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A cell or organism that lacks a membrane-bound nucleus and other organelles
A cell or organism that has a membrane-bound nucleus and usually other organelles
importance of microbes
- 1. shape our environment
- 2. effect our health
- 3. They teach us biology and the limits of life, giving us insights into potential life on other planets
- 1. life does not spontaneously generate
- 2. disease linked to micorbes
- 3. microscope- seeing is believing
showed that maggots in decaying meat were the offspring of flies à higher organisms (maggots) do not arise by spontaneous generation
lazzaro spallanzani 1799
showed that a performed sealed glass flask of beat broth sterilized by boiling did not grow microbes à microbes do not arise by spontaneous generation
Louis Pasteur 1861
1861 – demonstrated conclusively that microbes do not generate spontaneously
devised “swan-necked” flasks and showed that, after boiling, the contents remained free of microbial growth despite access to air
Lucretius 98-55 BC
98-55 BC – suggested that disease was caused by living, invisible creatures
1835 - discovered that silkworm disease is caused by a fungus, proposed that many diseases are microbial of origin
- friend died after cutting himself after an autopsy
- 40% mortality rate of medical students
drew attention to significance of disease in warfare and founded medical statistics
father of epidemiology
- antiseptic surgery
- prevented post-op infection
- germ theory
- developed pure culture techniques
- Koch's postulates!
- 1. microorganism is found in all cases of disease but is absent from healthy individuals
- 2. microbe isolated from diseased host and grown in pure culture
- 3. when microbe introduced into healthy, susceptible host, same disease occurs
- 4.. The same strain of microbe is obtained from the newly diseased host
germ theory/koch's postulate
antonie van leeuwenhoek
- 1676 - observed both protozoa and bacteria using a handbuilt microscope (single-lens magnifiers)
- 1st observe bacteria!
- 1.Built the first compound microscope
- 2.Used it to observe mold
- 3. Published Micrographia, the first manuscript that illustrated objects under the microscope
- 4.Coined the term cell
bend and focus light
bending of a ray of light as it passes from one medium to another
- the ability to separate or distinguish between small objects that are close together
how to optimize resolution
- 1. light entering lens
- 2. contrast: b and w vs. shades of grey
- 3. lens quality: small imperfections have HUGE impact
bright field microscopy
- 1. visualize organisms based on a difference in color or density from the surrounding medium
- 2. simple stain: directly stains an organism (e.g., crystal violet)
- 3. differential stain: differentiates cells into groups based on their staining properties
- 1. heat fixed to slide
- 2. Crystal violet stains cell reversibly
- 3. add iodine
- 4. wash w/ ethanol: gram - LOSES color
- 5. add safranin: stains gram - red/pink
dark field microscopy
visualize organisms due to the light that they reflect the light is introduced obliquely (e.g., from the side)
phase contrast microscopy
visualize organisms due to the light that they reflect the light is introduced obliquely (e.g., from the side)
visualize external features of a cell
transmission electron microscopy
features of a cell
- (light microscopy)
- 1. shares high intensity laser light power
- 2. Can visualize cells in three dimensions
- 3. Allows observation of live microbes in real time
- 4.Enables researchers to see if cells are inside, on top of or below other cells or structures.
atomic force microscopy
- 1. tip moves down, cantilever/mirror is deflected
- 2. sample is moved back and forth in the xy plane
- 1.Thick, complex outer envelope
- 2.Compact genome
- 3.Tightly coordinated cell functions
- 1. like bacteria, are prokaryotes
- 2. Have unique membrane and envelope structures
Eukaryotic cells have a nucleus and extensive membranous organelles
- Cytoplasm:consists of a gel-like network
- Cell membrane:encloses the cytoplasm
- Cell wall:covers the cell membrane
- Nucleoid: non-membrane-bound area of the cytoplasm that contains the chromosome in the form of looped coils
- Flagellum: external helical filament whose rotary motor propels the cell
- 1. backbone of RNA
- 2. pentoses
- 3. polysaccharides
- 1. backbone of DNA
- 2. pentoses
- 3. polysaccharides
- 1. leads to different molecules
- 2. alpha 1,4 : starch
- 3. alpha 1,6: glycogen
- 4. Cellulose B 1,4
phosphate containing head with fatty acid tail
- 2 fatty acid chains, phosphoryl head group
- A. photphatidylglycerol
- B. phosphatidylethanolamine
- two c's : one with amine and R, and then other as carboxylic acid group
two amino acids, bond between hydroxide and h to be removed to remove out water
- hydrogen bonds between nearby amino acids
different types of chains, z(A, B chain, b sheet) and all squiggly mess
- 1. nucleic acids
- 2. pyridimine bases:
- a. cytosine
- b. thymine
- c. uracil
- 3. purine:
- a. adenine
- b. guanine
- made of nucleic acids
non membrane bound area of cytoplasm that contains chromosome in form of looped coil
- help bacteria move to and from stimuli, external helical filament whose rotary motor propels the cell
- to food, away from bleach, etoh, etc.
