Exam One Flashcards
How do microbes help in agriculture?
Bacteria can help plants get Nitrogen
How do microbes help in energy?
Can take sugars from plants (cellulose and cornstarch) to make ethanol - biofuels
How do microbes help in food production?
Preservatives keep pH low and environment unfriendly for microbes
How many cells are there on earth?
25E29cells
Where are the majority of microbes?
On marine surfaces (66%)
How old is planet Earth?
around 4.5 billion years old
When was the origin of cellular life?
around 3.5-3.8 billion years ago
What was early earth like?
Anoxic (mostly CO2), much hotter than the present earth.
How were the first biological molecules likely made?
They were likely made in mounds of montmorillonite clay associated with hydrothermal springs that have the ability to precipitate so molecules can grow
What is the evidence for RNA as the first genome?
RNA can bind small molecules (ATP, nucleotides, amino acids), and catalytic RNA has enzymatic activity
What was the primitive metabolism of early life?
Anaerobic, autotrophic, and chemolithotrophic
When was the first evidence for microbial life found? Where?
around 3.5 billion years ago in stromatolites
When did oxygenic phototrophic cyanobacteria appear?
around 2.8 billion years ago
How did earth shift from an anoxic to an oxic environment?
oxygenic phototrophic bacteria appeared, iron was oxidized, oxygen accumulated, an ozone layer formed
What do all prokaryotic cells contain?
Cell wall, cytoplasmic membrane, nucleic, cytoplasm, plasmid (in some bacteria), and ribosome
What do all eukaryotic cells contain?
Cytoplasmic membrane, ER, ribosomes, nucleus, nucleolus, nuclear membrane, Golgi, cytoplasm
Theory of endosymbiosis
Mitochondria and chloroplasts came from chemoorganotroph and cyanobacterium
Supportive evidence for the theory of endosymbiosis
Mito and Chloroplasts: have their own genomes, contain their own ribosomes (70S), antibiotics are effective, rRNA sequences are similar to prokaryotic rRNA
How long have prokaryotic cells been on earth
about 4.3 billion years
How does the Hydrogen hypothesis explain how the first eukaryotic cell was formed?
Archaea cell engulfed a bacterial cell that produced hydrogen. Kept it alive to make hydrogen for the archaea cell because hydrogen is an electron donor
When did the early photosynthetic eukaryotic cell come?
1.5 billion years ago
What gene is sequenced in bacteria and archaea to measure phylogeny?
16S
What gene is sequenced in eukarya to help phylogeny
18S
What are the steps in SSU RNA sequencing?
Isolate DNA
Amplify gene by PCR
Run on agarose gel
sequence
Why use SSU RNA instead of another gene?
Universally distributed, functionally constant, slow changing, adequate length
If 16S rRNA sequence differed by more than 3%
different species
If 16S rRNA sequence differed by more than 5%
difference genus
Why is kingdom not included in our taxonomic hierarchy?
Kingdom was in place before archaea were discovered. No agreement on wether or not kingdoms should be in the taxonomic hierarchy
How many species are there
As of August 2013, there are 10,599 species
How would one identify an organism?
Asses its phenotypic properties from general to specific
What are some examples of phenotypic analyses?
Morphology, motility, metabolism, physiology, cell lipid chemistry, cell wall chemistry, etc.
tests ability of denatured DNA in a single strand formed from 2 organisms to bond to one another
DNA hybridization
In DNA hybridization, if 70-100% of the DNA will anneal
same species
In DNA hybridization, if at least 25% of the DNA will anneal
same genus
Sequence comparison of several housekeeping genes. Useful for determining different strains of the same species
Multilocus Sequence Typing
Steps in multi locus sequence typing
Isolate DNA, amplify 6-7 target genes, sequence, analyze alleles, compare with other strains and generate tree
Steps in Fatty Acid Methyl Ester (FAME) Analysis
Bacterial culture, extract fatty acids, derivative to form methyl esters, gas chromatography, graph with peaks, compare pattern of peaks, identify
regulates naming of prokaryotes
The International Code of Nomenclature of Bacteria
Major taxonomic compilations of Bacteria and Archaea
“Bergey’s Manual of Systematic Bacteriology” and “The Prokaryotes”
Formal recognition of a new prokaryotic species requires:
Deposition of a sample in 2 international culture collections, and official publication in IJESM
first person to describe microorganisms
Robert Hooke (1665)
first person to describe bacteria
Antoni van Leeuwenhoek (1676)
Simplest type of microscopy, illuminates specimen and specimen is stained
Bright Field
microscopy with a black bacground
Dark Field
microscopy that casts a shadow over the cell, a little 3D
Phase Contrast
What are the benefits of phase contrast and dark-field microscopy?
