Msu Mmg 301 Exam 2

Front 1

Bacteriostatic

Back 1

antimicrobials that inhibit microbial growth without killing them

Front 2

Bacteriocidal

Back 2

antimicrobials that kill microbes

Front 3

Bacteriolytic

Back 3

antimicrobials that kill microbes by lysing them

Front 4

antiseptic

Back 4

nontoxic antimicrobial compounds used on living tissues (topical agents)

Front 5

germicide

Back 5

kills germs

Front 6

HEPA filter

Back 6

High Efficiency Particulate Air-- depth filters tested and certified to remove 0.3 micrometer particles at above 99.97% efficiency

Front 7

facemask

Back 7

personal filters that are loose fitting and surround the mouth and nose

Front 8

N95 respirator

Back 8

personal filters that are tight-fitting devices that form a seal with the face

Front 9

Kirby-Bauer test

Back 9

agar plate test with cultures to see which antibiotics they are sensitive to by "zones of inhibition"

Front 10

What is pasteurization and how can it be done?

Back 10

short term heating used on heat-sensitive liquids;

reduce but not eliminate microorganisms;

increases self-life;

batch method or continuous flow

Front 11

What types of damage are caused by ionizing radiation and UV light; what is a decimal reduction time for radiation exposure?

Back 11

Damages DNA; the time it takes for the survival fraction of microbes to reduce by 10 fold

Front 12

What types of filters are commonly used to remove microbes?

Back 12

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

Front 13

Know the 4 BSL categories and what type of pathogens they are used for.

Back 13

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

Front 14

Understand the types of chemical antimicrobial agents based on their effect on microbial growth.

Back 14

"-static:" inhibits growth

"-cidal:" kills microbes

"-lytic:" kills microbes by lysing them

Front 15

What are sterilizers, disinfectants, antiseptics, and sanitizers each used for?

Back 15

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

Front 16

Review factors that influence effectiveness of antimicrobial agents; what forms of microbes are most or least resistant?

Back 16

Concentration

Duration

Temperature

Presence of other organic material

Level of microbial resistance

Most Resistant: Bacterial Spores

Least Resistant: Enveloped Viruses

Front 17

What is the minimum inhibitory concentration (MIC) and how is it determined?

Back 17

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)

Front 18

How is the disc agar diffusion test performed; how are the results interpreted?

Back 18

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"

Front 19

alignment:

Back 19

When data is fed into a computer to be overlapped and sequenced.

Front 20

overlap:

Back 20

two fragments that have regions of identical sequences that are stacked on each other

Front 21

contigs:

Back 21

longer, continuous sequences of data after alignment and overlap

Front 22

scaffolds:

Back 22

how contids are linked together

Front 23

gene prediction:

Back 23

when you analyze a sequence for an ORF to obtain a protein sequence

Front 24

annotation:

Back 24

when you compare protein sequences with regions of known proteins to assign function

Front 25

open reading frame (ORF):

Back 25

regions of DNA that code for genes;

usually separated by short regulatory regions

Front 26

bioinformatics:

Back 26

branch of biology dealing with computational approaches to storage, analysis, and comparison of genomes

Front 27

RNA-seq:

Back 27

isolation and sequencing of all RNA in a cell

Front 28

hybridize:

Back 28

when you stick DNA onto a chip to analyze

Front 29

transcriptome:

Back 29

k

Front 30

metagenomics:

Back 30

analyzing microbial communities by genome and/or RNA sequencing

Front 31

comparative genomics:

Back 31

comparison of genome sequences

Front 32

pathogenicity islands:

Back 32

clusters of genes that a pathogenic strain of a gene has

Front 33

Understand the basic method of Sanger dideoxy sequencing.

Back 33

k

Front 34

What is involved in shotgun sequencing (without too much detail)?

Back 34

fragmenting genomic DNA and cloning the fragments into plasmids

Front 35

What technical improvements allowed pyrosequencing to increase sequence throughput; what is detected in the pryrosequencing reactions?

Back 35

k

Front 36

Understand what sequence alignment is and how is this used to build long contiguous sequences?

