Final Review Flashcards
1
Q
Be able to distinguish between prokaryotic and eukaryotic cells based on their cellular organelles and components
A
Prokaryotes -> no membrane bound nucleus, no membrane-bound organelles, cell wall, ribosomes, cytoplasm, plasma membrane, flagella/pili
Eukaryotes -> nucleus (membrane bound), ER, Golgi, lysosomes, chloroplasts, ribosomes, cell wall, cytoskeleton, plasma membrane
2
Q
Know what the properties of acellular life are.
A
Examples: viruses, viroids (RNA), prions (proteins); no cells, cannot carry out metabolic processes, require a host for reproduction, have either DNA or RNA, can evolve, dependent on host
3
Q
Know the characteristics that distinguish the three domains of life.
A
Archaea -> prokaryotic, no nucleus, no membrane bound organelles, no peptidoglycan, binary fission
Bacteria -> prokaryotic, no nucleus, no membrane bound organelles, peptidoglycan, binary fission
Eukarya -> eukaryotic, mitosis, bound organelles, variable cell wall
4
Q
Know what the theory of spontaneous generation is and which scientist is credited with debunking the theory.
A
Spontaneous generation -> living things can arise from nonliving things, debunked by Pasteur
5
Q
Know what the germ theory and which scientists contributed to this theory
A
Germ Theory -> infectious diseases are caused by the transmission of microorganisms from one host to another (Pasteur/Lister)
6
Q
Know what Koch’s postulates are and how they need to be modified due to our expanded understanding of microbiology, genetics, and epidemiology today.
A
- Causative agent is absent from unaffected, present in affected
- Isolation
- Inoculation
- Reisolation
7
Q
Robert Hooke
A
identifying and naming the cell
8
Q
Anton van Leewuenhoek
A
microscopist
9
Q
Carl Woese
A
1977, archaea closer to eukarya, rRNA sequencing, LUCA
10
Q
Joseph Lister
A
antisepsis, applied germ theory to surgery
11
Q
Norman Pace
A
rRNA, study more microbes
12
Q
Louis Pasteur
A
germ theory, pasteurization, vaccines
13
Q
Robert Koch
A
postulates, microorganism cause infectious disease
14
Q
Onesimus
A
smallpox
15
Q
Edward Jenner
A
first successful smallpox vaccine
16
Q
Maria Gloria Dominguez-Bello
A
c-sections
17
Q
Alexander Fleming
A
penicillin
18
Q
Mary Hunt
A
cantaloupe, penicillin, mass production
19
Q
William Augustus Hinton
A
syphilis
20
Q
Fanny Hesse
A
agar
21
Q
John Snow
A
father of epidemiology
22
Q
Dark Field
A
Light is directed at an angle, dark black background, no stain, live specimens
23
Q
Bright Field
A
Light passes directly through the specimen, bright white background, staining required, fixed/stained
24
Q
Phase Contrast
A
enhances contrast using phase shifts in light passing through transparent parts, gray background with high contrast, internal structures appear light/dark with high detail, live specimens
25
Amplitude Object
specimen that alters intensity of light passing through
26
Phase Object
specimens change phase of light without affecting amplitude
27
NA
the numerical aperture of the objective lens, which is a measure light-gathering ability
28
Abbe Resolving Power
d = Lamba/(2xNA), smallest resolvable distance between two points
29
Basic Stain
carries a positive charge, attracts negatively charged surface of cell
30
Fixation
specimens attached to the slide by either heat or chemical treatment
31
Cocci
one singular circular bacterial cell
32
Diplococci
two circular bacterial cells
33
Neimcocci
coffee bean shaped double cocci
34
Streptococcus
chain of cocci, S. pyogenes
35
Staphylococcus
grape of cocci, S. aureus
36
Capsule
polysaccharide layer, slimy
37
Nucleoid
site of chromosomal DNA, circular, double stranded DNA
38
Plasmid
site of accessory DNA, smaller, double stranded, transferable
39
Ribosomes
site of protein synthesis, smaller than eukaryotic ribosomes
40
Cytoskeleton
protein elements unique to bacteria, MinB/ParA
41
Bacteria
ester bonds, bilayer, unbranched, flagellin (proton motive force), peptidoglycan (NAM)
42
Archaea
ether bonds, monolayers, branched (Type IV pilus (ATP)), pseudomurein (NAT)
43
Eukarya
ester bonds, bilayer, unbranched, microtubules (dynein motor/ATP)
44
Be able to think critically about how antimicrobials might affect archaeans based on their envelope structure
Archaea have no peptidoglycans, ineffective, lysozymes are also ineffective since they do not have B-1,4 linkages
45
Gram +
outer layer of thick peptidoglycans, stains purple because of the thick layer, falls harder because of thick layer
46
Gram -
two membranes, with thin layer of peptidoglycans in the middle, stains pink, LPS
47
What does it mean to say a bacterium is acid fast? What does the bacterium’s membrane contain?