Visualize live samples and don’t require staining
visualization of auto-fluorescent molecules or fluorescent stians
fluorescent microscopy
Limit of resolution of a compound light microscope
0.2 micrometers
limit of resolution of an electron microscope
0.2-0.4 micrometers
for observing internal cell structures
Transmission Electron Microscope
for 3D imaging and viewing surfaces
Scanning Electron Microscope
bacteria that is 0.2 micrometer and have no cell wall
Mycoplasma sp.
What is the effect of a high surface area to volume ratio
aids in nutrient and waste exchange with the environment
What is the size of a eukaryote?
around 1 micrometer
What are the four basic components of all microbial cells
cytoplasm, cytoplasmic membrane, ribosomes, DNA
What is a cytoplasmic membrane made up of?
lipid and proteins forming a lipid bilayer
What is an archaea lipid bilayer made up of that helps it survive in extreme environments?
Phylantyl instead of fatty acids and ether linkages that form strong covalent bonds
What connects the lipids in bacteria and eukarya
ester linkages
What other lipid in the cytoplasmic membrane helps to strengthen eukarya
sterols
What other lipid in the cytoplasmic membrane helps to strengthen bacteria
hopanoids
How does the cytoplasmic membrane act as a permeability barrier?
Prevents leakage and functions as a gateway for nutrients and wastes
What is simple transport driven by?
proton motive force
What is group translocation driven by
phosphoenolpyruvate
What is ABC transporter driven by
ATP
How does the cytoplasmic membrane work in terms of energy conservation?
Bacteria and Archaea make ATP in the membrane
How does the cytoplasmic membrane act as a protein anchor?
site of many proteins that participate in transport, bioenergetics, and chemotaxis
What makes up the eukaryotic cytoskeleton?
Microfilaments and microtubules
polymers of actin; define, maintain, change cell shape; cell motley - cytoplasmic streaming
microfilaments
polymers of tubulin; maintain cell shape; cell motility - from flagella and cilia; movement of organelles and chromosomes
microtubules
What makes up the prokaryotic cytoskeleton?
FtsZ, FtsA, and MreB
protein structure similar to tubing that determines where cell division will occur
FtsZ
Protein structures similar to actin; (1) helps hold FtsZ proteins; (2) determine where new cell wall will be inserted in an expanding/dividing cell
- FtsA
2. MreB
Eukaryotic cell organelle that is continuous with nuclear outer membrane; contains ribosomes - site of protein synthesis; makes glycoproteins and new membrane material
rough ER
Eukaryotic cell organelle that is continuous with the rough ER; site of lipid synthesis and carbohydrate metabolism
smooth ER
chemicals modifies carbohydrates on ER glycoproteins and sorts molecules from the ER
Golgi complex
produced by budding of the golgi complex, pH 5, contains digestive enzymes (lipase, nuclease, protease), recycle macromolecules, kills foreign bacteria, apoptosis
lysosome
organelle site of oxidation; contains catalase, superoxide dismutase to degrade H2O2 and O2 respectively
peroxisome
What are the inner and outer membranes of the mitochondrion are? What about the matrix?
Inner: cristae, less permeable and rigid, sites of ETC and ATP
Outer: rigid, somewhat permeable
Matrix: contains enzymes of the citric acid cycle
Replaces mito in anaerobic eukaryotes, site of ATP production and citric acid cycle
hydrogenosome
Aqueous part of the chloroplast, site of the Calvin-Benson Cycle
Stroma
stacks of flattened membrane disks, contain light harvesting pigments, site of ETC and ATP
grant of thylakoids
fixes CO2 into organic compounds
RuBisCO
What is the structure of a cell wall
proteins, glycoproteins, and polysaccharides
What are the main functions of the cell wall
protection, cell shape, preventing osmotic lysis, interact with the environment
Cell walls of algae
cellulose - polymer of glucose
Cell walls of fungi
chitin - polymer of N-acetylglucosamine
2 bacteria that lack cell wall
Mycoplasma & Chlamydia sp.
has protein cell wall
Planctomycetes sp.