Back 36

when a DNA sequence is aligned, overlapped, and formed into contigs

Front 37

Review the steps of a genome sequencing project from small fragment sequences to annotation.

Back 37

k

Front 38

What can a genome sequence reveal about uncultured organisms?

Back 38

k

Front 39

Understand the basics of what a DNA microarray is and what they are used for; how do the microarrays quantitate mRNA levels?

Back 39

contains a gridded chip that has oligonucleotides that can base pair with mRNA from a sequenced genome

Front 40

Know the two general strategies for performing environmental genomics.

Back 40

k

Front 41

Understand the difference between vertical and horizontal gene transfer.

Back 41

vertical: inherited genes passed through cell division

horizontal: non-inherited transfer of genes from one cell to another

Front 42

Transcription:

Back 42

first step in gene expression where DNA is transcribed into RNA

Front 43

Translation:

Back 43

MRNA is translated from AA as codons into proteins

Front 44

Dimer:

Back 44

a molecule containing two identical subunits

Front 45

Inverted repeats:

Back 45

regions of DNA that the dimers bind to

Front 46

diauxic growth:

Back 46

k

Front 47

signal transduction:

Back 47

process of transmitting external chemical signals to relevant regulatory targets

Front 48

feedback inhibition:

Back 48

when the end product of a reaction inhibits the activity of the first enzyme in the pathway

Front 49

effector molecule:

Back 49

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

Front 50

Understand what is meant by "gene expression."

Back 50

the conversion of DNA genetic information into a functional protein

Front 51

Be able to state the difference between an operon and a regulon.

Back 51

operon: the region of DNA that controls transcription

regulon: genes or operons throughout the genome under the same control as operons

Front 52

What is the basic structure of a repressor protein, what is an inverted repeat?

Back 52

k

Front 53

Review regulation of transcription by negative control with a repressor protein: arg operon (repression by arginine), lac operon (induction by lactose).

Back 53

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)

Front 54

Review positive control regulation with an activator protein: mal operon (induction by maltose).

Back 54

Mal operon: maltose binds to the activator binding site and transcription proceeds

Front 55

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?

Back 55

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

Front 56

Describe quorum sensing and the role of "autoinducers."

Back 56

quorum sensing is a method of cells to measure chemical signals to detect population density;

autoinducers are signals that nearby cells pick up

Front 57

What are the roles of a sensor kinase and response regulator protein in signal transduction?

Back 57

sensor kinase binds the extracellular signal molecule and phophorylates itself;

response regulator protein picks up the phosphate and binds to the operator of DNA

Front 58

How can small RNA molecules control translation?

Back 58

sRNA binds to the mRNA and can stimulate or prevent translations-- sometimes needs a Hfq protein, in which case it prevents transcription

Front 59

How do riboswitches control translation?

Back 59

they bind small regulatory molecules that changes base-pairing, making the binding site unavailable (no translation)

Front 60

What is allosteric regulation of enzyme activity?

Back 60

regulation found in enzymes catalyzing the first step of a pathway (i.e, feedback inhibition)

Front 61

Capsid:

Back 61

a protein coat surrounding a virus

Front 62

Nucleocapsid:

Back 62

protein coat surrounding the Nucleic Acid of of virus

Front 63

Virion:

Back 63

the entire virus in its extracellular form

Front 64

Bacteriophage:

Back 64

viruses of bacteria

Front 65

Capsomers:

Back 65

the individual proteins or subunits that make up capsids

Front 66

Filamentous viruses:

Back 66

structure of virus (long? straight? with filiament down middle)

Front 67

Icosahedral viruses:

Back 67

structure of virus that coils (ie, Tobacco Mosaic Virus)

Front 68

Plaque:

Back 68

a single virus cell?

