Exam 1 Flashcards
(215 cards)
1
Q
a bacterial, viral, or fungal agent of disease
A
pathogen
2
Q
a method to amplify DNA in vitro using many cycles of DNA denaturation, primer annealing, and DNA polymerization using a heat-stable polymerase
A
polymerase chain reaction (PCR)
3
Q
a living organism that requires a microscope to be seen
A
microbe
4
Q
the sum of all genomes of all members of a community of organisms
A
metagenome
5
Q
a noncellular particle containing a genome that can only replicate inside of a cell
A
virus
6
Q
cells lacking a nucleus; includes bacteria and archaea
A
prokaryotes
7
Q
cells with a nucleus
A
eukaryotes
8
Q
the three domains
A
bacteria, archaea, eukarya
9
Q
the total genetic information contained in an organism’s chromosomal DNA
sequence of all the nucleotides in a haploid set of chromosomes
A
genome
10
Q
what does the genes in a microbe’s genome and the sequence of DNA tell us about
A
how that microbe grows and associates with other species
microbial capabilities are defined by genome sequences
11
Q
organisms exist in both _________ and ___________ forms
A
macroscopic and microscopic
12
Q
major categories of microbes include
A
bacteria
archaea
microbial eukaryotes
viruses
13
Q
microbes may grow in
A
communities, such as a biofilm
14
Q
includes all the microbes that live on or in us
may be commensalism or mutualism (mostly)
mostly harmless microbes but can cause problems sometimes
A
the human microbiome
15
Q
what parts of the body would not be included in the human microbiome
A
blood, cerebrospinal fluid, internal organs
16
Q
true or false: the composition of the human microbiome is unique to each individual
A
true
17
Q
what are the 3 domains
A
bacteria, archaea, eukarya
18
Q
humans harbor diverse species from a limited number of __________: Actinobacteria, Bacteriodetes, Firmicutes, Fusobacteria, and Proteobacteria
A
phyla
19
Q
what do microbiome differences arise from
A
genetics, age, lifestyle, environment, etc
20
Q
proportions of microbes in the microbiome are heavily influenced by
A
anatomical site
21
Q
your microbiome begins developing at birth and reaches a ________ state by age 3
A
stable
22
Q
what are some factors that can fluctuate your microbiome
A
puberty, weight changes, diet, pregnancy, stress, cohabitation, new pets, job changes, children, medications, sports, travel, menopause
23
Q
an imbalance in the microbial community that is associated with diseases
A
dysbiosis
24
Q
animals that are used to direct physiological impact of the microbiome, allowing us to prove causation
A
gnotobiotic animals
25
all microbes are known, includes germ-free
gnotobiotic
26
an increase in *Firmicutes* would result in
obesity
27
a decrease in bacteroidetes is associated with
obesity
28
a decrease in verrucomicrobia is associated with
obesity
29
an increase in actinobacteria is associated with
obesity
30
*a decrease in F. prausnitzii results in*
obesity
31
disadvantages of using a germ-free animal
* more susceptible to pathogens
* poorly developed immune system
* lack key nutrients
* lower cardiac output, thin intestinal walls, and altered behavior
32
failure of immunoregulation is due to inadequate exposures to the microorganisms that drive development of the immune system
old friends hypothesis
33
the process by which pathogens produce disease
pathogenesis
34
a microbe that causes disease
pathogen
35
causes disease in a healthy host; can breach host defense mechanisms
primary pathogens
36
causes disease only in immunocompromised hosts or in specific circumstances
opportunistic pathogens
37
started the notion of handwashing
Ignaz Simmelweis
38
theory that states that microbes can cause disease
germ theory
39
koch's postulates establish a __________ relationship between a microbe and a specific disease
causative
40
koch's postulates (4)
1. the microbe is found in all cases of the disease but is absent from healthy individuals
2. the microbe is isolated from the diseased host and grown in pure culture
3. when the microbe is introdued into a healthy, susceptible hsot, the same disease occurs
4. the same strain of microbe is obtained from the newly diseased host
41
