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by: Murphy Mante

Microbiology BIOL0004

Murphy Mante

GPA 3.68


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Class Notes
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This 79 page Class Notes was uploaded by Murphy Mante on Tuesday October 20, 2015. The Class Notes belongs to BIOL0004 at Sierra College taught by Staff in Fall. Since its upload, it has received 11 views. For similar materials see /class/225365/biol0004-sierra-college in Biological Sciences at Sierra College.

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Date Created: 10/20/15
Desmids microscopic algae D Eukawa K Protista Ph Chlorophyta Magnification 400x Often composed of two semicells connected by a narrow isthmus The 2 semicells appear as mirror images Pb Chiarophyta monmm an 100x A lamenth groan plane with ribbun lik spiral chloroplasts Oedogonium D Eukarya K Pm sta Ph chm me mani m nn F llamamaus amen algae xiii acid a AWE 9 w wrmidsmwfw Cladophora D Eukarya K Pmtista Ph Chloraphyta Magni cation 40x Murtiple radashaped malls mnnmea togethar forming Dmnahing filamenta Farm masslike an sail or aubrmar ed racka uo ln Diatoms D Eukarya K Pratiata Ph Bacillaricphyta Magni oalion 100x 12 different types cf diatams Ceratium D Euk awa K Protista Ph Dino agellata Magnification 400x 4 prominent horns and a transverse furrow containing a whip like flagellum which causes the living cell to spin Pe dinium distil D 5qu K mom Din aaia am Mwnl man 4mm Ea ml 5 39Wmd by gunman psiam chitin it an Ingmar upmmnm I r gram gnaw 43quot annulusi gunman the n la am WEEMZC S W lsaj39r39 rpseudobodi a rat 9 reef used for locomotion and food getting Radiolar ian skeletons D EuKBrya K Pmtlsta PH Rhizopoda Magni cation 100x Typically pa enated by humercuz halas Gr park39s anal equipped with 8 Was Pseu pads extent DUI the hole ls More SD than diatoms mtni l auntie arumlatfaa Paramecium caudatum aurelia 0r buma a u D Eukmwi Prmmm Ph Giliopsmm Magni cation 1 am rounded mspovared w39f cil DR sanctum insidga is thin nucleus T Q 39 3 y quot1 7 ridIQ 7 yfV 3 13 J1 7 81 o D Eukarya K Protista Ph Euglenozoa Magnification 400x Single celled usually linear but Without cell walls can Chan e shape Nucleus in the center Single flagella from one end Trypanosoma lewisi D Eukana K Protista Ph Euglenozoa Magnification 1 000x Seen w RBCs Eel like cells Ea with a dark oval shaped nucleus an a smaller kinetoplast Single flagellum exten 39 length of cell and is attached by an undulating membrane Fasciola hepatica Sheep Liver Fluke D Eukarya KtAnlmalia Ph Platyhalminmes Cl Tmmatoda Magni cation Fasciola hepatica Sheep Liver Fluke D Euknrya K Animalm Ph Hatymlmmmas CI Trammoda Magnificaiion 1 Ox Canada larval form that exams thb water snail and towns a cyst on grass unmet S ohiistosoma Blood fluke D iE ukarya 39 K Animalla gt P h39 P la39ty h39el minthes 39 QJ Tremat dd a Magnifi at ion 40x B cod fl like perca riae h39 ater snails Taenia pisifannis Dog Ta pewarm or a w w D Eularam K Mirna Ph Platyholmtntm CL Cumm Magni catmn 4m utwmd wing are used fur an mum w a SEE W quot 392 1 quot av 39 7 39h 5quot L ih I V w 7 quot I r lgix wrr h d i l 394 I i 1 w I m WM a i 3 M 1er i fur a Trichinella spiralis larvae Trichinosis D Euk a rya K Anlmalia PnAsahalrr nthm manmm bn 100x Larvaein muscle timprabphl mum Trichinela spira lis larvae Trichinosis if 0 D Eukarya 0 K Animalia 1 PhAscheminthes Magnification 400x Encysted larvae in muscle tissue NeCator ameriCanus d 1 D Eukarya KAnimalia PH Asahairnimhas Magni m bn 2132 Adult male hoakworrn Maul contains sham cutting wailL F E e m mg w h w mgng e gw Q a E kg m m U a Vii I r 39 6quot afgyelshbwn39 bay quot lt2lt39 393quot51w quot30 quotc3 3 0amp1 g 3956 quotQ 1 I HNTl Onchocerca mlvulus River Blindness D Eukarya Kt Animalia Ph Awhalminthas Magnification 1 09 X8 of an adult warm uncaring uterus full of maria larva 09177730911100 andersoni Ixodes dammini Deer Tick D Eukarya PCAnimalia Ph Arthropods Magni ca on 16x 7 Wu V Cr E j v J turmm Pediculus humanus capitis Head louse v quot D Eukarya PCAnimalia PhArthwpoda Magni cationZ x Eatoparasite n Natice hoeked claws B jointed lags Xenopsylla cheopis Rat flea O o D Ema13m K mm Ph Anhmma Magni cation 40x Ectopams e F13 segment 6 legs Highly adapted hr jumplw Bristle painting backwardl Culefx pipiens 1 D Eukarya 0 K Anima lia 0 Ph Ar th ropoda MOSquito Magnification 1 0X Insect wiith 6 slehder j Oint ed legs Transmits WNV Amp hit ch ous Flagelilar39 Stain Magnificatibh 1 000x 0 Spiral shaped bacteria With polar or amphitrichous f lage39JJ ar 3 r39ra39i39fg39eimie nt Peritrichous agella v Magni ca an 1000 Rad shaped bactaria stained with a flagellar stain Introduction to Viroids and Prions Viroids Viroids are plant pathogens made up of short circular single stranded RNA molecules usually around 246 375 bases in length that are not surrounded by a protein coat They have internal base pairs that cause the formation of folded three dimensional rod like shapes Viroids apparently do not code for any polypeptides proteins but do cause a variety of disease symptoms in plants The mechanism for viroid replication is not thoroughly understood but is apparently dependent on plant enzymes Some evidence suggests