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94 Cards in this Set

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Compare characteristics of eukaryotes and prokaryotes: organelles, sterols, ribosomes, cell wall, mRNA half life, DNA
eukaryotes: many types of organelles, sterols in the PM, 80S ribosomes (60S + 40S), absence of cell wall or cellulose, long-lived mRNA, intervening introns
Prokaryotes: no true organelles, no sterols, 70S ribosomes (50S + 30S), peptidoglycan cell wall, short-lived mRNA, colinear
colearity of genes in prokaryotes
Continuous sequence of nucleotides in the DNA codes for a continuous sequence of amino acids in the protein. With colinearity, the number of nucleotides in the gene is proportional to the number of amino acids in the protein.
Virus sometimes have coat that contain lipids. T/F
T
Gram stain techniques:
1. crystal violet stains _____ blue-purple
2. iodine solution fixes crystal violet in ___ bacteria
3. acetone-alcohol washes dye out of _____ bacteria
4. safranin counter-stain _____ pink-red
1. G +
2. G +
3. G -
4. G -
Acid-fast (Ziehl-Neelsen) stain procedures:
1. stained with carbolfuschin
2. apply heat
3. wash the bacteria with acid-alcohol mixture
4. bacteria stained with methylene blue
1. -----
2. bacteria stains red
3. stain washes out of non-acid-fast cells
4. non-acid-fast cells counter-stain blue
examples of acid-fast bacteria
members of Mycobacterium
examples of mycobacterium that's important for dental practice
Mycobacterium tuberculosis
What other mycobacterium species is associated with a well known disease?
leprosy
bacteria cell shape
rods (short, long, curved), cocci, fusiform, spirochete, square
1. almost all G+ cocci are ____
2. almost all G- spirochetes are ____
3. almost all G- cocci are ___
4. all G- bacteria with star colony morphology _____
5. all G- rods with brown-black pigmented colonies _____
1. Streptococcus species
2. Treponema species
3. Veillonella species
4. AA (aggregatibacter actinomycetemcomitans
5. Bacteriodes or Porphyromonas gingivalis species
Biotype is based on?
Serotype is based on?
1. metabolic characteristics (fermentation rx); MacConkey agar
2. immunospecific rx (Ag/Ab); ELISA
genotyping is analytical approach based on DNA sequence analysis. 3 techniques in genotyping.
1. 16S rRNA gene sequencing (species identification)
2. PCR (identify any gene)
3. genomic sequencing
staphylococcus characteristics
G+, cocci, facultative, catalase +
streptococcus
G+, cocci, facultative, catalase -
Neisseria
G-, cocci
Bacteroides and fusobacterium
G-, rods, anaerobes, nonmotile
Eikenella
G-, rods, facultative, asaccharolytic (incapable of metabolizing glucose, CHO)
G+ bacteria: structure on the cell wall
PG (thick), pilus/fimbriae, flagellum, cytoplasmic membrane, capsule/glycocalyx
G- bacteria: structure on the cell wall
cytoplasmic membrane, PG (thin), periplasmic space, outer membrane (OM), flagellum, pilus/fimbriae, capsule/glycocalyx
unique structures of acid-fast bacteria
enclosing membrane, intracytoplasmic membrane, plasma membrane, cell wall
mycoplasma: unique structures
lack peptidoglycan cell wall, uses exogenous sterols in their membrane.
does cytoplasmic membrane have symmetric phospholipid bilayer?
yes, all bacteria cytoplasmic membrane contain the common phospholipids.
PG cell wall of bacteria are composed of these 3 parts:
glycan backbone (repeating unit of NAG and NAM), tetrapeptide side chain, amino acid cross bridge
NAG and NAM are linked by what bond?
beta (1->4) linkage
tetrapeptide are linked to NAM or NAG?
NAM
order of tetrapeptide
L-alanine, D-glutamic acid, meso DAP*, D-alanine
*meso DAP = D,L-diaminopimelic acid
tetrapeptide side chain always end with which aa?
D-alanine
function of cross-bridge
It attaches D alanine (4) in one side chain to meso DAP (3) in another side chain of another glycan backbone.
plasmolysis - solution is ___ to cell
cytolysis - solution is ____ to cell
hypertonic
hypotonic
what bacterial structure lysozyme cleaves?
it cleaves btw NAM and NAG, and produce cross-linked disaccarides
Lipoteichoic acid (LTA) are present in which bacterial cell type?
Lipopolysaccharide (LPS)/endotoxin is present in which bacterial cell type?
LTA: G+
LPS: G-
2 types of LTA
1) glycolipids
2) polyglycerophosphate
or
1) glycolipid
2) ribitol and phosphate
LPS components
lipid A (toxic), core, O-Ag (serotype)
component of lipid A of LPS
2x NAG, FA, phosphate group, 8-carbon sugar (KDO)
LTA is anchored on _____ membrane.
LPS is anchored on ______ membrane
cytoplasmic membrane
outer leaflet of outer membrane
describe the outer membrane of G- bacteria
LPS anchors on the outer leaflet of outer membrane, lipid A is also at the outer leaflet of outer membrane. The inner leaflet is composed of the same phospholipid as the cytoplasmic membrane. This gives a asymmetry to the outer membrane.

