BIO 2402 Exam One Study Guide PDF

BIO 2402 Exam One Study Guide ============================= Unit One (1.1-1.3) Invisible World: =================================== ### Microbiology: - What is microbiology? - Microbiology is the study of organisms that need a microscope to be seen. - They maintain a simpl...

BIO 2402 Exam One Study Guide ============================= Unit One (1.1-1.3) Invisible World: =================================== ### Microbiology: - What is microbiology? - Microbiology is the study of organisms that need a microscope to be seen. - They maintain a simple morphology. - What are some contradictions to microbiology? - Not all microbes are "microscopic" (like worms/ helminths) - Not all microbes are living: - Viruses (acellular) - Prions (specific type of protein) - What are the major groups of microorganisms? - Prokaryotic (unicellular and lack a nucleus): - Bacteria - Archaea - Eukaryotic (uni and multicellular): - Protists - Fungi - Viruses and Helminths - Where do microbes live? - Ubiquitous (everywhere) - What are the microbial communities: - Biofilms (adhered to their environment) - Colonies (grouped together) - Free swimming - Not all microbes cause disease (pathogenic): - Types of microbes: - Beneficial - Harmful - How are microbes essential to the web of life? - Microbes can be producers - Microbes can be decomposers - Fungi and bacteria - Microbes can be (nitrogenous) fixers - Microbes can exist in symbiotic relations - Ex. humans and normal flora/ microbiota - How can humans use microorganisms? - Agricultural technology and environment - Bioremediation: the use of microorganisms/ microbes to clean the environment. - Healthcare - Microbes can be used to create antibiotics - Fuels - Industrial Naming, Classifying, and Identifying Microorganisms: ---------------------------------------------------- - What are the two basic cell types? - Prokaryotes - Lack membrane bound organelles - Especially the nucleus - Unicellular - Eukaryotes - Have membrane bound organelles - Unicellular and Multicellular - What are the three branches of microbes? - Cellular - **Prokaryotes** - Bacteria - Archaea - **Eukaryotes** - Fungi - Protists - **Acellular** - Viruses - Viroid - Prions - Who created the basic microbial classification system? - Carolus Linnaeus created the initial two kingdom system consisting of: plants and animals. ### Domains: - What is a domain? - The broadest level of classification in the taxonomic system. - What are the three domains? - Bacteria - Prokaryotic - Unicellular - Archaea - Prokaryotic - Unicellular - Eukarya - Eukaryotic - Unicellular and multicellular - What are some differences between Archaea and Bacteria? - Bacteria: - Archaea: - Live in extreme environments - Do not contain peptidoglycan cell walls - Distinct replication - In some ways, more similar to Eukarya than bacteria - Domain Eukarya: - Unicellular and multicellular - Domain Eukarya includes which kingdoms? - Fungi - Plantae - Animilia - Protists - Protists include? ### Taxonomy: - What is taxonomy? - The ordered division and naming of organisms and viruses (extinct and living). - What is the order of taxons? - Domain - Supergroup - Kingdom - Phylum - Class - Order - Family - Genus - Species ### Binomial Nomenclature: - A two-part scientific name. - Consisting of a *Genus* and *species* name. - The formatting is seen as above. - The species is a more specific taxonomic group than the genus. - How can the name be abbreviated? - Ex*. G. species* - When and why? - This is because after a binomial nomenclature has been stated once, for simplicity it can be simplified as seen above. ### Classifying Organisms (and more): - Living organisms can be classified as prokaryotes (unicellular) and eukaryotes - Eukaryotes can then be classified as multicellular and unicellular. - Unicellular eukaryotes can then be classified as fungi or protists - Exception: - Some protists are multicellular - Most fungi are multicellular - Multicellular eukaryotes can then be classified as heterotrophs and autotrophs - Autotrophic eukaryotes are classified as plantae - They make their own sources of energy. - Heterotrophic eukaryotes can then be classified as absorptive and ingestive - Absorptive heterotrophs are classified as fungi - Ingestive heterotrophs are classified as Animalia - Recommended: draw a concept map using the information above: The Historical Foundations of Microbiology: ------------------------------------------- ### Ancient realizations: - Diseases are communicable, meaning: - They can spread from person to person - Survivors build some sort of immunity from being infected. - Who? - Hippocrates - Example? - Leprosy was believed to be communicable (It is.) - What did they believe? - Diseases were transmitted by things that cannot be seen. - Those who were infected would need to be isolated. - Survivors build some sort of immunity from being infected. - Where did we see this? - Egypt: mold bread - Rome: Sanitation and public health infrastructure - The Cloaca Maxima (great sewer) and the River Tiber - What is the miasma theory? - The theory that attributed disease to "bad air" created form decomposing material ### Microscopes: - Robert Hooke: - Created the first compact microscope - First to see and coin the term cell. - Viewed plant cells (from a piece of cork) - Antoni van Leeuwenhoek: - Created a single lens magnifier. - First to see single celled microbes, called them "animalcules." Unit One (3.1-3.2) The Cell: ============================ Historical Foundations of Microbiology: --------------------------------------- ### Spontaneous Generation: - What is spontaneous generation (abiogenesis)? - The belief that life can originate from "life force" or the elements? - Who? - Jan Baptista van Helmont - Aristotle - What is biogenesis? - The belief that life can only originate from life. ### Who supported abiogenesis? - John Needham: - Boiled/ heated vials with corked broths. - What were the results and what did they support? - The corked broths became turbid, signaling that there was microbial growth. - This supported abiogenesis. ### Who supported biogenesis? - Francesco Redi: - His experiment consisted of three jars, each covered differently (lid, cloth, and open). - Inside each jar was decaying meat, in which the meat exposed to flies grew maggots. - What were the results and what did they support? - The jar without a covering had maggot growth, which proved that maggots arose from