Module 1 PDF - Microbiology

Module 1 Created @January 3, 2025 10:08 PM Class MICR 002 Reviewed Introduction to Microbes and Microbiology Microbiology is the study of living things (“micro”) to be seen with the naked eye...

Module 1 Created @January 3, 2025 10:08 PM Class MICR 002 Reviewed Introduction to Microbes and Microbiology Microbiology is the study of living things (“micro”) to be seen with the naked eye The first human to view microbial life was a Dutch linen merchant named Antoine van Leeuwenhoek Seeing the Invisible: van Leeuwenhoek’s first glimpse most of life is invisible, and still have this idea that we are the “most central figure” in the world Leeuwenhoek, was a haberdasher in the city of Netherlands, and the quality of first microscopes were superb, and never shared how he made his lenses “Micrographia” by Robert Hooke is a book of the small things through lenses. This was Leeuwenhoeks first area of referencing to literature already there. Upon viewing these things, such as a leg of a louse, he discovered more than what Hooke did. Leeuwenhoek, grabbed a class container of algae that was later put into observation, and he found all these little animals, a thousand times smaller than anything he has seen before, naming them Diertgen, a derivative of the Dutch translation of little animals Module 1 1  Sperm, Red blood cells, Protozoam and bacteria were all discovered by Leeuwenhoek Vibrio Harveyi is a marine bacterium that glows in unison when joining together, a bioluminescent organism, that led to the discovery that bacteria can communicate with one other at the microbial level. CANVAS PAGE Microorganisms: aka microbes, are tiny living creatures that can’t be seen to the naked eye The vast majority of microbes on the planet either don’t interact with us or are helpful to us in some way! Microbial Benefit: Microflora Microflora: the beneficial microorganisms that live in our bodies We find floral organisms everywhere that the human body contacts the outside environment, which include our skins, mucous membrane, and throughout our digestive tract. Benefits of floral organisms: they keep tissues healthy by digesting excess oil and old skin cells They assist in digestion and produce needed vitamins They protect us against infections by pathogenic microbes Now re realize that they are likely responsible for out health in way we never imagined TEDx The Gut Flora YouTube Video Module 1 2  5 no million microbes in the planet compared to 5 billion people on the planet We harbor 100 trillion bacteria in and out of body at a time, in terms of cells, we are outnumbered 10 to 1, we are not humans but a walking microbial community Gut flora, genital flora, skin flora, Flora helps to train the immune system (not exact but is true) Microbium: the collective genome We have a second “genome” in and active on our body Enterotypes: microbial ecosystems in a microbiums, that work independently Diet dictates to gut composition and gut flora composition There are strong correlations with disturbed gut flora and gut diseases such as diarrhea, diabetes, Crohn’s disease, colon cancer. Gut flora are seeded at birth, and are inoculated by the flora of the mother, such as skin flora, gut flora, and etc Disrupting flora at early development, like in early infancy, could have negative effects on adulthood flora and correlation of disease Fecal Transfer: the transferring of flora from a heathy individual to a sick individual to help with disease CANVAS PAGE There are no microbial flora living internally, we expect to find flora on mucous membranes and throughout the intestinal tract but NOT on the liver or brain Any microbe found in the liver or brain would be from an infection! Module 1 3  Fermentation and Food Microbial Lots of foods rely on microbes in their production usually through a fermentation process that turns sugars into acid or alcohol. Examples include bread, beer, wine, cheese, yogurt, soy sauce, pickles, sauerkraut, kimchi, and even coffee and chocolate TEDx ED The beneficial bacteria that makes delicious food Yeast single celled fungi that make bread, beer, and wine Break down carbohydrates Anaerobic pathway is known as fermentation Aerobic pathway, where CO2 and water are created from Oxygen and Carbohydrates Overall sugar is broken down by different microbes to create cheese, milk, bread, wine. Most times its a bacteria that is breaking down the sugar CANVAS PAGE There are some microbes that are used as food themselves, such as Marmite and Vegemite are yeast extract originally developed as a cheap but nutritious food alternative