246 Cards in this Set
| Front | Back |
|---|---|
|
Bacteriostatic
|
antimicrobials that inhibit microbial growth without killing them
|
|
Bacteriocidal
|
antimicrobials that kill microbes
|
|
Bacteriolytic
|
antimicrobials that kill microbes by lysing them
|
|
antiseptic
|
nontoxic antimicrobial compounds used on living tissues (topical agents)
|
|
germicide
|
kills germs
|
|
HEPA filter
|
High Efficiency Particulate Air-- depth filters tested and certified to remove 0.3 micrometer particles at above 99.97% efficiency
|
|
facemask
|
personal filters that are loose fitting and surround the mouth and nose
|
|
N95 respirator
|
personal filters that are tight-fitting devices that form a seal with the face
|
|
Kirby-Bauer test
|
agar plate test with cultures to see which antibiotics they are sensitive to by "zones of inhibition"
|
|
What is pasteurization and how can it be done?
|
short term heating used on heat-sensitive liquids;
reduce but not eliminate microorganisms;
increases self-life;
batch method or continuous flow
|
|
What types of damage are caused by ionizing radiation and UV light; what is a decimal reduction time for radiation exposure?
|
Damages DNA; the time it takes for the survival fraction of microbes to reduce by 10 fold
|
|
What types of filters are commonly used to remove microbes?
|
Depth Filters: sheets or mats of paper, cellulose or glass
Membrane Filters: used for sterilization; uniform pore size
Personal Protection Masks: Facemasks or N95 respirators; filters both ways, prevents exchange
|
|
Know the 4 BSL categories and what type of pathogens they are used for.
|
BSL 1: least secure; non-pathogenic organisms
BSL 2: moderate pathogens
BSL 3: pathogens
BSL 4: most secure; life-threatening pathogens transmitted by air/aerosols
|
|
Understand the types of chemical antimicrobial agents based on their effect on microbial growth.
|
"-static:" inhibits growth
"-cidal:" kills microbes
"-lytic:" kills microbes by lysing them
|
|
What are sterilizers, disinfectants, antiseptics, and sanitizers each used for?
|
Sterilizers: kill all living organisms; lab equipment
Disinfectants: microbes/pathogens on inanimate surfaces; homes
Antiseptics: nontoxic compound used on living tissue; wound or surgical site
Sanitizers: reduce but not eliminate microbes; food prep
|
|
Review factors that influence effectiveness of antimicrobial agents; what forms of microbes are most or least resistant?
|
Concentration
Duration
Temperature
Presence of other organic material
Level of microbial resistance
Most Resistant: Bacterial Spores
Least Resistant: Enveloped Viruses
|
|
What is the minimum inhibitory concentration (MIC) and how is it determined?
|
the minimal concentration of an antimicrobial agent that will inhibit growth of a given bacterium;
tube dilution assay: given amt of bacterium in each tube, dilution of antimicrobial agent, measure of turbidity (growth)
|
|
How is the disc agar diffusion test performed; how are the results interpreted?
|
organism spread on culture, antibiotic disks applied, growth of organism on plate other than "zones of inhibition"
if it leaves a "zone of inhibition" it is sensitive to that antibiotic
"Kirby-Bauer test"
|
|
alignment:
|
When data is fed into a computer to be overlapped and sequenced.
|
|
overlap:
|
two fragments that have regions of identical sequences that are stacked on each other
|
|
contigs:
|
longer, continuous sequences of data after alignment and overlap
|
|
scaffolds
|
how contids are linked together
|
|
gene prediction:
|
when you analyze a sequence for an ORF to obtain a protein sequence
|
|
annotation:
|
when you compare protein sequences with regions of known proteins to assign function
|
|
open reading frame (ORF):
|
regions of DNA that code for genes;
usually separated by short regulatory regions
|
|
bioinformatics:
|
branch of biology dealing with computational approaches to storage, analysis, and comparison of genomes
|
|
RNA-seq:
|
isolation and sequencing of all RNA in a cell
|
|
hybridize:
|
when you stick DNA onto a chip to analyze
|
|
transcriptome:
|
K
|
|
metagenomics:
|
analyzing microbial communities by genome and/or RNA sequencing
|
|
comparative genomics:
|
comparison of genome sequences
|
|
pathogenicity islands:
|
clusters of genes that a pathogenic strain of a gene has
|
|
Understand the basic method of Sanger dideoxy sequencing.
