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158 Cards in this Set
- Front
- Back
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5 characteristics shared by most living systems.
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Metabolism
Evolution Reproduction (growth) Communication Compartmentalization |
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Cells as Machines
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"Chemical Machines" - supply energy and precursors for biosynthesis of macromolecules.
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Where are most prokaryotic bacteria on earth located?
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Water/Ocean
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Biotechnology
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Use of organisms, (usually genetically altered) in industrial, medical, or agriculteral applications.
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Genetic Engineering
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Apply gene/DNA tech to develop products by transferring genes into rapidly growing MO (in vivo)
(ex Vaccines, HGH) |
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Cells as Coding Devices
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"Computers" -stores and processes DNA to pass-on/replicate to daughter cells.
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Lysozyme
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-Is present in tears.
-Hydrolyzes/lyses the beta 1,4 glycosidic bond between the two amino sugars of peptidoglycan. -degrades the bacterial cell wall. |
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Membranes of eukaryotes
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-Contain Sterols
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Endospores of bacteria
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-calcium plays a role in dehydration.
-is very dehydrated structure not used for reproduction. -located w/in sporangium. -contains dipicollinic acid complexed with calcium -is released when the cell lyses (germination) -stains green -produced by certain Bacteria. -resistant to extreme conditions. -Can remain dormat for long periods of time -Most commonly found in soil. (Bacillus & Clostridium) |
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Koch's postualates
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1. The MO is found in the diseased organism but not in healthy
2. The microorganism can be isolated in pure culture from the diseased organism 3. Include that the disease is produced when a pure culture of the MO is in injected into a susceptible animal 4. The organism should be reisolated and shown to be the same as the original. |
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A long aliphatic hydrocarbon
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-is non-polar or hydrocarbon
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RNA differs from DNA
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-in that uracil replaces thymine
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In Carl Woese 3 biological kingdoms, which is a true bacteria?
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Eubacteria
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Bacteria were placed in what kingdom by Whitaker's 5 Kingdom scheme?
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Monera
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LPS
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-is endotoxic
-outer o-specific polysaccharide -Core polysaccharide layer -Lipid A layer |
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In the ABC transport, the binding protein that first binds the solute as it enters through the porin is found in what?
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periplasm
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Primary structure of a protein
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-a non-repetitive heteropolymer
(determined by a sequence of nucleotides in mRNA codes for sequence of amino acids) |
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Which structures may include a disulfide bride?
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-tertiary
-quaternary |
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Bonding between the carbonyl oxygen and the immino hydrogen of the nitrogen produces a coil region ...
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-that is called an alpha helix
-due to H bonding |
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What happens when a gram positive microorganism is treated with lysozyme in a hypotonic environment?
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-the cell membrance lyses
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As the A-T content of DNA gets higher ...
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-DNA melts at a lower temperature
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Naming Genus and Species
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-First letter of genus name is always capitalized
-Species name is not cap. -Genus & Species names are always italicized or underline |
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Integral proteins
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-are amipathic
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Ampipathic
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-have both hydrophobic and hydrophilic regions
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Antiport
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-active transport driven by an ion gradient
-one ion enters against the concentration gradient in one direction and another molecule in the opposite direction enters down the concentration gradient. |
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ATP hydrolysis
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-is associated with the ABC transport in addition to a transmembrane protein.
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Saturation Kinetics
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-facilitated diffusion
-at high external solute concentration, no increase in transport velocity -at low solute concentration, a linear increase in velocity transport |
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Ribosome
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-invariant structure
-of eucaryotes are ALL 80S |
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The major functions of the bacterial cell wall?
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-determine shape
-to prevent lysis of cells in dilute solutions |
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Which types of of molecules can most easily pass through the cell membrane without the help of a carrier?
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-small & nonpolar
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Hopanoids
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-are similar to sterols
-can be found in some procaryotic membranes -may stabalize membranes so they can survive in adverse environments |
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Penicillin
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-resembles Dalanyl-D Alinine
-inhibits the transpeptidase enzyme (cell wall) |
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What forms a phospholipid mole?
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-1 mole phosphate
-1 mole glycerol -2 moles fatty acid -removal of 3 moles H2O |
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Archae membranes may have ...
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-C-O-C linkages (ether)
-have isoprene instead of fatty acid chains -ether linkages are between glycerol & isoprene units |
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Bacterial cell walls
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-the first amino acid attached to muramic acid is alanine.
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What has mitochondria?
