Micro Notes Reading 1.pdf

- Additionally, mitochondrial and chloroplast ribosomes are structurally similar to bacterial ribosomes, rather than to the eukaryotic ribosomes of their hosts. - However, mitochondrial DNA and chloroplast DNA are reduced compared with nuclear DNA because many of the genes ha...

- Additionally, mitochondrial and chloroplast ribosomes are structurally similar to bacterial ribosomes, rather than to the eukaryotic ribosomes of their hosts. - However, mitochondrial DNA and chloroplast DNA are reduced compared with nuclear DNA because many of the genes have moved from the organelles into the host cell’s nucleus. - The binary fission of these organelles strongly resemble that of bacteria - Since Margulis original proposal sciences have observed various examples of bacterial endosymbionts in modern day eukaryotic cells The Endosymbiotic theory: - Infoldings of the plasma membrane of a cell give rise to endomembrane components ie nucleus and ER - First the ancestral Eukaryote consumes aerobic bacteria that evolved into the mitochondria - Second the early eukaryotes consumed photosynthesis bacteria that evolved into chloroplasts The germ theory of disease: - Before this there was a variety of other origins theories for where the origin of disease was form, For instance the greek suggested miasma theory which held that diseases originated from particles emanating from decomposing matter such as sewage, there particles infected humans that were within close proximity diseases like the Black death was that that it emerged this was - In the 11th century Ibn Sina proposed that tuberculosis was spread through people breath when in close proximity - Inm zhur documented that the skin condition scabies was caused through mites through the skin - In 1546 Italian physician Girolamo Francastry proposed that seed-like spores may be transferred between individuals through direct contact- those who may have had contaminated exposure this was the Early idea of the germ theory of Disease. However then after time his ideas were not widely accepted but then accepted again in the 19th century - A Hungarian Obstruction observed that people who gave birth in the hospital surrounded by physical and medical students were more likely to suffer and die of diseases than those who birthed near midwives. He noticed that medical students would perform Autopsy or dissection that construct vaginal exams  without washing HANDS- He suspected that students were transferring disease over, Assumptions came from when he lost a close friend - He didn't really understand the cause of the fever but predicted it could be reduced if students and physics washed their hands with chlorinated Lime Water. Finally when this was implemented- mortality rates reduced, Still many were slow to accept this handwashing concept - Around this Time snow was conducting research to understand the Cholera outbreaks in London and traced outbreaks to two water sources, hich were both contaminated by sewage- ie highlighting that these bacteria are transferred Via Sewage. His work was important as he highlighted the first known Epidemiological study- as this was one of the first considered Epidemics. The work of these two implemented Sanitation - Pasture then entered the chat again from his long swan flask experiment, he stated that if microbes could cause food spoilage they could also be the cause of infection - During this Same time…. British Surgeon Joseph lister was trying to determine the causes of post surgical infection, and then discovered this work, and implemented a sanitary operating room IE using an antiseptic spray during surgeries, this is why this is now a Common medical Practice - A few years Later Robert Koch proposed a series of Postulates, based on the idea that specific diseases could be attributed to a specific microbe using this they were able to identity the cause of pathogens for specific diseases 3.3 - All cells Possess a few essential Components, These includes a cytoplasm- A gel like substance composed of water and dissolved chemical needed for growth), this is contained within the plasma membrane, Must contain one or more chromosomes- which contain the genetic blueprints of the cell and Ribosomes, which are organelles used for the production of proteins. - Cells can vary between organisms. The two largest categories of cells are prokaryotic and Eukaryotic. And these are defined by the major difference in cell structure. - Prokaryotic cells lack a nucleus, surrounded by a complex nuclear membrane and generally have a single circular chromosome located in the nucleoid - Eukaryotic cells have a nucleus surrounded by a complex nuclear membrane that contains Multiple rod shaped chromosomes  - All plant and animal cells are eukaryotic. Some microorganisms are composed of Prokaryotic cells, and there by the other (eukaryotic). Prokaryotes are classified within the domain of archaea and bacteria and eukaryotic cells are classified in the domain Eukarya - Similar to the human body, each structure of a cell has its Own Function. Furthermore, there are some functions that are similar between prokaryotic and Eukaryotic cells and others are unique to prokaryotes - Although there are some exceptions, eukaryotic cells tend to be larger, this causes the need to compartmentalize, this is done using complex membrane organelles. In contracts prokaryotes generally lack membrane bound organelles and often contain inclusions that compartmentalize their cytoplasm Common Cell Morphologies and Arrangements: - Individual cells of a particular prokaryotic organism are typically similar in shape - Although a variety of prokaryotic organisms have been identified only a few shapes have been common( shape is morphology) - Certain species of prokaryotic cells of the same specific may group together in certain distinct arrangements SHAPES: coccus - Round Bacillus- Rod Vibrio- Curved rod Coccobacillus- Short rod Spirillum- Spiral Spirochete- Long loose helical Spiral ARRANGEMENTS: Coccus- Single Diplococcus- Pair of two cocci Tetrad- Grouping of 4 cells Arranged in a square Streptococcus- Chain of cocci Staphylococcus- Cluster of cocci Bacillus- Single rob Diplobacillus- Pair of ribs Streptobacillus Palisade- V or L Shaped Formation of rods  - In most prokaryotic cells, morphology is maintained by the cell wall, and cytoskeletal elements - The cell wall is found in most Prokaryotes and some eukaryotes- this envelopes the cell membrane protecting the cell from changes in osmotic pressure - Osmotic pressure occurs because of the difference of concentration in solutes on opposing sides of a semipermeable membrane - Water is able to pass through this semipermeable membrane but not solutes - When the concentration of solutes on one side is greater than the other of a membrane water diffuses across the membrane from the side with a lower concentration (more water) to the side with less water) until the concentration on the sides become equal this is osmosis - This can cause extreme osmotic pressure on the cell when there are environmental changes - The external environment of a cell can be described as isotonic, hypertonic and hypotonic - In an isotonic medium the solute concentration inside and outside the cell are approximately equal so there is no net movement of water across the membrane - In a hypertonic medium the solute concentration outside of the cell exceeds that inside of the cell so water Diffuses out of the cell into the external medium - In a hypotonic medium, the solute concentration inside the cell exceed that outside, so water will move in by osmosis into the cell, this causes the cell to well and potential burst - The degree in which each cell is able to withstand these conditions is called tonicity - Cells that have a cell wall, are better to withstand subtle changes in osmotics pressure and maintain their shape - In hypertonic environments, cells that lack a cell wall can become dehydrated, causing crenation or shriveling of the cell - Cells that do possess a cell wall undergo plasmolysis rather than crenation. - In plasmolysis the plasma membrane contracts and detaches from the cell wall to maintain its shape for a period of time - Likewise, cells that lack a cell wall are more prone to lysis in hypotonic environments. - The presence of a cell wall allows the cell to maintain its shape and Integrity for a longer time before lysins The Nucleoid  - Prokaryotic chromosomes are haploid( unpaired) - Prokaryotic Dna And DNA associated proteins are contracted within the nucleoid region of the cell.Prokaryotic DNA Interacts with nucleoid associated proteins that assist in the organization and packaging of the chromosomes. In bacteria, NAPS function similar to histones which are DNA organizing Proteins found in Eukaryotic cells Plasmids: -Prokaryotic cells may also contain extrachromosomal DNA or DNA that is not part of the chromosome this is found within the Plasmids These are small circular double stranded DNA molecules. Cells that have plasmids often have hundred of them within a single cell Plasmids are more commonly found within bacteria but can be found elsewhere These often carry genes that confer advantageous traits such as antibiotic resistance, this are importance to the survival of an organisms Ribosomes: - Responsible for protein synthesis - Are different within each of the three domains - Are constructed from proteins, along with rRNA - These within a prokaryote are found within the cytoplasm - They are called 70S Ribosomes- due to their size - Whereas eukaryotic cytoplasmic Ribosomes have a size of 80S (S being a unit of measure) - Although they are the same size bacterial and Archaeal Ribosomes have different protein and rRNA Molecules and the Real Version are more similar to their eukaryotic Counterparts than those found in bacteria Inclusions: - As single celled organisms that live in unstable environments, some pro cells have the ability to store excess nutrients within Cytoplasmic Structures called inclusis  - Storing Nutrients in a polymerized form is Advantageous because it reduces the building of osmotic pressure that occurs as a cell accumulates solutes. - Different types of inclusions store GLYCOGEN AND STARCHES, WHICH CONTAIN CARBON THAT CELLS CAN ACCESS FOR ENERGY. - Volutin granules, also called metachorics granules, because of the staining characteristics, are incluses that store polymerized inorganic phosphate that can be used in metabolism and assist in the formation of biofilms. - Microbes known to contain the Volutin granules include the Archers, the bacterium in the unicellular Eukaryotic alga - Sulfur granular another types of inclusio, are found in sulfur bacteria of the genus thiobacillus- these granules store elemental sulfur which the bacteria use for metabolism - Sometimes certain types of inclusion are surrounded by a phospholipid monolayer embedded with proteins Polyhydroxybutyrate (PHB), is an example of this - Some have inclusion for purposes other then storing nutrients - Some may produce gas molecules- they can help prokaryotic cells to adjust their location within the water column - Furthermore, there is Magnetic bacteria, which contain inclusion of magnetic iron oxide or iron sulfide surrounded by a lipid layer - these allow cells to align along a magnetic field aiding their movements - Cyanobacteria produce Carboxysome inclusions - These are made up of outershesls and thoushdans of protein subunits, their internet is filled with Ribulose and carbonic anhydrase- both of these are used for carbon metabolism - These structures are considered proto organelles because they compartmentalize important compounds or chemical reactions- like many Eukaryotic Organelles Endospores: - Bacterial Cells are observed as vegetative cells but some have the ability to form Endospores - structures that protect the bacterial genomes in a dormant state when environmental conditions are unfavorable - Endospores allow some bacterial cells to survives long periods without food or water, as well as exposures to chemicals, extreme temperatures or even radiation  - The process by which vegetative cells transform into endospores is called sporulation and it generally begins when nutrients become depleted or environment; conditions become otherwise unfavorable - The process begins with the formation of a septum in the vegetative bacterial cell. The septum divides the cell asymmetrical, sepeatin a NA forspore from the mother cell. - The forespore , which will form the core of the endospore, is essential a copy of the cells chromosomes and is separated from the mother cell by a second membrane - A cortex gradually forms around the foresporte by laying down layers of calcium and Diicolocine acide between membrane - A protein coat then forms around the cortex while the DNA Of the Mother Cell Disintegrates.Further Maturation of the Endospore occurs with the formation of an Outermost Exosporium. The endospore is released upon Disintegration of the mother cell. Completing Sporulation - Can persits dormitories for an extended period of time i.e. like A thousand years once the living conditions improve, they undergo germination, reentering a vegetative state. After germination the cell becomes metabolically active again and is able to carry out all of its normal function, including growth and cell division - Not all bacteria can form endospores, but there are many gram positive bacteria from the genera Bacillus and Clostridium, which has the ability to produce anthrax causing them to survives for many decades, these are hard to target because their endospores are so challenging to kill Plasma Membrane: - Structures that enclose the cytoplasm and internal structures of the cell are known collectively as the cell envelope - In prokaryotic cells the structure of the cell envelope varies depending on the type of cell and organism. Most prokaryotes have a cell wall but the makeup of this cell wall varies. All cells have a plasma membrane that exhibits selective permeability allowing for some molecules to enter or leave the cell while restricting the passage of others - This mode of this structure is often described as the fluid mosaic model , which refers to the ability of membrane components to move fluidly within the plan o the membrane as well as the mosaic like structure of all of the components, which include a diverse array of lipid and Protein components - The plasma membrane structure of most bacterial and Eukaryotic cell types is a bilayer composed mainly of phospholipids formed with ester linkages and  proteins. These phospholipids and proteins have the ability to love latterly within the plane of the membranes as well as between the two phospholipid layers - Archela membranes are fundamentally different from bacterial and Eukaryotic in a few ways, Ie Their phospholipids are formed with ether Linkages different from the other two groupings and they have branched chains whereas the other ones are straight. And mostly although some can be bilayers, these are mostly only mon layer - Protinese on cells surfaces have an import functions such as cell to cell communication and sensing environmental conditions and pathogenic virulence factors - Membrane Proteins and Phospholipids may have Carbohydrates associated with them and are called glycoproteins or Glycolipids. These extend out form the surface of the cell allowing them to interact with the external environment - Glycoproteins and Glycolipids in the palms ambrane can vary considerable in chemical composition among area ca, bacteria and eukaryotes, allowing scientist to use them to characterize unique species Membrane transport mechanism - One of the most important function of the Plasma membrane is to control the transport of molecules into and out of the cell - Internal condition must be also maintained within a certain range despite any changes within the external environment the transport of substances across the Plasma Membrane allows to cells to do so - Cells use a vanity of modes of transportation to cross the plasma membrane. FOR EX moles moving from a higher conc to a lower conc with a conc gradient are transported by simple diffusion also known as Passive transport. Some small Molecules like CO2 may cross the membrane Bilayer directly by simple diffusion. However charged Molecules as we;; as large molecules need the help of carriers or channels in the membrane These structures ferry molecules across the membrane a process known as facilitated Diffusion - Active transport occurs when cells move molecules across their membrane against concentration gradient - A major difference between passive and Active Transport, is that active requires ATP or another form of energy to move the Molecules Uphill! Therefore active transport structures are often called Pumps - Gripu translocation also transports substances into bacterial cells. In this case as a molecule moves into a cell against its conc gradient it is chemically modified so that it does not require transport against any unfavorable conc gradient - A common example of this is the bacterial phosphotransferase system, a series of carriers that phosphorylates which ads phosphate ion to glucose or other  sugars upon entry into cells - Since the early application ie required during the early stages of sugar metabolism this is required to be an energy neutral system Photosynthesis Membrane Structures - Some prokaryotic cells, namely cyanobacteria and Photosynthetic bacteria, Have membrane structures that enable them to perform photosynthesis. These structures consist of an infolding of the plasma membrane that encloses photosynthetic pigments such as green chloro physics and Bacteriochlorophylls - In cyanobacteria, these membrane structure are called Thylakoids, in photosynthetic bad cierta they are called chromatophores, lamellae or Chlorosomes Cell Wall - The primary function of the cell wall is to protect the cell from harsh conditions in the outside environment. When present there are notable similarities and differences among these walls of archaea, bacteria and Eukaryotes - The major Component bacterial cell wall is called peptidoglycan; it is only found in bacteria. Sturclly, peptidoglycan resembles a layer of Meshwork or fabrics - Each layer is composed of long chains of alternating molecules of NAG and NAM the structure of the long chain has significant two D tensile Strength due to the formation of peptide bridges that connect NAG and NAM within each Each peptidoglycan Layer - In gram negative bacteria tetrapeptide chains extending from each NAme unit are directly cross linked, whereas in gram positive bacteria, these tetrspeptide chains are linked by pentagycine cross bridges. Peptides;can subunits are made inside of the bacterial cell and then exported and assembled in layers given the cell its shape - Since Peptidoglycan is unique to bacteria, Many Antibiotic drugs are designed to interfere with peptidoglycan synthesis, weakening the call wall and making bacterial cells more susceptible to the effect of osmotic pressure - Addition,certain cells of the human immune system are able to recognize bacterial pathogen by detecting peptidoglycan on the surface of a bacterial cell these cells then engulf and destroy the bacterial cell, using enzymes such as lysozyme, which greeks down and digests the peptidoglycan in their cell walls - The gram Staining protocol is used to differentiate two common types of cell wall structure. Gram positive cells have a cell wall consisting of many layers of peptidoglycan totalying 30-100 nm in thickness. These layers are commonly embedded within teichoic Acids, Carbohydrate chains that extend through and beyond the peptidoglycan Layer. - TA is thought to stabilize peptidoglycan by increasing its rigidity. Ta also plays a role in the ability of pathogenic Gram Positive bacteria such as streptococcus to bind to certain proteins on the surface of host cells, enhancing their ability to cause infection. - In addition to peptidoglycan and TA bacteria of the family Mycobacteriaceae have an external layer of waxy mycolic acids in their cell wall, as describes in stian processes the bacteria are referred to as acid fast, since acid fast stains must be used to penetrate the mycolic acid layer for purposes of microscopy - Bacteria contain two common cell wall structural types. Gram-positive cell walls are structurally simple, containing a thick layer of peptidoglycan with embedded teichoic acid external to the plasma membrane.20 Gram-negative cell walls are structurally more complex, containing a thin layer of peptidoglycan and an outer membrane containing lipopolysaccharide. - Gram negative cells have a much thinner layer of Peptidoglycan than gram positive cells and the overall structure of the cell envelope is more complex. In gram negative cells a gel-like matrix occupides the periplasmic space between the cell and the plasma membrane and there is a second lipid bilayer called the outer membrane, which is external to the peptidoglycan layer. This outer membrane is attached to the Peptidoglycan by Murein Lipoprotein. The outer leaflet of the outer membrane contain the Molecules LPS which functions as an endotoxin infection involving gram negative bacteria, Contributing to symptomes such as fever hemorrhaging and septic shc - Is LAP models is composed of Lipids A, a core Polysaccharide and an O side chain that is composed of Sugar like molecules that compromises that external face of the LPS - The composition of the O side chain varies between different species and strain of bacteria - {art of the O side chained called antigen can be detected using serological or immunological tests to identity specific pathogenic strains like E coli a deadly strain of bacteria that causes bloody Diarrhea and Kidney Failure - Archaea cell wall structure differ from that of bacteria in several significant ways - First, the archaeal cell walls do not contain peptidoglycan instra they contain a similar polymer called Pseudopeptidoglycan in which NA is replaced with a different subunit. Other archaea may have a layer of Glycoproteins or Polysaccharides that serves as the call wa instead of of pseudopeptidoglycan and some appear to lack a cell wall entirely Glycocalyx and S layers - Although most prokaryotic cells have cell walls, some have additional cell envelope structures exterior to the cell wall such as Glycocalyx and S layers. A glycocalyx is a sugar coat of hih there are two important types capsules and Slime layers - A capsule is an organized layer located outside of the cell wall and usually composed of polysaccharides of proteins - A slime layer is a less tightly organized layer that is only loosely attached to the cell wall and can be more ealit washed off. Slime