they are related to introns and that they may also infect animals Disease processes may involve RNA interference or activities si1nilar to those involving mi RNA Prions Prions are proteinaceous infectious particles associated with a number of disease conditions such as Scrapie in sheep Bovine Spongiform Encephalopathy ESE or Mad Cow Disease in cattle Chronic Wasting Disease CWD in wild ungulates such as muledeer and elk and diseases in humans including Creutzfel dIacob disease CID 39 1 G88 Alpers syndrome in infants Fatal Familial Insomnia FFl and Kuru These diseases are characterized by loss of motor control dementia paralysis wasting and eventually death Prions can be transmitted through ingestion tissue transplantation and through the use of comtamjnated surgical instruments but can also be transmitted from one generation to the next genetically This is because prion proteins are encoded by genes normally existing within the brain cells of various ani1nals Disease is caused by the conversion of normal cell proteins glycoproteins into prion proteins Apparently the aInino acid sequences of normal and infective proteins are the saIne but prions have a unique three dimensional configuration that is induced by the presence of other prions Prions enter anilnal cells through endocytosis and accumulate within lysosomes but are not digested They cause the formation of aInyloid plaques within brain tissues The prion protein configuration is unusually stable but not functional in the usual sense By converting normal brain proteins into more prions the infective prions ulti1nately destroy brain function Prions are potentially very dangerous because they remain stable within the environment for an extended period of time They are resistant to denaturation by exposure to heat radiation or toxic chemicals Feed lots used to maintain stock animals have become contaminated by prions through contaminated feed and have remained infectious for years Although infection with prion proteins is almost always fatal researchers are working to develop therapeutic agents and a vaccine has been developed to prevent prion disease in mice This may eventually lead to a similar vaccine for humans See Internet links for more information Introduction to Viruses The term virus is Latin for poison and historically the name was applied to any agent that caused illness in humans Currently the term virus applies to a specific type of microbial agent A virus is a non cellular entity made up of a nucleic acid core DNA or RNA surrounded by a protein coat Viruses are obligate intracellular parasites hypotrophs and probably infect every type of living organism Most viruses tend to be host specific and are often categorized according to the type of organisms they infect They are generally much smaller than cells but they vary considerably in size A complete virus particle as it exists outside of its host is called a virion and is the infective form of a virus The origin of viruses is not entirely clear and it is possible that they came from cells Virology the science or study of viruses is a relatively new science because electron microscopes were required to observe viruses A virus that infects bacteria is called a bacteriophage meaning bacteria eater and a virus that infects E coli is called a coliphage Virion Structure in Greater Detail Though viruses vary considerably in size and structure they typically have common components e g a nucleic acid core and a protein coat or capsid Some viruses have additional structures as described below A The nucleic acid core or genome of a virus can be either DNA or RNA double or single stranded but viruses rarely contain both DNA and RNA the Mimivirus of Acanthamoeba polyphaga and certain human herpesviruses carry m RNA molecules In viruses that contain double stranded RNA the two strands are complimentary and antiparallel just as they are in DNA The viral genome may be either a closed loop or linear and may be made up of one or many segments Viral genomes range in size from around 4 to over 400 genes B The protein coat surrounding the nucleic acid core of a virus is called a capsid and is made of units called capsomers These are visible with an electron microscope and are often triangular in shape Capsomers are made up of smaller units called protomers that are protein complexes Many viral capsids are polyhedrons that are nearly spherical in shape but some are shaped like long slender rods C Some viruses have an additional layer called an envelope outside their protein capsid This is made of protein and lipids like those found in cell membranes lipid bilayer with integral and peripheral proteins A viral envelope is formed from a section of cell membrane taken from the host cell as the virus leaves D A tail assembly is another viral structure that may or may not be present Viruses known as T even coliphages have very complex tail assemblies that attach to the nucleocapsid capsid and nucleic acid core together Just below the nucleocapsid is a collar and below that the tail core surrounded by a tail sheath At the base of the tail core is a structure called a base plate equipped with tail pins short angular segments extending downward from the base plate and tail bers long