Front 69

Lawn:

Back 69

a continual covering of cells on a surface

Front 70

Lytic:

Back 70

life cycle of viruses in which the virus replicates and then lyses the host cell

Front 71

Lysogenic:

Back 71

life cycle of viruses in which the virus DNA gets incorporated into the host cell's genome

Front 72

Prophage:

Back 72

the incorporated virus genome in a host cell

Front 73

Lysogen:

Back 73

cells containing a viral genome (prophage)

Front 74

Overlapping Genes:

Back 74

a region of DNA that can encode for 2 or 3 proteins using different reading frames

Front 75

Latent infection:

Back 75

k

Front 76

Persistent infection:

Back 76

k

Front 77

Reverse transcriptase:

Back 77

enzyme used by viruses to convert RNA to DNA, to be expressed in the genome of a host cell

Front 78

Provirus:

Back 78

viral DNA that has entered into a host cells genome

Front 79

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?

Back 79

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

Front 80

Understand the steps in the life cycle of a virus that causes lysis of its host cell.

Back 80

virus attaches to host cell and injects viral DNA;

phage components are synthesized and virions assembled;

host cell lyses and virions expelled

Front 81

What is a virus "titer" and how is it determined; how is a plaque formed on an agar plate?

Back 81

titer is the concentration of a virus, determined through _______________;

plaque formed by pouring mix into a petri dish and collecting from agar

Front 82

Review the life cycle of the T4 bacterial virus; how are viral components made when they are needed; what is "packaging"?

Back 82

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

Front 83

What are the two paths that an E. coli cell can take after it is infected with lambda; what is induction?

Back 83

lytic or lysogenic;

induction is the process of which the prophage excises from the genome (leaving lysogenic for lytic)

Front 84

How do viruses make maximal use of the limited genome size?

Back 84

k

Front 85

Know the possible outcomes of infection by certain animal viruses; what is transformation?

Back 85

latent infection and persistent infection;

transformation is the process by which an animal virus converts a normal cell into a tumor cell

Front 86

What replication enzyme is a distinguishing feature of retroviruses; what are the three major gene regions in retroviruses; what are oncogenes?

Back 86

reverse transcriptase;

gag (core and capsid proteins), pol (rev. trans. integrase), env (envelope proteins);

oncogenes are __________________________

Front 87

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?

Back 87

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 _______

Front 88

wild-type:

Back 88

a strain of an organism as isolated from nature (presumably without mutation)

Front 89

spontaneous mutations:

Back 89

mutations that occur naturally without human intervention

Front 90

induced mutations:

Back 90

mutations resulting from intentional exposure to chemical agents of radiation

Front 91

truncated protein:

Back 91

a shortened protein produced by the stop codon UAG

Front 92

mutagen:

Back 92

anything that causes an increase in mutation rates above normal levels

Front 93

nucleotide base analogs:

Back 93

resemble DNA bases and leads to higher frequency of base subsitutions

Front 94

intercalating agents:

Back 94

bind between DNA bases and increase mutation rates

Front 95

SOS system:

Back 95

a regulon of about 40 genes involved in repair of DNA damage and damage tolerance

Front 96

repressor:

Back 96

slows or inhibits a process or an enzyme that controls a process

Front 97

single-strand binding protein:

Back 97

protein that helps detach a nicked strand from a whole strand

Front 98

Holliday junction:

Back 98

"crossover" pattern of a structure

Front 99

resolution:

Back 99

cutting of DNA strand to yield new DNA with heteroduplex regions (segments originating from different DNA molecules)

Front 100

heteroduplex:

Back 100

segments originating from different DNA molecules

Front 101

competence:

Back 101

ability to take up external DNA

Front 102

Understand the difference between genotype and phenotype.

Back 102

genotype: the nucleotide sequence of a genome

phenotype: observable manifestation of the genotype, physical attributes

Front 103

Review the 4 types of base pair substitutions.

Back 103

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

Front 104

What is a frame shift mutation and what can happen to the resulting protein?

Back 104

causes changes in all AA codons downstream of the mutation site; changes the codons/proteins made

Front 105

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?

Back 105

reversions can restore a phenotype;

can restore the reading frame with a second frameshift;

inserts a correct AA at the UAG codon

Front 106

What is the Ames test; how is it performed; why is a liver enzyme extract used; what phenotype is observed; how is it interpreted?

