soon as theAUG start codon is exposed, another ribosome can bind & start translation of thesame mRNA

- each sequence of 3 nucleotides (codon) following the start codon in mRNA specifiesan amino acid in the polypeptide

- most amino acids are coded for by more than one codon (code is degenerate)- tRNA molecules carry amino acids to the ribosome during translation (a tRNA for

each amino acid)

- anticodon on tRNA binds to codon on mRNA- One of 3 nonsense codons (stop codons; all other codons are sense codons) signals

the ribosome to stop translation of the mRNA following translation, a release factorcleaves the complete polypeptide from the last tRNA and the ribosome, and thepolypeptide leaves the ribosome


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- In eukaryotes, transcription occurs in the nucleus, while translation occurs in thecytoplasm transcription must be completed & mRNA sent into the cytoplasmbefore translation can begin- In bacteria, translation can begin before transcription is complete (no nucleus)

Regulation of Gene Expression in Bacteria:- some genes whose products are needed constantly by the cell (genes for glycolysis

enzymes) are transcribed & translated constitutively (at a fixed rate) in the cell

- regulation of gene expression is energy efficient only produce the gene productwhen needed

- Repression & Induction regulate gene expression at the transcriptional level (regulatemRNA synthesis for a gene)

- Repression inhibits gene expression, generally in response to the overabundanceof the gene product (usually an enzyme)

- Uses a repressor to block binding of RNA Polymerase to the promoter- Induction turns on (upregulates) expression of a gene product (also, usually an

enzyme enzyme induction)- Uses an inducer to block function of the repressor- A common example in bacteria is regulation of-galactosidase, an enzyme

involved in lactose metabolism

Operon Model of Gene Expression:

- formulated by Jacob & Monod in 1961 based on inducible enzymes for lactosecatabolism (lac operon) inE. coli

- structural genes code for enzyme gene products- in bacteria, a group of coordinately regulated structural genes with related metabolic

functions, pluspromoter& operatorsites controlling their transcription, is an operon

- in an inducible operon (e.g.: lac operon), a regulatory gene codes for a repressorprotein

- when induceris absent, the repressor binds to the operator & stops transcription- when inducer is present, it binds to the repressor & transcription is free to proceed

- in a repressible operon (e.g.: trp operon), a repressorrequires a corepressor to bindto the operator

- structural gene transcription is induced by the absence of glucose cyclic AMPbinds to its receptor protein, CRP, which binds to the lac promoter to turn ontranscription

- glucose effects catabolic repression when present, cAMP levels are low & CRPcannot bind to the operator to induce transcription

Mutation: a change in the base sequence ofDNA

- Base substitution: a single base is replaced with a different base- If the base substitution results in a codon change & an amino acid substitution, it

is called a missense mutation

- If the base substitution results in a nonsense codon, it is called a nonsensemutation


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- Nucleotide insertions or deletions can result in a frameshift mutation the readingframe & codons (& amino acids in the polypeptide) change from the site of themutation

- Spontaneous mutations occur in the absence of any mutation-causing agent- Mutagens are agents that cause DNA mutationsMutagens:

- Chemical mutagens: nitrous acid causes base modifications & subsequent basepairing anomalies; nucleoside analogs ( such as 5-bromouracil & AZT) arestructurally similar to normal nucleotides, but have altered base pairing properties

- Ionizing radiation causes ions & free radicals to form, that react with DNA & causebase substitutions & DNA breaks

- UV light causes thymine-dimers- UV damage to DNA can be repaired by repair enzymes that excise & replace the

damaged DNA (deficiency in these repair enzymes leads to disorders such asXeroderma pigmentosum (XP))

Mutation rate:

- expressed as 10 to a negative power- mutations generally occur at random locations along chromosome- low spontaneous mutation rates are beneficial for diversity of lifeMutant identification:

- mutants can be detected & selected by testing for an altered phenotype- replica plating used for negative selection

- auxotrophs (require a specific nutrient for growth) can be selected by growingcells in media without the nutrient

Identification of Carcinogens

- Ames testused for identification of chemical carcinogens- Tests reversion ofhistidine auxotrophs ofSalmonella

Genetic Transfer & Recombination:

- genetic recombination: the exchange of genes between 2 DNA molecules to formnew combinations of genes on a chromosome

- crossing over: homologous chromosomes break & rejoin, exchanging informationfrom the breakpoint on (occurs normally during metaphase I of meiosis)

- vertical gene transfer: genes are passed from an organism to its offspring- horizontal gene transfer: during conjugation in bacteria, a portion of a cells DNA is

transferred to a recipient cell

- when donor DNA has been integrated into a recipients DNA, the resulting cell is arecombinant

Bacterial Transformation: genes are transferred from one bacterium (or from thesolution) to another bacterium as naked DNA


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Bacterial Conjugation: DNA is transferred from one bacterial cell to another by meansof a (sex) pilus

- F+ cells have a plasmid (F factor) that is transferred to F- cells; when the plasmid isincorporated into the recipients chromosome, that cell is a Hfr cell

- Hfr cells can transfer portions of chromosomal DNA to F - cellsBacterial Transduction: DNA is transferred from one bacterium to another in abacteriophage, which is then incorporated into the recipients DNA

Plasmids: self-replicating extrachromosomal circular molecules of DNA carryingnonessential genes

- contain an origin of replication- antibiotic resistance genes can be included in a plasmid to select bacterial cells that

have taken up the plasmid

- -complementation uses a portion of the -galactosidase gene in both the plasmid &the recipient cell a gene of interest can be inserted in the plasmid within the

plasmids -galactosidase gene results in a nonfunctional -galactosidase- can be used in blue-white selection to identify recombinant bacteria containing

the gene of interest

Transposons: small DNA fragments that can jump from one region to another regionon the same or different chromosome or plasmid

