Lecture Exam 4 Flashcards
Mutualism
A reciprocal benefit accrues to both partners
What’s an example of a mutalistic relationship?
Buchnera sphidicola and aphids
Buchnera aphidicola
- Gram negative
- 617 kb genome
- Lives in the aphid
- Inside aphid cells -> bacteriocytes (mycetocyte)
- Transmitted vertically from mother to daughter
- Obligate mutualists
What does the aphid do for Buchnera?
The two have evolved together for millions of year
- ~75% of the Buchnera genome has been lost
- Asphid provides Buchnera with amino acids that Buchnera cannot make
What does Buchnera do for the aphid?
“gnotobiotic” aphids (gnotobiotics = germ free)
- Grow normally provided a diet supplemented with amino acids
- Aphids cannot make Trp. Buchnera must synthesize & provide Trp for the aphid
For the Trp operon what does it mean if there are low tryprophan levels?
transcription of the entire trp operon occurs
What happens to the trp operon if there are high tryptophan levels?
Repression occurs
- tryptophan binds, corepressor-repressor form active complex
- corepressor-repressor bind to operator and block transcription
Attenuation
Attenuation (in genetics) is a proposed mechanism of control in some bacterial operons which results in premature termination of transcription and which is based on the fact that, in bacteria, transcription and translation proceed simultaneously
Attenuation
What happens if Region 2 of the RNA pairs with Region 3 of the RNA?
- Nonterminating stem loop
- Transcription continues
thisis when trp is low so regions 2 and 3 on RNA will form together and create a raodblock so the ribosome is stuck on the operon and trascribes a ton of trp
Attenuation
What happens if Region 3 of the RNA pairs with Region 4 of the RNA?
- Terminating stem loop forms
- Transcription terminates
when there is enough Trp, the 2-3 roadblock is removed and the 3-4 pairing is formed, allowing the ribosome to move forward past the operon and hit the termination.
Cooperation
A reciprocal benefit accrues to both partners
canbe interspecific - btw two of the same species
Commensalism
one symbiont (the commensal) benefits while the other (host) isn’t harmed or helped
Example of commensalism
Staphylococcus epidermidis
- commonly found growing on skin
- Consumes human waste (oils, water, salts, dead skin cells) while normally having no impact on human health
Predation
one organism preys on another
Example of predation
Bdellovibrio
* Gram negative bacteria that preys on other Gram negative bacteria
* Enters the prey’s periplasmic space and feeds on the cytoplasmic contents
Parasitism
the parasite benefits while the host is usually harmed. Does not want to kill the host.
Amensalism
The adverse effect that one organism has on another
- unidirectional
Example of amensalism
*Streptomuces spp. *(penicillin)
* Produces many different antibiotics
* therefore they are studied heavily in the hunt for novel therapeutics
lots of this occurs in our gut
Competition
Two organisms try to acquire the same recource (location or nutrient)
* One outcompetes the other for the site’s resources
* Both coexist at lower levels, becuase they share the limiting resource
How many organisms make up the human microbiota?
- The human body contains ~10^13 human cells and ~ten times more microbial cells
- the mouth has 10^10 so .01% total
- the small and large intestine have 10^14 so 99% total
- the skin has 10^12 so 1% total
- the stomach has the least microbes becuase the stomach is highly acidic
Biofilm
- Biofilm: slime-encased aggregation of bacteria
- Composed of polysaccharide, protein, and extracellular DNA
*Staphylococcus aureus *biofilm formation
- Attachment, Multiplication, Exodus, Maturation
- Cells attach to a surface
- The cells multiply to a confluent “lawn” of cells on the surface
- An “exodus” phase occurs and some cells leave
- Biofilm then matures into towers of cells
Human microbiota
Not only provides nutrients for the host
- the human microbiota also protects teh body from invasion of harmful bacteria
Pathogen
any disease producing microorganism
C. difficile
- Gram (+), spore-forming anaerobe
- colonizes and infects people who have been treated with antibiotics
- Large problem in hospital and healthcare
Spore peptiodoglycan makeup
Composed of 2 layers
* A small inner layer of peptidoglycan that will make up the new cell wall upon germination
* A large layer of specialized peptidoglycan (cortex)
- Composed of NAG & NAM and nuramic-delta-lactam
- Not as highly crosslonked as call wall pepridoglycan
Stages of germination of spores
takes 30 min
Stage 1: Ca^2+ -DPA release Partial Core Rehydration. Some loss of resistance
(Grey)
Stage 2: Cortex Hydrolysis. Further Core Hydration. Loss of Dormancy.
