Introduction to Microbiology

• This text provides a detailed overview of microbiology, covering various aspects from the basic definition to complex applications.

Microbiology Basics

• Microbiology is the scientific study of microorganisms, including unicellular, multicellular, and acellular forms.
• Sub-disciplines of microbiology include virology, bacteriology, protistology, mycology, immunology, and parasitology.

Microbes—Ubiquitous and Essential

• Microbes are the origin point for all life on Earth.
• They are phylogenetically more diverse compared to plants and animals.
• Compose the majority of Earth's biomass.
• They are found in almost every habitat that contains water, mostly in Earth's surface.
• Microbes compose a large portion of biomass on Earth.
• They maintain the food chain, influence climate, cause diseases, and act as symbionts with other organisms.

Microbes and Human Life

• Infectious diseases were the leading cause of mortality in 1900, but have decreased in significance today.
• Microbes contribute beneficially to genetics, the environment, and human health.
• Most microbes are beneficial, not harmful.
• They produce mucus, antimicrobial chemicals, aid in digestion, and protect against pathogens.
• They are used in genetics, the environment, industry and on the skin.
• They can fortify the immune system fortify, produce scents to attract mates, and lubricate tissues.

Industrial Microbiology

• Processes of include products such as wine.
• Mutualistic symbiosis between nitrogen-fixing bacteria and leguminous plants are important.
• Cows are an example of a ruminant animal.
• Recombinant DNA technology allows the synthesis of insulin & other drugs.

Historical Milestones in Microbiology

• Antoni van Leeuwenhoek (1632-1723): Natural philosopher known for creating early microscopes and first observing bacteria.
• Louis Pasteur (1822-1895): Disproved spontaneous generation with the Swan-Necked Flask Experiment.
• Pasteur demonstrated infectious diseases are caused by microbes.
• Pasteur developed pasteurization and vaccines for splenic fever and rabies
• Robert Koch (1843-1910): Developed Koch's postulates, a universal method for proving cause and effect in infectious diseases.
• Koch received the Nobel Prize for his work on the infectious disease tuberculosis.
• Koch's work made diseases like anthrax, tuberculosis, and cholera manageable.

Koch's Postulates

• The suspected pathogen must be in all cases of the disease and absent from healthy animals.
• The suspected pathogen must be grown in pure culture.
• Cells from a pure culture of the suspected pathogen must cause disease in a healthy animal.
• The suspected pathogen must be reisolated and shown to be the same as the original.

Microbial Diversity and Size

• The phylogenetic tree consists of three domains: Bacteria, Archaea, and Eukarya.
• Hyperthermophiles are prokaryotes with optimal growth at 80°C or higher.
• Macroorganisms are highlighted in red.
• Formula for Size is Surface divided by volume
• The surface-area-to-volume ratio in cells decreases as cell size increases.
• Cell metabolism is inversely proportional to size.
• Biggest bacterium: Thiomargarita magnifica is >9000 mm.
• Cell diamater is between Ø: 0,2μm - 50μm

Cellular Life

• All cells have cytoplasmic membranes, cytoplasm, genomes made of DNA, and ribosomes.
• Cells use DNA's information to make RNA and protein through metabolism that transforms nutrients, conserves energy, and expels wastes (catabolism and anabolism).
• Information from DNA converts proteins, which convert nutrients from the environment into new cells during growth.
• Chance mutations in DNA cause new cell properties.

Cellular Properties

• Differentiation allows some cells to form new structures like spores.
• Communication allows cells to interact with each other by chemical messengers.
• Motility allows some cells to self-propel with flagella or other structures.
• Horizontal gene transfer enables cells to exchange genes.

Cell Shapes and Structures

• Representative cell shapes for prokayotes are coccus, hypha, spirillum, spirochete, budding and appendaged and filamentous.
• Bacteria may consist of a Cytoplasm, Nucleoid (DNA), Ribosomes, Plasmid, Cell Wall, and Cytoplasmic membrane
• Chromosome of a prokaryote is single circular, whereas a Eukaryote's is paired linear.
• A prokaryotes Chromosome is located in a Nucleoid with no membrane, while a Eukaryotes has the Nucleus with present membrane.
• A prokaryote has no Nucleolus while a Eukaryote has.
• A prokaryote's Extrachromosomal DNA consist of Plasmid, yet Eukaryotes consist of that plus Mitochondria and Chloroplast.
• The site of Respiration of prokaryote is Cell membrane, while a Eukaryotes site is Mitochondria.
• Prokaryote contains smaller 30S & 50S/70S Ribosomes. and Eukaryotes has larger 40S & 60S 780S Ribosomes in cytoplasm.
• Eukaryotes has Undulating flagella and cilia for Locomotion but prokaryote has Rotating rotating flagella and gliding.
• Pili only exists in prokaryote as pili for Sex or attachment.
• A prokaryote contains Peptidoglygan layer as the cell Wall, but a Eukaryotes cell wall is Usually absent.

