Untitled

• These are the answers to the study questions provided.

Chapter 1 - Microbial Life

• Microbes are microorganisms that include bacteria, archaea, fungi, protists, and viruses, found in nearly every environment on Earth.
• Microbiology is important in medicine, agriculture, biotechnology, and environmental science.
• Prokaryotic microorganisms: Bacteria and Archaea. Eukaryotic microorganisms: Fungi and Protists.
• Viruses are not microbes; they are not cells, but rather infectious particles.
• To differentiate microorganisms, consider cell structure, metabolism, genetics, and ecological role.
• A genome is the complete set of genetic material in an organism, useful for understanding organism's biology and evolution.
• Metagenome is the collection of genetic material from a mixed community of organisms.
• Microbes are crucial for nutrient cycling, decomposition, and human health.
• Florence Nightingale was a pioneer in nursing, recognized for improving sanitation in hospitals.
• Antonie van Leeuwenhoek discovered microorganisms using simple microscopes. Robert Hooke coined the term "cell". Louis Pasteur disproved spontaneous generation and developed pasteurization.
• Spontaneous generation is the idea that living organisms can arise from non-living matter, debunked by Louis Pasteur.
• Germ Theory states that specific diseases are caused by specific microorganisms, proposed by Robert Koch.
• Robert Koch developed a set of postulates to establish a causative link between a microorganism and a disease.
• Immunization is among the greatest medical developments because it provides protection against infectious diseases.
• Jenner's vaccination with cowpox demonstrated protection against smallpox, a critical milestone in understanding immunity.
• Antiseptics are used to kill microorganisms on living tissues, while antibiotics are used to treat bacterial infections internally.
• Penicillin, the first antibiotic, was discovered by Alexander Fleming.
• Scientists involved in virus discovery include D. Ivanovsky, M. Beijerinck, and F. Loeffler.
• The first virus identified was Tobacco Mosaic Virus (TMV), causing mosaic disease in tobacco plants.
• Sergi Winogradsky was a pioneer in microbial ecology, known for discovering chemolithotrophy and nitrogen fixation.
• Microbes in ecosystems play roles in nutrient cycling, decomposition, and maintaining balance.
• Endosymbionts live inside other organisms. Examples include nitrogen-fixing bacteria in plant roots and gut bacteria in animals.
• Astrobiology explores the possibility of life beyond Earth.
• Studying microbes on Earth can help us understand the potential for life in extreme environments elsewhere in the universe.
• Endosymbiosis is the theory that mitochondria and chloroplasts in eukaryotic cells originated as symbiotic bacteria.
• Carl Woese classified life into three domains: Bacteria, Archaea, and Eukarya, based on ribosomal RNA (rRNA) sequences.