|
K
|
|
What is involved in shotgun sequencing (without too much detail)?
|
fragmenting genomic DNA and cloning the fragments into plasmids
|
|
What technical improvements allowed pyrosequencing to increase sequence throughput; what is detected in the pryrosequencing reactions?
|
k
|
|
Understand what sequence alignment is and how is this used to build long contiguous sequences?
|
when a DNA sequence is aligned, overlapped, and formed into contigs
|
|
Review the steps of a genome sequencing project from small fragment sequences to annotation.
|
K
|
|
What can a genome sequence reveal about uncultured organisms?
|
K
|
|
Understand the basics of what a DNA microarray is and what they are used for; how do the microarrays quantitate mRNA levels?
|
contains a gridded chip that has oligonucleotides that can base pair with mRNA from a sequenced genome
|
|
Know the two general strategies for performing environmental genomics.
|
K
|
|
Understand the difference between vertical and horizontal gene transfer.
|
vertical: inherited genes passed through cell division
horizontal: non-inherited transfer of genes from one cell to another
|
|
Transcription:
|
first step in gene expression where DNA is transcribed into RNA
|
|
Translation:
|
MRNA is translated from AA as codons into proteins
|
|
Dimer:
|
a molecule containing two identical subunits
|
|
Inverted repeats:
|
regions of DNA that the dimers bind to
|
|
signal transduction:
|
process of transmitting external chemical signals to relevant regulatory targets
|
|
feedback inhibition:
|
when the end product of a reaction inhibits the activity of the first enzyme in the pathway
|
|
effector molecule:
|
molecule that binds to an enzyme, changing the shape of it so that the substrate molecule can no longer bind and react to the active site
|
|
Understand what is meant by "gene expression."
|
the conversion of DNA genetic information into a functional protein
|
|
Be able to state the difference between an operon and a regulon.
|
operon: the region of DNA that controls transcription
regulon: genes or operons throughout the genome under the same control as operons
|
|
What is the basic structure of a repressor protein, what is an inverted repeat?
|
K
|
|
Review regulation of transcription by negative control with a repressor protein: arg operon (repression by arginine), lac operon (induction by lactose).
|
Arg operon: when arginine is present, repressor binds and transcription is blocked (co-repressor)
Lac operon: when lactose is present, repressor is blocked and transcription proceeds (inducer)
|
|
Review positive control regulation with an activator protein: mal operon (induction by maltose).
|
Mal operon: maltose binds to the activator binding site and transcription proceeds
|
|
How is catabolite repression involved in diauxic growth using both glucose and lactose as carbon sources; how is cyclic AMP and the cyclic AMP receptor protein involved?
|
catabolite repression is the strategy for controlling which carbon source is to be used at a given time; cyclic AMP is involved in controlling that switch
|
|
Describe quorum sensing and the role of "autoinducers."
|
quorum sensing is a method of cells to measure chemical signals to detect population density;
autoinducers are signals that nearby cells pick up
|
|
What are the roles of a sensor kinase and response regulator protein in signal transduction?
|
sensor kinase binds the extracellular signal molecule and phophorylates itself;
response regulator protein picks up the phosphate and binds to the operator of DNA
|
|
How can small RNA molecules control translation?
|
sRNA binds to the mRNA and can stimulate or prevent translations-- sometimes needs a Hfq protein, in which case it prevents transcription
|
|
How do riboswitches control translation?
|
they bind small regulatory molecules that changes base-pairing, making the binding site unavailable (no translation)
|
|
What is allosteric regulation of enzyme activity?