- found in chromosomal DNA, plasmids & viral DNA- bacterial transposons may contain genes for enterotoxin or antibiotic resistance, but

there are likely no limits on the kinds of genes transposons can have


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Chapter 9: Biotechnology & Recombinant DNA

Biotechnology: the use of microorganisms, cells, or cell components to make a product

Genetic Engineering: manufacturing & manipulating genetic material in vitro using

recombinant DNA technology- genes from one organism can be inserted into the genome of another organism- transgenic: an organism carrying an inserted foreign in its genome

Recombinant DNA Techniques:

Vector: a plasmid or virus used to insert foreign DNA into a cell- should be self-replicatingClone: many identical cells originating from one cell

Tools of Biotechnology:

Selection:- natural selection: survival of fittest- artificial selection: used in biotechnology to select cells with desirable characteristics

(the gene of interest)

Mutation: alters the nucleotide sequence or chemical properties of nucleotides in a DNAmolecule

- site-directed mutagenesis: make a specific change in a geneRestriction enzymes: cleave DNA molecules at specific nucleotide sequences

- may be sensitive to methylated DNA- may produce blunt ends or sticky endsOther Important Enzymes:DNA Polymerase: makes DNA from a DNA templateRNA Polymerase: makes RNA from a DNA templateReverse Transcriptase: makes cDNA from an RNA template

Vectors: serve as vehicles for the introduction & replication of desired DNA sequences(genes) in a host cell

- must be self-replicating in host cell; need origin of replication- plasmid vectors (circular DNA constructs with required DNA sequences/genes)- viral vectors (from retroviruses, adenoviruses or herpesviruses)Polymerase Chain Reaction (PCR):

- amplify specific DNA sequences from a population of DNA molecules (that is, PCRmakes multiple copies of a desired DNA fragment enzymatically)

- can be used to increase amount of a DNA sequence in a sample to detectable levels- template DNA- product DNA


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- primer DNA- thermostable DNA Polymerase (from Thermus aquaticus or other thermophilic

microbe)

- thermal cycler: automates cycling process (20-30 cycles) 3 steps per cycle:o denaturation: double-stranded DNAo annealing: primer binds (anneals) to template DNA (and DNA returns to double-stranded state)o extension: DNA sequence between primers is filled in

Inserting Foreign DNA into cells:

Transformation: cells (bacteria) take up DNA from surrounding environment

- competent cells: cells treated chemically to enhance uptake of DNA from mediumo required for transformation of most organisms

Electroporation: uses electrical current to make pores in the plasma membrane; theDNA enters cells through the pores

- organisms with cell walls are converted to protoplasts (see below) firstProtoplast fusion: protoplasts are cells in which the cell wall has been enzymaticallyremoved

- the nuclei of protoplasts can be fused to incorporate new genes/DNAGene Gun: for plant cells shoots DNA through cell wall into plant cell

Microinjection: for animal cells DNA injected into nucleus of cell

Obtaining DNA:

Gene Library: a pool of DNA fragments cloned into vectors corresponding to a specific

portion of, or the complete, genome of an organism- uses restriction enzymes to create DNA fragments in a specific size range- eukaryotic genes contain introns & exons, that are spliced to form the mRNA for

producing the gene product (polypeptide)

- cDNA (complementary DNA) libraries can be constructed using mRNA & reversetranscriptase

Selection of a clone:

- uses selective media with an antibiotic the resistance gene for the antibiotic iscontained in the cloning vector

- alpha complementation: uses a portion of the beta-galactosidase gene in the cloningvector & the complementary portion of the gene in the competent cells

Colony hybridization: identify clones (colonies) with a gene of interest

- DNA probes used to screen colonies probe will bind to DNA from colonies withdesired gene

Making a gene product:

- transgenic bacteria


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- transgenic yeast- transgenic plants- transgenic animals/mammalian cells

Applications of genetic engineering:Therapeutic applications:

- large-scale synthesis of pharmaceutical products (e.g.: insulin) using bacteriatransformed with insulin genes

- subunit vaccines: contain only a portion of a protein from a pathogen- gene therapy

Scientific applications:

- Southern blotting: used to locate a gene/DNA sequence in cellular DNAo can be used to screen for mutations

- RFLPs (Restriction Fragment Length Polymorphisms): differences in DNAfragments created by restriction enzymes in different individuals

- DNA fingerprinting: comparison of a DNA sample with known DNA samples todetermine identity (can be used in forensics, to determine disease pathology, etc.)

Agricultural applications:

- Agrobacterium; Ti plasmid used to engineer plants with desired genes/characteristics- Antisense DNA technology: DNA complementary to mRNA for a troublesome gene

used to bind the cellular mRNA & prevent translation

Safety Issues & Ethics of Genetic Engineering:- cloning- human genome project


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Chapter 10: Classification of Microorganisms

Systematics (phylogeny): the study of the evolutionary history of a group of organisms

- reveals evolutionary or phylogenetic relationships- taxa: taxonomic categoriesThe 3 domains:

Archaea: prokaryotes with NO peptidoglycan in their cell wall

- often live in extreme environments & have unusual metabolism- methanogens: strict anaerobes that produce methane from CO2 & hydrogen- extreme halophiles: require high salt concentrations for survival- hyperthermophiles: grow in hot, acidic environments

Bacteria: prokaryotes with peptidoglycan in their cell walls

- includes all pathogenic prokaryotes & many nonpathogenic prokaryotes found in soil& water

- also includes photoautotrophic prokaryotes

Eukarya: all eukaryotes

- includes animals, plants, protists & fungi- endosymbiotic theory: eukaryotic cells evolved from prokaryotic cells living inside

one another (mitochondrion resulted from internal bacterium)

Classification of Organisms:

Scientific Nomenclature:- binomial nomenclature: each organism has 2 names- scientific name: genus & species name- examples:Homo sapiens, Rhizopus nigricans, Streptococcus pneumoniae- eukaryotic species: a group of closely related organisms that interbreed

