Class
When were proteins being studied? Explain
- 1950's - sequencing proteins - two organism that are closely related have similar shapes - antibodies are used to determine shape as they stick to certain shapes
Explain Stanly Miller and Harold Urey experiment
- 1952 - attempted to create conditions of early earth - tried to synthesize biochemical form from simpler organic molecules - filled a 5 liter flask with water and added methane, ammonia and hydrogen gas - electrical sparks were fired to simulate lightning - 5 amino acids where detected and later all 20 formed - nitrogenous bases in DNA and RNA were formed - Same animo acids have also been formed in N2-CO2 atmosphere - With nothing to consume or oxidize these materials they could increase in concentration in the ocean
Explain Carl Woese experiment
- 1970's - compaired rRNA - demonstrated that there are two very different groups of organisms with prokaryote cell structure, bacteria and archaea - studies based on rRNA comparison showed that protista is not a cohesive taxonomic unit and it should be divided into 3 or more kingdoms - three domains: bacteria, archaea and eukarya
When was there the first direct evidence of primitive cellular life found?
- 1977 - discovery of microbial fossils in Swartkoppie chert - Cert is granular sedimentary rock rich in silica - dated 3.5 BYA
Explain when ribosomes were first looked at
- 1977 - ribosomes are found in all cells - rRNA and protein in ribosomes - rRNA has the same function in every cell - rRNA has 3 types in prokaryotes: 5S, 16S and 23S - Bigger the number the bigger the rRNA molecule - Isolated 5S RNA from several different species was used -RNase was used to determine if sequences were the same, if RNase cut at the same place the 5S rRNA sequence is the same in both species - Use paper chromatography on RNA digests, this can be used to determine similarities and differences between species - Similarity coefficient: totally different = 0, completely the same =1 - 16SrRNA is now used for taxonomy of prokaryotes - 18SrRNA is used for taxonomy of eukaryotes
Explain Thomas Cech experiment
- 1981 - discovered catalytic RNA molecule in a protist - Could cut out an internal section of itself and splice the remaining sections back together - Other catalytic RNA molecules have been discovered - Ribozymes: catalytic RNA molecules - Discovery of ribozymes suggests that RNA at some time had the ability to catalyze its own replication using itself as a template
Explain James William Schopf discovery
- 1993 - disvovered fossils of filamentous bacteria in chert from the apex formation in pilabara region of western australia - cert was dated to 3.5 BYA
Explain Martin Hanczyc, Shelly Fujikawa and Jack Szostak discovery
- 2003 - showed that clay triggered the formation of liposomes containing RNA molecules
Explain stromatolites
- 3 BYA - look like large rocks but are actually living structures - layers of cyanobacteria - produce oxygen during the day and respire carbon dioxide at night - then next day move up through layer of carbon dioxide and start again - predominate form or marine living structure from 3.5 BYA to 800 MYA forming giant reef like structures
What are the differences in sizes for bacterial and eukaryotic ribosomes
- 70 S bacterial ribosomes - 80 S eukaryotic ribosomes - bacterial ribosomes are composed of two subunits 50s and 30S - S = Svedberg unit
Explain the evolution of cellular microbes
- Ancestral bacteria, archaea and eukaryotes possessed genetic information that could be duplicated, lost or mutated - mutations could have many outcomes - Some allowed new functions and characteristics to evolve - those mutations that allowed organisms to increase its reproductive ability were selected for and passed on to subsequent generations - Isolation of populations allowed some groups to evolve sepratly from others - selection and isolation led to the eventual development of new collections of genes and many new species - most eukaryotic species increase their genetic diversity by reproducing sexually - bacterial and archaeal species do not reproduce sexually, increase their genetic diversity by horizontal gene transfer (HGT) - during HGT genetic information from a donor organism is transferred to a recipient creating a new genotype - Genetic information can be passed from one generation to the next as well as between individuals of the same generation and even between different microbial species - outcome of HGT is that many bacterial archaeal species have mosaic genomes composed of bits and pieces of the genomes of other organisms
Explain some exceptions to the size of bacteria
- E. fishelsoni is 80 micrometers in diameter and 200-500 micrometers long, it is a giant vacuole - Oscullatoria is 7000 micrometers in diameter and is a type of cyanobacteria - Mycoplasma is the smallest microplasms and are between 0.1 and 0.2 micrometers in diameter
What are some properties of Eukarya?
- Eukaryotic - Protists, fungi, plants and animals
Explain the Square:cube law
- If you double the linear dimension then the area is squared and the volume is cubed - A cube with sides 1 micrometer long - 1 x 1 x 6 = 6 micrometers2 area - 1 x 1 x 1 = 1 micrometer3 volume - 6:1 surface area/volume ratio - A cube with sides 2 micrometers long - 2 x 2 x 6 = 24 micrometers2 area - 2 x 2 x 2 = 8 micrometers3 volume - 3:1 surface area/volume
Explain capsules
- Layer of material external to the cell wall and attached to bacteria - no easily washed off - composed of polysaccharides - rarely composed of amino acids - in gram positive and gram negative - makes things viscous - Bacilus antracis has a proteinaceous capsule composed of poly-D-glutamic acid - ex. levans/poly fructose, dextrans/poly glucose, colonic acid found in E. coli, glucose, alactose, fucose, glucuronic acid
Explain RNA world hypothesis
- Modern cells consist of plasma membrane enclosing water in which numerous chemicals are dissolved and subcellular structures float - first self replicating entity was much simpler then even the most primitive modern living cells - before there was life the earth was hot and anoxic with an atmosphere rich in water vapor, carbon dioxide and nitrogen - in the oceans hydrogen, methane and carboxylic acids were formed by geological and chemical processes - areas near hydrothermal vents or in shallow pools may have provided conditions that allowed chemicals to react with one another - Some reactions released energy and would eventually become the basis of modern cellular metabolism - Some reactions generated molecules that could function as catalysts - Some reactions aggregated with other molecules to form the predecessor of modern cell structures - Some reactions were able to replicate and act as units of hereditary information - In modern cells 3 different molecules fulfill the roles of catalysts, structural molecules and hereditary molecules - Proteins are structural and catalytic - Enzymes are catalytic proteins and speed up the myriad of chemical reactions that occur in a cell - DNA stores hereditary information and can be replicated to pass the information on to the next generation - RNA is involved in converting the information stored in DNA into protein - Any hypothesis about the origin of life must account for the evolution of these molecules - Proteins can do cellular work but their synthesis involves other proteins and RNA and uses information stored in DNA DNA cant do cellular work, it stores genetic information and serves as the template for its own replication a process that requires proteins - RNA is synthesized using DNA as the template and proteins as the catalyst for the reaction - there must have been a single molecule that could do both cellular work and replicate itself - believed this was RNA but a lipid membrane must have formed around the RNA - lipids spontaneously form liposomes which are vesicles bounded by a lipid bilayer - much of the cellular pool of RNA in modern cells exists in the ribosome - The ribosome consists largely of rRNA and uses mRNA and tRNA to construct proteins - rRNA catalyzes peptide bond formation for its importance in the development of proteins - RNA could have given rise to DNA - Once DNA evolved because the storage facility for genetic information because it provided a more chemically stable structure - proteins, DNA and cellular energy can be tracked back to RNA
Name 5 kingdoms
- Monera - Protista - Fungi - Animalia - Plantae - microorganisms except viruses are in monera, protista or fungi - all organisms with prokaryotic cell structure are in monera
Explain the functions of LPS
- Permeability barrier which restricts bile salts, detergents, antibiotics from entering the gram negative cell - helps stabilize the outer membrane - imparts negative charge to cell surface because core polysaccaride usually contains charged sugars and phosphate and can attach or repel cells from surface - protects the bacterium from immune system - O side chain is immunogenic but there are many different types of O chains in a population of bacteria - 180 different O antigens against certain strain you are infected with, if you survive you will produce antibodies against this strain and never receive disease from that particular strain again - role in pathogenicity of gram negative bacteria is endotoxin produced by lipid A and causes fever and shock
What are some properties of archaea?
