Exam I Flashcards by Annabella Moody

Symbionts that harm or live at the expense of their host:

parasitic organsims

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Microbes frequently found within the bodies of healthy persons:

Commensal organisms

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Commensal organisms may also be referred to as:

Normal microbiota

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What makes up the vast majority of normal flora:

Bacteria

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Colonization of ____ occurs rapidly after birth

Bacteria

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Locations in which large amounts of bacteria reside:

Skin (especially moist areas)
Respiratory tract (nose & oropharynx)
Digestive tract (Mouth & large intestine)
Urinary tract (anterior parts of urethra)
Genital system (vagina)

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Location in which small amounts of bacteria reside:

Remainder of respiratory & digestive tracts

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Locations in which no bacteria are present are considered:

sterile

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Sterile locations in the body:

Blood
CSF
Synovial fluid
Deep tissues

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Normal flora; found all over:

Resident organisms

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Resides in an area for a limited time:

Transient organisms

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Growth & multiplication of parasite on or within host:

Infection

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Disease resulting from infection:

Infectious disease

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Any parasitic organism that causes infectious disease by DIRECT interaction with host:

Primary (Frank) pathogen

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Causes disease only under certain circumstances (such as after antibiotic tx)

Opportunistic pahtogen

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Ability of a parasite to cause a disease:

Pathogenicity

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Any component of a pathogenic microbe that is required for or that potentiates its ability to cause disease:

Virulence factor

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Pathogenicity & virulence depend on:

The host

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What are the steps in an infectious disease:

Encounter
Entry
Spread
Multiplication
Damage
Outcome

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What are three types of encounters with a pathogen:

Exogenous
Endongenous
Congenital

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When a pathogen is externally derived such as a sneeze:

Exogenous encounter

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When a pathogen is internally derived such as a change in immunity/health; already inside:

Endogenous encounter

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When a pathogen is picked up during birth such as HIV; from mother to fetus:

Congenital encounter

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What are two forms of entry of a pathogen:

Ingress
Penetration

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Entry of pathogen via inhalation or ingestion:

Ingress

Entry of microbes through epithelia directly (via attachment & internalization)

Penetration

Insect bites, cuts & wounds, organ transplants, and blood transfusion are all examples of what type of pathogenic entry into the host:

Penetration

What are three components to the spread of a pathogen:

1. Lateral propagation vs. dissemination 2. Anatomical features 3. Active participation by microbes

Spread of a pathogen to neighboring tissue:

lateral propagation

Spread of a pathogen to distance sites:

dissemination

What are two components to the multiplication of a pathogen when causing an infectious disease?

1. Environmental factors 2. Subversion of host defenses

Damage inflicted by an infectious can be caused by:

1. Direct damage 2. Immune response

What are the outcomes of an infectious disease:

1. Microbe wins 2. Host wins 3. Learn to coexist

If an infection comes from our normal flora the source of infection is considered:

Endogenous

Overgrowth of particular bacteria in gingival crevices:

Periodontitis

When defenses are lowered and microaspirations of pneumococci occur:

Pneumococcal pnuemonia

Catheter-associated infections are typically a result of:

Staphylococci

What do the following have in common? -Periodontitis -Pneumococcal pneumonia -Catheter-associated infections

All have endogenous source of infection- normal flora act opportunistically

What are the roles of normal flora:

1. Immune stimulation 2. Keeping out pathogens 3. Assist in nutrition 4. Source of carcinogens vs. detoxification of carcinogens

Normal oral flora include:

Bacteria Fungi Protozoa Viruses

How many different species are estimated to be present in the oral cavity?

Over 500

What are the different oral habitats?

1. Buccal mucosa 2. Dorsal of tongue 3. Tooth surfaces 4. Crevicular epithelium 5. Dental appliances

What are three issues microbial cells face?

1. Nutritional fluxes 2. Maintaining occupancy 3. Resistance to damage

List all the factors modulating oral microbial growth:

1. Anatomical features that create areas that are difficult to clean 2. Saliva 3. Gingival crevicular fluid 4. Mircobial factors 5. Local pH 6. Redox potential 7. Antimicrobial therapy 8. Diet 9. Iatrogenic factors

______ are an absolute requirement for all living organisms

Membranes

Describe the plasma membrane:

-Highly organized -Asymmetric -Flexible -Dynamic

The lipid components of the plasma membrane form a:

Lipid bilayer

The polar ends of the lipids in the lipid bilayer are ____, while the non polar ends are _____

Polar --> Hydrophilic Nonpolar --> Hydrophobic

Proteins that are loosely associated with the plasma membrane that can easily be removed:

Peripheral proteins

Proteins that are embedded within the plasma membrane that are NOT easily removed:

Integral

Bacterial version of cholesterol that provides rigidity:

Bacteriohopanetetrol

Functions of the plasma membrane include:

1. Separation of cell from environment 2. Selectively permeable barrier 3. Location of crucial metabolic processes 4. Detection & response to chemicals via receptors

Granules of organic and inorganic materials that are stockpiled by the cell for future use:

Inclusion bodies

Some inclusion bodies are enclosed by a:

Single-layered membrane

The single-layered membrane that encloses some inclusion bodies: (2)

1. Vary in composition 2. Some made of proteins others of lipids

Complex structures consisting of proteins and RNA:

ribosomes

Sites of protein synthesis

Ribsosomes

Compare the size of eukaryotic and prokaryotic ribosomes:

Prokaryotic ribosomes are smaller

Size of prokaryotic ribosome: Size of eukaryotic ribosome:

70s 80S

Irregularly shaped region in bacteria in which the chromosome resides:

Nuceloid

Is the nucleoid membrane-bound?

In cells what do the nuceloid projections indicate?

Cells are actively growing; DNA being actively transcribed

Describe a prokaryotic chromosome:

Closed, circular double-stranded DNA molecule that is looped & coiled extensively

Proteins that help to fold a prokaryotic chromosome:

Nucleoid proteins

Describe some unusual circumstances of nucleoids:

1. More than one chromosome 2. Linear 3. Membrane-delimited nucleoids

Small, circular DNA molecules that exist and replicated independently of the chromosome:

Plasmids

Plasmids are NOT required for:

Growth & reproduction

Plasmids may carry genes that confer ______ such as _____

Selective advantage; drug resistance

Rigid structure that lies just outside the plasma membrane:

Prokaryotic cell wall

List all the functions of the prokaryotic cell wall:

1. Provides characteristic shape to cell 2. Protects the cell from osmotic lysis 3. May contribute to pathogenicity 4. May protect cell from toxic substances

Bacteria are divided into two major groups based on:

Response to straining (reaction due to cell wall structure)

Gram positive cells stain _____ Gram negative cells stain ____

Purple Pink

In a gram positive cell, the cell wall is composed of:

Primarily of peptidoglycan

Cells that contain large amounts of teichoic acids:

Gram positive cells

Polymers of glycerol or ribitol joined by phosphate groups:

Teichoic acid

Space between plasma membrane & cell wall:

Periplasmic space

Gram positive bacteria secrete:

Exoenzymes

In gram positive bacteria, exoenzymes serve as the _____ do in gram negative bacteria

Periplasmic enzymes

Cell wall consisting of a thin layer of peptidoglycan surrounded by an outer membrane:

Gram negative bacteria

The outer membrane in gram negative bacteria is composed of:

Lipids, lipoproteins, LPSs

NO teichoic acid present:

Gram negative bacteria

What type of bacteria are more permeable?