|
regulation found in enzymes catalyzing the first step of a pathway (i.e, feedback inhibition)
|
|
Capsid:
|
a protein coat surrounding a virus
|
|
Nucleocapsid
|
protein coat surrounding the Nucleic Acid of of virus
|
|
Virion
|
the entire virus in its extracellular form
|
|
Bacteriophage:
|
viruses of bacteria
|
|
Capsomers:
|
the individual proteins or subunits that make up capsids
|
|
Filamentous viruses:
|
structure of virus (long? straight? with filiament down middle)
|
|
Icosahedral viruses:
|
structure of virus that coils (ie, Tobacco Mosaic Virus)
|
|
Plaque:
|
a single virus cell?
|
|
Lawn:
|
a continual covering of cells on a surface
|
|
Lytic:
|
life cycle of viruses in which the virus replicates and then lyses the host cell
|
|
Lysogenic:
|
life cycle of viruses in which the virus DNA gets incorporated into the host cell's genome
|
|
Prophage:
|
the incorporated virus genome in a host cell
|
|
Lysogen:
|
cells containing a viral genome (prophage)
|
|
Overlapping Genes:
|
a region of DNA that can encode for 2 or 3 proteins using different reading frames
|
|
Latent infection:
|
k
|
|
Persistent infection:
|
k
|
|
Reverse transcriptase:
|
enzyme used by viruses to convert RNA to DNA, to be expressed in the genome of a host cell
|
|
Provirus:
|
viral DNA that has entered into a host cells genome
|
|
Review the components of viruses; what are capsids composed of; what are the two major structures of viruses; what is an envelope and where does it originate?
|
capsids are composed of capsomeres;
two major structures of viruses are the filiamentous and the icosahedral;
envelope surrounds the virus as a whole and originates from the host cell's membrane
|
|
Understand the steps in the life cycle of a virus that causes lysis of its host cell.
|
virus attaches to host cell and injects viral DNA;
phage components are synthesized and virions assembled;
host cell lyses and virions expelled
|
|
What is a virus "titer" and how is it determined; how is a plaque formed on an agar plate?
|
titer is the concentration of a virus, determined through _______________;
plaque formed by pouring mix into a petri dish and collecting from agar
|
|
Review the life cycle of the T4 bacterial virus; how are viral components made when they are needed; what is "packaging"?
|
T4 bacteriophages are lytic;
viral components made by diff genes at diff times so they are available, packaging is the process of which DNA is guided into the phage head
|
|
What are the two paths that an E. coli cell can take after it is infected with lambda; what is induction?
|
lytic or lysogenic;
induction is the process of which the prophage excises from the genome (leaving lysogenic for lytic)
|
|
How do viruses make maximal use of the limited genome size?
|
K
|
|
Know the possible outcomes of infection by certain animal viruses; what is transformation?
|
latent infection and persistent infection;
transformation is the process by which an animal virus converts a normal cell into a tumor cell
|
|
What replication enzyme is a distinguishing feature of retroviruses; what are the three major gene regions in retroviruses; what are oncogenes?
|
reverse transcriptase;
gag (core and capsid proteins), pol (rev. trans. integrase), env (envelope proteins);
oncogenes are __________________________
|
|
Review retrovirus life cycle, what type of genome, dsDNA intermediate, why are protease, reverse transcriptase, and fusion inhibitors helpful in treatment of HIV; how is the virus released by budding?
|
retrovirus enters cell, releases nucleocapsid and RNA genome, rev. trans. converts RNA-->DNA, viral DNA enters genome (provirus now), transcription of viral DNA, translation into viral proteins;
inhibit reverse transcriptase
budding is like _______
|
|
wild-type:
|
a strain of an organism as isolated from nature (presumably without mutation)
|
|
spontaneous mutations:
|
mutations that occur naturally without human intervention
|
|
induced mutations:
|
mutations resulting from intentional exposure to chemical agents of radiation
|
|
truncated protein:
|
a shortened protein produced by the stop codon UAG
|
|
mutagen:
|
anything that causes an increase in mutation rates above normal levels
|
|
nucleotide base analogs:
|
resemble DNA bases and leads to higher frequency of base subsitutions
|
|
intercalating agents:
|
bind between DNA bases and increase mutation rates
|
|
SOS system:
|
a regulon of about 40 genes involved in repair of DNA damage and damage tolerance
|
|
repressor:
|
slows or inhibits a process or an enzyme that controls a process
|
|
single-strand binding protein:
|
protein that helps detach a nicked strand from a whole strand
|
|
Holliday junction:
|
"crossover" pattern of a structure
|
|
resolution:
|
cutting of DNA strand to yield new DNA with heteroduplex regions (segments originating from different DNA molecules)
|
|
heteroduplex:
|
segments originating from different DNA molecules
|
|
competence:
|
ability to take up external DNA
|
|
Understand the difference between genotype and phenotype.