- Prokaryote - Distinctive rRNA sequences - Lack of peptidoglycan in cell walls - Unique membrane lipids - Unusual metabolic characteristics such as methanogens which generate methane gas - live in extreme environments including those with high temperatures and high concentrations of salt - some are members of a community of microbe involved in gum disease in humans
What is some evidence that RNA existed 4 BYA?
- RNA was autocatalytic - More RNA viruses then DNA viruses
What are bacilli/bacillus?
- Rod shape - shape of the ends of rods often varies between species and may be flat, rounded, cigar shaped or bifurcated
Explain the fluid mossaic model
- Singer and Nicholson - lipid bilayer in which proteins float - very thin - in TEM looks like two dark lines on either side of a light interior - Cleavage of membranes can be seen by freeze etching, allows proteins lying within membrane bilayer to be seen - membrane associated lipids are amphipathic - polar ends interact with water and are hydrophilic - nonpolar ends are insoluble in water and are hydrophobic - outer surface of bilayer are hydrophilic, inner ends are inside bilayer and are hydrophobic
Explain the hydrogen hypothesis
- States that the endosymbiont was an anaerobic bacterium that produced H2 and CO2 as end products of its metabolism - Over time host became dependent on H2 produced by endosymbiont - If endosymbiont developed the capacity to perform aerobic respiration it evolved into mitochondrion - If endosymbiont did not develop this capacity it evolved into a hydrogenosome - hydrogenosome is an organelle found in some protists that produces ATP by fementation
What are some properties of Protists?
- Unicellular - larger then bacteria and archaea - divided into protozoa and algae - algae, protozoa, slime molds and water molds
Explain group translocation
- a molecule is chemically modified as it is brought into the cell
Explain a sodium gradient
- accomplished by an antiporter that brings protons in as sodium ions are moved out of the cell - sodium gradient can then be used to drive uptake of nutrients by a symport mechanism
What are some properties of viruses?
- acellular infectious agents - must invade a host to multiply - simplest viruses are composed of only protein and nucleic acid - extremely small which bellies their power - viral diseases include smallpox, rabies, influenza, AIDS, common cold and some cancers - important role in aquatic environment
Explain iron uptake
- almost all microorganisms require iron for use in cyrochromes and enzymes - iron uptake is difficult due to extreme insolubility of ferric ion and its derivatives - bacteria secrete siderophores -sidrophores are low molecular weight organic molecules that bind ferric ion and supply it to the cell - microorganisms secrete siderophores when ion is scarce in medium - once ion-siderophore complex has reached cell surface it binds to siderophore-receptor protein and then either iron is released to enter cell directly or while iron-sideophore complex is transported inside by ABC transporter
Explain horizontal gene transfer
- bacterial and archaeal species do not reproduce sexually, increas their genetic diversity by horozontal gene transfer (HGT) - during HGT genetic infromation from a donor organism is transferred to a recipeiant creating a new genotype - Genetic information can be passed from one generation to the next as well as between individuals of the same generation and even between different microbial species - outcome of HGT is that many bacterial archaeal species have mosaic genomes composed of bits and peices of the genomes of other organisms
Explain cell organization
- bacterial cells are surrounded by many layers which are called the cell envelope - innermost layer is plasma membrane which surrounds the cytoplasm - cell wall covers the plasma membrane - capsule or slime layer external to cell wall - genetic material is localized in region called the nucleoid (NOT THE NUCLEUS) and is not separated from the surrounding cytoplasm by membranes - Ribosomes and larger masses are called inclusions and are scattered around the cytoplasm - many bacteria use flagella for locomotion
Explain FtsZ
- bacterial cytoskeletal protein - a homologue of the eukaryotic protein tubulin - forms a ring at the center of the dividing cell - is required for the formation of the septum that will separate daughter cells
Explain MreB
- bacterial cytoskeletal protein - not found in cocci - actin homologues - determine cell shape by properly positioning the machinery needed for peptidoglycan synthesis in rod shaped cells
Explain CreS
- bacterial cytoskeletal protein - discovered in C. crescentus - responsible for curved shape - homologue of lamin and keratin which are two intermediate filament proteins
Explain important events at 4BYA
- bombardment by meteroites decreased - water existed on the planet - planet was below 100 degrees - C, CH4, H2, N2, NH3, CO2 in atmosphere - no oxygen - earths atmosphere was formed - early ocean was acidic due to dissolution of CO2 and contained nitrogen in the form of ammonia or ammonium - acellular life may have existed - RNA existed - believed cyanobacteria existed
Explain the cell membrane
- border of all cells - separates the inside of the cell or the cytoplasm from the external environment - regulates the flow of materials from one side to the other - site of energy generating metabolism, including photosynthesis, electron transport chain, and enzymes involved with various types of oxidation - permeable to gases and water - molecules with a high amount of carbon will be permeable - charged compounds, sugars and hydrophilic compounds are not permeable - not permeable to protons - composed of phospholipids and proteins - somewhat different lipids composition than with eukaryotes -lipid bilayer - ester bond used to attach fatty acid onto hydroxyl group in glycerol - ester bond is very easy to make and break down - hydrophillic polar ends of the lipids interact with water both inside and outside of the cell - hydrophobic nonpolar parts of the lipids associate with eachother away from the water - prokaryotic membranes are thin (5-10 nm) - head groups of bacterial lipids are derivatives of glycerol phosphate - the tails of bacterial lipids are esters of fatty acids
How do bacteria reproduce?
- by binary fission, always double - bacilli grow longer and longer until they split down the middle - various lengths of cells will be seen when growing a bacterial culture
Explain macroelements/macronutrients
- carbon, oxygen, hydrogen, nitrogen, sulfur, phosphorous required in relatively large amounts - found in organic molecules such as proteins, lipids, nucleic acids and carbohydrates - potassium, calcium, magnesium and iron exist as cations and generally are associated with and contribute to the activity and stability of molecules and cell structures such as enzymes and ribosomes - important in many cellular processes including protein synthesis and energy conservation - some microbes are able to synthesize all organic molecules they need from macroelements
What are R plasmids
- carry antibotic resistance genes - have sex pili - can perform conjuation - have a resistance to Amp, Km, Nm and Tet
What are metabolic plasmids
- carry genes for enzymes - camphor degradation
What are virulence plasmids
- carry virulence genes - tumor introduction in plants
Explain swarming motility
- colony grows and then becomes motile outwards around the colony, this gives appearance of rings - have peritrichous flagella
Explain flagellar synthesis
- complex process involving 20-30 genes - 10 or more genes code for hook and basal body proteins, other genes are concerned with control of flagellar construction or function - new flagellin molecules transported though the hollow filament using type 3 like secretion system - filament subunits self assemble with help of filament cap at tip - flagellar protein is produced inside the cell and moves though motor and hook down filament and self assemble at end of filament
Explain Braun's lipoprotiens
- connects the outer membrane to the cell - very small and abundant in gram negatives - covalently linked to the peptidoglycan layer on one side - other end is hydrophobic and inserts into the inner layer of the outer membrane by fatty acid - has fatty acid attached at N-terminal - more lipoprotien in gram positive the gram negative - numerous places where the outer membrane and cytoplasmic membrane appear to be in direct contact
What are prokaryotic cells?
