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246 Cards in this Set
- Front
- Back
Bacteriostatic |
antimicrobials that inhibit microbial growth without killing them |
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Bacteriocidal |
antimicrobials that kill microbes |
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Bacteriolytic |
antimicrobials that kill microbes by lysing them |
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antiseptic |
nontoxic antimicrobial compounds used on living tissues (topical agents) |
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germicide |
kills germs |
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HEPA filter |
High Efficiency Particulate Air-- depth filters tested and certified to remove 0.3 micrometer particles at above 99.97% efficiency |
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facemask |
personal filters that are loose fitting and surround the mouth and nose |
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N95 respirator |
personal filters that are tight-fitting devices that form a seal with the face |
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Kirby-Bauer test |
agar plate test with cultures to see which antibiotics they are sensitive to by "zones of inhibition" |
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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 |
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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 |
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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
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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 |
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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 |
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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 |
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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 |
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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) |
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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" |
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alignment: |
When data is fed into a computer to be overlapped and sequenced. |
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overlap: |
two fragments that have regions of identical sequences that are stacked on each other |
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contigs: |
longer, continuous sequences of data after alignment and overlap |
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scaffolds: |
how contids are linked together |
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gene prediction: |
when you analyze a sequence for an ORF to obtain a protein sequence |
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annotation: |
when you compare protein sequences with regions of known proteins to assign function |
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open reading frame (ORF): |
regions of DNA that code for genes; usually separated by short regulatory regions |
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bioinformatics: |
branch of biology dealing with computational approaches to storage, analysis, and comparison of genomes |
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RNA-seq: |
isolation and sequencing of all RNA in a cell |
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hybridize: |
when you stick DNA onto a chip to analyze |
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transcriptome: |
k |
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metagenomics: |
analyzing microbial communities by genome and/or RNA sequencing |
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comparative genomics: |
comparison of genome sequences |
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pathogenicity islands: |
clusters of genes that a pathogenic strain of a gene has |
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Understand the basic method of Sanger dideoxy sequencing. |
k |
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What is involved in shotgun sequencing (without too much detail)? |
fragmenting genomic DNA and cloning the fragments into plasmids |
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What technical improvements allowed pyrosequencing to increase sequence throughput; what is detected in the pryrosequencing reactions? |
k |
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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 |
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Review the steps of a genome sequencing project from small fragment sequences to annotation. |
k |
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What can a genome sequence reveal about uncultured organisms? |
k |
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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 |
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Know the two general strategies for performing environmental genomics. |
k |
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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 |
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Transcription: |
first step in gene expression where DNA is transcribed into RNA |
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Translation: |
MRNA is translated from AA as codons into proteins |
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Dimer: |
a molecule containing two identical subunits |
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Inverted repeats: |
regions of DNA that the dimers bind to |
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diauxic growth: |
k |
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signal transduction: |
process of transmitting external chemical signals to relevant regulatory targets |
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feedback inhibition: |
when the end product of a reaction inhibits the activity of the first enzyme in the pathway |
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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 |
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Understand what is meant by "gene expression." |
the conversion of DNA genetic information into a functional protein |
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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 |
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What is the basic structure of a repressor protein, what is an inverted repeat? |
k |
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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) |
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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 |
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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 |
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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 |
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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 |
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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 |
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How do riboswitches control translation? |
they bind small regulatory molecules that changes base-pairing, making the binding site unavailable (no translation) |
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What is allosteric regulation of enzyme activity? |
regulation found in enzymes catalyzing the first step of a pathway (i.e, feedback inhibition) |
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Capsid: |
a protein coat surrounding a virus |
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Nucleocapsid: |
protein coat surrounding the Nucleic Acid of of virus |
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Virion: |
the entire virus in its extracellular form |
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Bacteriophage: |
viruses of bacteria |
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Capsomers: |
the individual proteins or subunits that make up capsids |
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Filamentous viruses: |
structure of virus (long? straight? with filiament down middle) |
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Icosahedral viruses: |
structure of virus that coils (ie, Tobacco Mosaic Virus) |
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Plaque: |
a single virus cell? |
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Lawn: |
a continual covering of cells on a surface |
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Lytic: |
life cycle of viruses in which the virus replicates and then lyses the host cell |
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Lysogenic: |
life cycle of viruses in which the virus DNA gets incorporated into the host cell's genome |
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Prophage: |
the incorporated virus genome in a host cell |
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Lysogen: |
cells containing a viral genome (prophage) |
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Overlapping Genes: |
a region of DNA that can encode for 2 or 3 proteins using different reading frames |
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Latent infection: |
k |
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Persistent infection: |
k |
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Reverse transcriptase: |
enzyme used by viruses to convert RNA to DNA, to be expressed in the genome of a host cell |
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Provirus: |
viral DNA that has entered into a host cells genome |
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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 |
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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 |
