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Med Micro
Exam 1
| Question | Answer |
|---|---|
| types of organisms to be studied in this class | protozoans, fungi, algae, bacteria, helminths, viruses, archaea |
| ubiquitous | microorganisms are found EVERYWHERE |
| Epidemiology | determines the source, cause, and mode of transmission of disease |
| Three domains... | Eukaryotes, Prokaryotes, Archaea |
| Bacteria | prokaryotic, 10 million species, found in spherical, spiral, and rod shapes, some can photosynthesize, small portion cause disease or spoil food |
| Archaea | live in extreme environments....considered prokaryotes because no nucleus |
| Algae | eukaryotes, photosynthetic, uni and multicellular, both salt and fresh waters...not so involved in human illness |
| Protozoa | eukaryotes, single celled organisms that live in association with plants or animals , can photosynthesize, 30 thousand species |
| helminths | eukaryotic, parasitic worms, can live in the digestive tract of animals/humans |
| fungi | eukaryotes, (yeast, mushrooms, mold) unicellular or multicellular, tend to live in their own food supply |
| Viruses | DNA or RNA and protein only...not living, infect organisms in order to replicate |
| ionic bonds | between ions of opposite charge |
| covalent bonds | between atoms that share electrons |
| hydrogen bonds | between a polar molecule including hydrogen and another polar molecule |
| properties of water | polar, cohesiveness, high specific heat, important solvent |
| the biomolecules | lipids, proteins, nucleic acids, carbohydrates |
| important carbohydrates | cellulose, chitin, peptidoglycan, lipopolysaccharide, glycocalyx |
| important lipids | triglycerides, phospholipids, steroids, waxes,....... cholesterol, fatty acids, ketone bodies |
| polar molecules | water, -OH, -C=O, -NH2, -SH, -OPO3..... hydrophilic |
| nonpolar molecules | hydrocarbons....hydrophobic |
| relative percentages of organic compounds in cells | in bacteria.... 70% water.....the organic compounds in the remaining 30%....half is protein, a third nucleic acid, a little lipid and a little carbohydrate |
| Roles of carbohydrates | energy supply in all cells, have a role in cell wall structure, make up the backbone of nucleic acids (pentose sugar)- polysaccharides are polymers of monosaccharides |
| Lipids | hydrophobic molecules found mostly in cell membranes, good energy source for cells |
| a triglyceride | glycerol backbone and three fatty acid tails...storage form of fatty acids. The melting point depends on saturation. More saturated=fat, less saturated=oil |
| phospholipid | important membrane lipid, glycerol backbone with two fatty acid tails and a phosphate/alcohol head group, are an amphipathic molecule |
| phospholipid bilayer | has hydrophobic interior, hydrophilic exterior |
| Steroids | example: cholesterol, also amphipathic, also in membrane |
| Waxes | typically in plants...coating the outer surface of cells |
| Proteins | responsible for catalysis, structure, mobility, cell regulation, transport, hormone signaling, defense, and storage.....made up of 20 different amino acids |
| amino acid | amino end, carboxyl end, H, R group with different properties that give the identity |
| linking amino acids | amino acids join into a chain called a polypeptide....dehydration reactions form the peptide bonds between backbone atoms |
| primary structure | polypeptide chain, bonds between backbone atoms of the amino acids |
| secondary structure | alpha helices and beta sheets, common structures, linkages are Hydrogen bonds between backbone atoms |
| tertiary structure | weak interactions between the R groups of amino acids (ionic, Hydrogen, disulfide bridges, hydrophobic interactions) |
| quaternary structure | multiple folded polypeptides come together...also held by weak forces |
| Nucleic acids | DNA is the genetic material of all life forms (except some viruses) RNA helps copy and translate gene information into proteins |
| the bases of DNA | adenine, guanine, cytosine, thymine (A+G are purines) (C+T are pyrimidines)...(G+C make three H bonds....better hold) |
| the bases of RNA | adenine, guanine, cytosine, uracil |
| ATP | an adenosine with three phosphates...is a nucleotide precursor to DNA...important for energy in the cell |
| DNA structure | 2 complimentary, antiparallel strands, base form rungs in-between the right handed double helix |
| DNA | genetic material for all life forms...contains detailed instructions for each organism's identity, polymer of individual nucleotides...the order determines what proteins are made in the cell |
| RNA | also long polymer of nucleotides, but single stranded. relays the information coded in the DNA so proteins can be made...transcription and translation |