Acid-fast bacteria like M. tuberculosis have cell envelope with waxy substance called mycolic acid, slow-growing due to limited nutrient uptake by waxy wall, more resistant to many antibiotics
48
How do capsules benefit bacteria?
Reduce binding by phagocytes, water tight, barrier against toxins, aid in adherence
49
What is LPS? What is endotoxin/endotoxemia?
LPS, endotoxin unit, gram negative only, Toll receptor TLR4, lipid A, oligosaccharide, O-antigen polysaccharide. Endotoxin refers to the lipid A of LPS (Gram-), Endotoxemia is the presence of endotoxins in the bloodstream, caused by an infection of a gram-neg bacteria.
50
TLR4
LPS
51
TLR5
Flagellin
52
TLR 7/8
single stranded RNA, viruses, ssRNA
53
Tetanus
-> Blood Stream
-> Uptaken by motor neuron (endocytosis of endotoxin)
-> Transferred to CNS (subunit A specifically)
-> Enters inhibitory neuron
-> Cleaves synaptobrevin
-> Inhibits GABA release
-> Unregulated ACTH release
-> Muscle Contractions
54
Botulism
-> Blood Stream
-> Endocytosis by motor neuron
-> Light chain cleaves syntaxin
-> ACTH vesicles can no longer bind
-> Muscle paralysis
55
What are acetoclastic methanogens?
Acetoclastic = acetate splitting, acetate is converted to methane and carbon dioxide (CH3COO- + H -> CH4 + CO2) This rxn provides energy for growth and metabolism
56
Know strategies that microbes use to cope with osmotic stress in salty environments
Actively pump K+ and Cl- ions to balance external salt concentrations, efflux pumps, biofilm formation, membrane modifications, stress response genes
57
Outline the mechanism that turns on the bioluminescence genes in V. fischeri
When the light organ reaches a high enough population density, production of signaling molecules, HSL, activate genes responsible for bioluminescence, camouflaging the squid
Excretion of HSL interacts with the regulator, LuxR, and activates transcription of the lux operon at high-cell density
58
Outline the process of biofilm formation
Bacterial communication of autoinducers, allow for the monitoring of population density and coordinated group behaviors only when a sufficient number of bacteria are present, counting before initiating actions like formation of biofilms or toxin production
59
Role of the Min system in septation and cytokinesis.
Ensuring division happens at mid-cell, MinD - an ATPase that recruits MicC, MinE - forms dynamic ring that chases MinD/C away from mid-cell
60
Cytoplasmic Stage
Building of NAM and NAG
61
Membrane Stage
movement of NAM and NAG across the membrane by bactoprenol
62
Extracellular Stage
Crosslinking by the transpeptidase
63
Penicillin
targets transpeptidation
64
Vancomycin
targets the terminal alanine of the peptidoglycan stage
65
Know the mechanism of penicillin resistance.
B-lactamase, breaks open the B-lactam ring of penicillin -> inactivating the drug
66
Mechanism of action for lysozyme.
Breaking down bacterial cell walls (peptidoglycan), hydrolyzes B-1,4 glycosidic bonds
67
Halophile
5-10 NaCl %
68
Acidophile
acid tolerance
69
Alkaliphile
exchange internal sodium ions for external protons
70
Barophile
pressure adversely affects them but not as much as non tolerant microbes
71
Psychrophile
most cold tolerant, -10 C
72
How can oxygen, salt, pH, temperature, pressure, and radiation be manipulated to prevent and promote microbial growth?