Gram Staining

• Developt by Hans Christian Joachim Gram (1853-1938), it stains bacteria with basic substances (crystal violet).
• Iodine solution is added to form a crystal violet-iodine complex, causing all cells to appear blue.
• After the organic solvent, gram-negative bacteria appear colorless.
• Counter stain uses safranin, stains the gram-negative cells red/pink, gram-positive bacteria remain blue.
• Gram-positive: thick peptidoglycan layer, no outer membrane.
• Gram-negative: thin peptidoglycan layer and an outer membrane.

Cell Wall Structure - Murein/Peptidoglycan

• The peptidoglycan backbone is formed by N-acetylglucoseamine (NAG) and N-acetylmuramic acid (NAM).
• Very fine mesh protects and maintains cell shape.
• Without the protective net bacteria would only occur in isotonic environments.
• Penicillin-binding proteins (PBPs) catalyze the polymerization of NAG and NAM (transglycosylation).
• Archaea: use the Pseudopeptidoglycan and S-Layer, especially peptide crosslinks between N-acetyltalosaminuronic acid residues (NAT) in place of muramic acid.

Gram-negative Bacteria - Outer Membrane and Gram-positive Bacteria cell Walls

• The gram-negative envelope contains hydrophobic lipopolysaccharides and requires Calcium2+ ions to maintain its lipopolysaccharide layer; this membrane is asymmetrical.
• Gram-positive bacteria have thick cell walls (20-80 nm) made of peptidoglycan layers with Teichoic acids.
• Polymers are made of glycerophosphate and ribitolphosphate moieties.
• The interaction of bacteria with eukaryotic host cells, including: symetric bilayer, fluid mosaic model, Phospholipid Bilayer Membrane.
• Homeoviscous Adaptation is composition adaptation of lipid bilayer to environmental conditions to maintain membrane fluidity.

Membrane Transport

• There are three major import mechanisms include: passive diffusion, facilitated diffusion, active transport selectively with energy input.
• Passive diffusion facilitates: water, glycerol, ethanol, carbon dioxide, and oxygen.
• Import uses transport of Binding protein
• There are three catagories transported substances. A Sodium-proton anti porter, a Lac permease, simple transport, and a Binding protein.

Ultramicroscopic Characteristics of Bacteria

• Are flagella that can occur at only one pole, anchored inside the cell.
• These structures cause the rotation cannot be changed in speed but only in direction. These include: Peritrichous, Monotrichous and polar, Amphitrichous and polar.
• Chemotaxis is the movement pattern that allows the a bacterium.
• Fimbriae serves mechanically attach plus anchor cells to the surfaces; This happens to the specific receptors on the mucous membrane etc.
• Pili are used Conjugation to transfer genetic material between bacteria.
• Capsules are composed of protein (poly-Dglutamic acid) or polysaccharides (e.g., glucose, rhamnose, uronic acids).
• Capsule-forming strains grow in large, slimy colonies though are very important during unfavorable conditions plus virulence.
• Sulfur-oxidizing bacteria can convert stored intracellular sulfur that stored sulfur globules (strongly refractive).

Formation of Endospores

• Bacteria do not divide in the middle, but do in a small area where mother surrounds the spore.. These stages:
• Free endospore
• Germination
• Growth cell devision
• Vegetative cycle
• Cell division asymetric sprorgulation
• Engulfment
• Maturation
• Moter cell lysis
• Cotex
• Coat

DNA Storage and Replication

• The hallmarks of cellular life include DNA replication and gene expresson.
• In bacteria, the chromosome is circular and organized in 100 minutes; it consists of Pyrimidine & Purine bases, consisting of Sugar phosphate, and Hydrogen
• The RNA is predominantly single-stranded, which makes it much more unstable but it is assumed it was the original variant of information storage.
• The genes encoding the rRNA are amplified by PCR to analyse rRNA gene sequences before generating a phylogenetic tree.
• Supercoiled and negative strand of DNA is introduced by Gyrase or DNA Topoisomerase during Cell growth.
• During replication there is a one specific place an Origin of replication an each chromosome and the forks that are used for Replication Occure on each.
• DNA-polymerase catalyses the nucleophilic attack to complete the DNA strand.
• RNA polymerase consists of five subunits, The subunits react with to to form the active enzyme which the Sigma factor dissociates from.
• Termination of transcription can result in the formation of a RNA stem-loop structure,.
• RNA is converted by nucleotiode code to proteins by a ribosome that starts at a start codon from a tRNA.

Molecular structure of proteins

A proteins Primary Structure must be built with Amino acids blocks, that form poly peptides by linking into the proteins Secondary, Tertiary and Quaternary Structure.