Taxonomic Hierarchy:

DomainKingdomPhylum or Division

ClassOrderFamilyGenusSpecies


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Prokaryotes:

- divided into 2 domains: Bacteria & Archaea- Kingdom: Prokaryotae orMonera (domain names typically used)- classification based on rRNA similarities- prokaryotic species: a population of cells with similar characteristics- strain: a collection of cells derived from a single cell

o a single prokaryotic species may have several strains that differ in certain featuresEukaryotes (domain Eukarya):

- Kingdom Protista: simple eukaryotes; mostly unicellular- Kingdom Fungi: includesunicellular yeasts & multicellular molds & mushrooms

o extracellular digestion & absorption of nutrientso cells join to form hyphaeo develop from spores or hyphal fragments

- Kingdom Plantae: includes some algae & all mosses, ferns, conifers & floweringplantso multicellular; carry out photosynthesis

- Kingdom Animalia: includes sponges, worms, insects & animals with backboneso multicellular; obtain nutrients by ingesting organic matter

Viruses: acellular; abiotic; obligate intracellular parasites

- not classified in 3 domains because they dont have ribosomes- use anabolic machinery in living host cells to multiply- viral species: population of viruses with similar characteristics occupying a particular

ecological niche

Methods for Classification:

Morphological characteristics: uses differences in cell shape & arrangement, &differences in such structures as endospores & flagella to distinguish organisms

Differential staining:

- Gram stain- Acid-fast stain- Endospore stainBiochemical tests: enzymatic activities- some examples:

o ability to ferment a particular carbohydrate end products of fermentation

o synthesis of a specific enzymeSerology: studies blood serum & immune responses evident in serum

- antiserum: antibody solutions used in identification of medically important microbes


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- slide agglutination test: tests bacteria for antigens that react with antibody ifpositive, agglutination or clumping is observed

- ELISA: enzyme-linked immunosorbent assay; tests ability of bacteria to react withknown antibody placed in wells of microplate

- Western blotting: used to identify bacterial antigens in a patients serumo proteins from serum separated by size, placed on filter & subjected to knownantibody

Phage typing: tests which phages a bacterium is susceptible to

- phage added to bacteria on plate & observed for evidence of plaques (clearing) due tolysis of bacteria by phage

Fatty acid profiles: separates cellular fatty acids from bacteria & compares them to fattyacid profiles of known bacteria

Flow Cytometry: fluid is passed through a small opening; scattering of light provides

evidence for presence & characteristics of contaminating bacteria- can be used to identify bacteria in a sample without culturing the bacteriaDNA base composition: percentage of guanine + cytosine (G + C) in DNA frombacterium compared to known bacterial species

DNA Fingerprinting: compares fragments of DNA created by restriction enzymebetween 2 bacteria

Ribosomal RNA sequencing: used to determine phylogenetic relationships(classification of bacteria)

Polymerase Chain Reaction (see Chapter 9)

Nucleic Acid hybridization (see Chapter 9)

- Southern blotting with DNA probesClassification methods

Dichotomous keys: identification of unknown bacterium based on the answers to a seriesof questions

- questions can involve the morphological characteristics as well as the outcome ofvarious biochemical tests

Cladograms: maps that show evolutionary relationships among organisms

- branchpoints define features shared by species on that branch- originally based on fossil evidence for vertebrates; confirmed with rRNA sequences- bacterial cladograms based on rRNA sequences (no fossils)


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Chapter 11: The Prokaryotes: Domains Bacteria & Archaea

Important Groups:

- Gram negative obligately anaerobic rods:Bacteroides, Prevotella,Porphyromonas, Fusobacterium

- Intracellular parasites:oRickettsia: gram-negative rods or coccobacilli; obligate intracellular parasites

require vector (insects or ticks) for transmissionoChlamydia: gram-negative coccoid; obligate intracellular parasites

- Bacteria without cell wall:Mycoplasma, Ureaplasma (mycoplasmas)- Acid-fast bacteria:Mycobacterium, (Nocardia is weakly acid-fast)- Gram negative aerobic rods: Pseudomonas, Legionella, Brucella, Bordetella,

Bartonella, Francisella, Burkholderia, Rickettsia

- Gram negative aerobic cocci:Neisseria, Moraxella, Acinetobacter- Gram negative facultatively anaerobic rods:Escherichia (E. coli), Salmonella,

Shigella, Klebsiella, Proteus, Yersinia, (Pasteurella, Haemophilus, Vibrio)

- Gram-negative vibrios: Vibrio (comma-shaped or S-shaped)- Gram-negative enteric rods:Escherichia strains (E. coli), Salmonella, Shigella,

Klebsiella, Proteus, Enterobacter

- Gram-negative rods - respiratory pathogens:Haemophilus, Bordetella, Legionella- Gram-negative zoonotic rods: Yersinia, Brucella, Francisella, Pasteurella- Gram positive anaerobic rods: Clostridium, Propionibacterium, Gardnerella- Gram positive facultatively anaerobic rods:Bacillus, Listeria- Gram positive cocci: Staphylococcus, Streptococcus, Enterococcus- Gram positive endospore-forming rods:Bacillus, Clostridium- Gram positivenon-endospore-forming rods:Lactobacillus,Corynebacterium,

Listeria, Propionibacterium

- Spirilla:Helicobacter, Campylobacter, Spirillumogram-negative aerobic bacteria with a helical or spiral shape (Campylobacter are

curved rods;Helicobacter are spiral/curved rods; Spirillum are helical/spiral)origid cell wall & motile by means of ordinary polar flagella (unlike spirochetes)oHelicobacter pylori causes peptic ulcers