Chapter 2 - Observing Microbes

• Microscopic refers to organisms or structures too small to be seen with the naked eye, requiring magnification.
• Resolution is the ability to distinguish between two adjacent objects or points. Average resolution for the human eye is approximately 0.2 mm.
• Fovea is the central focal point in the retina, responsible for sharp, central vision.
• Detection is the ability to perceive that an object exists, while resolution is your ability to see the separate parts of an object.
• Magnification is the process of enlarging the apparent size of an object, achieved usually through lenses.
• Bacteria can be classified as cocci (spherical), bacilli (rod-shaped), and spiral (curved)
• Light is a form of electromagnetic radiation with wavelengths visible to the human eye ranging from approximately 400 nm to 700 nm.
• Three conditions for object resolution in microscopy: sufficient contrast, wavelength of light is smaller than the object, and high-quality lens.
• Light interacts with objects through absorption, where light is absorbed by the object; reflection, where light bounces off the object; refraction where light bends as it passes through the object; and scattering, where light spreads out in multiple directions.
• Refractive index is a measure of how much light bends when passing from one medium to another, and is important for focusing light in microscopy.
• Lenses help in forming a focal point by refracting light rays to converge at a single point.
• Resolution can be increased in microscopy by using shorter wavelengths of light, increasing the numerical aperture of the lens, or using immersion oil.
• A compound microscope uses multiple lenses to magnify an image.
• Parfocal means that when one lens is in focus, other lenses will also be approximately in focus.
• Total magnification calculation requires multiplying the magnification of the objective lens by the magnification of the eyepiece lens.
• A wet mount is a specimen preparation technique where the sample is suspended in liquid between a slide and a coverslip. Advantages: viewing live organisms. Disadvantages: can dry out quickly and may not provide sufficient contrast.
• Steps for observing a specimen under a light microscope: prepare the slide, focus using low power, adjust light and contrast, switch to higher power gradually, and refocus.
• Simple stains use one dye to color the entire organism, whereas differential stains use multiple dyes to distinguish between different types of organisms or structures. Gram stain is an example of a differential stain.
• Gram staining steps involve: crystal violet, iodine, alcohol wash, and safranin counterstain.
• Gram staining differentiates bacteria based on cell wall structure.
• Gram-positive bacteria are usually considered Gram (+). Gram-negative bacteria are usually considered Gram (-).
• Acid-fast staining identifies bacteria with mycolic acid in their cell walls; spore staining identifies bacterial endospores; negative staining stains the background, making the object appear transparent.
• Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation.
• A fluorophore absorbs light at one wavelength (excitation) and emits light at a longer wavelength.
• The main advantage of confocal laser microscopy: ability to obtain high-resolution optical sections of specimens.
• Chemical imaging microscopy allows one to visualize the distribution of specific chemicals within a cell or tissue.
• Dark-field microscopy observes specimens by scattering light, making them appear bright against a dark background. Phase-contrast microscopy enhances contrast in transparent specimens by exploiting differences in refractive index.
• Two main types of electron microscopes: transmission electron microscope (TEM) and scanning electron microscope (SEM). TEM produces high-resolution images of internal structures, while SEM produces high-resolution images of external surfaces.
• Magnets are used instead of lenses in TEM or SEM to focus electrons due to their charge.
• X-ray crystallography provides information about the atomic and molecular structure of crystals.