|
genotype: the nucleotide sequence of a genome
phenotype: observable manifestation of the genotype, physical attributes
|
|
Review the 4 types of base pair substitutions.
|
Point mutations: changes to a single base pair, or insertion/deletion of a base pair
Frameshift mutations: causes changes in all AA codons downstream of the mutation site
Reversions:
Second-site mutations: can restore a phenotype
|
|
What is a frame shift mutation and what can happen to the resulting protein?
|
causes changes in all AA codons downstream of the mutation site; changes the codons/proteins made
|
|
Understand what reversion are; how can a second site mutation restore a correct reading frame; how can a suppressor tRNA produce a normal protein from a mutated DNA?
|
reversions can restore a phenotype;
can restore the reading frame with a second frameshift;
inserts a correct AA at the UAG codon
|
|
What is the Ames test; how is it performed; why is a liver enzyme extract used; what phenotype is observed; how is it interpreted?
|
a test to measure mutation rates;
to mimic what happens in the body;
only revertants grow;
if high colonies near the disk, positive Ames test, chemical is a possible mutagen
|
|
Understand mutagenesis, the types of DNA repair mechanisms and the enzymes involved; how is damaged DNA detected; what are the roles of RecA and LexA in DNA repair?
|
K
|
|
Review the sequence of steps involved in homologous recombination; what 2 proteins promote strand invasion?
|
nick in a strand, single-strand protein separates strands, nicked strand displaces homologous region, crossed-stranded exchange, new DNA from both molecules
|
|
Know the differences between transformation and transduction; what are generalized and specialized transduction?
|
transformation: horizontal genetic transfer process where external free DNA is taken up into a cell
transduction: horizontal gene transfer where viruses transfer DNA from a donor cell into a recipient cell
generalized transduction: when a random piece of chromosomal DNA is packaged into…
|
|
plasmid:
|
an extrachromosomal genetic element of double-stranded DNA;
can exist in one to many copies in a single cell
|
|
sex pilus:
|
aids in the transferring of genes
|
|
F+ cells:
|
cells containing the F plasmid, which can transfer a copy of itself into a cell
|
|
insertion sequences:
|
sequences on the F plasmid that are homologous to regions on the chromosome
|
|
OriT:
|
first DNA to copy and move into the recipient cell
|
|
cloning
|
putting DNA into a larger molecule that can be replicated and manipulated
|
|
sticky ends:
|
when the DNA is cut with a hanging edge to be paired/matched
|
|
blunt ends:
|
when the DNA is cut with no single-stranded end
|
|
amplification:
|
the replication of specific small regions of DNA
|
|
DNA ligase:
|
an enzyme that joins DNA ends
|
|
recombinant DNA:
|
DNA in which a plasmid has been incorporated
|
|
What is a conjugative plasmid; how is sex pilus involved?
|
plasmid that inserts a copy of itself into another cell;
transfers via the sex pilus
|
|
Understand how the F plasmid of E. coli works- either when a separate plasmid or intergrated into a host chromosome; know what an Hfr strain is and how the F plasmid gets inserted into the chromosome.
|
K
|
|
Know what restriction enzymes are and how they can be used for genetic engineering and cloning.
|
restriction enzymes are proteins that cut DNA at specific sequences;
they can cut at specific sites to insert plasmids and alter genes
|
|
How can PCR be used for generating specific DNA fragments?
|
by targeting and amplifying a given DNA sequence
|
|
How can DNA fragments be connected with a cloning vector to produce recombinant DNA?
|
the sticky ends match and are sealed/glued via DNA ligase
|
|
In what ways are plasmids designed to simplify molecular cloning of DNA fragments?