Oxygen -> anaerobic conditions, vacuum-sealed
Salt -> high salt concentration, halophilic exceptions
pH -> Acidic Conditions
Temperature -> Cold Temperature, freezing, high temperature = denature proteins
Pressure -> high pressure, except barophiles
Radiation -> UV, x-rays
73
Stages of microbial growth in a closed system.
Lag phase -> Exponential (log) phase -> stationary phase -> death phase
74
Sterilization
everything dead
75
Disinfection
killing of disease causing pathogens
76
Sanitation
public health level safety
77
Antisepsis
no living on tissue
78
Define pasteurization and relate it to these terms
repeated warming of milk to eliminate all pathogens, but not sterilized, more disinfection
79
What antibiotics are the most selectively toxic?
Cell wall synthesis inhibitors, such as penicillins, cephalosporins, vancomycin (target structures or processes not in human cells) and protein synthesis inhibitors such as tetracyclines and macrolides are the most selectively toxic.
80
What antibiotics are the least selectively toxic?
Least selectively toxic: Cell membrane disruptors (polymyxin) -> nephrotoxicity is common, also DNA/RNA synthesis inhibitors (ciprofloxacin) -> interfere with host machinery)
81
Cell Wall Synthesis Inhibitors
alter peptidoglycan synthesis -> penicillin, cephalosporins, vancomycin
82
Protein Synthesis Inhibitors
Bacterial ribosomes (70S) -> block translation (tetracyclines, aminoglycosides => 30S) (macrolides => 50S)
83
Metabolic Antagonists
bacterial metabolic pathways -> (sulfonamides/trimethoprim)
84
Nucleic Acid Synthesis Inhibitors
(fluoroquinolones -> inhibit DNA gyrase and topo IV)
85
Why is it harder to develop selectively toxic anti-fungals?
Fungi and eukaryotes are similar in cell structure, organelles, gene machinery, and lipid membranes, fungal membranes contain ergosterol instead of cholesterol (azoles, polyenes exploit this), still highly toxic
86
MIC
lowest concentration of an antibiotic that inhibits visible growth (ug/mL)
87
Kirby Bauer
diameter of zones is measured, lower MIC = more effective = larger size diameter
88
What are the four methods bacteria use to resist antibacterials?
1. Enzymatic Inactivation of the drug (B-lactamases)
2. Alteration of the Target Site
3. Reduced Permeability of Increased Efflux
4. Bypass of the Target Pathway
89
Examples of antimicrobials as inhibitors of metabolism.
Sulfonamides (blocks folate synthesis) and trimethoprim
90
Why is bacterial respiration less efficient than eukaryotic respiration?
In bacteria the ATP ratio per NADH is 1.3 in high oxygen and 0.67 in low oxygen, compared with 2.5 for eukaryotes.
91
Nitrifying
Nitrogen to oxidized forms (NH3 -> NO2- -> NO3-)
92
Denitrifying bacteria
Nitrate (NO3-) -> Nitrite (NO2-) -> Nitric oxide (NO) -> Nitrous Oxide (N2O) -> Nitrogen Gas (N2)
93
Role of fermentation
Fermentation - NADH is oxidized back to NAD+ to keep glycolysis going
94
What are SCFAs? How do they regulate gene expression? Tregs?
Acetate is the most abundant SCFA. Acetate is also a regulator of immune intolerance and evidence that asthma is a developmental origin disease. Acetate enters the bloodstream and travels to the lungs where it binds to GPR41/43 receptors on lung epithelium -> signaling cascade inhibits HDACs -> increased expression of genes like Foxp3 -> Foxp3 is a marker for T-regulatory cells linked with increased T-reg pools -> suppression of airway inflammation. Short-Chain-Fatty-Acids - 60 acetate: 20 propionate: 20 butyrate
95
What is a metagenome? How does this compare to a genome?
Genome - whole organism
Metagenome - every organism in a sample
96
What are the three steps of PCR?
Step 1: Denaturation at 94C for 1 min
Step 2: Primer annealing -> lower temperature to 56C for 1.5 min Anneal with primers
Step 3: Elongation by DNA polymerase -> increase temperature 72C for 1 min (Taq DNA polymerase + dNTPs)
97
F-factor plasmid
bacteria need this plasmid to carry out conjugation, F+ if positive, F-factor can be inserted into the bacterial genome from the plasmid or excised.
