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Final Study Guide MICRO 3050

by: Katie Kessler

Final Study Guide MICRO 3050 81382 - MICR 3050 - 001

Katie Kessler
GPA 3.7
General Microbiology
Krista Barrier Rudolph

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Here is the final study guide for Micro! This covers everything from the beer making to immunity. Good luck studying! If you have any questions, please contact me!
General Microbiology
Krista Barrier Rudolph
Study Guide
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This 26 page Study Guide was uploaded by Katie Kessler on Monday November 30, 2015. The Study Guide belongs to 81382 - MICR 3050 - 001 at Clemson University taught by Krista Barrier Rudolph in Fall 2015. Since its upload, it has received 93 views. For similar materials see General Microbiology in Biological Sciences at Clemson University.

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Date Created: 11/30/15
UNIT 4 STUDY GUIDE MICR 3050 Fall 2015 OBJECTIVES Chapter 411 413 415 416 1 Understand in general the production of beer ale and distilled beverages Be able to compare and contrast the processes Alcoholic beverages It is produced by yeast from the fermentation of sugar to ethyl alcohol and C02 It begins with formation of liquid containing carbohydrates in readily fermentable form Wine is usually a fermented form of grape juice Beer is fermented of malted grain Distilled beverages are distilled from fermented solutions Beers and Ales Mash gets the sugar out of the grain The grains are fermented which softens the grain up and activates the enzymes to yield malt Wort fermentable sugarsclear liquid that has fermenting carbohydrates The mash is heated with hops owering vine in a brew kettle The hops add avoring and assist in clarification because they are antimicrobial Heating inactivates hydrolytic enzymes which also helps clarify the beerales The hops are removed and sugar is available Now it is ready for the yeast The wort is inoculated pitched with the desired yeast It can be bottom yeasts used in production of lager beers It settles to the bottom and there is not a lot of C02 production Top yeast is used with production of ales The C02 bubbles oat to the top Fermentation o Lager Lasts 712 days for lager beers These ferment longer at cold temperatures This gives the beer a heavierdarker taste 0 Ales lasts 57 days around room temperature This ferments for a shorter time at room temperature In ales the pH drops lower Bottling C02 is added in the bottle Beer can be pasturized or sterilized by filtration Process of making beers and ales Use a moist oor for germinating the grain Dry and crush the grain The mash tun crushes the grain Add water to release the sugars which results in mash Add the hops and put it in a brew kettle Steep it and take out the hops Pitch it to the wort and put it in a fermentation bath Store it and then package it Processing step Biological change j d I j Heat in brew Spoilage organism inhibition 1 quvmaquot rem Enzymemacuvauon 1 l re leasle Flavoring from hops 39 5 b e Clarification carbohydrates Malling oor Brew kmquot Add VeaS F Remove hops Barley moistening and germination Drying and crushing Fermentation Alcoholic fermentation Funherenzymatic Storage Iagering Q J gt lgag m activity release p of maltose dextrins 1 Packaging l Distilled Spirits and proteins 0 Whiskey and burbon begin with sour mash which is mash inoculated with homolactic bacterium to make Lactic Acid It sours 0 Fun facts vodka is grain in potatoes gin vodka and gin berries brandi distilled red wine rum fermented sugar canemolasses tequila agave Mashing Add hops Chapter 431 432 2 Know the potential waterborne diseases discussed and how drinking water is purified Waterborne diseases 0 Typhoid fever salmonella typhi it was a major public health threat before drinking water treatment 0 Cholera vibrio cholera 7 major pandemics since 1817 It occurs in areas with inadequate or no sewage treatment 0 Protozoan infections giardia cryptosporidium entamoeba may be present in surface waters and may survive water treatment facilities as cysts It forms a cyst that can get through filters It is also resistant to chlorine Drinking water 0 Remove the sand sediment ect Coagulation removes the oc containing insoluble material and microorganisms Then filtrate remove all organic and inorganic compounds Chlorination and storage killed the remaining microorganisms and prevents growth of incola Then it is distributed 0 Chlorine is added in case anything gets through the filters although it is considered a carcinogen because it forms chlorinated organics 0 Why do we use chlorine instead of UV and radiation Chlorine leaves residuals and UVradiation doesn t 3 Describe the goals of wastewater treatment 0 Protect our health 0 Recycle valuable resources to enhance the environment 4 Know the terms associated with wastewater treatment ex BOD clarifiers sludge oc etc BOD biochemical oxygen demand the higher the oxygen consumpter the higher the oxygen in the matter Sludge semi solid slurry Clarifiers settling tanks built with mechanical means for continuous removal of solids being deposited by sedimentation Floc loosely clumped mass 5 Distinguish between primary secondary and tertiary wastewater treatment Primary treatment It grates and screens It allows to settle in the clarifiers Separates solids It may be discharged but it still has a lot of BOD It basically has water ow into it and the solids are removed on the bottom and the water ows out onto the top The scum baf e keeps the grease out of the water Secondary treatment It has an aeration basin where the water ows to after the primary clarifier Then it ows to the final clarifier and operates in the same way as the primary one It dissolves oxygen and recycles the