layers may be composed of polysaccharides, Glycoproteins and Glycolipids - Glycolic allows cells to adhere to surfaces aidenn in the formation of biofilms- colonies of microbes that form in layers on surfaces - In nature most microbes lived in mixed communities within biofilms, partly because the biofilm afford them some level of protection - Biofilmes generally hold water like a sponge, preventing desiccation. - They also protect cells form predation and Hinder that action of antibiotics and Disinfectants - All of these properties are advantages to the mcribs long in a biofilm but the present challenges in a clinical setting, where the goal is often to eliminate microbes - The ability to produce a capsule can contribute to a microbes pathogenic, because the capsule can make it more difficult for phagocytic cells- such as white blood cells to engulf and kill the microorganism- streptococcus Pneumoniae, produces a capsule that is well know to aid this bacteria,is Pathogenicity, bt capsules are different to stain for Microscopy, negative staining techniques are commonly used - An S layer is another type of cell envelope structure. It is composed of a mixture of structural proteins and Glycoproteins - In bacterial S layers are found outside of the cell wall but in some archaea the s layer serves as the cell wall - The extract function of an S layer is not entirely understood and they are difficult to study, but the available evidence suggests that the may play a variety of function in different prokaryotic cells such as he;ping the cell withstand osmotic pressure and, for certain pathogens, interacting with the host immune System Filamentous Appendages  - Many bacterial cells have protein appendages embedded within their cell envelopes that extend outwards, allowing interaction with the environment - These apprenages can attached to other surfaces, transfer DNA or Provide Movements - Filamentous Appendages include fimbriae, pili and flagella FImbriae and Pili - Fimbriae and Pili are structurally similar and because differentiation between the two is problematic - These terms are often used interchangeably - The term fimbriae commonly refers short bristles like proteins projecting from the cell surface by the hundred - Fimbriae enabled a cell to attached to surfaces and to other cells - For pathogenic bacteria, adherence to host cells is important for colonization, infectivity and Virulence - Adherence to surfaces is also important in biofilm formation - The termopili commonly refers to longer, less numerous proteins appendages that aid in attachment to surfaces a specific type of Pilus called the F pilis or Sex Pilus is important in the transfer of DNA between bacterial cells, which occurs between embers of the same gernagesstion when two cels physical transfer or exchange parents of their respective genomes Flagella - Flagella are structures used by cells to move in aqueous environments bacterial flagella act as propellants, they are stiff spiral filaments composed of flagellin protein subunits that extend outward from the cell and spin in solution - The basal body is the motor for the flagellus and is embedded in the plasma membrane - The hook region connects the basal body to the filament. Gram positive and gram negative bacterial have different basal body configuration due to difference in cell wall structure - Different types of motile bacterial exhibit different arrangements of flagella - A bacterium with a single flagella, typically located at one end of the cell (polar) is said to have a monotrichous flagella, An examples is vibrio cholerae, a gram negative bacteria that causes cholera - Cells with Amphitrichous flagella have a flagellum or tufts of flagella at each ends, An examples of Spirillum minor, the cause of Spirally Asian rate bit fever  - Cells with Lo[horticous flagella have a tuft at one end of the cell. The gram negative bacilli Pseudomonas, an opportunistic pathogen known for causing many infections including swimmers ear and Burn wound infection had lophotrichous Flagella that cover the entire surface of a bacterial cell are called peritrichous flagella. - The gram negative bacteria E coli shows a peritrichous arrangement of flagella - Directional movement depends on the configuration of the flagella - Bacteria can move in response to a variety of environmental signals including light (phototaxis) magnetic Field (magnetaxis) ising magnetosomes and most commonly chemical graidatents (chemotaxis). Purposeful movement towards a chemical attraction like a food cause oe away from a repelled like a poisonous chemical is archives by increasing the length of runs and Decreasing the lengths of tumbles - While running flagella rotates in a counterclockwise direction allow the bacterial cell to move forwards - In a peritrichous bacteria the flagella are all bundled together in a very streamlined way allowing for efficient movements - When tumbling flagella are splayed out while rotation in a clockwise direction, creating a looping motion and preventing meaningful forward movement but reorienting the cell toward the direction of the attractant, when an Attractant exists runs and tumbles still occur, however the length of the run is longer hle the length of tumbles is reduced allowing overall movement towards the higher concentration of the attractant when no chemical gradient exists then length of runes and Tumbles are more equal and overall movement is more random 3.4 - Eukaryotic organisms include protozoans, algae, fungi, plant and animals - Some eukaryotic cells are independent single celled microorganisms, wherehas other parents are multicellular organisms. The cells of Eukaryotic organisms have several Distinguishing characteristics - These organism are distinguishable by the presence of a nucleus surrounded by a complex nuclear membrane and by the presence of membrane Bound Organelles in the cytoplasm - Organelles such as Mitochondria the ER golgi Apparatus, lysosomes and Peroxisomes are held in place by the cytoskeletons, an internal network that support transport of intracellular components and helps maintain cell shape  - The genome of Eukaryotic cells is packaged in multiple rod shaped chromosomes as opposed to the single circular shaped chromones that characterizes morse prokaryotic cells Cell Morphologies - Eukaryotic cells have variety of shapes, including Spheroids, ovoid, cuboidal, Cylindrical, Flat, Lenticular,fusiform,Discoidal,crescent, ring stellate and polygonal - Some of these cells are irregular in shape and some are capable of changing shapes - The shape of a particular type of Eukaryotic cell may be influenced by factors such as its primary function, the organization of its cytoskeleton, the Viscosity of its cytoplasms, the rigidity of its cell membrane or cell wall and the physical pressure exerted on it by the surrounding environment and/or adjoining walls Nucleus: - These possess a nucleus, which is surrounded by a complex nuclear membrane that houses the DNA genome - By containing the DNA the Nucleus ultimately controls all activities of the cell and also serves an essential role in reproduction and heredity - Euk cells typically have their DNA organized into multiple linear chromosomes. The DNA Within the Nucleus is highschool organized and conceded to fit inside, which is accomplished by wrapping the DNA around proteins called Histones - Although most Euk cells only have 1 nucleus- there are some exceptions it protozoans has two ones used for reproduction and a large one that directs cellular metabolism - Some fungi form cells with two nuclei called heterokaryotic cells, during secually reproduction, cells whose nuclei divide, but whose synapse does not are called coenocytic - The nucleus is bound by a compass of Nuclear membrane, often called the nuclear envelope that consist of two distinct lipid bilayer that are contagious with each other - Desporte these connection between the inner and outer membranes each membrane contain unique lipids and proteins on its inner and outer surface, - The nuclear envelope contain nuclear pores which are large rosette shaped proteins complexes that control the movement of material into and out of the nucleus - The overall shape of the nucleus is determined by the nuclear lamina, a meshwork of intermediate filaments found just inside the nuclear envelope membrane - Outside of the nucleus additional intermediate filaments form a looser mesh and serve to anchor the nucleus in position within the cell - These cells are able to multiple through asexlul reproduction, during which a single parent cell becomes two identical daughter cells, this process is called mitoose, this process is very different to asecual binary fission - Euk cells possess multiple chromosomes that must be replicated and strategically divides between daughter cells, therefore meiosis is a much more complex cellular process than binary fission - Te euk cell culces is an ordered and carefully regulated series of events involving cell grown DNA, replication and cell divisions, to provide two clonal Daughter cells, One cycles of the cell cycles consist of two general phases Interphase and Mitotic Phase - During interphase the cell is not dividing but rather undergoing normal growth processes and Dna is replicated preparing for cell division the three stages of the pase are called, G1,S, G2 - The Mitotic Phase is a tulip step process during which the duplicated chromosomes are aligned, separated, moved to opposite poles of the cell and then are divided into two identical daughter cells. The first portion of the phase is called karyokinesis or nuclear division. Karyokinesis is divided into a series of phases prophase, prometaphase, metaphase,anaphase, and telophase- that results in the division of the cell nucleus. The second portion is called cytokinesis, and this is the ohmically separation of the Cytoplasms Componses into their two daughter cells in addition to mitosis asecl reponses, most euk microorganisms also have the option of secual repordcution invloin meiosis, Although Mitosis and Meiosis both require DNA replication, nuclear division, and Share Procedural similar ires there are important difference between the process and Outcomes - In contrast to the singular nuclear divisions that complete mitosis, meiosis involves two separate nuclear divisions. Rather than creating two colan daughter cells the goal of meiosis is the create 4 genetically distinct gametes,with each poses half the number of chromosomes found in the original cell  - This Reductionain is essential for the fertilization that occurs during sexual reproduction to produce in a zygote with a full complement of chromosomes Nucleolus: - This is a dense region within the nucleus where RNA biosynthesis occurs. And is the site where assembly of ribosomes begins - Ribosomal complex are assembled from rRNA and Proteins in the Nucleolus they are then Transported out to the ytoplases where the Ribosomes assembly is completed Ribosomes: - Ribosomes found in euk organelles such as mitochondria or chloroplasts of 70S ribosomes- the same size as prokaryotic ribosomes. However, organelles associated ribosomes in Eukaryotic cells are 80S ribosomes composed of a 40S small subunit and a 60S large Subunit in terms of Size and composition this makes them distinct from the ribosomes of prokaryotic cells - The two types of non organelles