Gram negative

Space between plasma membrane & outer membrane in gram negative bacteria:

Periplasmic space

In gram negative bacteria, what is contained within the periplasm?

Periplasmic enzymes

What are the roles of periplasmic enzymes?

1. Nutrient acquisition 2. Electron transport 3. Peptidoglycan synthesis 4. Modification of toxic compounds

Describe the structure of peptidoglycan:

-Polysaccharide formed from peptidoglycan subunits -two alternating sugars form backbone

What two alternating sugars form the backbone of peptidoglycan?

N-acetylglucosamine (NAG) N-acetylmuramic acid (NAM)

Within the peptidoglycan structure, ____ have a direct link between peptide chains, while _____ contain a peptide interbridge (GLY) between side chains

Gram negative bacteria Gram positive bacteria

What type of bacteria does this cell wall belong to?

Gram positive bacteria

What is under the thick peptidoglycan layer in a gram positive cell wall:

Single membrane bilayer

What type of bacteria does this cell wall belong to?

Gram negative bacteria

In a gram negative cell, there is a _____ structure with each being a bilayer

Double-membrane structure

Connect outer membrane to peptidoglycan in gram negative bacteria:

Braun's lipoproteins

Sites of direct contact between plasma & outer membrane in gram negative bacteria:

Adhesion sites

Substance may move DIRECTLY into gram negative bacteria via:

Adhesion sites

Lipopolysaccharides are found in what type of bacteria?

Gram negative

What are the components of a lipopolysaccharide (LPS):

1. Lipid A 2. Core polysaccharide 3. O side chain (O antigen)

Component of the LPS that inserts into the outer membrane structure for stabilization & can also act as an endotoxin:

Lipid A

The lipid A component of the LPS inserts into:

the outer membrane

Component of the LPS that contributes to the negative charge on the cell surface:

Core polysaccharide

What does the negative charge contributed by the core polysaccharide portion of LPS function to do?

Avoid/masks host defenses

What two components does the core polysaccharide portion of the LPS contains?

Keto-deoxoctogenic acid & heptose

Portion of the LPS that provides protection from host defenses:

O side chain (O antigen)

What component of the LPS is visible to our immune system?

O antigen

Which membrane is more permeable in a gram negative cell?

Outer membrane

Why is the outer membrane of a gram negative cell more permeable than the plasma membrane?

Due to presence of porin proteins & transporter proteins

Form channels in the outer membrane through which small molecules can pass:

Porin proteins

Layer outside of the cell wall that is well-organized, not easily removed from the cell & takes the shape of the underlying cell:

Capsule

Layer outside the cell wall that is similar to the capsule except diffuse, unorganized & easily removed:

Slime layer

Capsules & slime layers are both referred to as:

Glycocalyx

Network of polysaccharides extending from the cell surface:

Glycocalyx

What are the functions of the glycocalyx (4):

1. Protection from viral infection or predation by bacteria 2. Protection from chemicals in environment 3. Motility of gliding bacteria 4. Protection against osmotic stress

Short, thin, hairlike proteinaceous appendendages (1000/cell)

Fimbriae

What is the function of fimbriae:

Mediate attachment to cell surfaces

Similar to fimbriae except, longer, thicker & less numerous (1-10/cell)

Sex pilli

What are sex pilli required for?

Mating; transfer of genetic material

What is the function of flagella?

Motility

List the arrangements of flagella:

1. Monotrichous 2. Polar flagellum 3. Amphitrichous 4. Lophotrichous 5. Peritrichous

One flagellum:

Monotrichous

Flagellum at end of cell:

Polar flagellum

One flagellum at each end of cell:

Amphitrichous

Cluster of flagellum at one or both ends of cell:

Lophotrichous

Flagellum spread over entire surface of cell:

Peritrichous

Describe the ultrastructure of the flagellum:

Filament, basal body, hook

Portion of flagellum that projects out of cell surface:

Filament

Portion of flagellum that is anchored with the plasma membrane or within both plasma & outer membrane:

Basal body

Portion of the flagellum that is a protein component that gives a bend to the structure:

Hook

Dormant form created when the bacterium encounters environmentally challenging conditions that make it difficult for the cell to keep growing:

Endospore

The bacterial endospore is resistant to numerous harsh environmental conditions including:

-heat -radiation -chemicals -dessication

Overview of eukaryotic cells include:

1. Membrane-delimited nuclei 2. Membrane-bound organelles that perform specific functions 3. More structurally complex than prokaryotic cell 4. Generally larger than prokaryotic cell

Elements required in larger amounts:

Macroelements

List the macroelements required for microbial physiology that are cell components of carbs lipids, proteins & nucleic acids:

1. Carbon 2. Oxygen 3. Nitrogen 4. Hydrogen 5. Sulfur 6. Phosphorus

The macroelements required for microbial physiology make up components of:

1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic acids

List the macrolelements required for microbial physiology that exist as cations & play many roles, including cofactors of enzymes:

1. Potassium 2. Calcium 3. Magnesium 4. Iron

List the trace elements required for microbial physiology:

1. Manganese 2. Zinc 3. Cobalt 4. Molybdenum 5. Nickel 6. Copper

Trace elements are mainly needed as:

Cofactors of enzymes

Components required for ALL organisms survival:

1. Source of energy 2. Source of reducing equivalents (electron donors) 3. Source of carbon

Organisms that utilize light as a source of energy:

Phototrophs

Organisms that oxidize organic or inorganic compounds as a source of energy:

Chemotrophs

Organisms need electron donors for:

1. ETC (energy production) 2. Redox reactions (energy production) 3. Biosynthesis (in autotrophs from CO2)

Utilize INORGANIC molecules as a source of reducing agent:

Lithotrophs

Utilize ORGANIC molecules as a source of reducing agent:

Organotrophs

Utilize CO2 as the main/only source of carbon:

Autotrophs

Utilize reduced, preformed organic molecules (such as glucose) for source of carbon:

Heterotrophs

Due to the source of carbon utilized, most pathogenic bacteria are considered:

Heterotrophs

-Light energy source -Inorganic electron donor -CO2 carbon source

Photolithoautotrophy

-Light energy source -Inorganic electron donor -CO2 carbon source

Photolithotrophic autotrophy

-Light energy source -Organic electron donor -Organic carbon source

Photoorganotrophic heterotrophy

-Chemical energy source -Inorganic electron donor -CO2 carbon source

Chemolitotrophic autotrophy

-Chemical energy source -Organic electron donor -Organic carbon source

Chemoorganotrophic heterotrophy (ALL PATHOGENS)

Other nutrient sources required for bacteria include:

-nitrogen source -phosphate source -sulfure source -growth factors

List where bacteria may get their source of nitrogen from:

Amino acids, ammonia, or nitrate NO3- A few bacteria may obtain nitrogen from N2 (atmospheric/gaseous nitrogen)

List where bacteria may get their source of phosphate from:

Inorganic phosphate (PO4^3-)

List where bacteria may get their source of sulfur from:

Sulfate (SO4^2-) or reduced sulfur (Cysteine)

List where bacteria may get their growth factors from:

Amino acids Purines & pyrimidines Vitamins (small organic molecules)

-Perform aerobic respiration only -Final electron acceptor is oxygen (reduced to H2O)

Strict aerobes

-Perform anaerobic respiration -Final electron acceptor is an inorganic molecule (such as nitrate or Fe3+)

Strict anaerobe

-Perform fermentation -Final electron acceptor is an organic molecule (such as pyruvate reduced to lactase or acetyl-coA reduced to ethanol)