during world war 1. Microbial Benefit: Environmental Module 1 4  Microbes are also essential in our natural environment. There are microbes that decompose organic molecules to return nutrients to the soil like a fungus breaking down an orange. Microbes are also essential for cycling nutrients like phosphorus and nitrogen in the environment. Plants and other macroscopic life, rely on microbes to keep these nutrients available in the soil. Before plants were evolved to the point to produce oxygen, photosynthetic microbes like the cyanobacterium were responsible for creating an aerobic atmosphere on early earth and are STILL responsible for more than 50% of oxygen production on the planet Bioremediation: is where scientists utilize biological systems to remedy environmental problems. One common application is oil degreasing microbes in cleaning up oil spills. YouTube: Can Microbes Clean Up Our Oily Mess? bacteria and other microbes help to eat oil spills Microbes have evolved to take advantage of the abundance and lifelong of oil, thoroughly eating oil and as well as oil Scientists have continued to do research on microbe in order to speed up and biologically mediate the clean up of oils and plastic Diversity among Microbes Module 1 5  Intro there is tremendous diversity among microbes, the only aspect about themselves that they share in common are they are microorganisms Ubiquitous on Earth microbes are truly ubiquitous, meaning that they are found everywhere on the planet Unicellular vs Multicellular vs Acellular Unicellular: simple one celled organisms Multicellular: organisms compromised of 2 or more cells Acellular: don’t have a cell structure at all? Such as Viruses and Prions. Prokaryotes vs Eukaryotes All cellular organisms on the planet have one of two different types of cells, prokaryotic or eukaryotic cells. the prokaryotic cell structure is considered simplistic The eukaryotic cell structure is considered complex with organelles and the ability to build up to multicellular life. Khan Academy: Prokaryotic and Eukaryotic Cells Module 1 6  the most distinctive biological feature contrasting a eukaryote and prokaryote cell are membrane bound organelle and most notable a membrane bound nucleus, found within the eukaryote. In a eukaryote, the genetic information will be inside the nucleus In a prokaryote, the genetic information is found in a nucleiod, which isn’t membrane bound -kary = nut or kernel -pro = means before Eukaryotes also have membrane bound organelles such as mitochondria, a Golgi apparatus, which wont be find in a prokaryote In eukaryotes the DNA tends to be in multiple single strands where as in prokaryotes, is in swirls. Eukaryotes tend to be larger than prokaryotes Examples of Eukaryotes: multicellular organisms, animals, plants, protists,fungi Examples of Prokaryotic: bacteria, archaea(different domain of life tan bacteria) Free living vs Parasites most microbes are actually free living, compared to as being parasitic. Some microbes live in commensalism, with another organism, where one organism benefits from the interaction, while the other organism is neither helped nor hurt. Parasites live on another organism and harm that host organism Autotrophs vs Heterotrophs autotroph is an organism that obtains carbon from the carbon dioxide in the atmosphere such as algae and some bacteria Module 1 7  Heterotrophs are organisms that obtains carbon from organic molecules produced by autotrophs (fungus, worms, and many bacteria are heterotrophs) Chemotroph vs Phototroph another way to classify living organisms is to describe how they obtain energy Chemotroph is an organism that obtains energy from the breakdown of chemical bonds (most common way and most microbes do this) Phototrophs are organisms that obtain energy from light energy (algae and some bacteria are phototrophs. Important Terms for Describing Energy and Carbon Utilization These terms below are used to help define organisms on how they obtain both carbon and energy Photoautotroph: is where an organism uses carbon dioxide to get its carbon and light to get its energy. This process is called photosynthesis. Chemoautotroph: is where an organism carbon dioxide to get its carbon and breaks down chemical bonds to get their energy. There aren’t a lot of chemoautotrophs out there, but there are few groups of bacteria that live this lifestyle. Chemoheterotroph: is where an organisms use organic molecules to get both energy and carbon. It is the most common approach in all of biology. They include, worms (like all animals) fungi, and most protists and bacteria. Photo