|
contain multiple RE sites;
exist in many copies per cell;
possess one or more antibiotic resistance genes to allow for selection in host cells
|
|
What are expression vectors and shuttle vectors used for?
|
expression vectors: control expression of cloned genes
shuttle vectors: can be used in many organisms
|
|
alignment program:
|
program that finds overlaps in sequences of 16s rRNA genes
|
|
distance matrix:
|
how differences in the sequence overlaps of an alignment program are viewed/analyzed
|
|
branches:
|
how individual organisms are connected on a distance matrix
|
|
nodes:
|
where branches intersect on a distance matrix
|
|
core genome:
|
contains all genes shared by a group of organisms
|
|
pan genome:
|
all the genes unique to one particular genome
|
|
understand the major evolutionary events since the cooling of earth's crust; how did oxygen levels rise in the atmosphere?
|
cooling of earth's crust and formation of water;
conversion of prebiotic reactions into cellular life;
cellular common ancestor diverges into bacteria and archaea branches of life;
rise of photosynthetic bacteria in the anoxic earth;
the oxidation event;
multicellular life
|
|
What are microbial mats and stromalites?
|
microbial mats: layers of lawns of photosynthetic organisms
stromalites: fossilized microbial mats
|
|
Why are molecular sequences best for determining phylogenetic relationships; what sequence is most commonly used?
|
16s rRNA sequence from ribosomes
|
|
What are the steps in isolating 16s rRNA genes by PCR and building a phylogenetic tree?
|
DNA isolated from pure cultures of microbes or microbial communities;
16s rRNA genes amplified by PCR using specially designed primers;
PCR reaction products are checked by gel electrophoresis
|
|
What is fitness; what are major processes driving evolution; what is an example of evolution and fitness that has been observed in recent years?
|
fitness: the ability of an organism, with a given genotype or phenotype, to grow and reproduce, and to contribute its gentetic information to future generations;
mutations and recombination drive evolution;
antibiotic resistance
|
|
What is genetic drift and how has it been studied in E. coli populations; what studies have been done at MSU?
|
genetic drift: some members of a population reproduce slightly faster than others;
_____;
modern rapid genome sequencing methods
|
|
How can comparative genomics reveal genes important for causing disease?
|
by comparing pathogenic and nonpathogenic strains of bacteria
|
|
What are multilocus sequence typing and ribotyping and what are they used for?
|
multilocus sequence typing: analyzing DNA sequences of several essential genes
ribotyping: 16s rRNA classification by analyzing restriction enzyme fragments rather than DNA sequencing;
alternatives to DNA sequencing
|
|
Understand in a general way how FAME analysis works.
|
Fatty Acid Methyl Ester analysis:
derivatizes bacterial FA and examines profiles of them via gas chromatography
|
|
extremophile:
|
microbes that grow in extreme conditions (heat, salt, etc)
|
|
compatible solutes:
|
internal solutes that equalize the water activity between the inside and outside of the cell
|
|
bacteriorhodopsin:
|
protein contained in the membrane of some halophilic archaea
|
|
retinal:
|
molecule that moved protons from inside of a cell to the outside
|
|
phytanyl:
|
composed of a bilayer in membranes
|
|
biphytanyl:
|
composed in a monolayer in membranes
|
|
lipoglycan:
|
a membrane found in archaea with no wall
|
|
pleomorphic:
|
cells with no specific shape
|
|
sulfataras:
|
hot, acidic terrestrial sulfur springs; habitat of some extremophiles
|
|
hydrophobic cores:
|
stabilizes protein secondary structure; exclusion of water n internal regions of proteins by hydrophobic amino acids increases thermal stability (like two suction cups together)
|
|
salt bridges:
|
ionic bonds that create strong contacts between different parts of the polypeptide chain
|
|
chaperonins:
|
proteins that assist in the correct folding of proteins
|
|
reverse DNA gyrase:
|
enzyme that is more stable to heat denaturation
|
|
DNA-binding proteins
|
similar to histones; compact the DNA and help maintain double-strand structure at high temperatures
|
|
How do halophilic Archaea maintain water balance in high salt conditions?
|
with physiological adaptations such as compatible solutes
|
|
How do some Archaea generate ATP energy from light?