- so much like a bilayer
- lipid bilayer end up forming the membrane
- membranes where work is performed in order for cell to live
- H bonds between 2 columns
- column connects 5' to 3', opposite 3' to 5'
- cells must be broken up by techniques that allow subcellular parts to remain intact
- 2.ex/: mild detergent analysis, sonication, enzymes, mechanical disruption
- high rotation rate produces centrifugal forces strong enough to separate particles by size
- parts then tested for structural & biochemical analysis
- complimentary to cell fractionation
- strains can be intentionally mutated
- strains that are constructed w/ "reproter genes" fused to a gene encoding a protein of interest
common chemical components of bacteria
- 2. Essential ions
- 3.Small organic molecules
structure that defines existence of a cell
- 1. has equal parts phospholipids & proteins
- 2. 2 layers of phospholipids are called leaflets3. Membrane proteins serve numerous functions, including:
- a. Structural support
- b. Detection of environmental signals
- c. Secretion of virulence factors and communication signals
- d. Ion transport and energy storage
- 4.Have hydrophilic and hydrophobic regions that lock the protein in the membrane
- 5. cell membrane acts as a semipermeable barrier.
Small uncharged molecules, such as O2 and CO2, easily permeate the membrane
Water tends to diffuse across the membrane in a process called
Polar molecules and charged molecules require transport through specific protein
-molecules .move along their concentration gradient
molecules move against their concentration gradient
Cardiolipin or diphosphatidylglycerol
- 1.A double phospholipid linked by a glycerol
- 2. Concentration increases in bacteria grown to starvation
- 3.Localizes to the cell poles
Membranes also include planar molecules that fill gaps between hydrocarbon chains.
- 1.in eukaryotic membranes, the reinforcing agents are sterols, such as cholesterol.
- 2.in bacteria, the same function is filled by hopanoids, or hopanes.
- 1. the most extreme variations in phospholipid side-chain structures
- 2. Ether links between glycerol and fatty acids
- 3. terpenoids: hydrocarbon chains
- how prokaryotes protect cell membrane
- has peptidoglycan
- a few prokaryotes such as mycoplasmas, have a cell membrane with no outer layers
- single molecule
- bactreial cell wall
- single interlinked molecule
peptidoglycan structure (murein)
- 1. what most bacterial cell walls
- 2. long polymers of 2 disaccharides called N-acetylglucosamine & B-acetylmuramic acid bound to a peptide of 4 to 6 amino acids
- 3. peptides can form cross-bridges connecting the parallel glycan strands
- 1.unique to bacteria
- 2. enzymes responsible for its biosynthesis make excellent tragets for antibiotics
- a. penicillin inhibits transpeptidase that cross-links the peptides
- b. vancomycin prevents cross-bridge foramtion by binding to terminal D-Ala_D-Ala dipeptide
- 2. widespread use of such antibiotics selects for evolution of resistant strains
gram positive bacteria (thick cell wall)
- phylum firmicutes
- thick cell wall
gram negative bacteria
- thin cell wall
- phylum proteobacteria
- reinforicing agents (sterols) that are planar molecules that fill gaps between hyddrocarbon chains
- in eukaryotic membranes
- sterol in cell membrane that are planar molecules that fill gaps between hydrocarbon chains
- in bacteria
most diversity in phospholipid side-chain structures
- 1. ARCHAEA
- 2. ether links between glycerol and fatty acids
- 3. Hydrocarbon chains are branched terpenoids
- 1. The cell wall confers shape and rigidity to the cell, and helps it withstand turgor pressure
- 2. peptidoglycan
- 3. The cell wall confers shape and rigidity to the cell, and helps it withstand turgor pressure
- 1. Most bacterial cell walls are made up of peptidoglycan (or murein).