flies. - This supported biogenesis. - Lazzaro Spallanzani: - Retested John Needham's experiment. - What were the results and what did they support? - Spallanzani's experiment yielded nonturbid broth. - Concluded: - Needham failed either: - Heat the vials sufficiently to kill all the microbes - Failed to sufficiently seam the vials - Microbes exist in the air and can contaminate experiments - This supported biogenesis. - Louis Pasteur: - Created the "swan-neck" flask, which used the irregular shape of the glass to kill all microbes in the flask and still keep them accessible to air. - What were the results and what did they support? - His results concluded that after boiling, the contents remained free of microbial growth. - This supported biogenesis. ### Infection Control: - Ignaz Semmelweis: - Connected high maternal mortality to unwashed hands and cadaver particles. - Instituted preliminary aseptic techniques. - Joseph Lister: - First aseptic technique - Carbolic acid - Considered the "Father of Antiseptic Surgery" Germ Theory of Disease: ----------------------- - What is the Germ Theory of Disease? - The germ theory of disease is defined as "specific diseases being caused by specific kinds of microbes" - Who created the germ theory of disease? - Louis Pasteur - "The father of Microbiology" ### Major Contributions: - Louis Pasteur: - Germ Theory of Disease - Pasteurization: - The ability to kill harmful microbes in liquids without ruining them. - Fermentation - Disproved spontaneous generation - Vaccinations - Microbial Metabolism - Different microbes have different metabolic processes - Aseptic Techniques - Robert Koch: - Identified bacterial as a distinct species - Causative agents and etiology - Simple staining - Bacterial photos - Steam sterilization - The use of petri dishes - Bacterial transfer techniques Unit One (3.3-3.4) The Cell: ============================ Cell Theory: ------------ - What is cell Theory? - All organisms are made of cells - All cells are produced by other cells - Biogenesis - A cell is the fundamental unit of life. - What are the shared features of living organisms? - Cells and organization - Energy processing - Responses to environmental changes - Regulation and homeostasis - Reproduction - Growth - Evolution - What are the two types of cells? - Prokaryotes - Eukaryotes - What characteristics do they share? - DNA - RNA - Ribosomes - Prokaryotic: 70s - Eukaryotic: 80s - Proteins - Plasma membrane - Cytosol/ cytoplasm ### What is the Central Dogma Theory? - DNA is transcribed into RNA which is then translated (by ribosomes) into proteins. - Recommended: draw a mini concept map. Cell Membrane: -------------- - Why is the cell membrane called a fluid mosaic model? - This is because the cell membrane is composed of many parts: - Phospholipids - Proteins - Sugars - Carbohydrates - Steroids - Phospholipids: - Phospholipids are amphipathic, meaning the have hydrophilic heads and hydrophobic tails. - Their heads face the inside of the cell and the outside of the cell. - This dual layer structure is called a bilayer. - The polar head attracts water, while the tails repel water. - This affects molecules ability to pass through the semipermeable membrane. - Steroids: - Provide fluidity to the bilayer. - Temperature can cause fluctuations in how phospholipids act. - Proteins: - What are the functions of proteins? - Support - Signaling and communication - Transport - Import: entering the cell - Export: exiting the cell - Establishing the concentration gradient ### Membrane permeability: - Freely permeable molecules: - Small in size - Lack of charge - Gases - Hydrophobic - This allows the molecule to pass through the hydrophobic center of the bilayer. - Semipermeable molecules: - Small in size - Lack of charge or charge that is unevenly distributed (water) - These often have to "sneak in" - Impermeable molecules: - Large in size - Polar/ have a charge Cellular membrane movements: ---------------------------- ### Passive Transport: - What are shared characteristics of passive transport? - Does not require ATP. - Movements flow with the concentration gradient. - High to low concentration (solutes). - What is simple diffusion? - Transport of solutes directly through the semipermeable membrane. - Moves with the concentration gradient (which is necessary) - What is dynamic equilibrium? - When there are no differences in the concentration gradient inside and outside the cell. - What is facilitated diffusion? - Transport of solutes with the use of a transport protein. - Carrier protein (aquaporins, specific) or channel. - What is osmosis? - Osmosis is the movement of water across a semi-permeable membrane. - What is osmotic pressure? - The pressure necessary to stop movement of water across the membrane. - How does water move across the membrane? - Some sneak in. - Others move through aquaporins. - What is tonicity? - The strength of a solution. - What is a solution? - A solute and a solvent. - What are the types of environmental tonicities? - Isotonic - Hypotonic: the environment is less concentrated (water moves in the cell) - Prokaryotic: turgid - Cellular swelling - Eukaryotic: lyse - Cellular bursting - Hypertonic: the environment is more concentrated (water leaves the cell) - Prokaryotic: plasmolysis - Cell membrane separates from cell wall - Eukaryotic: crenate - Shrink ### Active Transport: - ATP is necessary for solute movements against the concentration gradient. - Low to High - Carrier proteins are necessary. - What are symports, antiport, and uniports? - Symports are low to high movements that allow molecules to move through the same carrier protein. - Antiports are low to high movements that allow molecules to move through the same carrier protein in different directions. - Uniports are low to high movements that allow a molecule to move through the carrier protein in one direction. ### Bulk Transport: - What is bulk transport? - A energy required process that transports large molecules or particles into the ell (endocytosis) or outside the cell (exocytosis) via vesicles. - Eukaryotes Cells: ------ ### (Summary) Prokaryotes and Eukaryotes: - How do prokaryotes and eukaryotes differ? - Prokaryotes: - Lack of nucleus - Haploid chromosome - No membrane bound organelles - Simple - Asexual reproduction - Include: - Bacteria - Archaea - Eukaryotes: - True nucleus - Chromosomes and chromatin - Membrane bound organelles - Complex - Include: - Algae - Protists - Fungi - Plants - Protozoa - Animals - How do bacteria and archaea differ? - Bacteria: - Ubiquitous - Cell walls made of peptidoglycan (or lack of cell wall) - Archaea: - Harsh environments - Cell walls composed of polymers aside from peptidoglycan ### Bacterial Reproduction (Binary Fission): - What are the steps of Binary Fission? - Replicate the DNA - Cellular elongation and expansion of cytoplasm - DNA is separated into two chromosomes (haploids) - Septum forms between the chromosomes - The cell divides Bacterial/ Prokaryotic Components: ---------------------------------- - What are the characteristics all bacteria share? - Plasma membrane - Ribosomes - Cytoplasm - Cytoskeleton - DNA ### Cytoplasm: - What are the components of cytoplasm? - Cytosol: - The gel-like portion of the cytoplasm. - Ribosomes - Nucleoid - Inclusion bodies - What are additional components that only some have? - Fibers that act as a cytoskeleton - Endospores ### Bacterial Genome/ Genetic Material: - What is the nucleoid? - The dense center of a prokaryotic cell that holds the genetic material; however, is not bound by a membrane. - What is the shape of the chromosome? - A singular haploid: - A singular chromosome that connects into one large circle. - What holds the DNA together? - DNA binding proteins. - These genes found in the nucleoid are essential for bacterial survival and functioning. - What is a Plasmid? - Extra chromosomal pieces of DNA. - Smaller that the haploid. - Nonessential genes for the bacterium but can provide adaptive advantages. ### Ribosomes: - What is the function of ribosomes? - To conduct protein synthesis. - What are the types of ribosomes found in the prokaryotic cell? - 70s (know this one of the two) - 80s - Antibiotics: - Specific antibiotics are used to target bacterial ribosomes, to prevent protein synthesis, which is essential for binary fission. ### Inclusions: - What is an inclusion? - Cellular storage sites that have various uses, contents, sizes, and numbers. ### Endospores: - What is an endospore? - Endospores are dormant spores that can be created in a cell (and exist inside or outside the cell) through sporulation. - What is sporulation? - The process of making endospores - What are the two bacterium that have endospores? - Bacillus - Clostridium - What does an endospore give rise to? - Once an endospore (which kills the bacteria once it is expelled) deems environmental conditions favorable, it will give rise to a vegetative/ functioning cell. - What are the concerns when it comes to endospores? - Endospores are extremely resistant and can live dormant in unfavorable environmental conditions. - Makes killing bacteria much more difficult. Bacterial Cell Wall and Outer Layers: ------------------------------------- ### Glycocalyces: - Where are Glycocalyces located? - Glycocalyces are located external to the cell wall. - What are the two types of Glycocalyces? - Capsules: - A capsule is a dense tightly bound layer with a mucoidal texture. - How is this beneficial to bacteria? - The mucoidal texture of the capsule allows the bacteria to slip out from phagocytic white blood cells. - This gives them greater ability to cause damage. - Slime layers: - A slime layer is characterized as being looser than capsules. - What is the function? - Protects the cell from water and nutrient loss. - The slime layer also helps the cells adhere to their environment - Biofilms. ### The Bacterial Cell Wall: - What are the functions of the cell wall? - Provides shape - Protection from lyse (cellular bursting) - Attachment - Pathogenicity: - Cell wall components can have the potential to cause disease ### The S Layers: - What is the S Layer? - An additional protective layer that if found in free living bacteria and archaea. The Cell Wall: -------------- ### What is Peptidoglycan: - What is the structure of Peptidoglycan (murein)? - Peptidoglycan is composed of alternating sugars and amino acid units. ### Gram Positive Cell Wall: - What is the structure of the Gram-Positive Cell Wall? - The gram-positive cell wall is composed of peptidoglycan and teichoic acid. - Teichoic acid can bind with lipids to become lipoteichoic acid, which then binds the cell wall and plasma membrane. - Proteins can also be present on the Gram-positive cell wall. - What are the functions of Lipoteichoic acid? - Cell wall maintenance - Establishing a charge - Enlargement of cells during binary fission ### Gram Negative Cell Wall: - What is the structure of the Gram-Negative Cell Wall? - What is the outermost layer? - The outermost layer is the Outer membrane. - The outer membrane is composed of: - Lipopolysaccharides - Proteins - Phospholipids - What is the middle layer? - The middle layer is called the Periplasmic Space. - The periplasmic space is composed of: - Peptidoglycan - What is the key characteristic of the gram-negative peptidoglycan? - The layer is extremely thin. - Enzymes and transport proteins - What is the function of these? - They protect and make the cell wall (binary fission). - What is the innermost layer? - The innermost layer is the Cytoplasmic Membrane: - The cytoplasmic membrane is composed of: - Phospholipids - Proteins - What is the outer membrane and where is it found? - What are the components of the outer membrane? - Lipopolysaccharides - The lipopolysaccharides form a bilayer outside of the cell wall. - These two are connected through: lipoproteins. - How can lipopolysaccharides pathogenic? - Lipid A is an endotoxin that can be released after bacterial cell death (caused by antibiotics). - What does this do? - This can then cause a cascade of immune responses, which then decrease BP and can lead to shock. - What are the functions of lipopolysaccharides? - Structural integrity of the membrane. - Protection against chemical attacks. - Proteins - What are porins? - Proteins that span the outer membrane and transport molecules. - Phospholipids ### The Gram Stain Reaction: - What dictates the gram stain reactions? - The nature of the cell wall dictates the gram stain reaction. - What is the nature of a Gram-Positive cell wall? - The shrinkage of pores allows for the cells to retain crystal violet better. - The cells have thicker cell walls. - What is the nature of a Gram-Negative cell wall? - The larger pores allow for crystal violet to be washed away by the decolorizer. - The cells have thinner cell walls. ### The Cell Wall is a Selective Target: - What is the cell wall a target of? - Peptidoglycan/ cell wall