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Microbiology 303 > Exam 3 > Flashcards

Exam 3 Flashcards

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1
Q

What are the steps of DNA cloning?

A
  1. Plasmid and target DNA isolation
  2. Restriction digest
  3. Mixing
  4. Ligation - molecular glue
  5. Transformation
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2
Q

What do you use to assign a function to an ORF?

A

BLAST (Basic Linear Alignment Search Tool)

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3
Q

Cryptic Pathways

A

Metabolic pathways in a microbe that may encode for something useful but are not normally expressed.

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4
Q

What is the “Plug and Play” method?

A

It involves making a plasmid with the gene cluster of interest, but modified so that it will express in high levels. You put it into another organism that is easy to culture/work with, thus allowing you to study the secondary metabolite.

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5
Q

Why is succinate of interest to microbiologists?

A

It is a starter for all sorts of chemical syntheses, especially plastics and pharmaceuticals.

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6
Q

Virion

A

Name for a virus when it is outside of the cell (as we see it in pictures)

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7
Q

Are most viral genomes linear or circular?

A

LINEAR

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8
Q

Capsid

A

The protein shell surrounding the viral genome

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9
Q

What are the two main types of viral capsid shapes?

A

Icosahedral: Spherical (most efficient)
Helical: Rod-shaped (depends on length of nucleic acid)

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10
Q

Capsomere

A

Protein subunit that aggregates to form the capsid.

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11
Q

Nucleocapsid

A

A complete viral capsid that has the nucleic acid packed inside.

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12
Q

What is a viral envelope? What is it made of? What function does this serve?

A

It is a membrane surrounding the nucleocapsid. It is a lipid bilayer with embedded proteins (like a cell membrane). It allows for easier entry into a cell by merging membranes.

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13
Q

What are 3 enzymes that viruses often have that are critical to infection, and what do they do?

A

Lysozyme: puts hole in cell wall, aids in lysis
Nucleic Acid Polymerases: For replication
Neuraminidases: Cleave glycosidic bonds, enabling liberation of viruses from cell.

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14
Q

Titer

A

Number of infectious units per volume of fluid

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15
Q

What are the 5 phases of viral replication?

A
  1. Attachment
  2. Entry
  3. Synthesis
  4. Assembly
  5. Release
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16
Q

Positive-strand (+) RNA virus

A

Its ssRNA genome essentially serves as mRNA, no coding required.

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17
Q

Negative-strand (-) RNA virus

A

Its ssRNA genome is complementary to mRNA, and must therefore be “read” and decoded into mRNA to function.

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18
Q

Which type of virus usually carries its own RNA polymerase?

A

ssRNA(-) viruses, as the (-)RNA HAS to be transcribed from RNA into mRNA…something a cell’s native RNA Polymerase cannot do.

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19
Q

What kinds of viral proteins are synthesized soonest after infection? How much are made?

A

“Early” Proteins. Ones necessary for replication of nucleic acid. Made in low amounts.

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20
Q

What kinds of viral proteins are synthesized later after an infection? How much are made?

A

“Late” Proteins. Ones necessary for making the viral coat/structure and cell lysis. Made in high amounts.

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21
Q

What form of nucleic acid is most common in bacteriophage genomes?

A

dsDNA (double stranded DNA)

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22
Q

What are the two modes of viral life cycles?

A

Virulent Mode: Lysing host cells

Temperate Mode: Replicating genome along with host.

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23
Q

Lysogeny

A

State where most virus genes are not expressed and virus genome (AKA prophage) is replicated in synchrony with host chromosome.

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24
Q

Lysogen

A

A bacterium containing a prophage.