- contents are not divided into compartments by membranes - lack membrane bound nucleus
Explain size of bacteria
- dimensions of bacteria are generally in micrometer range - usually bacteria are smaller than eukaryotic cells but larger then viruses - sometimes viruses and eukaryotes overlap in size with prokaryotes - single cell algae and yeasts which are eukaryotes can be smaller then large prokaryotes - bacteria can be larger or smaller based on how you grow them
What are some properties of fungi?
- diverse group of microorganisms that range from unicellular forms of yeast to mold and mushrooms - molds and mushrooms are multicellular fungi that form thin, thread like structures called hyphae - absorb nutrients from their environment including organic molecules they use as sources of carbon and energy - many fungi play beneficial roles including bread rising, producing antibiotics and decomposing dead organisms - some fungi associate with plant roots to form mycorrhizae
Describe archaea cell walls
- dont have peptidoglycan - most similar to peptidoglycan is pseudomurein which is a polymer of N-acetyl glucosamine and N-acetyl talosaminuronic acid with peptide inter chain bridges - contains other polysaccarides and protein layers
Explain the evolution of metabolism
- early earth was a hot environment that lacked oxygen - cells that arose must have been able to use the available energy sources under these harsh conditions - Today there are heat loving archaea capable of using inorganic molecules such as FeS as a source of energy, remnant of the first form of energy metabolism - oxygen releasing photosynthesis may have occurred 2.5 BYA, we know this from fossils of cyanobacteria and stromatolites - stomatolites are layered rocks that are formed by incorporation of mineral sediments into layers of microorganisms growing thick mats on the surface - oxygen they released changed the atmosphere to oxygen rich state allowing the evolution of aerobic respiration which is an oxygen consuming metabolic process
Explain micronutrients/trace nutrients
- elements are required in small amounts, maganese, zinc, cobalt, molybdnum, nickel and copper - part of certain enzymes and aid in the catalysis of reactions and maintenance of protein structure
Explain transport protiens
- embedded in membranes - channels and carriers
Explain the endosymbiotic origin of mitochondria, chloroplasts and hydrogenosomes
- endosymbiotic hypothesis is accepted as the origin of mitochondria, chloroplasts and hydrogenosomes - endosymbiosis is an interaction between two organisms in which one organism lives inside the other - Initial statement of endosymbiotic hypothesis proposed that over time a bacterial endosymbiont of an ancestral cell in the eukaryotic lineage lost its ability live independently and becoming either a mitochondrion in the intracellular bacterium used aerobic respiration or a chloroplast of the endosymbiont was a photosynthetic bacterium - mitochondria and chloroplasts contain DNA and ribosomes - Both organelles belong to the bacteria lineage based on SSU rRNA analysis - Further evidence of the origin of mitochondria comes from the genome sequences of the bacterium Rickettsia prowazkii, the genome is more similar to that of modern mitochondrial genomes then to any other bacterium - Chloroplasts of plant and green algae are thought to have descended from an ancestor of cyanobacterial genus Prochloron
What are the enzymes found in gram negative periplasm for
- energy production: often on inside surface of cytoplasmic membrane, ex. electron transport proteins - Nutrient transport: nutrients are broken down into amino acids outside of the cell and then amino acids are transported into the cell, ex. hydrolytic enzymes and transport proteins - nutrient macromolecule degration - detoxification - peptidoglycan synthesis: precursors of peptidoglycan are synthesized in cytoplasm and then exported to periplasm for peptidoglycan synthesis - transport to the outer membrane
When several transport systems exist for a nutrient they differ in
- energy source - affinity for the solute transported in the nature of their regulatiuon - gives competitive advantage to bacteria in variable environment
Explain the cytoplasm
- everything inside the cell membrane which is called the protoplast - mostly water - very dense and full of enzymes, intermediate metabolites and ribosomes - almost every water molecules is associated with a protien
Explain bacterial cell walls
- everything outside of cytoplasmic membrane is the cell envelope - all bacteria have cell walls except class Mollicutes/mycroplasms and the genus Chamyia - composed of rigid layer of peptidoglycan which is a component of the cell wall that gives strength to resist osmotic pressure and shape to the cell - located outside the membrane - helps maintain cell shape and protect cell from osmotic lysis - protect cell from toxic substances - in pathogens it can contribute to pathogenicity - bacterial cell wall synthesis is targeted by several antibiotics
Explain spirochete motility
- flagella in periplasm - multiple flagella form axial fibril which winds around the cell - flagella remain in periplasmic space inside the outer sheath - corkscrew shape exhibits flexing and spinning movements
Explain the mechanism of flagellar movement
- flagellum is 2 part motor producing torque Rotor: C (FliG protein) ring and MS ring interact with stator Stator: Mot A and Mot B proteins - form channel though plasma membrane - protons move though mot A and mot B channels using energy of proton motive force - torque powers rotation of the basal body and filament - MS ring in the membrane is in gram negative and gram positives and does the work - around the MS ring are mot A and mot B proteins that surround the MS ring - protons into the cell down the gradient though mot A and mot B proteins which creates energy for the MS ring and turns the ring which allows the flagella to spin
Explain bacterial flagellar movement
- flagellum rotates like a propeller - very rapid rotation 1100 revolutions per second - usually counterclockwise rotation causes forward motion - clockwise rotation disrupts forward motion and causes cell to stop and tumble
What are spirochetes?
- flexible, spiral shaped bacteria - unique internal flagellar arrangement - all belong to single phylum spirochaetes - usually only visible on wet mounts - move in corkscrew fashion
Explain how fatty acid composition of the membrane changes in different environments
- growth at lower temperatures leads to an increase in the percentage of unsaturated fatty acids in the membrane, this is because the membrane tends to go rigid when cold, by adding a double bond from unsaturation the fatty acid is kinked to prevent freezing from occurring and preserves fluidity - unsaturated fatty acids make membranes more fluid by increasing the amount of saturated fatty acids, this occurs at high temperatures
What are eukaryotic cells?
- have a nucleus and other membrane bound organelles
Explain hydroxyl group substitutions in bacterial fatty acids
- hydroxyl group can be on some carbons in the fatty acid tail - usually only occurs on one of the carbons in a given fatty acid
Explain the gram staining procedure
- if cell wall is removed typical gram positive bacteria stain gram negative - bacteria that never make cell walls such as mycoplasmas stain gram negative - Bacteria first stained with crystal violet which is a positively charged dye that is attracted to bacteria cells negative charge - Next treated with iodine which is a mordant that interacts with crystal violet forming an insoluble complex and promoting dye rention - Bacteria are treated with ethanol in a decolorization step and shrinks pores of thick peptidoglycan found in cell walls of gram positive bacteria which causes peptidoglycan to ask as a permeable barrier preventing the loss of crystal violet - The dye iodine complex is retained during decolorization step in gram positive bacteria and bacteria remain purple - Peptidoglycan in Gram negative cells is very thin, not highly cross linked and has larger pores - Alcohol treatment extracts enough lipids from the outer membrane to increase cell walls porosity further - Alcohol more readily removes crystal violet-iodine complex in gram negative cells and decolorizes these cells - Counterstain safranine is a dye with a negative charge and easily stains decolorized cells so gran negative cells appear pink
How can negative staining show if a capsule exists?
- if no capsule is present the background is dark - if capsule is present the negative stain shows a large white middle and when looking closely you can see a small cell within the white space
What is the function of the periplasmic space?
