Term
capsid
capsomer
nucleocapsid |
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Definition
capsid is protein shell surrounding virus genome
capsomer is the protein subunits of capsid
nucleocapsid=capsid+genome
-(helical or icosahedral symmetry
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Term
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Definition
| lyse/pore in cell wall peptidoglycan |
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Term
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Definition
| viral enzyme: txn (host has no RNA-dep enzymes) |
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Term
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Definition
| (animal) viral enzyme: cleave gly bonds for relase |
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Term
| restriction-modification systems |
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Definition
| host resistantance to viral restriction enzymes via methly mod of rec sites (ds DNA virus only) |
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Term
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Definition
| T4 base mod gives resistance to restriction enzymes |
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Term
| mRNA and complement/template |
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Definition
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Term
| temporate lamba repressors |
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Definition
C1: repress lytic
Cro: repress C1 -> allow lytic |
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Term
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Definition
Titer: #infect units
Plaque:clearing
In a two layer agar plate used to visualize phage concentraction, which layer is the phage within? Top layer. What is the other layer? Nutrient layer. |
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Term
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Definition
early: DNA txn, catalytic enzymes (sm amounts)
late: building head/tail/enzymes |
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Term
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Definition
| virulent(lyse) vs. temporate(genome) |
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Term
| temporate/lambda lifecycles |
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Definition
lysogenic: insert into chromosome
lytic: assembly/release of virons |
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Term
| lysogen, lysogeny, prophage |
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Definition
lysogen: infected host
prophage: virus genome incorporated
Lysogeny: state virus genes not expressed |
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Term
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Definition
| plasmid that can integrate into chromosome |
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Term
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Definition
| removing plasmid from cell |
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Term
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Definition
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Term
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Definition
cell able to take up plasmid.
induced by electroporation, heatshock, or Ca2+ |
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Term
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Definition
generalized: accentently packaged in virus (virulent or temporated
specialized: spec. seq (temporate only) highes eff at att site |
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Term
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Definition
(fertility/conjugation episome), rolling rep
tra gene: encodes transposase
oriT
IS: mobile element |
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Term
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Definition
F+:plasmid not integrated (donor)
Hfr: integrated (recipient with plasmid) |
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Term
| bacteria vs virus mutation rates |
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Definition
virus 1000x more because no repair mech
bacteria 10^-6 mutations/kb |
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Term
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Definition
for nonselective (not adventageous) mutations
axotroph/prototroph
use velveteen filter (instead of toothpicks) |
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Term
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Definition
| chemical mutagen point mutation |
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Term
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Definition
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Term
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Definition
| chemical mutagen: bulge bw bp |
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Term
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Definition
non-ionizing: UV pyrimidine dimers
ionizing: free radicals damage DNA |
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Term
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Definition
| detect axotroph/mutation in response to suspected mutagen |
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Term
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Definition
direct reversal
single strand: using template
double strand: break in DNA req more error-prone repair mech |
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Term
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Definition
| bacterial strain that carries 2 copies of chromosomal segment (introdiced by transformation, transduction, conjugation) |
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Term
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Definition
fxn copy compensates for defective
used by geneticist
if compensate for mutant, must contain wt |
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Term
| transposable elements (2) |
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Definition
Tn: transposons allow exchange of antibiotics
-Tn5=KanR; Tn10=tetracyclineR
IS: insertion seq one gene (trn) simplest |
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Term
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Definition
rec inverted repeats (palindromes)
cut->blunt or sticky ends |
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Term
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Definition
| protect own DNA from restriction enzyme (meth mod) |
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Term
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Definition
ethidium bromide
south=DNA |
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Term
| nucleic acid hybridization |
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Definition
| DNA or RNA probe for cDNA |
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Term
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Definition
mix of cells/clones with diff frag
shotguns made by cloning random frag |
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Term
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Definition
pUC19
ori: rec host DNA polymerase
selectible marker: AMPr
polylinker: MCS w/in lacz
lacz: distinguish plasmid w/insert
-expressed=no insert -> B-gal cleaves x-gal => blue/wht screen |
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Term
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Definition
Taq: thermus aquaticus
Pfu: Pyrococcus furiosus (more therm stable+proofreading) |
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Term
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Definition
RT-PCR: reverse transcriptase mRNA->cDNA
qPCR: determine # of target genes |
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Term
| site directed vs. cassette mutagenesis |
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Definition
site directed: no RE mut spec. loc
cassette: RE, antibioticR disrupt target gene->KO mutation selection |
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Term
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Definition
| lacz, GFP, luxAB(luciferase) |