Outer membrane have porin, provide aqueous channel. Anything larger than pentasaccharide is excluded from entrance thru porin.
acid-fast bacteria surface polymers
mycolic acid, arabinogalactan

LAM, mannophosphoinositide, phosphoinositol
the Ag on the surface of capsules (glycocalyx) is refer to?
K-Ag
3 types of flagella
polar, peritrichous (more than 1), axial filament (found on spirochete)
2 types of pilli
common, sex
3 functions of pili
adherence, coaggregation (involve >2 species), conjugation
the Ag on the surface of flagella is refer to ?
H-Ag
elements required for bacteria growth
C, H, N, O2, S
all oral bacteria are heterotrophs. T/F
T
obligate aerobic and facultative bacteria express ______ to eliminate superoxide anion
superoxide dismutase
superoxide are eliminated in 2 steps
step 1: catalyzed by superoxide dismutase to produce hydrogen peroxide.

step 2: hydrogen peroxide is catalyzed by catalase or peroxidases to produce water.
optimal growth temperatures of:
thermophiles
mesophiles
psychrophiles
thermophiles: 50 - 60 oC
mesophiles: 20 - 40 oC
psychrophiels: 10 - 20 oC
mesophiles mostly inhabit where
host commensals and pathogens
type and substrate of phosphotransferase system (PTS)
type: active
substrate: glucose, fructose, sucrose
components of PTS
Enzyme I, HPr: soluble cytoplasmic components, transport of phosphate group from PEP to donate to sugars
Enzyme II and III: membrane bound components used for transport of specific sugars.
Does PTS for glucose contain enzyme III?
Yes
Embden-Meyerhof-Parnas (EMP) pathway: ___ net ATP, ___ NADH.
2 ATP, 2 NADH
which intermediate of PPP is shunted to EMP.
pentose-5-phosphate
pentose phosphate pathway (PPP): ___ net ATP, ___ NADH, ____ NADPH
1 ATP, 1 NADH, 2 NADPH
properties of plasmids
linear array of genes: DNA has info on it.
characteristic copy number: there's finite numbers of plasmids in a bacteria. there's a gene that dictates the copy number.
types of plasmids
drug resistance factors
bacteriocinogenic factor: bacteriocin (proteins that kill other bacteria). colicin if produced by E coli.
fertility (F) factor: codes for proteins that facilitate conjugation (F pilus)
toxinogenic factor: codes for bacterial toxins that kill plant or animal cells, surface Ag (capsules or pili)
metabolic factor
cloning vector: commercially available
cryptic plasmid: unidentified functions
properties of transposons
linear molecule
move by non-homologous recombination
transposon are composed of 3 structures
inverted repeat, genes for transposition, core region (structural genes)
transposon are always flanked by ____ repeat
direct repeat
what proteins are involved in bacteria transformation
competence factor, autolysin, niclease, DNA-binding proteins, competence specific protein
During transformation, is it dsDNA or ssDNA that bind initially to the cell membrane?
dsDNA
During transformation, why are foreign DNA needed to be coated with competence-specific protein before entering the cell?
Because PG and DNA are both negatively, so competence-specific protein prevent repelling.
Define Hfr cells
During transformation, sometimes F plasmid become incorporated into the chromosome in low frequency. This creates Hfr (high frequency recombinance) cells. The cell become super DNA donor. It can mate with an F- cells at higher frequency than the original donor.
Define F' cells
F' strain is when F plasmid incorporate a small portion of the host cells. This F' plasmid can be transformed into another F- cells, and bacterial genome is transferred.
when Hfr are transferring its genome to F- cell, what's the last part to be transferred
the integrated F plasmid
2 types of phage
virulent and temperate
virulent:lytic cycle
temperate:_____
lysogenic cycle
temperate phages may be induced to become virulent, and go through lytic cycle.
one-step growth curve describe intracellular or extracellular phage?
extracellular phage
molecules involves in allosteric enzymes
effector, enzyme and substrate. binding of effector changes conformation of the enzyme
types of feedback inhibition
cumulative feedback inhibition
sequential feedback inhibition
feed-forward inhibition or activation
enzymes that regulate these pathways:
PEP -> pyruvate
pyruvate -> lactate
pyruvate -> to 3 other acids.
pyruvate kinase
lactate dehydrogenage
pyruvate formate lyase
limited sucrose results in _____ fermentation
excess sucrose results in _____ fermentation
heterolactic fermentation
homolactic fermentation
lactose operon : negative control
arabinose operon : positive control
negative control: repressor not bound to the DNA = transcription

