Exam 3 Flashcards
(201 cards)
1
Q
dichotomous key
A
a series of yes/no questions that successively narrows down the possible categories of species
- most traits are phenotypic, such as cell size and motility
2
Q
rapid pathogen identification
A
multiple color tests
- results scored to give most probable species
3
Q
random mutations
A
occur as the chromosome replicates
4
Q
reductive (degenerative) evolution
A
loss or mutation of DNA encoding unselected traits
5
Q
organisms diverge from one another through several fundamental mechanisms: (3)
A
- random mutations
- natural selection and adaptation
- reductive (degenerative) evolution
6
Q
molecular clock
A
temporal information contained in a macromolecular sequence
- based on the acquisition of new random mutations in each round of DNA replication
7
Q
genes show that most consistent measures of evolutionary time encode components of the _____ and _____ apparatus
A
transcription, translation
8
Q
which components of transcription/translation are a consistent measure of evolutionary time? (3)
A
ribosomal RNA and proteins, tRNA, and RNA polymerase
9
Q
the most widely used molecular clock is the gene that encodes….
A
small subunit rRNA (SSU rRNA)
- 16s rRNA in bacteria
- 18s rRNA in eukaryotes
10
Q
use of a molecular clock requires…
A
the alignment of homologous sequences in divergent species or strains
11
Q
the frequency of differences between homologous sequences can be used to generate a _____ _____
A
phylogenetic tree
12
Q
what do phylogenetic trees show?
A
estimates the relative amounts of evolutionary divergence between sequences of DNA
- can be used to infer the length of time since two species shared a common ancestor
13
Q
symbiosis
A
microbes interacting with other organisms
14
Q
mutualism
A
symbiosis that benefits both partners
15
Q
parasitism
A
symbiosis that only benefits one partner, the other is harmed
16
Q
commensalism
A
symbiosis that benefits one partner while the other is unaffected
17
Q
rhizobium
A
mutalist bacteria that helps plants grow and absorb nutrients; fixes nitrogen in roots of plants
18
Q
alphaproteobacteria
A
nitrogen-fixing bacteria
- rhizobium
19
Q
gammaproteobacteria (4)
Name the bacteria.
A
- Enterics - E. Coli and relatives
- Vibrios and relative
- Pseudomonas - p. Aeruginosa
- Legionella
Gram negative, catalase positive, oxidase negative, rod-shaped facultative anaerobes which are bile-salt tolerant and often inhabit the gastrointestinal tract
20
Q
gammaproteobacteria: vibrionales (3)
A
found in coastal water
- Vibrio cholerae causes cholera
- V. parahaemolyticus causes gastroenteritis
21
Q
epsilon proteobacteria (3)
A
smallest group of proteobacteria
- Campylobacter causes diarrhea
- Helicobacter pylori: cause of stomach ulcers, stomach cancer
22
Q
Barry Marshall and Robin Warren
A
awarded the Nobel Prize for their discovery that peptic ulcer disease was primarily caused by Helicobacter pylori
23
Q
Chlamydia (3)
A
obligate intracellular parasites
- Trachomatis: causes STD and conjunctivitis
- Psittaci: causes psittacosis (parrot fever)
- Pneumoniae: causes and atypical pneumonia
24
Q
chlamydia life cycle characteristics (3)
A
elementary body: non growing ‘spore-like’
reticulate body: vegetative cell
given up much metabolism: can’t make ATP
25
spirochaetes (3)
1. spiral organisms with a sheath and axial filaments
2. slow growing, aquatic free-living or parasitic
3. several human pathogens
26
spirochaetes: human pathogens (2)
1. Treponema pallidum: syphilis
2. Borrelia burgdorferi: lyme disease
27
Firmicutes
low GC, gram-positive rods and cocci
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Bacillales
aerobic or facultative anaerobes
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bacillus (5)
endospore-forming rods; obligate aerobes; grow in soil
- B. subtilis: gram-positive model system
- B. anthracis: anthrax
includes extremophiles
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listeria (2)
non-spore forming rods
- L. monocytogenes: enteric intracellular pathogen
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staphylococcus (3)
non-spore forming cocci; hexagonal clusters
- S. aureus: toxic shock and lethal flesh infections
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Clostridiales
anaerobic rods
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clostridium (2)
| what do they form?
