BIOSC 1850 1st EditionExam 1 Study GuideEvery single organism falls into one of the following categories:- Bacteriao More bacteria than anything else, more bacteria in human body than there are human cellso Wide diversity of morphology o No nucleus or membrane-bound organelleso Gram-positive vs. Gram-negative Levels of peptidoglycan present in the cell wall- Archeao No nucleus or membrane-bound organelles o Small diversity of morphology o Extremophiles (but not all are such)- Eukaryao Contains nucleus and other membrane-bound organelles- Viruso Replicates only inside the cells of living organisms Archeavirus, bacteriophageo Virus particles (virions) consist of 2-3 parts: Genetic material  Protein coat to protect the genes OPTIONAL lipid coating outside the protein coatSome microbes are essential to human life (synthesize essential compounds, aid in digestion of molecules, etc) Timeline of the Earth:4.5 billion years ago (BYO) to 1BYO: just microbial life ~2BYO: microbes started producing oxygen for atmosphere Coincides with emergence of eukaryotes ~1-0.5BYO: endosymbiosis of mitochondria and chloroplasts0.25BYO: mammals appear Prokaryotes/Archea show more diversity than Eukaryotes Archaeviruses: viruses that exclusively infect archea. - Archea can thrive in extreme environments, although not all are extremophiles. - Archaeviruses have atypical appearances (not typically phage-like or spherical)- ALL have DNA genomes. Lipid-containing outer shell Viral DNA, if a phage, is inserted into the host via a viral DNA pump. This pump is the strongest for its size! Bacteriophage Lambda (Λ)- Smaller than T4, less aggressive tail, no sheath wrapping - Lytic cycle, but under certain conditions can be lysogenic - Capsid, tail, tail fibers- The genome is replicated both rightward and leftwardo Rightward: transcribes the O, P, and Q genes, all involved in initiating replication and the expression of structural genes o Leftward: transcribes genes important for recombination, genes that prevent genome degradation by the host cell  N protein and Cro protein:- N: antiterminator (the termination signal is ignored so replication, transcription, and translation continues- Cro: represses the lytic cycle until conditions are right (works withCII to initiation lytic cycle) - CII proteins assess the state of the cell via susceptibility to protease (enzymes that break down proteins) o If the protease levels are high, the cell is healthy, and it enters the lytic cycleo If the protease levels are low, the cell is healthy, and it enters the lysogenic cycleMu Phage- Operates through replicative transposition o The same base pairings get inserted into the genome o Each time the base pairing set gets re-inserted into the genome, the entire genome replicated Average cell infected with Mu has ~200 copies of the new viral genome - Mu uses the host machinery to express its genes- The Mu DNA gets cut out, with a ~50bp buffer on either side, packaged, and sucked into a verionMS2- ssRNA genome (3500bp), but only 4 genes! o 180 copies of the shell gene **First to be transcribed!!o 1 copy of the maturation proteino 1 copy of the genome o As ribosome move through the shell genes, they disrupt the secondary structure of the genome and make the other genes available for transcription  Synthetase + 3 host cell proteins = RNA replication complex- Lytic cycle- The genome has a secondary structure that needs to unfold in order to be replicated (folds onto itself once, creating a hairpin)o 5’ ---- 3’ strand is the “PLUS strand”o 3’ ---- 5’ strand is the “MINUS strand” o The plus strand codes for the virion, and the minus strand is the template for the plus strandsT4 Bacteriophage- Lytic cycle only!- Terminally redundant DNA genomeΦ6- dsRNA SEGMENTED genome o ***Cells HATE dsRNA! Have mechanisms to destroy it, so the viral dsRNA genomeis always contained within the shell. The membrane comes off when in the cell, but the protein shell stays in placeo 3 separate dsRNAso 11 genes total- Polycistronic “many genes” - Also contains RNA-dependent RNA polymerases: uses RNA as a template for new RNAo Uses the MINUS strand as the template. New PLUS strand displaces the old strand. The old plus strand is displaced into the cytoplasm and now functions as mRNAo Once enough new RNA has been replicated, it gets sucked into new shells to form new Φ6 phages- Φ6 has an unknown mechanism for entering the host cell - Similar appearance to reovirus Influenza- Irregularly shaped (globular) - Presents 2 main lipoproteins on its membrane: H and No N: neuraminidase: cleaves polysaccharides on host cells o H: hemoglutinin: sticks to the cleaved polysaccharides o ***Polysaccharides have been cleaved so that the new virion doesn’t stick to the old host cell - 8 segments of ssRNA, packed in an elaborate structure - Taken up by host cell via endocytosis and taken to the lysosome for digestion. Influenza somehow makes a pore in the lysosome and escapes - Influenza’s RNA polymerases are not as effective as they could be! There are no proofreader, so lots of mutations occuro Mutations mainly effect H and N - Antigenic Drift: simultaneous infections lead to mismatched progeny virusesEbola- Filoviruso Variant looks like filamento Long, tube-like, helical array of genome o Solid genome- Starts with headache, muscular pain, progresses to nausea/vomiting. Progresses to bleeding: both internal and through orifices (eyes, nose, etc), leads to death.- Not very contagious—only passed through bodily fluids - No cure, no vaccine Plant Viruses - Most have ssRNA genomes- Relatively small - Plant viruses mainly enter cells via insect vectors—“pollination” of viruses- Viruses can also enter through the cell wall via microbreaks (usually due to environmental conditions, like windstorms)o Once inside, can very easily travel from cell to cell via plasmodesmata- MP=movement protein“Phage Rage” when phage genes and proteins show up in unexpected places - Pyocins:o Offensive weapons, look like bacteriophage tailso Drill holes in cell envelopes - Encapsulins:o Enzymes contained within a protein shello Defenses against oxidative stress - Gene Transfer Agents:o Mediates horizontal gene transfer Cap-snatching: host genome incorporated into virion so it can be exported out of the cell Textbook Chapter 3: EUKARYAL MICROBES3.1 The