98
Hfr
high frequency recombinants, have F factor integrated into their chromosome
99
Hfr x F
conjugation cannot equal an F+ cell only recombinant
100
F’ cells
F factor disintegrates from the Hfr host chromosome
101
competent
carry out transformation
102
Auxotroph
inactivates biosynthetic pathway
103
Prototrophic
acquire of a secondary mutation that makes up for first mutation
104
Generalized Transduction
a virus produces new phage particles during lytic cycle, some host cell DNA can be carried off in the phage head
105
Specialized Transduction
a prophage from the lysogenic cycle exits from the bacterial genome, leaves from genes behind and takes some bacterial genes with, infection of other cells but new phage will not kill
106
Lytic
lyse cells
107
Lysogenic
dormant until stress
108
What three aspects of NGS make it more accurate than traditional sequencing.
NGS - Massively Parallel - all sequence fragments can be sequenced at the same time
NGS - Deep Sequencing - replicated via PCR on the flow cell, creating replicate sequences, and enhanced accuracy
NGS - High Throughput - genomes of many organisms can be sequenced simultaneously
109
Know the three steps of the CRISPR-Cas system
1. Acquisition - if a cell survives infection, it adds portions of viral genome to the CRISPR region, added closest to CAS genes
2. CRISPR RNA Biogenesis - CRISPR region transcribed to yield large RNA containing repeats and spaces, Cas proteins associate with this RNA and process it into mature crRNA
3. Interference - CAS-crRNA complexes associated with viral mRNA or DNA, cleave these nucleic acids, preventing the virus from replicating
110
3 capsid structures
Icosahedral (soccer ball), helical, (spiral rod), complex
111
Why do viruses only infect certain species and certain areas of the body?
Specific cell surface proteins as viral receptors
112
Acute Infection
cell death and virus release
113
Latent Infection (persistent)
viral components are present, host is not harmed
114
Chronic Infection (persistent)
slow release of virus without cell death
115
Transformation
activation of host proto-oncogene, insertion of oncogene, or inactivation of tumor suppressor protein
116
PB1
RNA polymerase
117
PB2
cap snatcher
118
NP
cap attacher (encapsulates)
119
Antivirals for HIV. What do they target?
ART -> block the virus from entering the host cell (Maraviroc/Enfuvirtide), reverse transcriptase inhibitors (NRTIs/NNRTIs) (Zidovudine, Efavirenz), Integrase inhibitors (dolutegravir), protease inhibitors (ritonavir)
120
dsDNA
HSV
121
+RNA
Covid
122
-RNA
flu
123
Retroviruses
HIV
124
SARS-COV-2
Spike protein to ACE2
125
Influenza
HA (hemagglutinin) to Sialic acid
126
HIV
gp120 tp CD4/CCR5
127
Prion
proteinaceous infectious particle, normal cellular protein that becomes misfolded into a disease causing form, once misfolded it can cause other normal proteins to misfold in the same way, a chain reaction, can accumulate in the brain tissue, and lead to neurodegenerative diseases, no DNA/RNA, purely protein based infectious agents
128
Innate
first responders, non-specific (macrophages, neutrophils)
129
Adaptive
specialized, T/B cells
130
Natural
immune system comes in contact with antigen, responds by producing antibodies
131
Artificially
vaccine immunity
132
Direct ELISA
Patient sample loaded onto plate
Equivalent antibody is added with an enzyme to incubate
Wash
Substrate is added which will be cleaved and color change will be induced on antibodies that bind
133
Indirect ELISA
- Precoated antigen is loaded onto well
- Patient sample is added, primary antibody will bind if present
- Wash
- Anti-species antibody added with enzyme to bind to antibody
- Wash
- Substrate is added which will be cleaved and color change will be induced on antigen present plates
134
CD19
B cells
135
CD4
Helper T cells
136
CD3
T cells
137
CD8
cytotoxic T cells
138
FSC
forward scatter (size)
139
SSC
side scatter (granularity/internal structure)
140
What receptor would you use to identify T regulatory cells?
CD3/CD4/CD8
141
Can we use flow cytometry to identify bacterial cells? What receptor/marker on gram-negative cells could be used to identify gram negative from gram positive bacteria?
