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17- Chapter Metabolic Diversity PART I The Phototrophic Way of Life 17.1 Photosynthesis, p. 533 Phototrophs- use light as energy source 2 types of photosynthesis: Anoxygenic- no oxygen is produced Most photosynthetic bacteria are anoxygenic phototrophs Oxygenic- water is split to produce oxygen Cyanobacteria and photosynthetic eukaryotes (plants) are oxygenic phototrophs 17.2 Photosynthetic Pigments and Their Location within the Cell, p. 534 Pigments of photosynthesis: Chlorophylls in oxygenic phototrophs Bacteriochlorophylls in anoxygenic phototrophs Located in photosynthetic membranes where the light reactions of photosynthesis are carried out Photosynthetic eukaryotes have chloroplasts that contain the photosynthetic membranes known as the thylakoids Since photosynthetic prokaryotes do not have chloroplasts, the photosynthetic membranes are: The cytoplasmic membrane in many bacteria Chlorosomes in green bacteria Thylakoid membranes in cyanobacteria The ultimate in low-light efficiency is found in the chlorosome of green sulfur bacteria and Chloroflexus. Can grow at lowest light intensities of all known prokaryotes Antenna chlorophyll molecules harvest light and funnel energy to the reaction center where the conversion of light to ATP occurs Different pigments absorb different wavelengths of light There are several different chlorophylls and bacteriochlorophylls, each with a unique absorption spectra Different species have different pigments making it easy for two organisms to coexist in a habitat without competing for light energy 17.3 Carotenoids and Phycobilins, p. 537 Carotenoids (always in phototrophic orgs) and phycobilins (in cyanobact and red algal chloroplasts)- accessory pigments that absorb light and transfer the energy to reaction center chlorophylls Chlorophylls can only absorb certain wavelengths of light. Accessory pigments allow organisms to capture additional wavelengths of light Phycobilins absorb yellow (around 550nm) or red light (620, 650nm) depending on the pigment Carotenoids absorb blue light around 475nm 1 Carotenoids also play an important photoprotective role in preventing photooxidative damage (due to toxic forms of oxygen) to cells In photosynthesis, a series of electron transport reactions in the photosynthetic reaction center of phototrophs results in the formation of a proton motive force and the synthesis of ATP 17.4 Anoxygenic Photosynthesis, p. 538 Photosynthesis that does not produce oxygen Anoxygenic phototrophs include members of the following bacterial phyla: - Proteobacteria (both purple sulfur and purple nonsulfur) - Chloroflexus (green nonsulfur) - Chlorobium (green sulfur) - Heliobacteria (gram positives) A general scheme of electron flow (cyclic photophosphorylation) in anoxygenic photosynthesis in a purple bacterium (Fig 17.14) The arrangement of protein complexes in the photosynthetic membrane of a purple phototrophic bacterium (Fig 17.15) Reducing power in the form of NADH or NADPH needed for CO2 fixation comes from reductants (usually H2S) in the environment and requires reverse electron transport in purple phototrophs - Reverse Electron Transport- energy requiring process of moving electrons against the thermodynamic gradient to convert a weak electron donor to a strong electron donor Rhodobacter species are used for studying anoxygenic photosynthesis - They use photosynthesis in the light, respiration in the dark, and grow in the presence or absence of oxygen 17.5 Oxygenic Photosynthesis, p. 543 Algae and cyanobacteria use electrons from H2O to reduce NADPH for CO2 fixation producing O2 as a by-product 2 separate light reactions involved in oxygenic photosynthesis: photosystems I and II Photosystem I resembles the system in anoxygenic photosynthesis Photosystem II splits H2O to yield O2 Electron flow in (Fig 17.2) 17.6 Autotrophic Fixation: The Calvin Cycle, p. 545 Autotrophs- use CO2 as sole carbon source Convert CO2 into organic carbon compounds- CO2 fixation Many use the Calvin-Benson cycle - Calvin cycle- CO2 + ribulose bisphosphate (RubisCo) are used in cycle to eventually make glyceraldehyde 3 phosphate then fructose-6-phosphate Requires large amount of ATP F-6-P goes into glycolysis Glycolysis & TCA occur just as mentioned previously starting with F-6-P Several autotrophic prokaryotes that use the Calvin cycle for CO2 fixation produce polyhedral cell inclusions called carboxysomes that store molecules of RubisCo 2 The Calvin cycle is an energy-demanding process in which CO2 is converted into sugar (Fig 17.22) - Hexose sugars can be used by the cell or put into storage polymers like glycogen, starch, or poly--hydroxyalkanoates 17.7 Autotrophic Fixation: Reverse Citric Acid Cycle & the Hydroxypropionate Cycle Green sulfur bacteria use the reverse citric acid pathway for CO2 fixation Green nonsulfur bacteria Chloroflexus uses the Hydroxypropionate pathway - Chloroflexus is the oldest anoxygenic phototrophic Bacteria Possibly the first attempt at autotrophy in anoxygenic phototrophs PART II Chemolithotrophy: Energy from the Oxidation of Inorganic Electron Donors 17.8 Inorganic Electron Donors and Energetics, p. 548 Chemolithotrophs- oxidize inorganic chemicals as their sole sources of energy Most are also autotrophs Some are mixotrophic- although they are able to obtain energy from the oxidation of an inorganic compound, they require an organic compound as a carbon source Use inorganic compounds such as hydrogen sulfide, hydrogen gas, ferrous iron, and ammonia as electron donors (Fig 5.23) Typically oxygen is the terminal electron acceptor so aerobic respiration takes place it just starts with an inorganic molecule instead of an organic molecule 17.9 Hydrogen Oxidation, p. 549 Hydrogen Bacteria: Oxidize H2, thereby generating a proton motive force and ATP synthesis (Fig 17.25) These chemolithotrophs are also autotrophs and fix CO2 via the Calvin cycle Generate energy by oxidizing hydrogen gas Electrons from hydrogen are passed down an ETC to oxygen (ex of aerobic resp.) Hydrogen ion gradient formed ATPase uses potential energy from this gradient to make ATP Example: Ralstonia If organic compounds are present, most hydrogen bacteria will grow as chemoorganotrophs, but if organic compounds are absent they grow chemolithotrophically and fix CO2 by the Calvin cycle cytoplasm H2 2H+ electron transport chain periplasm H+ 2H+ + 1/2 O2 H2O H+ 3 17.10 Oxidation of Reduced Sulfur Compounds, p. 550 Sulfur Bacteria: Oxidize