Bacteria and Viruses PDF

Page 1 of 16 BIO 122 BACTERIA AND VIRUSES TEXT: CHAPTERS 26 AND 27 READ: “A brief history of microbiolog...

Page 1 of 16 BIO 122 BACTERIA AND VIRUSES TEXT: CHAPTERS 26 AND 27 READ: “A brief history of microbiology,”, pages 561-562 ————————————————————————————————————————— EUBACTERIA (TRUE BACTERIA) AND ARCHAEA - As we study the bacteria, we will see a tremendous amount of diversity. Since prokaryotes can be found in EVERY location on Earth, different species use different metabolic pathways in order to survive sometimes very extreme environments. According to your text, “there is significantly greater metabolic and nutritional diversity amongst the prokaryotes than amongst the eukarya.” - DNA evidence indicates that the organisms classified in the Eubacteria and Archaea are as different as Eubacteria and Eukarya. But, what do organisms in the Eubacteria and Archaea have in common? - It is interesting to note that humans are excellent hosts for bacteria. These bacteria share a type of symbiosis with humans called mutualism which means: - Some benefits: - assist in digestion of polysaccharides - produce nutrients needed by humans - protect us from pathogenic bacteria - Bacteria live on our skin, and in our digestive tract, urogenital tract and respiratory tract. Examples: A. _________________________________________ live on__________________________. If the skin becomes too oily, these bacteria can cause acne. But, they also reduce the chance of developing skin diseases caused by oxidative stress.  Page 2 of 16 B. _________________________________________ live in__________________________. These bacteria produce Vitamin K and Vitamin B12 which is absorbed into the human bloodstream. - Vitamin K is important for: - Vitamin B12 is important for: C. _________________________________________ live in__________________________. Lactobacilli produce lactic acid (by fermentation) which lowers the vaginal pH to 3.5-4.5. - All the bacteria living in and on us are referred to as the: - The ratio of human cells to bacteria is 1:1, meaning that there are: —————————————————————————————————————————— CHARACTERISTICS OF PROKARYOTIC CELLS 1. No membrane-bound nucleus - DNA in a single, circular chromosome located in the nucleoid of the cytoplasm. - Prokaryotic cells also contain extrachromosomal, small circular DNA molecules called:  Page 3 of 16 - Plasmids carry genes for specific functions that confer a selective advantage on the bacteria that have the plasmid. -example: carry genes for antibiotic resistance - Plasmids can be copied and transferred to other bacteria (even of other species) through: 2. No membrane-bound organelles - Some species do have structures that can be used for storage or to contain enzymes for certain metabolic pathways or protect the cell from toxins produced from basic metabolism. These are called: - folds of the cell membrane serve as sites for cell respiration and photosynthesis - prokaryotic cells DO have ribosomes - function of ribosomes: - Why do we say that prokaryotic cells don’t have membrane-bound organelles if they do have ribosomes? - Ribosomes differ in structure from that of eukaryotic ribosomes, and are smaller. Who cares??  Page 4 of 16 3. Unicellular - In certain species of prokaryotes, the individual cells form filaments, but each cell still functions independently of the others. 4. Cell size - Most prokaryotes are 1um or less in diameter. (Most eukaryotic cells are approximately 10 times larger). 5. Asexual Reproduction (no sexual reproduction) - Prokaryotes reproduce asexually by the process of: - bacterial reproduction is very fast……WHY? - Prokaryotes DO exchange genetic information (thus alter their genome) through a process through conjugation, as already discussed. - Prokaryotes can also take up bacterial DNA from their environment and incorporate it into their genome. This process is called: - Transformed cells have new DNA and can therefore produce new protein(s). As a result, they have a new characteristic(s). - When environmental conditions are not good, some prokaryotes will grow a thick wall around a small amount of cytoplasm and their DNA. This is called an:  Page 5 of 16 - What do you think will happen to the endospore when environmental conditions are no longer stressful? ex. Tetanus - Endospores driven into the skin where environment is favorable for germination of endospores. Disease and often death result. 