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25
How does bacteriophage Lambda form a prophage?
On its dsDNA genome, there are complementary 12nt "sticky ends" on the 5' terminus of each strand. Upon penetration, they pair to form the COS SITE, the DNA ligates to form a double stranded circle, and integrates into the E.coli chromosome at the lambda attachment site.
26
What is different about the entry of virus into bacterial vs animal cells?
In bacteria, only the DNA usually enters. In animals, the entire virion enters the animal cell.
27
What dictates where an animal virus can attach?
Cell receptors, which are usually tissue-specific.
28
Persistent infection
A viral infection where the host cell is not killed/lysed, but continues to live and produce virus
29
Latent infection
Delay between infection by the virus and lytic events.
30
What is "Transformation" in the context of viruses?
When a cell is converted from a normal cell into a tumor cell.
31
Since bacteria do not have proper immune systems, what do they use to fight off viruses?
CRISPR system: similar to RNAi (RNA interference) | Restriction modification system
32
Symbiosis
Intimate association of 2+ different species.
33
Mutualism
A type of symbiosis where both partners benefit
34
Commensalism
A type of symbiosis in which one partner benefits and the other is unaffected
35
Amensalism
A type of symbiosis where one partner benefits and the other is harmed/damaged AKA Parasitism, predation, pathogenesis
36
Colonization
multiplication of microbes after it has attached to host tissue
37
Infection
Growth of microorganism in/on host
38
What is the difference between a RESIDENT and a TRANSIENT infection?
RESIDENT infection is when the organism is constantly there | TRANSIENT infection is when the organism is there temporarily and then moves on
39
Pathogen
an organism capable of colonizing a host where the interaction results in disease
40
Parasite
Microbe that colonizes and causes damage to host.
41
Disease
Damage/injury that impairs host function
42
Virulence
Degree/severity of damage to the host.
43
Virulence factor
A gene product or metabolite involved in pathogenesis
44
Symbiont
Microbial partner in a host-microbe interaction
45
Microbiome
The COLLECTIVE GENOME of a microbiota
46
Axenic
Sterile, without microbes. AKA germ-free
47
Gnotobiotic
A host with a KNOWN biota, generally introduced into an axenic host
48
What are the 3 initial steps in the interaction of a microbe with a host?
Attachment, colonization, and invasion
49
What is the name of the signal molecules that nodulating bacteria detect?
FLAVONOIDS
50
How does a microbe sense a host?
Diffusable signals from host Cell surface components Enviro cues (temp, nutrients, etc)
51
How does the host recognize the microbe?
Diffusible signals Specific surface components on microbe General surface components (MAMPs)
52
What are some examples of MAMPs in gram positive and gram negative cells? (3,2)
POSITIVE: Teichoic Acid, Lipoteichoic Acid, Peptidoglycan NEGATIVE: LPS, PG
53
What are factors that affect ability of microbe to invade tissues?
Adapt to host environment Able to replicate Able to infect new host
54
What factors allow Vibrio Fischeri to colonize its host?
Sticky mucus at entrance to host Active flagellar motility Periplasmic catalase
55
Describe the Riftia pachyptila (tubeworm) symbiosis.
Tubeworm heart pumps blood carrying CO2, H2S, and O2 to the trophosome (microbe clusters) for food. In exchange, they synthesize chemicals that the tubeworm uses as food.
56
What degrades wood in termites' guts?
Protozoa: P.grassii
57
What are Kochs original postulates?
1. Suspected pathogen must be present in ALL cases of the disease and absent from healthy animals. 2. Pathogen should be grown in pure culture. 3. Cells from a pure culture should cause disease in a healthy host. 4. Pathogen should be re-isolated and shown to be the same as the original.
58
What are the faults of each of Koch's Postulates?
1. Opportunistic pathogens 2. Not able to see unculturables. Lose virulence factors upon plating. Viruses/prions don't grow on plates. 3. Assumes animal model works. 4. Unculturables again. How to define "same"?
59
Where are genes for most toxins located?
Temperate phages (and some on plasmids)
60
How do endotoxins and exotoxins differ?
Endotoxins (LPS) are part of the cell and are less potent than exotoxins. They also are more heat stable. Exotoxins are produced proteins that leave the cell to cause damage and are highly toxic.
61
What are some primary immune tissues?
Bone marrow and Thymus
62
What are some secondary immune tissues?
Spleen, Lymphatic system, lymph nodes, MALT
63
Where is complement produced and where does it go?
Produced in macrophages, liver cells, and GI epithelial cells. Circulate in blood stream until activated
64
Mast Cells
Histamine releasing cells
65
Opsonin
Molecules that increase efficiency of phagocytosis
66
What are the three pathways for activation of the complement cascade?
Classic (Abs react w/Ag, C1 starts cascade) Alternative (C3 interacts w/pathogen and starts it) Lectin (Mannose Binding Lectin protein forms a complex to start it)
67
What signals do NK cells need for activation?
CD4+ T cell secretions, NOT MHC
68
Where do DCs originate from and where are they found?
Bone Marrow. | Thymus, LNs and spleen (and blood stream)
69
What types of cells have MHC-I? What types have MHC-II?
MHC-I: ALL | MHC-II: B cells, Macrophages, and DCs