Chapter 3 - Cell Structure and Function

• Bacterial cells share the characteristics of a plasma membrane, cytoplasm, genetic material (DNA), ribosomes, and a cell wall.
• Archaeal cells are similar to bacteria, but differ in their cell wall composition, membrane lipids, and ribosomal RNA.
• Bacteria and Archaea belong to the prokaryotic domain.
• Prokaryotes lack membrane-bound organelles and a nucleus.
• Bacterial cell envelope includes the cell membrane, cell wall, and capsule.
• Cell cytoplasm is the gel-like substance within the cell membrane, containing water, enzymes, nutrients, and organelles.
• The nucleoid is the region in a prokaryotic cell where the genetic material (DNA) is located.
• The ultracentrifuge is important for cell study for separating cellular components based on size and density.
• The cell (plasma) membrane is composed of a phospholipid bilayer with embedded proteins. Its function is to regulate the passage of substances in and out of the cell.
• Inner membrane in bacterial cells is the cell membrane. Outer membrane is found only in Gram-negative bacteria and is located outside the cell wall.
• Mycoplasmas are interesting due to their lack of a cell wall, making them resistant to certain antibiotics.
• Molecules interaction with water terminology: hydrophilic (water-loving), hydrophobic (water-fearing), and amphipathic (having both hydrophilic and hydrophobic regions).
• Phospholipids are composed of a glycerol backbone, two fatty acids, and a phosphate group.
• Saturated fatty acids have no double bonds, unsaturated fatty acids have double bonds.
• The saturation state affects membrane fluidity: saturated fatty acids decrease fluidity, while unsaturated fatty acids increase fluidity.
• Hopanoids are steroid-like lipids in bacterial membranes, functioning to stabilize the membrane.
• A known difference between bacteria and archaea membrane structure is that archaea have ether linkages and isoprenoid chains, while bacteria have ester linkages and fatty acids.
• Proteins in cell membrane structure can function as transporters, receptors, enzymes, or structural components.
• A semi-permeable barrier allows some molecules to pass freely while restricting passage of others.
• Small, nonpolar molecules can pass "for free" (passively). Charged or large polar molecules need transport proteins.
• Membrane transport includes passive (diffusion) and active (requires energy) transport mechanisms.
• Osmosis is water movement across a semipermeable membrane, driven by differences in solute concentrations. Passive diffusion is the movement of molecules from an area of high concentration to low concentration.
• The cell wall provides structural support and protection to the cell. It is made of peptidoglycan in bacteria or other polysaccharides in other organisms.
• The two sugars are N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). They are connected by peptides.
• Penicillin and vancomycin kill bacteria by inhibiting peptidoglycan synthesis, weakening the cell wall.
• Transpeptidase is important in cell wall integrity because it cross-links peptidoglycan chains.
• Gram (+) bacteria have a thick peptidoglycan layer. Gram (-) bacteria have a thin peptidoglycan layer and an outer membrane.
• Mycobacteria are unique because they have mycolic acid in their cell walls, making them acid-fast.
• Bacterial capsules are made of polysaccharides, and located outside the cell wall.
• S-layer is a protein layer found on the surface of some bacteria and archaea.
• Outer membrane is present in Gram-negative bacteria, and consists of lipopolysaccharide (LPS), phospholipids, and proteins.
• LPS (lipopolysaccharide) is important due to its role as an endotoxin, eliciting a strong immune response in animals.
• Mycolic acid in mycobacteria cell envelopes is unique, providing increased resistance to antibiotics and environmental stress.
• Bacteria have cytoskeletons: proteins such as FtsZ, MreB, and CreS provide shape, support, internal organization, and cell division.
• Cell fission is the process of cell division in bacteria, which is different because mitosis is more complex and involves nuclear division.
• Septation involves the formation of a septum that divides the cell into two daughter cells. FtsZ protein plays a key role.
• The nucleoid is important as it contains the bacterial chromosome, essential for genetic information and cell function.

