Final Flashcards
Transcription:
DNA produces RNA
Translation:
RNA makes protein
Characteristics of Living Systems
Metabolism: chemical transformation of nutrients
Reproduction: generation of two cells from one
Differentiation: synthesis of new substances or structures that modify the cell (only in some microbes)
Communication: generation of, and response to, chemical signals (only in some microbes)
Movement: via self-propulsion, many forms in microbes
Evolution: genetic changes in cells that are transferred to offspring
Most microbial cells are found in
oceanic and terrestrial subsurfaces
The role of microbes in cleaning up pollutants
Bioremediation
Louis Pasteur
Discovered that living organisms discriminate between optical isomers
Discovered that alcoholic fermentation was a biologically mediated process (not abiotic chemistry)
Developed the Germ Theory that proposed and showed that germs cause disease
Developed vaccines for anthrax, fowl cholera, rabies
Disproved theory of spontaneous generation
Led to the development of methods for controlling the growth of microorganisms (aseptic technique)
Koch
Demonstrated the link between microbes and infectious diseases
Koch’s postulates
Identified causative agents of anthrax and tuberculosis
Developed techniques (solid media) for obtaining pure cultures of microbes, some still in existence today
Bright-field scope
Specimens are visualized because of differences in contrast (density) between specimen and surroundings
Two sets of lenses form the image
Objective lens and ocular lens
Total magnification = objective magnification ocular magnification
Phase-Contrast Microscopy
Phase ring amplifies differences in the refractive index of cell and surroundings
Improves the contrast of a sample without the use of a stain
Allows for the visualization of live samples
Resulting image is dark cells on a light background
Dark-Field Microscopy
Light reaches the specimen from the sides
Light reaching the lens has been scattered by specimen
Image appears light on a dark background
Excellent for observing motility
Fluorescence Microscopy
Used to visualize specimens that fluoresce
Emit light of one color when illuminated with another color of light
Some cells fluoresce naturally (autofluorescence)
Fluorescent dyes are used
Example: DAPI
Widely used in microbial ecology for enumerating bacteria in natural samples
What is used for phylogeny?
Ribosomal RNA (rRNA)
What are the organelles of the endosymbiotic theory?
Chloroplasts Evolved from phagocytosed photosynthetic Bacteria Mitochondria Evolved from phagocytosed oxygen utilizing Bacteria Nucleus Evolved from phagocytosed Archaea
All cells have the following in common
Cytoplasmic membrane Cytoplasm Ribosomes rRNA valuable comparison Genetic material
Nucleoid
Non membrane enclosed, but condensed region of genetic material
Bacteria, Archaea, and organelles
Plasmid
Extra chromosomal DNA
All domains, mainly Bacteria and Archaea
Histones
Eukaryotes and Archaea
Proteins associated with DNA to compact it
DNA wraps around histones
One human cell’s DNA is 6 feet long, wouldn’t fit without histone coiling
Size of Bacteria and Archaea
Range: 0.2 µm to > 700 µm Most: 0.5 and 4.0 µm wide and <15 µm long Average: rod 1 x 2 µm Smallest: M. pneumoniae 0.2 µm Largest: T. namibiensis 750 µm
Size of Eukaryotes
Range: 10 to >200 µm in diameter
Bacterial vs. Archaeal Membranes
Bacteria and Eukarya:
Ester linkages in phospholipids, only
Fatty acids, only
Straight carbon chain, only
Bilayer, only
Archaea:
Ether linkages in phospholipids
Lack fatty acids, have repeating isoprenes instead
Major lipids: glycerol diethers (20C) and teraethers (40C)
Side chains and/or rings (ex: cyclohexyl)
Can exist as lipid monolayers, bilayers, or mixture
At least 3 major classes of transport systems
Simple transport Single protein Group translocation Series of proteins ABC system 3 components
Three transport events are possible:
Uniporters transport in one direction across the membrane
Symporters function as co-transporters
Antiporters transport a molecule across the membrane while simultaneously transporting another molecule in the opposite direction
Lipoteichoic acids
teichoic acids covalently bound to membrane lipids
on the outisde of gram positive cell walls
channels for movement of hydrophilic low-molecular weight substances
Porins
Periplasm:
space located between cytoplasmic and outer membranes
~15 nm wide
Contents have gel-like consistency
Houses many proteins
Pseudomurein
Polysaccharide similar to peptidoglycan
Composed of N-acetylglucosamine and N-acetyltalosaminuronic acid
Found in cell walls of certain methanogenic Archaea
S-Layers
Most common cell wall type among Archaea Consist of protein or glycoprotein Paracrystalline structure Interlocking molecules with ordered appearance Variety of symmetries Hexagonal, tetragonal, trimeric, etc.