- Spirochetes: Treponema, Borrelia, Leptospiraothin, flexible, spiral-shaped bacteria that move by means ofaxial filaments or

endoflagella (unlike spirilla, no polar flagella)omost are free living (in mud and sediments), or live in associations with animals

(e.g. in the oral cavity or GI tract); a few are pathogens of animalsoTreponema pallidum causes syphilisoBorrelia burgdorferi causes Lyme disease

- Actinomycetes:Mycobacterium, Nocardia, Corynebacterium,Propionibacterium,Gardnerella

- Haemophilus:Haemophilus influenzae are coccobacilli (pleomorphic if no capsule)responsible for meningitis, otitis media, bronchitis & atypical pneumoniaoclinical labs use tests for requirement of X factor (heme fraction of hemoglobin) &

V factor (NAD+ or NADP+) in growth medium


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In Bergeys manual, prokaryotes are divided into 2 domains: Archaea & Bacteria

- gram-negative bacteria are divided into proteobacteria & nonproteobacteriao proteobacteria are divided into 5 groups: , , , ,

- gram-positive bacteria are divided into low G + C gram-positive bacteria and highG + C gram-positive bacteria

Domain Bacteria:

Proteobacteria: most gram-negative chemoheterotrophic bacteria

- largest taxonomic group of bacteria- few photosynthetic, although thought to be derived from common photosynthetic

ancestor phylogeny based on rRNA similarities

- subgroups designated by Greek letters-proteobacteria:

- includes most proteobacteria capable of growth with low nutrient levels- some have prosthecae (stalk- or bud-like protrusions- some agriculturally important (nitrogen fixation)- some plant & human pathogens- Azospirillum: found associated with plant roots fix nitrogen- Acetobacter & Gluconobacter: aerobic; convert ethanol into acetic acid- Rickettsia: gram-negative rods or cocci

o Pathogenic; transmitted to humans by insect bites cause epidemic typhus,endemic murine typhus & Rocky Mountain spotted fever

- Ehrlichia: gram-negative pathogens; live in white blood cells cause ehrlichiosis- Caulobacter &Hyphomicrobium: prominent prosthecae; found in low-nutrient

aquatic environments (lakes); budding

- Rhizobium &Agrobacterium: invade plant rootso Rhizobium: agriculturally important; fix nitrogen; symbiotic relationship with

plantso Agrobacterium: pathogen in plants; insert bacterial DNA plasmid into plant

DNA cause crown gall

- Brucella: obligate mammalian parasites; cause brucellosis; can survive phagocytosis- Nitrobacter &Nitrosomonas: nitrifying bacteria; chemoautotrophs use reduced

nitrogenous compounds for energyo Nitrosomonas are in -proteobacteria

-proteobacteria: some overlap with -proteobacteria- can use hydrogen gas, ammonia & methane for nutrient production; some pathogenic- Thiobacillus: chemoautotrophs; oxidize reduced forms of sulfur- Spirillum: large gram-negative, aerobic, motile bacteria with polar flagella- Sphaerotilus: gram-negative with polar flagella; sheathed bacteria live in

freshwater & sewage in hollow filamentous sheath

- Burkholderia: motile with polar flagella;B. cepacia best known capable of growthin disinfectant


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- Bordetella:B. pertussis pathogen that causes pertussis (whooping cough)- Neisseria: aerobic gram-negative cocci; pathogenic species causegonorrhea &

meningococcal meningitis

- Zoogloea: important in sewage treatment processes

-proteobacteria: largest subgroup of proteobacteria

- Beggiatoa: gliding motility; uses H2S as energy source- Francisella: Francisella tularensis transmitted by wild animals & arthropods causes

tularemia

- Pseudomonaleso Pseudomonas: motile by polar flagella; many produce water-soluble pigment

(blue-green in Pseudomonas aeruginosa) common in soil & other natural environments resistant to many antibiotics can cause opportunistic/nosocomial infections (UTIs, burn/wound infections,

septicemia)o Azotobacter &Azomonas: free-living nitrogen-fixing bacteria in soilo Moraxella: coccobacilli; species implicated in conjunctivitis

- Legionellaleso Legionella: common in streams; can grow in water-supply lines

Legionella pneumophila causes legionellosis; a bacterial pneumoniao Coxiella: intracellular parasites transmitted by arthropods

Coxiella burnetii causes Q fever (a bacterial pneumonia)- Vibrionales

o Vibrio: rods that are often curved or comma-shaped Vibrio cholerae causes cholera, characterized by profuse, watery diarrhea Vibrio parahaemolyticus causes less severe gastroenteritis

- Enterobacteriales (enterics)o inhabit intestinal tracts of animals; most actively ferment sugarso produce bacteriocins that lyse/kill closely related specieso Escherichia:

E. coli is common in biological research E. coli is not usually pathogenic, but can cause UTIs, and enterotoxin-

producing strains can cause travelers diarrhea and gastroenteritiso Salmonella: almost all members can be pathogenic; divided into serological types

or serotypes (strictly not species) by types of antigens on flagella, capsule & cellwall Salmonella typhi causes typhoid fever, a severe gastroenteritis other Salmonella members cause less severe gastroenteritis

o Shigella: Shigella species cause a severe form of diarrhea called bacillarydysentery (shigellosis), as well as travelers diarrhea

o Klebsiella: found in soil & water; many are nitrogen-fixing Klebsiella pneumoniae causes a serious pneumonia

o Serratia: Serratia marcescens produces a red pigment


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can be isolated from hospital environments; may cause nosocomial infectionssuch as UTIs and respiratory tract infections

o Proteus: motile by peritrichous flagella; exhibit swarming growth on agar produce urease enzyme; implicated in many UTIs

o Yersinia:

Yersinia pestis causes plague; transmitted by rat flea (respiratory droplets maybe involved as well)

o Erwinia: primarily plant pathogens (cause plant rot)o Enterobacter: found in animals, water, sewage & soil