what known disease do they cause?
forms endospores
- C. botulinum and C. difficile: tetanus
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streptococcus (4)
non-spore forming cocci; chains
- Human throat flora
- group A streptococci causes strep and scarlet fever
35
Mollicutes
| what do they lack? require?
what do they cause?
lacks cell wall and s-layer
requires animal host
- Mycoplasma genitalium: smallest known genome
- M. pneumoniae: causes pneumonia
36
firmicutes and actinobacteria (3)
- gram-positive
- peptidoglycan multiple layers; cross-linked by teichoic acids
- aerobes and facultative anaerobes
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actinomycetes (3)
filamentous, producing aerial hyphae and spores
- Streptomyces: produce many antibiotics
- S. coelicolor, S. griseus
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corynebacteriaceae
irregular rods
- Corynebacterium diphtheriae: diphtheria
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mycobacteriaceae
exceptionally thick cell envelope holds acid-fast stain
- Mycobacterium
- M. tuberculosis: tuberculosis
- M. leprae: leprosy
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proteobacteria and nitrospirae (4)
- gram-negative
- outer membrane contains LPS
- diverse metabolism
- lineage includes mitochondria
41
rhizobiales (3)
| What kind of microbes are these?
plant mutualists and pathogens, methyl oxidizers, and animal pathogens
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agrobacterium
A. tumefaciens: causes plant tumors; trasngenic plant vector
43
rhizobium (2)
related to agrobacterium, rhizobium, bradyrhizobium, sinorhizobium
- fix nitrogen intracellularly in legumes
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rickettsia (4)
| what does their lineage include?
includes intracellular parasites; lineage includes mitochondria
- R. rickettsii: rocky mountain spotted fever
- R. prowazekii: typhus
45
SAR11 cluster (2)
marine photoheterotrophs uses proteorhodopsin
- Pelagibacter
46
microbes are ubiquitous (2)
- in every habitable environment
- fill every potential niche
47
what can microbes use as a source of carbon or energy?
every component or product of a living cell
48
what determines a microbe's ability to fill a niche? (2)
genome and environment factors
49
microbe producers (3)
algae, bacteria, phytoplankton
50
microbe consumers (3)
bacteria, archaea, eukaryotes
51
microbe decomposers (2)
fungi, viruses
52
environmental factors that determine microbial growth (5)
1. oxygen levels
2. availability of other nutrients
3. temperature
4. salinity
5. pH
53
mutualistic microbes (3)
| name three types
lichens: fungus + alga/cyanobacterium
rhizobium: inside leguminous plants
mixotricha: bacterial endosymbionts + termites
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synergism
bother benefit through growth, but the partners are easily separated and they can grow independently of one another
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amensalism
one species benefits by harming another; relationship is nonspecific
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subdivisions of the environment surrounding roots (2)
1. rhizoplane
2. rhizosphere
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rhizoplane
plant root surface
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rhizosphere
region of soil outside the rhizoplane that receives substances from the roots
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rhizobium-legume mutualistic interaction (4)
- legumes secrete flavonoid attractants
- rhizobium enters cortical cells where they differentiate into bacteroides with no cell wall
- bacteroides remain in symbiosome
- plant supplies catabolites, bacterium supplies fixed nitrogen, plant leghemoglobin sequesters excess O2
60
agrobacterium tumefaciens
- an alpha-proteobacterium
- causes crown gall disease
61
how does agrobacterium tumefaciens infect its host?
through a wound
62
how does agrobacterium tumefaciens affect its host?
