microbiology_ch28

The Microbial World

• Antonie van Leeuwenhoek (1632-1723) improved the quality of the microscope in the late 1600s.
• He described "animalcules," which are microscopic life forms in water.
• Leeuwenhoek believed in spontaneous generation.
• Louis Pasteur disproved the theory of spontaneous generation in 1859.
• Pasteur suggested that a virus can cause rabies.
• Louis Pasteur designed experiments to figure out where bacterial cells come from.
• In the first experiment sterilized broth flasks exposed to indoor or outdoor air contaminated with microbial growth.
• In the second experiment the flask neck was curved to prevent microbes from entering broth from the air, and no microbial growth was observed.
• Pasteur demonstrated that the bacteria did not arise spontaneously.

The Science of Microbiology

• Microbiology is the study of microbes, including living organisms like bacteria, archaea, protists, and fungi.
• Microbiology also studies non-living infectious agents such as viruses, viroids, and prions.
• A microbe is an organism too small to be seen without a microscope.
• A microbe isn't a classification of life.
• Bacteria and other microbes are abundant in air, soil, water, and on objects.
• While some microbes cause human disease, others provide benefits.
• Microbiota are on and inside our bodies.
• Microbiota on skin crowds out harmful microbes.
• Microbiota in intestines aids in digestion and synthesizes vitamin K and vitamin B12.
• Microbes contribute to the proper functioning of ecosystems and the biosphere.
• Some bacteria and fungi are decomposers that recycle nutrients that organisms can reuse.
• Photosynthetic algae and protists are primary producers that capture solar energy or material that is inorganic.
• Primary producers also provide nutrients for complex organisms.
• Beneficial bacteria include photosynthetic bacteria.
• Bacteria processes waste products, oil spills, or toxic compounds.
• Microbes are used in food processing.
• Antibiotics are discovered in certain microbes.
• Microbes are used for the mass production of drugs such as insulin and vaccines.

The Origin of Microbial Life

• All life on Earth can be traced back to the last universal common ancestor (LUCA).
• LUCA is common to all organisms that live and have lived, since life began.
• The first organisms on Earth would have had similar characteristics compared to today's organisms.
• Metabolism, response to and interaction with environment, replicating, natural selection are similar characteristics from earliest organisms to today's.
• Earth had mainly inorganic substances when life originated on Earth.
• Scientific studies provide evidence that life originated 3.5 to 4 billion years ago from nonliving matter in a series of four stages.
• Stage 1: Organic monomers involved the evolution of simple, organic molecules from inorganic compounds, such as amino acids and nucleotides.
• Stage 2: Organic polymers involved the evolution of polymers, such as DNA, RNA, and proteins.
• Stage 3: Protobionts involved the evolution of protobionts (protocells), which are polymers enclosed in a membrane.
• Stage 4: Living cells involved the evolution of living cells.

The Evolution of Monomers

• In the 1920s, the A. Oparin and J. B. S. Haldane hypothesis (“primordial soup" hypothesis) was proposed.
• Early Earth had very little oxygen.
• Early Earth also had water vapor, hydrogen gas, methane, and ammonia.
• Methane and ammonia are reduction agents in the absence of oxygen.
• Early Earth had a reducing atmosphere where redox reactions could have driven organic monomers from inorganic molecules in the presence of strong energy sources.
• Stanley Miller and Harold Urey (1953) performed a famous experiment to test the primordial soup hypothesis.
• Proposed energy sources included heat from volcanoes, radioactivity from isotopes, electrical discharges from lightning, and solar radiation.
• Miller placed a mixture of methane (CH4), ammonia (NH3), hydrogen (H2), and water into a closed system.
• Over a week, the heated mixture produced amino acids and organic acids.
• The "iron-sulfur world" hypothesis (Günter Wächtershäuser) proposed that thermal vents at the bottom of Earth's oceans synthesized organic monomers.
• Gases such as carbon monoxide, ammonia, and hydrogen sulfide emitted from ocean vents.
• The gases passed over iron and nickel sulfide molecules, acting as catalysts to drive evolution from inorganic to organic molecules.
• Some scientists hypothesize that life began in hydrothermal vents deep in the ocean.
• Organic molecules have been confirmed on some meteorites.
• Some scientists hypothesize that bacterium-like cells could have evolved on another planet and then been carried to Earth; this an idea known as panspermia.