- in gram negitive bacteria contains hydrolytic enzymes and binding protiens for nutrient processing and uptake - in gram positive bacteria may be smaller or absent
Explain KDO
- in the inner core of LPS - has 8 carbons - two KDO or more in linear chain, branches can occur on these chains - Last KDO will connect to first sugar in outer core
Explain storage inclusions
- include glycogen inclusions, polyhydroxyalkonate granules, sulfur globules and polyphosphate granules and cyanophycin granules which are only present in cyanobacteria - some store end products of metabolic processes, the microbe can use these when it is in different environmental conditions
Explain glycogen
- inclusion body - a polymer of glucose - long linear changes of glucose with branching - low osmotic pressure - rare in bacteria - energy source - may have excess glucose, bacteria often packs this away in capsules - must depolymerize glucose to use it - almost all storage molecules are stored as polymers because this helps with osmotic pressure
Explain poly-beta-hydroxy butrate (PHB)
- inclusion body - a polymer of hydroxyl butyric acid - carbon storage material - more common in bacteria - stores energy - sugar is converted to PHB in the cell - accumulates in larger bodies in the cell which can be easily isolated - PHB can be made into a biopolymer similar to polyethylene but is biodegradable by heat - has ester bonds - surrounded by a single layered shell composed of proteins and a small amount of phospholipids
Explain cyanophycin
- inclusion body - a polypeptide of arginine and aspartic acid - not a protein but has the structure of a protein - stores amino acids - stores amino nitrogen - limiting nutrient for bacteria
Explain gas vesicles
- inclusion body - cylindrical tubes composed of protein molecules - impermeable to water - trap gas inside them - protein is small and hydrophobic - allow bacteria to change their buoyancy - a gas vacuole is many gas vesicles lumped together - when air in gas vacuole increases the bacteria move up, when air decreases the bacteria move down
Explain sulfur granules
- inclusion body - inorganic inclusion - composed of elemental sulfur - usually found in anaerobic photosynthetic bacteria which can convert H2S to sulfur - oxidize or reduce sulfur containing compounds to get elemental sulfur - elemental sulfur is not very soluble so precipitates as granules - sulfur metabolism can also be used to gain energy
Explain carboxysomes
- inclusion body - present in cyanobacteria and other CO2 fixing bacteria - polyhedral coat is composed of 6 different proteins - enclosed by the shell is enzyme carbonic anhydrase which converts carbonic acid into CO2 - carboxysome shell prevents CO2 from escaping and therefore CO2 accumulates within carboxysomes - storage of the enzyme ribulose-1,5-bisphospate carboxylase - RibisCO is the important enzyme in carbon dioxide fixation in the Calvin Cycle which is the process of converting CO2 to sugar - ribulose-1,5-bisphosphate carboxylase is used for photosynthesis and is the most abundant enzyme on the planet - this enzyme can also be used for making proteins when photosynthesis is not occurring - Bacteria keeps the ribisCO - ParA helps ensure appropriate segregation of carboxysomes and is a cytoskeletal protein
Explain magnetosomes
- inclusion body -aquatic magnetotactic bacteria use magnetosomes to orient themselves in earths magnetic field - intracellular chains of magnetite particles - enclosed within invaginations of the plasma membrane because invaginations have distinctive proteins that are not found in the rest of the plasma membrane - each iron particle is a tiny magnet - cytoskeletal protein called MamK is responsible for establishing a framework upon which the chain can form
Explain polyphosphate
- inclusion body -inorganic inclusion - phosphate granules found throughout the cytoplasm - a polymer of ortho-phosphate which can act as both an energy reserve and a source of phosphate - rare in bacteria - releases energy - stores phosphate needed for synthesis of important cell constituents such as nucleic acids - used to take out phosphorous in sewage
Explain plasmids
- independently replicating segments of DNA - range from 1kbp to 1mbp in size - usually circular but can be linear - usually less then 30 genes - usually encode genes which are not always necessary for the cell to survive - cell can survive without their plasmids - often carry antibiotic resistance genes and are transmissible from one cell to another
What are some properties of prions?
- infectious agents composed of only protein - cause variety of spongiform encephalopathies such as scrapie and mad cow disease
What are some properties of viroids and satellites?
- infectious agents composed only of RNA - viroids cause plant disease - satellites cause plant diseases and some animal diseases such as hepatitis
Explain Thylakoids
- internal membranes of photosynthetic cyanobacteria - contain the chlorophyll and photosynthetic reaction centers responcible for converting light energy into ATP
What is LUCA
- last universal common ancestor - Archaea, bacteria and eukarya all came from a common ancestor - all cells contain DNA, RNA and protein - the more similar you are the shorter the time you evolved from a common ancestor
What is glycocalyx?
- layer consisting of a network of polysaccharides extending from the surface of the cell - capsules and slime layers - aids in attachment to solid surfaces
Explain S Layer
- layer of protein or glycoprotien external to outer membrane in gram negatives and the peptidoglycan in gram positives - also found in archaea - regular array of subunits which resembles floor tiles - large surface area - in gram negative bacteria the S layer attaches directly to the outer membrane - the S layer is associated with the peptidoglycan surface of gram positive cell walls
Explain how bacterial lipid composition varies with temperature
- lipid composition varies with temperature in such a way that the membrane remains fluid during growth - bacteria growing at lower temperatures have more unsaturated fatty acids in their membrane phospholipids, there are one or more double bonds in the long hydrocarbon tail - At higher temperatures the phospholipids have more saturated fatty acids, those in which the carbon atoms are connected only with single covalent bonds
Explain peptidoglycan elasticity in E. coli
- live cells stretch about 25% and shrink about 33% under osmotic stress - if you destroy the membrane the peptidoglycan will suddenly contract about 45% - length changes but diameter is almost constant - May be related to structure of peptioglycan, glycan chains go around the diameter of the cell while peptide links are in direction of the length of the cell
Explain filamentous cyanobacteria
- live inside a tube called a trichome - filaments can fuse together and become visible which is the black stuff on the beach
Explain sex pili
- longer, thicker and less numerous - 1-10/cell - genes for formation found on plasmids - required for conjuagation -plasmid in donor allows conjuation/mobility to occur - initiates conjugation by producing pili, plasmid replicates itself and sends replica to recipient - allows plasmids to be moved into different cells and plays roles in antibiotic resistance since plasmids are resistant to many antibiotics - genes/genomes can be transferred between donor to recipient though sex pili - recipient will end up with 2 genomes and recombination can occur
Explain peripheral membrane protiens
- loosely connected to the membrane and can easily be removed - can be on outside or inside of cytoplasmic membrane - can be washed by buffer - soluble in aqueous solutions - make up 20-30% of total membrane protien
Explain what lysozyme and penicillin do in terms of osmotic pressure.
- lysozyme enzyme attacks peptidoglycan by hydrolyzing the bond that connects N-acteylmuramic acid with N- acetylglucosamine - Penicillin inhibibits the enzyme transpeptidase which is responsible for making the cross links between peptidoglycan chains - if bacteria are treated with either of these substances while in a hypotonic solute they lyse - if bacteria are treated with either of these substances in an isotonic solution they can survive and grow normally - treatment of gram positive bacteria with lysozyme or penicillin results in complete loss if cell wall and cell becomes a protoplast - when gram negative bacteria are exposed to lysozyme or penicillin the pepotidoglycan is destroyed but the outer membrane remains, these are sphereoplasts - because they lack a cell wall both protoplasts and spheroplasts are osmotically sensitive
Explain the bacterial cytoskeleton
- made of actin filaments, microtubules and intermediate filaments - actin filaments are made from actin - microtubules are made from tubulin - intermediate filaments are composed of a mixture of one or more members of different classes of proteins - participate in cell division, localize proteins to certain site in the cell and determine the cell shape - bacterial cytoskeletal proteins include FtsZ, MreB and CreS
Explain filamentous bacteria
- many cyanobacteria are filamentous - being filamentous allows some degree of differentiation among cells in the filament - some filamentous cyanobacteria from heterocysts within the filament, these are specialized cells that carry out nitrogen fixation - myxobacteria sometimes aggregate to form fruiting bodies - actinomycetes
How far does cellular (single cell) life go back?