T DNA transferred from bacterium to plant directs the host to overproduce phytohormones that cause tumor production, and to produce opines that attract more A. tumefaciens
63
where are the genes for infection and virulence encoded for in agrobacterium tumefaciens?
Ti, tumor inducing, plasmid
64
where is the carbon cycle's major reservoir?
the ocean, atmospheric reservoir is MUCH smaller
65
aerobic carbon cycling (3)
1. photosynthesis fixes CO2 into biomass, producing O2 and organic carbon compounds
2. lithotrophs also reduce CO2 to biomass
3. respiration returns CO2 to the atmosphere with a net gain of O2 and loss of CO2 in the photic zone
66
hydrologic cycle
1. water flowing over ground picks up nutrients
2. carbon and nitrogen runoff allows respiration
3. respiring microbes deplete O2 in water
- BOD: biochemical oxygen demand
4. high BOD ---> hypoxic costs ---> fish die
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the nitrogen triangle
both reduced and oxidized N is used for biomass
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the nitrogen cycle (6)
1. microorganisms decompose proteins from dead cells and release amino acids
2. ammonia is liberated by microbial ammonification of the amino acids
3. the nitrogen in ammonia is oxidized to produce nitrates for energy by nitrifying bacteria
4. denitrifying bacteria reduce the nitrogen in nitrates to molecular nitrogen
5. N2 is converted to ammonia by nitrogen-fixing bacteria
6. ammonium and nitrate are used by bacteria and plants to synthesize amino acids that are assembled into proteins
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nitrogen cycle:
proteins and waste products ---(?)---> amino acids
| what is this process called?
microbial decomposition
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nitrogen cycle:
amino acids ---(?)---> ammonia
| What is this called?
microbial ammonification
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nitrogen cycle:
ammonium ion ---(?)---> nitrite ion
nitrosomonas, nitrification
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nitrogen cycle:
nitrite ion ---(?)---> nitrate ion
nitrobacter, nitrification
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nitrogen cycle:
nitrate ion ---(?)---> N2
pseudomonas, denitrification
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nitrogen cycle:
N2 ---(?)---> ammonia
nitrogen-fixation
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sulfur triangle
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sulfur cycle (3)
1. SH2 is oxidized by anaerobic respirers to sulfate, removing toxic gas
2. others reduce S into SH2
3. algae excrete dimethyl sulfide, adding to atmospheric S
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sulfur cycle:
proteins and waste --(?)--> amino acids
microbial decomposition
78
sulfur cycle:
amino acids (-SH) --(?)--> H2S
microbial dissimilation
79
sulfur cycle:
H2S --(?)--> SO4^2-
thiobacillus, for energy
80
sulfur cycle:
SO4^2- --(?)--> amino acids
microbial and plant assimilation
81
natural water treatments
wetlands filter water
- slow water passage
- bacteria in wetland denitrify water
82
municipal treatment
reduce nutrients to reduce BOD
- allow microbes to grow, digest nutrients
- aerate to restore oxygen levels
83
opportunistic pathogen
can cause disease if reach abnormal location or in immunodeficient host
84
why is skin difficult to colonize? (4)
dry, salty, acidic, protective oils
85
propionibacterium
degrades skin oils, inflames sebaceous glands, and causes acne
86
staphylococcus epidermidis
colonizes human skin
gram-positive tolerates salt well
87
an infant's mouth is colonized with: (3)
Nonpathogenic neisseria
- gram-negative cocci
Streptococcus + Lactobacillus
- gram-positive rods
88
as an infant's teeth emerge, these bacteria colonize: (3)
Prevotella + Fusobacterium
- between gums and teeth
Streptococcus mutans
- on teeth
89
nasopharynx and oropharynx are populated by _____ _____ and _____ _____
Staphylococcus aureus and Streptococcus epidermidis
- harmless
90
why do few microbes survive in the stomach?
very high acidity
91
helicobacter pylori
- survive at pH 1
- burrow into protective mucous
- cause of ulcers
92
achlorhydria (3)
loss of acidity in the stomach
- caused by malnourishment
- allows pathogen growth
93
which bacteria grows in achlorhydric conditions?