a complex bidirectional network of communication between the Central Nervous System, the intestine, and the intestinal microbiota
microbiome-gut-brain axis
42
which cranial nerve is an important part of the microbiome-gut-brain axis
the vagus nerve
neurochemicals made by the brain initiate efferent vagus nerve impulses that travel from the brain to the gut, whereas gut bacteria make neurotransmitter-like chemicals that acan fire afferent signals back along the axis to the brain
43
the serial passage of a pathogenic organism from an infected individual to an uninfected individual, thus transmitting disease
chain of infection (transmission of disease)
44
a culture containing only a single strain or species of microorganism
pure culture
45
a visible cluster of microbes on a plate, all derived from a single founding microbe; usually consists of a clone, except for infrequent mutations
colony
46
exposure of an individual to a weakened version of a microbe or microbial antigen to provoke immunity and prevent development of disease upon reexposure
vaccination
47
a body's resistance to a specific disease
immunity
48
an organism's cellular defense against pathogens
immune system
49
the stimulation of an immune response by deliberate innoculation with a weakened pathogen, in hopes of providing immunity to disease caused by the weakened pathogen
immunization
50
a chemical that kills microbes
antiseptic agent
51
free of microbes
aseptic
52
a molecule that can "kill" or inhibit the growth of selected microorganisms
antibiotic
53
provide a set of criteria to establish a causative link between an infectious agent and a disease
Koch's postulates
54
established the practice of vaccination, or inoculation with cowpox to prevent smallpox
Edward Jenner
55
developed the first vaccines that were based on attenuated strains
Louis Pasteur
56
showed that antiseptics could prevent the transmission of pathogens from doctor to patient
Ignaz Semmelweis and Joseph Lister
57
discovered that the Penicillum mold generates a substance that kills bacteria
Alexander Fleming
58
purified the substance penicillin, the first commercial antibiotic to save human lives
Howard Florey and Ernst Chain
59
discovered viruses as filterable agents of infection that aren't cells
Dmitri Ivanovsky and Martinus Beijerinck
60
first crystallized viral particles
Wendell Stanley
61
a period of the infection process during which a pathogenic agent is dormant in the host and cannot be cultured
latent state
62
an organism's ability to cause disease
pathogenicity
63
how easily an organism causes disease
infectivity
64
a measure of the degree, or severity of disease
virulence
65
a measure of virulence; the number of bacteria or virions required to kill 50% of an experimental group of hosts
Lethal Dose 50% (LD50)
66
the route of transmission an organism takes
infection cycle
67
two main forms of transmission
horizontal transmission and vertical transmission
68
a mode of transmission in which an infectious agent is transferred from one person or animal to the next
horizontal transmission
69
a mode of transmission whereby the agent is transferred from an infected parent to offspring
vertical transmission
70
how can vertical transmission occur in humans
transplacental transmission or during birth
71
the process by which certain pathogens in maternal blood can pass through the placenta and infect the fetus
transplacental transmission
72
modes of horizontal transmission (5)
direct contact
airborne transmission
indirect contact
vehicles
vectors
73
pathogens that spread horizontally from person to person by physical contact with skin, blood, or bodily fluids
direct contact
74
in disease, the transfer of a pathogen via dust particles or on respiratory droplets produced when an infected person sneezes or coughs
airborne transmission
75
a broad term that covers all types of transmission that are not directly passed from person to person (fomites, food, and water)
indirect contact
76
an inanimate object on which pathogens can be transmitted from one host to another
fomites
77
the transfer of a pathogen when an infected person deposits it on a surface or in food or drink that another person touches or consumes
vehicle transmission
78