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Term
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Definition
2 or more host (BAC,YAC, M13)
-RBC
-codon bias ORF
-no introns (cDNA)
-eu ori and centromere |
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Term
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Definition
| time to reduce viability by 10 |
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Term
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Definition
HEPA: depth
nucleopore: membrane |
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Term
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Definition
| amount of agent needed to kill (dep on envir cond) |
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Term
| antiseptics vs sterilizers/disinfectants/sanitizers |
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Definition
antiseptics (non-corrosive): alc, phenol, cationic, H2O2, I
sterilizers also includes chlorine, ozone |
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Term
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Definition
| w/out killing host (synth antimicrobial drugs) |
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Term
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Definition
| stucturally sim to growth factos block normal fxn (synth antimicrobial drugs) |
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Term
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Definition
| PABA analog inhibits bacteria but alos folic acid and nucleic acid synth (synth antimicrobial drugs) |
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Term
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Definition
| inhib GNA gyrase (Cipro) (synth antimicrobial drugs) |
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Term
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Definition
| Penicilins and Cephalosporins |
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Term
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Definition
prokaryote antibiotic
aminosug glcosidic link
eg. kanamycin, neomycin (neuro/neph toxic) |
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Term
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Definition
prokaryote antibiotic
lactone rings broad spec 50S
eg erythromycin |
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Term
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Definition
prokayote antibiotic
broad spec 30S |
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Term
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Definition
dec permeability
inactivation
alt target
pathway
efflux
R-plasmids |
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Term
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Definition
| seq of genes/proteins to measure evolutionary chnge |
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Term
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Definition
| links phylogeny + taxonomy |
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Term
| membrane lipids in bacteria, archaea, and eukarya |
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Definition
archaea: ester links isoprenes+glycerol
bacteria and eukayotes: ester link FA+glycerol |
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Term
| RNA polymerases in in bacteria, archaea, and eukarya |
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Definition
| similar in archaea and eukarya |
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Term
| promoter strcture in in bacteria, archaea, and eukarya |
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Definition
-10&-35 sq bacteria
TATA for eu and arch |
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Term
| initiator tRNA in bacteria, archaea, and eukarya |
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Definition
bacteria formylthione
methione for eu and arch |
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Term
| histones in bacteria, archaea, and eukarya |
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Definition
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Term
| txn factors in bacteria, archaea, and eukarya |
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Definition
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Term
| introns in bacteria, archaea, and eukarya |
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Definition
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Term
| operons in bacteria, archaea, and eukarya |
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Definition
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Term
| capping and polyA in bacteria, archaea, and eukarya |
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Definition
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Term
| plasmids in bacteria, archaea, and eukarya |
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Definition
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Term
| nitrogen fixation in bacteria, archaea, and eukarya |
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Definition
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Term
| polyphasic taxonomy (3 types) |
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Definition
phenotypical, genotypical,
phylogenic |
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Term
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Definition
| alcoholic, homolactic, heterolactic, propione, mixed acid |
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Term
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Definition
1. FAs activated by CoA
2. 2-c removed -> acetly-CoA
3. acetyl-CoA catabolized->citric acid cycle
Negative 1 ATP. Payoff is in the metabolism of acetyl-CoA in citric acid cycle. |
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Term
| assimilative vs. dissimilative |
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Definition
in anaerobic resp
assimilation uses fermentation froducts for biosynth
dissimilative->prod not used, excreted |
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Term
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Definition
6CO2->1glucose
req ATP, NADPH, Rubisco |
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Term
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Definition
| chemolithotroth uses organic acids as carbon |
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Term
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Definition
use PMF->ATP (anerobic)
e-carrier ferredoxin
hyrogenase oxidizes H2 |
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Term
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Definition
N2->NH3
nitrogenase reg by nif |
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Term
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Definition
inhib by effectors O2 and NH3
3 nifHDK: nitrogenase polypeptides
FeMo-Co: iron molybdenium cofactor (synth+insert
--reg nefA and nifL |
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Term
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Definition
wine has sulfates added
beer malt breaks down polysacc, hops add flavor |
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Term
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Definition
(chlorophyll) capture light nrg ->convert to chemical
bound to protein
NADP->NADPH
donates e- to ETC |
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Term
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Definition
| funnel light enery into reaction centers |
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Term
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Definition
antenna pigment
prevents photooxidative damage |
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Term
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Definition
antenna pigment
cyano and red algae (more than chlorophyll alone) |
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Term
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Definition
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Term
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Definition
flourecent
non-specific; stain nucleotides |
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Term