heterotroph: is where an organism would use light energy and carbon molecules in their environment. Prokaryotes Module 1 8  Prokaryote Shapes Prokaryotic cells come in 3 common shapes: a coccus is a round cell a baciccus is a rod shaped cell a coccobacillus is a short rod shape that is in between a coccus and bacillus There are several terms for spiral shaped cells, so here are the ones provided on Canvas. Module 1 9  Vibrios are comma-shaped Spirilla (or Spirillum) are cells with 2 or more twists Spirochete are very flexible spring like cells that look like corkscrews and within them they have an axial filament Module 1 10  In addition to shape terms, prokaryotes also have specific arrangements when multiple cells are arranged together Diplo means two, so two cells in a pair, whether it’s a diplococci, or diplobacilli. Strepto means chain, so there are streptococci and streptobacilli where the cell don’t fully detach at cell division and instead from longer chains Tetras are packs of 4 cocci together, and Sarcinae are packs of 8 cocci together Straphylococci are irregular clusters of cocci’s that look like grape clusters Prokaryote Cell Parts and Function Module 1 11  Extensions from the Cell Module 1 12  Flagella: only some bacteria have them and they are used for motility. Aka Flagellum, is a specialized appendage attached to the cell by a basal body that holds a long rotating filament. Pilus: a hollow tube that SOME bacteria can make and use to transfer DNA to another cell(which is called Conjugation). A hollow tube that exits out of the cell like an appendage, functions for transfers of DNA to other cells, note only some bacteria can do this. Fimbriae: these are sticky hairs that only SOME bacteria have and are used for attachment to surfaces and other cells. Cell Envelope Glycocalyx: a sticky carbohydrate coating around the cell wall that SOME bacteria have. The glycocalyx can be called a slime layer or capsule depending on hoy tightly the carbohydrates are stacked. Its main function is for attachment, protection against dehydrate ion, and protecting against immune cells. It is the pink coating and most superficial coating of the cell envelope Cell Wall: a strong and flexible structure around the cell that is made up of peptidoglycan in bacteria. There are two main types of bacterial cell walls, Gram + and Gram -. Cell Membrane: the lipid bilayer around the cell that regulates what enters and exits the cell. It is very similar to the eukaryotic cell membrane (except the lack of sterols) Internal Structures Cytoplasm: the jelly like solution in every cell that contains the other internal structures and has lots of nutrients and ions dissolved in it. Nucleoid: the region of the cell where the chromosome is kept, and its not called a nucleus because there is no membrane around it Chromosome: the bacterial chromosome is a double stranded DNA in a large folded circle. Bacteria usually contain only 1 copy of their circular Module 1 13  chromosome Plasmid: a small ring of “bonus” DNA that only SOME prokaryotes have. The plasmid DNA would be non-essential for living in most conditions but may be helpful in more unusual condition. Common genes to find on plasmids are antibiotics resistance genes and genes that give the ability to digest unusual sugars. Ribosomes: protein production sites are made out of both protein and RNA. Prokaryotic ribosomes are called 70S ( as opposed to Eukaryotic 80S ribosomes) and are made up of 2 subunits called 50S and 30S subunits. The math in adding up doesn’t follow arithmetic but instead a different rule of density measurement. Inclusions/Granules: Some bacteria have inclusions and/or granules to store excess substances like nutrients or metal ions. Endospores: SOME bacteria can make this structure to survive poor conditions and then germinate back to a regular vegetative cell when conditions improve. Prokaryotic Flagella: in the prokaryote flagella, the flagella are made of a protein called flagellin. The flagella are attached to the cell wall, via a ring and piston type model that allows the flagella to rotate 360 degree. The rotating flagellum pushes the cell through the media its in. In eukaryotic cells, the flagella is made up of microtubules and move side to side, mimicking a whip like motion to push the cell. Therefore the prokaryotic flagellum is an appendage that is on the surface of the cell, where as the eukaryotic flagellum is part of the cell itself and is completely enclosed by the cell membrane. Both have the same function but very different design. Axial Filament Module 1 14  when talking