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-algae (never bacteria)
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Gram positive cells
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-have teichoic acids
-may have a glycine pentapeptide bridge for the crosslink |
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Messelsohn Stahl experiment
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-N15 was used to grown the cells initially (prior to first generation growth)
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Coenzyme
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-made by a microorganism
-necessary for the growth of the cell -primary a metabolite (because it's growing) |
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Bacterial flagellum
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-rotates like a propellar
-single microfibril -MS & C rings are in the cell membrane & cytoplasm -Mot proteins surround MS&C and generate torque and proton motive force provides the energy |
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The outer membrane
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-contains the LPS endotoxic layer of gram negative cells
-has porins that serve as channels to bring in hydrophilic low molecular weight substances -is impermeable to small hydrophobic molecules |
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DNA
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-are antiparallel
-one strand runs 5' to 3' and the other 3' to 5' from top to bottom -in procaryotes is double stranded and in form of a circle -in PC is not separated from nucleus by a nuclear membrane -in PC has introns and exons -in EC binds with basic proteins called histones |
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Gram negative cell walls
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-have less crosslinks in peptidoglycan than gram+.
-lack teichoic acids. |
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As the radius of the cell decreases ...
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-its surface area to volume equals 3/r
-it transports nutrients more efficiently. |
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The Central Dogma of Molecular Biology ...
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-includes DNA serving as template for its own replication
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Viruses
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-are acellular
-could consist of both RNA and protein |
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Group translocation
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-when an amino acid is decarboxylated (converted to an amine) by an enzyme located in the membrane as it is transported across the membrane by a carrier.
-phosphoenol pyruvate is the phosphate donor. |
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Bonding between bases in DNA
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-a purine hydrogen bonds to a pyrimidine
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Pillus
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-is found in the F+ cell
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A Sugar or monosaccharide
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-consists of a poly-hydrocarbon with an aldyhyde or ketone when drawing the lnear structure.
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Viroids
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-acellular
-consist of ONLY RNA |
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As the G/C content of DNA increases ..
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-more hydrogen bonds stabilize DNA
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RNA
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-regions of hydrogen bonding may produce secondary structure
-the number 2 carbon has a hydrogen and a hydroxyl |
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Quaternary Structure
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-one polypeptide is connected to another by a covalent bond.
-usually forms a disulfide bond -Two alpha polypeptide chains associate with two beta polypeptice chains. |
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ABC transport
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-uses a periplasmic protein to bind solute prior to transmembrane protein.
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When a gram positive MO is treated w/lysozyme in an isotonic environment ...
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-a protoplast is produced
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Thymine
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-in the enol form hydrogen bonds to guanine
-in the keto form it hydrogen bonds to adenine -always hydrogen bonds to adenine |
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In the eukaryotic and eubacterial cytoplasmic membranes ...
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- some peripheral proteins have a lipid tail to anchor protein to membrane.
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Cell membrane
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-permeability barrier
-protein anchor -site of the generation of the proton motive force -site where 1 of the rings of the bacterial flagellum attach |
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The region that contains peptidoglycan is found were?
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-In the region between the outer membrane and the cytoplasmic membrane of gram negative cells.
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Symport
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-active trnsport driven by an ion gradient in which one ion enters against the concentration gradient in one direction and another molecule in the same direction enters down the concentration gradient.
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Hopanoids
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-stabilize membranes of eubacteria
-have a structure similar to sterols -can be found in some procaryots |
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Penicillin
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-is a competitive inhibitor of the transpeptidase enzyme.
-Resembles Dalanyl-D Alanine |
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Archaea cell membrane
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-has ether linkages (C-O-O)
-has side chains composed of repeating units of isoprene (instead of fatty acid chains) |
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Peptidoglycan
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-is a repetitive heteropolymer
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Teichoic Acids
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-are acidic polysaccharides embedded in gram+ cell walls
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What has no nuclear membrane?
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-eubacteria
-archaebacteria |
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The outer membrane of gram-
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-requires proteins called porins to serve as channels for small hydrophilic molecules
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Benzene
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-a six C ring that has alternating single and double bonds
-and aromatic hydrocarbon |
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Primary metabolite
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-an amino acid made by a MO and used to make the polypetides required by this MO (for growth).
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Carl Woese
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-used data from RNA fingerprinting of ribosomal RNA to create a 3rd biological kingdom/domain
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Where were Protozoans placed in the 5 kindom scheme?
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-Protista
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Terminal bond
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-removal of water between an alcohol and a phosphoric acid.
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Phospho-diester bond
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-removal of water between 3' hydroxyl on one nucleotide sugar and the 5' phosphate on another.
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Peptide bond
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-removal of water between the amino group on the alpha C of one amino acid and the carboxyl group of another
amino acid. -covalent bond joining amino acids in a polypeptide. |
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N terminal
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-the end of the molecule (by convention) on the left.