thin structures resembling spider legs Regardless of their structure all viruses tend to have a silnilar strategy that is 1 Gain access to a host 2 Reproduce within that host cell 3 Get out If a virus gets into a cell it will often disrupt the cell s activity sometilnes causing death If the cell is a bacterium it may be lysed If a virus gets into a multicellular organism such as a human the damage it causes depends on what cells it infects and how many of these are killed Host defense mechanisms in uence the outcome In some cases the entire organism dies Bacteriophages are often used as models for virus activity because they are readily available and not hazardous to humans Bacteria are easy to grow in vitro and the viruses that infect them are easily obtained Bacteriophages can be divided into two categories based on how they affect their host these are cytolytic and temperate phages a A cytolytic bacteriophage is one that causes cell lysis so kills its host b A temperate avirulent or asymptomatic bacteriophage does not kill its host at least not right away and may become a prophage ie may incorporate itself into the chromosome of its host Cytolytic Bacteriophage Life Cycle A group of viruses known as T even coliphages T stands for type and the T even phages include T2 T4 and T6 can be used to illustrate a typical virus life cycle These viruses are cytolytic like the phages T2 and X174 viewed in the laboratory The life cycle of a T even phage can be divided into stages or phases as indicated below and begins with a free virion outside the host cell 1 Adsorption The binding of a virus to the cell surface of its host is called adsorption This step involves interaction between the tail fibers of the virus and receptors on the host cell surface viruses are host specific due to this interaction The virion can only attach to a specific type of cell and can move around until each tail fiber is contacting a receptor site on the cell surface When all tail fibers are attached they ex and allow the tail core to snap down so that the tail pins are touching the cell surface Once the tail pins attach the virus is not likely to come off 2 Penetration During the penetration stage the viral nucleic acid core enters the host cell The tail sheath proteins undergo a molecular reconfiguration and the tail core penetrates the cell surface The capsid and tail assembly are just packaging and a method of transmitting the virus to a new cell During penetration the nucleic acid core enters the cell leaving the other parts behind on the outside 3 Latent period or eclipse phase During the latent or eclipse period the viral nucleic acid is transcribed and translated The virus is dependent on the host cells ribosomes for the translation process because the virus does not have any Transcription may involve viral enzymes after these have been made but is initially dependent on host enzymes unless viral enzymes have been packaged within the capsid The viral genome is transcribed in segments or in a sequence as follows a Immediate early phage genes These genes encode enzymes Some of these preferentially transcribe viral genes and others chop up the host cell s DNA This provides a large quantity of nucleotides that are then available to make viral DNA strands This also prevents the cell from carrying on its own DNA related activity b Delayed early phage genes These genes encode enzymes used to replicate the viral genome The viral DNA may be reproduced 200 times or more c Late phage genes These genes encode the proteins needed to build the viral capsid and the tail assembly Since during replication the viral DNA may experience mutation the proteins encoded by the various genomes may not be identical This can result in variation within the virus population 4 Assembly or maturation During the assembly phase the viral components are assembled put together to form new virions Some of the proteins come together by themselves and others require assistance from other proteins called chaperonins or chaperonin proteins 5 Release or liberation During the liberation phase the cell is lysed and new virions are released into the environment This process may involve viral enzymes that soften up the cell wall The new virions are now free to infect other cells The length of time required for viral replication is variable and is dependent on factors in uencing metabolism within the host For bacteria grown in a batch culture where fission can occur every 20 minutes bacteriophage replication tends to be rapid A single virus particle might cause the destruction of an entire population with a few hours Restriction enzymes within the host cells provide the main line of defense for the bacteria Cytolytic bacteriophages are used clinically in some countries because they can kill bacteria that would otherwise be damaging to humans In situations where antibiotics are not available or are too expensive bacteriophage cultures provide an alternative method for controlling gastrointestinal infections caused by E coli Salmonella Vibrio and other infectious agents According to a recent report October 2006 the FDA has approved the use of a bacteriophage preparation from the Netherlands sold as LISTEX to control Listeria monocytogenes in