reduced sulfur compounds such as H2S and S0 to sulfate (SO42-) Sulfate is exported to the environment where it reacts with hydrogen ions to form sulfuric acid When sulfur is oxidized, electrons are donated to ETC where electron acceptor is usually oxygen (aerobic) Causes hydrogen ion gradient which ATPase uses to generate ATP These chemolithotrophs are also autotrophs and use the Calvin cycle to fix CO2 Most are aerobic Example: Beggiatoa Some sulfur bacteria like Thiobacillus denitrificans are anaerobic and use nitrate as an electron acceptor See Fig 17.27 17.11 Iron Oxidation, p. 553 Iron Oxidizing Bacteria: Chemolithotrophs that generate energy by oxidizing ferrous iron (Fe+2) to ferric iron (Fe+3) Most are obligatory acidophilic Iron-oxidizing bacteria in a creek receiving drainage from an acid mine. Orange color is due to the oxidation of Fe2+ to the insoluble precipitate Fe(OH)3 by the bacteria (Fig 17.28) Natural proton motive force exists due to the large pH difference between the periplasm and cytoplasm (Fig 17.30). Periplasm has lower pH--higher [H+]. 17.12 Nitrification and Anammox, p. 555 Nitrifying Bacteria: Ammonia (NH3) and nitrite (NO2-) are the most common inorganic nitrogen compounds used as electron donors Chemolithotrophic nitrifying bacteria oxidize inorganic nitrogen aerobically by nitrification Nitrosifyers oxidize ammonia to nitrate Another group of bacteria oxidize nitrite to nitrate Most nitrifying bacteria are also heterotrophs- able to use glucose or other organic carbon source PART III The Anaerobic Way of Life: Anaerobic Respirations 17.13 Anaerobic Respiration, p. 557 Anaerobic respiration uses molecules other than oxygen as final electron acceptor less energy efficient but enables resp. in environments where oxygen is absent Obligate anaerobes solely use anaerobic respiration Some facultative anaerobes like denitrifying bacteria use aerobic respiration in the presence of oxygen but when oxygen is depleted switch to anaerobic respiration 4 17.14 Nitrate Reduction and Denitrification, p. 558 See Fig 17.36 Example of Denitrifying bacteria- Pseudomonas cytoplasmic membrane Reduce nitrate (NO3-) to gases such as nitrogen NADH (N2), nitrous oxide (N2O), and nitric oxide (NO) + flavoprotein H+ (Escape from the environment) Nitrate is the electron acceptor NAD + ETC process is same as aerobic respiration 2eDifference- electrons are used to reduce nitrate ironinstead of oxygen sulfur protein Fig 17.37 cytoplasm 2e- 2H+ periplasm quinone H+ 2eCyt b 2eNO3- + 2H+ nitrate reductase NO2- + H2O 17.15 Sulfate Reduction, p. 560 Sulfate-reducing bacteria use sulfate as an electron acceptor (anaerobic respiration), converting the sulfate to hydrogen sulfide Examples: purple bacteria such as Desulfovibrio & Desulfobacter Various electron donors, including H2, lactate and pyruvate are used to reduce sulfate to hydrogen sulfide (Fig 17.39) 17.16 Acetogenesis, p. 563 Homoacetogenesis (Fig. 17.41) - Use by some anaerobes to reduce CO2 to acetate using acetyl-CoA pathway - H2 is usually the electron donor used to generate proton or sodium motive force and ATP 17.17 Methanogenesis--carried out by a group of strictly anaerobic Archaea (methanogens), p. 564 Biological production of methane (CH4) either from CO2 plus H2 or form methylated compounds such as acetate or methanol A variety of unique coenzymes are involved and the process is strictly anaerobic (Archaea) Energy is produced using both proton and/or sodium ion gradient 5 17.18 Ferric Iron, Manganese, Chlorate, and Organic Electron Acceptors, p. 568 Besides inorganic nitrogen and sulfur compounds or CO2, a variety of other substances, both organic and inorganic, can function as electron acceptors for anaerobic respiration (Fig 17.47) Geobacter metallireducens can use toluene as an electron donor to reduce Fe3+ Bacteria such as Thauera selenatis that reduce selenate to elemental sulfur can be used to remove selenate from contaminated waters and soils The sulfate reducing bacteria Desulfotomaculum reduces arsenate to arsenite in addition to reducing sulfate to hydrogen sulfide ion producing arsenic trisulfide thereby detoxifying arsenic-containing waste PART IV The Anaerobic Way of Life: Fermentations and Syntrophy 17.19 Fermentations: Energetic and Redox Considerations, p. 571 In the absence of an external electron acceptor, organic compounds can be catabolized only by fermentation (Fig 17.49) Fermentation of pyruvate generated by glycolysis: o Stage I series of reactions to generate 2 molecules of glyceraldehyde 3phosphate from glucose o Stage II redox reactions generate ATP and 2 molecules of pyruvate from the glyceraldehyde 3-phosphate o Stage III redox reactions to convert pyruvate into fermentation products Only certain compounds are fermentable An energy-rich organic intermediate must be formed that can produce ATP by substrate-level phosphorylation Fig 17.50 & 17.51 Redox balance must also be achieved in fermentations, and H2 production is one way of disposing of excess electrons Production of H2 is generally associated with the presence of an iron-sulfur protein called ferredoxin 17.20 Fermentative Diversity, p. 573 A wide variety of fermentations are known (Fig 17.7) In many cases, the product of one organism's fermentation is fermented by a second organism Some fermentations employ ion gradients (H+ or Na+) as the basis of their energetics instead of using substrate-level phosphorylation or electron transport system (Fig 17.52) PART V Hydrocarbon Oxidation and the Role of O2 in the Catabolism of Organic Compounds 17.23 Hydrocarbon Oxidation, p. 578 17.24 Methanotrophy and Methylotrophy, p. 579 6 Many microorganisms can degrade aliphatic and aromatic hydrocarbons (benzene, toluene, etc.) Methanotrophy- use of CH4 as a carbon and energy source 17.25 Hexose, Pentose, and Polysaccharide Metabolism, p. 581 Fig 17.9- Polysaccharides are abundant in nature and can be broken down, usually by phosphorolysis, into hexose phosphate or pentose phosphates and used as energy sources Pentose phosphate pathway- major means for generating pentose sugars for biosynthesis from hexose sugars Pentoses (ribose and deoxyribose: sugars that make up DNA and RNA) are required for nucleic acid 17.26 Organic Acid Metabolism, p. 584 Organic acids are frequently metabolized through the citric acid cycle or the glyoxylate cycle 17.27 Lipids as Microbial Nutrients, p. 585 Fats are metabolized via hydrolysis by lipases or phospholipases to free fatty acids (Fig 17.68) The fatty acids