What are bacterial cell walls mostly made of
peptidoglycan
Where is the location of peptidoglycan in gram-negative bacteria?
in the periplasm
What is the surface of gram-negative bacteria
wavy/irregular
Attached to the outer membrane of gram-negative bacteria
liao-polysaccharides:
O-Specific and Core Polysaccharides
What is the surface of the gram-positive bacteria
smooth
negatively charged polymers on gram positive cells containing glycerophosphate or ribitol residues
Teichoic Acids
teichoic acids covalently linked to membrane lipids
lipoteichoic acids
2 sugars attached to N-acetylglucosamine and N-acetylmuramic acid. Linked by Beta(1,4) - lysozyme sensitive
peptidoglycan
has a pseudomurein cell wall
Methanobacterium
N-acetylglucosamine attached to N-acetylalosaminuronic acid by lysozyme insensitive Beta(1,3)
pseudomurein
has polysaccharide cell wall
Halococcus
Massive collection of sugars that bind sulfate which has utilities as an electron accepter
polysaccharide cell walls
destroys peptidoglycan by cleaving Beta(1,4) glycosidic bonds; found in animal secretions; major line of defense as infection by Bacteria
Lysozyme
Short protein filaments on the prokaryotic cell surface. Sticky because the proteins need it to stick to surfaces
Fimbriae
longer protein filaments on the prokaryotic cell surface; used in conjugation (exchanging genetic info); can help cells move or attach
Pili
glides via slime secretion
Cytophaga
glides by a twitching motility (extension/retraction of type IV pili)
Myxococcus
glides by the ratchet-protein mechanism and is helped by a proton force
Flavobacterium
Move back and forth by dyein motor proteins (like sperm), and is made of microtubules
Eukaryotic flagella and cilia
What are the parts of a bacterial flagellum
filament, hook, motor
embedded in the cytoplasmic membrane
motor
How fast can a flagellum move a bacterial cell
60 cell lengths/ second
multiple proteins make up filament; small diameter flagellum - less torque, slower speed; powered by ATP
archaea flagella
Flagella are attached at one or both ends of the cell; movement more rapid; Ex. Spirrilum
Polar
Flagella are all around
Peritrichous
Flagella are multiple on one end
Lophotrichous
CCW rotation gives movement opposite of CW rotation
Reversible Flagella
CW rotation moves one way, cell stops and reorients before continuing
Unidirectional
Run (bundled flagella in CCW rotation) & Tumble (flagella pushed apart in CW rotation)
Movement with peritrichous flagella
phototrophic bacterium that aggregates at light wavelengths at which its pigments absorb
Thiospirillum jenense
Small gas-filled structures made of protein that confer buoyancy on cells
gas vesicles
aquatic microorganism that uses gas vesicles to move up and down
Cyanobacteria
aquatic microbes that have magnetosomes - Intracellular particles of magnetite that orient cells in a particular direction
Magnetospirrilum
a prokaryote that has carboxysome - contains ~250molecules of rubisco used for CO2 fixation
Halothiobacillus neopolitamus
In the Carbon storage deposit
Glycogen, poly-beta-hydroxyalkanoate, poly-beta-hydroxybutyrate
In the Phosphate storage deposit
polyphosphate granules; RNA, DNA, and ATP all need a lot of phosphate
In the Sulfur storage deposit
sulfur granules stored in periplasm by gram-negative bacteria like the purple sulfur bacteria
Described the life cycle of Bacillus subtitles from vegetative cell
1876 Ferdinand Cohn
survival mechanism by some gram-positive bacteria like bacillus and clostridium
endospore
cell is not sporulating but is happy, healthy and content
vegetative cell
has an endospore at a terminal
Clostridium botulinum
has an endospore at a subterminal space
Bacillus subtilis
has an endospore at a central space
Bacillus anthrax
What essential macromolecules are in an endospore
nucleic acids, proteins, carbohydrates, lipids, some water
What are the layers of an endospore
DNA to Cortex to Core Wall to Spore coat to Exospore
What is the cortex of an endospore made of
lipids
released from vegetative cell; can survive indefinite periods of time; resistant to heat, chemicals, radiation, desiccation
spore
Spore transforms into a vegetative cell that made the spore when conditions become favorable
germination