(Black)
Outgrowth: Metabolism. Escape from spore coats
Nutrient limiation
(White)
C. difficile treatment options
Current Therapy
* Vancomycin
* Difficid (Fidaxomicin)
* Zinplava (bezlotoxumab)
Alternate Therapies
* Toxiod Vaccine (failed Phase III clinical trial)
* Probiotics (hit or miss)
* Recal Replacement (very cuccessful)
The spleen
- Most highly organized lymphoid organ
- FIlters blood
- Macrophages and dendritic cells trap microbes and antigens
- Present antigens to B and T cells
- Most common way that lymphocytes become activated to carry out their immune functions
Lymph nodes
- Most highly organized lymphoid tissue
- Filter lymph
- Microbes and antigens trapped and phagocytosed by macrophages and dendritic cells
- B cells differentiate into memory and plasms cells within lymph nodes
Nonspecific immune response
also called nonspecific resistance, innate immunity and natural immunity
- Acts as a first line of defense
- Offers resistance to any microbe or foreign material
- lacks immunological memory (does not evolve)
Specific Immune Response
aka acquired immunity, adaptive immunity, and specific immunity
- resistance to a particular foreign agent (adaptive to specific antigen)
- has “memory”: effectiveness increases on repeated exposure to agent
Specific and non specific immune response work together
Antimicrobial peptides
Cationic Peptides, what are the 3 classes? based on biological activity related to ability to damage bacterial plasma membranes
First class: linear, alpha-helical peptides that lack cysteine amino acid residues. (e.g., cathelicidin, produced by a variety of cells)
Second Class: defensins. Peptides that are open-ended, rich in arginine and cysteins, and disulfide linked. Found in neutrophils, intestial Paneth cells and intestinal and respiratory epithelial cells.
Third Class: larger peptides that are enriched for specific amino acids and exhibit regular structural repeats. (e.g., histatin, present in human salivia and has anti-fungal activity)
Cathelicidin (LL-37)
defense mechanism against bacterial, viral, or fungi infection of eukaryotic organisms
Broad spectru, activity
- Bacteria, Fungi, parasites
curved amphipathic helix-bend-helix
Bacteriocins
- peptides produced by normal microbiota
- lethal to related species
- produced by Gram-positive and Gram-negative cells
- e.g., colicins produced by E. coli
- e.g., lantibiotics produced by Gram-positive bacteria
Mucous Membranes
- Lysozyme- a muramidase
- cleaves or hydrolizes the B-1,4 brong between NAG and NAM
- Lactoferrin- sequesters iron (soaks up excess iron)
- Iron is required for growth
- can kill by another mechanisms - fenton rxn
complement
>30 serum proteins involved
- facilitates phagocytosis through opsonization
- bridges innate and adaptive immune system
- disposes of waste- dead cells and inflammatory products
opsonin
increases the efficiency of phagocytosis
Cytokines
- soluble proteins or glugoproteins that are released by one cell population that act as intercellular mediators or signaling molecules
- four families: chemokines, hematopoietins, interleukins, tumor necrosis faction (TNF) family
Granulocytes
- irregularly-shaped nuclei with two to five lobes
- cytoplasm has granules with reactive substances
- kill microbes, enhance inflammation
- three types: basophils, eosinophils, enutrophils (polymorphonuclear neutrophil (PMN))
Macrophages
- larger than monocytes, reside in specific tissues, highly phagocytic
- have a variety of surface receptors including (pattern recognition receptors)
- recognize pathogen associated molecular patterns (PAMPs)
Dendritic cells
- heterogeneous group of cells with neuron-like appendages
- present in small numbers in blood, skin, and mucous membranes of nose, lungs, and intestines
- also express pattern recognition receptors (PRRs)
- Main Goal: Phagocytosis and antigen processing -> display foreign antigens on their surfaces (antigen presentation) (present to T & B- cells)
Neutrophils
- have ability to explode and release contents
- extracellular traps
Phagocytosis
process by which phagocytic cells (monocytes, tissue macrophages, dendritic cells, and neutrophils) recognize ingest and kill extracellular micorbes
What are the two mechanisms for recognition of microbe by phagocyte?