Gram-Negative -> LPS
Gram-Positive -> Teichoic acid (on peptidoglycan layer)
142
Understand what a reservoir for infectious agents is
Where an infectious agent normally lives and multiples, examples: mice, bats, spiders, pigs, mosquitos
143
Know how to interpret an infectious dose 50
ID50 = dose of microorganism needed to infect 50% of hosts
144
Be able to identify virulence factors for infectious agents
Genes that enable the pathogen to attach to the host, move to other hosts, and harm hosts, anything that enhances the infectivity of the pathogen, encoded in chromosomes or plasmids, large groups of DNA that encode virulence factors are called PATHOGENICITY ISLANDS.
145
Be able to define epidemiology and understand its role in the current COVID-19 pandemic and previous outbreaks and pandemics discussed in class.
Epidemiology -> monitor public health (morbidity/mortality), determine the cause of outbreaks, institute control measures, determine risk factors, recommend control measures
146
Understand the role of public health experts and epidemiologists in disease surveillance
NIH (research), CDC, FDA, WHO
147
Explain why surveillance (until recently) has shifted to include more non-communicable diseases
In the 1900s infectious diseases were highly prevalent, increased understanding of the disease transmission and public health surveillance has dramatically decreased infectious disease prevalence, in parallel with this shift came a transition to a more sedentary lifestyle and more sanitized environment, this had brought about a myriad or metabolic and immune mediated diseases (heart disease, cancer, diabetes)
148
HAIs
ventilator-associated pneumonia, bloodstream, intestinal tract and liver, urinary tract, surgical sites (pneumonia, UTIs), devices such as catheters, antibiotics can kill healthy bacteria, disturbing balance of the microbiome, vulnerable patients and disrupted microbiomes
149
Know what factors contribute to the re-emergence or new emergence of infectious agents
Microbial adaptation and mutation, urbanization, changes in environment and climate, breakdown of public health systems, antibiotic misuse and resistance, contact with wildlife
150
Sporadic disease
occurs occasionally, at irregular intervals (bacterial meningitis)
151
Endemic
steady low frequency
152
Outbreaks
sudden, unexpected occurrence of the disease, usually in limited segment of a population
153
Epidemic
outbreak affecting many people at once
154
Pandemic
disease occurrence increases to larger populations spanning multiple countries
155
Index case
first case of an epidemic, patient zero
156
Propagated
strep throat
157
Common-source epidemic
food poisoning
158
Morbidity Rate
of new cases of a disease during a specific period / # of individuals in the population
159
Prevalence
Total # of cases in population / Total Population x 100
160
Mortality Rate
of deaths due to a given disease / Size of the total population with the same disease
161
Understand methods used to prevent and stop outbreaks of infectious diseases
Eliminate the source or reservoir (water supply, animal source, quarantine infected individuals)
Break the contact with any sustained risk (source) -> Pasteurization, Food Prep Laws
Decrease population susceptibility (immunization)
162
Know what herd immunity is and how vaccines establish herd immunity
Decrease in the number of people susceptible to infection
163
Attenuated Live Microbes
(reduced pathogenicity avirulent) -> MMR vaccine
164
Inactivated Microbes (killed)
flu
165
Acellular Vaccines
components of pathogen are purified and used as vaccine (exotoxins, surface antigens, capsular polysaccharides (Tdap)
166
Recombinant Vaccine
Recombinant DNA and mRNA vaccines (Gardasil/COVID)
167
DNA vaccines
introduce fragments of pathogen DNA directly into host muscle cell, when injected into muscle cells, the DNA is taken into the nucleus and the pathogen’s DNA is transiently expressed, generating foreign proteins to which the host’s immune system responds, slower than mRNA since more difficult to produce the right type of protein
168
mRNA vaccines
faster because mRNA molecules are easier to produce
169
Humoral Immunity
T-cell independent -> antigens bind and activate B cells resulting in B cell differentiation and proliferation into plasma cells that can secrete antibodies, antibodies bind to antigen and inactivate it
T cell dependent -> presents antigen to a helper T cell and this interaction activates the T cell and stimulates release of signaling molecules, these in turn activate B cell, B cell activation then triggers differentiation and proliferation into plasma cells and memory B cells, that can respond to subsequent exposures to the same antigen
170
Cellular Immunity
pathogen protein is processed and presented by an APC to a naive T cell, this generate an activated T-cell and a subsequent activation of cell-mediated immunity specific for the antigen and other T-cell types