Strict anaerobe

-Can perform respiration & fermentation -Most medically relevant bacteria

Faculative anaerobes

Final electron acceptor for strict aerobes:

oxygen (reduced to H2O)

Final electron acceptor is an inorganic molecule:

Strict anaerobe performing anaerobic respiration

Final electron acceptor is an organic molecule:

Strict anaerobe performing fermentation

Give & explain an example of a facultative anaerobe:

E. coli can survive on a Petri dish (aerobic) & can survive in the intestines (anaerobic)

The respiratory chain of E.Coli occurs in the ______; for use, it occurs in the ______

Membrane of cell; mitochondria

Unique to the oral cavity & requires a certain amount of CO2 in addition to oxygen:

Capnophilic

List the gram positive bacteria in the oral cavity:

1. Streptococcus 2. Peptostreptococcus 3. Actinomyces 4. Lactobacillus

List the shapes of the following gram positive oral bacteria: 1. Streptococcus 2. Peptostreptococcus 3. Actinomyces 4. Lactobacillus

1. Cocci 2. Cocci 3. Rods 4. Rods

List the oxygen requirements for the following gram positive oral bacteria: 1. Streptococcus 2. Peptostreptococcus 3. Actinomyces 4. Lactobacillus

1. Facultative anaerobes 2. Strict anaerobes 3. Strict/facultative anaerobes 4. Facultative anaerobes

List the gram negative bacteria found in the oral cavity:

1. Veilonella 2. Aggregatibacter 3. Capnocytophaga 4. Porphyromonas 5. Prevotella 6. Fusobacterium 7. Spirochetes

List the shapes of the following gram negative oral bacteria: 1. Veilonella 2. Aggregatibacter 3. Capnocytophaga 4. Porphyromonas 5. Prevotella 6. Fusobacterium 7. Spirochetes

1. Cocci 2-6. Rods 7. Spirals

List the oxygen requirements for the following gram negative oral bacteria: 1. Veilonella 2. Aggregatibacter 3. Capnocytophaga 4. Porphyromonas 5. Prevotella 6. Fusobacterium 7. Spirochetes

1. Strict anaerobes 2. Capnophilic 3. Capnophilic 4-7. Strict anaerobes

-Move from higher concentration to lower concentration -NO ENERGY requirements

Facilitated diffusion

What is facilitated diffusion uptake driven by?

Intracellular use of the compound

Compare the rate of facilitated diffusion vs. passive diffusion:

Facilitated diffusion is much fast =er

What happens to the rate of facilitated diffusion as the concentration gets smaller:

As concentration gets smaller, the rate gets smaller, however rate is more magnified at smaller concentrations

Carrier proteins embedded in the plasma membrane:

Permeases

An active transport mechanisms in which transported substances are chemically altered during the process:

Group translocation

Group translocation may also be called:

Phosphorylation-linked transport or Phosphotransferase system

An example of group translocation would be:

Glucose --> Glucose-6-phosphate

System that moves a phosphate group & covalently links it to a transporter molecule; very common within bacterial cells

Group translocation

Where does the phosphate bond come from in group translocation & what does this serve as?

Phosphoenolpyruvate (PEP); energy source

Some _____ & _____ are transported via group translocation:

Sugars & cariogenic bacteria

Energy use to drive the accumulation of substance, which remains unchanged by the transport process

Active transport

Form of active transport that uses proton notice force (proton gradient) by coupling to an energetically unfavorable transport event (concentration of substance against the gradient)

Ion-driven transport systems

Give an example of a molecule that would use ion-driven transport systems:

Amino acids

Coupling energetically favorable + unfavorable processes

Symport

Form of active transport that use membrane proteins that form a channel & drive substances through the channel using the energy from ATP hydrolyses:

Binding protein-dependent transport systems

Give an example of a molecule that would use binding protein-dependent transport systems:

Sugars & amino acids

In all active transport mechanisms, the transport processes use carrier that:

Can become saturated

Ferric iron is very ______ so ______ is difficult

Insoluble; uptake

Because ferric iron is insoluble & difficult to uptake, microorganisms use ____ to aid in the uptake

Siderophores

Describe the process of ferric iron uptake in microorganisms:

Siderophore complexes with ferric iron & the entire complex is then transported into the cell

E.Coli can grow on greater than 30 different _____ compounds, using each to obtain _____ , _____ & _____

Organic compounds; carbon, H+/Electrons, energy

Bacteria that can use several hundred compounds to obtain carbon, reducing agents & energy:

Pseudomonas

________ organisms have complex needs and can only grow in association with the human body or in complex culture medium (ex. Blood agar)

Nutritionally fastidious

Give an example of nutritionally fastidious bacteria:

Staphylococci & streptococci

Have to replicate within living cells, but unlike viruses, they can carry out metabolic processes:

Obligate intracellular parasites

Give an example of a bacteria that is an obligate intracellular parasite:

Chlamydia

Microbial growth in real world is considered:

Suboptimal

Different organisms have ______ growth rates

Variable

What is a factor that protects bacteria:

Stress responses

Bacteria can still cause damage to the host when not growing through:

Immunogenic processes & toxin production

Mechanisms of adaptation of bacteria function to:

1. Maximize efficiency in using energy & resources 2. Respond to changes

What are the results of regulation by microorganism:

1. Pathways can be switched on or off 2. Pathways can be turned up or down

How is control among microorganisms established?

1. Enzyme activity 2. Number of enzyme molecules

All enzymes have ______ for catalysis, but some enzymes also have _____ for regulation

Active sites; allosteric sites

_______ sites bind regulatory molecules

Allosteric sites

Describe the binding of a regulatory molecule to an allosteric site on an enzyme:

1. Noncovalent 2. Reversible 3. Affects activity of enzyme

Positive effectors ____ activity; while negative effectors ____ activity of an enzyme:

Increase; decrease

In allosteric regulation: Higher concentration of regulatory molecules =

More activity

In allosteric regulation, effectors act to:

1. Change affinity of enzyme for substrate 2. Change Vmax (rate of reaction)

Results in the prematures termination of transcription of mRNA:

Attenuation

In attenuation, the _____ becomes stalled in the _____ of the mRNA (upstream of the coding region on the enzyme)

Ribosome; attenuator region

During attenuation even though transcription is not complete, what can occur, & why?

Translation can begin, because transcription & translation occur simultaneously in bacteria

During attenuation, ______ are important for mRNA folding

Secondary structures (hairpin)

An example of a secondary structure used for mRNA folding during attenuation:

Hairpin

In attenuation, what happens when leucine is present?

When leucine is present, leucine-rich region allows ribosome to read & translate A & B regions causing formation of a C-D hairpin structure

In attenuation, when leucine is present and a C-D hairpin structure is formed, this causes:

The RNA polymerase to dissociate from the DNA, resulting in terminating transcription

In attenuation, when leucine is present and a C-D hairpin structure is formed, this causes the termination of transcription, ultimately:

Preventing the cell from making the enzyme to create more leucine

In attenuation, what happens when leucine is absent?