associated with eukaryotic ribosomes are defined by their location in the cell- free ribosomes and membrane-bound ribosomes. - Free ribosomes are found in the cytoplasm and serve to synthesize water soluble proteins, membrane bound ribosomes are found attached to the rough ER and make proteins for interaction into the cell membrane or [proteins destined for export from the cell - The difference between Eukaryotic and prokaryotic ribosomes are clinically relevant because certain antibiotic drudge are designed to target one or the other, since human cells re euk they generally are not harmed by antibiotics that destroy prokaryotic ribosomes in bacteria, however sometimes Negative Side effects may occur because mitochondria in human cells contain prokaryotic ribosomes Endomembrane System: - This system is unique to Euk cells - This is a series of membranous tubules, sacs, and flattened disks that synthesize many cell components and move material around within the cell. Because of their larger size cell euk cells require this system to transport materials that cannot be  dispersed by diffusions alone, The endomembrane system comprises several organelles and connection between the, including the ER, golgi Apparatus, Lysosomes and Vesicles Endoplasmic Reticulum - The ER is an interconnected array of tubules and cisternae (flattened sacs) with a single lipid bilayer, the spaces of the cisternae are called lumen of the ER, there are two types of ER rough and smooth. These two different types are sites for the synthesis of distinctly different types of molecules. RER is studded with ribosomes bound to the cytoplasmic side of the membrane. These Ribosomes make proteins destined for the plasma membrane - Following synthese, these proteins are inserted into the membrane of the RER. Small sacs of the R containing these newly synthesized proteins then bud off as transport vesicles and move either to the golgi apparatus for further processing directly to the plasma membrane to the membrane of another organelle or out to the the - Transport vesicles are single lipid bilayer, membranous, spheres with hollow interiors that carry molecules. SER does not have Ribosomes and therefore appears smooth it is involved in the biosynthesis of lipids, carbohydrate metabolism and Detoxification of Compounds within the cell Golgi Apparatus - Was discovered in 1898 by camilli Golgi who discovered a novel staining technique that showed stanced membrane structures - This is composed of a series of membranous discs called dictyosomes, each having a single lipid Bilayer, that are stacked together - Enzymes in the GA modify lipids and proteins transported from the ER to the Golgi, often adding carbohydrate components to them, producing glycolipids, Glycoproteins or Proteoglycans - Glycolipids and Glycoproteins are often inserted into the plasma membrane and are important for signal recognition by other cells or infectious particles. - Different types of cells can be distinguished from one another by the structure adaangeents of the glycolipids and glycoproteins contained in their plasma membrane - There glycolipids and proteins commonly also serve as cell surface receptors  - Transport vesicles leaving the ER fuse with a Golgi Apparatus on its receive cis or face - The proteins are processed within the google Apparatus and then addition transport vesicles containing the modified proteins and lipids pinch off form the golgi apparatus on its outgoing rams or face, these outgoing vesicles move to and fuse with the plasma membrane or the membrane of other organelles - Excitonics is the process by which secretory vesicles release their content to the cells exterior - All cells gave constitutive secretory pathways in which secretory vesicles transposer double proteins that are released from the cell contunelly - Certain specialized cells also have regulated secretory pathways, which are used to stro soluble proteins in secretory vesicles - Regulated secretion involves substances that are only released in response to certain events or signals, for example, certain cells of the Human immune system, secret histones in response to the pisces of foreign objects or pathogens in the body. - Histamines is a compass that triggers various mechanisms used by the immune system to eliminate pathogens Lysosomes: - In the 1960’s a belgian scientists discover lysosomes - These contain the digestive enzymes certain Euk cells use to break down particles i.e. food, damaged organelles or cellular debris \, microorganism or immune complexes. Compartmentation of the digestive enzyme within the lysosome allow the cell to efficelynu digest matter without harming the cytoplasmic components of the cell Peroxisomes: - The same guy also Discovered peroxisomes, membrane bound organelles that are not a part of the Endomembrane System. - These form independently in the cytoplasm from the Synthesis of peroxin proteins by free ribosomes and the incorepetat of these peroxin proteins into existing peroxisomes. Growing peroxisomes then divided by a process similar to binary fission - First named to produce hydrogen peroxide- a highly reactive molecule that helps to break down molecules such as uric acid, amino acid, and fatty acids  - Peroxisomes also possess the enzyme catalase which can degrade hydrogen peroxide along with the SER, promises also play a role in lipid biosynthesis - Like Lysosomes the compartmentalization of these degradative molecules within an organless helps protect the cytoplasmic contents form unwanted damde - The proxies of certina organism are specialized to meet their particles functional need - For examples Glyoxysomes are modified peroxisomes of yeats and plant cells that perform several metabolic functions include the production of sugar molecules - Similarly, Glycomsomes are modified peroxisomes made by certina Trypanosomes, the pathogenic Protozoans that cause chagas disease and African Sleeping sickness Cytoskeleton - These are made up of Microfilaments, Intermediate filaments and Microtubules - This gives structural support as well as a network for material to be transported - For examples the process of exocytosis involves the movement of a vesicles via the cytoskeletal network to the plasma membrane, where it can release its contents - Microfilaments are composed of two intertwined strands of actin, each composed of actin monomers forming filamentous cables 6nm in diapers - These filaments work together with motor proteins like myosin to affect muscles contraction in animals or the amoeboid movement of some euk microbes - In amyloid organism action can be found in two forms, a stiffer polymerized gel form and a more fluid, unpolymerized form - Actin in the gel form creates stability in the ectoplasm, the gel like area of cytoplasm just inside the plasma membrane - Temporary extensions of the Cytoplasmic membrane called pseudopodia- meaning false feet are produced through the forward flow of soluble actin filaments into the pseudopodia, followed by the gel sol cycling of the actin filaments, resulting in cell motility - Once the Cytoplasms extends outward forming a pseudopod the remaining cytoplasm flows up to join the leading edge thereby creating forward location - They are also involved with other processes in euk cells including cytoplasmic streaming , cleave furrow formation during cell division and Muscles movement in animals - They can polymerize and De polymerise relatively easily in response to cellular signals and their interaction with molecular motors - Intermediate filaments are a diverse group of cytoskeletal filament that act as cables within the cell  - They are termed this because of their 10 nm diameter is thicker than that of actin but thinner than that of microtubules they are composed of several strands of polymerized subunit that in turn are made up of a wide variety of monomers - These Intermediate filaments tend to be more permanent in the cell and Maintain the position of the nucleus - They also form the Nuclear lamina just inside the nuclear envelope - They also play a role in anchoring cells together in animal tissues - The intermediate filament protein desmin is found in desomeses the protein structure that join muscles cells together and help them resist external physical forces the intermediate filament keratin is a structural protein found in hair skin and nails - Microtubules are a tinder type of cytoskeletal fiber composed of tubulin dimers, these form hollow tubes 23 nm in diameter that are used as girders within the cytoskeleton - Like microfilaments, microtubules are dynamic and have the ability to rapidly assemble and disassemble. - Microtubules also work with motor proteins to move organelles and vesicles around within the cytoplasm - Microtubules are the main components of Eukaryotic flagella and cilia, composing both the Filament and the basal body components - Microtubules are involved in cell division, forming the mitotic spindles that serves to separate chromosomes during mitosis and meiosis - The meiotic spindle is produced by two centrosomes, which are essentially microtubule- organizing centers, at opposite ends of the cell - Each centrosomes is compose of a pair of centrioles positioned at right angles to each other, and each centro is an array od 27 parallel microtubules arranged in triplets Mitochondria - Large and complex and this is here aerobic respiration occurs - This term was coined by carl benda in 1898 - They learned that this organelles have their own genome and 70S ribosomes - The genome was found to be bacterial when it was sequenced in 1976, these finding supported the endosymbiotic theory propose by lynn Marguils which states that mitochondria originally arose through an endosymbiotic event in which a bacterium capable of aerobic cellular respiration was taken up by phagocytosis into a host cell and remind as a viable intracellular component - Each has two lipid membranes  - The intermembrane is a rename of the original hosts cells membrane structure - The inner membrane was derived from the bacterial plasma membrane - The electron transport chain for aerobic respiration uses integral proteins embedded in the inner membrane - The mitochondrial matrix, corresponding to the location of the original bacterium custom places is the current location of many metabolic enzymes - It also contained mitochondrial DNA and 70S Ribosomes - Invginations of the inner membrane =, called cristae evolved to increase surface area for the location of Biochemical reactions - The folding patterns of the Cristae different among various types of Eukaryotic cells and are used to distinguish different Eukaryotic organisms from each other Chloroplasts: - Plant and Algal cell contain chloroplast, the organelles in which photosynthesis occurs - All chloroplast have at least three membrane systems, the outer membrane the inner and the thylakoid - Inside the outer and the Inner membrane is the chloroplast stroma a gel like fluid that makes up much of a chloroplasts volume and In which the Thylakoid system floats - The thylakoid system is a highly dynamic collection of folded membrane scae - It is where the green photosynthetic pigment chlorophyll is found and the light reaction of photosynthesis occur - In most chloroplasts the thylakoids are arranged in stacks called grana, where in some algal chloroplasts the Thylakoids are free floating - Other Organelles similar to the mitochondria have arisen in other types of Euk but their roles differ - Hydrogenosomes are found in anaerobic eukas and serve as the location of anaerobic hydrogen produci - Hydrogosmes typically lack their own DNA and Ribosomes - Kinetoplasts are a variation of the Mitochondria found in some euk pathogens - In these organisms each cell has a single long branched mitochondria in which the kinetoplast DNA Organized as multiple circular pieces of DNA is found COncentrated at one pole of the cell Plasma Membrane - The plasma membrane of Euk cells is similar to the prokaryote - This is because it is mainly composed of phospholipids forming a bilayer with embedded peripheral and integral proteins - These membrane components move within the plane of the membrane according to the fluid mosaic model - Euk membranes contain sterols including cholesterol, that alter membrane fluidity - Many also contain some specialized lipids including Sphingolipds which are thought to play a role in maintaining membrane stability as well as being involved in signal transduction pathways and cell to cell communication Membrane transport Mechanisms: - All types of diffusions are used in both types of cells - However Euk cells can perform various types of Endocytosis, the uptake of matter through plasma membrane invagination and vacuole? Vesicles formation - A types of endocytosis involving the engulfment of large particles through the membrane invagination is called phagocytosis which means cell eating - In phagocytosis, particles are enclosed in a pocket within the membrane which then pinches off from the membrane to form a vaculor that completely surrounds the particles, Another type of endocytosis is called endocytosis which means cell drinking - In pinocytosis, small, dissolved material and liquids are taken into the cell through small vesicles - Saprophytic fungi for examples obtain their nutrients forms dead and Decaying matter largely through pinocytosis - Receptor Mediated Endocytosis is a type of endocytosis that Is united by specific molecules called ligands when they bind to cells surface receptors on the membrane - Receptor mediated endocytosis is the mechanism that peptide and amine derived hormones use to enter cells and is also used by various viruses and bacteria for the entry into host cells - The process by which secretory vesicles release their contents to the cells exterior is called Exocytosis - Vesicles move towards the plasma membrane and then meld with the membrane, ejectings their contents out of the cell. Exocytosis is used by cells to remove waste produces and may a;sp e used to release chemical signal that can be taken up by other cells  Cell wall: - In addition to a plasma membrane Some euk cells have a cell wall - Cells of fungi algae plants and even some protists have cell walls - Cells walls can be made of a wide range of materials including cellulose lose biogenic silica, calcium carbonate, agar, carrageenan or chitin - All cell walls provide structural stability for the cell and protection form envioemranetla stresses such as desiccation, changes in osmotic pressure and Traumatic Injury ExtraCellular Matrix: - Cells of animals and some Protozoans do not have cell well to help maintain shape and provide the structural stability, instead these types of eukaryotic cells produce an extracellular matrix for this purpose - They secrete a sticky mass of carbohydrates and Proteins into the spaces between adjacent cells - Some protein components assemble into a basement membrane to which the remaining extracellular matrix components adhere - Proteoglycans typically form the bulky mass of the extracellular matrix fibrous proteins Like collagen, provide strength - Both Proteoglycan and collagen are attracted to fibronectin, proteins, which in turn are attached to integrin proteins, - These proteins interact with transmembrane protein in the plasma membranes of EUK cells that lack cell walls - In animal cells the Extracellular matrix allows cells within tissue to withstand external stresses and transmits signals from the outside of the cell to the inside - The amount of extracellular matrix is quite extensive in various types of connective tissues and variation in the in extracellular matrix can give different types of tissue their distinct properties - In addition a host's cells extracellular matrix is often the site where microbial pathogens attach themselves to establish infection - For ex Streptococcus pyogenes the bacterium that causes strep throat and various other infection, binds to fibronectin in the extracellular matrix of the cells lining the oropharynx Flagella And cilia - Some Eukaryotic cells use flagella for locomotion, but Euk flagella are structurally distinct from those found in pork cells  - Pork flagella is a stiff, rotating structure, a eukaouic flagellum is more like a flexible whip composed of 9 parallel pairs of microtubules surrounding a central pain of microtubules - This arrangement is referred to as a 9+2 Array - The parrape microtubules use dynein motor proteins to move relative to each other causing the flagellum to bend - Cilia are a similar external structure found in some eukaryotic cells unique to the eukaryotes cilia are shorter than flagella and often cover the entire surface of a cell however they are structurally similar to flagella, and use the same mechanism for movement - A structure called a basal body is found at the base of each cilium and flagellum - This attaches the cilium or flagellum to the cell, and is compose of an array of triple microtubules similar to that of a centriole but is embedded within the plasma membrane - Because of their shorter length cilla use rapid flexible waving motion - They may also have other functions such as sweeping particles past or into other cells - Ie protozoans use cilia to sweep food into their mouth and mammals can use it to sweep debris out of the lung 4.1 Prokaryotes habitats and Functions - They can be found everywhere on the planet in hot springs to antarctica ice shields and under water with extreme pressure- one has ever survived being centrifuged at the gravity of jupiter (parapcoccu Dentrificans) - Also abunants on and within the human body - It is guessed that Prokaryotes outnumber nucleated human cells recent studies show the ratio is 1:1 but even then that means there can be a great number of bacteria in the human body - Bacteria Thrive in the human mouth, nasal cavity, throat and ears and vagina - Large colonies can be found in moist areas on the human body ie armpits however even drier skin is not free from bacteria - The existence of these creates is very important for the stability and thriving of ecosystems, for ex they are a necessary part of soil formation through the breakdown of organic matter and the development of biofilms - 1 gram of soil contains up to 10 billion microorganisms, belonging to about 1000 species - Many species of bacteria use substance released from plant roots, such as acids and carbohydrates as nutrients - The bacteria metabolize these plant substance and release the products of bacterial metabolism back to the soil and increasing the soil's fertility - In salty likes like the dead sea, salt loving halobacteria decompose dead brine shrimp and nourish young bring shrimp and flies with the products of bacteria metabolism - They are also abundant in the air even high up within the atmosphere - They are extremely resilient and adaptable, they are often metabolically flexible, which mean that they might easily switch from one energy source to another depending on the availability of sources or from one metabolic pathway to another - For ex certain prokaryotic cyanobacteria can switch from conventional type lipid metabolism which includes production of fatty aldehydes to a different types of lipid metabolism that generates biofuel such as fatty acids and wax esters - Ground water bacteria store complex high energy carbohydrates when grown in pure ground ware but they metabolize these molecules when the groundwater is enriched with phosphates - Some bacteria get their energy by reducing sulfates and sulfides but can switch to a different metabolic pathway when necessary, producing acids and free hydrogen ions prokaryotes perform function vital to life of earth by captures and reculing elements like carbon and nitrogen - Animals do require carbon to grow, but unlike prokaryotes they are unable to use inorganic carbon products that they can use - This process of converting carbon dioxide to organic carbon products is called carbon fixation - Plants and animals also rely heavily on prokaryotes for nitrogen fixation the conversion of atmospheric nitrogen into ammonia, a compound that some pants can use to form many different biomolecules necessary to their survival - Bacteria in the genus Rhizobium for example are nitrogen fixing bacteria they live in the roots of legume plants such as clove alfalfa and peas - Ammonium produced by these helps plants to survive by enabling them to make building block of nucleic cis, - In turn these plants are eaten by animals sustaining growth and survival or they may day in which the products of nitrogen fixation will enrich the soil ad be used by other plants - They Clean up the environment people have research and found that some bacteria play a unique role in degrading toxic chemicals that pollute water and soil  - Despite the good some are human pathogens and can cause illness or infection when they enter the body in addition some bacteria can contaminate food, causing spoilage of food borne illness, which makes them subjects of food safety concerns - Less the 1 percent of prokaryotes are thought to be human pathogens - Prokaryotes are thought to play a process in climate change, soil that was once frozen is now unfrozen and is thawing, carbon trapped in the permafrost is gradually released and metabolized by prokaryotes - These actions produce large amounts of carbon dioxide and methane greenhouse gasses that escape into the atmosphere and contribute to the greenhouse effect Symbiotic relationships: - They can have unique relationships with plants and Animals for examples bacteria living on the roots or leaves of a plant get nutrients from the plant and in return produce substance that protect the plant from pathogens on the other hand some bacteria are plant pathogens that uses similar mechanisms of infections to humans or animals - Prokaryotes live in a community, or a group of iterating populations of organisms. A population is a group of individuals organisms belonging to the same biological species and limited to a certain geographic area - Population can have cooperative interactions, which benefit the population or competitive interaction, in which one populations competes with another for resources the study of these interaction between microbial population and their environment is called microbial ecology - Any interaction between different species that are associated with each other within a community is called symbiosis such interaction fa along a continuum between opposition and cooperation - Interaction in a symbiotic relationship may be beneficial or harmful or have no effect on one or both species involved - When two species benefit from each other the symbiosis is called mutualism humans have this relationship with Bacteroides