-opsonin-independent (nonopsonic) recognition
-opsonin-dependent (opsonic) recognition
-phagocytosis can be greatly increased by opsonization
Opsonin-independant mechanism
pathogen recognition
- common pathogen components are non-specifically recognized to activate phagocytes
- singaling mechanism involved
- involves nonspecific and specific receptors on phagocytic cells
- four main forms
- recognition by lectin-carbohydrate interactions
- recognition by protein-protein interactions
- recognition by hydrophobic interaction
- detection of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs, e.g., toll-like receptors)
Opsonin-dependent mechanism
pathogen recognition
opsonized pathogens are recognized by the minding of opsonins to the phagocyte
Antigen
- self & nonself substances that elicit an immune response and react with the products of that response
- Antibody generators
- antigens are recognized as foreign
- Autoimmune disease: “self” recognized as foreign, elements of “self” become antigens
Epitope
regions/sites of the antigen that bind to a specific antibody or T-cell receptor
two types of aquired immunity
natural immunity and arificial immunity
Natural immunity, definition and the two types
Natural Immunity: is aquired through the noraml life experiences of a human and is not induced through medical means
Activite Immunity: is the consequence of a person developing his or her own immune response to a microbe (infection)
Passive immunity: is the consequence of one person receiving preformed immunity made by another person (maternal antibody- breast milk)
Artifiical immunity definition and two types
Arificial immunity: is that produced purposefully through medical procedures (also called immunization)
Active immunity: is the consequence of a perosn developing his or her own immune response to a microbe (vaccination)
Passive immunity: is the consequence of one perosn receiving preformed immunity made by another person (immune globulin therapy)
Antigens induce immune responses
Presence of antigen results in B cell activation and the production of antibodies
* antibodies bind to specific antigens, inactivating or eliminating them
* other immune cells also become activated
T-Cell Biology
- major players in cell-mediated immune response
- originate from CD34+ stem cells in the bone marrow but mature in thymus
- have major role in B cell activation
- immunologically specific and function in a variety of regulatory and effector ways
Major Histocompatibility Complex (MHC)
where is each class found?
Class I: found on all nucleated cells
Class II: Found on cells that process nonself materials. (Macrophages, dentritic cells etc)
Class III: Secreted products that have immune functions
What does MHC Class I do?
presents endogenously-derived antigens to cytotoxic T-cells
MHC Class II
What is it produced by? What does it do?
- Produced by: Macrophages, Dendritic cells, B cells, T cells
- Required for T cell communication
- Present exogenously-derived antigens
Types of T cells
- mature T cells are naive until they are activated by antigen presentation
- once activated they proliferate into effector cells and memory cells
- effector cells carry out specific function to protect host
- three types: T helper, cytotoxic T lymphocytes (CTL), an regulatory T cells
T-Helper Cells (TH Cells)
- Activated by antigens presented on MHC Class II
- 5 Types
- TH0 - undifferentiated precursor of 1, 2 & 17
- TH1 - promote CTL activity, mediate inflammation
- TH2 - stimulate antibody responses
- TH17 - found mainly in the skin/ epithelium
- respond to bacterial invaders
- T reg - recognize self antigens
- secrete IL-10to inhibit TH 1& 2 mediated inflammation
Cytotoxic T Cells
Naive CD8+ T-cells
- Expresses an antigen-specific T-cell receptor
- Mature into CTL upon antigen recognition (MHC Class I)
- kill the infected cell by the preforin pathway and Fas-FasL Pathway
T Cell Activation
requires binding a specific antigen
* occurs through antigen presentation which bridges MHC class II of the APC to the TCR of the T cell
* initiates a signaling cascade which involves other membrane-bound proteins and intracellular messengers
* a second signal is required for lymphocyte proliferation, differentiation, and expression of specific cytokine genes also occur
- if no 2nd signal, T cell becomes anergic (doesn’t respond to the specific antigen - becomes tolerant)
Superantigens
How do they differ to normal antigens?