Vibrio cholerae
94
organisms that inhabit the intestine (2)
1. Bacteroides thetaiotaomicron
2. Escherichia coli
95
Bacteroides thetaiotaomicron (2)
- anaerobe
- breaks down complex carbs into products the body can absorb
96
Escherichia coli (2)
- facultative anaerobe
- catabolizes gluconate, component of secreted mucus
97
innate immunity (3)
- barriers to infection
- nonspecific reaction to destroy invading cells
- complement proteins
98
adaptive immunity (3)
- reaction to specific antigens
- body reacts to the antigen when exposed because of "memory"
- basis for vaccines
99
innate defenses: skin
- epidermis consists of tightly packed cells with keratin, oil, and cells that phagocytose microbes
- washing removes dead skin and associated microbes
100
innate defenses: lungs
- mucous membranes trap and destroy pathogens
- the ciliary escalator sweeps mucous, containing microbes, away from the lungs
101
innate defenses: chemical
- acidic pH: stomach, skin, vagina
- lysozyme: tears, perspiration, saliva, tissue fluids
- antimicrobial peptides
102
what do antimicrobial peptides do?
destroy microbial plasma membrane
103
neutrophils/monocytes
- engulf and destroy microbes by phagocytosis
104
monocytes differentiate into _____ and _____
macrophages and dendritic cells
105
basophils and eosinophils
release toxins to poison microbes
106
lymphocytes
Tcells and B cells
107
T cells
modulate specific immune responses
108
B cells
produce antibodies to bind antigens
109
Natural killer (NK) cells
destroy infected and cancerous host cells
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healthy cells make surface antigens _____
MHC class I
111
what type of cells stop producing MHCI
cancerous and infected cells
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when an NK cell meets a cell lacking MHCI, it secretes _____ proteins into the target cell
perforin
113
what does perforin do?
creates membrane pores to lyse cells
114
inflammation signs (4)
redness, pain, heat, swelling (edema)
115
inflammation functions (3)
1. destroy injurious agent
2. limit the effect if destruction is not possible
3. repair or replace the tissue damage
116
humoral immunity
production of antibody proteins, each binding a different agent
117
cellular immunity
T cells that bind different antigens; kills pathogens, controls antibody production
118
stages of inflammation (4)
1. acute-phase proteins activated
2. vasodilation
3. phagocyte migration
4. tissue repair
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MAMPs
microbe-associated molecular patters
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MAMPs can be recognized by _____ or _____ receptors present on/in various cell types
Toll-like, NOD-like
121
PRRs
pattern recognition receptors
- very important to our body's alarm system
122
Toll-like receptors
evolutionarily conserved cell-surface glycoproteins present on cells of many eukaryotes
123
when a toll-like receptor is bound by its ligand, what happens?
it triggers an intracellular cascade to release cytokines, which bind to various cells to direct them to engage invadors
124
NOD-like receptors
important cytoplasmic sensors of MAMPs
125
NOD-like receptors (NLRs) are part of what family of proteins?
inflammasomes
126
what happens when a NLR binds it's ligand?
triggers a signal that stimulates inflammation and activated adaptive immune responses
127
interferons
low-molecular-weight cytokines
- action is host specific not virus specific
128
type I interferons (4)
- high antiviral potency
- IFN-a, IFN-B, IFN-w
- binds receptors of uninfected host cells, renders them resistant to infection
- cleaves dsRNA and blocks viral RNA translation
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type II interferon
- has immunomodulatory function
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complement proteins
serum proteins activated in a cascade
131
C3b causes....
opsonization
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C3a + C5a cause...
inflammation
133
C5b + C6 + C7 + C8 + C9 cause....
cell lysis through formation of the membrane attack complex
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classical pathway (4)
1. antibodies attach to antigen Ab-Ag complexes bind and activate C1
2. C1 activates C2 and C4 by splitting them
3. C2a-C4b activates C3 by splitting it into C3a and C3b
4. the C3 fragments initiate cytolysis, inflammation, and opsonization
135
alternative pathway (2)
1. activated by contact between complement protein and pathogen
2. C3 is split into C3a and C3b
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lectin pathway (4)
1. lectins are proteins bound to carbohydrates
2. binding of lectin to bacterial cell wall functions as an opsonin to enhance phagocytosis and..