Capsules
Tight matrix excludes India ink
Adhere firmly to the cell wall
Slime Layers
Looser matrix does not exclude India ink
Loosely attached to cell wall
Biofilm
Thick layer of cells (“multicellular”)
Exopolysacharies play key role in biofilm development
Fimbriae
Filamentous protein structures Enable organisms to: Stick to surfaces Form pellicles Form biofilms
Pili
Filamentous protein structures
Typically longer than fimbriae
Less pili per cell than fimbriae
Assist in surface attachment
Facilitate genetic exchange during conjugation
Type IV pili involved in twitching motility (gliding)
Can be conductive of electricity
Endospores
Highly differentiated cells resistant to heat, harsh chemicals, and radiation
“Dormant” stage of bacterial life cycle
Ideal for dispersal via wind, water, or animal gut
Only present in some gram-positive bacteria
Flagellum (pl. flagella):
structure that assists in swimming
Different arrangements: peritrichous, polar, lophotrichous, amphitrichous (two poles)
Helical in shape
Bacterial Flagellar Structure
Consists of several components Filament composed of single type of flagellin Move by rotation – rotary motor Energy required for rotation comes from proton motive force ~1000 protons translocated per rotation Gram negative: L ring, P ring, MS ring, C ring Gram positive: P ring, MS ring, C ring
Archaeal Flagella
Smaller diameter than Bacteria 10-13 nm vs 15-20 nm Lack central channel Great diversity of flagellin proteins Amino acid sequence of flagellin proteins show no phylogentic relationship to Bacterial More similar to type IV pili Powered by ATP instead of protons Flagellin added at base during synthesis
Eukaryote Flagella
A bundle of nine fused pairs of microtubule doublets surrounding two central single microtubules: “9+2”
Axoneme
Basal body base (kinetosome) is the microtuble organizing center
Flagellum encased within cell’s plasma membrane
Powered by ATP
Taxis:
directed movement in response to chemical or physical gradients
Phototaxis:
response to light
Aerotaxis:
response to oxygen
Osmotaxis:
response to ionic strength
Hydrotaxis:
response to water
Magnetotaxis:
response to Earth’s magnetic field
Chemoorganotrophs
Obtain their energy from the oxidation of organic molecules
Chemolithotrophs
Obtain their energy from the oxidation of inorganic molecules
Process not found in Eukaryotes
Aerobes
use oxygen to obtain energy
Anaerobes
obtain energy in the absence of oxygen
Phototrophs
Contain pigments that allow them to use light as an energy source
Oxygenic photosynthesis produces oxygen
Anoxygenic photosynthesis does not produce oxygen
Autotrophs
Use carbon dioxide as their carbon source
Sometimes referred to as primary producers or carbon fixers
Heterotrophs
Require one or more organic molecules for their carbon source
Feed directly on autotrophs or live off products produced by autotrophs
Catabolic reactions (catabolism)
Energy-releasing metabolic reactions
Anabolic reactions (anabolism)
Energy-requiring metabolic reactions
Defined media:
precise chemical composition is known
Complex media:
composed of digests of chemically undefined substances (e.g., yeast and meat extracts)
Selective Media
Contains compounds that selectively inhibit growth of some microbes but not others
IF it grows or not
Differential Media
Contains an indicator, usually a dye, that detects particular chemical reactions occurring during growth
HOW it grows in comparison
Free energy (G):
energy released that is available to do work
Exergonic
Negative G0′
Release free energy
Endergonic
Positive G0′
Require energy
Oxidation:
the removal of electron(s)
Reduction:
that addition of electron(s)
Electron donor:
is oxidized in a redox reaction
Electron acceptor:
is reduced in a redox reaction
Delta E
Energy released
Difference is reduction potential between donor and acceptor redox couple
The further electrons “drop” from a donor before they are “caught” by an acceptor the greater the amount of energy
Proportional to ΔG0’
NADH dehydrogenases:
Proteins bound to inside surface of cytoplasmic membrane
Active site binds NADH and accepts 2 electrons and 2 protons that are both passed to flavoproteins
e- AND H+
Complex I
NADH is oxidized and e- added to quinone pool ( is reduced)
Complex II
Bypasses complex I and feeds e- and H+ from FADH to quinone pool
Complex III
e- passed from quinone pool to cytochrome b-c1 complex
e- passed to cytochrome c – an e- shuttle
Complex IV
e- passed to cytochromes a and a3
Terminal oxidase – adds e- to terminal electron acceptor (i.e. O2)
proton motive force
The inside becomes electrically negative and alkaline
The outside becomes electrically positive and acidic
Respiration