- may go back 3.5 BYA - cells have DNA, RNA, protein and membrane enclosed, concentration gradients
Explain primary active transport
- mediated by carriers called primary active transporters - used the energy provided by ATP hydrolysis to move substance against a concentration gradient without modifying them - use uniporters - ATP-binding cassette transports are important primary active transporters - most ABC transporters consist of two hydrophobic membranespanning domains associate on their cytoplasmic surfaces with two ATP binding domains - membrane spanning domains form a pore in the membrane and ATP binding domains bind and hydrolyze ATP to drive uptake - ABC transporters employ substate binding proteins - substate binding protiens bind the molecules to be transported and then interact with the transporter protein to move the molecule into the cell
What are sortases?
- membrane bound enzymes that catalyze formation of the covalent bonds that join protiens to the peptidoglycan
Explain volume of bacteria
- metabolism is proportional to volume - surface area/volume ratio is very high in bacteria - cytoplasm has metabolic activities - area of membrane is limiting factor of metabolism - increase in metabolism means increase in the membrane to surface area ratio or make the cell smaller - when linear dimensions are larger metabolism slows down - small cells have high metabolic rates - prokaryotes have higher rates of metabolism then eukaryotic cells - as surface area to volume ratio increases the uptake of nutrients and the diffusion of molecules within the cell becomes more efficient which facilitate rapid growth rate - rod with same volume as coccus has higher S/V ratio - For bacteria to be large they must have other characteristics that maximize their S/V ratio or their size must be beneficial - E. fishelsoni has highly convoluted membrane which increases S/V ration - Cells that are filamentous have prostheca or are oddly shaped and are less susceptible to preditation
Explain the paturns of flagellar distributions
- monotrichous: one flagellum - polar flagellum: flagellum at end of cell - amphitrichous: one flagellum at each end of the cell - lophotirchous: cluster of flagella at one or both ends - peritrichous: spread over the entire surface of the cell
Explain bacterial plasma membranes
- most important because it encompasses the cytoplasm and defines the cell - if plasma membrane was removed the cells contents would spill into environment and the cell would no longer exist - selectively permeable barriers allow particular ions and molecules to pass either into or out of the cell while preventing the movement of others - prevents the loss of essential components through leakage while allowing the movement of other molecules - location of several crucial metabolic processes including respiration, photosynthesis and synthesis of lipids and cell wall constituents - some bacteria have extensive intracytoplasmic membrane sytesms, internal membranes and plasma membrane share a basic design but differ in lipids and protiens
What are the functions of the flagella?
- motility and swarming behaviour - attachment to surfaces - may be virulence factors
Explain chemotaxis
- move toward or away from chemical attractants or repellents - changing concentrations of chemical attractants and chemical repellents bind chemoreceptors of chemosensing system - in gram negative bacteria chemoreceptor proteins are located in the plasma membrane - in presence of attractant tumbling frequency is reduced and runs in direction of attractant are longer - behavior of bacterium is altered by temporal concentration of chemical
Explain secondary active transport
- move two substances simutaneously - ion whos gradient powers transport and the substance being moved across the membrane - can be symport or antiport - include major facilitarot superfamily (MFS) protiens - MFS transporters using ion gradients some of which are created by bacteria during their metabolic processes - Electron transport during energy conserving processes generate a proton gradient in which protons are at higher concentrations outside the cell than inside - protine gradient can be used to do cellular work including secondary active transport - sometimes proton gradient can be used to create another ion gradient such as a sodium gradient - lactose permease of E.coli
Explain the gram negative outer membrane
- only in gram negative - lies outside of think peptidoglycan layer - linked to cell by Braun's lipoprotien which is the most abundant cell in outer membrane - composed of phospholipids, a lipid bilayer, embedded proteins and lipopolysaccaride (LPS) - phospholipids are glycerol with 3 hydroxyl groups that things attach to - one hydroxyl group has a phosphate group, other two have fatty acid chains that are attached by an ester bond - glycerol phosphate is on outside of membrane - fatty acid chains are on inside of membrane - outer leaflet will have LPS - 1/3 LPS - 2/3 is phospholipids and protiens
Explain teichoic acids
- only in gram positives - polymer of glycerol phosphate or ribitol phosphate - covalently connected to peptidoglycan or plasma membrane lipids - if the polymers are attached to the peptidoglycan then they are called teichoic acids - if they pass through the cell wall and anchor into the cytoplasmic membrane they are lipoteichoic acids - contain glycerol and phosphate in a repeating pattern or ribitol and phosphate in a repeating pattern - phosphate groups are negatively charged - usually positive counter ion present - fatty acids can be added - fatty acids allow teichoic acid to be inserted into cytoplsamic membrane - teichoic acid without fatty acid insertes into peptidoglycan - all gram positives cells will have both fatty acid teichoic acids and non fatty acid teichoic acids - help create and maintain the structure of the cell envelope and protect the cell from harmful substances - may be involved in binding pathogenic species to host tissues and initiating infectious disease process
Explain lipopolysacharide (LPS)
- only in outer leaflet of the outer membrane - contain lipid and carbohydrate - composed of lipid A, core polysaccaride. O antigen - creates fever/septic shock when gram negative strains are lysised and LPS is released
What are microorganisms?
- organisms and acellular entities too small to be seen clearly by the unaided eye - marcroscopic organelles that we seen are colonies of microorganisms - some macroscopic microorganisms that we see are multicellular - distinguished from other life forms by a lack of highly differentiated tissues - some are motile like animals but also have cell walls like plants
What are extant organisms?
- organisms present today - some extant organisms have structures and molecules that represent relics of ancient life forms
What are anaerobic photosynthetic organisms?
- other groups of bacteria that are photosynthetic but do not produce oxygen
Explain the phylum cyanobacteria
- oxygenic photosynthetic - produce oxygen - blue green algae - no nucleus - cyanobacteria are believed to evolved into plants - fairly large 50 micrometers - live in freshwater -dont need extra electrons as electrons are not lost - when combining purple sulfur and greens plus oxygen involving process get organism that splits water and gives off oxygen
Explain core polysaccaride
- part of LPS - attach to lipid A - approx 10 monosacharides attached in a branching pattern - links lipid A to the O side chain - core divided into two parts the outer and inner core - inner core has sugar called KDO - outer core has several sugars, often glucose is found - O antigen connects to last sugar in outer core - Lipid A connects directly to KDO in inner core
Explain O Antigen
- part of LPS - composed of several monosaccarides - often unusual or rare sugars - 2-4 sugars link together in a subunit and is repeated many times in a linear chain - repeating unit often has one or more branches - chain points out into the environment - 50-150 sugars long in total - varies in composition between bacterial strains
Explain Lipid A
- part of LPS - composed of two molecules of glucosamine and phosphate - each glucosamine molecule has 2 or 3 fatty acids attached - the fatty acids anchor to the LPS into the outer membrane - Extremely toxic - causes gram negative septic shock - diamer of glucosamine - phosphate is attached to each glucosamine - two fatty acids are attached directly to glucosamine and many branch off from original fatty acid
Explain peptidoglycan structure
- peptidoglycan sacculus - enormous polymer composed of sugars and amino acids '- backbone of peptidoglycan is composed of 2 types of sugars linked together in long strands - contains lots of water - sugars alternate in the polymer: -NAG-NAM-NAG-NAM- - Sugar backbone is linear and unbranched - backbone chain about 50-150 sugars long, not long enough to reach around cell individually - N-acetylmuramic acid is linked to a short peptide chain of 4 amino acids: L-alanine, D-glutamic acid, meso-diaminopiemelic acid, D-alanine - when precursor is synthesized it has 5 amino acids, an extra D-alanine - presence of D-amino acids protects against degration by most peptidases which recognize only L-isomers of amino acid residues - On the sugar backbone every NAM carries a peptide chain - Peptide chains are crosslinked to eachother from the 3rd amino acid in one chain to the 4th amino acid in another - In some bacteria this linkage is though a peptide bridge - Strands of peptidoglycan are helical - Position 5 D-alanine is removed as the cross link is formed - Strong but elastic, stretches and contracts in responce to osmotic pressure - Very porous allowing globular proteins to pass through - Gram positive has more cross linking then gram negative - gram positive have thick cell wall with many layers of peptidoglycan (50-80 nm) - gram negative have thin cell wall with one or a few layers of peptidoglycan (3-6 nm) - E. coli about 6-7 nm but areas with 2.5 nm corresponds to 3 or 1 layer thick - pesudomonas aeruginosa about 2.5 nm thick everywhere - bacillus subtilus has 2 different layers, inner layer is newer peptidoglycan and about 22 nm thick, outer layer and teichoic acids about 15-30 nm thick - when cell shrinks peptidoglycan also shrinks - when cell expands peptidoglycan also stretches and expands - Peptidoglycan sacculus have protiens that are involved in interactions of the cell with its environment, some noncovalently bound to teichoic acids or other cell wall polymers, other surface protiens are covalently attached to peptidoglycan - Many covalently attached protiens have roles in virulence
What are some properties of Algae?