bacteria at a specific rate so the bacteria doesn t get into the system If a plant wanted to they could get rid of the primary clarifier and use membranes This allows you to keep the water in a smaller bath and you don t have to worry about the oc The downside is that they are much more expensive It is a bacterial farm with aeration water and BOD The bacteria chews up the organic matter in the water The bacteria gets put back into the tank so they eat the organic matter that they normally wouldn t eat Tertiarv treatment The purpose of this treatment is to remove things such as SS COD solid and colloidal phosphorus and specific compounds pesticides metals detergents and so on It is designed to improve the quality of purified water so that it can be discharged into the natural environment or reused The first step This is the nitrogen removal it makes the ammonia to nitrate Nitrogen is in sewage as ammonia The nitrosomonas and nitrobacteria convert ammonia to nitrate in aeration basins This is called nitrification and it consumes a great deal of oxygen This system is beneficial bc it reduces energy requires for wastewater treatment A lot of the energy is used to get oxygen in the aeration basin However the anoxic basin reduces the amount of oxygen requires because there is less organic matter than needs to be oxidized and it pumps less oxygen in the aeration basin In the anoxic basin the organic matter has ammonia groups and the ammonia is converted to nitrate The nitrate ows to the final clarifier Most of the things in the system such as the bugs use nitrate for the terminal e acceptor and makes the N gas bubble out of the tank resulting in N free water The second step nitrate N gas The nitrate is converted to N gas by denitrification by bacteria N gas steams out of the wastewater This is beneficial bc it reduces oxygen required for wastewater treatment Phosphorus removal A group of bacteria called PAO s phosphorus accumulating organisms will remove P under appropriate conditions It involves cycling bacteria between anaerobic and aerobic conditions 0 In this system the bacteria takes up the BOD to get the energy by the polyphosphate chains and break off the phosphates to bring organic matter into the cell Then everything ows into the aeration basin and the bacteria metabolizes the food to have excess energy They do this by Remaking the Phosphate chains 0 Haver process N from the atmosphere makes N fertilizer Wastewater disinfiectant Chlorine UV light damages bacterial DNA and prevents bacteria from reproducing Anaerobic digesters Reduces the sludge for disposal and produces methane 6 Describe indicator organisms their use in the analysis of water quality and the methods used to detect them Ideal indicator organisms Chapter 61 Suitable for all water types Present wherever enteric pathogens are Survives a long time Does not reproduce in contaminated water Detected by a highly specific test Harmless to humans Its level in water re ects degree of fecal pollution To test coliforms use the MPN method 65 7 Describe viruses structure genomes morphological types They replicate independently of a cells chromosome but NEED to live in a host cell to replicate They are obligate intracellular parasites and infect ALL cell types They are acellular this is why they take over the host cell They contain DNA and RNA as their genome It can be single double linear circular or segmented more than one genome The extracellular form is called a viron the complete virus particle nucleis acid surrounded by a protein coat and other layers Structure size ranges from 101000 nm in diameter It contains a nucleocapsid nucleic acid and capsid protein coat They can have peplimers which are the spikes 8 Compare and contrast bacterial and animal viruses Animal viruses can be ds DNA or ss RNA However all four types can be found in animals ds DNA ss DNA ds RNA ss RNA Something that helps me remember if it is a bacteriaanimal virus is that bacteria always has phage at the end of the name and animal viruses has virus at the end of the name o For ex from the picture below c Herpesvirus is the herpes virus in animals and f Teven coliphage is the T virus that infects E coli 0 Most bacteria viruses don t have an envelope Animal viruses have an envelope because it arises during viral replication 0 bacteriophage lysogenicprophage animal viruslatentprovirus 0 When the bacteriophage enters a bacterium only the DNARNA is released into the cell capsid remains outside However when viruses enter animal cells the capsid goes into the cell creating the extra step of uncoating o Bacteriophages use cell wall lipopolysacharides and proteins as receptors They can also use teichoic acids agella or pili 0 Animal causes conformational changes in virion proteins that facilitate interaction with secondary receptors Nucleocapsid enters cytoplasm with genome still enclosed Copyright The McGrawHill Companies Inc Permission required for reproduction or display 0 i 3 J I 39 K at h Adenovirus I e 0 f J e Rhabdovirus f T even coliphage g A flexuous i Influenza virus tailed phage T I e j Human k Picornavirus I mX174 phage m Tobacco mosaic virus papilloma virus L I 1 11m 9 Describe bacteriophages o It is a virus that infects bacteria and the common genome is ds DNA 0 They start multiplying after they enter the host cell It lyses the bacteria host for release and they use lytic pathways 10 Distinguish between virulent lytic and temperate lysogenic bacteriophages and their life cycles using T4 phage and lambda phage as examples respectively 0 Lytic DNA is injected into the host cell 0 An example T4 The virus on the outside injects the nucleic acid in the cell Inside the cell it is lysing and releasing more 0 Host cell lysis and releases viruses 0 Lysogenic remain within the host cell without destroying