Enterobacter aerogenes & Enterobacter cloacae can cause UTIs &nosocomial infections

- Pasteurellaleso Pasteurella: domestic animal pathogen; causes septicemia & cholera in fowl

Pasteurella multocida can be transmitted to humans by cat & dog biteso Haemophilus: requires blood in culture medium (heme fraction called X factor);

also requires NAD (V factor)

Haemophilus influenzae causes bacterial pneumonia and bacterial meningitis

Purple & Green Photosynthetic Bacteria: scattered in many taxonomic subgroups

- green nonsulfur bacteria- green sulfur bacteria- purple nonsulfur bacteria- purple sulfur bacteria-proteobacteria: some bacterial predators; some sulfur-reducing bacteria

- Bdellovibrio: attacks other gram - bacteria- Desulfovibrionales

o Desulfovibrio: obligately anaerobic sulfur-reducing bacteria- Myxococcales

o Myxococcus: move by gliding (slime trail); digest other bacteria for nutrients-proteobacteria: gram-negative rods; helical or vibrioid

- Campylobacter: microaerophilic vibrios (name means curved rod)o Campylobacter jejuni is a cause of foodborne intestinal disease

- Helicobacter: microaerophilic curved rods with multiple flagella- Helicobacter pyloriis a common cause of gastric ulcerNonproteobacteria Gram-Negative Bacteria: phylogeny based on rRNA

- Cyanobacteria: once called blue-green algae due to coloro Carry out oxygen-producing photosynthesis; many fix nitrogeno Unicellular, colonial & filamentous forms

- Chlamydiales: intracellular parasites (cultivated in cells, animals, embryonated eggs)o Chlamydia: coccoid bacteria; spread by interpersonal contact or airborne

Chlamydia trachomatis: causes blindness, nongonococcal urethritis (NGU) Chlamydia psittaci causes psittacosis (ornithosis) Chlamydia pneumoniae causes mild pneumonia


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o Spirochetes Treponema: Treponema pallidum causes syphilis Borrelia: bacteria transmitted by ticks or lice; cause relapsing fever

Borrelia burgdorferi causesLyme disease Leptospira: cause leptospirosis; spread though contaminated water from urine

of infected animals- Bacterioides: anaerobic bacteria; members of genus Prevotella in oral cavity

o Bacterioides: inhabit human intestinal tract & gingival crevice infect through puncture wounds or surgery; cause peritonitis

- Fusobacteria: pleomorphic but often fusiform (spindle-shaped)o Fusobacterium: may be responsible for dental abscesses

- Sphingobacteria: chemoheterotrophic bacteria; hydrolyze plant oils (commercial use)o Cytophagia: degrade cellulose in soil; important in sewage treatment

Gram-Positive Bacteria: divided into 2 groups, based on ratio of G+C (Guanine +cytosine nucleotides relative to total nucleotides in chromosome)

Low G + C Gram-Positive Bacteria

- Mycoplasmatales: do not form cell wallso have high sterol content in the plasma membraneo aerobes or facultative anaerobes; highly pleomorphico Mycoplasma- Can be grown on artificial media with sterols, but cell culture

methods are often usedo Mycoplasma pneumoniae - primary atypical pneumoniao Ureaplasma urealyticum - nongonococcal urethritis

- Clostridialeso Clostridium- obligate anaerobes that form endosporeso Clostridium tetani causes tetanuso Clostridium botulinum causes botulismo Clostridium perfringens causes gas gangrene, foodborne diarrheao Clostridium difficile - antibiotic-associated pseudomembranous colitis

- Epulopiscium large, originally thought be a protozoan- Veillonella: normal flora of the mouth (dental plaque), colon, vagina

o anaerobic cocci that occur in pairs or short chains; non-motile, non-endosporeforming

o opportunistic pathogen abscesses of sinuses, tonsils and brain- Lactobacillales

o Lactobacillus - normal flora of oral cavity, vagina and intestinal tract aerotolerant rods that produce lactic acid through fermentation

- Streptococcus aerotolerant cocci that grow in chainso catalase-negative; some produce exotoxins that destroy phagocytes & host tissueso -hemolytic streptococci produce -hemolysin, which reduces hemoglobin (red)

to biliverdin (green)o -hemolytic strep produce a hemolysin (streptolysin-O or S) that completely lyses

hemoglobin, producing a clear zone around colonieso -hemolytic strep are actually nonhemolytic; do not produce a hemolysin


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o S. pyogenes - Group A, -hemolytic strep; causes pharyngitis, impetigo, scarletfever, and rheumatic fever

o S. mutans - -hemolytic; causes dental carieso S. pneumoniae - -hemolytic; causes pneumonia, bacteremia, meningitis, otitis

and sinusitis

-Staphylococcus: aerobes or facultative anaerobes that grow in grapelike clusters,under high osmotic pressure/low moisture conditionso Staphylococcus epidermidis -normal flora of the skino Staphylococcus aureus - pyogenic infections such as endocarditis and

osteomyelitis; food poisoning, and toxic shock syndromeo Staphylococcus saprophyticus - urinary tract infections

- Listeriao Listeria monocytogenes - meningitis and sepsis in newborns and

immunosuppressed adults; can cause stillbirth or serious damage to thedeveloping fetus; contaminates foods, survives phagocytosis, grows atrefrigeration temperature.

- High G + C gram-positive bacteria phylum Actinobacteria- Mycobacterium - aerobic, non-endospore forming rods; fungus-like in that they

occasionally exhibit filamentous growtho mycolic acids in outer layer from waxy, water-resistant layer, resistant to

desiccation and many antimicrobial drugso Mycobacterium tuberculosis: causes tuberculosis (TB)o Mycobacterium leprae: causes leprosy

- Corynebacterium pleomorphic, varies with age of cellso Corynebacterium diphtheriae: causes diphtheria

- Propionibacterium forms propionic acid, species used for fermentation of Swisscheese.o Propionibacterium acnes: causes acne

- Gardnerellao Gardnerella vaginalis common cause of vaginitis, gram-variable and

pleomorphic.