- photosynthetic - together with cyanobacteria they produce 75% of planets oxygen - foundation of aquatic food chain
Explain osmotic pressure
- pressure arises when concentration of solutes inside the cell differes from outside the cells - responce works to equalize solute concentrations - can exceed the cells ability to acclimate so additional protection is provided by the cell wall - when cells are in hypotonic solutions (solute concentration is less then that in the cytoplasm) the water diffuses into the cell causing it to swell, without the peptidoglycan layer of the cell wall the cell would burst - Hypertonic solutions (water flows out of the cytoplasm) the cell shrivels up which is called plasmolysis
What are the 3 types of active transport in bacteria
- primary active transport - secondary active transport - group translocation
Explain passive diffusion
- process by which molecules move from a region of higher concentration to one of lower concentration - molecules move down a concentration gradient - rate depends on size of concentration gradient - large concentration gradient is required for adequate nutrient uptake - unless nutrient is used immediately upon entry the rate of diffusion decreases as more nutrient accumulates in the cell - gases easily diffuse across the plasma membrane - allows cell to adjust to differences in solute concentration - larger molecules, ions, polar substance cannot enter cell by passive diffusion
What are Col plasmids
- produce bacteriocins which are substances that destroy closely related species - coilicon E1 production
What are some properties of bacteria?
- prokaryote - single celled organisms - cell walls that contain peptidoglycan - few members of phylum Plantomycetes have their genetic material surrounded by a membrane - abundant in soil, water and air including sites that have extreme temperatures, pH and salinity
Explain structure and cellular organization of bacteria
- prokaryotes have very little sub-cellular organization as compared to eukaryotes - no internal membrane-enclosed structures - membrane invaginations are a part of the cytoplasmic membrane - prokaryotes are enclosed by a strong, rigid but porous cell wall - cell wall is external to a semi-permeable membrane and the cytoplasm -pili, fimbriae and flagella can be outside the cell wall - inclusion bodies, gas vesicles, the nucleoid, spores and internal membranes are located inside the cell wall
What are the functions of an S layer?
- protection against pH and ion changes - protection against predators, the immune system and enzymes - adhesion to surfaces - osmotic stress protection for archaea - helps maintain shape and envelope rigidity - s layer proteins can self assemble, contain the information required to spontaneously associate and form the S layer without the aid of additional enzymes or factors - very resistant to things that break down proteins - phenol is very strong substance that breaks down proteins but will not break down S layer, phenol can sometimes be used to identify an S layer
Explain the functions of capsules and slime layers
- protection against phagocytosis - capsules make bacteria larger which helps defend against being eaten - phagocytes have receptors to detect bacteria, a bacterial capsule prevents phagocyte receptors from detecting bacteria - protection against desiccation - deactivated by drying/desiccation - capsules are made of polysaccarides which absorb water - attachment to solid surfaces - biofilm when bacteria stick to something, extracellular polymeric substance keeps biofilm stuck together - protection against viruses/bacteriophage -motility for gliding bacteria
What are some properties of Slime Molds?
- protists that behave like protozoa in one stage of their life cycle but like fungi in another - in the protozoan phase they hunt for and engulf food particle consuming decaying vegetation and other microbes
What are some properties of water molds?
- protists that grow on the surface of freshwater and moist soil - feed on decaying vegetation such as logs and mulch - involved in great potato famine
Explain intracytoplasmic membranes
- provide a larger membrane surface for greater metabolic activity - may be aggregates of spherical vesicles, flattened vesicles or tubular membranes - often connected to the plasma membrane and arise from the plasma membrane though invaginations - enriched for proteins and other molecules that are involved in energy conservation - ex. thylakoids and anammoxome
Explain the nucleoid
- region of the cytoplasm where bacterial DNA is located - irregular shape, projections into the cytoplasm where transcription takes place - not membrane bound - blob of jello with DNA, RNA and protein in water - DNA associated proteins coil and package the DNA - may be in contact with the cell membrane - contains the bacterial chromosome which is a single circulate molecule of DNA and plasmids - covalently close circle of DNA - 4.5 million bp - in E. coli the chromosome is 1400 mircometers long - coiled and looped around condensins - bacterial genomes range from 0.6 mpb to more than 9 mpb - some have linear chromosomes some may have linear and circular chromosomes
Explain microcompartments
- relatively large polyhedrons formed by one or more different proteins - enclosed within the protein shell are one or more enzymes - examples are the ethanolamine utilization (Eut) microcompartments, the propandiol utilization (Pdu) microcompartments, and carboxysomes
Explain integral membrane protiens
- remaining proteins - not easily extracted from the membrane - insoluble in aqueous solutions when freeded from lipids - amphipathic with hydrophobic ends buried in lipid and hydrophilic ends projecting from membrane surface - transport proteins used to move material into or out of the cell - involved in energy conserving process - proteins with region exposed to outside of the cell enable the cell to interact with its environment - Cannot be washed by buffer
What are exoenzymes?
- secreted proteins and enzymes - degrade polymetric nutrients that would otherwise be too large for transport across the plasma membrane
Explain SSU rRNA molecules
- sequence of nucleotides in the genes that encode SSU rRNAs from diverse organisms are aligned and pairwise comparisons of the sequences are made - for each pair of gene sequences the number of difference in nucleotide sequences is counted - value serves as a measure of the evolutionary distance between the organisms - more differences counted the greater the evolutionary distance
Explain pili and fimbriae
- short, thin hairlike proteinanceous appendages - up to 1000/cell - slender tubes composed of helically arranged protein subunits - can mediate attachment to surfaces, motility and DNA uptake - self assemble - made of one type of protein - IV pili are involved in motility and the uptake of DNA during the process of bacterial transformation - gram positive bacteria usually have at least two types of pili and both are involved in attaching the bacteria to surfaces
Explain slime layers
- similar to capsules - easily removed by washing - dilute version of a capsule -gliding bacteria often produce slime
Explain lactose perease of E. coli as secondary active transport
- single protein that transports a lactose molecule inward as a proton simultaneously enters the cell - proton is moving down proton gradient and the energy released drives solute transport - when lactose and a proton bind to separate sites on the outward facing conformation the protein changes to its inward facing conformation and the sugar and proton are released into the cytoplasm
Explain Anammoxome
- site of anaerobic ammonia oxidation - contains group of lipids called ladderane lipids - ladderane lipids have two or more cyclobutate rings and they pack together very tightly
What is an anammoxosome?