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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 |
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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 |
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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) |
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How do viruses make maximal use of the limited genome size? |
k |
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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 |
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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 __________________________ |
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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 _______ |
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wild-type: |
a strain of an organism as isolated from nature (presumably without mutation) |
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spontaneous mutations: |
mutations that occur naturally without human intervention |
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induced mutations: |
mutations resulting from intentional exposure to chemical agents of radiation |
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truncated protein: |
a shortened protein produced by the stop codon UAG |
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mutagen: |
anything that causes an increase in mutation rates above normal levels |
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nucleotide base analogs: |
resemble DNA bases and leads to higher frequency of base subsitutions |
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intercalating agents: |
bind between DNA bases and increase mutation rates |
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SOS system: |
a regulon of about 40 genes involved in repair of DNA damage and damage tolerance |
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repressor: |
slows or inhibits a process or an enzyme that controls a process |
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single-strand binding protein: |
protein that helps detach a nicked strand from a whole strand |
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Holliday junction: |
"crossover" pattern of a structure |
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resolution: |
cutting of DNA strand to yield new DNA with heteroduplex regions (segments originating from different DNA molecules) |
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heteroduplex: |
segments originating from different DNA molecules |
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competence: |
ability to take up external DNA |
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Understand the difference between genotype and phenotype. |
genotype: the nucleotide sequence of a genome
phenotype: observable manifestation of the genotype, physical attributes |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 a phage specialized transduction: DNA that is adjacent to the prophage can be transferred into the recipient cell |
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plasmid: |
an extrachromosomal genetic element of double-stranded DNA; can exist in one to many copies in a single cell |
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sex pilus: |
aids in the transferring of genes |
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F+ cells: |
cells containing the F plasmid, which can transfer a copy of itself into a cell |
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insertion sequences: |
sequences on the F plasmid that are homologous to regions on the chromosome |
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OriT: |
first DNA to copy and move into the recipient cell |
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cloning: |
putting DNA into a larger molecule that can be replicated and manipulated |
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sticky ends: |
when the DNA is cut with a hanging edge to be paired/matched |
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blunt ends: |
when the DNA is cut with no single-stranded end |
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amplification: |
the replication of specific small regions of DNA |
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DNA ligase: |
an enzyme that joins DNA ends |
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recombinant DNA: |
DNA in which a plasmid has been incorporated |
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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 |
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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 |
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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 |
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How can PCR be used for generating specific DNA fragments? |
by targeting and amplifying a given DNA sequence |
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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 |
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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 |
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What are expression vectors and shuttle vectors used for? |
expression vectors: control expression of cloned genes
shuttle vectors: can be used in many organisms |
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alignment program: |
program that finds overlaps in sequences of 16s rRNA genes |
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distance matrix: |
how differences in the sequence overlaps of an alignment program are viewed/analyzed |
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branches: |
how individual organisms are connected on a distance matrix |
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nodes: |
where branches intersect on a distance matrix |
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core genome: |
contains all genes shared by a group of organisms |
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pan genome: |
all the genes unique to one particular genome |
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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 |
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What are microbial mats and stromalites? |
microbial mats: layers of lawns of photosynthetic organisms
stromalites: fossilized microbial mats |
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Why are molecular sequences best for determining phylogenetic relationships; what sequence is most commonly used? |
16s rRNA sequence from ribosomes |
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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 |
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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 |
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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 |
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How can comparative genomics reveal genes important for causing disease? |
by comparing pathogenic and nonpathogenic strains of bacteria |
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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 |
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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 |
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extremophile: |
microbes that grow in extreme conditions (heat, salt, etc) |
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compatible solutes: |
internal solutes that equalize the water activity between the inside and outside of the cell |
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bacteriorhodopsin: |
protein contained in the membrane of some halophilic archaea |
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retinal: |
molecule that moved protons from inside of a cell to the outside |
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phytanyl: |
composed of a bilayer in membranes |
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biphytanyl: |
composed in a monolayer in membranes |
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lipoglycan: |
a membrane found in archaea with no wall |
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pleomorphic: |
cells with no specific shape |
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sulfataras: |
hot, acidic terrestrial sulfur springs; habitat of some extremophiles |
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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) |
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salt bridges: |
ionic bonds that create strong contacts between different parts of the polypeptide chain |
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chaperonins: |
proteins that assist in the correct folding of proteins |
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reverse DNA gyrase: |
enzyme that is more stable to heat denaturation |
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DNA-binding proteins |
similar to histones; compact the DNA and help maintain double-strand structure at high temperatures |
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How do halophilic Archaea maintain water balance in high salt conditions? |
with physiological adaptations such as compatible solutes |
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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 |
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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 |
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Review the different ether lipids of Archaea; what are the major types of lipids? |
phytanyl: biphytanyl: lyopglycan: |
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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 |
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How does Nanoarchaeum live; what does it derive from its host? |