- Actinomycetes filamentous, soil bacteriao Frankia forms nitrogen-fixing nodules in alder tree rootso Streptomyces strict aerobes, produce asexual spores (conidiospores); source of

most commercial antibioticso Actinomyces facultative anaerobes, inhabit mouth and throat of humans and

animals Actinomycesisraeliicauses actinomycosis, tissue destroying disease of thehead, neck or lungs.

o Nocardia aerobic, produce filaments that fragment into short rods Nocardia asteroides may cause pulmonary infections or mycetoma

(localized destructive infection of feet or hands)

Domain Archaea: extreme halophiles, extreme thermophiles, and methanogens


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Chapter 12: The Eukaryotes: Fungi, Algae, Protozoa & Helminths

Fungi:

- Pros: decompose dead plants using extracellular enzymes like cellulases - importantfor food chains/webs

o mycorrhizae symbiosis with plants (live on roots), aids absorption of minerals &water from soil

o used as food (mushrooms), in baking/brewing (yeasts), & as source of antibiotics(penicillin)

- Cons: Fungal infections (hospital-acquired & from weakened immunity)o Fungal diseases of plants

Mycology: study of fungi

Characteristics of fungi:

- fungi are chemoheterotrophs (require preformed organic compounds for energy &carbon)

- fungi are generally aerobic or facultatively anaerobic; very few anaerobic fungi- Vegetative structures: fungal colonies cells involved in catabolism & growthMolds & fleshy fungi: thallus (body) composed of hyphae (long filaments of cells)

- septate hyphae have septa (cross-walls) dividing hyphae into uninucleate units- coenocytic hyphae have no septa appear as long continuous cells- hyphae fragments can grow fully into new hyphae- vegetative hyphae obtains nutrients reproduction occurs in reproductive or aerial

hyphae (project above media surface) that often bear spores

- mycelium: visible mass of hyphaeYeasts: nonfilamentous unicellular fungi; spherical or oval shape

- budding yeast (Saccharomyces): divide unevenly by formation of new cell fromsmall budo pseudohypha: undetached buds that form short chain of cells

- fission yeast (Schizosaccharomyces): divide evenly- yeast are facultative anaerobes carry out aerobic respiration when oxygen is present

& alcohol fermentation in the absence of oxygen

Dimorphic fungi: can grow as either a mold or yeast

- temperature-dependent in some pathogenic fungi (yeastlike at 37C, moldlike at25C); CO2 concentration-dependent in others

Life cycle:

- asexual reproduction in filamentous fungi is possible by fragmentation of hyphae- spores formed by aerial hyphae

o asexual spores: form fungus identical to parent


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conidium: unicellular or multicellular spore not enclosed in sac; produced inchain at end of conidiophore arthrospore: formed by hyphae fragmentation blastoconidia: buds from parent cell

chlamydospore: thick-walled spore from enlarged hyphal segment

sporangiospore: formed within sac (sporangium) at end ofsporangiophore(found inRhizopus)

o sexual spores: result from fusion of nuclei from opposite mating strains of thesame species (not identical to either parent) 3 phases of sexual reproduction: plasmogamy (donor nucleus enters recipient

cell); karyogamy (+ & - nuclei fuse); meiosis (diploid nucleus forms haploidnuclei)

sexual spores used in classificationNutritional adaptations of Fungi:

-low pH (~ pH=5) environment best for growth

- molds generally aerobic; yeast generally facultative anaerobes- fungi generally more resistant to high osmotic pressure- can grow in low moisture environment- reduced requirement for nitrogen- can metabolize complex carbohydrates (lignin, cellulose)Medically Important Phyla of Fungi:

Teleomorphs: produce both asexual & sexual sporesZygomycota: conjugation fungi; saprophytic molds with coenocytic hyphae

- example:Rhizopus nigricans (black bread mold)- asexual spores are sporangiospores- sexual spores are zygospores (large, thick-walled spore)Ascomycota: sac fungi; molds with septate hyphae, some yeasts

- asexual spores are conidia- sexual spores are ascospores (spores produced in saclike structure called ascus)Basidiomycota: club fungi; fungi with septate hyphae that produce mushrooms

- asexual spores are usually basidiospores (formed externally on base pedestal calledbasidium), sometimes conidiospores

Anamorphs: only produce asexual sporesDeuteromycota: undefined fungi; rRNA sequencing now being used to classify fungi inthis phylum

- example: Penicillium- most deuteromycetes may be anamorph phases of AscomycotaFungal Diseases:

Mycoses: fungal infection 5 groups:


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- Diatoms: unicellular or filamentous algae; cell wall with pectin & silica; responsiblefor domoic acid intoxication

- Dinoflagellates : unicellular algae (plankton) or free-floating; some produceneurotoxinso produce saxitoxins responsible forparalytic shellfish poisoningo large marine concentrations of some species produce red tides

- periodic/seasonal planktonic algae increases called algal blooms- algae believed to produce most atmospheric oxygenProtozoa: unicellular, eukaryotic chemoheterotrophs

- feeding & growing stage (trophozoite) feeds on bacteria & particulate nutrients- reproduce asexually by fission, budding or schizogamy (multiple fissions)- ciliates (Paramecium) reproduce sexually by conjugation (fusion of micronucleus

from one ciliate & macronucleus from another)

- some protozoa produce gametes that fuse to form a zygote- can form a protective capsule called a cyst phylumApicomplexa forms an oocyst

that can reproduce asexually- some have a protective covering called pellicleArchaezoa: eukaryotes with no mitochondria; spindle-shaped with 2 or more flagella