When leucine is absent, a high demand for leucine tRNA causes ribosome to stall, allowing for formation of B-C hairpin structure

In attenuation, what happens when leucine is absent and B-C hairpin has formed, this allows for:

Transcription to occur

In attenuation, what happens when leucine is absent and B-C hairpin has formed allowing for transcription to occur this and ultimately:

RNA polymerase will transcribe the rest of the operon & produce more leucine

In attenuation, if abundant leucine is present, the ribosome:

Reads through leucine-rich region

In attention, if no leucine is present, the ribosome:

Stalls with high demand for leucine tRNA

Controlling the NUMBER of enzyme molecules can be accomplished through:

Attenuation

Controlling the initiation of transcription can be accomplished through:

Catabolic & anabolic pathways

Controlling transcription initiation in a catabolic pathway is accomplished through:

Gene induction (by inducer)

When controlling transcription initiation, when lactose is absent:

Repressor molecule binds to operator region

When controlling transcription initiation, when lactose is absent and the repressor molecule binds to the operator region this:

Prevents RNA polymerase from beginning transcription process

When a repressor is bound to the operator region therefore preventing RNA polymerase from binding:

No mRNA or enzymes are produced

Describe what occurs in a catabolic pathway when lactose is absent:

Repressor molecule binds to operator region, preventing RNA polymerase from beginning transcription = no mRNA or enzymes produced

Describe what occurs in a catabolic pathway when lactose is present:

Inducer molecule binds to/inactivates the repressor & stops it from binding to operator region = increased transcription

When lactose is present in a catabolic pathway resulting increased transcription, ultimately:

Enzymes are produced to break down lactose for sugars

Catabolic pathways: ______ Anabolic pathways: ______

Gene induction (by inducer) Gene repression (by corepressor)

Controlling transcription initiation in an anabolic pathway is accomplished through:

Gene repression (by corepressor)

Anabolic pathways use of gene repression via a compressor is considered the:

Default - mRNA is produced

When is gene repression via a corepressor turned on in anabolic pathways?

When tryptophan (end product) us at very high levels

Discuss what happens in an anabolic pathway when tryptophan is at very high levels:

Tryptopan will act as corepressor by binding to repressor, allowing it to bind to operator site

When tryptophan (at high levels) acts as corepressor, this ultimately:

Inhibits transcription

Genetic complementation is a genetic approach to study:

Bacteria pathogenesis

In the provided example, we studied yersenia pseudotuberculosis genes that confer _____ on _____

Invasiveness on E.coli

List the first four steps of genetic complementation:

1. Isolate DNA & cut into restriction fragments 2. Splice (insert) donor DNA into the plasmid 3. Introduce into recipient 4. Enrich for invasive clones

In step three of genetic complementation "introduce into recipient" we are we introducing the Y. Pseudotuberculosis plasmid into E. coli?

E. coli is not invasive, so if we can cause it to become invasive with fragments of Yersinia DNA, we can identify the invasive gene

In genetic complementation, when we introduce the DNA into the recipient (E. coli), the plasmids will:

Divide & replicate right along with E. Coli

In step four of genetic complementation "Enrich for invasive clones" what is the goal?

Goal is to screen different yersinia genes to determine which one can invade a mammalian cell

In step four of genetic complementation "Enrich for invasive clones": Certain _____ that have acquired a plasmid with the _____ gene for _____ will enter the mammalian cells

E. coli; Yersinia; Invasiveness

In step four of genetic complementation "enrich for invasive clones" What is added to kill all the E.Coli cells that are outside the mammalian cells and why?

Gentamicin (antibiotic) is added to kill all E. coli cells that are outside mammalian cells because those did not invade

In step four of genetic complementation "enrich for invasive clones" After the antibiotic is added to kill the noninvasive E.coli, what next occurs?

Mammalian cells are then washed off, lysed & their contents (including an E. Coli that invaded) are plated onto antibiotic Petri dish

In step four of genetic complementation "enrich for invasive clones" After the mammalian cells are washed, lysed they are then plated onto antibiotic petri dish- what does this process allow for?

This process allows for positive selection of the cells that contain the invasive gene/antibiotic-resistance

In genetic complementation process, after the positive selection of the cells that contain the invasive gene/antibiotic resistance, what next occurs (4 steps)

1. Generate DNA sequence= INV gene 2. Deduce protein coding region= invasion protein 3. Manipulate (mutate) gene further 4. Reintroduce into yersinia

During genetic complementation process, when manipulating (mutating) the gene further & reintroducing it into yersinia, what is the first step to accomplish this?

1. INV gene is cloned into suicide plasmid for yersinia

During genetic complementation process, when manipulating (mutating) the gene further & reintroducing it into yersinia, following the INV gene being cloned into a suicide plasmid for yersinia what occurs next?

A majority of the INV gene on suicide plasmid is replaced with a Kanamycin-resistance gene (KM^r)

During genetic complementation, when reintroducing the manipulated/mutated back into yersinia, the INV gene on the suicide plasmid may be replaced with the KM^r gene what will this mutation result in?

Loss-of-function mutation

During genetic complementation, when reintroducing the manipulated/mutated back into yersinia, the INV gene on the suicide plasmid may be replaced with the KM^r resulting in a loss of function mutation, what will then be done with these plasmids containing mutated copies:

Suicide plasmids contains INV loss-of-function is transferred from E. coli to Yersinia

In genetic complementation, when the suicide plasmids containing the INV loss-of-function mutations are transferred from E. coli to yersinia, the suicide plasmid will:

Replicate in E. coli but NOT replicate in Yersinsia (so plasmid is lost after next cell division)

During genetic complementation, in the final steps, what is needed to replace the INV gene in yersinia chromosome with the loss-of-function INV all from the plasmid?

Double recombination even

During genetic complementation, in the final steps, what is needed to replace the INV gene in yersinia chromosome with the loss-of-function INV all from the plasmid?

Double recombination event

What is ultimately the final step of genetic complementation with yersinia?

Test Yersinia INV mutants and show that they DO NOT invade (due to loss-of-function mutation)

Genetic complementation is used to study:

Bacteria pathogenesis

Move from place to place within a genome; jumping genes:

Tranposons

Insertion of a transposon in a gene often creates a:

Loss of function mutation

What marks the site of the mutation in transposon-based methods?

Transposon

Unlike simple transposons, composite transposons contain:

Separate IS elements at either end & intervening genes in between

The intervening genes in between the IS elements in composite transposons are often responsible for:

Drug resistance

The intervening genes in between the IS elements in composite transposons are often responsible for:

Drug resistance

Tn-phoA is an example of:

Engineered transposon

Tn-phoA mutagenesis identifies ______ in Vibrio cholera:

Virulence genes

Transposon based methods function to identify:

Virulence factors

In Tn-phoA mutagenesis, experimenters are looking for vibrio goes that are:

1. Exported into the perioplasm 2. Expressed under certain physiologic conditions

Tn-phoA mutagenesis, experimenters are looking for vibrio genes under what physiologic conditions?

@ pH 6.5 & high osmolarity

What is the first step of Tn-phoA mutagenesis?

1. Introduce Tn-phoA on a suicide plasma

Tn-phoA mutagenesis when we introduce Tn-phoA on a suicide plasmid, the transposon may:

Jump into vibrio chromosome (transposition)

In Tn-phoA mutagenesis, after Tn-phoA is introduced on a suicide plasmid, we used ____ to select for cells containing a transposon (as some transposons jumped into the vibrio chromosome)

Kanamycin

In Tn-phoA mutagenesis what is required for colonies to grow?

Kanamycin-resistanve

In Tn-phoA mutagenesis the third step is to screen for blue colonies, what are we looking for?

PhoA+ gene

In Tn-phoA mutagenesis, phoA encodes the enzyme:

Periplasmic phosphatase

In Tn-phoA mutagenesis, the expression of phoA gene depends on:

Fusion of reading frame to an adjacent gene (V. cholera) AFTER transposition

In Tn-phoA mutagenesis expression of phoA gene depends on fusion of the reading frame to an adjacent gene (Vibrio cholera) AFTER transposition, what does this fusion do?