Back 106

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

Front 107

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?

Back 107

k

Front 108

Review the sequence of steps involved in homologous recombination; what 2 proteins promote strand invasion?

Back 108

nick in a strand, single-strand protein separates strands, nicked strand displaces homologous region, crossed-stranded exchange, new DNA from both molecules

Front 109

Know the differences between transformation and transduction; what are generalized and specialized transduction?

Back 109

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

Front 110

plasmid:

Back 110

an extrachromosomal genetic element of double-stranded DNA;

can exist in one to many copies in a single cell

Front 111

sex pilus:

Back 111

aids in the transferring of genes

Front 112

F+ cells:

Back 112

cells containing the F plasmid, which can transfer a copy of itself into a cell

Front 113

insertion sequences:

Back 113

sequences on the F plasmid that are homologous to regions on the chromosome

Front 114

OriT:

Back 114

first DNA to copy and move into the recipient cell

Front 115

cloning:

Back 115

putting DNA into a larger molecule that can be replicated and manipulated

Front 116

sticky ends:

Back 116

when the DNA is cut with a hanging edge to be paired/matched

Front 117

blunt ends:

Back 117

when the DNA is cut with no single-stranded end

Front 118

amplification:

Back 118

the replication of specific small regions of DNA

Front 119

DNA ligase:

Back 119

an enzyme that joins DNA ends

Front 120

recombinant DNA:

Back 120

DNA in which a plasmid has been incorporated

Front 121

What is a conjugative plasmid; how is sex pilus involved?

Back 121

plasmid that inserts a copy of itself into another cell;

transfers via the sex pilus

Front 122

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.

Back 122

k

Front 123

Know what restriction enzymes are and how they can be used for genetic engineering and cloning.

Back 123

restriction enzymes are proteins that cut DNA at specific sequences;

they can cut at specific sites to insert plasmids and alter genes

Front 124

How can PCR be used for generating specific DNA fragments?

Back 124

by targeting and amplifying a given DNA sequence

Front 125

How can DNA fragments be connected with a cloning vector to produce recombinant DNA?

Back 125

the sticky ends match and are sealed/glued via DNA ligase

Front 126

In what ways are plasmids designed to simplify molecular cloning of DNA fragments?

Back 126

contain multiple RE sites;

exist in many copies per cell;

possess one or more antibiotic resistance genes to allow for selection in host cells

Front 127

What are expression vectors and shuttle vectors used for?

Back 127

expression vectors: control expression of cloned genes

shuttle vectors: can be used in many organisms

Front 128

alignment program:

Back 128

program that finds overlaps in sequences of 16s rRNA genes

Front 129

distance matrix:

Back 129

how differences in the sequence overlaps of an alignment program are viewed/analyzed

Front 130

branches:

Back 130

how individual organisms are connected on a distance matrix

Front 131

nodes:

Back 131

where branches intersect on a distance matrix

Front 132

core genome:

Back 132

contains all genes shared by a group of organisms

Front 133

pan genome:

Back 133

all the genes unique to one particular genome

Front 134

understand the major evolutionary events since the cooling of earth's crust; how did oxygen levels rise in the atmosphere?

Back 134

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

Front 135

What are microbial mats and stromalites?

Back 135

microbial mats: layers of lawns of photosynthetic organisms

stromalites: fossilized microbial mats

Front 136

Why are molecular sequences best for determining phylogenetic relationships; what sequence is most commonly used?

Back 136

16s rRNA sequence from ribosomes

Front 137

What are the steps in isolating 16s rRNA genes by PCR and building a phylogenetic tree?

Back 137

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

Front 138

What is fitness; what are major processes driving evolution; what is an example of evolution and fitness that has been observed in recent years?

Back 138

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

Front 139

What is genetic drift and how has it been studied in E. coli populations; what studies have been done at MSU?

Back 139

genetic drift: some members of a population reproduce slightly faster than others;

_____;

modern rapid genome sequencing methods

Front 140

How can comparative genomics reveal genes important for causing disease?