thetaiotaomicron, which lives in our intestinal tract , they digest complex polysaccharide materials that human digestive enzymes cannot break down converting them into monosaccharides that can be absorbed by human cells - We have this same relationship with certain strings of E coli , E coli releases on international contents for nutrients and Humans derive certain vitamins form E coli partially vitamin K which is required for the formation of blood clotting factors - A type of symbiosis in which one population harms another but remains unaffected is called amensalism. An examples is that bacteria may kill other forms of bacteria For example Staphylococcus epidermidis and Cutibacterium acnes.both have the ability to cause infections disease when protective barriers are breached they both produce a variety of antibacterial bacteriocins and bacteriocin like compounds, they are unaffected by what they take when their products can target and kill pathogens - The type of symbiosis and commensalism is where one organisms benefits while the other in unaffected this occurs when the bacterium Staphylococcus epidermidis uses the dead skin cells of the human skin as nutrients - Billions of these bacteria live on our skin but in most cases we do not interact with them in anyway, some may consider this relationship mutualisms - If neither are effected it is called neutralism for ex the bacterium bacillus anthracite typically forms endospores in the soi when conditions are unfavorable, if the soil is warmed and enriched with nutrients some B. anthracite endospores germinate and remain in symbiosis with other species of endospore that have not germinated - The relationship where when is benefited while the other is harmed is called parasitism, the relationship between humans and pathogenic bacteria can be classified as this - Sciences have coined the term Microbiome to refer to all prokaryotic and Eukaryotic microorganism and their genetic material that are associated with a certain organism or environment within the human microbiome there are resident microbiota and Transient microbiota - The resident consists of microorganisms that can't live on our bodies the term transient microbiota referred to microorganisms that are only temporarily found in the human body and these may include pathogenic microorganisms- hygienist and diets can alter both - The resident microbiota is amazing diverse, not only in terms of the variety of species by also in terms of the preference of different microorganism for different areas of the human's body - For examples in the human outh thesea re thougsinar of commntala or mutals spcieices of bacteria - Some live on the tongue or cheeks, the inner surface of the cheek has the least diverse microbiota because of its exposure to oxygen - By contract the crypts of the tongue and the spaces between teeth are to site with limited oxygen exposure, so these sites have more diverse microbiota, including bacteria living in the absence of oxygen - Differences in the oral microbiota between randomly chosen human individuals are also significant. Studies have shown for examples that the presence of such bacteria are streptococcus, Haemophilus and other was dramatically different when compared between individuals - There are also significant differences between the microbitation of different sites of the same khan body. The inner surface have the cheek has the predominance of streptococcus whereas the throat, the palatine tonsil and the saliva there are two to three times fewer streptococcus and several times more fusobacterium, in the place removed from gums the predominant bacteria belong to the genus Fusobacterium However in the intestine Both streptococcus and fusobacteria Disappear and the Genus Bacteroides becomes predominant - The Microbiome can also change overtime within the same individuals Humans Acquire their first inoculation of normal flora during natural birth and shortly after birth - Before if there is a raise increase in the population of Lactobaccill spp in the vagine, and this population services as the first colonization of microbiota during natural birth - After birth additional additional microbes are acquired from healthcare providers, parents and other relatives and individuals who come in contact with the baby - This process creates a microbiome that will continue to evolve over the course of the individuals as new microbes colonize and are eliminated from the body - For examples it is estimated that it nhin a 9 hour pes the microbiota of the small intestine can change so that half of the microbial inhabitants will be different - The Importance of the initial Lactobacillus colonization during vaginal child birth is highlighted by studies demonstrating a higher inside of disease in individuals born by cesarean section, compare to those born vginall - Studies have shown that babies born vaginally are predominantly colonized by vaginal lactobacillus wheres babies born by C section are more frequently colonized by microbes of the romal Skin microbiota, including common hospital acquired pathogens - Throughout the body resident microbiota are important for human health because they occupy niches that might otherwise be tkrn by pathogenic microorganisms. For instance Lactobacillus spp are the dominant bacterial specie of the normal vaginal microbiota for most females, these provees lactic acid contributing to the acidity of the vagin and inhihitjng the growth of pathogenic yeast - However when the population of the resident microbiota is decreased for some reason the PH of the Vag increase making it a more favorable environment for  the growth of yeast.Antibiotic therapy can also disrupt the microbiota of the intestinal tract and respiratory tract, increment the risk for secondary infections or proteins the long term carriage and shredded of pathogens Taxonomy and systematics: - Assigning Prokaryotes to a certain species is challenging they do not reproduce secually so it is not possible to classify them according to the presence or absence of interbreeding - They also do not have many morphological features - Traditional classification was based purely on shape staining patterns and biochemical or physiological difference More recently as technology has improve the nucleotide sequences in genesis have become an important creation of microbial classification - In 1923 American Microbiologist Davide Hendrics Bergy Published a manual in determinative Bacteriology, here he attempted to summary the information about the kinds of bacteria known at the time, using latin binomial classification Bergey also induce moroso;ica psychological and biochemical properties of these organism - This has been updated multiple times to include newer types of bacteria found and their Properties Classification by staining patterns: - According to their staining patterns which depends on the properties of the cell wall, bacteria have traditionally been classified into gram negative and positive and atypical meaning neither - Gram Pos bacteria possess a thick peptidoglycan wall that retains the primary stain during decolorizing step they remain purples after the gram stain procedure because the crystal violet dominates the light red/pink color of the secondary counterstain, safrain - In contrast gram negative bacteria possess a thin peptidoglycan cell that does not prevent the crystal violets from washing away during the decolorizing step, therefore they appear light red/pink after staining with the safrin. Bacteria that can't be stained b the standard gram stain procedure are atypical - These include Mycoplasma and Chlamydia. Rickettsia are also considered atypical because they are too small to be evaluated by the Gram stain.  - More recently scientists have begun to further classify gram neg and gram positive bacteria they have added a special group of deeply branching bacteria based on a combination of physiological biochemical and genetic feature - They aso now further classify gram negative bacterial into proteobaciera Cytophaga-Flavobacterium-Bacteroides (CFB), and spirochetes - The deeply branching bacteria are thought to be a very early evolutions form of bacteria - They live in hot acidic UV light exposed and anaerobic conditions Protebactier i a phylum of very diverse gorus, of gram negative because it includes some important human pathogens ie E coli - The CFB group of bacteria inlcdes components of the normal human gut microbiota like bacteroides - The spiriochests are spiral shaped bacteria and include the pathogen treponema pallidum which causes syphilis - Based of their prevalence of Guanine and Cytosine nucleotides, gram positive bacteria are also classified into low G+C and high G+C gram positive bacteria, the Low positive bacteria have less the 50 percent of gunaina a dn Cytosine nucleotide in their DNA they include human pathogens such as those that cause anthrax and teturnat and listerois, High include the bacteria that cause Diphtheria, Tuberculosisand Other diseases 4.6 - Are all unicellular organism - These are structured differently from bacteria in several ways, the archaeal membrane is composed of ether linkages with branched isoprene chains, as opposed to ester linkages with unbranched fatty acids - Archeal cell wall lack peptidoglycan by some contain a structurally similar substance called pseudo peptiocal or pseumurin - The genomes of archaea, are larger and more complex than bac irta - Is is as diverse as the domain bacteria and its representatives can be found in any habitat - Some archaea are mesophiles and many are extremophiles perfreing extreme hot cold, sanity or other condition that are hostile to most other forms on earth - Their metabolisms is adapted to these harsh environments and they can performs methanogenesis, where other domains cant  - Their size and complexity makes it challenging to classify, but most have determined that there are 5 major groups - Crenarchaeota, Euryarchaeota, Korarchaeota, Nanoarchaeota, and Thaumarchaeota there are many other that have likely not been classified yet - With a few exception archa are not present in the human microbiota and nne are associated with infectious human disease Crenarchaeota - This is a class of archaea that is extremely diverse, containing generate and species that different vastly in their morphology and requirements for growth - All are aquatic organisms and they are thought to be the most abundant microorganisms in the oceans, Most but not all are hyper theophanies, some of them are able to grow at temperature up to 113 degrees c - Arecha of the genus Sulfolobus are theonlie that prefer temps around 70-0 degree c and aciophies that perfect a PH of 2-3 sl fobus can live in aerobic or anaerobic environments in the preset of oxygen, these use metabolic processes similar to those of heterophyes, in anaerobic environment they oxidize sulfur to produce sulfuric acid which is stored in granules. These are used in bio technology for the reduction of thermostable and acid resistant proteins called affitienes, can bind and neutral various antigens - Another genus thermoproteus is represented by strictly anaerobic organisms with an optimal growth temperature f 85 degrees C they have flagella and therefore are motile, they have acellular membrane in which lipids form a monolayer rather than a bilayer which is typical or archaea its metabolism is