Microbiology Lecture Notes PDF

9/22/24 Bacteria regulate internal pH. 1 5. Oxygen and Other Electron Acceptors § Many microorganisms can grow in the presence of molecular oxygen (O2). § Many organisms are killed instantly by O2. § Some even use oxygen as a terminal electron accep...

9/22/24 Bacteria regulate internal pH. 1 5. Oxygen and Other Electron Acceptors § Many microorganisms can grow in the presence of molecular oxygen (O2). § Many organisms are killed instantly by O2. § Some even use oxygen as a terminal electron acceptor (TEA) in the electron transport chain. 2 1  9/22/24 Oxygen Has Benefits and Risks § Oxygen is a benefit to aerobes, organisms that can use it as a TEA to extract energy from nutrients. § Oxygen is toxic to all cells that do not have enzymes capable of efficiently destroying the reactive oxygen species (ROS)—for example, anaerobes. § For example, catalase enzyme. § Oxygen rich atmosphere is lethal to many organisms!!! 3 Aerobes, Anaerobes, and More § Strict aerobes can only grow in oxygen. § Microaerophiles grow only at lower O2 levels. § Strict anaerobes die in the least bit of oxygen. § Aerotolerant anaerobes grow in oxygen while retaining a fermentation-based metabolism. § Facultative anaerobes can live with or without oxygen. - They possess both the ability for fermentative metabolism and respiration (anaerobic and aerobic). 4 2  9/22/24 Culturing Anaerobes in the Lab § Three oxygen-removing techniques are used today: 1. Special reducing agents (thioglycolate) or enzyme systems (Oxyrase) can be added to ordinary liquid media 2. An anaerobe jar - O2 is removed by a reaction catalyzed by palladium 3. An anaerobic chamber with glove ports - O2 is removed by vacuum and replaced with N2 and CO2 5 5.5 Nutrient Deprivation and Starvation § Starvation is a stress that can elicit a “starvation response” in many microbes. Enzymes are produced to increase the efficiency of nutrient gathering and to protect cell macromolecules from damage. § The response is usually triggered by the accumulation of small signal molecules such as cAMP or guanosine tetraphosphate, which globally transform gene expression. These highly soluble, small molecules can quickly diffuse throughout the cell, promoting a fast response. 6 6 3  9/22/24 Microbes Encounter Multiple Stresses in Real Life § Bacterial stress responses have traditionally been studied in terms of individual stresses. § In the world outside of the laboratory, environmental situations can be quite complex, involving multiple, not just single, stresses. For example, an organism could simultaneously undergo carbon starvation in a high-salt, low-pH environment. 7 7 Physical Agents That Kill Microbes § High temperature Moist heat is more effective than dry heat. Boiling water (100°C) kills most cells. Killing spores and thermophiles usually requires a combination of high pressure and temperature. At high pressure, the boiling point of water rises to a temperature rarely experienced by microbes. – Even endospores quickly die under these conditions. § Chemical Agents § Ethanol or Iodine or Chlorine (bleach) 8 4  9/22/24 Chapter 6: Virus Structure and Function! 9 What Is a Virus? § A virus is a non-cellular particle that must infect a host cell in order to reproduce. § The virus particle (virion), consists of a single nucleic acid (can be DNA or RNA) contained within a protective protein capsid. § Only discovered in 1892!! 10 5  9/22/24 Introduction § All life-forms can be infected by viruses. § Some viruses can be infected by viruses! § From dengue fever to influenza to AIDS to COVID- 19. § In research, viruses have provided both tools and model systems in molecular biology. 11 Figure 6.3 12 6  9/22/24 Viruses come in different sizes § Small viruses § Large viruses may commonly have a have more than small genome, 100 genes encoding under ten genes - Mimivirus encodes over - The genes may 1,000 genes actually overlap in sequence 13 Viruses have varying levels of lethality Marburg Virus- The mortality rate was more than 80% in the 1998-2000 outbreak in the Democratic Republic of Congo. One strain of Ebola (Reston), doesn't even make people sick. But the Bundibugyo strain is up to 50% and it is up to 71% for the Sudan strain Rabies- 100% lethal if you don’t get treatment SARS-CoV-2 Influenza 14 7  9/22/24 Viral Ecology § Viruses exist with host organisms in complex ecosystems. § Huge #’s in the environment! § Viruses fill important niches in all ecosystems. - Limiting host population density - Selecting for host diversity 15 § Virus-to-bacteria ratios range from 10:1 in marine and aquatic environments, to 1,000:1 in soils. § On a global scale, viruses play a significant role in the carbon balance. 16 8  9/22/24 § In the oceans, viruses are extremely numerous and genetically diverse. - The number of bacteriophages and algal viruses can reach 107 (10 million) per milliliter. § When marine algae overgrow, viruses play a decisive role in controlling the algal bloom. 17 18 9  9/22/24 Emergence of Viral Pathogens § Certain human-infecting viruses are well known to persist in the wild, such as Rabies virus and West Nile virus. § But how does a seemingly “new” virus emerge to sicken humans? 19 Virus Structure § The viral capsid is composed of repeated protein subunits. § The capsid packages the viral genome and delivers it into the host cell. § Different viruses make different capsid forms. 20 10  9/22/24 Symmetrical Viruses § Icosahedral viruses - Are polyhedral with 20 identical triangular faces - Have a structure that exhibits rotational symmetry 21 § In some icosahedral viruses, the capsid is enclosed in an envelope, formed from the host cell membrane. - The envelope contains glycoprotein spikes, which are encoded by the virus. 22 11  9/22/24 §Filamentous viruses - The capsid consists of a long tube of protein, with the genome coiled inside - Vary in length, depending on genome size - Filamentous viruses show helical symmetry A 23 Tailed Viruses § These have complex multipart structures § T4 bacteriophages - Have an icosahedral “head” and helical “neck” 24 12  9/22/24 Viral Genomes and Classification § Viral genomes can be: - DNA or RNA - Single- or double-stranded (ss or ds) - Linear or circular § Include genes encoding viral proteins - Capsid - Envelope proteins (if needed) - Any polymerase not found in host cell 25 Bacteriophage Replication § All viruses require a host cell for reproduction. - Thus, they all face the same needs for host infection: - Host recognition and attachment - Genome entry - Assembly of virions - Exit and transmission 26 13  9/22/24 Bacteriophages Infect a Bacterial Host 27 Bacteriophages Infect a Bacterial Host § Most bacteriophages (phages) inject only their genome into a cell through the cell envelope. - The phage capsid (now termed “ghost”) remains outside, attached to the cell surface. 28 14  9/22/24 § All bacteriophages can undergo one life cycle - 1. Lytic cycle Some bacteria can undergo a second lifecycle - 2. Lysogenic cycle § The “decision” between the two cycles is dictated by environmental cues. - In general, events that threaten host cell survival trigger a lytic burst. 29 § The lytic replication cycle requires these steps: - Host recognition and attachment - Genome entry - Assembly of phages - Exit and transmission § In a lytic cycle, when a phage particle injects its genome into a cell, it immediately reproduces as many progeny phage particles as possible. 30 15