Back 140

by comparing pathogenic and nonpathogenic strains of bacteria

Front 141

What are multilocus sequence typing and ribotyping and what are they used for?

Back 141

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

Front 142

Understand in a general way how FAME analysis works.

Back 142

Fatty Acid Methyl Ester analysis:

derivatizes bacterial FA and examines profiles of them via gas chromatography

Front 143

extremophile:

Back 143

microbes that grow in extreme conditions (heat, salt, etc)

Front 144

compatible solutes:

Back 144

internal solutes that equalize the water activity between the inside and outside of the cell

Front 145

bacteriorhodopsin:

Back 145

protein contained in the membrane of some halophilic archaea

Front 146

retinal:

Back 146

molecule that moved protons from inside of a cell to the outside

Front 147

phytanyl:

Back 147

composed of a bilayer in membranes

Front 148

biphytanyl:

Back 148

composed in a monolayer in membranes

Front 149

lipoglycan:

Back 149

a membrane found in archaea with no wall

Front 150

pleomorphic:

Back 150

cells with no specific shape

Front 151

sulfataras:

Back 151

hot, acidic terrestrial sulfur springs; habitat of some extremophiles

Front 152

hydrophobic cores:

Back 152

stabilizes protein secondary structure; exclusion of water n internal regions of proteins by hydrophobic amino acids increases thermal stability (like two suction cups together)

Front 153

salt bridges:

Back 153

ionic bonds that create strong contacts between different parts of the polypeptide chain

Front 154

chaperonins:

Back 154

proteins that assist in the correct folding of proteins

Front 155

reverse DNA gyrase:

Back 155

enzyme that is more stable to heat denaturation

Front 156

DNA-binding proteins

Back 156

similar to histones; compact the DNA and help maintain double-strand structure at high temperatures

Front 157

How do halophilic Archaea maintain water balance in high salt conditions?

Back 157

with physiological adaptations such as compatible solutes

Front 158

How do some Archaea generate ATP energy from light?

Back 158

the bacteriorhodopsin protein contain retinal, which transports protons outside the cell; these protons fall back down their concentration gradient into the cell, producing ATP

Front 159

What are methanogens and understand what the methanogenesis pathway does.

Back 159

anaerobes that convert CO2 to methane;

they utilize cofactors that make CH4 from CO2 and H2

Front 160

Review the different ether lipids of Archaea; what are the major types of lipids?

Back 160

phytanyl:

biphytanyl:

lyopglycan:

Front 161

How is Thaumarchaeota important for the global nitrogen cycle; what adaptation is important for its survival?

Back 161

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

Front 162

How does Nanoarchaeum live; what does it derive from its host?

Back 162

lives as a parasite;

derives genes from its host cell

Front 163

What habitats is Sulfolobus found in; how does it get energy?

Back 163

deep ocean hydrothermal vents;

chemolithotrophically or chemoheterotrophically

Front 164

What are challenges to organisms living at high temperatures and what adaptations to proteins and DNA do they have in order to survive?

Back 164

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

Front 165

hydrogenosomes

Back 165

similar to mitochondria but lack TCA cycle enzymes

Front 166

michondrion:

Back 166

organelle responsible for respiration and oxidative phosphorylation;

surrounded by two membranes;

folded internal membrane called cistae

Front 167

chloroplast:

Back 167

chlorophyll-containing organelle found in phototrophic eukaryotes (plant cells);

flattened membranes called thylakoids;

lumen called stroma which contains RubisCO (key in Calvin cycle)

Front 168

thylakoids:

Back 168

flattened membrane disks inside chlorplasts

Front 169

christae

Back 169

folded, internal membrane of mitochondria

Front 170

Rubisco:

Back 170

contained in the stroma of chloroplasts;

key enzyme in the Calvin cycle

Front 171

Calvin cycle:

Back 171

conducted in the chloroplast;

Front 172

Giardiasis:

Back 172

disease resulting in abnormal cramps, diarrhea, nausea;

pathogen transmitted through fecal-contaminated water

Front 173

African sleeping sickness:

Back 173

Trypanosoma brucei;

transmitted by a live vector, the tsetse fly;

Front 174

nagana:

Back 174

disease caused by Trypanosoma brucei in cattle

Front 175

vector:

Back 175

organism that transmits disease;

intermediate host

Front 176

pseudoplasmodium slug:

Back 176

unified organisms created by aggregated slime molds that move together

Front 177

chitin:

Back 177

type of fungi?