- Trichomonas vaginalis: infects vagina & male urinary tractMicrosporidia: lack mitochondria & microtubules; cause diarrhea in AIDS patients

Rhizopoda: amoeba

- Entamoeba histolytica causes amoebic dysenteryApicomplexa: nonmotile in mature form; obligate intracellular parasites- Plasmodium reproduces inAnopheles mosquito & is transferred to human blood cells

by mosquito bite; lyse blood cells causes malaria

Ciliophora: move by means of cilia

Euglenozoa: photoautotrophs; move by flagella; lack sexual reproduction

Slime Molds:

- cellular slime molds resemble amoebas; ingest bacteria by phagocytosis- plasmodial slime molds are a multinucleate mass of protoplasm engulf bacteria &

debris as they move

Helminths:

- parasitic flatworms in phylum Platyhelminthes- parasitic roundworms in phylumNematoda- multicellular animals; some are human parasites- adult stage found in definitive host- larval stages require intermediate host


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- can be monoecious (male & female sex organs in same animal) or dioecious(separate male & female organisms)

- Platyhelminthes: dorsoventrally flattened; parasitic flatworms may lack digestivetract

o Adult trematodes (flukes) have oral & ventral sucker to attach to hosto A cestode (tapeworm) consists of a scolex (head) & proglottids (segments)o intermediate host consumes eggs (from feces/soil); larvae encyst in muscle; when

definitive gost consumes meat; larvae mature & migrate to other tissues (GI tract)o humans as definitive host:

beef tapeworm (Taenia saginata); cattle are intermediate host pork tapeworm (Taenia solium); humans can also be intermediate host

o humans as intermediate host: tiny tapewormEchinococcus granulosus; dogs & coyotes are definitive hosts

o diagnosis based on presence of mature proglottids in feces- Nematoda: roundworms with a complete digestive systemo most species are dioecious

o males are smaller than females & often have a hooked tail with spiculeso free-living (soil & water) and parasitic specieso can be divided into those in which egg is infective & those in which larva is

infectiveo egg infective for humans:

pinwormEnterobius vermicularis Ascaris lumbricoides: large roundworm that lives in the digestive tract of

humans & domestic animals eggs excreted in feces into soil & ingested by another host

olarvae infective for humans hookworm (Necator americanus): live in small intestine of humans; eggs are

excreted in feces/soil; larvae enter host by penetration of skin Trichinella spiralis: causes trichinosis in humans through ingestion of

encysted larvae in undefcooked pork or game animals (bears)

Arthropods as Vectors

- arthropods (Phylum Arthropoda) are animals characterized by segmented bodies,hard external skeletons & jointed legs

- include arachnids (spiders, mites, ticks), crustacea (crabs, crayfish) & insects (bees,flies, lice)

- arthropods that carry disease are called vectors- control or eradication of vectors is best approach to elimination of diseases they carry


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Chapter 13: Viruses, Viroids & Prions

Viruses:

- are obligatory intracellular parasites- contain a single type ofnucleic acid either DNA or RNA- contain aprotein coatsurrounding the nucleic acid (& some have an envelope

composed of lipids, proteins & carbohydrates surrounding the protein coat)

- multiply in living cells using the cells metabolic machinery (do not have their ownenzymes for protein synthesis or ATP generation)

- cause synthesis of structures that can transfer viral nucleic acids to other cells- viral size: ranges from 20-14,000 nmViral Host Range: viruses exist that infect invertebrates, vertebrates, plants, protists,fungi & bacteria

- viruses that infect bacteria are called bacteriophages or phages- the host range depends on the presence on the surface of the host cell of viral

receptors for a given virus

Viral Structure: virion infectious viral particle

- Nucleic Acid: either DNA or RNAo Can be either single-stranded or double-stranded; size varies

- Capsid & Envelope:o the capsid is the protein coat of the virus surrounding the nucleic acido the capsid is composed of protein subunits called capsomereso in some viruses, the capsid is enclosed by an envelope consisting of proteins,

lipids & carbohydrates some envelopes are covered by carbohydrate-protein complexes called spikes

that may aid in attachment to the host cell in nonenveloped viruses, the capsid protects the nucleic acid from nucleases &

promotes attachment to host cellGeneral morphology:

- Helical viruses: helical capsid;o examples: rabies & Ebola viruses

- Polyhedral viruses: polyhedral (many-sided) capsid; usually icosahedral (20 sides)o examples: adenovirus, poliovirus

- Enveloped viruses: capsid enclosed by envelopeo examples:Influenzavirus (helical enveloped), herpes simplex virus (icosahedral

enveloped)

- Complex viruses: complicated structureo example: bacteriophage

Viral taxonomy:

- viruses grouped into families based on: nucleic acid type, replication strategy, &morphology

- order names end inales- family names end inviridae


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- genus names end invirus- species names use common names (e.g.: human immunodeficiency virus)

o subspecies use a number (e.g.: HIV-1)Viral Families by Genome & important viruses

- single-stranded DNA, nonenvelopedo Parvoviridae (human parvovirus B19)- double-stranded DNA, nonenveloped

o Adenoviridae (Mastadenovirus)o Papovaviridae (Papillomavirus (human papillomavirus or HPV))

- double-stranded DNA, envelopedo Poxviridae (Orthopoxvirus (vaccinia virus, smallpox virus))o Herpesviridae

Simplexvirus (herpes simplex virus HHV-1 & HHV-2) Varicellovirus (varicella zoster virus HHV-3) Lymphocryptovirus (Epstein-Barr virus (EBV) HHV-4) Cytomegalovirus (CMV, HHV-5) Roseolovirus (HHV-6)

o Hepadnaviridae (Hepadnavirus (hepatitis B virus (HBV)))- + strand single-stranded RNA, nonenveloped

o Picornaviridae (Enterovirus,Rhinovirus, hepatitis A virus (HAV))o Calciviridae (hepatitis E virus (HEV),Norovirus)