|
the bacteriorhodopsin protein contain retinal, which transports protons outside the cell; these protons fall back down their concentration gradient into the cell, producing ATP
|
|
What are methanogens and understand what the methanogenesis pathway does.
|
anaerobes that convert CO2 to methane;
they utilize cofactors that make CH4 from CO2 and H2
|
|
Review the different ether lipids of Archaea; what are the major types of lipids?
|
phytanyl:
biphytanyl:
lyopglycan:
|
|
How is Thaumarchaeota important for the global nitrogen cycle; what adaptation is important for its survival?
|
they participate in nitrification, which oxidizes ammonia to nitrite;
its adapted to very low nutrient levels, allowing it to live in hot springs and sea ice habitats
|
|
How does Nanoarchaeum live; what does it derive from its host?
|
lives as a parasite;
derives genes from its host cell
|
|
What habitats is Sulfolobus found in; how does it get energy?
|
deep ocean hydrothermal vents;
chemolithotrophically or chemoheterotrophically
|
|
What are challenges to organisms living at high temperatures and what adaptations to proteins and DNA do they have in order to survive?
|
stability of small molecules (ATP) is reduced, proteins and enzymes unfold at higher temperatures, DNA and RNA can denature and degrade, ability of membrane lipids to function is lower;
hydrophobic cores, salt bridges, chaperonins, reverse DNA gyrase, DNA-binding proteins
|
|
hydrogenosomes
|
similar to mitochondria but lack TCA cycle enzymes
|
|
michondrion:
|
organelle responsible for respiration and oxidative phosphorylation;
surrounded by two membranes;
folded internal membrane called cistae
|
|
chloroplast
|
chlorophyll-containing organelle found in phototrophic eukaryotes (plant cells);
flattened membranes called thylakoids;
lumen called stroma which contains RubisCO (key in Calvin cycle)
|
|
thylakoids:
|
flattened membrane disks inside chlorplasts
|
|
christae
|
folded, internal membrane of mitochondria
|
|
Rubisco:
|
contained in the stroma of chloroplasts;
key enzyme in the Calvin cycle
|
|
Calvin cycle:
|
conducted in the chloroplast;
|
|
Giardiasis:
|
disease resulting in abnormal cramps, diarrhea, nausea;
pathogen transmitted through fecal-contaminated water
|
|
African sleeping sickness:
|
Trypanosoma brucei;
transmitted by a live vector, the tsetse fly;
|
|
nagana:
|
disease caused by Trypanosoma brucei in cattle
|
|
vector:
|
organism that transmits disease;
intermediate host
|
|
pseudoplasmodium slug:
|
unified organisms created by aggregated slime molds that move together
|
|
chitin:
|
type of fungi?
|
|
achlorophyllous:
|
type of chemoorganotrophs
|
|
basidiocarp:
|
macroscopic sexual spore-bearing structures
|
|
mycoses:
|
infections on or in the body, 3 types:
superficial, subcutaneous/invasive,
|
|
superficial:
|
infection only on the surface layer; skin, hair, etc;
Ex: athlete's foot, ringworm, etc
|
|
subcutaneous:
|
infection under the skin?
|
|
systemic:
|
infection that affects internal organs
Ex: histoplasmosis, thrush, etc
|
|
primary producer:
|
main producer?
|
|
endolithic:
|
"inside rocks"
|
|
Briefly review key features of a eukaryotic cell but do not memorize all the details.
|
dual membrane nucleus, ribosomes, nucleolus, organelles, etc
|
|
What is the endosymbiosis theory and what evidence supports it?
|
that the organelles of eukaryotes orginated from prokaryotes;
some organelles have
|
|
review the three major energy production organelles of eukaryotes.
|
mitochondria:
hydrogenosome:
chloroplast:
|
|
What type of diseases are caused by Protists such as Giardia and Trichomonas?
|
K
|
|
What are pathogenic and non-pathogenic examples of Euglenozoans?
|
Pathogenic: Trypanosoma brucei (African sleeping sickness, nagana) and cruzi (chagas)
Non-pathogenic: Euglena
|
|
Briefly review Plasmodium falciparum life cycle and the different stages during the cycle.