autotrophic - To synthesizes ATP they reduce sulfur or molecular hydrogen and use Carbon monoxide as a Source of carbo, this is thought to be the deepest branching genus of Archaea and thus is a living examples of our plant in rarely form Euraychoatea - Includes several Distinct classes Methanobacteria, Methanococci, and Methanomicrobia represent Archaea that can be generally described as methanogens. - These are unique in that the ca reduce carbon dioxide in the presents of hydrogen producing methane - They can live in the most extreme environments and can reproduce at temps from below freezing to above boiling - They have been found in a variety of places and also produce glasses in ruminants and humans some sciences have even hypothesized that  methanogens may inhabit the plant marks because of the mixture of gasses produced by methanogens resembles the atmosphere - The cass Halobactier includes halophilic (Salt loving) - Halobacteira require a very high concentration of sodium chloride in their aquatic environment the require consent is close to saturation at 36 percent such environments include the Dead seas as well as some salty lake in antarctica and south central asian, One remarkable feature of these organisms is that they perform photosynthesis using the protein, Bacteria Isipin, which give them and the bodies of water the inabit a beautiful purple color - These may be the oldest living species on earth READING 2 Chapter 5 Intro - Although bacteria and viruses account for a large number of infectious disease that affect humans, many serious illness are caused from eukaryotic organisms - One examples is Malaria which is caused by plasmodium, a eukaryotic organism transmitted through mosquito bites - This is a major illness and threatened 3.4 billion people worldwide - Organ failure and blood or metabolic abnormalities contributes to medical energies and sometimes death And relapses may occur - In countries where malaria is endemic, the disease represent a more public health challenge, that can place a tremendous trains on developing economies - Efforts to stop this disease include distribution of insecticide treated bed nets and the spraying of pesticide - Researchers are also working on creating a vaccine that are effective - In late 2021 R21/matrix M became the first vaccine to be recommended for widespread use by the world health organization and at least 10 other candidate vaccines are in development this is a multinational Involvements working with governments, universities nonprofits and pharmaceutical companies  - The Malaria Research and Training center in mali has done the most research and they have critical clinical trial 6.1 - Despite their small size there was a discovery of a filterable component smaller than a bacteria that causes tobacco mosaic disease, that dates back to 1892 - At the time Dmitir Ivonvski discovered the source of TMD by using a porcleicle filtering devices first invented by charles chamberlain and Louis Pasteur , these have a pore size of 0.1 um, which is small enough to move all bacteria less than 02 from any liquids passed through the device - An extract obtained from TMD infected tobacco plants was made to determine the cause of the disease, initially it was thought to be bacterial. - Ivanvoski using the filter found that the cause of TMJ was not removed after passing the extract through the poricling filter - Therefore is a bacteria was not the cause of TMD what could be cueing the disease, he concluded must be an extremely small bacterium or bacterial spore - Other scientists continued looking into thai - It was Beijerinck in 1899 who concluded that is was not a bacteria but instead possibly a chemical, like poison or what we would describe today as a toxin - As a result the word Virus- Latin for poison was used to describe the cause of TMD- a few years after his initial discovery - Even though he was not able to see the virus that caused TMD and did not realize the cause the cause was not a bacterial, he is credited as the original discovery of Viruses and founder of the field of virology - Today we see virus using an electron microscope - Viruses are distinct biology entities, however there is not a lot known about their evolution - In terms of taxonomy they are not included in the tree of life as they are Acellular - In order to survive and reproduce viruses must infect a cellular host, making them Obligate intracellular parasites - The genome of a virus enters a host cell and direct the production of the viral components, Proteins and Nucleic Acids needed to form new Virus particles called Virions  - New virions are made in the host cell by assembly of Viral components, these new virions transport the viral genome to another host cell to carry out another round of infection Hosts and Viral transmission - Viruses can infect every types of host cell, Including those of plants, animals, fungi, protists, bacteria and Archaea - Most viruses will only be able to infect the cells of one or a few species of an organism- this is called the host ranged - However having a wide host range is not common and viruses will typically only infect specific hosts and only specific cell types within those hosts - The viruses that infect bacteria are called Bacteriophages, or simply phases - the word phase comes from the greek word for devour - Other viruses are just identified by their host ground, such as animal or plant viruses - Once a cell is infected, the effects of the virus can vary depending on the type of virus - Viruses may cause abnormal growth of the cell or cell death, alter the cell's genome or cause little noticeable effect in the cell - Viruses can be transmitted through direct contact, indirect contact with fomites, or through a vector - which is an animal that transmits a pathogen from one host to another - Arthropods such a mosquitos, ticks and flies are typical vectors for viral diseases, and they may act as mechanical vectors or biology vectors - Mechanical transmission occurs when the arthropod carrier a viral pathogen on the outside of its body and transmits it to a new host by physical contact - Biological transmission occurs when the arthropod carrier the viral pathogen inside of its body and transmits it to the new host through biting - In humans a wide variety of viruses are capable of causing various infection and disease - Some of the deadliest emerging pathogen in humans are viruses, yet we have few treatments or drugs to deal with viral infections, making them difficult to eradicate - Viruses that can be transmitted from an animal host to a human host can cause zoonoses - For examples the avian influenza virus originates in bird but can cause disease in humans - Reverse zoonosis are caused by infection of an animal by a virus that originated in a human Viral Structure: - In general Vernons are small and can't be observed using a regular light microscope - They are much smaller than prokaryotic and eukaryotic cells, this an an adaption allowing viruses to infect these larger cells - The size of a virion can range from 20 nm for small viruses up to 90090 for typical large circles - Recent discoveries however have identified new giant viral species such as panoavirus salinus and Pithovirusi sibicum with sizes approaching that of a bacterial cell - After the development of the electron Microscope, Wendall Stanly was the first scientist to crystallize the structure of the tobacco mosaic virus and discovered that is is composed of RNA and Protein - In 1943 he isolated Influenza B vistus which contributed to the development if ab Influenza vaccine - This discovery unlocked the nature viruses that had been puzzling sciences for over 40 years and was awarded the nobel prize in 1946 - Because of research we now know that viruses consist of a Nuclieic acid- Either RNA or DNA surrounded by a protein coat called a capsid- the interior is not filled with cytosol, as in a cell but contains the bare necessities in terms of genome and enzymes needed to direct synthesis of new virions Each capsid is composed of proteins subunit called Capsomeres made of one or more different types of capsomere proteins that interlock to form the closely packed capside - There are 2 categories of viruses based on general composition, Viruses formed from only a Nucliec acid and Capsid are called naked viruses or nonenveloped viruses - Viruses formed with a Nucleic acid packed capside surrounded by a lipids Layer are called enveloped viruses with a nucleic acid packaged capsid, - The viral envelope may either be intracellular or cytoplasmic in origin - Extending outward and away from the capsid of some naked viruses and enveloped virus are protein structure called spikes - At the topics of these spikes are structures that allow the virus to attach and enter a cell, like the Influenza viruses spikes that allow the virus detach from the cell surface during release of new VirensInfluenza viruses are often identified by their H&M Spike Spike's for example each one and and one influenza viruses are  responsible for the pandemics in 1918 in 2009 H2 n two for the pandemic in 1957 H three n 2 for the pandemic in 1968 - Viruses vary in the shape of their capsids which can be either helical polyhedral or complex a helical capsid forms the shape of tobacco mosaic virus and naked here cofire us and a bola virus an envelope Tellico virusThe caps it is cylindrical or rod shaped with the genome fitting just inside the length of the capsid polyhedral capsids from the shapes of poly viruses and rhinoviruses and consist of nucleic acid surrounded by a polyhedral many sided capsid in the form of an icosahedron. - A icosahedral capsid is a 3-D at three dimensional 20 sided structure with 12 vertices; these caps somewhat resemble a soccer ball; both helical and polyhedral viruses can have envelopes. - King on viruses can have envelopes Viral shapes seen in certain types of bacteriophages such as T4 Fage And poxvirus is like Vikina virus may have features of both polyhedral and helical viruses so they are described as complex viral shape. - In the bacterial phage complex form the genome is located within the polyhedral head and the sheath connects head to the tail fibers and tell pens that help the virus attached to receptors on the host cell's surface. - Poxviruses that have complex shapes are often brick shaped with intricate surface characteristics not seen in other categories of the capsid. Classification and Taxonomy of virus - Other viruses are not classified in the three domains of life their numbers are great enough to require classificationSince 1971 the international union of microbiological societies virology division has given the task for developing refining and maintaining a universal virus taxonomy to the international committee onTaxonomy of viruses - Since viruses commuted so quickly it can be difficult to classify them into genus and species apathy using the bio Romeo name and culture system since the ICTV is viral nomenclature system classifies viruses into familiesAnd Genera based on the viral genetics chemistry morphology and mechanism of her multiplication - Today at the ICTV has classified no one viruses and seven orders 96 families and 350 Ginera bio families names end in Viridae Ingenious names and with virusThe names of viral orders family and Genera are all italicize when referring to a viral species we