- Stimulate stronger immune response than normal antigens by “trickling” T cells into activation although they have not been triggered by a specific antigen
- Stimulate T cells to proliferate nonspecifically
What do super antigens stimulate the release of?
stimulate release of massive quantities of cytokines form T cells. May result in circulatory shock and multiorgan failure. Examples such as staphlyococcal enterotoxin B that can cause good poisoning and toxic shock syndrome.
B-Cells
- antibody producing cells
- must be activated by an antigen binding the B-cell recepor
- Transmembrane antibodies
- Are specific for 1 antigen
- upon binding, signals to the B-cell nucleus
- Transmembrane antibodies
- Normally require TH to differentiate into antibody secreting cells
Antibodies
- found in blood serum, tissue fluids, and mucosal surfaces of vertebrate animals
- an antibody can recognize and bind antigen that caused its production
- 5 classes: IgG, IgM, IgA, IgE
Class Switching
- IgM is the first antibody to be made
- IgG then replaces IgM through class switching
- Any antibody class switch is mediated through this process
- antibody genes are split into many gene segments
Splice-site variability
DUring splicing, the junction between the V and D and J segments can be changed
- this changes the codons
- resulting in an amino acid change
Somatic hypermutation of V regions
- Somatic hypermutation - a region of DNA that can have a high rate of induced mutaion (estimates are 10^5v- 10^6 fold greater than rest of the DNA). These mutations are only in the cell undergoing the mutation and not in the germline
- V regions are susceptible to a high rate of somatic hypermutation
Clonal selection
Remember - B-cells only make 1 antibody each
- during a response, there are many different -cells generated. Each expressing a separate anitbody
how does Staphylococcus aureus Portein A brind?
- virulence determinant
- secreted and deposited on the S. aureus cell surface
- specifically binds antibodies
- binds the Fc region
Epidemiology
science that evalulates occurence, determinats, distribution, and control of health and disease in a defined human population
John Snow
studied Cholera
father of epidemiology
investivated cholera deaths in London
* interviewed families of deceased
* noticed they all had similar sympotoms
* identified that all of the deceased drank from the same water pump. Sewage pit has leaked fecal bacteria into the well.
Endemic disease
a disease that maintains a steady, low-level at a moderately regular interval
(in a specific population or populated place when that infection is constantly present, or maintained at a baseline level, without extra infections being brought into the group as a result of travel or similar means
Incidence
number of new cases
outbreak
the sudden, unexpected occurrance of a disease
Attack Rate
proportional number of cases that develop in a population exposed to the agent
Epidemic
an outbreak affecting many people at once
Index case
the first case in an epidemic
Pandemic
an increase in disease occurence over a large area (worldwide)
public surveillance
- public health
- use methodical approaches to identify a health problem
Typhoid Mary
was a carried but has no symptoms (asymptamatic) but infected peopel with her cooking
Typhoid fever in Philadelphia
How did they get the number of cases down?
implementing filtration of water which helped drop cases but even mroe casses dropped when chlorination of water began.
Morbidity
Morbidity = number of **new **cases of a disease during a specified time / number of individals in the population
Prevalence
Prevalence = **Total **number of cases in a population / total population
Mortality
Mortality = Number of deaths due to the disease / size of the total population with the same disease
common source epidemic
results form single common contaminated source such as food or water.