6. Flagella - bacteria may have one or more flagella - function: - NOT composed of microtubules; these flagella are made up of a protein called: 7. Classification of Bacteria A. Use of cell shape a. Coccus (cocci) b. Bacillus (bacilli) c. Spirillum (spirilla) d. Vibrio (vibrios)  Page 6 of 16 B. Use of cell wall for classification - the cell wall consists of many layers, maintains the shape of the cell and protects it from rupturing in hypotonic conditions. What is a hypotonic environment? - Eubacteria cell walls contain peptidoglycan (polysaccharide strands cross-linked by peptide side chains); Archaebacteria cell walls do not contain peptidoglycan - An important staining process called the Gram stain (crystal violet dye) can be used to identify true bacteria. The gram stain is usually the first test used by microbiologists to identify a bacterium. - Gram positive bacteria - have a thicker peptidoglycan wall - stain: - Gram negative bacteria - have a thinner peptidoglycan wall as well as an outer lipopolysaccharide membrane - due not take up the Gram stain, so a counterstain (safranin) is used and these bacteria stain: Who cares?  Page 7 of 16 - Speaking of bacteria that cause disease, some bacteria have an outer capsule surrounding the other outer layers of the organism. The capsule: 1. Allows the bacteria to stick to a surface 2. Makes it difficult for phagocytic cells of the immune system to identify the organism 8. Antibiotics and Bacteria - antibiotics are chemicals that kill: - many strains of bacteria have acquired antibiotic resistance which means: - antibiotic resistance occurs due to the rapid rate of mutations that occur in prokaryotes (remember, prokaryotes reproduce very quickly, so “good” mutations can be spread rapidly in a population) - Note that bacterial populations are adapting to environmental stressors in the human body, What are these stressors: - Those bacteria that can survive in the presence of antibiotics will live and reproduce. - Example: - Staphylococcus aureus - a number of strains are antibiotic-resistant 1. MRSA: methicillin-resistant S. aureus and, of even more concern: 2. VRSA: Vancomycin-resistant S. Aureus because vancomycin is our “last resort” antibiotic  Page 8 of 16 9. Diversity of Bacteria - Bacteria are very diverse with regard to their metabolism. As a group, bacteria can metabolize almost anything!!! The goal is to convert a source of potential energy into the chemical bonds of ATP. - ATP is the source of chemical potential energy for ALL living organisms. - A. Heterotrophs - cannot produce their own food - get nutrition from forms of organic carbon. What is organic carbon? 1. Chemoorganotrophs - Note: all animals are chemoorganotrophs 2. Chemolithotrophs - Note: Since prokaryotes are the only organisms that are chemolithotrophs, they are an important part of the ecosystem in terms of biogeochemical cycling of many nutrients. B. Autotrophs - can produce their own food - produce complex organic compounds using carbon from inorganic sources  Page 9 of 16 1. Photolithoautotrophs Note 1: During photosynthesis, carbon is converted from an inorganic form (CO2) to an organic form (C6H12O6 (glucose)). This is important because (1) carbon is fixed and (2) these organic compounds are passed up the food chains to ALL heterotrophs, even YOU! fixation: conversion of nutrients from oxidized inorganic compounds to reduced organic compounds Note 2: prokaryotic photosynthesis differs from that of eukaryotes Do prokaryotes have chloroplasts? 2. Chemolithoautotrophs - Note: The use of reduced inorganic nutrients in this process is very important to nutrient recycling in the ecosystem. 10. Many forms of bacteria are beneficial to humans - Example 1: Escherichia coli in human intestine (as discussed earlier) - Example 2: Fermentation - anaerobic process - There are many different metabolic pathways in prokaryotic organisms resulting in a variety of alcohols and acids. - used for milk and cheese flavors  Page 10 of 16 - production of CHOCOLATE!! (cocoa is fermented in the process) - Clostridium botulinum - may be inadvertently added to food during the canning process - can ferment the amino acids of proteins in the food in order to produce ATP so they can reproduce - result: 11. Pathogenic bacteria - cause disease - represent a small number of bacterial species, but their pathogenicity leads to the death of many humans (and other organisms) - some bacteria that are always pathogenic: - Example 1: Salmonellosis - Example 2: Tuberculosis READ: Section 27.6: Bacterial Diseases in Humans, pages 578 - 582  Page 11 of 16 12. Decomposition and Fixation - Nutrients are constantly recycled between living organisms and the physical environment. Prokaryotes (and fungi) are the most important organisms in breaking down dead bodies, returning essential nutrients to the environment to be re-used by living organisms. - In addition to fixing carbon, prokaryotes are also essential in fixing nitrogen. - N2 - only a few species of prokaryotes have the enzymes that can break that bond and reduce nitrogen to ammonia - This process is critical to ALL living organisms because ____________________, the building blocks of proteins, require NH2 in their structure.  