| RNA structure | contains ribose sugar instead of deoxyribose...has U instead of T to pair with A, typically single stranded |
| many types of RNA | mRNA, rRNA, tRNA, |
| Inoculation | a sample of microbes must be introduced into an environment in which they are able to grow...involves specialized containers with nutrient mediums providing the nutrients for the microbes |
| Incubation | kept in a temperature controlled chamber to encourage growth and multiplication..can also control atomospheric gases...CO2 or O2 |
| liquid media | broths, will not solidify at temperatures above freezing |
| solid media | 1-5% agar, allows media to stay in place when containers are moved |
| Defined media | a media in which all the ingredients and their amounts are precisely known...have an exact formula- can have organic and inorganic materials...used so that metabolic processes of the microbe can be precisely monitored |
| Complex media | contains extracts of plants, animals, yeasts....rich supply of nutrients, can't determine exact amounts of each component |
| Enriched media | contains a complex organic substance like blood, serum, growth factors etc. that the species needs to grow... |
| Bacteria that require growth factors and complex nutrients | are called fastidious |
| Differential media | designed to visibly display differences in microbes (colony color, media color, gas bubbles, precipitates) as they grow... differentiate one type from another |
| Selective media | allows one type of growth but not others.....can be used to isolate a specific microorganism from a sample containing many different species |
| Isolation techniques | streak plates and pour plates... an individual call that is separated form other cells will grow into a discrete mound called a colony |
| Colony | an individual call that is separated form other cells will grow into a discrete mound called a colony |
| bright field microscope (aka compound microscope) | light transmitted through a specimen...specimen absorbs some light...produces darker image. limit is 2,000x and may need oil |
| calculating magnification | multiply objective lens and ocular lens |
| dark field microscope | adds a stop to condenser of bright field... all lights blocked except the light scattered off the edge of the specimen- dark background but bright outline of specimen |
| Phase contrast | transforms the subtle changes in light waves passing through a specimen into differences in light absorbance... used to observe bacterial endospores, granules, and organelles---can view things live! no need to heat-fix |
| Fluorescence | add fluorescent material to target particular parts of the cell, shows up in different colors |
| Confocal | uses laser beam of light to scan various depths in the spectrum to deliver a sharp image of just a singular plane....looks 3D |
| Electron microscopes | (SEM and TEM) can examine much smaller objects!...use electrons instead of light |
| resolution | gets better with light of shorter wavelengths....electrons have very short wavelength...better resolution |
| Transmission Electron Microscopes | produce image by transmitting electrons through the specimen....has to be extremely thinly cut...electrons do not penetrate well |
| Scanning electron microscope | bombards surface of the metal-coated specimen with electrons...scanning back and forth- best for studying the surfaces of viruses and bacteria |
| stains | staining enhances visualization, gives colors to cells or parts of cells through a chemical reaction (can be basic + or acidic-) |
| simple stains | mostly basic (+) and acidic (-) |
| Differential stains | use two different colored stains (primary stain and counter stain) to distinguish between two cell types |
| Gram stain | distinguish between different bacteria due to cell wall structure |
| Acid Fast Stain | used to identify bacteria with a heavy waxy coating on their cell walls |
| Special stains | used to emphasize certain cell parts that are often difficult to stain (capsules, endospores, flagella) |
| cell theory | all life consists of one or more cells---cells only arise from pre-existing cells |
| cell | the basic unit of structure for all organisms |
| characteristics of all cells | most are relatively small, 1 to 100 micrometers, all oxidize sugar molecules for energy, all are surrounded by membrane, all have double stranded DNA for genome, all use ribosomes for protein synthesis |
| bacteria sizes | about 1 micrometer, 0.2 to 2 micrometers in diameter, 2-8 micrometers in length |
| Coccus | spherical or round in shape (can be in 2 -Diplococci) (in 4-Tetrad) (in 8- Sarcinae) (in chain- Streptococci) (In bunch- Staphylococci) |