- 2. -Long polymers of two disaccharides called N-acetylglucosamine and N-acetylmuramic acid, bound to a peptide of four to six amino acids
- 3.The peptides can form cross-bridges connecting the parallel glycan strands
how antibiotics work
- 1. attack enzymes responsible for its biosynthesis make excellent targets for antibiotics
- 2. Penicillin inhibits the transpeptidase that cross-links the peptides
- 3.Vancomycin prevents cross-bridge formation by binding to the terminal D-Ala-D-Ala dipeptide
- 4.Unfortunately, the widespread use of such antibiotics selects for evolution of resistant strains
- 1. has glycocosyl chains
- 2. s-layer
- 3. peptidoglycan with teichoic acid
- 4. cell membrane and proteins
- 1. lipopolysaccharides (LPS)(outer membrane)
- 2. lipoproteins
- 3. periplasm
- 4. inner membrane
Gram-Positive Cell Envelope
- 1. Has multiple layers of peptidoglycan
- 2. Threaded by teichoic acids: give added rigidity to layer
- 3. capsule
- 1. most exterior layer?
- 2. -Made of polysaccharide and glycoprotein
- 3. -Protects cells from phagocytosis
- 4. -Found also in Gram-negative cells
- 1. An additional protective layer commonly found in free
- 2.living bacteria and archaea
- 3.Crystalline layer of thick subunits consisting of protein or glycoprotein
- 4. May contribute to cell shape and help protect the cell from osmotic stress
- 5. part of gram + cell envelope
mycobacterial cell envelopes
- 1. very complex cell envelopes
- 2. have mycolic acids:
- 3. arabinogalactans: unusual sugars
outer membrane of gram -
- 1. thin peptidoglycan layer consists of 1 -2 sheets
- 2. lipoprotein: INNER facing leaflet
- 3. lipopolysaccharides/porins: outward-facing leaflet, saccharide chains:
- A. increase diffusion rate
- B. helps attract water
- C. LPS can complicate antibody's perofrmance
- D. for pathogens, helps disguise its host
- 4. anything with lipo will go into membrane
- 5. LPS helps balance bacteria w/immediate environment
eukaryotic micorbes and osmotic shock
- 1. algae: form cell walls of cellulose.
- 2. Fungi: form cell walls of chitin
- 3. Diatoms: form exoskeletons of silicate
- 4. Paramecia: possess a contractile vacuole to pump water out of the cell
- 1.shape determining proteins
- 2. FtsZ = forms a "z-ring" in spherical cells
- 3. MreB: forms coil inside rod-shaped cells
- 4. CreS "crescentin": -forms a polymer along the inner side of crescent-shaped bacteria
Nucleus: euks vs. prok.
- 1. euks: have well-defined nucleus delimited by nuclear membrane
- 2. proks: have a nucleoid region that extends throughout the cytoplasm
- 1. in nucleoid
- 2. excluding a lot of protein
- 3. nucleoid forms about 50 loops or domains. Within each domain, the DNA is supercoiled by DNA-binding proteins.
- 1. proteins and DNA floating around "flag" or "anchor"
- 2. specific proteins recognize parts of DNA and code it back to flag "the origin"
- 3. proteins help bind, organize, and store DNA
Transcription and Translation
- 1. RNA polymerase transcribes DNA into a single strand of RNA.
- 2. For most genes, it is messenger RNA.
- A. mRNA immediately binds to a ribosome for translation into a polypeptide.
- B. This is aided by transfer RNA (tRNA), which brings the amino acids to the ribosome.
- D. In prokaryotes, translation is tightly coupled to transcription. (saves time!)
tells amino acids their own order to make proteins
PROKARYOTE Protein Synthesis and Secretion
- 1. membrane proteins and secreted proteins are synthesized in association with the cell membrane.
- 2. aided by signal recognition particle (SRP) which binds to growing peptide
- 3. proteins supposed to be outside
- 4. SRP takes protein sequence to transport protein that knows that specific code
- 5. SRP is recognized by protein
- 1.also named cell fission
- 2. , requires highly coordinated growth and expansion of all the cell’s parts.
- 3. Unlike eukaryotes, prokaryotes synthesize RNA and proteins continually while the cell’s DNA undergoes replication.
- 4. Bacterial DNA replication is coordinated with the cell wall expansion and ultimately the separation of the two daughter cells.
- 1. BIDIRECTIONALLY
- 2. In prokaryotes, a circular chromosome begins to replicate at its origin, or ori site.
- 3. Two replications forks are generated, which proceed outward in both directions.
- a. -At each fork, DNA is synthesized by DNA polymerase with the help of accessory proteins (the replisome).
- B. As the termination site is replicated, the two forks separate from the DNA
- 1. Replication of the termination site triggers growth of the dividing partition, or septum.