expansion (inhibits binary fission): - Penicillin - Cephalosporins - Vancomycin - Bacitracin - Cell wall breakdown: - Lysosomes ### Atypical Cell Walls: - What are cells with Atypical Cell Walls? - Acid fast bacterium - What are acid-fast bacterium? - Acid-fast bacterium have thick cell envelopes and contain mycolic acid in their cell walls. - Mycolic acid makes them waxy. - What does this mean for the bacterium? - The acid-fast bacterium experience a longer cellular envelope generation time, in which slows reproduction and development. - What diseases and their bacterium can this diagnose? - Tuberculosis - Etiology: mycobacterium tuberculosis - Leprosy (Hansen's Disease) - Etiology: mycobacterium leprae ### Do All Bacteria have Cell Walls: - Which bacteria don't have cell walls? - Mollicutes - Mycoplasma - What is a characteristic of bacteria without cell walls? - They become pleomorphic. - They can change shape depending on their environment. Specialized Structures: ----------------------- ### Attachment Based Structures: - What bacterial structures can be used for attachment? - Pili (pilus) and fimbriae: - What do the two have in common? - Both are straight filaments of pilin protein. - Both can contribute to biofilms. - What is unique about fimbriae? - Shorter in length - Often more numerous - What is unique about pili? - Longer in length - Often less numerous - What is a sex pili? - A sex pili is a "bridge" between to cells, allowing DNA transfers. ### Mobility Struture: - What bacterial structure allows for movement? - The flagella: - Flagella is composed of flagella protein. - What is the function of the flagella? - Movement - What are the flagellar arrangements? - Peritrichous: - A cell is covered in flagella. - Monotrichous: - A cell has one flagella. - Lophotrichous: - The cell has more than one flagella on one end of the cell. - Amphitrichous: - The cell has one flagella at each end of the cell. - Atrichous: - The cell does not have a flagella - Endoflagella: - Specific to spirochete, on both ends of the bacterium. - What bacterial morphology doesn't have a flagellum? - Coccus (spehere) ### Bacterial Motility: - What are the terms to describe moving towards or away from a substance? - Towards: Positive - Away: Negative - What are the types of bacterial motility? - Chemotaxis: - Bacterial movement regarding nutrients - Phototaxis: - Bacterial movement regarding light - Alternating runs and tumbles: - What is tumbling? - The cell stops and changes directions. - What is an alternating run? - The cell swims with a counterclockwise movement. - Movement towards. Domain Archaea: --------------- - How is domain archaea the most primitive of all domains? - This is because archaea are currently the most related to cells from 4 billion years ago. - Aka little evolutionary change. - What are extremophiles? - Archaea are extremophiles in that they often thrive/ live in extreme environments. - What are some types? - Psychrophile: - Cold environment - Hyperthermophiles - Hot environments - Extreme halophiles - High salt concentration - How are archaea different from other cells? - Unique sequencing or rRNA (ribosomal) - Unique DNA compaction - Cell walls are composed of pseudomurein Eukaryotic Cells: ----------------- ### Eukaryotic Cell Components: - What are the components of all eukaryotic cells? - Cytoplasm - Nucleus - Cytoplasmic membrane - Mitochondria - Endoplasmic reticulum - Golgi apparatus - Vacuoles - Cytoskeleton - Glycocalyx - What are some characteristics found in some eukaryotic cells? - Cell wall - Locomotor appendages - Chloroplasts (allow for photosynthesis) ### Eukaryotic External Structures: - What is the outermost layer an eukaryotic cell can have? - Glycocalyx: - This layer allows for cell-to-cell recognition. - What is present in some eukaryotic cells? - Cell walls: - What are cell walls for plants made of? - Cellulose - What are cell walls for fungi made of? - Chitin ### Nucleus: - What is the nucleus? - A nucleus is a membrane bound organelle composed of a phospholipid bilayer (nuclear envelope) and the cells genetic material. - What lies inside the nuclear envelope? - Nucleoplasm - This is cytoplasm for the nucleus - Chromatin - How is chromatin organized? - Chromatin is wrapped around DNA proteins. - Vertical chromosomes - What is the chromosomal structure necessary for? - Cellular division. - Nucleolus - What is nucleolus? - The nucleolus is the densely concentrated center of the nucleus. - Contains: - RNA and ribosomes - What is the function? - Ribosomal RNA synthesis ### Ribosomes: - What are eukaryotic ribosomes? - Eukaryotic ribosomes are complexes of rRNA and proteins - What is the eukaryotic ribosomes size? - 80s (60s+40s) - What is the function of ribosomes? - Protein synthesis - Where is protein synthesis conducted? - In the cytosol (free floating) - On the outside of the rough endoplasmic reticulum or on the nuclear envelope. ### Vacuoles and Vesicles: - What are vacuoles and vesicles? - Vacuoles are single membranes surround solid or liquid contents. - What are the varieties of vacuoles? - Storage for particles needing to be digested, excreted, or stored. - Contractile: - Contractile vacuoles are present in cells without cell walls, in which they can contract to extract water. - How does this benefit the cell? - This excretion can prevent osmotic shock and cellular lysis - Vesicles are small membrane sacks. ### Endomembrane Secretory Pathway: - What is the Endomembrane Secretory Pathway? - Genetic information originates from the nucleus. ↓ - Ribosomes synthesize proteins in the rough endoplasmic reticulum. ↓ - The endoplasmic reticulum pinches off into a vesicle. ↓ - The vesicle goes to the cis face of the Golgi apparatus. ↓ - The Golgi apparatus then modifies the proteins. ↓ - The Golgi apparatus then pinches off into a vesicle on the trans face. ↓ - This vesicle then exits the cell membrane. ### Endoplasmic Reticulum: - What is the endoplasmic reticulum? - What is the general function of the endoplasmic reticulum? - Both smooth and rough endoplasmic reticulum function as transport systems. - What is the structure of the endoplasmic reticulum? - The endoplasmic reticulum is composed of various flat membrane folds, cisternae. - Where are cisternae also present? - The Golgi apparatus - What are the two types of endoplasmic reticulum? - Smooth: - What is unique about the smooth endoplasmic reticulum? - Lack of ribosomes on the membrane - Produces phospholipids (lipids) - Performs detoxification - Rough: - What is unique about the rough endoplasmic reticulum? - Ribosomes present on the membrane - Protein creation and packaging ### Golgi Apparatus: - What is the Golgi Apparatus? - What is the general function of the Golgi apparatus? - To modify, store, and determine transportation routes of endoplasmic reticulum products. - What is the structure of the Golgi apparatus? - The Golgi apparatus is composed of various flat disc shaped sacs called cisternae. - What are the two faces of the Golgi apparatus? - Cis face: receives / the entrance, faces the endoplasmic reticulum - Trans face: leaves / the exit, faces the plasma membrane ### Lysosomes: - What are lysosomes? - Lysosomes are membrane bound sacks that contain hydrolytic enzymes (modified proteins) - What gives rise to the lysosome? - The Golgi apparatus receives proteins from the endoplasmic reticulum and modifies them into hydrolytic enzymes. - What does hydrolytic mean? - Hydrolytic is broken down into two word parts: Hydr/o (water) and -lytic (to break). - Meaning, water is used to break down molecules. - How does a lysosome work? - A lysosome will merge with vesicles to break down particles/ molecules being carried within. ### Peroxisome: - What are peroxisomes? - Peroxisomes are membrane sacs that contain a variety of enzymes, in which are used to rid the cell of toxic substances. - What is a specific toxic substance? - Hydrogen peroxide - What is hydrogen peroxide? - Hydrogen peroxide is a common byproduct of cellular metabolism. ### Bulk Transport: - What type of cells can engage in bulk/ vesicle transport? - Cells that lack a cell wall can engage in bulk transport by forming membrane-enclosed vesicles. - What are the two types of vesicle movements? - Endocytosis: - The cell engulfs/ take sin extracellular substances. - What are the different types of endocytosis? - Phagocytosis - Cellular eating - Pinocytosis - Cellular drinking - Receptor mediated endocytosis - A process that brings specific molecules in. - Exocytosis: - The cell expels substances. ### Mitochondria: - What is the function of the mitochondria? - The function of the mitochondria is to produce ATP. - What is the structure of the mitochondria? - The mitochondria is composed of two phospholipid bilayer membranes, seen as: - The outer membrane - The inner membrane - The matrix lies inside the inner membrane - What is the matrix composed of? - 70s ribosomes - These ribosomes are the same as? - Ribosomes that are in prokaryotes. - Circular DNA - And metabolic enzymes - The folds of the inner membrane are called cristae. - Do all cells have the same number of mitochondria? - No, they can vary in number. - What are shared traits between mitochondria and chloroplasts? - They both divide independently of the cell. - Binary fission - Both are thought to have originated as a bacterium phagocytized by eukaryotic cells. - Both are not present in prokaryotes. ### Chloroplasts: - What is the function of chloroplasts? - Chloroplasts are light harvesting structures allow cells to go through photosynthesis. - What organisms have chloroplasts? - Plants - Algae - These two are primary producers of organic nutrients (carbohydrates) and oxygen. - What is the structure of chloroplasts? - Chloroplasts is composed of a double membrane. - The stacks inside the chloroplasts are called grana or granum. - The individual disks composing the grana are called thylakoids. - 70s ribosomes and circular chromosomes - What are the origins of chloroplasts? - Chloroplasts are seen to originate from cyanobacteria through the process of endosymbiosis. - What are cyanobacteria? - Photosynthetic bacteria (oxygenic photosynthesis) - They are found in freshwater, marine, and terrestrial environments. - What is the significance of cyanobacteria? - Oxygen production - Nitrogen fixation - Symbiotic relationships with plants, fungi, and algae ### Cytoskeleton: - What is the cytoskeleton? - The cytoskeleton is an extension network of fibers and tubules. - The cytoskeleton has motor proteins that move along the fibers and tubules. - What are the functions of the cytoskeleton? - The cytoskeleton anchors organelles - Moves RNA and vesicles - This is done through a road track like movement, with motor proteins moving along the microtubules. - Permits shape changes and movement - What are the three main types of cytoskeleton elements: - Actin filaments - Red or pink in color. - Known for cellular shape changing - Intermediate filaments - Tan in color. - Known for nucleus shape. - Microtubules - Green in color. - Hollow cylinders that allow for: - Maintaining cell shape - Essential in cell division - Vesicle transportation and motor proteins Eukaryotic Movements: --------------------- - What are the structures used in eukaryotic movements? - Flagella - Cilia - Pseudopodia - What are pseudopodia? - An amoeboid type movement in cells without cell walls - Also called false feet or projections. ### Eukaryotic Flagella: - How do eukaryotic flagella different from prokaryotic flagella? - The flagella are 10x thicker - Structurally complex - Covered by an extension of the cell membrane - Longer with the 9+2 arrangement ### Eukaryotic Cilia: - What are the characteristics of Cilia? - They are similar in structure to flagella - They are shorter and more numerous - Only present in a single group of protozoa and certain animal cells - What is the function of cilia? - Feeding and filtering functions History of Eukaryotes: ---------------------- - Endosymbiotic Theory: - Eukaryotes formed from a union of small aerobic prokaryotes with larger anerobic prokaryotes - What does this mean? - Smaller prokaryotes come internal parasites (used for cellular respiration). - What does this mean for symbiotic organisms? - Smaller parasites cannot exist independently. - The larger cell becomes dependent on the smaller parasites for ATP or photosynthesis production. Unit One (15.1-15.4) Microbial Pathogenicity: ============================================= Normal Microbiota: ------------------ - What is normal microbiota? - Normal microbiota are organisms that colonize the body's surfaces without normally causing disease. - This consists of a large and diverse collection of microbes on and in the body. - What terms are normal microbiota interchangeable with? - Normal flora - Indigenous microbiota - Indigenous microflora ### Types of Microbiotas: - What is resident microbiota? - Microbiota that