BIOL 209 1st EditionFinal Exam Study GuideWhat are the different methods used to identify specific microorganisms?Polymerase Chain Reaction (PCR) assay: based on DNA sequences unique to a particular microbeELISA assay: uses antibodies to detect structures unique to a particular microbeInformal classification: (used if microbe has not developed reagents) uses cell shape, dye staining properties, metabolic properties, and growth requirements unique to a particular microbeWhat are the differences in envelope structure that distinguish Gram-positive and Gram-negative bacteria? Gram-positive bacteria (firmicutes) contain teichoic acid and lipoteichoic acid with a thick cell wall/peptidoglycan layer surrounding an inner cell membrane. Gram-negative bacteria (proteobacterials) contain porin proteins, lipoproteins, and lipopolysaccharides with a thin cell wall/peptidoglycan layer sandwiched between an inner and outer cell membrane.List 3 extracellular appendages and describe their function.Flagella provide mobility, and in some cases adhesion. Conjugation pili are long protein fibers that mediate the initial attachment of conjugating bacteria, which allows the transfer of DNA from one bacterium to another. Fimbrae are relatively short protein fibers that contribute to adherence to inanimate surfaces, other microorganisms, and select host tissues. Biofilms are complex communities of microbes that adhere to a surface and each other through the production of a very thick and sticky slime layer.Compare a slime layer and a capsule; list their similarities and differences. A slime layer consists of loosely associated glycocalyx, which helps retain water and nutrients. A capsule is a thicker glycocalyx associated closely with the envelope. It can provide protection by blocking phagocytosis by host immune cells. What are the characteristics of a biofilm? What advantage does a cell gain by living in it? A biofilm is complex, dynamic, and sticky. A cell that lives on biofilm becomes highly resistant to physical and chemical treatments, including many host immune mechanisms.Compare and contrast endospores and cysts, bacterial and eukaryotic flagella, biofilms and hyphae. Endospores are more durable than cysts, but both protect bacteria from harm. Some forms of cysts and spores can survive higher temperatures for a limited time. Both spores and cysts can lay dormant for long periods of time. Bacterial flagella are smaller and simpler in structure, made up of protein flagellin, move in rotation, and are proton driven. Eukaryotic flagella are larger and complex in structure, made upof tubulin, bend to move, and are ATP driven.Biofilms are made up of multiple species. Hyphae are made up of one single species. Both function in adhesion and protection, are multicellular, and obtain food by absorbing nutrients. Name the different classes of Protozoans. Compare protozoans to fungi - how are they similar? How are they different? Ciliates, flagellates, sporozoans, and amoebas are the four classes of Protozoa. Fungi are multicellular while protozoa are unicellular. Fungi invade tissues and digest material externally by digesting enzymes.What are the basic classes of viruses? What are the components of virus structure and what aretheir functions? The basic classes of viruses are enveloped, naked, and complex. They consist of nucleocapsid proteins and specific enzymes necessary for replication. Viruses attack a host cell’s functions and utilize them for their own benefits. Viruses control host cells function to promote viral genome replication and viral protein production.In what ways are viral genomes "diverse"? What determines which cells viruses infect? How do viruses enter cells?Viral genomes are either DNA or RNA and can be either single or double stranded. Their structure is usually circular or linear, or otherwise packaged as separate segments. Size varies, but they are relatively small. A host cell’s specific surface receptors must match that of a virus for the virus to infect it. Enveloped viruses enter cells through either fusion or endocytosis. Naked viruses enter cells through endocytosis only. Bacteriophages bind to specific receptors onthe cell enevelope and directly inject their genome into the host cell.Why do cells have receptors for viruses? *Trick question! Cells have receptor proteins designed to do a specific job, and the virus borrows the receptor for its own benefit. What is viral latency?Some viruses have the option of persisting in a host cell (hanging out for a while) without killingit, but reactivate later on. This is referred to as viral latency. How do bacteria grow? What determines their growth rate? What are the phases of their growth? What are the conditions affecting their growth? Bacteria grow exponentially. Their growth rate is determined by nutrient availability. The four phases of growth include the lag phase, which consists of adjusting metabolism, the exponentialphase, which is the maximum growth rate, the stationary phase, consisting of depleted nutrients, increased toxic products, and reduced cell size, and finally death, where more cells are dying than dividing. The conditions effecting growth include changes in pH, temperature, salt concentration, and oxygen availability. Describe the different ways that a microbe may adapt to changing growth conditions.1. Conjugation: genetic transmission through direct contact – a plasmid or fragment of DNA is transferred from a donor to a recipient cell through direct connection- Gram - and gram + bacteria can conjugate, but only gram -‘s can operate with a specialized plasmid (fertility/F factor)- Both the donor and recipient have to be alive- Bridge forms between cell surfaces to interact with pilus to transfer plasmid or just DNA in general- Rarely is the entire genome transferred – just a portion usually- High frequency transfer: the donor cell retains one strand of DNA and the other strand is transported to the recipient, in a higher frequency than other cells- Biomedical importance: R plasmids/factors bear genes resistant to antibiotics and other drugs, and are shared by bacteria through conjugation2. Transformation: capturing free DNA from solution – nonspecific, indirect acceptance of small fragments of soluble DNA from the surrounding environment- Griffith’s experiment with rats – live non-virulent cells picked up loose DNA from dead mice (who carried dead virulent cells) that had broken open, so