| Bacillus | cylindrical or rod like in shape...most appear as single cells, but can have 2-Diplobacilli, or a chain- Streptobacilli, or Palisades each connected at only one end...accordion fold |
| Vibrio | look like curved rods and have a comma-like shape |
| Spirillum | have a corkscrew-like shape, are fairly rigid, have many flagella for motion---typically the flagella are at both ends of the bacteria |
| Spirochete | also helical, but are more flexible and use axial filament for motion---an endoflagella (on the inside) for movement |
| Flagella | long filamentous appendages that propel bacteria through an aqueous environment |
| three parts of the flagella | filament, hook, basal body---allows to turn in a 360ยบ rotation all spirilla, half of bacilli, and small number of cocci have flagella |
| flagella participate in chemotaxis | bacteria can move to or from light, moisture, other chemicals.. |
| Axial filaments (periplasmic flagella) | internal flagellum in spirochetes....bundles of fibrils that spiral around the cell |
| Fimbriae | one cell can have a few to hundreds...help the bacteria to adhere to each other, and allowing attachment to epithelial cells in the body...NOT FOR MOTILITY |
| Pili | form an attachment between two bacterial cells that allow one cell to transfer DNA to a neighboring cell....NOT FOR MOBILITY |
| Nanotubes | much smaller than pili...very thin tubular extensions of cytoplasmic membrane that bacteria use to transfer amino acids to each other or harvest energy by shuttling electrons from an electron rich surface in the environment |
| from inner to outermost...bacterial layers | cytoplasmic membrane---> peptidoglycan cell wall---> S layer---> Glycocalyx |
| S layer | single layer of many thousand cross linked proteins....protein chain mail.....usually only produced in severe environmental conditions for protection , can be used in attachment as well |
| Glycocalyx | sugar substance secreted on to the outermost cell surface...usually viscous and helps protect the cell-aids in attachment( can be either a capsule or slime layer) |
| Capsule | if the glycocalyx is organized and firmly attached to the cell wall |
| Slime layer | if the glycocalyx is unorganized and only loosely attached to the cell wall |
| the cell envelope | a term referring to the cytoplasmic membrane and the peptidoglycan cell wall....and in some cells the outer membrane...act together as a single protective unit |
| Cell wall | semi-rigid structure responsible for the shape of the cell, almost all prokaryotes have a cell wall... Major component---peptidoglycan |
| peptidoglycan | long glycan chains cross linked by short peptide fragments (protein and carb) it is often targeted by antibiotics |
| Gram positive bacteria | have cell walls made up of MANY layers of peptidoglycan, embedded with a polymer called techoic acid |
| techoic acid | functions on cell wall maintenance and enlargement during cell division |
| Gram negative bacteria | have only a thin layer of peptidoglycan, but have an outer cell membrane like the cytoplasmic membrane but with specialized types of polysaccharides and proteins------have no techoic acid |
| periplasmic space | the space between the inner and outer membranes |
| non-typical cell walls | can be different cell envelope structures than Gram pos or neg or no cell wall at all.....some can have cell walls mainly made up of unique lipids |
| cell walls with mycotic acid | gives the cell walls of these bacteria a waxy nature (leprosy and tuberculosis) |
| the cytoplasmic membrane | a thin structure inside the cell wall that encloses the cytoplasm of the cell...a lipid bilayer made up of 30-40% lipid, 60-70% protein |
| membrane proteins | act as enzymes for cell wall synthesis and for energy metabolism....anchor DNA to membrane during replication, act as cell surface receptors ....transport essential molecules and nutrients |
| the DNA of most prokaryotic cells | usually found as a single, circular chromosome |
| bacteria have no nucleus, but there is a nucleoid | their DNA is aggregated in a dense area of the cell called the nucleoid |
| plasmids | smaller pieces of DNA that carry additional genes used by the cell--can be transported with pili....not essential for growth and development, but can give survival tools |
| ribosomes | sites of protein synthesis...large RNA/protein complexes that function to assemble amino acids into polypeptide chains based off RNA templates |
| Inclusion bodies | sites in the cytoplasm where particular molecules have accumulated...can store nutrients to respond to periods of low food availability, or store gas to provide buoyancy in an aquatic environment |
| cytoskeleton | long polymers of proteins that function in cell shape and cell division...arranged in helical ribbons just under the cytoplasmic membrane |