are oxidized to acetyl- CoA, which are then oxidized to CO2 by the citric acid cycle PART VI Nitrogen Fixation 17.28 Nitrogenase and the Process of Nitrogen Fixation, p. 586 Nitrogen fixation is the reduction of atmospheric N2 to ammonia (NH3) Most organisms must use oxidized nitrogen compounds (NO3-, NH3) from environment as nitrogen source. Some can use nitrogen gas (nitrogen fixation)- convert it into NH3 which is used to make organic compounds Requires large amounts of ATP Occurs in some prokaryotes, not in eukaryotes Nitrogen fixation requires an enzymes complex called nitrogenase Nitrogenase is inhibited by oxygen Many organisms only fix N when growing anaerobically Aerobic nitrogen-fixing bacteria prevent the oxygen needed for respiration from interacting with nitrogenase by: - Rapid removal of O2 by respiration - Producing O2 retarding slime layers - Compartmentalization of nitrogenase in special cells (some species of cyanobacteria have heterocysts where nitrogen fixation occurs) Others - Rhizobium provides plants with N. plant protects bacteria & keeps nitrogenase from being destroyed by oxygen 7 Chapter 7- Essentials of Molecular Biology PART I Genes and Gene Expression 7.1 7.4 p. 167 176 The three key processes of macromolecular synthesis are: (Fig 7.1) (1) DNA replication - Making a copy of DNA (2) Transcription - Synthesis of RNA from a DNA template (3) Translation - Synthesis of proteins using messenger RNA as a template Although the basic processes are the same in prokaryotes and eukaryotes, the organization of genetic information is more complex in eukaryotes (Fig. 7.2) - DNA is a double stranded helix (twisted ladder) - The two strands in double helix are anti-parallel (run in opposite directions) - The 2 DNA polynucleotide strands have base sequences that are complementary: o Adenine always pairs with thymine (A=T) o Guanine always pairs with cytosine (G=C) - Hydrogen bonds hold the two strands together G = C is a stronger b/c t is held together by three hydrogen bonds instead of two DNA is made of deoxyribonucleotides linked by phosphodiester bonds Deoxyribonucleotide= sugar deoxyribose + nitrogenous base + phosphate Nitrogen Bases purines (adenine and guanine) and pyrimidines (cytosine and thymine) 8 DNA structure (Fig 7.3- 7.5) Prokaryotic circular DNA molecules can be packaged into the cell b/c it is supercoiled. DNA gyrases assist in supercoiling (Fig 7.8 & 7.10) In addition to the chromosome, a number of other genetic elements exist in cells (Table 7.1) Plasmids- DNA molecules that exist separately from the chromosome of the cell Mitochondria and chloroplasts contain their own DNA chromosomes Viruses contain a genome either DNA or RNA, that controls their replication Transposable elements exist as a part of other genetic elements Table 7.2 PART III DNA Replication 7.5 7.6 p. 176 181 Both strands of the DNA helix serve as templates for the synthesis of two new strands by semi-conservative replication. (Fig 7.11) Enzymes involved in DNA replication (Fig 7.3) Most prokaryotes have a singular circular chromosome DNA replication begins at a unique site called the origin of replication - Eukaryotes have multiple origins of replication - Prokaryotes have a single origin of replication Replication proceeds in both directions (bidirectional replication) from the origin and ends at a site halfway around the chromosome called the terminus. (Fig. 7.17) Formation of the replication bubble - For chromosome to be replicated, it must first be unwounded by enzyme called helicase - Helicase breaks the phosphodiester bond (connects one nucleotide to the next) in one strand (a nick), unwinds the strands a small amount and seals the nick - The unwound area is called a replication bubble DNA polymerization - DNA polymerase- enzyme that ads deoxyribonucleotides to the 3' end of the growing DNA chain - Can only add to the 3' end. Not the 5' end - DNA polymerase cannot begin a new DNA chain Fig 7.5 & 7.12 - To begin DNA replication, there must be a primer- site at which DNA polymerase can attach the first deoxyribonucleotides 9 - Primer- short stretch of RNA (ribonucleotide) made by the enzyme primase Deoxyribonucleotides can then be added to the 3' OH at the end of the RNA primer See Fig 7.13 & 7.14 Starting the leading & lagging strands o Since DNA polymerase can only make DNA in the 5' to 3' direction (nucleotides added to the 3' end), only one stand is made toward the replication fork leading strand o The other strand is made in the direction away from the replication fork lagging strand leading strand replication fork 5' 5' lagging strand Extending the leading & lagging strands - As replication fork opens, leading strand continues to be made toward the replication fork (5' to 3') - Lagging strand can't be made toward the fork so a gap is formed leading strand 5' 5' lagging strand Fig 7.5, 7.18, 7.19 - Primase and DNA polymerase fill this gap by starting a new chain at fork and extending it to the lagging strand - These fragments are Okazaki fragments - Process continues until terminus is reached - Primers are then removed and replaced with DNA 5' leading strand Okazaki fragment lagging strand 10 Sealing the nicks - Once both strands have been copied, there are still nicks between the Okazaki fragments - These nicks are sealed by DNA ligase - Cell has 2 complete chromosomes; each chromosome has 1 old strand and 1 new strand that is semi-conservative replication Fig 7.16 - Most errors in base pairing are corrected by proofreading functions of the DNA polymerases (Fig 7.20) PART V RNA Synthesis: Transcription 7.10 7.13 p. 188 193 Differences between DNA & RNA: DNA- made of deoxyribonucleotides Double stranded Thymine Sugar- deoxyribose RNA made of ribonucleotides Single stranded Uracil Sugar- ribose Three major types of RNA: - messenger RNA (mRNA) - transfer RNA (tRNA) - ribosomal (rRNA) Template strand- DNA strand that is being copied into complementary mRNA Non-template strand- DNA strand that is not being copied into mRNA The non-template strand is identical to the mRNA except that T's in the DNA are replaced by U's in the mRNA. RNA polymerase- enzyme that transcribes DNA into RNA Process of transcription 3 phases: - Initiation - Elongation - Termination Transcription of RNA from DNA involves the enzyme RNA polymerase, which adds ribonucleotides onto the 3' ends of growing RNA chains Unlike DNA polymerase, RNA polymerase needs no primer and recognizes a specific start site on the DNA called the promoter 11 