it by integrating genome into host genome in a relationship called lysogeny ex lambda o It reproduces as lytic o Pathway A prophage exits the bacterial chromosome initiating the lytic cycle The phage DNA circularizes The phage DNA integrates into the bacterial chromosome becoming a prophage the genetic material of a bacteriophage incorporated into the genome of a bacterium and able to produce phages if specifically activated The bacterium reproduces normally copying the prophage and transmitting it to the daughter cells Then the cell diVides many times producing a colony of bacteria infected With a prophage Here is the lambda pathway Keep in mind that induction occurs When prophage hops out and goes into the lytic pathway haemriail calm hum h 39 l h h E Z 5 l lmfiilx a vim aTTaEHraEMT m EEML K mm museum or mama tum l Miranda DNA unutuumsza IEIIFITE IElll TIIDN EIF L i DIME4 IHI39I39U H UEJUWEH f ha E E FMTHEEHE IEIF 39i lHLvi39gfL FHDTTEB Q E NEEDED Fl lFl lFEIIHiI39IaR39la TII M 39 NEW JIHUJEEES C p 739 H F iilEI HElP JE TEEITr HF lg l u39l t l EllJill EMFHQ I39ITE FELEHELEIMG WHITE E IQMFEETHE VIHUEE GE LIL L f ll HE LEAHEE A N LEIMEJE FIE EF INTEGRATED L a ENE FEEFHJIEEJHEE ALIENEJ Ia39islliTHl imamukmruu gwg f l I FH FkMEE FELTHWEV I Lame Hummus 1 DillE iHWIHUEJ EEi T4 infection lifecycle The Viral DNA injects itself into the cell Early mRNA is made and the host DNA is degraded Phage DNA is replicated Late RNA is made along With the head and tails Virions are forming and the host cell lyses until it degrades the host cell and releases the Viral DNA Copyright The McGrawHill Companies Inc Permission required for reproduction or display DNA injection 39 12 min 5 m V Head and 39 RNA tails made made 9 min a ll wji iufi g canwigihm PEEIEEIII I Enjugaaiim um publishing as Benjamin umminga 11 Explain lysogeny and how the lytic cycle may be induced in lysogens o It is the process in which a Virus incorporates its genetic material into the genome of its host This allows the Virus to lie dormant within the host until it enters the lytic stage when the Virus reproduces o It always integrates between galactose and biotin operons attachment site 0 Lytic cycle may be induced by lysogens by induction This is triggered by a drop in the levels of lambda repressor caused by UV lightchemical mutagens This is also known as the temperate phage see below Copyright The McGrawHill Companies Inc Permission required for reproduction or display Phage DNA Bacterial chromosome v Phage injects Exposure to New phages I its DNA into a r stress such as bacterial excision from host cells V chromosome L ic e cle 39 armawwi L so enic c cle Vt Y 2 Y 9 y r I p x K quot N I 1931 1 HWVW M 2 I 3x r3 5 I I I39 R 5quot I I I i z I I I x migir t u A I 1 i 3 1 ma73 39 39 quot3 I 5 le39 quot 39 1A Iquot39 Cell lyses integrates 39 and releases into host the new phages chromosome if 7 Phage DNA r W A Prophage DNA quot directs the vVI x is copied when H synthesis of a 39 I cell divides 39 many new phageS 3quot Prophage 12 Describe the effects of animal viruses on their hosts Most use dsDNA or ssRNA Animal Viruses can bud from their cells and it takes over the genetics Since Viruses don t have metabolic pathways it shuts the metabolic pathway off in the host 13 Distinguish between acute latent and chronic viral infections know examples of each Acute rapid onset and gets over quickly Ex common cold and u The symptoms relate to cell damage Latent Viral DNA gets into the cell and hangs out persistent infection It doesn t replicate with the host chromosome No antibodies show up at this time which is why you don t show symptoms all the time Ex cold sore on lip Chronic incorporates onto chromosome to make a Virus factory but doesn39t kill the host cell Virions released by budding carcinogenic tumors It uses a slow release and can eventually cause death There are constant antibodies EX HIV to T helper cells The T helper cells are infected and the symptoms are related to suppressed immune system Cancer The Virus can either a insert an oncogene cancer gene into the chromosome of the cell Proliferation occursundifferentiation and the shape of the membrane changes B inserts into a protooncogene normal gene in body but it is susceptible to turn into a cancer gene EX HPV is caused by a Virus 14 Understand the replication process of HIV a retrovirus A retrovirus uses reverse transcriptase to change RNA to DNA It integrates into the host DNA and undergoes transcription and budding to release It is ssRNA segmented genome It specifically attaches to helper T cells The whole Virus goes into the host uncoated at the membrane Reverse transcriptase is brought with the Virus to go from ssRNA to dsDNA It is then incorporated in to the host DNA Envelope is from the host cell lipid bilayer and the rest is made through transcription and translation of DNA Virus particle 55 RNA two copies 1 Entrance 2 Uncoating 5 ss RNA 1 3 Reverse transcription LTR ds DNA LTR 1 4 Travel to nucleus and 1 integration into host DNA Host DNA LTR Provirus LTR 5 Transcription 5 Viral mRNA and 39 genomic RNA 6 Encapsidation l 1 55 RNA 39 Nucleocapsid R 55 RNA 7 Budding Host cytoplasmic 39o membrane Release 39 Virus 0 o 0 particle O 0 Figure 926 Brock Biology of Microorganisms 1 1e 2006 Pearson Prentice Hall Inc 15 Explain the role of viruses in causing cancer oncoviruses 0 Viruses cause cancer by inserting into a protonocgene turning it into an oncogene This causes overreproduction of the cell or by inserting an oncogene into the DNA Chapter 161 162 164 168 172 16 Know the basic structure of DNA 0 DNA is tightly structured 0 DNA is made up of six smaller molecules a five carbon sugar called deoxyribose a phosphate molecule and four different nitrogenous bases adenine thymine cytosine and guanine o The rails of the ladder