Page 12 of 16 VIRUSES VIRUSES ARE NOT MADE UP OF CELLS. THEREFORE THEY ARE NOT CLASSIFIED AS LIVING ORGANISMS. THEY ARE NOT CLASSIFIED INTO ANY OF THE THREE DOMAINS. (Note size of viruses, textbook figure 26.4) Characteristics: 1. A virus is a PARTICLE called a virion. A virus is made up of two parts: A. outer protein coat called a: B. inside capsid 2. The goal of a virus is to: - Viruses cannot reproduce or carry out metabolism unless inside a host cell. Therefore, infection of a host cell involves: A. Attachment: virus binds to a host cell using a protein receptor B. Viral DNA injected into host cell C. Incorporation of the viral DNA into the host DNA. - Viruses then use the “host cell machinery” (organelles) and host cell ATP to make more virus. Note that viruses will use the host cell to: 1. replicate the viral genome 2. express viral genes 3. use the resulting proteins to build new virions - One host cell can be used to produce thousands of new virions. Production of virions will continue until the host cell dies. As virions are released, other host cells are infected.  Page 13 of 16 - Note that when retroviruses (which contain RNA, not DNA) infect host cells, they must first convert themselves into double stranded DNA. RNA ————DNA Note that this is the OPPOSITE of transcription, so this process is called reverse transcription. The viral enzyme used for this process is: - Viruses have two forms of replication: the lytic cycle and the lysogenic cycle. A. Lytic Cycle - Once virions have been produced inside the host cell, the virions are released by “busting” the host cell open or by budding out of the host cell. - Host cell DIES. A. Lysogenic Cycle - Once the viral DNA enters the host cell and is incorporated into the host cell DNA, that’s it! The virus just sits there. The phage genome is known as the: The cell containing the prophage is the: - The problem is that, as the host cell replicates, the viral DNA is replicated as well. So, will all daughter cells and their daughter cells and their daughter cells etc. have a copy of the virus? - Due to an environmental stressor (UV light, hormonal changes, suppression of the immune system), at some point, the prophage undergoes induction. The virus is now activated, and the lytic cycle begins. - Example: Herpes simplex viral infection - Of the 8 herpes viruses, we will consider: HSV-1 and HSV-2 which cause oral and genital herpes. 1. When host cells are first infected, the viruses replicate quickly. The immune system responds, causing tissue damage as the host cells are killed, therefore symptoms (swellings, blisters) result.  Page 14 of 16 2. Symptoms abate as immune system responds. 3. Meanwhile, the virus migrates via nerve cells to ganglia (collection of nerve cell bodies) where they enter the lysogenic (latent) phase. 4. Upon reactiviation due to an environmental stressor, new viruses are produced. These travel back down the nerve cells to the original site of infection, and the lytic cycle commences, thus causing more symptoms. THIS IS THE POINT AT WHICH THE VIRUS IS MOST LIKELY TO SPREAD TO ANOTHER HOST. 3. Most viruses are specific to their host species and host cell(s). How is the host cell identified? - example 1: SARS-CoV-2 and ACE2 receptor - example 2: Rhabdovirus, which causes rabies, can only infect and reproduce itself in neurons. 4. Viruses can increase risk for cancer. Think about their “behavior,” and predict an answer as to why.  Page 15 of 16 - Example 1: HPV: human papillomavirus - sexually transmitted infection (STI) - causes _____________________________ and increases risk for: - There are more than 100 types of HPV, classified as A. low-risk: genital warts or no symptoms B. high-risk: increase risk of cancer Note: 70% of cases of cervical cancer occur in women with HPV infection. - Example 2: HBV, hepatitis B virus, increases risk for ______________________ cancer Page 16 of 16