| endospores | dormant bodies that allow bacteria to survive extreme heat, lack of water, and exposure to toxic chemicals......can be anywhere, very hard to kill |
| Archaea | classified as prokaryotes, but share many eukaryotic features (ribosomal RNA and protein synthesis ribosomal subunits) ...they live in extreme environments and can be called extremophiles |
| characteristics of all eukaryotic cells | cell membrane, nucleus, mitochondria, Golgi apparatus, vaculoles, cytoskelekton, and glycocalyx....some have a cell wall, appendages for moving, or chloroplasts |
| flagella and cilia in eukaryotes | used for cellular locomotion or for moving substances along surfaces of the cell common in protozoa, algae, and a few fungi and animal cells |
| eukaryotic flagella | are structurally different than prokaryotic flagella...more of a whip like motion than the rotation in prokaryotes....is ten times thicker, covered by an extension of the cell membrane |
| eukaryotic cilia | similar to flagella, are shorter and more numerous....found only on one kind of protozoa and certain animal cells....they beat back and forth like oar strokes ...not in bacteria! |
| eukaryotic glycocalyx | the outermost layer that comes into direct contact with the environment...can be like a slime layer or a capsule...contributes to protection, adherence of cells to surfaces, reception of signals form other cells and from the environment |
| many plant cells and fungi have cell walls (protozoa, helminths, and animal cells don't) | these cell walls are much simpler than the prokaryotic cell wall, they are rigid and provide structural support and shape.....different in chemical composition from bacteria/archaea |
| cell walls in eukaryotes | have an inner layer of polysaccharide fibers (chitin or cellulose) and an outer layer of mixed glycans |
| cell membrane eukaryotes | typical bilayer of phospholipids in which protein molecules are imbedded serves as the selectively permeable barrier for the cell |
| Nucleus! makes the eukaryotes unique | a compact sphere that is the most prominent organelle of eukaryotic cells...houses genetic information...surrounded by a double membrane....nuclear envelope...has pores |
| nucleolus | the site for ribosomal RNA synthesis and a collection area for ribosomal subunits |
| ER (rough and smooth) | an extensive network of flattened membrane used for transport and storage |
| Rough ER | a continuation of the outer membrane of the nuclear envelope and extends into the cytoplasm....has ribosomes on the surfacee |
| Smooth ER | extends from the rough ER, has no ribosomes on the surface, functions in nutrient processing, and site of synthesis of phospholipids, fats, and steroids |
| Golgi apparatus | flattened sacs called cistern...process the proteins destined for the plasma membrane or for release to the outside of the cell (site of post translational modification)....always closely associated with the ER |
| Lysosomes | enclosed vesicles that bud off the Golgi.....contain powerful acids and enzymes able to break down various molecules.....digest food particles, protect against invaders, clean up cell debris |
| Mitochondria | double membrane-bound organelles, main site of ATP production....has smooth continuous membrane forming the external contour, and an inner folded membrane that fits inside (folds are called Cristae...have enzymes and electro carriers needed in respiration |
| Chloroplasts | only in plants and algae...responsible for photosynthesis energy of sunlight and CO2 is converted into chemical energy and O2 |
| Ribosomes | sites of protein synthesis, a little larger in eukaryotes than prokaryotes...can be free in cytoplasm or attached to the rough ER (there are enough differences that bacterial ribosomes can be targeted by antibiotics) |
| Fungi | can be yeasts (round shapes, performs asexual reproduction...swells into buds) can be hyphae (long, threadlike cells.....bodies of filamentous fungi or molds) |
| Fungi as pathogens (only about 270 species that effect humans) | mycoses (fungal infections) vary in the way the pathogen enters the body and the degree of tissue involvement they display....also pathogenic to agriculture, causing disease in animals that eat rotten crops |
| fungi are saprobes | they acquire nutrients from the remnants of dead plants and animals in soil or aquatic habitats |
| fungi are parasites | they can live on the bodies of living animals or plants (a living host) |
| Fungi have crazy enzymes | the fungi penetrate a substance by secreting enzymes that reduce it to small molecules it can absorb...wide range of capabilities! |