- 2.The septum grows inward, at last constricting and sealing off the two daughter cells
- 3. orientation of septum determines shape of cocci
- 1.parallel planes
- a. streptococci
- 2. Random planes
- 3. Perpendicular planes
- 1. polar aging: when bacterial cell poles differ in origin & "age"
- 2. In bacteria that appear superficially symmetrical, polar differences may appear at cell division
- 3. Some bacteria generate two kinds of daughter cells: one stationary and the other mobile
- 4. Example: the flagellum-to-stalk transition of the bacterium Caulobacter crescentus
- 5. poles of each daughter cell differ chemically from each other
- extensively folded intracellular membranes
- (a specialized structure)
- polyhedral bodies packed with the enzyme Rubisco for CO2 fixation
- (a specialized structure)
- to increase buoyancy
- (a specialized structure)
- 1. Specialized Structures
- 2. Glycogen, PHB, and PHA, for energy
- 3. Sulfur, for oxidation
- 1. Membrane-embedded crystals of magnetite, Fe3O4
- 2.Orient the swimming of magnetotactic bacteria
- 1. also named fimbriae
- 2. straight filaments of pilin protein
- 3. Used in attachment
- 4. sex pili used in conjugation- to pass DNA transfer between 2 bacterial cells
- 5. twitching motility
- 1. membrane-embedded extensions of the cytoplasm
- 2. Tips secrete adhesion factors called holdfasts
- 3. "glue" hold bacteria to specific surface
- 1. intercellular connections that pass material from one cell to the next.
- 2. can share cytoplasm to share food, communicate, etc.
- 1. how Prokaryotes that are motile generally swim by means of rotary
- 2. peritrichous cells have flagella randomly distributed around cell, hair all over bacteria!
- a. hair rotate together in a bundle behind the swimming cell
- 3. each is made of flagellin: a spiral filament of protein monomers
- 4. filament rotates by a omtor driven by proton motive force
- a. moves CW or CCW
- 1. movement of a bacterium in response to chemical gradients
- 2. Attractants cause CCW rotation.
- aFlagella bundle together - Push cell forward - “Run”
- 3. Repellents cause CW rotation.
- a. Flagellar bundle falls apart
- b. “Tumble” = bacterium briefly stops, then changes direction
- 4. alternating runs and tumbles cause a “random walk.”
- 5. receptors detect attractant concentrations
- a. sugars, amino acids
- 6. attractant concentration increases and prolongs
- a. sugars, amino acids
- 7. attractant concentration increases and prolongs run
- a. "biased random walk"
- b. causes net movement of bacteria toward attractants (or away from repellents)
Spore formation as virulence factor
- 1. Gram-positive rod; rods occur in chains
- 2. causes anthrax, which was the disease studied by Robert Koch when formulating the famous Koch's Postulates
- 3. forms endospores that can survive in soil and animal products for decades
- 4. most commonly mentioned candidate for biological warfare because the endospores are so resistant to drying that they can survive dissemination in the air; infection via inhalation has nearly 100% mortality rate
- function in attachment
- short and very thin
- up to 1000/cell
- functions in motility
motility in spirochetes
- 1.protoplasmic cylinder: inner cylinder
- rigid, generally helical
- 2. endoflagellum: rigid, rotates attached to one end of protoplasmic cylinder
- 3. outer sheath (flexible)
- 1. mitochondria and chloroplasts became eukaryotic organelles following the intracellular engulfment of prokaryotic cells
- 2. EVIDENCE, both m and c:
- a. outer and inner membranes: outer like euk's, inner like prok.s
- b. contain ribosomes that resemble those of bacteria (70s instead of 80s)
- c. contain DNA (unusual for an organelle) and that DNA is circular like a bacterial chromosome
- 4. replicate semi-autonomously, replication not fully coordinated with rest of cell
- -Major elements in cell macromolecules -
- C, O, H, N, P, S-
- Ions necessary for protein function - Mg2+, Ca2+, Fe2+, K+
- 1.Trace elements necessary for enzyme function
- 2.Co, Cu, Mn, Zn
defined minimal medium
- contains only the compounds needed for an organism to grow.
- Some organisms have adapted so well to their natural habitat that we still don’t know how to grow them in the lab.
1.obtain energy from oxidation-reduction reactions
- inorganic molecules as a source of electrons
- considered an autotroph
use organic molecules
proton motive force.
- 1.the H+ gradient plus the charge difference form an electrochemical potential
- 2.(A membrane potential is generated when chemical energy is used to pump protons outside of the cell)
- 3. The potential energy stored can be used to transport nutrients, drive flagellar rotation, and make ATP by the F1FO ATP synthase.
- 1. makes 79% of earths atmosphere
- 2. nitrogen fixers:possess nitrogenase, which converts N2 to ammonium ions (NH4+).