- site of anaoxic ammonia oxidation which is an unusual metabolic process that is important in the nitrogen cycle
Explain ribosomes
- site of protein synthesis - made up of a number of specific ribosomal proteins and RNA - 15 by 20 nm - bacterial ribosomes are smaller then eukaryotic ribosomes - bacterial ribosomes have two subunits - bacterial ribosomes are composed of different proteins and RNAs than eukaryotic ribosomes - 3 individual RNAs : 5S, 16S and 23S - 55 ribosomal proteins - cytoplasm full of ribosomes 20,000/cell - number of ribosomes per cell depends on growth rate and nutrition - more ribosomes the faster the growth rate - to increase protein synthesis more ribosomes must be made as the speed of protein synthesis does not change within a ribosome - some ribosomes may be attached to the plasma membrane - cytoplasmic ribosomes synthesize proteins that will remain in the cell - plasma membrane ribosomes make proteins that will reside in the cell envelope of get transported outside of the cell - since ribosomes are the site of protein synthesis and protein synthesis is vital for the bacteria to live and bacterial ribosomes are different from eukaryotic ribosomes there are organic compounds which can inhibit bacterial protein synthesis without also inhibiting bacterial synthesis - these compounds are selectivly toxic to bacterial but not eukaryotes, these include: streptomycin, tetracycline, erythromycin, chloramphenicol
Explain gliding motility
- slime released from cell and this slime pushes the cell forward - may involve IV slime - smooth movements
Explain the differences in the ribosomal subunits
- small and large subunit - 50S and 30S - 16S rRNA in the small subunit - 23S rRNA and 5S rRNA in the large subunit - 21 ribosomal proteins in the small subunit - 34 ribosomal proteins in the large subunit
Explain inclusion bodies
- small particle like structures usually visible by light microscope found in the cytoplasm - formed by aggregation of substances - usually contain storage material - reduce osmotic pressure by tying up molecules in a particulate form - not always present, depends on nutritional status and environment - culture dependent some amorphous - some lie free in cytoplasm, some enclosed by shell that is single layered and may consist of proteins and phosphoplipids - some surrounded by invaginations of the plasma membrane - ex. glycogen, poly-beta-hydroxy butrate (PHB), cyanophycin, polyphosphate, sulfur granules, carboxysomes, gas vesicles, magnetosomes
Explain motility in mycococcus xanthus
- social motility occurs when large groups of cells move together in a coordinated fashion and is mediated by type IV pili - adventurous motility by gliding and observed when single cells move independently
Explain phylum Planctomycetes
- some members of this phylum have their genetic material enclosed in a membrane - others have membrane bound organelle called the anammoxosome
Explain growth factors
- some microbes are unable to synthesize certain molecules needed for survival and they must be obtained from the environment - amino acids - purines and prymidines - vitamins
Explain cyclo rings in bacterial fatty acids
- sometimes rings can occur in the fatty acid tail - often a stress responce
Explain periplasmic space
- space between cytoplasmic membrane and cell wall - consists of periplasm - molecules can get into and out of periplasm - external compartments for bacteria - proteins cannot go through peptidoglycan so they are put in periplasm - gram positive bacteria have thin periplasm - gram negative have large periplasm, 30-70 nm wide and 20-40% of cell volume - gram negative peptidoglycan sits inside the periplasm - in gram positive bacteria some enzymes are found in the periplasm because peptidoglycan is porous and many proteins translocated across the plasma membrane pass through peptidoglycan - toxins diffuse out of periplasm
Explain porin protiens
- special portions found in outer membrane - narrow tube shaped and water filled - nutrients cannot diffuse though the outer membrane - Clumps in 3's - associated together as trimmers to form a pore though outer membrane - allows various molecules up to 600-700 Da to diffuse through outer membrane - larger molecules cross the outer membrane through specific carrier proteins that deliver the molecule to ABC transporters - Different types of porins allow different molecules to pass though - porins are selective for size, charge, etc
Explain the black death plauge
- struck europe in 1347 - arthropod borne disease - killed 1/3 of population within 4 years - disease struck repeatedly through next 80 years - killed 75% of european population
Explain hopanoids
- structure similar to cholesterol - bacteria does not contain cholesterol - hydrocarbon lipids - function is unknown, may contribute to stability of the membrane - when a bacteria dies, hopanoids are slow to degrade and their degration products build up in the environment
Explain facilitated diffusion
- substances move across the plasma membrane with the assistance of channels or carriers - rate increases with the concentration gradient - when transporter is a carrier the diffusion rate reaches a plateau above a specific gradient value because the carrier protein is saturated and transports as many solute molecules as possible - concentration gradient spanning the membrane drives the movement of molecules - no metabolic energy input is required - gradient can be maintained by transforming the transported nutrient to another compound which occurs when nutrient is metabolized - after solute molecule binds to outside the carrier changes conformation and release the molecule on the cell interior - carrier subsequently changes back to original shape and is ready to pick up another molecule - hydrophilic molecule can enter cell in responce to concentration gradient - not a major uptake mechanism
Explain gram positive cell walls
- thick - contain teichoic acids - many belong to phyla Firmicutes and Actinobacteria - large number of enzymes attached to peptidoglycan layer at cell surface - these enzymes have characteristic tail which allows them to covalently attach to peptidoglycan - enzymes are often involved with pathogenesis
Explain flagella
- threadlike, locomotor appendages extending outward from plasma membrane and cell wall - some bacteria are more virulent because they are motile - protein is specific to the particular bacteria - runs off of membrane potential - protons move down flagellum to the cell to create energy as they are moving down a concentration gradient, when protons move away from the cell down the flagellum this uses energy - L and P rings are only in gram negitives
What are conjugative plasmids
- transfer of DNA from one cell to another - have sex pili and can perform conjugation
Explain PTS
- transport a variety of sugars while phospholating them using PEP as the phosphate donor - PEP is high energy molecule that can be used to synthesize ATP - when used in PTS reactions the energy present in PEP is used to energize uptake rather then ATP synthesis - transfer of phosphate from PEP to the incomeing molecule involves several proteins and is an example of phosporelay system - E.coli and Salmonella the PTS consists of two enzymes and a low moleculear weight heat stable protien (HPr) - phosphate is transfered from PEP to enzyme II with the aid of enzyem I and HPr - Enzyme II then phsophorylates the sugar molecule that is carried across the membrane - Many facilitativly anaerobic bacteria have PTS - Most aerobic bacteria lack PTS - Many carbohydrates are transported by PTS - PTS can bind chemical attractants toward which bacteria move by chemotaxis
Explain the functions of membrane associated protiens
- transport of nutrients across the membrane - energy generation by photosynthesis and oxidations - chemotaxis and motility
Define active transport
- transport of solute molecule to higher concentrations with the input of energy - involves carrier proteins - carrier proteins bind particular solutes with great specify
What are carriers?
- transport protein - carry nutrients across the membrane - shows alot of specificity
What are channels?
- transport protein - form pores in membranes in which substances can pass - often involved in facilitated diffusion - show some specifity for substance that pass through
Explain methyl group substitutions in bacterial fatty acids
- two methyl groups can be on the end of a fatty acid tail
What is T3SS
- type 3 secretion system - may have evolved from flagellar secretion system
Explain actinomycetes
- typically form long filaments called hyphae ex streptomyces - hyphae can branch and produce network called mycelium which is similar to eukaryotic filamentous fungi - bacilli that branch - long thin tubes - when growing on petrie dish will form areal mycelia that look fuzzy and form spores that are often differently colored
What are some properties of protozoa?