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Definition
| 2 dyes differenciate dead and living (2nd dye enders dead only) |
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Term
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Definition
time and money
tag specific binding to a specific protein, lipid or polysaccharide on the target cell’s membrane |
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Term
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Definition
| tracking acting as reporter gene |
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Term
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Definition
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Term
| single gene biodiv anaylysis |
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Definition
DGGE: denaturing gel electrophoresis
T-RFLP: terminal restriction frag length polymorph |
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Term
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Definition
richness: total # of species present
abundance: proportion of species |
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Term
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Definition
| links organisms based on metabolism |
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Term
| primary vs secondary metoabolites |
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Definition
primary: made durng exp growth; essential
secondary: non essential; provides advantage |
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Term
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Definition
| virulence lethal dose: kills 50% |
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Term
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Definition
| dec virulence in lab setting |
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Term
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Definition
| coating pathogen with fibrin to disguise as blood cell to avoid macrophage endocytosis |
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Term
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Definition
| genetically engineered (use cDNA) |
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Term
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Definition
assembly pathway using genes from mult orgs
eg ecoli+another for indigo dye |
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Term
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Definition
Ti plasmid
T-DNA
eg Bt toxin |
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Term
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Definition
strong promoter: txn
RBS (tln)
MalE: carrier protein
lacl: encodes repress of Ptac
lPTG induces by inactivating repressor |
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Term
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Definition
| vaccine mild infection for immunity |
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Term
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Definition
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Term
| recombinant vaccine (3) types |
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Definition
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Term
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Definition
recombinant
inset gene into harmless virus |
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Term
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Definition
recombinant
protein from pathogen |
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Term
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Definition
recombinant
genes for immunogenic proteins cloned in |
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Term
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Definition
lactic acid bacteria
Streptococcus subrinus/mutans |
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Term
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Definition
stomach: Helicobacter (ulcers)
LI: Enterococcus (opportunistic) |
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Term
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Definition
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Term
| intestinal flora organic acid production |
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Definition
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Term
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Definition
(mostly upper)
staphylococci, streptococci, diphtheroid bacilli, gram-cocci |
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Term
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Definition
SpoIIA activation (phos due to stress)
SpoIIABsigma complex binds and activates sigmaF
(EK=Mom; FG:Endospore)
sigmaF->pro-sigmaE->pro-sigmaK and sigma G->sigma G activates pro-sigmaK to sigma K |
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Term
| endospore-forming bacteria (3 eg Genera) |
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Definition
| Bacillus, Clostridium, Heliobacterium |
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Term
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Definition
final step in cell wall synthesis
making crosslink (lysine+ or DAP-)
G-M glycosidic
a-a covalent |
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Term
Vibrio fischeri
Pseudomonas aeruginosa |
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Definition
quarum sensing discovered with light prod V. fischeri
biofilm/independent behavior change P. aeruginosa |
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Term
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Definition
| use a metabolic process that produces methane, a greenhouse gas. (rememeber methanogens = archaea) |
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Term
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Definition
long overhangs - sticky
blunt cuts around center |
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Term
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Definition
| most commonly used Eukaryote in lab settings |
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Term
| How old are the oldest multicellular fossils estimated to be? |
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Definition
| 0.9 billion to 1.4 billion years ago |
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Term
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Definition
refers to the oxidation of iron which preceded the oxidation of the atmosphere
can be visualized by a layer of oxidized Iron in sedentary rock called the banded iron formations |
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Term
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Definition
| prokaryotes are classified within a species if they have 70% similar DNA-DNA hybridization and 97% similar 16s(SSU) rRNA |
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Term
| How many different phyla make up the domain bacteria? |
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Definition
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Term
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Definition
| resistant to radiation because it has adapted to rapid reversal of dessication(drying) induced DNA damage. |
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Term
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Definition
| How does a TMV (Tobacco Mosiac Virus) get past the plant cell wall and into the cytoplasm? TMV is spread by insects that eat leaves, causing plant cell wall damage. |
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Term
| early/late virus proteins |
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Definition
| Viral polymerase is an example of an (early/late) protein. Capsomers are generally (early/late) proteins. Note- genome replication proteins/enzymes are almost always early proteins, all other proteins come later. |
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Term
| methanigenesis involves a series of reactions including |
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Definition
H2 as e- donor
CH4 as a product
prod ATP
PMF, Na+ MF |
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