70
What do MHC-I and II present antigens to?
TCR's
71
Which type of antibodies are passed from mother to child?
IgG
72
What abilities allow antibodies to attain almost limitless diversity? (4)
Somatic recombination Random Heavy/Light chain reassortment Coding for joint diversity Hypermutation
73
What are the different reactions/functions antibodies can do? (5)
``` Complement activation Agglutination Toxic neutralization Opsonization Steric hindrance ```
74
What is the difference between active and passive immunity?
ACTIVE: Host makes own immune response PASSIVE: Host receives premade antibodies or immune cells
75
Hypersensitivity
Inappropriate immune response that results in host damage
76
Type I Hypersensitivity
Antibody-mediated IMMEDIATE hypersensitivity. Caused by IgE antibody-coated mast cells AKA Allergy Ex: Pollen/fungal spores, insect venom, foods, dander, dust mites
77
Type IV Hypersensitivity
Cell-mediated, Delayed-type hypersensitivity (DTH). Characterized by tissue damage from inflammatory responses from Th1 cells Ex: Microbes, self antigens, and chemicals that covalently bind skin
78
Type II Hypersensitivity
Cytotoxic Hypersensitivity. IgG antibodies against cell surface antigen Ex: Type 1 Diabetes
79
What are the common phylotypes of bacteria in the human microbiome?
Firmicutes, Bacteroidetes, and Actinobacteria
80
What is the human microbiota like in INFANTS?
As an infant, we inherit "founder species" from our mother, depending on delivery mode. C-Section has Staph, Propioni etc and higher susceptibility to certain pathogens.
81
What is the human microbiota like in CHILDREN?
New strains replace old and diversity increases rapidly, depending on diet/illness. High instability as it develops.
82
What is the human microbiota like in ADULTS?
Highly distinct/differentiated. Slow to change.
83
What is the human microbiota like in the ELDERLY?
Much different than in younger adults, nearly no change.
84
What roles do our microbiota play for us? (4)
Nutrition Barrier (Colonization resistance) Immune (education) Community (interactions with each other, host)
85
Dysbiosis
Disease resulting from a disruption to the normal microbiota
86
What are two barriers human GUT epithelial surfaces have to microbes?
``` Lipids/lipoproteins (Surfactants) Mucin Proteins (Mucus) ```
87
What are three barriers human SKIN has against microbes?
Keratin Layers/loss of cells Antimicrobial peptides (AMPs)
88
Where are most immune cells located in the body?
The GUT
89
Is the gut microbiome more diverse in OBESE people or LEAN people?
LEAN people.
90
Probiotics
Pure cultures of microbial strains that yield a measurable health benefit with tested data from controlled trials.
91
Prebiotics
Food you feed your probiotic microbes
92
Synbiotics
Prebiotics and Probiotics together
93
Emerging Infectious Disease
A new infection resulting from the evolution or change of an existing pathogenic agent, a known infection spreading to a new geographic area/population, or a previously unrecognized pathogenic agent/disease diagnosed for the first time and which has a SIGNIFICANT impact on animals or the public.
94
Epidemic
Spreading rapidly and extensively by infection and affecting many individuals in an area or population at the same time, as of a disease or illness.
95
Pandemic
A widespread epidemic that affects whole countries or the entire world.
96
Endemic
Referring to a disease that is usually present or often present in a certain area
97
Incidence
The rate of a disease in a specific population/time period
98
Prevalence
Number of cases of a specific disease present in a given population at a certain time
99
Outbreak
The occurrence of an infection of a particular disease, usually in a geographic area
100
Carriers
An individual who harbors a disease organism, is not visibly ill, but can often transmit the microbe to others
101
Reservoirs
The habitat in which an infectious agent normally lives, grows and multiplies. Ex: Humans, animals, environment.
102
Morbidity
Any departure, subjective or objective, from a state of physiological or psychological well-being.
103
Mortality
Death
104
How do the incidence curves differ in a common source vs host-to-host epidemic?
Common Source: Sharp rise, rapid decline | Host-to-Host: Slower and more progressive rise
105
Herd immunity
When most people in a population are immune, it limits the chances a disease has to spread.
106
What are the different types of vaccines? (2+4)
``` Live attenuated Inactivated/Dead Subunit Toxoid Polysaccharide Adjuvants ```
107
How do live/attenuated and dead/inactivated vaccines differ?
LIVE: Pathogen has reduced virulence but can still replicate -> allows fuller immune response/education. DEAD: Pathogen is dead, only provides patient with antigens for presentation. No effect on cell-mediated immunity.
108
What are the O, H, and K antigens on E.coli?
``` O = LPS K = Capsule H = Flagella ```
109
What is rheumatic fever and what causes it?
Immunologic attack of the heart caused by overactivation of the immune system from Streptococcus pyogenes.
110
What does shiga toxin do?
Inhibits protein synthesis, killing cells
111
What do Clostridium difficile toxins do?
Damage cells by inactivating Ras and Rho GTPase (signaling molecules)
112
What does Toxic Shock Syndrom Toxin (TSST) do?
Causes over-stimulation of immune system because it is a superantigen

Microbiology 303 (3 decks)

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