are always present, most being neutral. - What is transient microbiota? - Microbiota that are present for short periods of time in the body. Colonization and Infection: --------------------------- - Colonization leads to infection. ### Colonization: - What is colonization? - Colonization is the attachment of microbes in the body. ### Infection: - What is infection? - When microbes enter and multiply in the body. - These microbes may or may not cause illness and can then either present themselves as asymptomatic or lead to disease. Disease: -------- - What is a disease? - Disease is a condition in which homeostasis is altered. - What are the two types of microbes that can cause disease? - Endogenous: - Disease caused by microbes in the body. - Exogenous: - Disease caused by microbes outside the body. ### Infectious Disease: - What is an infectious disease? - An infectious disease is a disease caused by a microbe. - What are the characteristics of infectious diseases? - Signs - Observable characteristics. - Symptoms - Subjective, defined by the patient. - Syndrome - A collection of signs and symptoms. - Asymptomatic - Sequela - Effects seen after recovery, aftermath. ### Classification of Disease: - What are Infectious vs. non-infectious diseases? - An infectious disease is a disease caused by a microbe. - A non-infectious disease is a disease not caused by a microbe. - What are communicable vs. non-communicable diseases? - Communicable diseases will spread from person to person. - Non-communicable diseases will not spread from person to person. - What are zoonotic diseases? - Infections indigenous to animals that are transmitted to humans. ### Periods of an Infectious Disease: +-----------+-----------+-----------+-----------+-----------+-----------+ | Order: | 1 | 2 | 3 | 4 | 5 | +===========+===========+===========+===========+===========+===========+ | Name: | Incubatio | Prodromal | Illness | Decline | Convalesc | | | n | | | | ence | +-----------+-----------+-----------+-----------+-----------+-----------+ | Definitio | Initial | The onset | Signs and | The | Healing, | | n: | contact | of | symptoms | immune | repair, | | | at portal | disease. | are most | system | and low | | | of entry. | | severe, | kicks, | microbial | | | | | there is | there is | levels. | | | The agent | | rapid | microbial | | | | is | | microbial | decline. | | | | multiplyi | | multiplic | | | | | ng | | ation. | | | | | but | | | | | | | hasn't | | \- Acme: | | | | | caused | | gradual | | | | | damage to | | | | | | | elicit | | \- | | | | | symptoms. | | Fulminati | | | | | | | ng: | | | | | | | sudden | | | +-----------+-----------+-----------+-----------+-----------+-----------+ ### Acute, Chronic, and Latent Disease: - What are acute diseases? - Diseases with short duration and symptoms appear suddenly. - Can be treated with medication. - Can be fatal. - What are chronic diseases? - Diseases that develop slowly, and last months, years, or a lifetime. - Can be fatal. - What are latent diseases? - Diseases that can last for years with extended dormant periods. - The organism is present without active replication. - No symptoms during dormant periods; disease can recur later. - Is screening recommended? - Yes. Robert Koch's Postulates: ------------------------- A close-up of a text AI-generated content may be incorrect. - What is the general process of this experiment? - A diseased organism will have their causative agent collected and plated, this will be done until there is a pure culture. - That pure culture will then be inoculated into a healthy organism, in which it should cause the living organism to be diseased in the same as the initial diseased organism. - The same causative agent must be reisolated from the inoculated organism. - What are the exceptions to Koch's postulates? - Microbes (specifically viruses) cannot be grown on artificial media. - More than one microbe can produce the same disease - Diseases can be caused by combinations of pathogens - One microbe can cause multiple diseases - There are ethical considerations for strictly human diseases that cannot be tested on a human model. Pathogens: ---------- - What is a pathogen? - A pathogen is a microorganism that causes disease. - Reminder, most microbes do NOT cause disease. - What microorganisms cause disease? - Viruses - Bacteria - Fungi - Parasites - What are parasites? - Parasites are organisms living on or in a host, benefiting at the host's expense. - What are the types of parasites? - Ectoparasites: - Parasites that live on the surface of the host. - Endoparasites: - Parasites that live in the host's body. - What do pathogens do? - Pathogens invade the host and cause disease. ### Pathogenicity: - What is pathogenicity? - Pathogenicity is the ability of a pathogen to cause disease. - What are the factors that influence pathogenicity? - Invasion - The pathogens' ability to enter and colonize the host. - Evasion - A pathogen's mechanisms to evade or inhibit the host's immune response. - Toxin production - The ability to produce toxins that damage the host. - Adherence - The ability to attach to host tissues. ### Virulence: - What is virulence? - The degree of pathogenicity (severity) of a pathogen. - What virulence factors? - Virulence factors are molecules or structures that enhance a pathogen's pathogenicity. - Host factors: - Host immune status - Genetic factors - Pre-existing conditions - What are diseases with low virulence? - Rhinovirus (cold like symptoms) - What are diseases with high virulence? - Ebola Virus (hemorrhagic fevers) ### Invasiveness: - What is invasiveness? - Invasiveness is the ability of a pathogen to spread within the host. - What are invasiveness factors? - Enzyme production - The ability for pathogens to create enzymes. - Cell penetration - Allows for pathogen multiplication while evading immune detection - Immune evasion - Motility - Pathogen movement. ### Primary vs. Opportunistic Pathogens: - What is a primary pathogen? - A primary pathogen is a pathogen that can cause disease in healthy individuals. - What is an opportunistic pathogen? - An opportunistic pathogen is a pathogen that causes diseases in immuno-compromised individuals. - Also referred to as potential pathogens. - What are conditions ideal for opportunistic pathogens? - Weakened immune system - Pathogen relocation within the body - Fluctuations in normal flora - Uneven balance - What is an example of a fluctuation in normal flora? - The