| primary reproductive mode of fungi | production of spores (asexual and sexual) spores are responsible for multiplication, dispersal, and helping gian genetic diversity |
| Asexual spores | product of mitotic division of a single parent cell |
| Sexual spores | formed by the fusing of two parental nuclei followed by meiosis |
| Protozoa characteristics | all single celled, have remarkable movement, feeding, and behavior, only a few are pathogens.....have all the same major organelles as eukaryotes except chloroplasts |
| cytoplasm of prokaryotes | divided into an outer layer--ectoplasm--- and granular inner region---endoplasm |
| protozoan mobility | can move through fluids with pseudopods, flagella, or cilia....lack a cell wall so have lots of flexibility (shape can remain constant or be constantly changing) |
| protozoans must live in moisture | can scavenge dead plants or animal debris...or eat live cells of bacteria and algae----live in fresh and salt water, soil, plants and animals, few in extreme environments |
| the motile feeding stage of protozoa | the trophozoite stage |
| other stages of the protozoa life cycle | can enter into a dormant, cyst stage--in hostile environments, will become trophozoite again when exposed to proper environment |
| Helminths characteristics | multicellular organisms, visible to eye.....tapeworms, flukes, and roundworms, have organs and organ systems |
| helminth life cycle | can be picked up by host either orally or by penetration of skin, typically being stepped on barefoot......sources of human infection are contaminated food, soil, water, or infected animals |
| cytoskeleton for eukaryotes | a flexible framework of molecules that crisscross the cytoplasm of a cell, anchors organelles, provide a means of movement to RNA and vesicles in the cell, and permit some cell shape change |
| three kinds of cytoskeletal filaments | actin filaments, intermediate filaments, microtubules |
| viral characteristics | intracellular parasite of all kinds of cells....more viral particles on earth than all bacteria and archaea....SUPER tiny....they are not cells- dont meet the qualifications for living |
| viruses are not cells | lack enzymes needed for most metabolic processes...lack machinery for making proteins |
| build of a viral particle | a very compact and economical....a protein shell around a nucleic acid (either DNA or RNA but never both) core |
| viewing viruses....need special stains.... | most cannot be seen with a light microscope...need an electron microscope so tiny, many million can fit in one human cell |
| biggest known viruses (up to 450 nm) | Pandoravirus and mimivirus |
| smallest known viruses ( around 20 nm) | poliovirus and yellow fever viruses |
| viruses contain only what they need to invade and control a host cell | external coating---made of proteins---called the capsid/// surrounding either DNA or RNA and sometimes one or two enzymes |
| protein capsid | a shell that surrounds the nucleic acid in the central core, made up of identical protein subunits called capsomeres |
| nucleocapsid | a term referring to both the capsid and the nucleic acid |
| enveloped virus | many animal viruses possess an additional covering to the nucleocapsid called an envelope.....can take many shapes from spherical to filamentous |
| naked virus | viruses with no envelope, only the nucleocapsid, are called naked |
| spikes | carbohydrate-protein complexes that project from the nucleocapsid or the envelope....allow viruses to dock onto their host cells |
| virions | fully formed virus capable of infecting a host |
| capsomeres | each capsomere can be composed of one protein or multiple proteins that spontaneously self-assemble into the finished capsid |
| enveloped viruses steal membrane from their host cell | the viruses are released and bud out from the host cell, take part of the cell membrane with them as an envelope...others can bud from the ER or the nuclear envelope..... |
| genome | the sum total of the genetic code carried by an organism |
| virus can have either DNA or RNA as their genome | will not have a mix.....can be single or double stranded, linear or circular, or in several segments |
| number of genes varies | can have 4 genes (Hep B virus) or hundreds of genes (some herpes viruses) only contain the genes needed to invade host cells and redirect their activity, |
| genes in a virus | must contain genes needed to synthesize viral capsid and genetic material, regulate the actions of the host, and packaging the mature virus |
| enzymes needed by virus | enzymes for protein synthesis, ribosomes, tRNA, and energy production are all supplied by the host cell...used to synthesize new viral proteins |