Initiation Process of starting an mRNA chain Promoter- site on the DNA where RNA polymerase binds to the DNA and begins transcription In Bacteria, promoters are recognized by the sigma subunit of RNA polymerase Prokaryotes have a single RNA polymerase with a sigma factor attached. The sigma factor binds to the DNA promoter to initiate transcription. Elongation RNA polymerase moves down the template from 3' to 5' direction RNA strand is made 5' to 3' (ribonucleotides are added to the 3' end) complementary to the DNA Termination When RNA polymerase reaches the terminator, transcription stops and RNA chain is released. Terminators: (Fig 7.12) inverted repeat forms a stem and loop structure causing RNA polymerase to dissociate Rho factor- a protein that moves up RNA to reach RNA polymerase causing it to dissociate See fig 7.29- transcription overview Eukaryotes do not have sigma factors. Transcription factors help eukaryotic RNA polymerases to bind to promoters (Fig 7.31) In prokaryotes, genes that code for the enzymes in a specific pathway are often lined up in groups called operons Ex: There are 3 enzymes involved in lactose utilization so there are 3 genes. These are lined up in an operon called the lac operon lacZ lacY lacA DNA 12 There is 1 mRNA transcript for the entire lac operon lacZ lacY lacA DNA transcription lacZ lacY lacA mRNA Once the mRNA is made for the lac operon, it is used to make 3 proteins Translation- process of making a protein using mRNA as template There is 1 protein for each gene in the lac operon lacZ lacY lacA DNA transcription lacZ lacY lacA mRNA translation proteins -galactosidase lac permease transacetylase Multiple genes can be co-transcribed forming a polycistronic mRNA (Fig 7.2a & 7.33) In eukaryotes a single gene is transcribed at a time (Fig 7.2b) PART VI Protein Synthesis 7.14 7.17 p. 193 203 Translation- Process of making a polypeptide chain from mRNA Codons: There are 20 amino acids found in proteins How can 4 RNA bases (A, U, G , C) code for 20 amino acids? A group of 3 RNA bases code for each amino acid this is called a codon 13 The genetic code is degenerate There are 64 possible codons, but only 20 amino acids Some amino acids have several codons Ex: There are 3 codons for isoleucine: AUU, AUC, AUA A single amino acid may be encoded by several different but related codons(Table 7.5) Transfer RNA (tRNA) tRNA- small RNA molecules that act as adapters Each tRNA has a binding site for a _codon at one end_, and a binding site for an amino acid at the other end There are tRNA molecules for 61 of the 64 codons these are called sense codons The other 3 codons are called nonsense codons One or more transfer RNAs exist for each amino acid found in a protein (Fig 7.36) Enzymes called aminoacyl tRNA synthetases attach an amino acid to a tRNA(Fig 7.37) The anticodon 3 nucleotides at the bottom of the tRNA that are complementary to a codon on the mRNA In drawing above, the anticodon is UAC The anticodon is written from 3' to 5' direction What codon is this anticodon complementary to? Answer: AUG complements UAC AUG (usually the start codon) AUG is the codon for which amino acid? Met A codon will base-pair with a sequence of three bases on a tRNA called the anticodon Translation of mRNA occurs from a start codon to a stop codon From start codon to stop codon is called an open reading fram (ORF) Table 7.5- Codon table- shows all possible codons & the amino acid each codes for Each of the 61 sense codons specifies an amino acid There are tRNA's for the 61 sense codons There are no tRNA's for the 3 nonsense codons UAG, UGA, UAA The ribosome Ribosome- large complex of proteins and RNA that links amino acids together to form proteins 14 There are 2 ribosomal subunits, 30s and 50s in prokaryotes (Table 7.6) s stands for svedberg unit, a measure of mass and shape The 2 subunits together form a 70s ribosome The ribosome brings together mRNA and aminoacyl tRNAs for protein synthesis There are 3 sites on the ribosome: (Fig 7.38) Acceptor (A) site, where the charged tRNA first binds Peptide (P) site, where the growing polypeptide chain is held Exit (E) site Translation Initiation Shine-Dalgarno sequence/ribosome binding site- mRNA sequence involved in binding mRNA to ribosome The mRNA fits into a groove in the 30s subunit of the ribosome The 50s subunit has 3 holes, called the P (peptide) site, the A (acceptor) site, and the E (exit) site ribosome binds to mRNA so there is one codon in the P site and 1 codon in the A site Aminoacylated tRNA's with correct anticodons fit into these 2 sites & hydrogen bond with the mRNA codons Ribosome forms a peptide bond between the 2 amino acids After peptide bond forms, there is a chain of 2 amino acids hooked to the tRNA in the A site Translation elongation Translocation- ribosome moves up the mRNA 1 codon, so the tRNA with the chain of amino acids is in the P site. A new aminoacylated tRNA binds to the vacant A site Chain of amino acids is linked to the amino acid in the A site Now there is a chain of 3 amino acids Ribosome moves up the mRNA 1 codon & repeats the cycle until the complete chain is made. 15 During each step of amino acid addition, the ribosome advances three nucleotides (one codon) along the mRNA, and the tRNA moves from the acceptor to the peptide site. See fig 7.38 Translation Termination Occurs when a nonsense codon which does not code for an amino acid is in the A site Protein and ribosome are released from the mRNA Eukaryotic translation occurs in the cytoplasm spatially separated from transcription (Fig 7.2b) Several ribosomes can translate a single mRNA molecule simultaneously, forming a complex called a polysome (Fig 7.39) In prokaryotes, transcription & translation can occur at the same time- coupled Polysome- more than 1 ribosome translating an mRNA at once To function correctly, proteins must be properly folded Folding may occur spontaneously or may involve proteins called molecular chaperones Many proteins must be transported into or through the cell membranes Such proteins are synthesized with a signal sequence that is recognized by the cellular export apparatus and is removed either during or after export Regulation of Transcription by Positive and Negative Control 8.5 8.7 p. 212 - 218 The amount of an enzyme in the cell can be controlled by decreasing (repression) or increasing (induction) the amount of mRNA that encodes the enzyme Repression occurs when sufficient product is present Induction occurs when substrate is present For negative control