Front 178

achlorophyllous:

Back 178

type of chemoorganotrophs

Front 179

basidiocarp:

Back 179

macroscopic sexual spore-bearing structures

Front 180

mycoses:

Back 180

infections on or in the body, 3 types:

superficial, subcutaneous/invasive,

Front 181

superficial:

Back 181

infection only on the surface layer; skin, hair, etc;

Ex: athlete's foot, ringworm, etc

Front 182

subcutaneous:

Back 182

infection under the skin?

Front 183

systemic:

Back 183

infection that affects internal organs

Ex: histoplasmosis, thrush, etc

Front 184

primary producer:

Back 184

main producer?

Front 185

endolithic:

Back 185

"inside rocks"

Front 186

Briefly review key features of a eukaryotic cell but do not memorize all the details.

Back 186

dual membrane nucleus, ribosomes, nucleolus, organelles, etc

Front 187

What is the endosymbiosis theory and what evidence supports it?

Back 187

that the organelles of eukaryotes orginated from prokaryotes;

some organelles have

Front 188

review the three major energy production organelles of eukaryotes.

Back 188

mitochondria:

hydrogenosome:

chloroplast:

Front 189

What type of diseases are caused by Protists such as Giardia and Trichomonas?

Back 189

k

Front 190

What are pathogenic and non-pathogenic examples of Euglenozoans?

Back 190

Pathogenic: Trypanosoma brucei (African sleeping sickness, nagana) and cruzi (chagas)

Non-pathogenic: Euglena

Front 191

Briefly review Plasmodium falciparum life cycle and the different stages during the cycle.

Back 191

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 -->

Front 192

Why are some dinoflagellates toxic; what habitat are they found in?

Back 192

k

Front 193

What are two types of slime molds; how do cellular slime molds differentiate?

Back 193

cellular: individual cells with amoeboid motility

plasmodial (acellular): produce masses of multinucleated protoplasm called plasmodia;

Front 194

Know the key features of fungi; roles in nature, major impacts to humans.

Back 194

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

Front 195

What disease can Candida albican cause; what is histoplasmosis?

Back 195

thrush;

?

Front 196

In what habitats are algae commonly found; what types of cell walls can they have?

Back 196

rocks?

cellulose/pectin, silica, calcium carbonate

Front 197

phylotypes:

Back 197

method of expressing richness of a species

Front 198

allochthonous:

Back 198

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

Front 199

viability stains:

Back 199

stains that discriminate live cells from dead cells

Front 200

DAPI:

Back 200

becomes fluorescent blue only when bound to DNA

Front 201

Acridine orange:

Back 201

fluoresces orange when bound to DNA

Front 202

metagenomics:

Back 202

analysis of community diversity by looking at genes

Front 203

Review populations, guilds, communities, habitats, ecosystem; how is a freshwater lake and example of a microbial ecosystem, what are the energy inputs?

Back 203

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

Front 204

Understand the difference between species richness and species abundance.

Back 204

species richness: reference to the number of different species present (diversity)

species abundance: reference to the fraction or proportion of each species

Front 205

Review the methods used to determine microbial community composition; what staining methods are used for microscopic analysis; what is a live/dead stain?

Back 205

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

Front 206

Understand the basic method of Fluorescence In Situ Hybridization; what is it used for?

Back 206

it can "tag" a certain molecule or sequence with a neon "marker";

recognizing specific organsims within populations

Front 207

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?

Back 207

do not require growth of an organism;

medical diagnostics and ;

microscopic analyses and genetic analyses

Front 208

How can PCR products be analyzed by terminal restriction fragment length polymorphism, 1st generation sequencing, or next generation sequencing?