use of antibiotics can kill good and bad bacterium, which gives space to let normally controlled flora experience overgrowth. - This leads to an infection. ### Host-microbe Relationships: - What is symbiosis? - Symbiosis is a term describing the relationship between two organisms. - What are the symbiosis types between hosts and microbes? - Mutualism - What is mutualism? - Both organisms benefit. - Commensalism - What is commensalism? - One organism benefits, while the other is neutral. - Antagonism - What is antagonism? - One organism benefits, the other is harmed. - Parasitism - What is parasitism? - The parasite benefits, while the host is harmed. Stages of Pathogenesis: ----------------------- ### Step 1- Exposure - What is exposure? - Exposure is the stage in which the pathogen encounters the host. - How does the pathogen enter the body? - Portals of entry. - What is a portal of entry? - A portal of entry is a site in which the host enters the body. - What are the two types of microbes that pass-through portals of entry? - Exogenous: - Microbes that originate outside the body - Endogenous: - Microbes that already exist in/ on the body - What are the major pathways? - Skin - Mucous membranes - What are some specific examples? - Gastrointestinal tract (oral) - Respiratory tract - Parenteral route - The parenteral route in a portal of entry created by a piercing of the skin or mucosal membrane - Ex. Contaminated needles - Transplacental - The transplacental route is when microbes pass across the placenta from the blood of the mother to the fetus. - Perinatally - The transmission of infections by passing through the birth canal ### Step 2- Adhesion: - What is adhesion? - Adhesion is the attachment of the pathogen to host tissues. - What is adhesion reliant on? - Adhesion is reliant on the binding between specific molecules of host and pathogens. - What are binding molecules? - Adhesins - What are some examples of Adhesins? - The end of fimbriae - Capsules - How is host range important? - Host range is important because it is the range in which pathogens can bind to specific host cells/ tissues. - This is essential for colonization, incubation, and infection. ### Step 3- Invasion: - What is invasion? - Invasion is the pathogen surviving host defenses and disseminating throughout host tissue. - What is phagocytosis? - Phagocytosis is the process in which white blood cells engulf and destroy pathogens. - What are virulence factors in relation to phagocytosis? - Bacterial capsule - The bacterial capsule makes it difficult for WBCs to phagocytize pathogens, increasing their virulence - Antiphagocytic chemicals - Antiphagocytic chemicals allow for pathogens to: - Prevent lysosome and vesicle fusion - Leukocidins - Destroy WBCs ### Step 4- Infection: - What is infection? - Infection is the stage in which the pathogen establishes itself, replicates, and causes damage, leading to disease symptoms. - What are the types of infection? - Localized - Systemic - Focal - An infection in one area that can spread and cause a secondary infection. - What is a secondary infection? - A secondary infection is an infection that takes place during or after treatment of the primary (initial) infection. - Mixed infection - An infection caused by \>2 microbes, at the same time and area. ### Step 5- Transmission of Disease: - What is the transmission of disease? - The transmission of diseases is when pathogens vacate the host. - How is this done? - The transmission of disease is done through the portals of exit. - What is a portal of exit? - An avenue of departure for pathogens to exit the host. - What are some portals of exit? - Bodily fluids - Ex. Mucus, sputum, and blood - Excretion - Ex. Feces and urine Factors That Influence Pathogenicity: ------------------------------------- - What are the factors that influence pathogenicity? - Virulence - The degree of severity a pathogen can cause. - Attenuation - The reduction of virulence or pathogenicity - What does this mean? - This is when the severity or a pathogens ability to cause disease is weakened. - Transmission - How quickly or likely? - Portal of entry - If the pathogen can properly adhere and colonize tissue within their host range. - Invasiveness - The pathogen's ability to invade and live inside of a host. ### Virulence Factors for Bacterial Pathogens: - What are the Virulence Factors for Bacterial Pathogens? - Adaptations to invade and establish infections. - Why is this important? - These adaptations can allow a pathogen to better invade, cause infections, and damage, allowing for the potential of increased severity. - Adhesions: - Cell wall components - Capsules - Both useful for attachment and protection from phagocytosis - Fimbriae and pili - Flagella - Important for mobility - Bacterial Exoenzymes: - Bacterial Exoenzymes can increase invasiveness. - What do enzymes do? - Enzymes work as catalyst to accelerate reactions to cause damage and breakdown host tissue - "Spreading factors" - What are some Bacterial Exoenzymes? - Hyaluronidase: - Breaks down hyaluronic acid which acts as cellular glue for epithelial cells. - Collagenase (next barrier): - Breaks down collagen. - What are some Bacterial Exoenzymes that act on host cells or tissues? - Coagulase: - Released by bacteria to form a clot around the pathogen, aiding in invasion (evade) and infection (replication). - Coagulase produces a clot around the bacterium, allowing them to go undetected by the immune system, and allowing them to replicate inside the clot. - Kinases: - Released by bacteria to break down the clot formed around the pathogen, aiding in infection (establishment) and its invasiveness (ability to spread). - Kinase breaks down the clot made by the bacterium, releasing the pathogen. - Catalase: - Released by bacterium to neutralize hydroperoxide. - 2H~2~O~2~ 2H~2~O + O~2~ - Why? - Hydrogen peroxide is harmful to bacteria. - Bacterial Toxins: - What is a toxin? - Toxins are a biological poison that causes damage to tissues. - What is toxigenicity? - Toxigenicity is the ability of a pathogen to produce toxins. - What is Toxemia (intoxication)? - Toxemia is the presence of toxins in the blood. - What are the two types of toxins? - Exotoxins: - Exotoxins are toxins produced by the bacterium and are then released - Endotoxins: - Endotoxins are toxins produced by the bacterium that then become part of the cell wall. - Why is this a problem? - When a bacterium dies, the toxin will