an organism that maintains a virus or bacterial pathogen in an area by serving as a high-titer host
reservoirs
79
a vector that conveys pathogens to a susceptible individual or food without the pathogen needing to replicate in the vector
mechanical vector
80
an infectious disease that is primarily seen in animals but can be transmitted to humans either by vector or other means
zoonotic disease
81
the transfer of a pathogen from parent to offspring via infection of the egg cells
| typically seen in insects
transovarial transmission
82
a person who harbors a potential disease agent but has no symptoms of disease
asymptomatic carrier
83
portals of entry
respiratory
oral
ocular
urogenital
parenteral
wound
84
agents that are transmitted only by mosquitos or ticks; injection into the bloodstream
parenteral route
85
applies when the immune response to a pathogen is a contributing cause of pathology and disease
immunopathogenesis
86
a trait of a pathogen that enhances a pathogen's disease-producing capability
| toxins, attachment proteins, capsules, and other devices used by pathoge
virulence factors
87
true or false: if you become infected with a pathogen, you will become diseased
false
88
what are the requirements for Molecular Koch's Posulates
1. the phenotype under study should be associated with pathogenic strains of a species
2. specific inactivation of the suspected virulence gene(s) should lead to a measurable loss in virulence or pathogenicity. the genes should be isolated by molecular methods
3. reversion or replacement of the mutated gene should restore pathogenicity
88
an organism that can carry infectious agents from one animal to another
vectors
88
a type of genomic island in which the stretch of DNA contains virulence factors and may have been transferred from another genome
pathogenicity island
88
a measure of how easily a disease spreads
basic reproduction number (R0)
89
replication of pathogen in host
infection
90
factors that influence infection after exposure
(host and pathogen) genetics
risk factors to developing disease
prior exposure to pathogen
91
measures the proportion of infected people who develop disease
case-to-infected ratio (CI)
92
how do you calculate R0
determine the ratio of new cases to existing cases
93
a measure of virulence
case-fatality-ratio (CFR)
94
what is the CFR equation
CFR = M / (Ir + Ip + Id)
## Footnote
M= mortality
Ir = infected + recovered
Ip = infected and presented
Id= infected and died
95
what does a pathogen need to do to cause disease
* make contact w/ appropriate host tissues/cells
* outcompete the resident microbiota for resources
* survive host defense mechanisms
* multiply and eventually transmit to a new susceptible hsot
96
how do we identify virulence factors?
* compare genomes of related virulent/avirulent pathogens
* identify genes in the virulent strain that are absent from a virulent strain
* use molecular koch's postulates
97
used to prove a gene encodes a virulence factor
molecular koch's postulates
98
measures the dose that it takes a microbe to cause infection (but does not kill host)
infectious dose 50 (ID50)
99
form, elevation, margin, size, texture, and opacity
colony characteristics
100
bacteria arranged in a spherical shape
coccus (pl. cocci)
101
cocci cells are arranged based on what
plane of cell division
102
chains of spherically shaped cells
streptococcus
103
grapelike clusters of spherically shaped cells
staphylococcus
104
rod-shaped cells
bacillus (pl. bacilli)
105
rigid, short spiral-shaped cells
spirillum (pl. spirilla)
106
flexible, long spiral-shaped cells
spirochetes
107
comma-shaped cells
vibrio (pl. vibrios)
108
most bacteria are typically between what size in length?
0.5-5.0 micrometers
109
what are the constraints on small cells?
cells must be big enough to have essential genetic material and machinery
110
smallest known bacterial cells
0.2 micrometers
smallest known genomes (~650 genes)
Mycoplasma
111
cannot reproduce outside their host cell, meaning that the parasite's reproduction is entirely reliant on intracellular resources
obligate intracellular parasite
112
large cells are constrained by the limits of
diffusion
113
how does *E. fishelsoni* compensate for its large size?