about flagellum, the spirochetes have an unusual one, called the axial filament. the structure and function of the axial filament is the same as the flagella found in other prokaryotes except that the axial filament is wrapped around the cell, covered by a thin outer membrane. When a spirochete rotate their axial filament, it causes the entire cell to bend and flex, thus the motility of the cell looks like it is spiraling through the media like a corkscrew Flagellar Arrangements We often describe bacteria according to their flagella arrangements: Monotrichous: one flagellum on the cell Amphitrichous: flagella at both ends of the cell Lophotrichous: a bundle of flagella at one end Peritrichous: multiple flagela all over the cell Bacterial Endospores only a few Gram Positive genera are capable of forming this thick protein coat around their DNA. The spore is incredibly resistant to heat, chemicals, UV light, dehydration These spores can survive for millions of years and then germinate when the spore encounters a more hospitable environment to return to a vegetative cell. Bacterial Cell Walls & Glycocalyx Module 1 15  Bacteria Cell Walls: The vast majority of bacteria have wither a Gram positive of Gram negative Gram positive vs Gram negative Cell Wall and the Glycocalyx (carbohydrate structure for protection against white blood cells, and dehydration, and also enables attachment) along with the cell membrane, make up the cell envelope the bacterial cell wall is generally composed of peptidoglycan (and can only be found in bacteria) Peptidoglycan is a structure of individual strands that are lashed together It is composed of two different carbohydrates, NAG (N-acetlyglucoamine) and NAM (N-acetlymuramic acid) and they are the strands that are held together by protein crosslinks called polypeptides. Only ever found in bacterial cell walls Gram positive cell wall thick peptidoglycan layer Teichoic and lipoteichoic acids (teichoic acids act as an anchoring point, going through the peptidoglycan and holds it down to the membrane) Periplasmic space is the space in between the peptidoglycan layer and the cell membrane Module 1 16  Gram negative cell wall still has a cell membrane with a lipid bilayer But gram negatives have a second membrane called an outer membrane, which is another entirety of a lipid bilayer Has a thin peptidoglycan layer along the peripasmic space The outer membrane , has an outer layer where lipopolysaccarides on the edge on the outer membrane layer and are toxic to humans and other mammals Gram negatives don’t have teichoic acids CANVAS PAGE The vast majority of bacteria have wither a Gram Positive or a Gram Negative cell wall structure. However there are a few oddball bacteria that don’t have neither. Mycoplasma is a bacterial genus that has cells that entirely lack a cell wall. They are the only bacterial genus without any peptidoglycan. They are also the only bacteria with sterols. Mycobacterium is a bacterial genus that has a Gram positive structure with the addition of mycolic acids, which made a waxy structure. These mycolic acids allow the cell to stain “acid fast” during the acid fast stain, while all other cells stain “non acid fast” Lastly, there is never peptidoglycan in an archaea, peptidoglycan is only found in Domain Bacteria. The Gram Stain The Gram stain, first developed by Hans Christian Gram, is still used to differentiate between Gram positive and Gram negative. It is the quintessential differential staining process in microbiology that is usually the first step in identifying any bacterium. Module 1 17  Biofilms: all prokaryotes are unicellular organisms, but live in complex communities. Microbes growing in these Biofilms often have different characteristics than they would growing individually and it is harder to treat infection that are caused by microbes living in biofilms YouTube: Biofilms Biofilms are sometimes referred to as slime or a type of bacterial colony that creates a sticky substance that sticks them close together Planktonic bacteria = lone, alone some bacteria Scientists have found that bacteria spend the majority of their lives living in biofilms Mucus is a type of biofilm? Scientists suggest that the 60-80% of bacteria that causes infection, live as biofilm Plaque is the most widely known and popular form of biofilm Sometimes biofilm infested tissues with surgery CANVAS PAGE The genesis of biofilm starts when early colonizing bacteria find a solid surface with enough nutrients to support its survival, and those first bacteria attach via their fimbrae, pili, capsule, etc. When the