The Evolution of Polymers

• Protein-first is a hypothesis that proteins came first.
• Amino acids in oceans could have collected in shallow puddles along rock shores
• The solar heat could have caused them to form proteinoids.
• Proteinoids are small polypeptides with some catalytic properties.
• When proteinoids are placed in water they form microspheres.
• Proteinoids enzymatic activity have provided an over others advantage.
• RNA-first hypothesis is the contrasting belief that only RNA needed to progress toward the formation of the first cell.
• The discovery of catalytic RNA in the 1980s supports this hypothesis.
• RNA can be both a substrate and an enzyme.
• If RNA evolved first, it could have functioned as both genes and enzymes.
• It was an "RNA world" 4 billion years ago.

The Evolution of Protobionts

• Protobionts (or protocells) would have emerged before the first true cell.
• Protobionts have an outer membrane that helps regulate and maintain cellular activities.
• Fatty acids likely formed the first membranes, and can form micelles, which are small spheres with a single layer of fatty acids.
• Vesicles are larger than micelles and surrounded by a bilayer of fatty acids.
• Fatty acids in a bilayer can flip and move molecules from outside to inside.
• Micelles can merge to form vesicles.
• The first protobiont was likely a type of vesicle
• In the 1960s, Alec Bangham discovered when lipids extracted from egg yolks are put into water, they organized into double-layered bubbles.
• Those structures were named liposomes and might have provided life's first membranous boundary.
• The membrane-first hypothesis suggests that liposomes would protect and concentrate molecules early so they could evolve.
• The first cell would have had a plasma membrane before any other parts.
• Protobionts would need nutrition to grow.
• Protocells were likely heterotrophs, and consumed preformed organic molecules.
• This implies that heterotrophs preceded autotrophs.
• If protobionts evolved at thermal vents, they may have carried out chemosynthesis.
• Chemosynthesis involved the synthesis of organic molecules from inorganic molecules and nutrients.
• Many modern-day bacteria are chemoautotrophs: they obtain energy by oxidizing inorganic compounds, such as H2S, abundant in thermal vents.
• ATP is a critical energy-carrying molecule.
• ATP was likely first synthesized by fermentation, which is a process because there was no oxygen available on early Earth.
• Oxidative phosphorylation evolved later; it is a reaction of ATP per unit of energy.
• In eukaryotes, oxidative phosphorylation occur in mitochrondria, which share a common ancestor with a group of bacteria that synthesize ATP via an electron transport chain.
• The evolution of complex biochemical pathways took millions of years.

The Evolution of Living Cells

• The central dogma of genetics state that DNA directs protein synthesis and information flows from DNA to RNA to protein.
• The RNA-first hypothesis suggests that the first true cell would have had RNA genes.
• The genes would have directed and enzymatically carried out protein synthesis.
• Some viruses have RNA genes.
• RNA viruses contain the enzyme reverse transcriptase, which produce DNA from RNA.
• This suggests a mechanism how cells that have DNA genes evolved.
• Proteins may have evolved before DNA and RNA.
• Complex enzymatic processes and a plasma membrane may have been necessary for the formation of DNA and RNA.
• Enzymes may have been required to produce nucleotides and nucleic acids.
• RNA is not likely to have spontaneously arose from chemicals.
• Cairns-Smith hypothesis: Polypeptides and RNA evolved simultaneously.
• RNA genes replicated when proteins catalyzed the reactions.
• Cairns-Smith hypothesis supposes that RNA and the formation of protein occurred at once.
• The genetic code evolved before DNA could store genetic information.
• Present genetic code minimizes effects of mutations.

Archaea

• Bacteria and Archaea are prokaryotes.
• Archaea and Bacteria are separated by differences that are molecular and cellular.
• Prokaryotes are single-celled organisms lacking a nucleus and membrane-bound cytoplasmic organelles found in eukaryotic cells.
• Archaea and bacteria are not related, but diverged from common ancestor after life began.
• Archaea and Bacteria are found in extreme environments (hot springs, thermal vents, salt basins).
• The Eukarya come from the archaeal line of descent.
• Eukarya are more closely related to archaea than bacteria.
• Archaea shares some of the same ribosomal proteins of Eukarya.
• Archaea and Eukarya initiate transcription in same manner.
• Archaea and Eukarya have types of tRNA that are similar.
• Archaea (Domain Archaea) range from 0.1 to 15 micrometers in size.
• Archaea have a genome with a single, closed, circular DNA molecule.
• They reproduce asexually by binary fission.
• The archaea plasma membrane differs sharply from plasma membranes of bacteria and eukaryotes.
• Has a single lipid layer with branched side chains.
• They tolerate acid and heat.
• Most archaea have cell walls.
• Lack peptidoglycan distinguishing them Feature of bacteria
• For some archaea, the cell wall is largely polysaccharide; in others, it is pure protein.
• Three main types are based on unique habitats and metabolism: Halophiles, thermoacidophiles, and methanogens.
• Some are found in moderate environments (lake sediments and soil).
• Some can recycle nutrients.
• Some archaea have symbiotic relationships with sponges, sea cucumbers, and digestive tracts of humans.