* with a highly folded membrane that increases surface area
* multiple genome copies to make materials at different locations
* vesicles help to excrete waste
114
includes everything that surrounds the cells cytoplasm
(plasma membrane, cell wall, specialized outer layers)
cell envelope
115
how do bacterial cell membranes closely resemble eukaryotic cell membranes
* regulate traffic
* detect signals from the environment
* contains cholesterol-like structures to help maintain membrane fluidity
116
cholesterol-like structure in bacteria that helps maintain membrane fluidity
hopanoid
117
fatty acid chain saturation change in response to what stimuli
temperature and pH
118
saturated fatty acid chains can pack very tightly and are more present in what environment
hotter
119
unsaturated fatty acid chains are present in what type of environment
| contain kinks due to *cis* bonds
cooler environments
120
cyclopropane fatty acids help resist what type of change and how do they maintain this?
* pH
* decrease permeability of membrane to protons, helping bacteria to survive in acidic environments
121
some archaeal membranes are ______________ that withstand very high temperatures
monolayers
122
the bacterial cell wall is made up of
peptidoglycan
123
the bacterial cell wall helps prevent lysis in what type of tonic environment?
hypotonic
124
qualities of gram positive bacteria
* stains purple
* teichoic acids
* many layers (up to 30) of peptidoglycan
* only one membrane
125
qualities of Gram negative bacteria
* Lipopolysaccharides
* stains pink
* inner and outer membrane with a periplasm in the middle
* 1 or 2 layers of peptidoglycan
* porins
* lipoproteins
126
scaffolds for enzymes that remodel peptidoglycan in Gram-positive bacteria
teichoic acids
127
what are lipopolysaccharides (LPS) composed of? (most internal to external)
* Lipid A
* Core polysaccharide
* O antigen
128
why is LPS a virulence factor?
* the composition of the O-antigen varies in different strains, making it resistant to host defense mechanisms
* Lipid A is an endotoxin (can overactivate immune response, leading to organ failure and septic shock)
129
steps to Gram-staining
1. crystal violet
2. iodine
3. ethanol
4. safranin
130
the cell wall has what type of charge
negative
131
crystal violet has what type of charge
positive charge
132
safranin has what charge
negative
133
what genera of bacteria are Gram positive?
* Staphylococcus
* Streptococcus
* Listeria
* Clostridium
134
what genera of bacteria are Gram-negative
* Neisseria
* Escherichia
* Salmonella
* Campylobacter
* Borrelia
* Treponema
135
* an organized, crystalline-like layer of protein or glycoprotein found in archaea and bacteria
* contributes to cell shape and helps protect cell from osmotic stress, bacteriophages, and predatory bacteria
S-layer
135
* a well organized layer of polysaccharides, tightly associated
* acts as a virulence factor and adheres to surfaces and host cells, aids in biofilm formation, protection from dessication, evasion of phagocytosis by white blood cells
capsule
136
* diffuse, unorganized layer of extracellular material (polysaccharides, glycoproteins, glycolipids); loosely associated
* adheres to surface and host cells, aids in biofilm association, protection from dessication, evasion of phagocytosis by white blood cells
slime layer
137
virulence factors that help bacteria form biofilms
capsules and slime layers
137
specialized, surface-attached, collaborative communities that are hard to treat
biofilms
138
how do nutrients cross the cell membrane in gram positive cells
* simple diffusion
* facilitated diffusion
* active transport
139
use ATP directly to move molecules against their electrochemical gradient
primary active transport
140
steps to primary active transport
1. solute binds to its cognate periplasmic binding protein, and the complex then binds to the membrane transporter
2. the ATPase activity of one component powers the opening of the channel and movement of the solute into the cell
140
what is an example of primary active transport
ABC (ATP-Binding Cassette) Transporters
141
use the energy stored in a gradient (one molecule moving from high-to-low) to transport molecules
secondary active transport
142
examples of secondary active transport
symporters and antiporters
143
* a mechanism of transport across a membrane in which two different molecules move in the same direction
* one molecule moves up the electrochemical gradient because the movement of the other molecule is more favorable
symporters
144
* membrane transporters that co-transport two or more dissimilar molecules in the opposite direction across a membrane
* the movement of one ion or molecule is against its electrochemical gradient and is powered by the movement of another ion or molecule with its electrochemical gradient
antiporters
145
* a bacterial active transport mechanism that uses metabolic energy
* goes down the electrochemical gradient in a favorable way
* unique to bacteria
group translocation
146
example of group translocation
phosphotransferase system (PTS)
147
how do nutrients from the environment enter Gram negative cells?