|
production of gametes, transmission to mosquito, maturation of gametes in mosquito, fertilization, growth, development of sporozoites, release of sporozoites, transmission from mosquito, infection of RBC -->
|
|
Why are some dinoflagellates toxic; what habitat are they found in?
|
K
|
|
What are two types of slime molds; how do cellular slime molds differentiate?
|
cellular: individual cells with amoeboid motility
plasmodial (acellular): produce masses of multinucleated protoplasm called plasmodia;
|
|
Know the key features of fungi; roles in nature, major impacts to humans.
|
contain cell walls of chitin, commonly filamentous;
contributors to decomposition and mineralization of organic carbon, dominate microbial biomass in soils, symbiotic with plant roots;
mushrooms and unicellular yeast
|
|
What disease can Candida albican cause; what is histoplasmosis?
|
thrush;
?
|
|
In what habitats are algae commonly found; what types of cell walls can they have?
|
rocks?
cellulose/pectin, silica, calcium carbonate
|
|
phylotypes:
|
method of expressing richness of a species
|
|
allochthonous:
|
enters the ecosystem from the outside;
Ex: allochthonous carbon enters from outside the ecosystem in ways such as leaves falling from trees into a river
|
|
viability stains:
|
stains that discriminate live cells from dead cells
|
|
DAPI:
|
becomes fluorescent blue only when bound to DNA
|
|
Acridine orange:
|
fluoresces orange when bound to DNA
|
|
metagenomics
|
analysis of community diversity by looking at genes
|
|
Review populations, guilds, communities, habitats, ecosystem; how is a freshwater lake and example of a microbial ecosystem, what are the energy inputs?
|
populations: individual cells of the same type
guilds: populations of organisms doing similar metabolism
communities: interaction of different guilds that conduct complementary processes
habitats: communities living together in parts of a larger environment
ecosystems: communities tha…
|
|
Understand the difference between species richness and species abundance.
|
species richness: reference to the number of different species present (diversity)
species abundance: reference to the fraction or proportion of each species
|
|
Review the methods used to determine microbial community composition; what staining methods are used for microscopic analysis; what is a live/dead stain?
|
culture-independent methods (microscopic analysis, genetic analysis, PCR analysis);
live/dead staining with DAPI or Acridine orange;
differentiates between live and dead cells by fluorescence
|
|
Understand the basic method of Fluorescence In Situ Hybridization; what is it used for?
|
it can "tag" a certain molecule or sequence with a neon "marker";
recognizing specific organsims within populations
|
|
Review what culture-independent methods are and the examples shown in class; what are the two types of analysis that can be done using culture-independent methods?
|
do not require growth of an organism;
medical diagnostics and ;
microscopic analyses and genetic analyses
|
|
How can PCR products be analyzed by terminal restriction fragment length polymorphism, 1st generation sequencing, or next generation sequencing?
|
RFLP: label fragments with fluorescent dye, cut with RE, gel electrophoreis
1st generation: PCR amplification and then clone plasmids into bacterial hosts to be sequenced
next generation: PCR products sequenced directly
|
|
What are phylochips and what are they used for; what is hybridization of DNA?
|
tool to measure the different phylotypes in a community without sequencing;
base pairing
|
|
How have these methods been applied in analyzing microbial communities in the Sargasso Sea and the human microbiome?
|
Sargasso Sea: DNA extracted and sequenced to get idea of marine microbe diversity
Human Microbiome: to determine what microbes live in a healthy human and how that changes in response to factors like nutrition, disease, etc.
|
|
microenvironments:
|
local habitats of microbial cells
|
|
antagonism:
|
(ammensalism) one organism inhibits gorwth of another organism (ie, antiibiotics)
|
|
competition:
|
demand for food exceeds the supply (limited resources)
|
|
predation:
|
microbes can be food for other organisms
|
|
parasitism
|
parasite (such as a virus) harms its host microorganism
|
|
cystic fibrosis:
|
K
|
|
benthic
|
organisms that grow on the sides or bottom surfaces of aquatic systems
|
|
Be able to describe what a niche is.
|
a set of resources and conditions that are utilized by microorganisms
|
|
What are the benefits of living in biofilms; what happens in each stage of biofilm development?