ATP produced from proton motive force formed by transport of electrons
Aerobic Respiration
O2 is the terminal electron acceptor
Anaerobic Respiration
Alternative element as the terminal electron acceptor
NO3-, NO2-, Fe3+, SO42-, CO32-
Redox tower
Respiration generally higher ATP yield than fermentations
ATP produced at the expense of the proton motive force, which is generated by electron transport
Fermentation:
Substrate-level phosphorylation
ATP directly synthesized from an energy-rich intermediate
Glycolysis:
catabolism of glucose
Chemolithotrophy
Uses inorganic chemicals as electron donors
Examples include hydrogen sulfide (H2S), hydrogen gas (H2), ferrous iron (Fe2+), ammonia (NH3)
Typically aerobic
Begins with oxidation of inorganic electron donor
Uses electron transport chain and proton motive force
Autotrophic; uses CO2 as carbon source
Phototrophy
uses light as energy source
Photophosphorylation:
light-mediated ATP synthesis
Photoautotrophs
use ATP for assimilation of CO2 for biosynthesis
Photoheterotrophs
use ATP for assimilation of organic carbon for biosynthesis
Divisome:
cell division apparatus
FtsZ: forms ring around center of cel
Fts (filamentous temperature-sensitive) proteins
Essential for cell division in
ZipA: anchor that connects FtsZ ring to cytoplasmic membrane
FtsA: helps connect FtsZ ring to membrane and also recruits other divisome proteins
Doubling time
of the exponentially growing population is
dt = t/n
t is the duration of exponential growth
n is the number of generations during the period of exponential growth
Growth rate
is calculated as
v = 1/dt
Psychrophile
low temperature
Mesophile:
midrange temperature
Thermophile
high temperature
Hyperthermophile
very high temperature
Water activity (aw):
water availability; expressed in physical terms
Defined as ratio of vapor pressure of air in equilibrium with a substance or solution to the vapor pressure of pure water
Xerophiles:
organisms able to grow in very dry environments
Osmophiles:
organisms that live in environments high in sugar as solute
Aerobes:
require oxygen to live
Anaerobes:
do not require oxygen and may even be killed by exposure
Facultative organisms:
can live with or without oxygen
Aerotolerant anaerobes:
can tolerate oxygen and grow in its presence even though they cannot use it
Microaerophiles:
can use oxygen only when it is present at levels reduced from that in air
Chemolithoautotophs
As early Earth was anoxic, energy-generating metabolism of primitive cells was exclusively anaerobic and likely chemolithotrophic
Obtained carbon from CO2
Obtained energy from H2 (probably)
H2 available at deep sea hydrothermal vents
H2 is energetic (very positive Eh)
H2 promotes high energy redox reactions of anaerobic respiration
Virion:
Virus particle
Extracellular form of a virus
Exists outside host and facilitates transmission from one host cell to another
Contains:
Nucleic acid genome
Surrounding by a protein coat
Other surrounding layers (only in some virions)
Capsid
the protein shell that surrounds the genome of a virus particle
Composed of a number of protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid
Capsomere:
subunit of the capsid
Smallest morphological unit visible with an electron microscope
Lysozyme
Makes hole in cell wall
Lyses bacterial cell
Neuraminidases
Enzymes that cleave glycosidic bonds
Allows liberation of viruses from cell
Titer
number of infectious units per volume of fluid
Plaque assay
one way to quantify virus infectivity
Plaques are clear zones that develop on lawns of host cells
Lawn can be bacterial or tissue culture
Phases of Viral Replication
Attachment (adsorption) of the virus to a susceptible host cell
Entry (penetration) of the virion or its nucleic acid
Synthesis of virus nucleic acid and protein by cell metabolism as redirected by virus
Assembly of capsids and packaging of viral genomes into new virions (maturation)
Release of mature virions from host cell
Restriction enzymes
Aka restriction endonucleases
Cleave DNA at specific sequences
Degrades all foreign nucleic acid
Have to distinguish self vs non-self
Modification of host’s DNA prevents cleavage of own DNA
Addition of methyl groups at restriction enzyme recognition sites
Lysogeny
state where most virus genes are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome
Temperate viruses:
can undergo a stable genetic relationship within the host
But can also kill cells through lytic cycle
Lysogen:
a bacterium containing a prophage
Under certain conditions lysogenic viruses may revert to the lytic pathway and begin to produce and release virions
Regulation of lytic vs. lysogenic events in lambda is controlled by a complex genetic switch
Regulation of gene expression