- 3. Nitrifiers: oxidize ammonia to nitrate (NO3–).
- 4. Denitrifiers: convert nitrate to N2
Selective permeability is achieved in three ways:
- 1.Substrate-specific carrier proteins, or permeases
- 2. Dedicated nutrient-binding proteins that patrol the periplasmic space
- 3.Membrane-spanning protein channels or pores
- 1. helps solutes move across a membrane from a region of high concentration to one of lower concentration.
- 2. -It does not use energy and cannot move a molecule against its gradient.
Coupled transport systems
- 1. are those in which energy released by moving a driving ion down its gradient is used to move a solute up its gradient
- 2. symport : travel in same direction
- 3. antiport: actively transported molecule moves in direction opposite to driving ion
- 1. largest family of energy-driven transport systems is ATP-binding cassette superfamily, or ABC transporters
- 2. found in all 3 domains of life
- 3. 2 main types:
- a. uptake ABC T's: critical for transporting nutrients
- b. Efflux ABC transporters: generally used as multidrug efflux pumps.
- 1. are specialized molecules secreted to bind ferric ion (Fe3+) and transport it into the cell.
- 2. iron released into cytoplasm and reduced to more useful ferrous (fe2+) form
- 3. recognizes transferin, protein stores iron
- 1.a process that uses energy to chemically alter the substrate during its transport.
- 2.phosphotransferase system (PTS) is an example present in all bacteria.
- 3. PTS attaches phosphate added to sugars so you get overall influx of sugars
- 1.We have succeeded in culturing only 0.1% of the microorganisms around us.
- 2. Microbes in nature exist in complex, multispecies communities, but for detailed studies they must be grown separately in...
2 main types of culture media
- 1. liquid or broth
- 2. solid (usually gelled with agar)
- a. useful for trying to separate mixed cultures form clinical specimens or natural environment
-Dragging a loop across the surface of an agar plate
-Tenfold serial dilutions are performed on a liquid culture-A small amount of each dilution is then plated
- are nutrient rich but poorly defined.
- liquid leftover from grinding meat
are precisely defined
are complex media to which specific blood components are added.
favor the growth of one organism over another
exploit differences between two species that grow equally well
Petroff-Hausser counting chamber
Microorganisms can be counted directly by placing dilutions on a special microscope slide,
Fluorescence-Activated Cell Sorter (FACS)
- laser hit cells emits fluroescent light off of bacteria cells and count those cells w/out destroying them
A viable bacterium is defined as being capable of replicating and forming a colony on a solid medium.-Viable cells can be counted via the pour plate method
Microorganisms can be counted indirectly via biochemical assays of cell mass, protein content, or metabolic rate.
where one parent cell splits into two equal daughter cells
- how long it takes bacteria to double
- 2^n , n = # of generations
or rate of increase in cell numbers or biomass, is proportional to the population size at a given time.
The simplest way to model the effects of a changing environment is to culture bacteria in a
cells in a population achieve a steady state, which allows detailed study of bacterial physiology.
- ensures logarithmic growth by constantly adding and removing equal amounts of culture media.
- ex/human gastrointestinal tract
- 1. In nature, many bacteria form specialized, surface-attached communities
- 2. one or multiple species, and can form on a range of organic or inorganic surfaces.
- 3. Bacterial biofilms form when nutrients are plentiful.
- Once nutrients become scarce, individuals detach from the community to forage for new sources of nutrients
- 4.Biofilms in nature can take many different forms and serve different functions for different species.
- 5.The formation of biofilms can be cued by different environmental signals in different species.
- 1.Clostridium and Bacillus species can produce dormant spores that are heat resistant.
- 2.Starvation initiates an elaborate 8-hour genetic program that involves:
- 3.An asymmetrical cell division process that produces a forespore and ultimately an endospore
- 4Sporulation can be divided into discrete stages based primarily on morphological appearance.
- 1.Bacteria faced with environmental stress undergo complex molecular reprogramming that includes changes in cell structure.
- 2.Examples include:-Endospores of Gram-positive bacteria-Heterocysts of cyanobacteria-Fruiting bodies of Myxococcus xanthus-Aerial hyphae and arthrospores of Streptomyces
Anabaena differentiates into specialized cells called heterocysts.-Allow it to fix nitrogen anaerobically while maintaining oxygenic photosynthesis
Myxococcus xanthus uses gliding motility.-Starvation triggers the aggregation of 100,000 cells, which form a fruiting body.
- 1.Streptomyces bacteria form mycelia and sporangia analogous to those of fungi.
- 2. As nutrients decline, aerial hyphae divide into arthrospores that are resistant to drying