are made of alternating sugar and phosphate molecules The steps of the ladder are made of two bases joined together With either two or three weak hydrogen bonds 0 The basic building block of DNA is called a NUCLEOTIDE 0 A nucleotide is made up of one sugar molecule one phosphate molecule and one of the four bases Here is the structural formula for the four nucleotides of DNA Note that the purine bases adenine and guanine have a double ring structure While the pyrimidine bases thymine and cytosine have only a single ring The Nucleotides of DNA imp H I 39 H Era H 2 N H NEH HH N H Ag N H fa CH Ndfuikwa N N 39 HCI EHn HID EH H 339 3 Ill HU TH E c mH EHH mH mH Adenine Guanosine Thymine m i Furines Pyrimidines o The nucleoid location of chromosome and associated proteinsit is irregularly shaped bc there is no membrane around it o Plasmidsextra chromosomal DNAsmall closed circular DNA molecules They exist and replicate independently They contain a few genes that are nonessential genes and this gives the cells an advantage 0 There are no housekeeping genes on these 0 Smaller than a chromosome 0 Plasmids can keep making copies even when the chromosome isn t replicating o If they aren t transcribed it degrades and must be grown in antibiotics if that s how plasmids grow 17 Understand the terms associated with bacterial genetics 0 Gene DNA segment that codes for polypeptide rRNA or tRNA 0 Example hisC 0 Genotype specific set of genes an organism possesses the nucleotide sequence 0 Phenotype set of observable characteristics 0 Example His His Wildtype strain strain isolated from nature 0 Mutation stable heritable change in nucleotide sequence genotype is altered may or may not have an effect on the phenotype of an organism 0 Example hisCI 18 Explain how mutations arise 0 Spontaneously arise without exposure to external agentsmay result from errors in DNA replication 0 Induced develop after exposure to a mutagen 0 Base analogs the base looks like the nucleotide but it is not the same The cells will put in those analogs and it will put in these analogs and it will be wrong 0 DNA modifying agents 0 Intercalating agents I Causes a break bubble deletions additions 0 Sitedirected mutagenesis technique whereby a gene with a specific mutation can be constructed in vitro 19 Compare and contrast point and frameshift mutations and their effects 0 Point mutations this mutation occurs when a single nucleotide is replaced with another nucleotide base 0 Insertion and deletion fall under this category 0 Sometimes this is caused by heat or radiation that causes an error in DNA replication 0 This occurs on a single DNA molecule or an exon I Ex sickle cell anemia 0 These mutations are subdivided into 0 Nonsense mutations code for the stop codon o Missense mutations occurs in the genes that code for a different AA 0 Silent mutations don t effect the function of the proteins and code for different or same AA Frameshift mutations mispairing of the DNA molecule causes the frameshift mutations o This usually occurs by insertions or deletions o The entire info changes because of frameshift mutations o The results errors in DNA replication damage to DNA the action of the mobile genetic elements such as transposons 0 Possible effects alters reading frames that can be nonfunctional protein or code death 20 Distinguish between the various point mutations Missense mutation single nucleotide change results in a codon that codes for a different amino acid Nonsense mutation DNA that results in a premature stop codon or a nonsense codon in the transcribed mRNA and in a truncated incomplete and usually nonfunctional protein product Silent mutation mutations in DNA that do not significantly alter the phenotype of the organism in which they occur Silent mutations can occur in noncoding regions outside of genes or within introns or they may occur within exons Wild type most normal allele Keep in mind transition purine for a purine or pyrimidine for pyrimidine and transversion pyrimidine or purine as well 21 Understand the expression of mutations forward vs reverse Wildtype most prevalent form of a gene Forward mutation Wild type to mutation form aka a new allele Reverse mutation mutant phenotype into a Wildtype phenotype Revertant the process by which mutant DNA is changed so that the protein inactivated by the first mutation is reactivated by the second 0 Same site revertant the mutation is the same as the second site but the mutation occurs in the stop where the original mutation occurred 0 Second site revertants one mutation occurs and the original mutation is still there but it is a different mutation that fixes that mutation suppressor mutations 22 Describe the phenotypic effects of mutations in bacteria Morphological change in colonial or cellular morphology Lethal kills the organism Conditional expressed only under certain environmental conditions Resistance resistance to pathogen chemical or antibiotic mutation caused it be resistant to Ab or a pathogen Biochemical change in metabolic capabilities o Auxotrophic mutant form of the wildtype this is unable to make an essention macromolecule such as an AA or a nucleotide It has a conditional phenotype The wild type strain arose from a protoroph nutritional wild type 23 Distinguish between prototrophs and auxotrophs Prototroph bacteria CAN grow on minimal medium which only contains inorganic salts a carbon source and water wild type Auxotrophic bacteria will NOT grow on minimal medium but it can GROW on minimal medium plus one or more specific nutrients or supplements or on rich media mutant 24 Describe how to detect and isolate mutants including the replica plating technique Mutant detection observation of changes in phenotype screening Selectable mutations confers advantage to the organisms that possesses them 0 EX