* through the outer membrane: porins and TonB-dependent transporters
* through the inner membrane: same as Gram positive cells
148
* passive water-filled pores that have less specificity
* act via facilitated diffusion
* allows small (<600 Da) solutes to diffuse, driven by their concentration gradient (from high to low) [ex: amino acids and glucose]
porins
149
* active transporter
* energy intensive
* undergoes a conformational change
* used for very limited nutrients (high specificity and affinity)
* linked to inner membrane via TonB
* needs another active transporter
TonB-dependent receptor
150
TonB-dependent receptors use energy from
proton motive force transmitted from inner to outer membrane
151
the force that promotes movement of protons across membranes down the electrochemical gradient
proton motive force
152
* often a limiting nutrient
* a key part of the ETC and an important cofactor for certain enzymes
iron
153
have an extremely high affinity for iron, function primarily to scavenge iron
siderophores
154
siderophores utilize what type of transport
ABC transporters
| active
155
steps to iron transport
1. the siderophore called enterochelin is secreted and binds iron
2. the complex is transported to the periplasm through an outermembrane protein FepA
3. a periplasmic binding protein escorts the complex to an ABC transporter
4. the enterocherlin-iron complex enters the cell
5. inside the cell, the iron is released and reduced to iron
156
specialized appendages of bacteria
* pili/fimbriae
* sex pili
* flagella
157
* protein-based (pilin) finger-like appendages
* responsible for adherence
* can act as a virulence factor
pili / fimbriae
158
* thin protein appendage
* connects cells during conjugation (horizontal gene transfer)
sex pilus
159
* not common in coci
* rigid spiral filament of protein monomers called flagellin, extends from the cell surface
* responsible for cell motility powered by proton motive force
* spins like a propeller
flagella
160
spirochetes have what kind of flagella
endoflagella
161
* wraps around cell body within periplasm
* better at moving through viscous envronments
endoflagellum
162
bacteria house their DNA in what rather than a defined nucleus
nucleoid region
163
what allows for the condensing of DNA into a nucleoid region
DNA-binding domains
164
critical for cell shape and division
bacterial cytoskeleton
165
* forms a ring inside almost all bacteria
* tubulin homolog
* critical for cell division
* responsible for contraction and separation, remodeling of peptidoglycan
FtsZ
166
* forms a coil inside rod-shaped and elongated cells
* actin homolog
* critical for cell shape determination
MreB
167
* forms a polymer along the inner side of crescent-shaped bacteria
* intermediate filament homolog
* critical for cell shape determination
crescentin (CreS)
168
* protein "vesicles" filled with air
* provide buoyancy to cells for movement in response to light and nutrients
* present in aquatic organisms/photosynthetic bacteria
gas vesicles
169
* protein "vesicles" that contain CO2 and RubisCO
* responsible for carbon fixation
carboxysomes
170
* built when carbon sources are abundant / responsible for carbon storage
* store nutrients in nutrient-limited environments
* lipid polymers
inclusion bodies (PHB granules)
171
* consist of magnetite enclosed by a lipid membrane
* directed motility based on a magnetic field (magnetotaxis)
magnetosomes
172
* dormant structure composed of DNA, ribosomes, and severall tough protective coverings
* ensure survival through periods of environmental stress
endospores
173
how has human control of infectious disease made incredible progress in the last century?