3. activates C2 and C4
4. then C2a and C4b activate C3 etc.
137
what temperature is the hypothalamus 'set' at normally?
37 deg C
138
what induce temperature rise in the body?
pyrogens
139
exogenous pyrogens
substances, which originate outside the body and which are capable of inducing interleukins; LPS
140
endogenous pyrogens
interferons, TNF, IL-6
- signal to the brain to raise temperature
- reduce iron availability to bacteria
141
disadvantages of a fever (4)
- tachycardia
- acidosis
- dehydration
- seizures in children
142
immunoglobulin
antibodies in the body
143
what are the two chains of an antibody? what are they held together by?
light and heavy; disulfide bonds
144
antibody constant region
highly conserved amino acids; CH and CL for heavy and light chains
145
antibody variable region
highly different amino acid area, VH and VL; form the antigen binding site
146
IgG (3)
- monomer with four subclasses
- most abundant in blood and tissue fluids
- opsonin, can cross placenta; activates complement
147
IgA (3)
- commonly found as a dimer
- secreted across mucosa
- abundant in tears and breast milk
148
IgM (2)
- monomer on B cells, but also a pentamer
- first antibody detected during immune response
149
IgD (2)
- monomer
- found abundantly on B cells, rare in blood
150
IgE (2)
- monomer found on mast cells and basophils
- mediates inflammatory response
151
primary antibody response
the first time your body interacts with an antigen, via disease or vaccination
152
when do antibodies appear in serum after a primary antibody response?
after several days
153
After B cells bind antigens and make antibodies the immunoglobulin....
switches from IgM to IgG, aka isotype switching
154
secondary antibody response
second exposure to a pathogen via disease or vaccination
155
B plasma cells
secrete antibodies
156
B memory cells
store how to fight the pathogen
157
clonal selection
the process through which B and T cells are selected in the maturation process
158
what increases diversity of antibody production?
high point mutation rate
159
the variable region is made up of three different section
variable, diversity, and joining
160
helper T cells
- displays the surface antigen CD4
- assists activation of B cells and other T cells
161
cytotoxic T cells
- displays the surface antigen CD8
- destroys bacteria and infected host cells
162
T helper 0
precursor that can differentiate into other T cell types
163
follicular helper T cells
drive B cell differentiation into antibody secreting plasma cells
164
T helper 1 cells
assist in activation of cytotoxic T cells
165
T helper 2
recruit eosinophils to combat parasitic infections and can inhibit T helper 1 proliferatin
166
T helper 17
cells stimulate inflammatory response by secreting IL-17
167
regulatory T cells
dampen inflammatory responses
168
MHC class I present....
intracellular antigens
- microbial proteins that make it into the hot cytoplasm are degraded, loaded into the ER, and placed on MHCI molecules for presentation
169
MHC class II present...
extracellular antigens
- microbial proteins outside the cell are endocytosed into the cell, degraded, and loaded onto MHCII
170
T cell receptors only bind antigens if they are attached to...