drug resistance Selection placing organisms under conditions where the growth of those with a particular genotype will be favored 0 Ex conditions Replica plating can be used to detect auxotrophic mutants This is a negative selection 25 Know the difference between screening and selection Selection selecting for bacteria to grow Screening this is used for individual bacterial colonies to find one that contains a plasmid of correct structure this is done by looking at the DNA sequence 26 Describe the possible fates of donor DNA during horizontal gene transfer HGT can happen when the cell is competent For instance a donor bacterium dies lyses and releases DNA into the environment The other bacterium takes in the DNA and expresses the DNA known as transformation Or it can happen through a virus when a virus makes a mistake Instead of carrying VIRAL DNA it carries BACTERIAL DNA Once it gets in it picks up the traits from the virus known as transduction It can happen by conjugation plasmid or chromosomal transfer Copyright The McGrawHill Companies Inc Permission required for reproduction or display ReDr W Pop laton U I of stable ll Reproducm recombinants integration of donor DNA Donor DNA Partially diploid conjugation recipient cell l i Ye Transformation Donor DNA Se Transduction Keg a plasmdl Don Recombinant Semi QNA can7 pl cate 0t R Recrpient s v39 chromosome No stable recombinants 27 Describe homologous recombination in bacteria 0 One or more nucleic acid molecules are rearranged or combined to produce a new nucleotide sequence 0 Homologous recombination is a way that foreign DNA gets on the chromosome It usually involves a reciprocal exchange between a pair of DNA molecules with the same nucleotide sequence 0 DNA strand breakage and reunion leads to crossover I DNA strand is nicked I SSB protein and RecA protein complex formed picks up foreign piece of DNA and drives through the DNA called strand invasion I Recipient DNA invaded I Crossover leads to exchange which is then ligated to form two recombinant DNA molecules Donor DNA Endonuclease nicks DNA Donor Nick Binding of 558 protein 558 protein Donor ReCipiENt A DNA a Strand invasion RecA protein 0 o Development of l crossstrand exchange gt 4 Resolution Resolution at D sites at Vsites v Figure 1 0 9 Brock Biology of Microorganisms 1 We 2006 Pearson Prentice Hall Inc 28 Compare and contrast insertion sequences and transposons 0 Insertion sequence only carries the gene for transposaseshort segents 1000 base pairs 0 Transposons contains genes other than those used for transposition It is large than IS 29 Understand the mechanisms of transposition simple and replicative 0 Segments of DNA that move about the genome in a process called transposition o It can be integrated at a target site in the chromosome and it is usually site specific be it is important to get the gene in a specific place 0 It has a transposase gene recognizes target sequence and puts it somewhere else or makes a copy of it o It is bound by inverted terminal repeats 30 Describe bacterial plasmids their signi cance in a bacterial host and their role in horizontal gene transfer 0 Bacterial plasmids extra chromosomal elementcircular 0 3 important elements origin of replication selectable marker gene and a cloning site a place to insert foreign DNA 0 Significance plasmids can copy themselves independently of the bacterial chromosome so there can be many copies of a plasmid 0 Transformation transduction and conjugation are how plasmids are transfered 31 Be able to read a plasmid map i l ri iabl Moniker mmuicr Eianab il i39iud 5m 5 j 397 l I I 39iir39i E tj Filli E P laamnd Mp Imertr ame 5 d Er Y 1 39 Heazrlt39 kirlw 51 u g I39ll39rlr rsr quot3J1 f mobmac Itquot A l eaigaame f A firm a Iquot L 39h fr EHriw39 m tJg iutistnrm 32 Know why plasmids are useful as cloning vectors 0 Small autonomously replication DNA molecules that can eXist independently or as episomes It can eXist as single or multiple copies 33 Describe the process of bacterial conjugation 0 In bacteria the direct transfer of DNA between two cells that are temporarily joined 0 Conjugative plasmids tra region gene for conjugation It can transfer copies of themselves to other bacteria through conjugation o pili connects the two cells F plasmid nicked in one strand strand goes into F cell while simultaneous replication of same strand occurs in F cell synthesis of complementary strand in recipient cell both end as F cells both are donors Bacterial chromosome quotH PIIUS F ell donor F plasmid recipient y l 39 Cell pairs stabilized F plasmid nicked in one strand Transfer of one strand from Fcell to F cell F plasmid simultaneously replicated in Fcell Synthesis of complementary strand begins in recipient cell 5 IEO u v l I fquot Completion of DNA transfer it and synthesis Cells separate Figure 1022a Brock Biology of Microorganisms 11e 2006 Pearson Prentice Hall Inc 34 Understand the process of transformation in general and the concept of cell competence 0 It is the uptake of naked DNA by a competent cell followed by incorporation of the DNA into the recipient cell s genome 0 Competent Bacteria Bacteria that can take up naked DNA DNA strands for transformation Used by Molecular Biologists to transform in laboratory experiments 0 Competence Factor This is released by competent bacteria into the medium before cells will open up to DNA fragments Hell 35 Know the significance of the following abbreviations RecA IS Tn tnp F F tra ori 0 protein used in homologous recombination insertion sequence transposon transposase gene positive for fertility negative for fertility gene not able to do conjugation transfer genes 0 origin of replication 36 Compare and contrast generalized and specialized transduction o Transduction transfer of bacterial genes by a Virus 0 Generalizedalmost