- unicellular - animal like protists - motile - free living protozoa function as the principle hunter and grazers of the microbial world - some are normal inhabitants of the intestinal tracts of animals where they aid in digestion of complex materials such as cellulose
Explain Svedberg unit
- unit of sedimentation coefficent - a measure of sedimentation velocity in a centrifuge - the faster the particle travels when centrifuged the greater its Svedberg value - function of the particles molecular weight, volume and shape - heavier and more compact particles have larger Svedberg numbers
What is anarobic microbiology?
- use glass box with gloved holes - filled with N2, 5% CO2, 5% H2/CH4
Explain light microscope and section of focus
- when looking through light microscope you only have small section of focus and therefore when your focus is in the middle of the cell the object will be bigger/fatter then other areas
Explain twitching motility
- when pili become shorter, jerky movements result - may involve type IV pili - hydrolysis of ATP powers extension/retraction of IV pili
What was the earths atmosphere before 2.5 BYA
- world was anaerobic - CO2, N2 and a little H2
Explain the great oxidation event
-2.5 BYA - concentration of oxygen went up from 0.1% to 1% - world contained N2, CO2 and O2 but no H2 - world was aerobic - Oxygen releasing photosynthesis occurred by cyanobacteria - all iron in ocean was oxidized to FeO to make oxygen in the atmosphere
When did the earth form? How do we know?
-4.5 BYA - date is obtained from decay of radioisotopes, uranium 238 decay to lead-206 with a half life of 4.5 billion years
What is the function of the plasma membrane?
-Selectively permeable barrier - mechanical boundary of cell - nutrient and waste transport - location of many metabolic processes - detection of environmental cues for chemotaxis
How do bacilli and cocci vary in size?
-baciili varies in length from 1-3 micrometter and in width by 0.5-1 micrometers - cocci vary from 0.5-5 micrometers
Explain spectrum of activity
-certain antibiotics kill only certain types of bacteria - gram negative bacteria are harder to treat then gram positive - magnessium is counter ion for gram negative outer membrane which is why gram negative are protected from many antibiotics - hard to diffuse something into gram negative cell because of barrier
What are prochlorococcus?
-cyanobacteria - thought to be the most abundant photosynthetic organism
Explain cell membrane lipid fatty acids
-fatty acids are generally medium in chain length (C12, C14, C16) - usually fully saturated fatty acids, not many unsaturated - bacterial fatty acids may include many modifications not often seen in eukaryotes such as methyl group substitutions, hydroxyl group substitutions and cyclo rings - the fatty acid composition of the membrane changes in different environments
What are hopanoids
-synthesized from the same precursors as steroids and they stabilize the membrane - bacterial membranes dont have cholesterol instead they have hopanoids
What is the minimum DNA size for free living cells
0.58 mpb
When did multicellular organisms exist?
1 BYA
When did multicellular eukaryotic organisms first appear?
1.5 BYA
When did eukaryotic cells first appear?
2.5-2.0 BYA
When did diasours and mammals first appear?
225 MYA
When did dinosaurs exist?
270 MYA
When did fossils of primitive filametous microbes appear?
3.5 BYA
When did the first cells appear?
3.8-3.5 BYA
When did first reptiles appear?
300 MYA
When was the first fossilized cyanobacteria?
4 BYA - inside had organic carbon/kerogen, this was believed to be the living part of the cell
How long could life not live on earth?
4.5-4 BYA life could not live on earth, conditions on earth were too harsh to sustain life
When did large terrestrial colonization of plants and animals appear?
450 MYA
When was the Cambrian explosion?
500 MYA
When did first vertebrates and first land plants appear?
520 MYA
When did hominids first appear?
7 MYA
When did sponges exist>
700 MYA
What is the reducing/neutral atmosphere?
CO2 and N2
What are diplococci/diplococcus?
Cocci divide and remain in pairs
Explain the parts of the flagella
Filament - extend from cell surface to the tip - hollow, rigid cylinder of flagellin protein - ends with a capping protein and may have sheath covering it Hook - links filament to basal body - hook attaches to basal body and turns 90 degrees to attach to filament - wider then filament - made of different protein subunits Basal body - series of rings that drive flagellar motor -embedded in the cell envelope - in gram negatives have 4 rings: L, P, MS, and C which are connected to the central rod - L, P and MS rings are in the cell envelope - C ring is on the cytoplasmic side of the MS ring - gram positive bacteria have 2 rings, an inner ring connected to the plasma membrane and an outer ring attached to peptidoglycan
What is phototaxis?
Move in responce to light
What is osmotacis?
Move in responce to osmotic pressure
What is aerotacis?
Move in responce to oxygen
What is thermotaxis?
Move in responce to temperature
What are Hyphomicrobium?
Oval to pear shaped members produce a bud at the end of long hypha
What are viroids composed of?
RNA
What are coccobacilli?
Short bacilli that resemble cocci
What are cocci/coccus?
Spheres
Explain what microbial evolution is based on
The scientific method Formulation of hypothesis, the gathering and analysis of data, reformation of hypothesis based on newly acquired evidence
What is the function of the gas vacuole?
an inclusion that provides buoyancy for floating in aquatic environments
What is the function of the fimbriae and pili?
attachment to surfaces, bacterial conjugation and transformation, twitching and gliding motility
What are sarcina?
cocci divide in 3 planes producing cubical packet of 8 cells
Explain species in bacteria and archaea
collection of strains that share many stable properties and differ significantly from other groups of strains
What are vibrios?
comma shaped bacilli
Define strain
consists of the descendants of a single, pure microbial culture
All aerobic organisms have blank
cytochrome oxidase molecules
What are morphovars?
differ morphologically
What are staphylococcus?
divide in random planes to generate irregular grapelike clumps
What are tetrads?
divide in two planes to form square groups of 4 cells ex. Micrococcus
What are mycorrhiza?
fungi transfer nutrients to the roots, improving growth of plants
What is GRAS?
generally regarded as safe
Explain species in plants and animals
group of interbreeding or potentially interbreeding natural populations that is reproductively isolated from other groups, also appropriate for many eukaryotic microbes that reproduce sexually
What are serovars?
have distinctive properties that can be detected by antibioties
What are some enzymes found in gram positive periplasm
in gram positive bacteria some enzymes are found in the periplasm because peptidoglycan is porous and many protiens translocated across the plasma membrane pass through peptidoglycan - exoenzymes which degrade macromolecular nutrients -periplasmic enzymes are usually attched to the cytoplasmic membrane and involved in interactions of the cell with its environment, some are noncovalently bound to teichoic acids
What is the function of the nucleoid?
locatization of genetic material
What are streptococcus?
long chains of cocci that have divided in only one plane
What is curing
loss of plasmids during replication
Define uniporter
move single molecule across the membrane
What are satellite composed of?
nucleic acid often RNA
What is a phylogentic taxonomy?
organizing living things into system based on decent
What are pathovars?
pathogenic strain distinguished by the plants in which they cause disease
Define cell envelope
plasma membrane and all surrounding layers external to it
What are episomes
plasmids that can integrate into the chromosome
What is the function of the cell wall?
protection from osmotic stress helps maintain cell shape
What are viruses composed of?
protein and nucleic acid
What are prions composed of?
protien
What is the function of the Ribosomes?
protien synthesis
What is the function of the capsules and slime layers?
resistance to phagocytosis adherence to surfaces
What are spirilla?
rigid spiral shaped cells, many have tufts of flagella at one or both ends
What is the function of the inclusions?
storage of carbon phosphate and other substances
What is the function of the endospore?
survival under harsh environmental conditions
What is the function of the flagella?
swimming and swarming motility
What is phenetic?
using characteristic traits to classify bacteria
What is pleomorphic?
variable in shape and lacking single characteristic form ex. corynebacterium
What are biovars?
variant strains characterized by biochemical or physiological differences
Define symport
when ion and other substance both move in the same direction
Define antiport
when ion and other substance move in opposite directions