Chapter 6 - Viruses

• Viruses are found everywhere and are important due to their impact on ecosystems, human health, and biotechnology.
• A virus (or virion) consists of genetic material (DNA or RNA) enclosed in a protein coat (capsid).
• Bacteriophages infect bacteria, while viriophages infect viruses.
• The first virus identified was Tobacco Mosaic Virus (TMV). It was found through experiments showing it could pass through filters that retain bacteria.
• Viruses differ from most cells in their small size, simple structure, and obligate intracellular parasitic lifestyle.
• Prophages are bacteriophage genomes integrated into a bacterial chromosome. Proviruses are viral genomes integrated into a eukaryotic host cell chromosome.
• A provirus is a viral genome integrated into the host cell's DNA, while an endogenous virus is a viral sequence that has become a permanent part of the host's genome.
• Viruses can be found as free virions, integrated into host genomes, or in association with specific cells or tissues.
• Virome is the entire population of viruses present in a particular environment or organism.
• Viruses are important for nutrient cycling because they can lyse cells, releasing nutrients back into the environment.
• Acute virus infections are short-term, with rapid onset and clearance. Chronic virus infections are long-term, with persistent viral replication.
• Host range refers to the spectrum of cells that a virus can infect. Host trophism refers to the specific cells or tissues within a host that a virus can infect.
• Antibiotics target bacterial-specific processes and structures.
• Virus genome options: DNA or RNA, single-stranded (ss) or double-stranded (ds), linear or circular.
• Viral capsids are made of proteins and function to protect the viral genome and facilitate entry into host cells.
• A viral envelope is made of lipids, proteins, and glycoproteins, and functions to help the virus enter host cells and evade the immune system.
• Three main types of shape-groups for viruses: icosahedral, helical, and complex.
• Common symmetrical structures of viruses: icosahedral and helical.
• Viroids are small, circular RNA molecules (infectious to plants). Prions are infectious proteins, studied for their role in causing diseases like mad cow disease.
• A virus genome can be DNA or RNA, single-stranded or double-stranded, linear or circular.
• Virus genome size can range from a few thousand to several hundred thousand base pairs.
• The ICTV classifies viruses based on characteristics such as genome type, virion structure, and host range.
• Baltimore classification categorizes viruses based on their method of mRNA production and replication. There are seven groups identified using this system.
• Bacteriophage replication types: lytic and lysogenic cycles.
• Lytic replication cycle steps: attachment, entry, replication, assembly, and release.
• Lysogenic viruses integrate their DNA into the host's genome and replicate along with it.
• Some bacteriophages undergo a pseudo-lysogenic cycle, establishing a chronic, non-lytic infection without integration.
• Bacteria protect against virus infections through mechanisms such as restriction enzymes and CRISPR-Cas systems.
• Animal and plant virus infections and replication steps: attachment, entry, uncoating, replication, assembly, and release.
• Uncoating is important for some viruses as it releases the viral genome from the capsid, allowing replication to begin.
• Reverse transcriptase is an enzyme that synthesizes DNA from an RNA template, required by retroviruses.
• Animal viruses released in two ways from host cell: lysis (bursting of the cell) and exocytosis / budding.
• Oncogenic viruses are viruses that can cause cancer. Examples include human papillomavirus (HPV) and Epstein-Barr virus (EBV).
• Plant viruses differ because they often require mechanical damage or vectors for entry, unlike bacteriophages and animal viruses.
• Defense mechanisms in animals and plants against viruses: immune responses (antibodies, interferon) and RNA silencing in plants.
• COVID-19 caused by SARS-CoV-2; the genome is a single-stranded RNA virus.
• Zoonotic disease can be transmitted from animals to humans.
• Pandemic is a global spread of a disease. Spillover is the transmission of a virus from one host species to another.
• SARS-CoV-2 targets cells in the respiratory tract, entering host cell through the ACE2 receptor.
• Virus growth in a lab requires host cells for replication.
• Batch culture involves growing viruses in a liquid medium with host cells, while plate culture involves growing viruses on a solid medium with host cells.
• In batch culture, virus growth is seen by measuring viral titer over time. Plate culture, growth is seen by observing plaques (clear areas) in the cell monolayer.

Chapter 11 - Viral Molecular Biology

• Lambda phage is a temperate bacteriophage, often studied as a model for understanding viral replication and gene regulation.
• Lambda phage structures include: a head containing the DNA genome, a tail for attachment to the host cell, and tail fibers.
• Lambda phage replicates through either a lytic or lysogenic cycle.
• The virus that causes the flu is the influenza virus.
• Influenza virus is an RNA virus.
• Key components of the flu virus: hemagglutinin (HA) responsible for host cell attachment and neuraminidase (NA) responsible for virus release.
• Gene reassortment is when genetic material from different viral strains mixes during infection, especially in segmented viruses like influenza.
• Segmented genomes in viruses can lead to greater diversity and rapid evolution through gene reassortment.
• Viruses that infect animals, such as bird flu, are worrisome due to their potential to jump to humans and cause pandemics.
• Virus causing AIDS is HIV (human immunodeficiency virus).
• AIDS transmitted: sexual contact, blood transfusion, sharing needles.
• HIV genome unique due to its RNA genome and the need for reverse transcriptase to integrate into the host cell genome.
• Single antiviral drug ineffective against HIV due to rapid mutation and resistance development.
• Quasispecies are populations of genetically distinct but closely related viruses within an infected individual.
• HIV enters host cells by binding to CD4 receptors and co-receptors on immune cells.
• HIV replication: attachment, entry, reverse transcription, integration, replication, assembly, and release.
• Gene-transfer vector is used to deliver genetic material into cells.
• Viral vectors used to treat diseases due to ability to efficiently deliver genetic material into target cells.