any part of bacterial genome can be transferred during viral assembly fragments of host DNA are mistakenly packaged into phage head transducing particle Occurs during lytic cycle 0 Specialized carried out only by temperate phages that have established lysogeny Only specific portion of bacterial genome is transferred and it occurs when prophage is incorrectly excised 37 Understand how to detect recombinants 0 Trp cells placed on tryptophan lacking agar nothing grows o Trp cells with DNA from Trp cells placed on tryptophan lacking agar if growth occurs transformation happened 38 Describe PCR and its uses Know the three steps of PCR in order and what is needed for each step 0 It synthesizes large quantites of a DNA fragment It targets DNA primers taq polymerase and deoxyribonucleotide triphosphates o 3 steps 0 Denature target DNA with heat around 95 degrees Celsius o Anneal primers bind to target DNA around 55 degrees Celsius 0 Extension copies of target DNA are synthesize with a temp of 72 degrees Celsius Chapter 322 323 39 Know the locations of the normal microbial ora inon the human body and its role in maintaining good health Know where bacteria should not be found in the human body 0 microbes regularly found at an anatomical site associated with healthy body tissue relationship begins at birth from vagina and breast milk found on surfaces of the body warm places normally not found on the internal tissues should not be found in heart lymph or internal organs 0 infection does not always cause disease bacteria can just be growing on your body vs disease 40 Describe the characteristics of the bacteria found in and on the skin nose nasopharynx oropharynx respiratory tract eye external ear mouth stomach small intestine large intestine and genitourinary tract 0 Skin 0 Propionibacterium acnes and S aureus 0 has both resident and transient mircobiota mechanically strong barrier inhospitable environment slightly acidic pH high levels of NaCl many areas low in moisture inhibitory substances lysozyme cathelicidins acne vulgaris and body odor sebum oilywaxy matter secreted from sebaceous Propionibacterium acnes slowgrowing typically aerotolerant anaerobic Grampositive bacterium linked to the skin condition acne O o comedo zit 0 body odor caused by gram bacteria amp moist area Nose o S aureus and S epidermidis 0 can be opportunistic pathogens Nasopharynx o Streptococcus pneumoniae Neisseria meningitidis and Haemophilus in uenzae 0 may contain low numbers of potentially pathogen microbes Oropharynx o alphahemolytic streptococci semibreakdown on blood agar diphtheroids gramnegative cocci anaerobes in tonsillar crypts Respiratory tract 0 no normal microbiota 0 only particles smaller than 10um in diameter reach the lungs o microbes removed bycontinuous mucus stream generated by goblet cells 0 ciliated epithelial cells 0 phagocytic action of alveolar macrophages 0 lysozyme in mucus Eye 0 primary bacteria staphylococcus epidermidis 0 small numbers of bacteria found on the conjunctiva of the eye 0 conjunctivitis pink eye 0 bacterialgreenyellow pus very itchy stuck shut 0 viral itchy eyes and watery discharge External ear 0 coagulasenegative staphylococci and Corynebacterium 0 similar to skin ora o fungi can be a part of natural bacterial ora but not as high in number Mouth 0 Streptococcus sp 0 contains organisms that survive mechanical removal by adhering to gums and teeth saliva conditions teeth to allow this 0 contribute to formation of dental plaque dental caries gingivitis and periodontal disease 0 anaerobes present in space between the teeth amp gums o biofilms can form in the mouth Stomach o Helicobacter pylori can cause ulcers 80 asymptom can benefit in keeping pH higher and acid re ux down most microbes killed by acidic conditions pH2 some survive if they pass through really quickly some survive if ingested in food particles small intestine o Enterococcus faecalis and lactobacilli o as you move into intestines the pH increases and number of bacteria increases large intestine O O O O o Bacteroides thetaiontaomicron o colonizes exfoliated host cells food particles and sloughed mucus 0 largest microbial population of the body 0 10A12 microbes per gram of wet weight 0 colonic bacteria produce essential vitamins B 12 ribo avin K and thiamine o bacteria eliminated from body by peristalsis desquamation shedding of outer layer of a tissue and movement of mucus o bacteria make up 13 of the weight of fecal matter 0 replaced rapidly 2 doublings per day 0 c diff nosocomial diarrheatoxic colon fecal implant 90 effective in fixing this 0 pH continues to increase from small intestine 0 Genitournary tract 0 kidneys ureter and bladder o normally free of microbes 0 some microbes in the distal portions of the urethra but when you get bacteria that should not be there it leads to a UTI E coli is most common cause 0 female genital tract complex microbiota in a state of ux due to menstrual cycle 0 Lactobacillus acidophilus predominates in vagina maintains acidic conditions 0 if you knock out normal ora of the vagina with antibiotics it can lead to yeast infection 41 Know the discussed examples of bacteria found in each of the mentioned locations 0 This is mentioned above 42 Describe the conditions of each location that support or do not support microbial growth ex pH of intestines 0 This is mentioned above 43 Understand how normal microbial ora can cause infection and sometimes disease usually normal microbiota and the host mutually benefit each other prevent colonization by pathogens produce vitamins stimulate immune response opportunistic pathogens normal microbiota that produce disease under certain circumstances compromised host debilitated host with lowered resistance to infection Chapter 33 34 35 37 36 38 Selected Topics 44 Define immunity and