biofilm matures, it can release cells that disperse into the environment and start their own new biofilms. Module 1 18  Eukaryotic Cell Structure Nucleus: the double membrane bound organelle that contains the eukaryotic chromosomes. Chromosome: Eukaryotic chromosomes are linear segments (as opposed to the ring structure of prokaryotic chromosomes) and eukaryotes carry 2 or more copies of their chromosomes Cytoplasm: The jelly like substance that’s inside of all cells and contains lots of ions, protein and nutrients dissolved in it. Cytoskeleton: A rigid structure inside the cell made of microtubules, actin filaments and intermediate filaments. It provides structure and support to the cell, holds the organelles in place and transports vesicles around the cell. Microtubules make up a scaffolding structure inside the cell and also extend Module 1 19  to form the eukaryotic flagella. Actin filaments are fibers that run along the inside surface of the cell membrane and flex/contract to change the cell shape and allow cellular movement. 80S Ribosomes: there are very in similar and function to prokaryotic ribosomes but they are a little larger. Eukaryotic ribosomes are 80S and they are composed of 2 subunits, the 60S and 40S subunits. Some ribosomes are free floating in cytoplasm making proteins that will stay in the cell. Other ribosomes are attached to the RER making proteins that will be transported in vesicles. Rough Endoplasmic Reticulum: a membranous organelle that extends from the nuclear envelope and has ribosomes attached to its surface. Because of the ribosomes there, the main job of the RER is to make proteins. Smooth Endoplasmic Reticulum: Another membranous organelle that is connected to both the nuclear envelope and the RER but, it does not have ribosomes attached. The SER is responsible for making lipids, including new membrane, and it also involved with cell communication and signaling. Vesicles: a sack of membrane that contain something. There are lots of different kinds of vesicles. For example, transport vesicles move things from one organelle to another and there are other vesicles that have enzymes used to digest things. Golgi: a membranous organelle that is not connected to the nuclear envelope, SER, RER. The Golgi receives vesicles from all of the cell, processed the vesicles contents and then tags vesicles so they go to the right location. Mitochondria: the organelle that produces large amounts of ATPfor the cell. The mitochondria has 2 membranes ( a smooth outer membrane and highly folded inner membrane) and the innermost space of the mitochondria is called the matrix. The mitochondria also carries its own chromosome (its a circular chromosome) and its own ribsomes (they are 70S ribosomes) Chloroplast: this organelle is only found in plants and some protists since it is the site of photosynthesis for a eukaryotic cell. There are lots of similarities in the structure between the mitochondria and chloroplast. The chloroplast also has 2 membranes with the inner highly folded to increase Module 1 20  surface area, it also has its own circular chromosome and its own 70S ribosome Khan Academy: Organelles in eukaryotic cells for a cell to be eukaryotic it means that inside the cells there are membrane bound organelles. The genetic information in a eukaryotic cell, well be held inside a membrane bound organelle, the nucleus. CANVAS PAGE The Theory of Endosymbiosis the theory of endosymbiosis explains how mitochondria, chloroplasts and other membrane-bound organelles in eukaryotic cell likely arose from a symbiosis between aerobic prokaryotes and host eukaryotic ancestors. This theory was developed by Lynn Margulis, and is our current understanding of how Eukaryotes evolved from Prokaryotes. Scientists believed it happened starting with an early ancestral cell engulfing aerobic bacteria, that is able to utilize oxygen to produce energy. Over the many following generations, this aerobic bacteria lost its ability to live independently and became part of a larger cell, eventually leading to the creation of the mitochondria. After many generations later, this cell later engulfed another bacteria creating chloroplasts. Some of the evidence that scientists use to help prove this theory: both mitochondria and chloroplasts have their own circular DNA like bacterial DNA Both mitochondria and chloroplast have two membrane Module 1 21  Both mitochondria and chloroplast divide independently of the cell through a mechanism very similar to bacterial cell division Both mitochondria and chloroplast have 70S ribosomes inside them Module 1 22