- + strand single-stranded RNA, envelopedo Togaviridae (Rubivirus (rubella virus))o Flaviviridae (Flavivirus, hepatitis C virus (HCV))o Coronaviridae (Coronavirus)

- - strand single-stranded RNAo Rhabdoviridae (Lyssavirus (rabies virus))o Filoviridae (Ebola virus)o Paramyxoviridae (Paramyxovirus (measles virus))o Deltaviridae (hepatitis D virus)

- multiple strand RNA (- strand)o Orthomyxoviridae (Influenzavirus A, B & C)o Bunyaviridae (Hantavirus)o Retroviridae (Lentivirus (HIV))

- double-stranded RNA, nonenvelopedo Reoviridae (Reovirus, Rotavirus)

Viral Isolation:- bacteriophage growth visualized on agar plates asplaques (clearings where bacteria

have been lysed)

- can be counted plaque-forming units- animal viruses are more difficult can use:

o living animalso embryonated eggso cell cultures


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cause cytopathic effect can be counted similarly to plaques primary cell lines cells isolated from tissue; short life span

diploid cell lines isolated from embryos; about 100 generations possible continuous cell lines: immortal; infinite generations usually isolated from

cancerous tissue

-Viral Identification: can use serological methods (Western blotting), RFLPs, PCR

Viral Multiplication: (bacteriophage model)

- Lytic cycle: (T-even bacteriophages)o Attachment: phage attaches to host cell (wall)o Penetration: phage penetrates host cell (using tail core) & injects its DNAo Biosynthesis: host cell used to synthesize phage proteinso Maturation: synthesized viral components packaged into virionso Release: host cell lysed (phage lysozyme breaks down cell wall) & new virions

released

- burst time: time from phage attachment to release- burst size: number of new phage particles released from a single infection- Lysogenic cycle: (bacteriophage )

o Lysogenic phages may use a lytic cycle, but can also integrate their DNA into thehost cell chromosome the inserted phage DNA is known as a prophage

o If the integrated phage DNA is excised (removed from host DNA by UV light;chromosome break), it can enter the lytic cycle

o During lysogeny, the phage remains latent (inactive), & the host cell is known as alysogenic cell

o Lysogenic cells are immune to reinfection with the same phageo Phage conversion: lysogenic cell may acquire new properties (from phage gene

products)

o Specialized transduction: excised phage DNA can carry adjacent bacterial geneswhich will be packaged into phage capsids recombinant phageMultiplication of animal viruses:

- Stages:o Attachment: virus attaches to plasma membrane receptors of host cell using

surface attachment sites (capsid fibers, spikes,) on viruso Penetration: virus taken into cell by endocytosis or byfusion with the plasma

membrane (enveloped viruses)o Biosynthesis: synthesis of capsid & viral nucleic acid (see below)o Uncoating: viral nucleic acid separated from capsid (by enzymes, etc.)o Maturation & Release:enveloped viruses released by budding from host cellplasma membrane (membrane may become viral envelope) host cell may

survive; nonenveloped viruses released through ruptures in plasma membrane host cell usually dies


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Biosynthesis of Viral Nucleic Acid:

- DNA viruses: viral DNA synthesized in nucleus using enzymes from early genes& capsid synthesized in cytoplasm using mRNA from late genes capsid proteinsmigrate to nucleus for packagingo ssDNA viruses: family Parvoviridae (parvovirus)o

dsDNA viruses: families Herpesviridae (herpesvirus), Papovaviridae(papillomavirus) & Poxviridae (smallpox & cowpox viruses)

- RNA viruses:o ssRNA viruses:

+ strand ssRNA viruses use + strand as mRNA for viral proteins, as templatefor synthesizing strand (useRNA-dependent RNA polymerase make more +strand) & as viral genome example: picornaviruses (poliovirus)

- strand ssRNA viruses use strand to make + strand & as viral genome example: rhabdoviruses (rabiesvirus)

o dsRNA viruses:RNA-dependent RNA polymerase copies the strand to make +strand (mRNA) example: reoviruses

o multiple strand RNA viruses: reverse transcriptase uses RNA as template tosynthesize; DNA is integrated into host cell chromosome (provirus) & used astemplate for viral mRNA synthesis example: retroviruses (HIV)

Viruses & Cancer:

- oncogenes: mutation in these genes makes the cell more susceptible to oncogenictransformation

- transformation: tumor cells acquire properties unlike normal cells (loss of contactinhibition, virally transformed cells may express viral antigens)

Viral Infections:

- latent viral infection: viral activity may be reactivated by immunosuppression orother conditionso e.g.: infections by HSV-1 (cold sores, fever blisters) & HSV-2 (genital herpes)

- persistent viral infection (slow viral infection): disease caused by a viral infectionthat progresses slowly over a long time period; usually fatalo e.g.: subacute sclerosing panencephalitis caused by measles virus

Prions: proteinaceous infectious particles

- suspected cause of nine types of neurological diseases (mad cow disease (BSE), kuru,Creutzfeldt-Jacob disease (CJD))- diseases called spongiform encephalopathies large vacuoles develop in brain- sheep scrapie: infectivity of infected sheep brain reduced with proteases- human prion protein (PrP) gene found located on chromosome 20- normal PrP is PrPC (cellular); abnormal PrP is PrPSc (scrapie); injection of PrPSc in

normal animal brains causes disease (and refolding of existing PrPC to PrPSc)

- fragments of abnormal prion protein accumulate in plaques in infected brain


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Plant Viruses & Viroids:

- cell wall reduces plant susceptibility to viral infection, yet plant viruses (bean mosaicvirus, wound tumor virus) cause many plant diseases

- viroids: short pieces of naked RNA

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Microbio - Review Exam 2