This fusion tells the protein to go into the periplasm

In Tn-phoA mutagenesis, why do we see a blue color only if the cell was exported into the periplasma?

PhoA enzyme will cut the X-P dye to produce a blue color ONLY if cell was exported

In Tn-phoA mutagenesis: PhoA is expressed ______ of bacterial cells:

Outside

In Tn-phoA mutagenesis: Within the blue colonies, the ______ is no longer present:

Tn-phoA plasmid

In Tn-phoA mutagenesis, after screening for blue colonies (PhoA+), what is measured in the next step?

Measure phoA activity after growth in liquid medium

In Tn-phoA mutagenesis, after measuring phoA activity following growth in a liquid medium, we will ONLY select for bacteria that have _____ activity at pH 6.5 and ______ osmolarity while having _____ activity at pH 8.0 and _____ osmolarity

High; high Low; low

The final step in Tn-phoA mutagenesis is to:

Test virulence in mouse model

In Tn-phoA mutagenesis, what should we expect to see when testing virulence in a mouse model?

Expect to see DECREASED virulence, because the transposon creates a loss-of-function mutation

What is used in the mouse model for typhoid fever?

Signature-tagged mutagenesis

Examines individual bacteria for desirable trait:

Genetic SCREEN

Only bacteria with desirable trait grow:

Genetic SELECTION

Genetic screening is based on:

Phenotype (color, something you can see)

Genetic selection is based on:

What survives vs. what dies (antibiotic resistance)

Signature-tagged mutagenesis (mouse model for Typhoid fever) is a _____ for ______trait: inability to grow in spleen

Screen; negative trait

What is the negative trait that is screened for in the signature-tagged mutagenesis (mouse model for Typhoid fever):

In ability to grow in spleen

In signature-tagged mutagenesis (Mouse model for Typhoid fever), by screening for a negative trait (inability to grow in spleen) we are looking for:

Mutants of salmonella that CAN'T infect a mouse

In signature-tagged mutagenesis (Mouse model for Typhoid fever): What is put into each transposon?

KM^r maker +DNA sequence tag (that is a tiny variable region)

In signature-tagged mutagenesis (Mouse model for Typhoid fever): What is responsible for creating a slight difference between the transposons?

PCR

In signature-tagged mutagenesis (Mouse model for Typhoid fever): After PCR of transposons, all tranposons are transferred into:

Salmonella genome

In signature-tagged mutagenesis (Mouse model for Typhoid fever): All transposons are transferred into the salmonella genome, by using a ______ that moves ______ from E. coli into salmonella:

Suicide plasmid; Mini-Tn5

In signature-tagged mutagenesis (Mouse model for Typhoid fever): All transposons are transferred into the salmonella genome by using a suicide plasmid that moves mini-Tn5 from ____ to ____

E. coli to salmonella

In signature-tagged mutagenesis (Mouse model for Typhoid fever): If transposition has occurred, all will have:

Kanamycin resistance

In signature-tagged mutagenesis (Mouse model for Typhoid fever) What do we select for after all transposons are transferred into the salmonella genome?

Kanamycin resistance

In signature-tagged mutagenesis (Mouse model for Typhoid fever) Selecting for Kanamycin resistance will create:

A library of tagged salmonella mutants that each contain a unique mini-Tn5 insertion

In signature-tagged mutagenesis (Mouse model for Typhoid fever) What do we inject the mouse with?

Inject mouse with pooled mutants

In signature-tagged mutagenesis (Mouse model for Typhoid fever) Once mouse in injected with pooled mutants, we then:

Recover bacteria from the spleen

In signature-tagged mutagenesis (Mouse model for Typhoid fever) What do we do with the recovered bacteria from the spleen & why?

Placed recovered bacteria on a kanamycin dish to identify those with transposon insertions

In signature-tagged mutagenesis (Mouse model for Typhoid fever) What are the DNA sequence tags (variable region) used for?

Used to compare the input and recovered pools of bacteria

In signature-tagged mutagenesis (Mouse model for Typhoid fever) What do the blank spots in the recovery pool blot represent?

Bacterial mutants that did NOT grow in mice

In signature-tagged mutagenesis (Mouse model for Typhoid fever) The mutants not recovered are:

Avirulent

IVET

In-Vivo Expression Technology

What mechanism is used in IVET?

Promotor-trapping

In IVET we are looking for genes of salmonella that are:

Expressed in infection but not in the lab

What is the first step of IVET?

1. Put fragments of salmonella DNA into plasmid with PurA, LacZ & ampicillin resistant gene

What type of plasmid is used in the first step of IVET?

Suicide plasmid

In IVET, what happens in the first step to the suicide plasmid?

Undergoes double recombination

In IVET following the creation of a suicide plasmid contain salmonella, PurA, LacZ & Ampicillin resistance gene, we engineer the bacteria further by inserting:

Loss-of-function PurA mutant

In IVET after further engineering the bacteria with a loss-of-function PurA mutant, what occurs?

Integration of plasmid onto the chromosomes

In IVET, after the integration of plasmid onto the chromosomes what is the following step?

Screen for PurA by injecting pool of fusions into mouse

In IVET once the mice have been injected with the pool of fusions we then:

Recover bacteria from spleen of mouse

In IVET, the bacteria recovered from mouse spleen must have:

Functional promotor fused to purA-LacZ operon because they were able to be recovered

Gene used to identify virulence genes that are transcriptionally active in the mouse (IVET)

PurA

In IVET, the gene used to select for salmonella bacteria that contain the plasmid inserted within their genome

Ampicillin resistance gene

In IVET, after the bacteria have been recovered from the spleen _____ is screened for in-vitro:

LacZY

In IVET, the gene used to identify virulence genes that are not expressed during laboratory growth:

LacZY

In IVET _____ do NOT contain LacZ protein

Light colored colonies

In IVET the light colored colonies that do NOT contain LacZ protein are the ones that are:

Linked to a promotor expressed in infection (in mouse) but NOT in lab

DFIT

Differential Fluorenscence Induction Technique

In DFIT what are we looking for?

Looking to identify genes containing potential macrophage survival factors

(DFIT) _____ can survive within macrophages, while _____ cannot

Pathogenic salmonella; normal salmonella

In DFIT, fragments of ____ chromosome are placed into _____

Salmonella; GFP fusion plasmid

(DFIT) GFP can only be expressed if:

It is inserted next to a gene with an open reading frame & promotor

In the second step of DFIT, macrophages are infected with transformed GFP salmonella and separated by:

Fluorescence activated cell sorting (FACS)

In DFIT what happens to the macrophages with fluorescent bacteria after separation via FACS?

They are lysed, grown on media & then sorted again using FACS

In DFIT why are cells ran through FACS a second time?

In order to identify bacterial cells that do NOT fluoresce on their own

In the final step of DFIT what are we looking for?

Bacterial cells that fluoresce within macrophages from the bacterial cell population that did NOT fluoresce when growing on their own in lab environment

IVIAT

In vivo-induced antigen technology

IVIAT is a _____ approach

Antibody-based

Uses patient serum to identify genes of bacterial pathogens expressed during infection:

IVIAT

In IVIAT what do antibodies typically respond to?

Antibodies typically response to protein on the surface or secreted by bacteria

In IVIAT why do only some of the pathogen proteins react with patient serum?

Because only a subset of the pathogens proteins are secreted or expressed on the bacterial cell surface

In IVIAT what vector is used:

Bacteriophage

In IVIAT the bacteriophages are placed into:

E. coli

In IVIAT when the bacteriophages are put in to & replicated in E. coli what results?

