TOPIC 1: Introduction Flashcards
What are the three domains of life?
archaea (extremophiles)
bacteria
eukarya
what are prokaryotes?
bacteria and archaea
single celled organisms
lack a nucleus
how to interpret a phylogenic tree?
COMMON ANCESTOR
count back clades
what are the traditional ways to differentiate bacteria?
shape/structure –> electron microscope
Gram staining –> positive or negative
aerobic/anaerobic –> indicates genes for metabolism
physiology –> nutritional requirements, metabolism
describe the cell wall structure for GRAM POSITIVE bacteria from top to bottom
GLYCOSYL CHAINS
S LAYER
PEPTIDOGLYCAN (thick layer)
MEMRANE (+ proteins)
cytosol
describe the cell wall structure for GRAM NEGATIVE BACTERIA
S LAYERS
LIPOPOLYSACCHARIDES
OUTER MEMBRANE
LIPOPROTEINS
PEPTIDOGLYCAN (thin layer)
PERIPLASM
INNER MEMBRANE (+ proteins)
What is the structure of peptidoglycan?
glycan chains crossed linked with amino acid chains
peptide chains attached to NAM cross link to adjacent glycan chains
describe the steps in a Gram stain
cells fixes to slide
CRYSTAL VIOLET stain
add IODINE (forms complex in +)
wash with ETHANOL (removes stain in -)
add SAFRANIN (dyes - PINK)
modern way to differentiate bacteria
comparison of GENES (16s RNA)
do NOT need to grow in lab
what is the 16s rRNA sequence
binds complementary to the Shine-Dalgarno sequence
AKA ribosome binding site
first AUG codes for formyl-methionine in bacteria
what is a svedberg?
measure of sedimentation velocity
depends on WEIGHT and SURFACE AREA
heavy w/ small surface area = bottom of flask
describe 16S rRNA sequencing
analyzing the sequence of DNA that ENCODES for this gene, NOT the RNA
16S rRNA performs an important part on translation by forming the shone-dalgarno sequence
FOUND IN ALL PROKARYOTES
9 variable regions
cannot distinguish between closely related bacteria
what are the advantages of 16S rRNA sequencing?
do not need to culture/grow bacteria
not time consuming
what are the disadvantages of 16S rRNA sequencing?
must match sequences to database (no newly identified bacteria)
lacks resolution to distinguish between certain strains or species
cannot reveal metabolic capabilities
high risk of contamination
at what percentage is a species considered the same genus?
95%
what are the two subclasses of bacteria?
gram positive and negative
what are the types of metabolism?
PHOTOSYNTHETIC (cyanobacteria)
LITHOTROPHS (energy from minerals)
HETEROTROPHS (metabolize organic molecules)
what environments can bacteria inhabit?
thermal vents (THERMOTOGA)
cold environments (PSYCHROBACTER)
high radiation (DEINOCOCCUS RADIODURANS)
what kinds of bacteria can metabolize organic matter?
FUNGI and HETEROTROPHIC bacteria (ex. ACTINOMYCETES and PROTEOBACTTERIA)
what are the layers of soil?
organic horizon
aerated horizon
eluviated horizon
B horizon
water table
water saturated horizon (anaerobes)
bedrock
what is lignin?
energy source for other organisms
broken down by fungi into smaller molecules which become food
component of plant cell wall
what is competition?
some microbes secrete chemicals that kill other microbes (antibiotics)
what environmental factors must we consider when culturing bacteria?
[O2]
pH
temperature
pressure
osmolarity
sometimes we cannot grow bacteria since we don’t have correct conditions