cheese and poultry meat products Bacteria in the genus Listeria are psychrophiles capable of growing under refrigerator conditions and commonly associated with poultry especially turkeys They can cause potentially fatal listeriosis a disease usually causing gastrointestinal symptoms diarrhea fever malaise but can also cause neurological symptoms encephalitis and meningitis Temperate Phage Bacteriophage lambda Temperate phages also called avirulent or asymptomatic phages are those that do not kill their host cell at least not right away These bacteriophages can reside within the host without causing damage and may become incorporated into the host chromosome ie can exist as prophages A temperate phage known as Bacteriophage lambda is one example of a bacteriophage that can become a prophage but can also revert to a lytic life cycle This virus has a double stranded DNA genome that may be represented as a loop being closed by overlapping cohesive termini These cohesive termini are sometimes referred to as cos sites and are the basis for the naIne cosrnid applied to cloning vectors made from bacteriophage laInbda as described earlier The cohesive termini allow the phage genome to enter into the chromosome of the host at a specific location ie an endonuclease cut site that would have complimentary cohesive termini The viral genome has numerous genes and the regulation of these genes is somewhat complex The short version of the regulation is as follows a When the bacteriophage laInbda genome enters the host cell it is initially not committed to either a lytic or a lysogenic pathway Under certain circumstances a portion of the viral genome known as the cI gene is expressed This gene codes for a repressor protein that can block the transcription of the viral lytic genes Recall operon function an active repressor protein will bind to the operator site of an operon and block the transcription of the structural genes in that operon As long as the repressor protein is present the expression of lytic genes is repressed and the virus will not be able to complete a lytic cycle Other genes on the viral genome code for enzymes that allow the virus DNA to integrate itself into the host chromosome When these are expressed the viral genome can enter the chromosome and become a prophage b Whether the viral genome stays within the host chromosome or not is determined by a variety of factors one being the activation of a host gene called RecA The RecA gene of E coli codes for a proteolytic enzyme that catalyses the cleavage and inactivation of the cl repressor protein The RecA gene is activated when the E coli cells are stressed ie when they are exposed to stressful environlnental conditions such as exposure to ultra violet light or toxic chemicals Thus host cells that are stressed produce a protein coded for by the RecA gene that ultjlnately causes the viral genome to exit the host chromosome and revert to a lytic cycle In a sense the dying cell releases the viral genome genetic information much as passengers in a sinking ship might release a message in a bottle Temperate phages are associated with a condition or phenomenon known as lysogeny Lysogeny occurs when a temperate phage the genome of a virus establishes a stable non lytic relationship with its host cell In most cases the viral genome enters into the chromosome of the host and is then referred to as a prophage This viral DNA will be copied along with the host chromosome and maintained within the progeny population In other instances the viral genome is maintained outside the chromosome as a plasmid The presence of viral genes within a bacterial population will sometjlnes result in phenotypic changes ie the phenotype of the bacteria is in uenced by the expression of viral genes This phenomenon is referred to as lysogenic conversion sometimes as bacteriophage conversion A characteristic of bacteria that is often attributed to the expression of viral genes is toxin production Bacteria such as Cl ostridium tetam39 Cl ostridium botulinum C orynebacterium diphtheriae and other bacteria that frequently produce potent toxins are expressing viral genes Thus the Latin meaning for the term virus poison is quite appropriate A bacterium that is carrying a prophage may be referred to as a lysogenic cell If we consider the origin of this term it had to do with bacteria populations that appeared to initiate self destruction under certain circumstances ie they generated their own lysis Lyso lysis and genic generation These lysogenic bacteria when grown under laboratory conditions would appear to generate their own lysis when subjected to stressful conditions exposure to toxic substances ultra violet light etc As it turns out the viral genome plays a significant role in this lytic process as explained above Viral Classification Viruses are non cellular entities that reproduce only when within living host cells and most viruses are host specific for this reason viruses are often categorized according to the type of host they infect Those infecting tomatoes corn beans etc can be called plant viruses and those infecting cats horses and humans are called animal viruses Viruses that infect bacteria are called bacteriophages bacteria eaters or sometimes just