* improvements in sanitation and hygiene
* antimicrobial drugs (antibiotics, antifungals, antivirals)
* vaccines
174
compounds produced naturally in nature that adversely affects other microbes
antibiotics
175
harms target organism but does not affect humans; drug should affect microbial physiology that does not exist, or is greatly modified in humans
selective toxicity
176
antibiotics that target cell wall synthesis
* penicillins
* cephalosporins
* bacitracin
* vancomycin
177
antibiotics that target protein synthesis
* chloramphenicol
* tetracyclines
* aminoglycosides
* macrolides
* lincosamides
178
antibiotics that target cell membrane integrity
* polymyxin
* daptomycin
* amphotercin
* imidazoles (fungi)
## Footnote
these drugs are typically topical agents
179
antibiotics that target nucleic acid function
* nitroimidazoles
* nitrofurans
* quinolones
* rifampin
* some antiviral compounds, especially antimetabolites
180
antibiotics that target intermediary metabolism of bacteria
* sulfonamides
* trimethoprim
181
antibiotics can typically be classified as
* broad spectrum
* narrow spectrum
182
a type of antibiotic that targets a wide range of microbes
broad spectrum
183
a type of antibiotic that has a narrow range of the organisms they affect
narrow spectrum
184
in regards to arresting bacteria/killing them, antibiotics can be classified as
bacteriostatic or bactericidal
185
* does not lyse cell and prevents septic shock form gram negative cells
* not very useful if pt is immunocompromised
* arrests growth, does not kill bacteria
* gives immune system time to catch up
bacteriostatic antibiotics
186
* lyses cell
* kills bacteria
* brings potential for lipid A toxicity
bactericidal drugs
187
1. NAG and NAM precursors are made in the cytoplasm
2. they are carried across the cell membrane by a lipid carrier: bactoprenol
3. precursors are polymerized to the existing cell wall structure by transglycosylases
4. the peptide side chains are cross-linked by transpeptidases
peptidoglycan synthesis
188
drugs that target peptidoglycan are typically seen as
bactericidal
189
what drug inhibits NAG and NAM precursors from being made in the cytoplasm
cycloserine
190
what drug prevents NAG and NAM precursors from being carried across the cell membrane by bactoprenol
bacitracin
191
what part of penicillin chemically resembles the D-Ala-D-Ala part of peptidoglycan
B-lactam ring
192
mechanism of penicillin
1. target bacterial penicillin binding proteins (PBP)
2. interfere with transpeptidation (D-Ala-D-Ala is the substrate of transpeptidase)
3. competitive and irreversible covalent bond forms
4. unstable cell wall
5. cell death
193
active against gram positive bacteria
penicillin G
194
active against gram positive bacteria and is acid resistant
penicillin V
195
B-lactamase resistant
methicillin
196
active against a broad range of bacteria
* carbenicillin
* amoxiciliin
197
198
active against a broad spectrum of bacteria and is acid resistant
ampicillin
199
* antimetabolites that interfere with bacterial metabolism
* bacteriostatic
sulfa drugs
200
static drugs that interfere with the bacterial ribosome
* macrolides (erythromycin and azithromycin)
* chloramphenicol
* tetracyclines (doxycycline)
201
block transfer of the peptide
macrolides (erythromycin and azithromycin)
202
obstructs formation of the peptide bond
chloramphenicol
203
interfere with the binding of the tRNA with the mRNA codon
tetracyclines (doxycycline)
204
* interferes with elongation causing misreading
* produces junk proteins
* bactericidal
aminoglycosides (streptomycin and gentamycin)
205
how do bacteria become resistant to antibiotics
* prevent entry into cell or destroy antibiotic
* prevent binding to target by altering target or modifying antibiotic
* reverse binding by disoldging the antibiotic bound to target
206
how can antibiotic resistance be acquired from other microbes
horizontal gene transfer
207
* microbes that produce antibiotics in nature must also be resistant and competitors must have defense mechanisms
* have genes encoding resistance proteins
intrinsic resistance
208
selective pressure from what promotes survival of antibiotic resistant strains
overuse of drugs
209
bacteria exhibit a high frequency of
random mutations and recombination