of transcription, the regulatory molecule is called a repressor protein and it functions by inhibiting mRNA synthesis The lac operon an as example of negative control of transcription (Fig 8.14 & 8.12) The lac operon is under the control of catabolite repression as well as it s own specific negative regulatory system Two requirements for induction of the lac operon: 1. cAMP levels high enough for CAP protein to bind to the CAP-binding site 2. Lactose must be present (Fig 8.20) For positive control of transcription an activator protein binds to activator-binding sites on the DNA to stimulate transcription 16 For transcription of the maltose operon: 1. Maltose (inducer) binds to the maltose activator protein 2. Maltose activator protein binds to the activator binding site on the DNA RNA polymerase can then proceed with transcription The mal operon as an example of positive control of transcription (Fig 8.15) Chapter 11 Microbial Evolution and Systematics PART I Early Earth, the Origin off Life, and Microbial Diversification 11.1 Evolution of Earth and Earliest Life Forms, p. 300 Earth is believed to be about 4.6 billion years old First evidence of microbial life can be found in rocks about 3.86 billion years old Stromatolites are fossilized microbial mats consisting of layers of filamentous prokaryotes and trapped sediment Early Earth was anoxic and much hotter than the present Earth The first biochemical compounds were made by abiotic syntheses that set the stage for the origin of life 11.2 Primitive Life: The RNA World and Molecular Coding, p. 303 See figure 11.5 11.3 Primitive Life: Energy and Carbon Metabolism, p. 304 Primitive metabolism was anaerobic & chemolithotrophic, using the abundant sources of FeS and H2S Carbon metabolism may have included autotrophy since CO2 was abundant Oxygenic photosynthesis arose ~2.8 billion years ago Oxygenic phototrophic cyanobacteria produce oxygen. Oxygen could accumulate creating an oxic environment and allowing for aerobic organisms to arise PART II Methods for Determining Evolutionary Relationships 11.5 Evolutionary Chronometers and 11.6 Ribosomal RNA Sequences as a Tool of Molecular Evolution, p. 309 The phylogeny of microorganisms is their evolutionary relationships Certain genes and proteins are evolutionary chronometers- measures of evolutionary change Comparisons of sequences of ribosomal RNA can be used to determine the evolutionary relationships among organisms SSU (small subunit) RNA sequencing of 16S or 18S is commonly performed The Ribosomal Database Project (RDP) contains a large collection of rRNA sequences Phylogenetic trees based on ribosomal RNA have now been prepared for all the major prokaryotic and eukaryotic groups Comparative ribosomal RNA sequencing has defined the three domains of life (Fig 11.16) 17 PART III Microbial Evolution 11.8 Microbial Phylogeny Derived from Ribosomal RNA Sequences, p. 314 11.9 Characteristics of the Domains of Life, p. 316 Feature Bacteria Peptidoglycan Planctomyces-Pirella have protein cell wall Mycoplasma-Chlamydia lack cell wall Feature Lipids Membrane lipid bilayer Membrane lipid monolayer Membrane lipid bilayer Bacteria Ester-linked fatty acids Archaea Ether-linked fatty acids Eukarya Ester-linked fatty acids Archaea Pseudopeptidoglycan Protein Eukarya Protozoans lack a cell wall Cell wall Feature RNA polymerase Bacteria 4 subunits Archaea 2 different ones with 8-10 subunits each Eukarya 3 different ones with 10-12 subunits each Feature Protein synthesis Bacteria 70S ribosomes FormylMethionine Archaea 70S ribosomes but functionally similar to eukaryotes Methionine Eukarya 80S ribosomes Methionine PART IV Microbial Taxonomy and Its Relationship to Phylogeny 11.10 Classical Taxonomy, p. 318 11.11 Chemotaxonomy, p. 320 Conventional bacterial taxonomy emphasizes phenotypic properties of the organism (Table 11.4 ) To identify an organism, one must assess several of its phenotypic properties, from general to specific (Fig 11.20) 18 Molecular taxonomy involves molecular analyses of specific cell components: GC ratio DNA:DNA hybridization Ribotyping Multilocus Sequence Typing (MLST) Fatty Acid Methyl Ester (FAME) analysis GC ratio Percentage of guanine plus cytosine in an organism's DNA Greater than 5% difference in GC ratio between 2 organisms indicates they are different species and unlikely to be closely related DNA: DNA Hybridization o Tests ability of denatured DNA in single strand to form 2 organisms to bond to one another o DNA single strands from 2 individuals of the same species will anneal with 70% to 100% accuracy o To consider 2 individuals in the same genus, at least 25% annealing is required Ribotyping o Comparison of enzyme digested 16S ribosomal RNA Multilocus Sequence Typing Sequence comparison of several genes Useful for determining different strains of the same species Fatty Acid Methyl Ester (FAME) Analysis (Fig 11.24 b) 11.12 The Species Concept in Microbiology, p. 324 Bacterial speciation is affected to some degree by lateral (horizontal) gene transfer Lateral flow is the transfer of genes between species by: Conjugation plasmid transfer by cell to cell contact Transduction genomic DNA transfer via a virus Transformation uptake of free DNA from environment Taxonomic Hierarchy: Domain Phylum Class Order Family Genus 16S ribosomal RNA sequence difference of more than 5% Species 16S ribosomal RNA sequence difference by more than 3% 7029 Prokaryotes recognized but there are many more out there 11.13 Nomenclature and Bergey's Manual, p. 326 Binomial system of nomenclature: descriptive genus name and species epithet - EX: Bacillus subtilis The International Code of Nomenclature of Bacteria regulates naming of prokaryotes Formal recognition of a new prokaryotic species requires: - Deposition of a sample of the organism in 2 international culture collections - Official publication of the new species name and description in International Journal of Systematic and Evolutionary Microbiology (IJSEM) 19 Bergey's Manual of Systematic Bacteriology and The Prokaryotes are major taxonomic compilations of Bacteria and Archaea Chapter 12 Prokaryotic Diversity: The Bacteria 12.1 12.38, p. 331-417 Phylum 1: Proteobacteria Largest most metabolically diverse group of bacteria; ALL are Gram negative 5 major (phylogenetic) subdivisions: alpha, beta, gamma, delta, and epsilon 12.2 Purple phototrophic bacteria Anoxygenic phototrophs Purple sulfur bacteria Use H2S as electron donor Most form sulfur globules Found in illuminated anoxic