lives as a parasite; derives genes from its host cell |
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What habitats is Sulfolobus found in; how does it get energy? |
deep ocean hydrothermal vents; chemolithotrophically or chemoheterotrophically |
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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 |
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hydrogenosomes |
similar to mitochondria but lack TCA cycle enzymes |
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michondrion: |
organelle responsible for respiration and oxidative phosphorylation; surrounded by two membranes; folded internal membrane called cistae |
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chloroplast: |
chlorophyll-containing organelle found in phototrophic eukaryotes (plant cells); flattened membranes called thylakoids; lumen called stroma which contains RubisCO (key in Calvin cycle) |
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thylakoids: |
flattened membrane disks inside chlorplasts |
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christae |
folded, internal membrane of mitochondria |
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Rubisco: |
contained in the stroma of chloroplasts; key enzyme in the Calvin cycle |
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Calvin cycle: |
conducted in the chloroplast;
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Giardiasis: |
disease resulting in abnormal cramps, diarrhea, nausea; pathogen transmitted through fecal-contaminated water |
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African sleeping sickness: |
Trypanosoma brucei; transmitted by a live vector, the tsetse fly;
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nagana: |
disease caused by Trypanosoma brucei in cattle |
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vector: |
organism that transmits disease; intermediate host |
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pseudoplasmodium slug: |
unified organisms created by aggregated slime molds that move together |
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chitin: |
type of fungi? |
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achlorophyllous: |
type of chemoorganotrophs |
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basidiocarp: |
macroscopic sexual spore-bearing structures |
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mycoses: |
infections on or in the body, 3 types: superficial, subcutaneous/invasive, |
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superficial: |
infection only on the surface layer; skin, hair, etc; Ex: athlete's foot, ringworm, etc |
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subcutaneous: |
infection under the skin? |
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systemic: |
infection that affects internal organs Ex: histoplasmosis, thrush, etc |
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primary producer: |
main producer? |
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endolithic: |
"inside rocks" |
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Briefly review key features of a eukaryotic cell but do not memorize all the details. |
dual membrane nucleus, ribosomes, nucleolus, organelles, etc |
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What is the endosymbiosis theory and what evidence supports it? |
that the organelles of eukaryotes orginated from prokaryotes; some organelles have |
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review the three major energy production organelles of eukaryotes. |
mitochondria: hydrogenosome: chloroplast: |
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What type of diseases are caused by Protists such as Giardia and Trichomonas? |
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What are pathogenic and non-pathogenic examples of Euglenozoans? |
Pathogenic: Trypanosoma brucei (African sleeping sickness, nagana) and cruzi (chagas) Non-pathogenic: Euglena |
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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 --> |
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Why are some dinoflagellates toxic; what habitat are they found in? |
k |
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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;
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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 |
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What disease can Candida albican cause; what is histoplasmosis? |
thrush;
? |
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In what habitats are algae commonly found; what types of cell walls can they have? |
rocks?
cellulose/pectin, silica, calcium carbonate |
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phylotypes: |
method of expressing richness of a species |
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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 |
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viability stains: |
stains that discriminate live cells from dead cells |
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DAPI: |
becomes fluorescent blue only when bound to DNA |
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Acridine orange: |
fluoresces orange when bound to DNA |
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metagenomics: |
analysis of community diversity by looking at genes |
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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 that interact with communities of macroorganisms different categories; sunlight, organic carbon, inorganic compounds |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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. |
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microenvironments: |
local habitats of microbial cells |
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antagonism: |
(ammensalism) one organism inhibits gorwth of another organism (ie, antiibiotics) |
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competition: |
demand for food exceeds the supply (limited resources) |
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predation: |
microbes can be food for other organisms |
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parasitism: |
parasite (such as a virus) harms its host microorganism |
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cystic fibrosis: |
k |
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benthic: |
organisms that grow on the sides or bottom surfaces of aquatic systems |
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Be able to describe what a niche is. |
a set of resources and conditions that are utilized by microorganisms |
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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 environmental factor such as nutrient availability |
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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 growth rates (antibiotics work best against growing bacteria) |
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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; ? |
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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?? |
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What are the bacterial and eukaryotic primary producers in open ocean waters? |
bacterial: Prochlorococcus and Trichodesmium eukaryotic: Ostreococcus |
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soil separates: |
sand, silt, and clay |
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epiphytes: |
microbes that colonize plant surface |
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endophytes: |
microbes that colonize plant interior |
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phyllosphere: |
aerial leaf surface of plants |
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rhizosphere: |
region adjacent to the root |
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rhizoplane: |
the root surface |
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legumes: |
pod-bearing angiosperms that can fix nitrogen |
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bacteroid: |
k |
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membrane: |
k |
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nodule: |
the product of root hair after curling |
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Nod factors: |
lipochitin polysaccharides that are recognized by root hair |
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infection thread: |
line of infection as it expands into root cells |
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leghemoglobin: |
hemoglobin in a legume; protein that delivers oxygen to electric transport chain |
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inter-domain: |
transfer of DNA from a bacterium to a plant |
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flavinoid: |
compound excreted by roots that are taken up by bacteria to express nodulation genes |
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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? |
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How does water affect oxygen levels in the microenvironments within soil aggregates? |
k |
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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 |
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What are the 3 main locations for microbes associated with plants? |
phyllosphere, rhizosphere, rhizoplane |
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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 |
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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 |
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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 |
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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 |