Bacterial Growth

• Bacteria divide with Binary Fission in phases: cell elongation, DNA and Spetum bilding.
• An exponential growth phase: one cell becomes two, two become four, etc.
• The cycle can be graphed like this
  • Lag phase: before growth
  • Log phase: each cell divides
  • Stationary phase: Growth stops due to nutrient limitations
  • Death phase: the number of dying bacteria exceeds growht
• The Number of cells can be measured by:
• Viable count
• Optical density
• Total number of cells
• Abiotic parameters affecting growth of microorganisms are:
  • Temperature
  • Osmolarity
  • pH
  • Oxygen supply
  • Water activity (Humidity

Growth Temperature of bacteria

• Bacteria can be: Psychrophile, Mesophile, Thermophile, Hyperthermophile depending on their enzymes reactions on the cell membranes etc.
• How thermophiles and extreme thermophiles stay at high temperatures is due to thier proteins in their cell and a larger number of ionic bonds between basic and acidic amino acids. And hydrophobic interior of the the protein

Conditions for Bacterial Growth (pH and Osmolarity)

• Bacteria can grow at different pH levels but the intracellular pH is generally close to neutral!
• There are both, Acidophiles or Alkaliphiles species of bacteria.
• Bacteria need Osmolarity to halotolerate the correct amount of water, wich must be solved to prevent from the inhibition by a solution. This means that the bacteria will need a water activity or a moist atmosphere.
• There are Halotolerant or Nonhalotolerant types of bacteria, wich need higher or low water-activity.

Oxygen and Anti Microbal Grow Conditions

• Bacteria are categorises to Aerobic, anaerobic, facultative, microaerophilic and aerotolerant anaerobic growth
• How to prevent microbial gowth includes: using Heat sterilization or Pasteurization and lonizing radiation or Filtration and with Chemicals growth contro. Heat sterilization (under pressure): The autoclave sterilizes bacteria by:

1. In a large chamber under pressure and heat everything gets killed
2. Spores could be eliminated by circulair autoclaving.
3. Biosafety cabinet with shortwave UV light kills microbiological contaminants, and lot of sugers.
4. Different filters in liquids is used to filter out some of bacteria

Chemical Control

• Phenols destroy all enzymes.
• Alcohols (60-85%) can disinfect surfaces.
• Hydrogen peroxide is an oxidizing agent and used for medical instruments.
• Antibiotics are natural and come from different bacteria, but are classified 3 ways dependen on their effec.
• Most common Antibiotic treatment is the:
  • Bacteriostatic agents inhibitors that cause protein binding
  • Bacteriocidal agents binds firmly
  • Bacteriolytic agents kills the cells. But this can cause Antibiotic resistance.

Bacterial resistance

This is a problem due to multidrug resistant pathogens that cannot be treated in conventional ways. These are Bacteria such as: Acinetobacter sp. , Streptococcus pneumoniae, Haemophilus influenzae, Salmonella sp and Staphylococcus aureus. The resistance has many Mechanisms, such as: Efflux pumps, antibiotics inactivation or Target modification, that is then by-passed.

Metabolic and Growth Neccasary things

• Schematic representation of anabolism and catabolism with in the key role of ATP.
• Bacteria need nutrients like Carbon, Hydrogen and Magnesium for growth, so that it has at least a Macronutriens like: C or N or P, or just a Micronutrients. The macromolecules a re also necessary for cell to exist ( DNA, RNA and Proteine). In order to grow.

Vitamin Support and Culture Growth

• Micronutriens and Vitamins are also necessary to mainting cells, without them the cell wont need to be added to the media for growing.
• Culture media for bacteria needs to be split into Defined or complex media.
• A culture needs ATP, for the Metabolism or enzymes. This need can be achieved via:
  • Phosphoenolpyruvate for the Fermentation
  • ATP during Glycolysis
• Sulfur-oxidizing bacteria can convert stored intracellular sulfur (Strongly refractive).

Redox Reactions

• Redox is the energy-efficient electron-transfer from the reducing agent to the oxidant.
• Both the Oxidation and Reduction both variants occur in a coupled redox reaction.

Gen regulation

• To Survive bacteria adapt to environmental changes; This can be light, pH , nutrition, ionic strength, antiobodys…
• The cells use different mechanisms called:
  • No Controle: enzmyes will constitutively use products
  • Translation Controle: Not synthesizing enzymes
  • Transcription Controle: Not synthesizing mRNA
• mRNA needs also a synthesis by controle, the core enzyme. It reacts with the DNA thanks to the 3D Form.

Active genes and how it works.

• mRNA polymerase is brought on spot.
• bubble in the DNA - Double helix becomes open.
• Transcription can happen at 3’ to 5’
• Synthesis continue (the protein is independant)
• The chain starts from the start codon (AUG) and continues until the end codon

Proteine Binding.