| host range | the number of different hosts that a virus can infect...can be narrow to one type of cell in one organism, or can be broad and infect cells of many species |
| cells that lack compatible virus receptors | they are resistant to absorption and infection by that virus....the virus cannot dock |
| viral particle absorption | a virus must encounter a compatible host cell, absorb specifically to receptor sites on the cell membrane....outer surface of virus must chemically interact with specific receptor sites on the surface of the cell |
| receptor sites on host cell | can be parts of cell wall, part of fimbriae or flagella, or on plasma membrane of host cells |
| endocytosis | the entire virus is engulfed by the cell and is enclosed in a vacuole or vesicle...host enzymes act to dissolve the envelope and capsid, release viral nucleic material into the cytoplasm |
| virus is uncoated | the host cell dissolves the capsid and envelope and releases the DNA or RNA |
| virus can directly fuse with the host cell membrane | envelope merges directly with the cell membrane...releases the nucleocapsid into the cell's interior |
| after viral entry... | viral nucleic acid begins to synthesize the materials to make new viruses |
| DNA containing viruses use viral enzymes in the host nucleus | they replicate their DNA in the host cell nucleus and make capsid in the cytoplasm with host cell enzymes....the capsid proteins migrate into nucleus and join the viral DNA to form virions |
| budding | envelope develops around the capsid when the assembled capsid pushes through the plasma membrane , some part of the plasma membrane adhere to the capsid and forms an envelope |
| cytopathic effects | the damage a virus does to a host cell....most times it will eventually kill the host cell |
| sometimes the virus does not kill the host | the cell can harbor the virus for a long time (in a latent, not harming, not making more viruses... stage) a persistent infection! can be few weeks to years |
| viruses can incorporate its DNA into the DNA of the host | called a provirus when it incorporates its DNA (measles, herpes, chicken pox viruses can remain latent for a long time and start reproducing due to stress and other factors) |
| some viruses permanently alter genetic material and lead to cancer | the disruption to host cell DNA can cause mutations that lead to cancer.... maybe 13% or more of cancers are caused by viruses |
| the stages of animal virus replication | Absorption---Penetration and Uncoating---Synthesis, replication and uncoating---Assembly and release |
| bacteriophage | a virus which attacks bacteria...have an icosahedral capsid head containing DNA, a central tube, collar, base plate, tail pins, and fibers |
| the lytic life cycle- absorption | tail fibers on the virus attach to a complementary receptor site on the bacterial cell- weak bonds (Hydrogen and ionic) form between the attachment and receptor sites |
| the lytic life cycle - penetration | the phage DNA is injected into the bacterium, phage releases phage lysozyme which breaks down a portion of the bacteria cell wall, capsid remains outside of the host cell--injects its DNA like a hypodermic needle |
| the lytic life cycle - biosynthesis | DNA has reached the cytoplasm of the host cell...viral nucleic acid and protein production takes over the normal cell functionings.....viral proteins interfere with transcription, translation, or degrade host DNA |
| the lytic life cycle- maturation | phage DNA and capsids are assembled into complete virions.....many virions housed in the bacterial cell!---cell lyses to free viruses |
| the lysogenic life cycle | some viruses don't cause cell death....capable of incorporating their DNA into the host cell's DNA , phage remains latent but its DNA is replicated every time the host cell replicates its genome |
| prophage | the DNA inserted by the virus that gets incorporated in the host cell's DNA |
| Prions | purely protein...newly discovered type of infectious agent....cause misfolding and malfunctioning of body proteins......fatal diseases often including deposition of human fibrils in the brain tissues |
| Viroids | just RNA, non-coding RNA fragments that have no protein coat....bind to other compatible RNA's and block translation-----problem for agriculture |
| around 260 viruses effect humans | viral infections do not commonly result in death, but some have high mortality rates and can lead to long term effects |
| hard to eradicate | the viruses borrow host proteins and functions to replicate....hard to find drugs that will impact the virus but not the host cells....the antiviral drugs in existence are designed to target one of the steps in viral life cycle |
Created by:
Gracie Cook
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