Zones of clearing

In IVIAT what causes the zones of clearing?

Clear areas remain after local population of bacteria are lysed

In IVIAT in addition to the zones of clearing , what else is present following the replication of bacteriophages in E. coli?

Phage debris (plaque) and Recombinate bacterial proteins

In IVIAT we want to remove intact E. coli because some antibodies will bind to the E. Coli and we don't want those antibodies, we only want:

Antibodies for TB

In IVIAT, we must remove antibodies from patient serum because antibodies will bind to each phage plaque replicate, generating a signal from all plaques which would appear as:

Black spots

In IVIAT once antibodies are removed, the remaining serum is:

Incubated with plaques on membrane filter

In IVIAT once the TB antigens will turn:

Black

In Microarray scheme, genes encoding potential virulence factors are identified by identifying:

Genes whose mRNAs are expressed in different levels in bacteria growth in the lab compared to bacteria isolated from a patient

In the microarray scheme, we convert ____ to ____, label with ___ and then mix _____ with array on glass slide

RNA to DNA; Fluorescent dye; copy-DNA

In the microarray scheme, PCR can be used to:

Amplify individual coding regions of particular bacterial genome

(Microarray scheme) Single for a gene that has increased expression during infection:

Green fluorescent signal

(Microarray scheme) Green fluorescent signal= signal for a gene that has increased expression during infection=

Cy3 > Cy5

(Microarray scheme) Signal for "house-keeping" gene expressed at the same level in cholera both during an infection and during growth in a lab:

Yellow fluorescent signal

(Microarray scheme) Yellow fluorescent signal= Signal for "house-keeping" gene expressed at the same level in cholera both during an infection and during growth in a lab=

Cy3 = Cy5

(Microarray scheme) Signal for a gene that has an increased expression during growth in a laboratory:

Red fluorescent signal

(Microarray scheme) Red fluorescent signal= Signal for a gene that has an increased expression during growth in a laboratory=

Cy5 > Cy3

Chemical compounds used to treat disease:

Chemotherapeutic agent

Destroy pathogenic microbes or inhibit their growth within host:

Antimicrobials

Destroy or inhibit bacteria; a class of chemotherapeutic agent:

Antibiotics

Most antibiotics are ______ or their _____

Microbial products; derivatives

When bacterial produce material to kill each other & we use those materials to kill bacteria:

Germ warefare

What are some bacterial sources of antibiotics:

1. Streptomyces 2. Micromonospora 3. Bacillus

What are some fungal sources of antibiotics:

1. Penicillium 2. Cephalosporium

What are the four general characteristics of ANTIMICROBIAL drugs?

1. Selective toxicity 2. Therapeutic dose 3. Toxic dose 4. Therapeutic index

Ability of a drug to kill or inhibit a pathogen while damaging host as little as possible:

Selective toxicity

Drug level required for clinical treatment:

Therapeutic dose

Drug level at which drug becomes too toxic for patient (i.e., produces side effects):

Toxic dose

Ratio of toxic dose to therapeutic dose:

Therapeutic index

What are the four general characteristics of ANTIBIOTICS?

1. Bacteriocidal 2. Bacteriostatic 3. Broad-spectrum 4. Narrow-spectrum

Kill bacteria:

Bacteriocidal

Inhibit growth of bacteria:

Bacteriostatic

Attack many different bacteria (Gram + & Gram -)

Broad-soectrum

Attack only a few different bacteria:

Narrow-spectrum

How is the effectiveness of antimicrobial drug therapy expressed?

1. Minimal inhibitory concentration (MIC) 2. Minimal bactericidal concentration (MBC)

Lowest concentration of drug that inhibits growth of pathogen:

Minimal inhibitory concentration

Lowest concentration of drug that kills pathogen:

Minimal bactericidal concentration

What are the techniques used to determine MIC & MBC?

1. Dilution susceptibility tests 2. Disk diffusion tests

Involves inoculating media containing varying concentrations of drug:

Dilution susceptibility test

In a dilution susceptibility test, how do we know which is the MIC?

Broth or agar with lowest concentration showing no growth

To introduce an infective agent or vaccine into organism/medium to produce immunity:

Inoculate

In a solution susceptibility test, how do we know which is the MBC?

Broth from which microbe cannot be recovered

In a dilution susceptibility test, if broth is used, tubes showing _____ can be subcultured into drug-free medium

No growth

Process in which disks impregnated with specific drugs are placed on agar plates inoculated with test microbe:

Disk diffusion test

How does a disk diffusion test work?

Drug diffuses from disk into agar, establishing concentration gradient

In a disk diffusion test, what signifies no growth?

Clear zones of inhibition around disk

What is the standardized method for carrying out disk diffusion test?

Kirby-Bauer method

In the Kirby-Bauer method for carryng out a disk diffusion test, sensitivity and resistance are determined using tables that relate:

Zone diameter to degree of microbial resistance

In the Kirby-Bauer method for carrying out disk diffusion test, the table values are plotted and used to determine:

If concentration of drug reached in body will be effective

In the Kirby-Bauer method for carrying out disk diffusion test, the zone of inhibition depends on:

How effective the antibiotic is at stopping bacterial growth

In the Kirby-Bauer method for carrying disk diffusion test, a larger zone of inhibition =

Smaller MIC

In the Kirby-Bauer method for carrying disk diffusion test, designations are based on studies to establish:

The levels a drug can safely reach in the human body

In the Kirby-Bauer method for carrying disk diffusion test, what is considered RESISTANT? What does this mean?

Less than 12mm Weaker antibiotic, requires higher concentration to stop growth

In the Kirby-Bauer method for carrying disk diffusion test, what is considered SENSITIVE? What does this mean?

Greater than 17mm Stronger antibiotic

In order to be considered effective in the blood, concentration of drug at infection site must be:

Greater than or equal to the MIC

Describe the growth of colonies when antibiotics are effective:

No colonies will grow

What can be used to determine the concentration of Drug in blood? (5)

Microbiological, chemical, immunological, enzymatic or chromatographic assays

What are the three factors influencing effectiveness of antimicrobial drugs?

1. Ability of drug to reach site of infection 2. Ability of drug to reach concentrations in the body that exceed MIC of the pathogen 3. The susceptibility of the drug

The ability of the drug to reach site of infection depends in part on:

Mode of administration

What are the three modes of administration of drugs:

1. Oral 2. Topical 3. Parenteral routes

What does parenteral routes of drug administration mean?

Non-oral routes of administration

Orally administrated drugs, must be able to overcome:

Stomach acid- some drugs destroyed by this

What are two cases in which drugs can be excluded:

1. Blood clots 2. Necrotic tissue

The ability of a drug to reach concentrations in the body that exceed MIC of pathogen depend on:

1. Amount administered 2. Route of administration 3. Speed of uptake 4. Rate of clearance (elimination) from body

When discussing susceptibility of pathogen to drug: A drug requires ______ to be effective

bacterial cell growth

How soon a drug stops bacterial growth:

Speed of action

When discussing the mechanism of action of antimicrobial agents, the agent can impact the pathogen by targeting:

Some function necessary for its reproduction or survival

Mechanism of action- antimicrobial agents: Ideally, targeted function is:

Very specific to pathogen

Mechanism of action- antimicrobial agents: If targeted function is very specific to pathogen this means:

High therapeutic index

What are four mechanisms of action of antimicrobial agents?