The Transcription can happen, when controle is in the right spot. Lac - Operon This is important for the genes, all occurig, to the same sequence and have to absord the correct lactose amount to grow. These parts called the promoter

• Lacz
• Laci
• Laca

Bacteria inductions methods

1. Direct binding
2. Allosteric regulation
3. repression
4. binding to operator
5. Induction by an activator
6. Transcription of some proteins

What happen, when there are to much sugars?

One of the methods is Diauxic growth. The cell then selects an carbon uptake system Another mechanism is that the cellule send several sigma factors

Signal-Transduction an Regulatory Systems

Cells and how they Communicate. To use Proteins as Kinases

• They help with:

1. Osmolarity
2. Chemo sensory
3. Oxygene- There are Quorum sensing signals like autoinducer LuxI to send signals to the the host, wich are transkribed to help with Amino acids

• Then Transkribtiola Attenuation by Amino acids.

regulation of protein

• How an why does that work?

1. Start codon
   • SD
2. Secondary structurs These things help with the Riboregulation or Riboswitch, where the translation is turned to an non translation part by force and can never be used.

• Post-translational: Allosteric feedback inhibiton
• How allosteric changes enzmyes. That can affect the enzyme if the correct glutamin is in the site.

Viruses

Viruses and Phases

• no living entities
• require the machinery of the host cell to replicate
• obligate intracellular parasites
• infect all organisms on earth
• source for genetic diversity
• All have a Nucleocapsid
• These have a diversity which means that some viruses have preferences. The diversity of viral genomes

1. Class Double-stranded DNA (Ds DNA)
2. Single stranded DNA(ss DNA)
3. Double-stranded RNA (dsRNA)
4. Positive single-stranded RNA
5. Negative single-stranded RNA
6. Retroviruses :Viruses need the other cells to replicate with DNA

Phages

• The Replication Cycle of a Lytic Bacteriophage takes up the Virion by Virus injection

• The phases are.

• Attachment of the

• Penetration

  • Synthesis nucleic acids
  • Packing the new virus

• The cell lysis

• Phages is the lysis of the host cell which then is transported into new cells. They are used for Calculation of a diluted Phage solution to determinate conclusions on other medium

• The Timeline of Lytic phage are in different stages through the virus infection

• To protect themselves the can be used to to make it clear it is a Bacteria that happens with Bacteriophage receptors.

• Also Temperate virus can go after injection into a Lysogenic or Lytic pathway

• The Linear- Lambda genes make it possible to create an circle for integration.

What viruses can do for cell manipulation

• Invertase and reverse the order with specific manipulation
• Can make little DNA and RNA that can help with cell activation
• MS2 is a small RNA phage that is often used to build antibodies against bacteria'

Host- and Cell-Defenssystems

• Defence Systems happen if the virus:

  • Blocks Adsorption
  • Injection

• If assembly happens of the RM Sytems a self destruction code will be activated A bacterium will have receptors . All depend of the target. These attacks create immune systems.

• There a diffrent mechanisms called:

  • Innate
  • Cell-mediated
  • Pattern recognitation by Phagocytes

Molecular-Mechanismus in Cells

• In cells there will be an activation for the enzymes in production of oxygen compounds as a response for the Immune activation.
• If that happens the cells release cytokines wich will increase the body temperature.
• Adaptive actions
  • t Cells, B Cells and also Memory will be activated to heal the cell.
  • They will create antigens
  • That can lead to the Cell Death or Lyse

Antigen-Presentation

• The Major histocompatibility complex needs to be the correct relation to TCell receptor activation
  • Antigenic presentation happens in the Endoplasmic reticulum of the cell to activate a Target with the MCH1.
  • There are also T Helper cells that can help to activate the the response of TH1
  • It requires the B cell to be right a the spot And to trigger them correct the can th17. So make it to the right to help with the immunity . The adaptive system must know it what not to affect the T cells to harm the body because if the interaction if wrong a high autoimmune reaction can happen!

Cell-Reactions for anti Immune Systems

• Immunoglobulins can contain

  • several epiloes
  • Antibodies Can react and lead to cell-death

• Also the system needs specific Compliment Activaation

Imunology Diseases Transmission

• Epidemiology*:

• Endemic Diseases: Consistently present in a geographic area.

• Epidemic Diseases: Outbreaks affecting a larger area, often originating from an endemic region.

• Pandemic Diseases: Global outbreaks.

• Major Means of Transmission*

• Diseases can transmit through Direct or Indirect.

• Herd Immunity:* Protection of a population from infection due to a large proportion being immune.

  • Herd immunity threshold depends on R0: the higher R0, the higher the herd immunity needed.

• Countermeasures*:

  • Include sanitation; filtration; sterilization, in order to reduce the transmission