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Endospore components
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-Exosporium (protein)
-Spore coat (protein) -Cortex (peptidoglycan) -Core (protoplast) |
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Chemical substance found in endospores but not in vegetative cells
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-Dipicolinic acid
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Monera
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-One of Whitaker's 5 Kingdoms
-prokaytotic & unicellular includes: bacteria, blue-green algae |
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Removal of water between a hydroxyl group of one deoxy-sugar and the phosphate group of a second deoxy-sugar produces a ____ bond between the nucleotides in DNA?
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3'5' phosho-diester
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Periplasm
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the binding protein that first binds the solute as it enters through the porin during the ABC transport.
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Primary protein structure
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-non-repetitive heteropolymer
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What type of proteins are embedded in the cell membrane?
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-ampipathic
-integral |
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Secondary metabolites
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-molecules made by the bacterium that are not necessary for growth
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What happens when a gram- MO is treated with lysozyme in a isotonic environment?
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-a spheroplast is formed containing pieces of undigested wall material
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As a cell increases in size
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-it transports nutrients less efficiently
-the surface area to volume ratio decreases |
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Pasteur
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-developed heat as a sterilization technique.
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What 2 functional groups are present for a sugar or monosaccharide?
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-hydroxyl
-aldehyde |
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Secondary Structure
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-alpha helix
-beta pleated sheet -occurs when the sequence of amino acids are linked by hydrogen bonds |
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Protozoa were placed in what kingdom by Whitaker's 5 Kingdom scheme?
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-Protista: Eukaryotic & unicellular (also includes algae)
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What is NOT a characteristic of all cells?
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-presence of cell wall
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Five major characteristics of cells
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-self-feeding or nutrition
-self-replication -evolution -chemical signaling |
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Periplasm
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-the whole region between the cell membrane and the LPS
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Nucleoside phosphate
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-consists of a base bound to a sugar phosphate
-is the subunit of nucleic acids -is a nucleotide |
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What would not be aromatic?
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-a aliphatic carbon chain containing single bonds between C & H and C & C.
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What would be aromatic?
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-benzene
-pyrimidine -non-polar or hydrophobic -a ring containing alternating double & single carbon to carbon bonds |
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Gram negative bacteria
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-have a direct crosslink between diaminopimelic acid on one chain & alanin on another.
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Phosphate ester
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Removal of water between a phosphoric acid and an alcohol.
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Hydrophobic attractions
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-nonpolar - non polar attractions
-2 R groups of amino acids that are nonpolar attracting one another in the interior of the polypeptide. -oil droplets in water comming together -most of the surface amino acids in a polypeptide attracting to water |
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Hydrophilic attractions
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C16 fatty acid tails associating with one another
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Cytochrome electron transport chain & Krebb's cycle enzymes are located in ...
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-cell membrane
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Eukaryotic Flagellum
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-wave-like motion
-(9x2)+2 microfibril arrangement |
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Bonds between the carbonyl oxygen of one amino acid in a polypeptide and the immino hydrogen in another (N-H......O=C)
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-are hydrogen bonds
-are part of secondary structure |
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Bonding between a pyrimidine and a purine
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-is hydrogen bonding between nucleotide bases
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What are Carl Woese 3 biological kingdoms?
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-Eukaryotes
-Eubacteria -Archaebacteria/Archaea |
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Hydrogen bond
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-the bond which stabilizes the alpha helix in the secondary structure of protein
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Sulfahdral bond
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-the covalent bond participating in tertiary structure
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The R groups of the fatty acids esterfied to glycerol in the cell membrane phospholipids are ...
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long nonpolar aliphatic hydrocarbon chains.