zones of lakes Purple non-sulfur bacteria Use H2S as electron donor Most can fix N2 Rhodobacter Vampirococcus This bacterium attaches to its prey, the purple sulfur bacterium Chromatium, through pilus structures and sucks it dry of cytoplasm. Don't worry, it won't attack you! 12.3 Nitrifying bacteria Chemolithotrophs Use reduced nitrogen compounds 2 groups Ammonia-oxidizing or Nitrosifyers (NH3 to NO2) Ex: Nitrosococcus Nitrite-oxidizing or nitrifying (NO2 to NO3) Ex: Nitrobacter 12.4 Sulfur and iron-oxidizing bacteria Chemolithotrophs Use reduced sulfur (H2S, S0) or Fe for energy Acidithiobacillus Oxidizes sulfur to sulfuric acid Can also oxidize ferrous iron Beggiatoa Large, filamentous, gliding, sulfur-oxidizing 12.5 Hydrogen-oxidizing bacteria Able to use H2 as electron donor Require nickel (Ni2+) as metal cofactor for hydrogenase Many are autotrophic and use the Calvin cycle Ralstonia 20 12.6 Methanotrophs and Methylotrophs Sterols in membranes Widespread in aquatic and terrestrial environments Methylotrophs Oxidize one-carbon compounds for energy and as a carbon source Methanotrophs A methylotroph that can also use methane (CH4) 12.7 Pseudomonads Polar flagella Oxidase positive Wide variety of organic compounds as carbon sources Some species can use over 100 different compounds Widespread in nature Some animal and plant pathogens Nosocomial infections Pseudomonas 12.8 Acetic Acid bacteria Incomplete oxidation of alcohols and sugars Accumulation of organic acids such as acetic acid High tolerance for acidic environments Some can synthesize cellulose Vinegar, cider, wine Acetobacter 12.9 Free-living aerobic nitrogen-fixing bacteria Atmospheric N2 is reduced to ammonia that can then be converted to organic nitrogen compounds Non-symbiotic In soil Some produce capsules or slime layers Azotobacter resting structures called cysts that are dormant, resistant to desiccation and UV but NOT heat 12.10 Neisseria and relatives Some pathogenic (G-cocci) Neisseria gonorrhoeae causes gonorrhea 12.11 Enteric Bacteria Facultative anaerobes, fermentative Intestinal tract of warm-blooded animals, soil, water Some are pathogenic Typhoid Fever by Salmonella typhi Serratia, Shigella, Salmonella Escherichia, Enterobacter Proteus 21 12.12 Vibrio and Photobacterium Rods and curved rods Most aquatic Some are pathogenic Vibrio cholerae- cholera Some bioluminescent Vibrio, Photobacterium 12.13 Rickettsias Small cocci or rod-shaped Most are obligate intracellular parasites Typhus fever, Rocky Mountain spotted fever, Q fever Have not been cultivated in absence of host cells Deficient in most metabolic functions, must get metabolites from host Transmitted between animals by arthropods Rickettsia 12.14 Spirilla Bdellovibrio is a bacterial predator Campylobacter and Helicobacter are human pathogens Magnetospirillum contains magnetosomes 12.15 Sheathed Proteobacteria Filamentous Common in freshwater habitats Form flagellate swarmer cells with a sheath to be released in unfavorable conditions 12.16 Budding and Prosthecate/Stalked Bacteria Budding bacteria Prosthecate/Stalked bacteria Appendage used for attachment Aquatic environments Caulobacter, Stella 12.17 Gliding Myxobacteria Vegetative cells Move by gliding across surfaces Nutrients obtained from lysis of other bacteria Multicellular fruiting bodies Form under nutrient deplete conditions Contain resting structures called myxospores that are desication and radiation resistant Myxococcus 12.18 Sulfate- and Sulfur-Reducing Bacteria Sulfate (Desulfovibrio) and sulfur (Desulfuromonas) used as electron acceptors under anoxic conditions to produce H2S 22 Phylum 2 and 3- Gram positive bacteria & Actinobacteria Includes ALL Gram Positive Bacteria Divided into 2 groups: high GC and low GC based on % guanine and cytosine in DNA Phylum 2: Gram-positive bacteria with low GC content (12.19 12.21) 12.19 Nonsporulating Catalase (+), salt tolerant, some pathogenic Staphylococcus Micrococcus Sarcina Catalase (-) Lactic acid bacteria Homofermentative produce only lactic acid Streptococcus, Enterococcus, Lactobacillus (Yogurt) Heterofermentative produce other products like ethanol and CO2 in addition to lactic acid Leuconostoc 12.20 Endospore-forming Bacillus Bt toxin- endospores of one species sold as insecticide Clostridium Obligate anaerobe Some fix N2 Soil Heliobacteria (Heliobacterium) Anoxygenic phototrophs Fix N2; associated with rice fields 12.21 Cell wall-less Small genomes Pleomorphic (no distinct shape) Classified with Gram + due to phylogenic relatedness Parasitic plant, animal, insect hosts Mycoplasma Phylum 3: Gram-positive bacteria with high GC content, Actinobacteria (12.22 12.24) 12.22 Coryneform and Propionic Acid bacteria Coryneforms Snapping division Some animal and plant pathogens Diphtheria caused by Corynebacterium Propionic Acid bacteria Produce Propionic acid Swiss cheese (produce gases that allow for the holes in the Swiss cheese) Propionibacterium 12.23 Mycobacteria Acid fast due to mycolic acids Some human pathogens 23 12.24 Tuberculosis, leprosy Slow-growers vs. fast-growers (salt tolerant) Mycobacterium Filamentous Branching filaments called mycelia like that of filamentous fungi Reproductive spores called conidia Sporulation triggered by nutrient depletion Streptomyces earthy odor of soil 60+ antibiotics 12.25 Phylum 4: Cyanobacteria and Prochlorophytes (12.25 12.26) Cyanobacteria Large group of oxygenic photosynthetic bacteria; phycobilins Fix Carbon Dioxide; many also fix Nitrogen and have heterocysts Can cause nuisance blooms in freshwater habitats Many have gas vesicles for buoyancy Many secrete neurotoxins- animals ingesting water where bloom has occurred may be killed Only group of bacteria that are oxygenic phototrophs Anabaena 12.26 Prochlorophytes Prochlorococcus Possibly the most abundant photosynthetic organism of Earth 12.27 Phylum 5: Chlamydia group Obligate intracellular parasites of animals Little metabolic capacity No peptidoglycan All 3 species can cause human disease such as venereal disease (Chlamydia- most common STD bacteria in US), conjunctivitis, pneumonia Psittacosis- epidemic in birds, can cause pneumonia in humans Trachoma- leading cause of blindness in humans 12.28 Phylum 6: Planctomyces/Pirellula S layer protein cell wall Reproduce by budding Some species have stalks (non-cellular appendages) made of protein that function in attachment Have cell compartmentalization: there are membranes around certain things in the cell Gemmata has membrane-bound nuclear