1. Disruption of bacterial cell wall 2. Inhibition of protein synthesis 3. Inhibition of nucleic acid synthesis 4. Antimetabolites

Disruption of bacterial cell wall: ______ is unique to bacteria

Peptidoglycan

Disruption of bacterial cell wall: Many antibiotics target this pathway:

Peptidoglycan synthesis

Acts as a carrier and links to NAM prior to addition of peptide side chain

Uridine Diphosphate (UDP)

Steps to peptidoglycan synthesis: 1. Peptidoglycan repeat unit forms in _____ 2. Repeat unit is the transported across membrane by _____ 3. Repeating unit attached to ______ 4. Cross-links formed by _____

1. Cytoplasm 2. Bactoprenol (lipid) 3. growing peptidoglycan chain 4. Transpeptidation

The exchange of one peptide bond for another:

Transpeptidation

Inhibits transpeptidation:

Beta-Lactam antibiotics

What is an example of a B-lactamase inhibitor?

Clavulanic acid Sulbactam Tazobactam

Are not antibiotics but help B-lactam antibiotics by preventing their degredation by B-lactamases

B-lactamase inhibitors

Enzymes produced by some bacteria that are resistant to B-lactam antibiotics

B-lactamases

Used in combination with B-lactam antibiotic:

B-lactamase inhibitor

The 1st combination of B-lactam antibiotic + B-lactimase inhibitors: Specifically what was used?

Augmentin Amoxicillin + Clavulanic acid

Binds terminal D-Ala-D-Ala and sterically inhibits the addition of peptidoglycan subunits to the cell wall:

Vancomycin

Vancomycin binding to existing peptidoglycan chains inhibits the:

Transpeptidation reaction that cross-links the chains

Important for the treatment of antibiotic resistant staph & eneteroccocal infections

Vancomycin

Penicillins Cephalosporins Carbapenems & Monobactams Are all:

B-Lactams

Vancomycin & Teichoplanin are both:

Glycopeptides

Bacitracin & Polymixins are both:

Polypeptides

Polypeptides, Glycopeptides, & B-lactams are all responsible for:

Disrupting cell wall

Second line treatment for mycobacterium tuberculosis:

Cycloserine

Sulfonaides, Trimethoprim, Dapsone, P-aminosalicylic acid are all:

Anti-metabolites

Unlike, bacteria, humans do not make ______, we require it in our diet:

Folic acid

Antimetabolites act to inhibit _______ in bacteria

Folic acid synthesis

Prevents recycling of lipid carrier:

Polypeptides (bacitracins & polymixins)

Binds phospholipids & disrupts outer & inner membranes of Gram negative bacteria (topical because of more general mode of action= toxic)

Bacitracin & Polymixins (Polypeptides)

Once resistance originates in a population, it can be transmitted to other bacteria via:

1. New mutations 2. Pre-existing resistance genes

Resistance mechanism: Hydrolysis of b-lactam ring by b-lactamase: Plasmidborne?

Penicllin & Cephalosporins Yes

Resistance mechanism: Change in Penicllin-binding protein: Plasmidborne?

Methicilin No

Resistance mechanism: Efflux pump pushes drug out of cell: Plasmidborne?

Tetracyclines Yes

Resistance mechanism: Mutations in 23s rRNA: Plasmidborne?

Oxazolidinones No

Resistance mechanism: Mutations in genes encoding DNA gyrase & topoisomerase IV: Plasmidborne?

Quinolones No

Resistance mechanisms: How do bacteria resist antibiotics?

1. Impermeable barrier 2. Target modification 3. Antibiotic modification 4. Efflux-pump mechanism

Resistance mechanism in which the bacterial cell membrane develops an impermeable barrier which blocks antibiotics:

Impermeable barrier

Resistance mechanism in which modification of components of the bacteria which are targeted by the antibiotic, meaning the antibiotic can no longer bind properly to its target in order to destroy the bacteria:

Target modification

Resistance mechanism in which the cell produces substances, usually an enzyme, that inactivate the antibiotic before it can harm the bacteria:

Antibiotic modification

Resistance mechanism in which the antibiotic is actively pumped out of the bacteria so that it cannot harm the bacteria:

Efflux pump

Genetic elements involved in resistance gene dissemination include:

1. plasmids 2. transducing bacteriophage 3. bacterial chromosomal genes 4. transposons 5. integrons

Genetic elements involved in resistance gene dissemination: Some plasmids can promote their own transfer by:

Conjugation

Genetic elements involved in resistance gene dissemination: Some transducing bacteriophage can package non-phage DNA resulting in transfer by:

Transduction

Genetic elements involved in resistance gene dissemination: Bacterial chromosomal genes can undergo _____ or transfer by ____

Mutations; transformation

Development and spread of drug-resistant pathogens caused by drug treatment, which destroys sensitive strains:

Superinfection

What steps can be taken to prevent emergence of drug resistance?

1. Give drug in high concentrations 2. Give two or more drugs at the same time 3. Use drugs only when necessary

What are two possible future solutions for preventing emergence of drug resistance?

1. Continued development of new drugs 2. Use of bacteriophages to treat bacterial disease

Common organisms in superinfection include:

1. C-Diff 2. MDR Gram-negative rods 3. MRSA 4. Candida

Resistance to infectious disease:

Immunity

Collection of cells, tissues & molecules that mediate resistance to infections:

Immune system

Coordinated reaction of the immune system to infectious microbes:

Immune response

Study of the immune system, including its responses to microbial pathogens & damaged tissues & its role in disease:

Immunology

Immune response that acts immediate:

Innate

Immune response that is NOT antigen specific

Innate

Innate immune response recognizes _____ that are shared by many different microbes, as well as _____

PAMPs & DAMPs (pathogen-associated molecular patterns) (damage-associated molecular patterns)

Genes encoding Pattern Recognition Receptors (PRRs) are present in the:

Germ line

Genes encoding receptors that recognize PAMPs are present in the germ line and do not undergo:

Somatic recombination or hyper mutation

In response to infection innate immune cells do NOT undergo:

Clonal expansion

Immune system characterized by no memory & cells that are nonreative to self:

Innate

The adaptive immune system requires _____ before it is effective:

Days to weeks

The adaptive immune system is highly:

Antigen-specific

The adaptive immune system recognizes _____ on _____ of _____

Specific epitopes; specific proteins; specific pathogens

In the adaptive immune response, functional genes encoding antigen receptors are:

NOT present in the germ line

In the adaptive immune system, functional antigen receptor genes are generated by ____ & _____ of germ line genes during maturation of B cells & T ells

Somatic recombination & mutation

In the adaptive immune system the functional antigen receptor genes that are generated by somatic recombination and mutation of germ line genes, are produced:

Prior to exposure to any antigens

In the adaptive immune response, clonal selection and proliferation of B & T lymphocytes specific for particular antigens occurs:

Following exposure to those antigens

The adaptive immune response is _____ to self:

Non-reactive

Gives rise to immunologic memory:

Adaptive immune system

Innate or adaptive: Provide initial defense against infections

Innate

Innate or adaptive: Develops later & is mediated by lymphocytes & their products

Adaptive

Innate or adaptive: Some mechanisms (epithelial barriers) prevent infections:

Innate

Innate or adaptive: Other mechanisms (phagocytes, NK cells, complement system) eliminate microbes:

Innate

Innate or adaptive: Involves humoral & cell-mediated immunity:

Adaptive

B lymphocytes secrete antibodies that block infections & eliminate extracellular microbes:

Humoral immunity

______ secrete antibodies that block infections & eliminate extracellular microbes:

B lymphocytes

T-lymphocytes eradicate intracellular microbes

C-mediated immunity

T-lymphocytes eradicate ______ microbes (in cell-mediated immunity)

Intracellular

Eliminate phagocytosed (ingested) mivrobes

Helper T-cells

Kill infected cells & eliminate reservoirs of infection:

Cytotoxic T-cells

Feature of adaptive immunity which ensures that distinct antigens elicit specific responses:

Specificity

Feature of adaptive immunity that enables the immune system to respond to a large variety of antigens:

Diveristy

Feature of adaptive immunity that increases number of antigen-specific lymphocytes from a small number of naive lymphocytes:

Clonal expansion

Lymphocyte clones with diverse receptors arise in primary lymphoid organs:

Clonal selection

In clonal selection, lymphocyte clones with diverse receptors arise in:

Primary lymphoid organs

A population of lymphocytes with identical antigen receptors (same specificity; all derived from same precursor cell):

Clone

In clonal selection, clones of mature lymphocytes specific for many antigens enter:

Lymphoid tissue

In clonal selection, after entering lymphoid tissue, antigen-specific clones are activated by:

Antigens

In clonal selection, what occurs when antigen-specific clones are activated by antigens?