Back 208

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

Front 209

What are phylochips and what are they used for; what is hybridization of DNA?

Back 209

tool to measure the different phylotypes in a community without sequencing;

base pairing

Front 210

How have these methods been applied in analyzing microbial communities in the Sargasso Sea and the human microbiome?

Back 210

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.

Front 211

microenvironments:

Back 211

local habitats of microbial cells

Front 212

antagonism:

Back 212

(ammensalism) one organism inhibits gorwth of another organism (ie, antiibiotics)

Front 213

competition:

Back 213

demand for food exceeds the supply (limited resources)

Front 214

predation:

Back 214

microbes can be food for other organisms

Front 215

parasitism:

Back 215

parasite (such as a virus) harms its host microorganism

Front 216

cystic fibrosis:

Back 216

k

Front 217

benthic:

Back 217

organisms that grow on the sides or bottom surfaces of aquatic systems

Front 218

Be able to describe what a niche is.

Back 218

a set of resources and conditions that are utilized by microorganisms

Front 219

What are the benefits of living in biofilms; what happens in each stage of biofilm development?

Back 219

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

Front 220

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?

Back 220

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)

Front 221

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?

Back 221

in winter, colder near top, in summer, colder near bottom;

it has low levels of dissolved O2;

?

Front 222

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?

Back 222

?

less O2, higher BOD??

Front 223

What are the bacterial and eukaryotic primary producers in open ocean waters?

Back 223

bacterial: Prochlorococcus and Trichodesmium

eukaryotic: Ostreococcus

Front 224

soil separates:

Back 224

sand, silt, and clay

Front 225

epiphytes:

Back 225

microbes that colonize plant surface

Front 226

endophytes:

Back 226

microbes that colonize plant interior

Front 227

phyllosphere:

Back 227

aerial leaf surface of plants

Front 228

rhizosphere:

Back 228

region adjacent to the root

Front 229

rhizoplane:

Back 229

the root surface

Front 230

legumes:

Back 230

pod-bearing angiosperms that can fix nitrogen

Front 231

bacteroid:

Back 231

k

Front 232

membrane:

Back 232

k

Front 233

nodule:

Back 233

the product of root hair after curling

Front 234

Nod factors:

Back 234

lipochitin polysaccharides that are recognized by root hair

Front 235

infection thread:

Back 235

line of infection as it expands into root cells

Front 236

leghemoglobin:

Back 236

hemoglobin in a legume; protein that delivers oxygen to electric transport chain

Front 237

inter-domain:

Back 237

transfer of DNA from a bacterium to a plant

Front 238

flavinoid:

Back 238

compound excreted by roots that are taken up by bacteria to express nodulation genes

Front 239

Name the 3 phases found in soils; review the four vertical horizons found in mature soils; what are soil aggregates?

Back 239

solids, liquids, and gasses;

O, A, B and C horizons;

fill space in soil?

Front 240

How does water affect oxygen levels in the microenvironments within soil aggregates?

Back 240

k

Front 241

What is rhizodeposition and what is its effect on nearby soil microbes?

Back 241

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

Front 242

What are the 3 main locations for microbes associated with plants?

Back 242

phyllosphere, rhizosphere, rhizoplane

Front 243

Why is N2-fixing symbiosis important to agriculture; describe the steps of plant-rhizobia symbiosis; what chemicals are used for plant-microbe communication?

Back 243

can develop N2-fixing root nodules, N2 is the most common limiting nutrient

Front 244

Review nitrogen-fixation; what is the overall reaction for nitrogen fixation; how much energy is expended for each N2?

Back 244

N2 + 8H + 8e- +16 ATP +16H20

-->

2NH3 + H2 + 16 ADP + 16 Pi

16 ATP

Front 245

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?

Back 245

via a Ti plasmid;

carried genes for tumor formation on the plant;

VirA: sensor kinase

VirG: response regulator

Front 246

What are the two types of associations of fungi with plant roots; how to plants and mycorrhizal fungi benefit from each other?

Back 246

ecto- and endomycorrhizae;

fungi can take nutrients from the soil and make them more readily usable by plants