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Influenza
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-early 1900s
-more Americans died than were killed in 4 wars. |
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Small pox
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-10 million people killed
-brought by spanish -no new cases since 1977 |
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Black plague
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-1/3 pop of Europ (25 mil) died
-Antibiotics have controlled |
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Emerging Diseases
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-Legionnaires' Disease
-Lyme Disease -AIDS -Hantavirus Pulmoney Syndrome -Mad Cow Disease -SARS |
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Industrial Microbiology
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conversion of raw materials into desirable end products by selected microorganisms
(Primary & Seconday metabolites) |
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Primary Metabolites
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production of products necessary for microbial growth
(amino acids, organic acids, alcholo, certain enzymes, etc) |
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Secondary metabolites
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production of products by microorganisms NOT necessary for its growth (antibiotics, steroids, etc)
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Gentech
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-microbiology hits wall st. 1980s
-apply gene technology/recombinant DNA tech to development of products |
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Bioremediation
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the use of living organisms to degrade pollutants in the environment
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Anton van Leeuwenhoek
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1684- first observation of bacteria
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Jenner
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1798- introduces sm pox vaccination
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Pasteur
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1864- developed heat sterylization methods
-disproved spontaneous generation |
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Robert Koch
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1881- grows pure culture of anthrax
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Development of Microbiology
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latter 1800's/ 1850-1900
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Resolving power
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diameter of smallest resolvable object = wavelength/2xNA
-the smaller the # the better the resolution (.2 better than 1) |
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Phylogeny
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permits groupiing of organisms based on the evolutionary lines of decent
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Taxonomy
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groups organisns for convenience of laboratory study
-focuses on phenotypic differences |
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E.H. Haekel
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1866- proposed a 3rd biological kingdom: Potista (added onto the Linean System: Animalia & Plantae)
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Haekel's Protista
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-unicellular, or if muticellular they do not develop diff. tissues (algae, fungi, protozoa, bacteria, cyanobacteria)
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Stainer's division
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divided protista: 1)Higher (eukaryotic cell structure)-algae, protozoa, fungi. 2)Lower (prokaryotic)-cyaobacteria & bacteria
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Whittaker
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1969- 5 Kingdom (3 levels)
I. Monera: Prokaryotic & Unicellular II. Protista: Eukaryotic & Unicellular III. Plantae:Photosynthesis> IV. Fungi: Absorption>Eukaryot V. Animalia Ingestion>& MultiC |
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Carl Woese
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1977- discovery of comain Archaea
-used rRNA 3 Domains: I Baceria (Eubacteria=all procaryotes) II Archaea=all procaryotes III Eukarya= all eukaryotes |
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5 Kingdoms vs. Domains
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-5 kingdoms do not represent 5 evolutionary lines.
-Cell life evolved from 3 lineages called domains -2 D are microbial -3 D includes the original 5 K-Monera |
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Eukarya classification scemes
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-Diplomonads
-Trichomonads -Flagellates -Slime Molds -Diatoms -Ciliates* (early-branching lack Mitochondria) |
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Classification and ID
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I. Staining properties
II. Cultural Characteristics III Biochemical & Physiological Properties IV. Serological Properties V. Genetic Studies |
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Staining properties
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-Simple or Negative stains-Morphology & size
-Differential Stains-Gram reaction -Structural Stains: spore, capsule, flagellum |
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Spore
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-Clostridium (Gm+, anaerobic rod)
-Bacillus (Gm+, aerobic rod) -Sporosarcina (coccus) |
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Biochemical & Physiological Properties
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(at enzyme level)
-Most classification is done at this level. |
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Cultural Characteristics
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-macroscopic appearance of growth (ex. Broth, deeps, dlants, colonies)
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Serological Properties
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Immunological, antibodies, etc.
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Genetic Studies
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GC/AT ratios, hybridization, sequence analysis
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Naming
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Genus (first letter Caps)& Species (not caps)-both are always italicized or underlined
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Viruses
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-DNA or RNA(usually smaller genome size than bacteria-cause bacteria have both DNA & RNA)
-Protein coat |
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Viroids
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-ONLY RNA
-No protein coat |
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Prions
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-ONLY Protein
-No protein coat |
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Organic Chemistry
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-study of carbon containing compounds (central importance to living organisms)
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Carbon
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-4 valance electrons
-can share 4 e- to from 4 covalent bonds |
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Carbon Skeletons
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-carbon atoms can join to form: chains, branched trees, or rings
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Covalent Bond
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-2 atoms share one or more electrons
-Intramolecular bond |
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C-H Compounds
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-C & H together make stable compounds=hydrocarbons
-nonpolar -do not form hydrogen bonds -insoluble in water |
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Weak Non-covalent Bonds
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-Important in DNA
-tight binding only when many are formed simultaneously (Van Der Waals, Hydrogen, Hydrophobic, Ionic) |
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Hydrogen Bonds
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-form when "sandwiched" between 2 electron attracting atoms (usually O or N)
-are weak in water because of competition with water molecules |
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Hydrophobic Forces
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-attraction is caused by a repulsion from the water
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Ionic Bonds
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-force of attraction between two opposing charges
-in the absence of water are very strong -very weak in water or salt |
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Proteins in a cell
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(Amino Acids)
-Wall -Membrane -Cytoplasm |
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Nucleic Acids in a cell
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(nucleotide)
-Nucleoid (DNA/RNA) -Ribosomes |
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Polysaccharides
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(Carbohydrates/sugar)
-storage granules in a cell -many monomeric (individual glucose)covalently bonded= Glycosidic Bonds -long chain |
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Lipids in a cell
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(Fat)
-storage granules -cell membrane |
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Disaccharide
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-2 sugars(monosaccharides) joined by a glycosidic bond
(also trisaccharides=3, or oligosaccharide=several) |
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Carbohydrates (sugars)
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-organic compounds containing C, H, & O in a ratio of 1:2:1
-The most biologicallly relevant carbohydrates are those containing 4,5,6,&7 C |