Archaea Examples

• Halophiles, or "salt-loving" archaea live in salty habitats that range from 12% to 15% salt concentration, ocean water is at 3.5% salt.
• Halophiles have also been isolated from environments (Great Salt Lake, Dead Sea, and hypersaline soils).
• Contain membranes with chloride pumps that have a light-powered protein (halorhodopsin).
• Halophiles pump chloride and water into the cell to prevent dehydration.
• some halophiles also carry photosynthesis that uses pigment bacteriorhodopsin and not cholorophyll.
• Thermoacidophiles live in hot, acidic, aquatic environments which include hot springs, geysers, and volcanoes that are underwater.
• Lipid membranes and proteins have evolved to temperatures as high as 80 degrees Celsius.
• Picrophilus torridus survives at a pH of less than 1.0.
• 12% of genes encode transport proteins on the plasma membrane.
• The proteins pump excess H+ ions outside of the cell.
• Methanogens mostly use carbon dioxide and hydrogen as energy sources.
• Methanogens produce methane as a by-product.
• They live in anaerobic environments such as swamps, lake sediments, rice paddies, and animal intestines. Methane is a greenhouse gas that might contribute to global warming, which is produced by cattle.

Bacteria

• Bacteria (domain Bacteria) are the most common type of prokaryote on Earth.
• More than 11,000 different species have been identified.
• Millions of unnamed species are estimated.
• Bacteria are found in virtually every environment on Earth.
• The classes and species of bacteria are constantly discovered.
• Bacteria are found in various shapes/sizes.

Bacterial Size and Structure

• Most bacteria are between 0.2 to 10 micrometers in size; smallest living organisms.
• Bacteria have three basic shapes: Rod, spherical, and spiral-shaped.
  • Rod: Bacillus
  • Spherical: Coccus
  • Spiral-Shaped: Spirillum
• Bacillus or coccus can occur singly or in arrangements/associations (e.g. chains).
• Bacteria have protective cell walls (molecule, peptidoglycan).
• Some bacteria have a capsule ( layer outside cell wall).
• Gram stain classifies bacteria by cell walls.
• Gram-positive bacteria have a thick peptidoglycan layer and stain purple.
• Gram-negative bacteria have a thinner/lacking layer of peptidoglycan and stain pink.
  • Can lead to the selection of useful antibiotics to treat infection.
• Motile bacteria have flagella for locomotion (structure eukaryotic flagella).
• Some bacteria used fimbriae to bind surfaces (e.g., urinary tract bacteria).
• One chromosome (single circle) located in a nucleoid region
• Plasmids (accessory rings of DNA that can carry genes, e.g. antibiotic resistance)
• Ribosomes; types of storage granules

Bacteria Reproduction and Gene Transfer

• Bacteria reproduce asexually by binary fission.
• The bacterial cell replicates its genome and divides into two new daughter cells.
• Each daughter cell is a close copy of the other one (Exact Clones).
• Generation time ranges from 20 minutes to a day or more.
• Some bacteria form resistant endospores in harsh conditions, like a thick-walled dehydrated structure).
• The endospore exists to survive harsh conditions and not for reproduction.
• There is no sexual reproduction in prokaryotes.
• Horizontal Gene Transfer:
  • Conjugation: donor cell transfers DNA to recipient cell
  • Transformation: bacterium takes up DNA released by dead bacteria
  • Transduction: Viruses carry portion of bacterial DNA (one to another)

Bacterial Metabolism

• Bacteria can display a range of metabolism.
• Most bacteria are heterotrophic.
  • Require sources from an outside source of outside compounds (e.g. glucose, sucrose).
• Anaerobic bacteria cannot use oxygen as final electron acceptor in ETC (Instead may use sulfate, or nitrate).
• Chemoautotroph:
  • Electrons for energy from ammonia and hydrogen as a product
  • CO2 is reduced to organic compounds
• Cyanobacteria have chlorophyll and other pigments.
• Evolved 3.8 billion years; introduced most of the O2 into Earth’s atmosphere
• Capable of nitrogen fixation & carbon fixation
• Some form lichens with fungi Other bacteria (photosynthetic) can split hydrogen sulfide vs. water (sulfur created as a by-product).