immunology and describe the human immune system 0 Immunity ability of host to resist a particular disease or infection 0 Immunology the study of immune responses 45 Compare and contrast nonspeci c innate and speci c adaptive immunity know the characteristics of each 0 Nonspecific innate innate and natural This is the ability to be born with this o It acts as a first line of defense 0 The bodys built in ability to recognize and destroy pathogens or their products offers resistance to invaders or microbes o It doesn t rely on the previous exposure 0 Lack immunological memory 0 Includes barriers chemical mediators and phagocytes 0 Specific adaptive this is an acquired ability Two types cell mediated T cells and antibody mediated B cells and the antibodies it makes 0 Recognizes antigens from oathogens 0 memory 0 Discriminates bw self and nonself 46 Know the role of phagocytes in nonspecific immunity and how some can initiate a speci c immune response 0 Phagocytes engulf things in nonspecific immunity which means it could engulf LPS acids fungal components 0 Results in in ammation 0 It includes neutrophils macrophages and dendritic cells I Macrophages and dendritic cells do something neutrophils cant they can act as APC s Neutrophils secrete in ammatory cells and the other ones have antigens on an immune cell 0 Some act as antigen presenting cells 0 APC s peptides from the engulfed pathogen are presented outward from the cell It links a nonspecific response to a specific immune response and activated lymphocytes 47 Compare and contrast cellmediated and antibodymediated speci c immunity 0 Cell mediated Cell mediated immunity is an immune response that does not involve antibodies but rather involves the activation of phagocytes antigenspecific cytotoxic Tlymphocytes and the release of various cytokines in response to an antigen 0 T cells 0 Make up most of the lymphocytes in the blood 0 Mature in the thymus o Require antigen binding to T cell R for activation and continued replication Differentiate into effector cells known as T cells and cytotoxic cell and lastly memory T cell 0 T cells play a role in B cell activation I Helper T cells secrete chemicals to stimulate other cells and in ammation 39 Cytotoxic T cells killers carry digestive enzymes make holes in the cell and kills it o Antibody mediated an Adaptive immunity mediated by soluble globular host proteins called antibodies or immunoglobulins B cells Mature in bone marrow Not mobile hang around in lymphoid tissue Activated by binding a specific antigen and needs T cells for activation O 0000 o Differentiates into plasma cells and memory cells lIumoral antibodymediated immune response Cellmediated immune response Engutzd by Allacrophag Antigens di Iayed by APC infected cel activate Stim Iates ceil Stimulates Helper Stimulates cto Ql T T cell Gives ise to Stim Iates Stimtates Stim lates 97 7 rl a l a lggaamplgt3lt 35211113 Stim Iates 39 quotquot 39Kc tiv 9333 lcytotoxicD T cell a39 nix 39AMIbOdIeS Vi 4 6quot Defend against extracellular pathogens by binding to antigens and Defend against intracellular pathogens and cancer by binding to making the pathogens easier targets for phagocytes and complement and lysing the Infected cells or cancer cells Copyright 53 Pearson Education Inc publishing as Benjamin Cummings 48 Describe T cells and B cells and their roles in speci c immunity 0 T cells don t last as long as B cells 0 T cells secrete chemicals to stimulates other cells and in ammation while cytotoxic cells are the killer T cells that carry digestive enzymes and make holes in the cell and kills it 0 Look at question above for the major di erences 49 Distinguish between a primary and secondary immune response 0 Secondary production of antibodies after a second or subsequent exposure to an antigen faster than primary response 0 Primary initial production of antibodies in response to the presence of an antigen often takes several days 50 Explain how antibodies eliminate pathogens 0 Agglutination cells bind one Ab can bind 2 cells which is Why they clump up It keeps bacteria from infecting other cells 0 Complement fixation serum protein if Ab bind and compliment bind then it will lead to sequence of lysing the bacterial cells and destroys them 0 Neutralization Antibodies inhibit the biological action of growth factors by binding to their receptors Target cells starve to death without the stimulation of growth factors 0 Precipitation This describes the reaction between soluble antibody and soluble antigen in which an insoluble product results 0 Opsonization enhanced phagocytosis Engulfs it a lot faster and recognizes it more Neutralization Antibodies block binding Copyright The McGraw Hill Companies Inc Permission required for reproduction or display Antibody Precipitation Opsonization Cellfree molecule in solution a lt Epitope Antigen Opsonized bacteria engulfed more readily Crosslinked bacterial cell antigens Lysing bacterial cells 51 Distinguish between the types of acquired immunity active vs passive natural vs artificial Natural immunity can get active immunity by getting sick Getting active be you make memory cells and Ab s another natural way is passive when a baby gets Ab from milk This protects the baby s immune system Passive bc baby have no memory and no Ab Artificial vaccine gives you active immunity You make memory and Ab s another way passive immunity forget to get shot and got tetanus so you get preformed Ab s from someone else Copyright The McGraw Hill Companies Inc Permission required for reproduction or display Acquired Immunity I l I Natural immunity Artificial immunity is acquired through the normal life experiences of is that produced purposefully through a human and is not induced through medical means medical procedures also called immunization I I I I l I Active