then be released. - Where is this seen? - This is seen in gram negative cells that contain lipid A (in phospholipids). - What are common bacterial exotoxins? - Membrane disrupting toxins: - Membrane disrupting toxins can be categorized into three groups based on how destructive they are. - Hemolysis: - The breakdown of red blood cells: - Alpha: - Partial breakdown - Green in color - Beta: - Complete breakdown - Transparent - Gamma: - No breakdown - How is hemolysis beneficial to bacteria? - The breakdown of RBCs releases iron, which is favorable for bacterial growth. Unit One (16.1-16.4) Disease and Epidemiology: ============================================== Epidemiology: ------------- - What is epidemiology? - Epidemiology is how diseases are spread. ### Study of Disease in Populations: - What are terms related to diseases in populations? - Index case: - The first case of a disease. - Incidences vs. Prevalence - What is incidence? - Incidence is the number of new cases for a certain population of a certain time. - What is prevalence? - Prevalence is the total number of cases of a disease over a certain population of in a certain time. - Morbidity vs. Mortality - What is morbidity? - Morbidity is the total number of people with a disease (all diseases) in a certain population of a certain time. - What is mortality? - Mortality is the number of deaths due to a disease in a certain population of a certain time. - How are diseases within populations classified? - Endemic: - Diseases continually present, usually at low levels. - Sporadic: - Disease that has random unpredictable outbreaks. - Epidemic: - Disease that has a sudden increase in population larger than originally predicted. - Pandemic: - Diseases that spread worldwide. ### Etiology agent: - What are etiologic agents? - Etiologic agent's are pathogens that caused disease. - What are the two ways that sources can spread? - Common source of spread: - This is when a pathogen originates from a common location or source, this often causes a fast spread and fast decline. - Propagated spreads: - Horizontal transmission: This is when pathogens spread from person to person, experiencing a slow spread and slow decline. ### Public Health Organizations: - What is the Center for Disease Control: - The CDC is a public health organization that sets guidelines for safety, store infrequently used drugs, and the Morbidity and Mortality Weekly Report. ### Notifiable diseases: - What are Notifiable diseases? - Notifiable diseases are disease that must be reported if found in a patient. Pathogens: ---------- ### Where pathogens persist: - What is a Reservoir? - Reservoirs are permanent places for an infectious agent reside. - These can be living or nonliving. - What is a Carrier? - A carrier is a subclinical or inapparent infection. - These carries can be: - Passively infected: able to spread pathogens, but not infected - Asymptomiatic: Lack of signs or symptoms - Active Disease Transmission: --------------------- - What are the three types of disease transmission? - Contact transmission: - Direct contact transmission: - Vertical - What is vertical direct contact transmission? - This is parent to offspring transmission. - Horizontal - What is horizontal direct contact transmission? - This is person to person transmission. - What are the types? - Contact - Droplet - Indirect contact transmission: - Fomites - What are fomites? - Fomites is transmission through inanimate objects. - Vehicle transmission - Vector transmission ### Direct Contact Transmission of Infectious Disease: - What is vertical transmission? - This is parent to offspring transmission. - How can this be done? - Transplacental - Parturition (childbirth) - Breastfeeding - What is horizontal direct contact transmission? - This is person to person transmission. - How can this be done? - Contact (touching) - Droplet (closer in proximity, larger in size) - What are some examples? - Sneezing - Coughing - Talking ### Indirect Contact Transmission of Infectious Disease: - What are fomites? - Fomites are intimate objects that spread disease. - How can this be done? - Parenteral transmission: (contaminated needles) ### Vehicle Transmission: - What are the types of vehicles (non-living) transmission? - Airborne - Airborne particles remain suspended in air longer than droplets, are smaller in size and travel a greater distance. - Examples? - Dust - Droplet nuclei - Waterborne: - Waterborne is when there is contaminated water. - Foodborne, Fecal-Oral: - This is when there is contaminated food. ### Vector Transmission: - What is mechanical transmission? - Mechanical transmission is done through mechanical vectors. - Mechanical vectors spread pathogens (like a fly). - What is biological transmission? - Biological transmission is done through biological vectors (mosquitoes with pathogens inside them). Healthcare Associated Infections: --------------------------------- ### Nosocomial Infection: - What is a nosocomial infection? - A nosocomial infection is an infection acquired while at the hospital. - What are the most common nosocomial infection? - UTIs - Surgical wounds - Respiratory infections - What is the cause? - Lack of infection control - Types of Nosocomial Infection: - Exogenous - Something outside of the body that makes you sick. - Endogenous - Something inside your body that makes you sick. - Iatrogenic - Infections caused by medical procedures - Nosocomial Transmission: - What are the common nodes of nosocomial transmission? - Urinary Tract - Surgical Wounds ### Communicable Disease: - How are communicable diseases controlled? - Quarinitine - Quarantine is when someone is not sick but may be exposed. - Isolation - Isolation is when someone is sick and must be separated. - Immunization (Vaccinations) - Herd immunity - Herd immunity is when a person without immunity is surrounded by many immune people. - Vector Control (living) - Vector control can be done through habitat control. Infectious Disease: ------------------- ### Past: - What was the number one past killer? - Infectious disease. ### Present: - Was is the current number one killer? - Cancer. - What are current factors that can negatively affect this? - Risk factors have changed: - Drug resistance - Anti-vaccination movements - Emerging diseases - Remerging diseases - What are the barriers to disease eradication? - Availability of meds and doctors - Adaptability of organisms - Social behaviors and conditions - Immigration and travel