Bacterial Diseases

Streptococcus infections cause damage.

• Streptococcus pneumoniae: cause pneumonia, meningitis, and middle ear infections.
• Streptococcus mutans: contributes to dental caries.
• Streptococcus pyogenes: Most causes of diseases. - Pharyngitis (strep throat) - Impetigo in infants (mild skin disease) - Scarlet fever (red rash) - Rheumatic fever (endotoxins) - Necrotizing fasciitis (flesh-eating" bacteria)
• Staphylococcus aureus and MRSA _ 20% of people are carriers on their skin with any symptoms Disease is usually limited to skin infections. A strain resistant to methicillin is called MRSA (kills young healthy individuals) Often possesses toxins that cause death and the spreading of germs
• Tuberculosis TB is a lung condition caused by a slow growth of bacteria leading to infectious disease (1/3 of human is infected, millions of death occurring each year).
• Causes inflammation of the lung region from the infection, causes tubercles to undergo damages.
• This damage in lung tissue can harden and calcify, leading to cancer.
• Two types of bacteria cause food poisoning: - Some produce a toxic substance that causes vomiting/diarrhea when not cooked properly. - Others are infections such as the clostridium botulinum which can cause toxic botulism. - Salmonella can grow after days of growing.

Antibiotics

• Antibiotics prevents bacteria in metabolic path
• Not harmful to human cells as a medicine.
• Work in two different ways: - protein -Erythromycin/Tetracycline Inhibit cell wall biosynthesis. -Penicillins/Cephalosporins
• Antibiotics cause problems -Allergic reactions -Kills Bacteria (Overgrowth in digestive /reproduce track) - Bacterial resistance to drugs
  • Mutations
  • Genetic material shares to resist antibiotic drugs

Viruses, Viroids, and Prions

• Viruses are non-cellular structures that require a host/ reproduction
• Viruses use Machinery to replicate (certain enzymes)
• Genetic information causes for replication
• Viroids: code and reproduce inside a cell
• Prions: cause infections (change shape into different proteins)

Viral Size and Structure

• Smaller in size - Variety of shapes
• Two parts: Capsid & Nucleic Acid Core
  • Capsid (protein):
    • It closes in nucleic acid core.
    • Spikes bind to a cell
    • Nucleic acid core (DNA/RNA)

Viral Reproduction

• Viruses (every organism on Earth)
  • Bacteriaphages infect bacteria
  • Certain infect Humans/Animals/Plants only - Specifics
• Reproduction cycle 6 steps for animal virus RNA - Attachment - Entry - Replication - Biosynthesis - Budding - Assembly.
• Latency virus lies dormant in human host
• Escape from immune system - Herpesviridae family - New Viruses are produced (Genome is reproduced).
• Retroviruses (Enzyme transcribes through the RNA)
  • DNA forms new strand
  • Integrate with the cell genome (provirus) - It cannot produce an antiviral or escape the immune system

Viral Human Diseases

Common Cold/Flu - Caused by viruses Symptoms and duration are variable - Antigens Can change flu viruses COVID-19 - Infection in Animals (Zoonotic Species) Cause problems (respitory or diseases) - Involves Corona virus

• Highly Contagious Measles - Spreads from respitpry System - Vaccine to protect people
• Herpesviruses
  • Cold Sores - Fever Blister Varicella Chickenox/Shingles Infectious - Mononucleosis
• Antiviral medication and drugs
• Hard to develop a certain way to affect the viral replication
• Antibiotics: Not the option help
• Helps prevent certain cells when replication occurs
• Viroids are a disease (Infectious)
• Code and reproduce inside a cell
• Potato Spindle/Apple and Skin Problems.

Priods

• Particles that are infections - Normal Proteins change shapes when normal proteins occur
• Causes the generate diseases Ingestion -- Scrapie: sheep -Bovine -Creutzfield -KarU (transmission with human) - Chronic (Deer Elks.)