phages Since the presence of viruses within their host often results in the development of disease symptoms many viruses were initially named according to the diseases they caused Plant viruses were named for the most common first recognized or most important type of host plant they infected and for the primary symptoms they caused under natural conditions for example tobacco mosaic virus barley yellow dwarf virus and apple chlorotic leafspot virus Animal viruses were initially classified in a similar manner but this was problematic because some are not host specific Thus although human wart viruses infect only humans in uenza viruses can infect humans water fowl and swine and the rabies virus infects a wide variety of mammals During the 1960s virologists proposed that all viruses should be classified according to their own shared properties rather than according to the organisms they infected the symptoms they caused or other properties relating to their hosts As a consequence two classification systems were developed The Hierarchical virus classification system and the Baltimore Classi cation System The Hierarchical virus classification system This system proposed by A Lwoff R W Horne and P Tournier 1962 and modified by the International Committee on Taxonomy of Viruses lCTV bases viral classification on four main characteristics 1 Nature of the nucleic acid RNA or DNA 2 Symmetry of the capsid 3 Presence or absence of an envelope 4 Dimensions of the virion and capsid Currently this viral classification scheme is most important from the family level down since higher taxa phyla classes orders are still being determined In general virus families are determined through genomics and proteomics ie the elucidation o evolutionary relationships through the analysis of nucleic acid and amino acid sequence similarities The names of virus families contain the suffix viridae e g Retroviridae Rhabdoviridae Reoviridae and genera include the suffix virus e g enterovirus cardiovirus rhinovirus etc The definition of species is difficult but usually includes a group of viruses sharing the same genetic information and host range e g human immunodeficiency virus HIV Viral subspecies or strains are indicated by number eg HIV 1 and HIV 2 The Baltimore Classification system Not included on Exam 2 The Baltimore classification system David Baltimore 1971 is based on the viral genome composition and viral strategy for gene expression By convention m RNA is designated as positive sense or positive strand RNA DNA with the same sequence written in the 5 3 direction is positive sense or positive strand DNA Complimentary sequences are designated as negative sense or negative strand RNA or DNA All viral genomes whether DNA or RNA generate m RNA molecules that allow for the production of viral proteins and facilitate viral replication The precise mechanisms involved differ for each virus family According to the Baltimore system of classification all viruses can be classified into seven arbitrary groups as follows II V I 1 1 1 Doublestranded DNA Adenoviruses Herpesviruses Poxviruses etc These viruses function like cellular DNA in that the strands separate and the negative sense DNA strand codes for m RNA Some of these replicate in the nucleus eg adenoviruses using cellular enzymes Poxviruses replicate in the cytoplasm and make their own enzymes for nucleic acid replication Singlestranded positivesense DNA Parvoviruses These viruses replicate within the nucleus to form complimentary negativesense DNA strands These then serve as templates for positive strand m RNA and DNA synthesis Doublestranded RNA Reoviruses Birnaviruses These viruses have segmented genomes Each negative strand genome segment is transcribed separately to produce monocistronic m RNA molecules Singlestranded positivesense RNA Picornaviruses Togaviruses etc These viruses enter their host in a form that can be translated directly genomic RNA is m RNA and occur in two forms a Polycistronic m RNA eg Picornaviruses Hepatitis A where naked RNA is infectious and does not code for viral RNA polymerase Translation results in the formation of a polyprotein product that is later cleaved to form mature proteins b Complex Transcription e g Togaviruses where two or more rounds of translation are necessary to produce genomic RNA Singlestranded negativesense RNA Orthomyxoviruses Rhabdoviruses etc These viruses require RNA polymerase enzymes directed toward viral RNA specifically and occur in two forms a Segmented e g Orthomyxoviruses where the first step in replication involves transcription of the negative sense RNA genome by viral RNA dependent RNA polymerase enzymes This results in the formation of monocistronic m RNA molecules that serve as the template for genome replication b Non segmented e g Rhabdoviruses where replication occurs as above and monocistronic m RNAs are formed Singlestranded positivesense RNA with DNA intermediate in lifecycle Retroviruses These viruses have a positive sense genome but are unique in that it is diploid occurs as two copies and does not serve as m RNA The viral genome RNA must be reverse transcribed to form DNA before new copies of viral genome can e generated


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