Stimulation of proliferation & differentiation of that clone

The secondary response to a specific antigen is:

Larger and more rapid (due to memory)

The primary response to one antigen is:

Different than to a different antigen (specificity)

Antigen recognition of B lymphocytes:

Soluble or cell surface antigens

The effector function of ______ includes: Secretion of antibodies -neutralization of microbe -phagocytosis -complement activation

B-lymphocyte

Antigen recognition of helper T cells:

Antigens on surfaces of APC

The effector function of _____ includes: Secretion of cytokines -activation of macrophages -inflammation -activation of T & B lymphocytes

Helper T cells

Antigen recognition of cytotoxic T cells:

Antigens in infected cells

The effector function of ______ includes: Killing of infected cells

Cytotoxic T cells

Regulatory T cells function to:

Suppress immune response

Antigen recognition of natural killer cells:

Recognize changes on surface of infected cells

Natural killer cells respond by:

Killing infected cell

After lymphocytes are activated by antigen, _______ cells migrate towards eachother and meet at the edge of follicle:

B & T cells

After lymphocytes are activated by antigen, B & T cells migrate towards each other and meet at the edge of follicle and there, helper T cells interact with and help B cells:

Differentiate into antibody-producing cells

-Innate defensive mechanisms to keep out microbes -If defensive barrier are crossed= inflammation & antiviral mechanisms

Early innate immune response

Secreted antibodies, phagocytes & helper T cells, cytotoxic T cells:

Adaptive immune response

Includes microbial antigen through vaccine or infection:

Active immunity

Is active immunity specific? Does it cause memory?

Yes & Yes

Includes serum antibodies, from immune individual, administered to uninfected individual:

Passive immunity

Is passive immunity specific? Does it cause memory?

Yes & Yes

In innate immunity, specificity is based on:

PAMPs & DAMPs

In adaptive immunity, specificity is based on:

Structural detail of microbial molecules (Antigens)

The receptors of the innate immune system are encoded in the: This results in:

Germ line; limited diversity

The receptors of the adaptive immune system are encoded by: This results in:

Genes produced by somatic recombination; greater diversity

The distribution of receptors in the innate immune system are:

Nonclonal

Identical receptors on all cells of the same lineage:

Nonclonal (seen in innate immunity)

The distribution of receptors in the adaptive immune system are:

Clonal

Clones of lymphocytes with distinct specificities express different receptors:

Clonal (seen in adaptive immunity)

The two principle types of reaction in the innate immune system:

1. Stimulate acute inflammation 2. Anti-viral defenses

The accumulation of leukocytes, phagocytic cells, plasma proteins and fluid derived from the blood at an extravascular tissue site of infection or injury:

Acute inflammation

NK Cell-mediated killing of virus-infected cells

Anti-viral defenses

Interferon A/B (Type I interferons), are secreted by virus-infected cells, bind to receptors on surrounding ells, and induce and induce an anti-viral state in those cells:

Anti-viral defenses

List the prominent cell-associated pattern recognition receptors and sensors of innate immunity:

1. Toll-like receptors (TLRs) 2. NOD-like receptors (NLRs) 3. RIG-like receptors (RLRs)

Where are the prominent cell-associated pattern recognition receptors & sensors of innate immunity located?

Extracellularly, cytoplasm or in endosomes

TLRs that recognize microbial products (such as PAMPs) will be found in the _____ while TLRs that recognize nucleic acids will be present within the ______

Cytoplasm; endosome

TLR engagement by bacterial or viral molecules ultimately leads to:

1. Acute inflammation 2. Stimulation of adaptive immunity 3. Antiviral state

A family of more than 20 different cytosolic proteins that recognize PAMPs and DAMPs in the cytoplasms and recruit other proteins to for signaling complexes (such as inflammasomes) that promote inflammation:

NOD-like receptors (NLRs)

Cytosolic sensors of viral RNA that respond to viral nucleic acids by inducing production of the antiviral type I interferons:

RIG-like receptors (RLRs)

Physical barrier to infection

Epithelial barrier

-Killing of microbes by locally produced antibiotics & killing of microbes and infected cells by intraepithelial lymphocytes are both function of the:

Epithelial barrier

Secrete cytokines that induce inflammation, and ingest and destroy microbes:

Macrophages (can survive long periods of times in tissues)

-circulating phagocytic cells -most abundant leukocyte in blood -first responder to most infections -live only a few hours in tissues

Neutrophils

What happens to blood monocytes after entering into tissues:

Differentiate into macrophages

What cells are the phagocytes of the innate immune response:

Neutrophils & monocytes/macrophages

-Microbes binding to TLRs -Cytokines binding to cytokine receptors -Complement fragments binding to complement receptors These all cause:

Activation of macrophages

Component of the innate immune system: -secretes cytokines -presents antigenic peptides to T cells

Dendritic cells (Sentinel cells)

Component of the innate immune system: -abundant cytoplasmic granules -present in skin & mucosal epithelium -contain vasoactive amines (e.g. histamine) -cause vasodilation & capillary permeability

Mast cells

Component of the innate immune system: -lymphocyte-like cells -produce cytokines but lack T cell antigen receptors (TCRs)

Innate lymphoid cells

Both mast cells and dendritic cells are part of:

Innate immune system

Induce inflammation, opsonize microbes enhancing their phagocytosis, cause osmotic lysis of microbes:

Complement

List the complement proteins involved in the early steps & late steps:

Early steps: C3a, C3b Late steps: C5a, C6-C9

C3a is responsible for:

Inflammation

C3b is responsible for:

opsonization & phagocytosis

C5a is responsible for:

Inflammation

C6-9 are responsible for:

Lysis of microbe

-Rolling -Integrin activation by chemokines -Stable adhesion -Migration through endothelium These are the steps in:

Migration of blood leukocytes to site of infection

-Kill virus-infected cells -Secrete interferon Y which activates macrophages

Natural killer cells

Secreted by virus-infected cells, induce anti-viral state in surrounding cells (local)

IFN A/B (Type I interferons)

_______ & ______ are combated mainly by an acute inflammatory response, in which neutrophils & monocytes are recruited to the site of infection & by the complement system:

Extracellular bacteria & fungi

______, which can survive inside phagocytes, are eliminated when the microbial killing functions of phagocytes are activated by TLRs and other sensors, as well as by cytokines:

Intracellular bacteria

Defense against _____ is provided by type 1 interferons (interferons a & b) & by natural killer (NK) cells

Viruses