|
protection from predators, better nutrient availability, physical protection from environment conditions;
attachment: adhesion of a few cells to solid surface
colonization: intercellular communication, growth and formation
development: more growth
active dispersal: triggered by enviro…
|
|
Understand the effects of biofilms on humans; what specific problems does Pseudomonas aeruginosa cause some patients; what human disease is this bacterium associated with; why are some bacteria in biofilms resistant to antibiotics?
|
used with inanimate prosthetic devices and organ tissues to protect from antibiotic and autoimmune, but can cause other bodily infections-- can also cause plaque and gingivitis;
pneumonia in human patients with cystic fibrosis;
biofilm protects them, and they have low metabolism and gro…
|
|
Describe seasonal turnover in lakes; how does thermal stratification result in anoxic conditions in the hypolimnion; why are lake nutrient content and dissolved O2 inversely proportional?
|
in winter, colder near top, in summer, colder near bottom;
it has low levels of dissolved O2;
?
|
|
Review the characteristics of O2, bacteria (+ organic carbon and BOD), algae, as they change downstream of a population entry point in a river; why is BOD proportional to the amount of dissolved organic pollution in a water sample?
|
?
less O2, higher BOD??
|
|
What are the bacterial and eukaryotic primary producers in open ocean waters?
|
bacterial: Prochlorococcus and Trichodesmium
|
|
soil separates:
|
sand, silt, and clay
|
|
epiphytes:
|
microbes that colonize plant surface
|
|
epiphytes:
|
microbes that colonize plant surface
|
|
endophytes:
|
microbes that colonize plant interior
|
|
phyllosphere:
|
aerial leaf surface of plants
|
|
rhizosphere:
|
region adjacent to the root
|
|
rhizoplane:
|
the root surface
|
|
legumes:
|
pod-bearing angiosperms that can fix nitrogen
|
|
bacteroid:
|
K
|
|
membrane:
|
K
|
|
nodule:
|
the product of root hair after curling
|
|
Nod factors:
|
lipochitin polysaccharides that are recognized by root hair
|
|
infection thread:
|
line of infection as it expands into root cells
|
|
leghemoglobin:
|
hemoglobin in a legume; protein that delivers oxygen to electric transport chain
|
|
inter-domain:
|
transfer of DNA from a bacterium to a plant
|
|
flavinoid:
|
compound excreted by roots that are taken up by bacteria to express nodulation genes
|
|
Name the 3 phases found in soils; review the four vertical horizons found in mature soils; what are soil aggregates?
|
solids, liquids, and gasses;
O, A, B and C horizons;
fill space in soil?
|
|
How does water affect oxygen levels in the microenvironments within soil aggregates?
|
K
|
|
What is rhizodeposition and what is its effect on nearby soil microbes?
|
process of which 25% of plant photosynthates are exuded from roots into surrounding soil;
increases nutrient enrichment near roots, promoting colonization of bacteria and fungal organisms
|
|
What are the 3 main locations for microbes associated with plants?
|
phyllosphere, rhizosphere, rhizoplane
|
|
Why is N2-fixing symbiosis important to agriculture; describe the steps of plant-rhizobia symbiosis; what chemicals are used for plant-microbe communication?
|
can develop N2-fixing root nodules, N2 is the most common limiting nutrient
|
|
Review nitrogen-fixation; what is the overall reaction for nitrogen fixation; how much energy is expended for each N2?
|
N2 + 8H + 8e- +16 ATP +16H20
-->
2NH3 + H2 + 16 ADP + 16 Pi
16 ATP
|
|
How does Agrobacterium tumefaciens cause Crown Gall disease; what plasmid mediates this process; what is T-DNA; what are the basic roles of VirA and VirG?
|
via a Ti plasmid;
carried genes for tumor formation on the plant;
VirA: sensor kinase
VirG: response regulator
|
|
What are the two types of associations of fungi with plant roots; how to plants and mycorrhizal fungi benefit from each other?
|
ecto- and endomycorrhizae;
fungi can take nutrients from the soil and make them more readily usable by plants
|
Study Guide: Final Exam