MHC molecules, they interact with other molecules on the membrane that cascade into activation and proliferation
171
cell-mediated immune response
T helper 0 binds MHCII on APC
172
CD4 binds MHCII =
recognition of presenting molecule
173
CD28 binds B7 =
recognition of antigen presenting cells
174
how to make live attenuated vaccines (2)
- serial passage of virulent virus
- deliberate alteration of genes, marker genes
175
advantages of live attenuated viral vaccines (5)
- effective in small amounts due to biological amplification
- duration is longer, often a lifetime
- better cellular responses, more antigens
- can be given orally to stimulate IgA
- adjuvants not needed
176
adjuvant
an ingredient used in some vaccines that helps create a stronger immune response in people receiving the vaccine
177
new approaches to vaccines (7)
- plasmid based
- mRNA vaccines
- subunit
- virus like particles
- new vectors/virus as vectors
- enhance immunogenicity
178
examples of bacterial vaccines (5)
1. extract vaccines - old pertussis
2. carbohydrate vaccines - meningococcus
3. toxoid vaccines - tetanus & diphtheria
4. attenuated vaccines - BCG strain for TB
5. conjugated bacteria vaccines - carbohydrate + protein Hib
179
examples of viral vaccines (3)
1. inactivated viruses - influenza and Salk polio
2. attenuated vaccines - Sabin polio, MMR
3. subunit vaccine - Hep B, recombinant protein from yeast; old version prepared from HBV carriers
180
tDAP vaccine components (3)
- diphtheria purified toxoid
- tetanus purified toxoid
- pertussis acellular fragments
181
meningococcal meningitis vaccine components
purified polysaccharide from N. meningitidis
182
haemophilus influenzae vaccine components
type B meningitis
polysaccharides conjugated with protein
183
pneumococcal vaccine components
S. pneumoniae antigens conjugated with proteins
184
smallpox vaccine components
live vaccinia virus
185
poliomyelitis vaccine components
inactivated virus and attenuated virus
186
rabies vaccine components
inactivated virus
187
Hep A vaccine components
inactivated virus
188
influenza vaccine components
inactivated (flu shot) or attenuated virus (flu mist)
189
measles, mumps, and rubella vaccine component
attenuated virus
190
chickenpox vaccine components
attenuated virus
191
Hep B vaccine components
antigenic fragments (recombinant vaccine)
192
diagnostic immunology (5)
1. precipitation reactions
2. agglutination reactions
3. ELISA test
4. Western blot tests
5. Fluorescent-antibody techniques
193
precipitation reactions (2)
immuno-diffusion
- antibodies lay on the bottom of a test tube, antigens are placed at the surface
- a noticeable "zone of equivalence" forms through the anitbody-antigen reaction
194
agglutination reactions (2)
- involves particulate antigens and antibodies
- antigens may be on a cell (direct) , attached to latex spheres (indirect/passive), or on red blood cells (hemagglutination)
195
antibody titer
the concentration of antibodies against a particular pathogen
196
hemagglutination
agglutination of red blood cells
197
direct ELISA (4)
1. antibodies are absorbed on a well
2. enzyme-linked antibody specific for test antigens are added and bind to the antibody
3. patient sample is added, complementary antigen binds to the antibody
4. enzyme's substrate is added and reaction produces a product that causes a color change
198
indirect ELISA (4)
1. antigen is absorbed to a well
2. enzyme linked anti-HISG is added and binds to the antibody
3. patient antiserum is added, complementary antibody binds to the antigen
4. enzyme's substrate is added and reaction produces a visible color change
199
serological tests - pregnancy test (3)
1. free monoclonal antibody specific for hCG
2. capture monoclonal antibody bound to substrate
3. sandwich formed by combination capture antibody and free antibody when hCG is present, creates color change
200
monoclonal antibody test (6)
1. mouse is injected with antigen to produce antibodies
2. spleen is removed, collected suspension of B cells
3. spleen cells are mixed with myeloma cells to help them proliferate; they fused together
4. mix of cells is placed in an active medium to grow
5. proliferate into hybridomas; screened for desired antibody
6. selected hybridomas are cultured into large monoclonal antibodies
201
monoclonal antibody vaccines (4)
- trastuzumab: herceptin for breast cancer
- muromonab-CD3: for kidney transplant
- infliximab: for Crohn's
- ibritumomab + rituximab: for non-Hodgkin's lymphoma