material (unique in prokaryotes) 12.29 Phylum 7: Verrucomicrobia Derived from Greek word "warty" Have cytoplasmic appendages celled Prosthecate 24 12.30 Phylum 8: Bacteriodes/Flavobacteria group Bacteroides- obligate anaerobe Predominant microbe in lower digestive tract of humans and other animals can be pathogenic In intestine, undigested food is fermented by Bacteroides. Fermentation products are used by animal as carbon and energy source Flavobacterium-rarely pathogenic; found in aquatic habitats 12.31 Phylum 9: Cytophaga group Rod-shaped, obligate aerobes that move by gliding Found in soil & water Many digest polysaccharides such as cellulose, agar, chitin Cellulase enzyme stays attached to the cell envelope Some species are fish pathogens Sporocytophaga produces microcysts-resisting structures 12.32 Phylum 10: Green sulfur bacteria Obligate anaerobes, carry out anoxygenic photosynthesis Possess chlorosomes Found at greatest depths of any phototrophic organism Use H2S as electron donor, oxidize it to sulfur sulfur granules are deposited outside the cells Autotrophs NO Calvin Cycle, reverse citric acid cycle 12.33 Phylum 11: The Spirochetes Motile, Gram Negative Endoflagella- located in the periplasm of the cell Treponema pallidum causes syphilis (never grown in laboratory culture) Borrelia burgdorferi causes Lyme disease (transmitted by ticks), has a linear chromosome 12.34 Phylum 12: Deinococcus group Deinococcus- highly resistant to radiation due to DNA repair mechanisms First isolated from foods sterilized by gamma irradiation (1,000 rads of ionizing radiation kills humans; 500,000 rads does not kill Deinococcus) Stain G+ due to thick peptidoglycan layer but has outer membrane like GramThermus aquaticus- thermophile Taq DNA polymerase used in PCR 12.35 The Green Nonsulfur Bacteria Green filamentous bacteria Most are thermophile Ex: Chloroflexus - anoxygenic phototrophic found in bacterial mats Contain chlorosomes- bacteriochlorophyll containing structures that are attached to the cytoplasmic membrane 12.36, 12.37 Phyla 14-16: Deeply branching hyperthermophilic bacteria Hyperthermophiles (optimum growth temp above 80C) found near marine hydrothermal vents & hot springs 25 Aquifex - Most ancient & thermophile genus of know Bacteria (grow up to 90C) Thermotoga - Cells surrounded by protein covering (toga) that balloons over ends 12.38 Phyla 17 & 18: Nitrospira, Deferribacter & relatives Nitrospira & Deferribacter were identified by rRNA sequencing; little is known about them Some species are found in microbial mats near hot springs Relatives- diverse metabolic capabilities Chapter 13- Prokaryotic Diversity: The Archaea 4 Phyla of Archaea Phylum 1: Euryarchaeota 4 groups of Euryarchaeota - Extreme halophiles - Methanogens - Thermoplasmatales - Hyperthermophiles Phylum Euryarchaeota 13.3 Extreme Halophiles Require at least 9% of NaCl for growth- most require 12-23% Common in salt lakes and salterns (ponds used to prepare solar salt by evaporation of sea water) - Give red color to water - Ex: Halobacterium salinarium To prevent water loss in hypertonic environment: - Pump inorganic ions (K+) into the cell - Make or concentrate an organic solute in the cell Light-mediated energy production: - Some extreme halophiles use light to produce energy - Don't have chlorophyll, have protein called bacteriorhodopsin - Light energy is used to pump protons to outside surface of cell membrane and generate a hydrogen ion gradient - ATPase uses this gradient to form ATP 13.4 Methanogens Release 100 million tons of methane into atmosphere each year Found in anaerobic environments Methanogenic habitats - Freshwater sediments rice paddies, marshes, etc. - Gastrointestinal tract of animals human large intestine - Rumen 10-20% of total methane emitted to atmosphere originates in rumen 13.5 Thermoplasmatales Lack cell walls Thermophilic & acidophilic Most strains have been isolated from self-heating coal refuse piles Thermoplasma Picrophilus optimum pH 0.7 26 13.6 - 13.7 Hyperthermophiles Optimum growth at 100 C Pyrococcus "fireball" Methanopyrus - Source of methane produced from hot oceanic sediments 2000m deep 13.8 13.10 Phylum Crenarchaeota Most are hyperthermophiles (hot springs), some are psychrophiles (sea ice) Most use sulfur as electron acceptor 13.11 Phylum Nanoarchaeota Nanoarchaeum cells are symbionts or parasites of Ignicoccus (Crenarcheote), none free-living Tiny cells- 1% of the volume of E. coli Smallest genome Lacks genes for most metabolic functions; depends on host Hydrothermal vents and hot springs Phylum Korarchaeota- pg 421 Found in Obsidian Pool at Yellowstone Hyperthermophiles- 85 C Originally detected from 16s rRNA sequence No pure cultures exist Not officially recognized in taxonomy Least evolved microbes? Origin of life? Chapter 14- Eukaryotic Cell Biology and Eukaryotic Microorganisms PART III Eukaryotic Microbial Diversity 14.9 Phylogeny of the Eukarya, p. 461 Based on 18s rRNA sequencing 14.10 Protozoa, p. 463 Unicellular Lack cell walls Most feed by phagocytosis Divided into 4 groups based on motility: Sarcodina cytoplasmic streaming Entamoeba histolytica- amebic dysentery serious, gastrointestinal disease Mastigophora flagella Trypanosomes (Causes African Sleeping Disease) & Giardia (gastrointestinal) Ciliophora cilia Paramecium Apicomplexa non-motile Plasmodium 27 14.11 Slime Molds, p. 467 Acellular slime mold- mass of motile protoplasm called plasmodium Cellular slime mold- mass of individual cells that aggregate to move and to form fruiting bodies that release spores 14.12 Fungi, p. 469 Cell walls made of chitin Produce spores Non-motile 3 major groups: Molds Yeasts Candida Saccharomyces Mushrooms 14.13 Algae, p. 472 Oxygenic phototrophs, have chloroplasts 3 groups: Dinoflagellates, Diatoms, Euglenoids Chapter 9- Essentials of Virology PART I Virus and Virion p. 231 9.1 General Properties of Viruses, p. 231 Obligate intracellular parasite made of nucleic acid surrounded by a protein coat Only replicate inside host No nucleus, organelles, cytoplasm AKA virions 9.2 Nature of the Virion, p. 232 Viral Components (3): Nucleic acid- either DNA or RNA Can be single-stranded or double-stranded Linear or Circular Capsid- protein coat surrounding nucleic acid Envelope- lipid bilayer surrounding the capsid; only found in some viruses Capsid proteins are arranged to give virion symmetry 1. Helical Symmetry Head Rod-shaped, protein subunits twist up 2. Icosahedral Symmetry Roughly spherical 20 equilateral triangles or