immunity Passive immunity Active immunity Passive immunity is the consequence of is the consequence of is the consequence of a is the consequence a person developing his or one person receiving person developing his or of one person receiving her own immune response preformed immunity her own immune response preformed immunity to a microbe made by another person to a microbe made by another person Infection Maternal antibody Vaccination Immune globulin therapy PhotoDisc RFGetty Immune globulin therapy CreatasPictureQuest 52 Understand how vaccines work and describe the types of vaccines used today 0 Preparation of microbial antigens to induce immunitiy 0 May consist of killed living weakened microbes or inactivated bacterial toxins called toxoids puri ed cell material recombinant vectors or DNA 53 Explain how herd immunity may protect susceptible individuals 0 When 8095 of herd is immune entire herd is protected Immune status of population rather than individual animal is considered 54 Describe antigenic shift and its impact on public health 0 Antigenic shift is an abrupt change Copyright The McGrawHill Companies Inc Permission required for reproduction or display Duck influenza virus Human influenza virus Duck influenza virus with human HA spike 55 Describe infectious disease and what factors will in uence the outcome CODVIIQIII The McGrawHill Companies Inc permission Icquucd lot rcptoduclxon or display 3912 Death I I Illness U I o E I C o a lt19 0 C Q 3 U s E gt g 2 8 D D U D 0 Q E 2 O C 9 u 339 9 o E 6 4 6 9 O c g D O 2 e Illness Initial Time exposure to microbe When you are exposed to the right amount of pathogens this brings you to incubation period pathogen getting into your body no symptoms during incubation You are not contagious during incubation To be contagious your body has to be secreting the disease Prodromal stage some uncharacteristic symptoms Illness period symptoms and contagious Once the symptoms level off you are not contagious Convalescent period getting better Prodomal and illness period is the only time youre contagious 56 Understand the terms associated with epidemiology Epidemiology the study of the occurrence distribution and control of diseases endemic disease always thereexz u maintains a relatively steady low level frequency at a moderately regular interval outbreak sudden unexpected occurrence of disease usually focal or in a limited segment of population epidemic sudden increase in frequency above expected number pandemic increase in disease occurrence within a large population over wide region usually worldwide 57 Distinguish between direct and indirect routes of disease transmission Direct infected host 9 susceptible host Indirect vectors living thing like a ee that can take the bubonic plague and giving it to humans 0 Fomites 9 susceptible host 58 Distinguish between commonsource and propagated epidemics DISEASES Common source Rapid rise in people who get sick a deep decline everyone got sick at the same time common source of pathogen noncommicable noncontagious common source Propagated Gradual increase and decrease one person infects someone propagated this helps determine measures to prevent the spread pathogen 59 For each of the microbial diseases listed below be able to brie y describe the following a cause name of bacterium or virus b general characteristics of the microbe bacteria Gram reaction and shape viruses type of genome and shape c route of transmission d characteristic symptoms Peptic Ulcer Disease 0 O O 0 cause name of bacterium or virus Hilcobacter pylori general characteristics of the microbe gram and motile route of transmission not clear but it is thought to be through kissing and food transmisson characteristic symptoms ulcers Nongonococcal Urethritis Chlamydia trachomatis 0 cause name of bacterium or virus Neisseria gonorrhea 0 general characteristics of the microbe gram o route of transmission sexually prenatal o characteristic symptoms buming sensation when peeing skin lesions and arthritis MRSA Infection 0 cause name of bacterium or virus staphbacteria 0 general characteristics of the microbe gram o route of transmission direct contactwound o characteristic symptoms soresboils Toxic Shock Syndrome 0 cause name of bacterium or virus S pyogenesaureus 0 general characteristics of the microbe gram o route of transmission growth on mucus membrane that produces a toxin 0 characteristic symptoms organ failure high fever Anthrax Inhalation 0 cause name of bacterium or Virus B acillus Anthracis 0 general characteristics of the microbe gram spore o route of transmission activated by growing cells in the body 0 characteristic symptoms death Hantavirus 0 cause name of bacterium or Virus bunyaVirus 0 general characteristics of the microbe Virus o route of transmission rodents urinefeces o characteristic symptoms abdominal pains soreness death gt Even if we do not cover these diseases in lecture you are still responsible for the information NOTE Unless otherwise stated you are responsible for all of the unit objectives even if they are not covered in lecture see textbook UNIT 4 ANIMATIONS TO WATCH Access Via httphigheredmcgrawhillcomsites0073402400student View0 choose the chapter then select animations Chapter 6 Lambda Phage Replication Cycle Steps in the Replication of T4 Phage in E coli Chapter 16 Addition and Deletion Mutations Bacterial Transformation Conjugation Transfer of the F Plasmid Simple Transposition Transposons Shifting Segments of the Genome Chapter 17 Polymerase Chain Reaction Access Via httphigheredmcgrawhillcomsites0073375268student View0indexhtml choose the chapter then select animations Chapter 14 Mechanism of Transposition Transduction Specialized Transduction by Temperate Phage Chapter 32 Phagocytosis


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