Lecture 13 Viruses are not living but influence life Living things Consist of cells Contain genetic info and use it to reproduce Genetically related evolve Convert molecules from the environment into new ones Extract energy from the environment Regulate internal environment Viruses are nucleic acids inside a protein coat Virions Have a protective coat Capsid and either RNA or DNA Lipid and glycoprotein envelopes only some Viruses can infect all types of organisms Host specific Pandemic Goes for one type of organism Goes for any living organism Viruses are organized into four categories based on their DNA RNA Double stranded DNA viruses dsDNA Nucleus HPV Pox RNA retroviruses 2 copies single stranded RNA Reverse transcribes RNA to DNA HIV Double stranded RNA viruses Sing stranded RNA viruses Negative sense cells can read RNA without manipulation Positive sense RNA can be put into cells and immediately translated Viruses are incredibly diverse You usually cannot categorize viruses Genetic diversity van be extracted from other cells Recombination Multiple hosts There are more viruses than living things in the world Viruses have multiple origins Escaped genes hypothesis Viruses arose from plasmids and transposable elements Symbiotic bacteria hypothesis Degradation of essential genes of eukaryotic symbionts led to parasitism Origin of life hypothesis Early RNA based life forms gave rise to viruses Viruses use host cell machinery to replicate Virus DNA or RNA set of instructions Viruses reproduce inside of a cell Gene expression Cells are basically hijacked by the virus Bacteriophages are viruses that infect bacteria Viruses are very small Phage have very complex structures Generalized life cycles Nothing too important or out of the ordinary occurs in their life cycle Can be used in biotechnology Bacteriophages have two reproductive cycles Lytic cycle Transduction Lysis bursting of the infected host cell occurs releasing progeny na ve baby viruses When a virion infects a bacterium the bacterial DNA is injected into the new host cell Mechanism of gene transfer Lysogenic cycle Lysogeny Postpones the bursting lysis of the cell Prophage Deemed a prophage when viral DNA becomes integrated into the host DNA As the host cell divides the viral DNA gets replicated along with that of the host Can remain inactive for thousands of generations When inactive still continues to produce more copies of viral DNA Retroviruses carry their information as RNA Reverse transcriptase DNA is then integrated into host cells DNA Acts as template for new viral genomes HIV Encodes a protein which makes DNA strand that is complementary to its own RNA strand No proofreading Allows for strand to change quickly and mutate with each host Viral recombination generates new flu strains Recombination Viral DNA segments are exchanged Novel many combinations of surface proteins New combinations often result in pandemics Ducks chickens and pigs are the most common flu hosts Viruses can cause cancer Viruses may contribute to 15 or more of human cancer Viruses cause the expression of cancer causing genes called oncogenes Vaccines are available for HPV and hepatitis Only for certain forms Have been linked to contraction of other forms Guardasil HPV Prokaryotes No The three domains of life had a single origin Domain Kingdom Phylum Class Order Family Genus Species Are prokaryotes monophyletic Domains bacteria and archaea are prokaryotes No cytoskeleton organelles or nucleus Binary fission is their method of reproduction Chromosomes are circular haploid Cell walls Unique flagella Shapes of prokaryotes include Cocci Bacilli Helical Prokaryotes form complex communities Solitary distinct units Colonial filaments Biofilms Communication Through signal molecules Cell walls are composed of many polymers Peptidoglycan In bacteria but not archaea Gram stain Positive Contains peptidoglycan shows up as a purple color Negative Does not contain peptidoglycan no color change Archaea DO NOT have peptidoglycan protein or other materials Prokaryotes have a variety of metabolic pathways Aerobic vs anaerobic Aerobic uses oxygen ATP Anaerobic does not Photoautotrophs Light Chemolitho auto trophs Inorganic compounds Photoheterotrophs Light for energy Carbon from organic molecules Chemoheterotrophs Carbon and energy from organic molecules Nitrogen and sulfur Prokaryotes are ecologically essential Most abundant organisms Nutrient cycling Nitrogen Carbon Sulfur Oxygen production Obligate symbionts ruminants Bacteria are pathogenic Cause diseases Lateral gene transfer generates variability in prokaryotes Conjugation requires the presence of an F plasmid Process DNA fragment is taken up by another cell DNA is incorporated by homologous recombination Transducing phage adheres to cell Cell death of a bacterium causes release of DNA fragments Cell contains DNA from dead donor cell Prokaryotes are not monophyletic However there are monophyletic domains Archaea and eukarya DNA replication Gene sequences DNA sequence data rRNA Prokaryote diversity Bacteria Spirochetes Gram negative Do not contain peptidoglycan Chemoheterotrophic Axial filaments They are parasites pathogens or free living Bacteria Chlamydias Some of the smallest of all bacteria Gram negative Solely parasitic Have two different life stages Cause eye infections in mammals STDs linked to heart disease in women Bacteria High GC Gram Positives Actinobacteria Have a high ratio of GC vs AT in DNA Reproduction with spores Common in soil and dental plaque also can be pathogenic Used to develop antibiotics Bacteria Low GC Gram Positives Low GC AT ratio some are gram negative smallest bacteria Form heat resistant endospores Include disease causing Staphylococcus Bacillus anthracis Bacteria Cyanobacteria Colonial and solitary Photoautotrophs most oxygen production on earth Have specialized cells for nitrogen fixation Gave rise to chloroplasts in Eukaryotes Responsible for green blooms in polluted waters Bacteria Proteobacteria Largest number of described species Evolutionary origin of mitochondria Cause human and plant diseases Symbioses Archaea have several synapomorphies Ether bonds Absence of peptidoglycan rRNA genes Hydrocarbon monolayer More similar to Eukarya Archaea Crenarchaetoa and Euryarchaetoa Poorly described in species number Most crenarcheota are thermophillic or acidophilic or both Euryarchaeota are methanogens extreme halophiles Archaea are not all extremophiles