positive control: repressor bound to the DNA = transcription
growth curve of bacteria on a single substrate include 4 phases
lag phase, log (exponential) phase, stationary phase, death phase
an example of global regulatory mechanism
catabolite repression
examples of natural sources of Ab:
Fungi
G+
G-
Fungi: beta-lactam
G+: aminoglycoside
G-: quinoline
Minimal Inhibitory Concentration (MIC)
serial dilution of antibiotics in test tubes that have bacteria. MIC is when the liquid is clear, indicating no bacterial growth.
Kirby-Bauer method
bacteria is plated on the agar plate and disk of different concentration of antibiotics is placed on the plate. zone of inhibition is observed.
function of D-cycloserine
D-cycloserine and D alanine look alike, D-cycloserine inhibits the formation of D-alanine dipeptide, which inhibit PG formation.
vancomycin
Inhibits NAM from crossing the membrane, also inhibits lipopolisaccaride synetheis in G-
bacitracin
Inhibit removal of Pi from C55 isoprenoid carrier lipid, the lipid carrier cannot be recycled,
penicillin (contain a b-lactam ring)
the terminal D alanine need to be cut in order for the aa crossbridging to attach at the position 4 D-ala. This reaction is carried out by the transpeptidase. penicillin is a structural analogue of D-ala-D-ala. The transpeptidase binds to penicillin and become unable to remove the terminal D-ala. The end result is PG is weakened.
two rings that are the basic structures of penicillin
thiazolidine ring and beta-lactam ring are the basic structures of the penicillin. beta-lactam is the more important structure, important for activity.
properties of antibiotics that inhibit cell wall biosynthesis
1. all are bactericidal
2. only effective on actively growing bacteria (must inhibit growing peptidoglycan matrix)
3. most potent class of antibiotics (selective toxicity)
polymyxin
alter permeability by insertion in cell membrane through interaction with phospholipids
polyenes
alter permeability by insertion in cell membrane through interactions with sterols. it's more specific for eukaryotic cells, control yeast infection.
quinolones: nalidixic acid, ciprofloxacin, norfloxacin, novobiocin
Inhibit DNA replication by binding to DNA gyrase. DNA gyrase is composed of subunits A and B. nalidixic acid, ciprofloxacin, norfloxacin bind to subunit A. novobiocin binds to subunit B.
metronidazole
inhibition of DNA replication by inducing host cells to produce more free radicals. Anaerobes is more susceptible to the effect of metronidazole.
Rifamycin
Inhibition of transcription by binding to RNA polymerase (subunit B)
sulfonamides
Inhibition of tetrahydrofolic acid (folic acid - vit B9 or M) synthesis by binding to enzymes required in nucleic acid synthesis. Toxic to humans.
antibiotics that inhibit nuclei acid biosynthesis /DNA replication
quinolones, metronidazole, sulfonamide
3 antibodies that inhibit mycolic acid biosynthesis
ethambutol (EMB), isoniazid (INH), pyrazinamide (PZA)
tetracycline family
tetracycline, oxytetracycline, chlorotetracycline, demeclocycline, doxycycline, minocycline
lac A
lac Y
lac Z
the protein they produce and pathway they act on
lac A: b-galactoside transacetylase
lactose -> galactose and glucose
lac Y: b-galactoside permease
transport lactose into the cell
lac Z: b-galactosidase
galactose-1P -> UDP-galactose