faces Complex viruses- multiple parts assembled separately Head genome surrounded by capsid Tail & tail fibers Tail 28 Enzymes- Some viruses have 1 or more enzymes; May help infect the host cell, or may be required for replication of the viral genome Bacterial Viruses Bacteriophage/phage- viruses that infect bacteria PART II Growth and Quantification 9.3 The Virus Host, p. 236 Must be grown with living host cells 3 types of hosts: prokaryotes, plants, animals - Bacterial viruses with their bacterial host o Bacteriophage lambda with E. coli - Plant viruses with their plant host o Tobacco mosaic virus with Tobacco - Animal viruses with their animal host o HIV with lymphocytes (wbc) 9.4 Quantification of Viruses, p. 236 Quantification methods (2): 1. Animal infectivity Inject sensitive animals with 10-fold serial dilutions of viral sample, determine % survival at each solution 2. Plaque assay Used to count bacterial and some animal viruses Depends on efficiency of infection PART III Viral Replication 9.5 9.7 p. 238 242 Attachment to a specific receptor on host cell, usually a membrane protein Penetration of either whole or virus (eukaryotic) or just its genome (prokaryotic) Host machinery replicates viral genome and makes viral proteins (like capsid proteins) Assembly and packaging of structural subunits and genome into capsid Release- lysis of host cell or by budding; new virions can infect new host cell 1. 2. 3. 4. 5. Viral Restriction and Modification by the Host Bacteria synthesize enzymes as protection against viral invaders Restriction endonucleases cleave DNA at specific sequences Viruses can modify their DNA to avoid digestion by the host's restriction endonucleases Glucosylation Methylation Encode proteins to inhibit host restriction systems Host cells also have similar means of protecting their DNA from degradation by viral endonucleases 29 PART IV Viral Diversity 9.8 Overview of Bacterial Viruses, p. 243 9.9 Virulent Bacteriophages and T4, p. 243 9.10 Temperate Bacteriophages, p. 245 9.11 Bacteriophage Lambda, p. 246 2 types of phage: Lytic Lysogenic Lytic Simple life cycle Infect host, make copies of themselves, lyse the host cell Ex: T4 which infects E. coli - T4 life-cycle: o Attachment & penetration Tail-fibers of T4 attach to cell wall T4 genome is 1 linear molecule of double-stranded DNA DNA is injected into host. Rest of phage remains outside host cell o Replication & synthesis of new proteins DNA is transcribed Resulting mRNA is translated to make proteins for new viral heads and tails 100's of copies of viral DNA are also made o Assembly & release of viral particles DNA is inserted into empty capsids and tails are added Host cell is lysed to release viruses Formation of a plaque When an infected cell lyses & releases phage, those phage infect neighboring cells which causes them to lyse. This cycle continues. This causes a clearing in a lawn of bacteria called a plaque Lysogenic phage/Temperate viruses- Fig 9.16 Enter a state called lysogeny where viral genome integrates into host chromosome and is replicated with host chromosome Don't immediately make new phage particles - The virus is called a prophage when its genome exists as part of host genome - Bacterial host cells that harbor prophages are called lysogens Eventually, new phage are made (lytic cycle occurs) and cells lyse - Induction of prophage lytic cycle host cell lysis Ex: Lambda which infects E. coli - The lambda life cycle- Lysogeny o Lambda genome is double-stranded linear DNA o Attaches to host cell wall & injects its DNA into cytoplasm o DNA is inserted into E. coli chromosome between the gal and bio genes o Lysogenic cell- cell with lambda DNA in its chromosome o When chromosome replicates, lambda DNA replicates with it o Regulation of lytic versus lysogenic events in lambda is controlled by several promoters and regulatory proteins 30 o Induction Change in environmental conditions causes lambda to come out of chromosome and form new viruses Hundreds of lambda chromosomes are formed Viruses are assembled then cell lyses to release viruses Bacteriophage with different types of nucleic acids: Single-stranded DNA phage Ex: M13 RNA phage Ex: MS2 Single-stranded Used as mRNA to make proteins Complementary copies are also made and used as templates for making more phage RNA New phage RNA is packaged, cells lyse 9.12 Overview of Animal Viruses, p. 250 4 Types of infection by animal viruses: 1. Lytic Destruction of host cells 2. Persistent New virions leave host by budding Cell does not die, but remains infected and will produce virions indefinitely 3. Latent Virus is not actively replicating, dormant Symptoms appear only when virus emerges from latency (like cold sores) 4. Transformation Virus can change normal cell into cancer cell Genetic changes that regulate growth Benign or malignant tumors Animal viruses Can be single or double stranded DNA or RNA RNA viruses Positive-strand RNA viruses (SS)- genomic RNA is used directly as mRNA for making proteins - Ex: poliovirus, coronaviruses & rhinoviruses Negative-strand RNA viruses (SS)- genomic RNA does not serve directly as mRNA but is transcribed into a complement that functions as mRNA - Ex: rhabdoviruses (rabies), Ebola virus, measles, influenza, RSV Double-stranded RNA viruses: - Reoviruses- only animal viruses with double-stranded RNA - Rotavirus- member of reovirus family, most common cause of infant diarrhea 31 DNA viruses Parvoviruses- only group with single-stranded DNA Herpesvirus group (DS)- causes cold sores, venereal disease, chicken pox, mononucleosis Are able to remain latent in the body for years, becoming active during stressful conditions Poxvirus group (DS) causes smallpox (vaccinia), cowpox, & some tumors 9.13 Retroviruses, p. 251 Retro means backward Cause HIV & some forms of cancer Single-stranded RNA genome Enzyme reverse transcriptase copies RNA into DNA DNA integrates into host genome like a temperate virus Viral DNA is transcribed into mRNA and RNA for new viruses New viruses are assembled and released Viral RNA AZT reverse transcriptase (RT) Viral DNA Host cell DNA Retrovirus DNA (provirus) 9.14 Viroids and Prions Viroids Small, naked (no capsid, no envelope, etc.) single-stranded RNA Mostly crop diseases Prions Protein-only infectious agent BSE (mad cow), scrapie (sheep), Creutzfeld-Jakob, kuru (humans), chronic wasting disease (deer, elk) Normal protein takes on abnormal shape, loses normal function (Fig 9.29) 32

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