often use a genus and species epithet Such asPanda virus door sis  - The Baltimore classification system is an alternative to ICTV nomenclature the Baltimore system classifies viruses according to their genomes a.k.a.DNA or RNA a single versus double stranded and motive replication this system plus create seven groups of viruses that have common genetics and biology - Aside from formal systems of nomenclature of viruses are often informally grouped into categories based on chemistry morphology and other characteristics they share in common categories may include naked or envelope structures single-stranded or double stranded DNA or RNAGenomesSegmented or unsegmented Gino's and positive strand or negative strand RNA - For example herpes viruses can be classified as Diaz DNAEnvelope virus human immunodeficiency virusIs a single-stranded RNA enveloped virus and Tobacco mosaic virus is a single-stranded RNA virusOther characteristics such as host specificity tissue specificity caps size and shape and special jeans and enzymes may also be used to describe groups of similar viruses Classification of Viral Diseases - What are the ICTV has been tasked with biological classification of viruses it has also played in important role in the classification of disease caused by viruses - Distillate take the tracking a virus of the related human diseases that I see TV has created classifications that link to the international classification of diseases the standard taxonomy of disease that is maintained an updated by the world health organization - The ICD assigns an alphanumeric code of up to six characters to every type of viral infection as well as all other types of diseases medical conditions and causes of death - This ICD code is used in conjunction With two other coding systemsThe current procedural terminologies in the healthcare common procedure coding system to categorize patient conditions for treatment and insurance reimbursement - For example when a patient six treatment for a viral infection ICD codes are routinely used by clinicians to order laboratory test and prescribe treatments specific to the virus specific acted of causing the illness - Does ICD code is then used by medical laboratories to identify test and must be performed to confirm the diagnosis ICD code is used by the healthcare management system to verify that all treatment in laboratory work performed are appropriate for the given virus  - Medical coders use ICD codesTo assign the proper code of for procedures performed and medical billers intern use this information to process claims for reimbursement by insurance companies Vital record keepers use ICD code to record cause of death on death certificates and epidemiologists use ICD codes to calculate morbidity and mortality statistics 6.2 - All viruses depend on sells for reproduction and metabolic processes by themselves viruses do not in code for all the enzymes necessary for viral replication but within a wholesale of Irish can commander cellular machinery to produce the viral particles - Bacteriophages replicate only in the cytoplasm since prokaryotic cells do not have a nucleus or organelles in eukaryotic cells most DNA viruses can replicate inside the nucleus with an exception observed in the large DNA viruses such as pox virus is that can replicate in the cytoplasm with a few exceptions RNA viruses that infect animal cells replicate in the cytoplasmImportant exception will be highlighted layer is the influenza virus The Life Cycles of Viruses with Prokaryotes Hosts - The life cycle of bacteriophages have been a good model for understanding out viruses affect the cells that they infect - Send similar processes have been is Herb for eukaryotic viruses which can cause immediate death of the cell or establish a latent chronic infection Byerland phages typically lead to the death of the cell through so lysis temperate phage is on the other hand can become a host chromosome and they are replicated with the cell genome until such time as they are inducing to make newly assembled viruses Or progeny viruses The Lytic Cycle: - During the light to cycle of violence phage the bacteriophage takes over the cell reproduces new faces and destroys the cell TVand  phage is a good example of a well characterize class of Ireland phages - There are five stages in the bacteriophage liked excel cycleAttachment is the first stage in the infection process in which the phase interact with specific bacterial surface receptors most pages have a narrow host range and may in fact one species of bacteria or stream within a species this unique recognition can be exploited for targeted treatment of bacterial infection by faze therapy or fish typing to identify unique bacterial subspecies are strange - The second stage of infection is entry or penetration there's a curse the contraction of the tail she's which accent like a hypodermic needle to inject a viral genome through the cell wall and membrane the fish head and remaining components remain outside the bacteria - The third stage of infection is biosynthesis of a new viral component after entering the host of the virus synthesizes virus in coded and don't nucleus is to grade the bacterial chromosomeThen hijacks the hotel to replicate transcribe and translate the necessary viral componentsCasemiro's, she is, base plates, tail fibresAnd viral enzymes for the assembly of new viruses polymerase jeans are usually expressed early in the in the cycle Well capsid and tail proteins are expressed later during the mature Asian Fage new Virens are created - To liberate free phages the bacterial cell wall is disrupted by face proteins such as Hollyn or laces on the final stages released mature viruses burst out of the host cell in a process called license and the parking viruses are liberated into the environment to infect new cells Lysogenic Cycle: - In a lysogenic cycle the phage genome also enter the souther attachment and penetration a prime example of a phase with this type of lifecycle is the land of age during the lights of Genex psycho instead of killing the house the phase genome integrate into the bacterial chromosome and becomes part of the hostIntegrated face genome is called a prophage a bacterial house with a prophage is often called a Lysogen - The process in which bacterium is infected by a temperate phage It's called a life so Jenny it is typical of temperate phage is to be latent or inactive within the cell  - As the bacterium replicates and it's chromosome it also replicates the phages DNA in passed it onto new daughter cells during reproduction the presence of the fish may alter the phenotype of the bacterium to take care bring extra jeansThis change in the hose phenotype is called lysogenic conversion or face conversion some bacteria such as Video chlorateAre less violent in the absence of the prophage the phases infecting these bacteria carry the toxin jeans and their genome and enhance their Virgins of the host when they toxic jeans are expressed in the case of the Cloria phage encoded toxin can becauseSevere diarrhea - During Leiser jenny the prophage will persistIn the host, Jean until induction which results in thatExcision of viral genome from the host comazon After induction has occurred the temperate phage can proceed through electric cycle and then undergo lysogenyIn a newly infected cell Transduction: - Transduction occurs when a bacteriophage transfers bacterial DNA From one bacterium to another during sequential infections there are two types of transduction generalized and specialized - During the late text cycle of viral replication the virus hijacked the hotel degrades the hose chromosome and makes more viral genomeIs it assembled in packages DNA into the fish head packing can occasionally makes a mistake instead of packaging viral DNA it takes a random piece of host DNA and inserted into the capsid once released is Byron will then inject the former host DNA into a newly infected hostThe asexual transfer of genetic information can allow for DNA recombination to occur that's providing the new house with NewJeans - Generalized transaction occurs when a random piece of bacterial chromosome DNA is transferred by phage during the light to cycle - Specialized transaction occurs at the end of the lights of Jenny cycle where the pro fish is exercise and the bacteriophage enters the light to cycle since the features integrated into the host gene on the prophage can replicate as part of the host have a some conditions e.g.Ultraviolet light exposure or chemical exposure stimulate The prophage to undergo induction causing the phage to exercise from the genome Intergalactic cycle and produce new phages to leave host cells - During the process of excursion from the host comazone a phase me occasionally remove some bacterial DNA near the site of viral integration the Faigin host DNA from one end or both ends of the integration site are packed within the capsid and her transferred to the new infected hostSince the DNA  transferred by the phages not randomly package but instead of specific piece of DNA near the side of integration this mechanism of gene transfer is referred to as specialized transactionThe DNA can recombine with host, zones giving the ladder new characteristics transduction seems to play an important role in the evolution airy process of bacteria giving them a mechanism for asexual exchange of genetic information Life Cycle of Viruses with Animal Hosts - Like took animal viruses follow similar infection stages to bacteriophages attachment penetration biosynthesis metrician and release however the mechanisms of penetration nucleic acid biosynthesis and release difference between bacterial and animal viruses - After binding to host receptors animal viruses enter through endocytosis engulfment by the host cell or through membrane fusion Biro envelope with the host cell membrane - Many viruses are host specific meaning they only infected certain type of host and most viruses only infect certain types of cells within tissuesThis specific tea is called A tissue tropism examples of this our demonstrated by the polio virus which exhibit tropism for the tissues of the brain and spinal cord or the influenza virus which has a primary tropisms for the respiratory tract - Animal viruses do not always expressed their jeans using the normal flow of genetic information DNA to RNA to protein some viruses have a dsDNA genome like cellular organisms and can follow the normal flow however others may have single-stranded DNA double stranded RNA are single-stranded RNA genomes the nature of the genome determines how the genome is replicated and expressed as viral proteinsIf a genome is single-stranded DNA host enzymes will be used to synthesize a second strand that is complementary to the genome strand that's producing double stranded DNA itThe double trying to DNA Kanell be replicated transcribed and translated similar to the host DNA - If the viral genome is RNA a different mechanism must be used their three types of RNA genomeDouble-stranded RNA a positive single-stranded RNA or negativeStranded RNAIf a virus has a single-stranded RNA genome it can be translated directly to make a viral proteins viral genomic Single-stranded RNA acts like a cellular mRNA however if it virus contains negative single-stranded RNA Gino the hose ribosomes cannot translate it until negative single-strand