- such as food poisoning outbreaks
- cholera
propagated epidemic
results from the introduction of a single infected individual into a susceptible population which is propagated to others
- person to person
- host to host
- influenza
what can cause the susceptible population size to decrease after the introduction of an infected individual?
it can cross below the threshold density (from the graph) because people are gaining adaptive immunity or can be from a vaccine
Heard Immunity
- resistance of a population to infection and to spread of an infectious organism because of the immunity of a large percentage of the population
- level can be altered by introduction of new susceptible individuals into population
- level can be altered by changes in pathogen
- antigenic shift: major change in antigenic character of pathogen
- antigenic drift: smaller antigenic changes
Immunity: population resistent to the infection
What disease has the lowest heard immunity? Highest?
Lowest: Influenza 29%
Highest: Measles and Pertussis 94%
human reservoir
- infected humans most significant reservoirs, primarily of communicable diseases
- symptomatic infections: obvious source of infectious agents
- asymptomatic carriers: individual harbors pathogen with no ill effects
Non-human animal reservoirs
Disease transmitted by non-human animal reservoirs are termed zoonotic
- disease often more server in humans than in normal animal
stread of an org
Direct contact
- requires physical contact
- hands are the primary source of contact
stread of an org
Indirect contact
organism can live on a surface and then transfer to an individual
spread of an org
Droplet
- respiratory particles
- not only transmit the organism freely but some lie within the small drops of liquid that come out
How are infections tracked?
Centers for Disease Control and Prevention (CDC)
- monitors and tracks infections : hospitals and PCP’s resport directly to the CDC what infections they are seeing
What are the three types of vaccines?
- Whole-cell vaccines
- inactivated
- attenuated
- subunit vaccines
- DNA Vaccines
What disease were vaccines first made for?
Polio by Jonas Salk and Albert Sabin
Salk’s Vaccine
- first effective vaccine against polio
- is an** inactivated** polio vaccine (IPV)
- Formalin inactivated
Sabin’s Vaccine
- Live attenuated vaccine
- oral polio vaccine
Acellular or Subunit Vaccines
the use of specific, purified macromolecules derived from pathogenic microbes help avoid some of the risks associated with whole-cell vaccines
What are forms of subunit vaccines?
- capsular polysaccharides
- recombinant surface antigens
- inactivated exotoxins (toxoids)
Recombinant-Vector Vaccines
- pathogen genes that encode major antigens inserted into nonvirulent viruses or bacteria which serve as vectors and express the inserted gene
- released gene products (antigens) can elicit cellular and humoral immunity
DNA Vaccines
- DNA directly introduced into host cell via air pressure or gene gun
- when injected into muscle cells, DNA taken into nucleus and pathogen’s DNA fragment is expressed
- host immune system responds to foreign proteins produced
- many DNA vaccine trials are currently being run
RNA Vaccines
RNA is coated and injected into a patient. The RNA is traslanted in the cytoplasm to generate the required protein. Protein is expressed.
Moderna Vaccine
COVID-19
Lipid-coated mRNA that fuses with host cells. The Pfizer-BioNTech is a similar mRNA Vaccine.
Johnson & Johnson Covid 19 vaccine
Genetically-modified Adenoviral vector to deliver the antigen
covid vaccine
AstraZeneca covid vaccine
Encodes the spike protein antigen
Spuntnik V covid vaccine
Genetically-motified Adenoviral vector to deliver the antigen
Adjuvants
- An agent that stimulates the immune system to aid in immunization
- Commonly combined with the vaccine antigen
- Alum
bioterrorism
intentional or threatened use of viruses, bacteria, fungi, or toxins from living organisms to produce death or disease in humans, animals, and plants
Alexander Flemings discovory?
- Discovered a bacteriolytic substance - Lysozyme
- Found a halo of inhibition of Staphylocccus around a mold contaminant
- observed penicillin activity on contaminated plate
selective toxicity
ability of drug to kill or inhibit pathogen while damaging host as little as possible
therapeutic dose
drug level required for clinical treatment
toxic dose
drug level at which drug becomes too toxic for patient (produces side effects)
therapeutic index
ratio of toxic dose to therapeutic dose
side effects
undesirable effects of drugs on host cells
narrow-spectrum drugs
attack only a few different pathogens
broad-spectrum drugs
attack many differnt pathogens
cidal agent
kills microbes
static agent
inhibits growth of microbes
Minimal inhibitory concentration (MIC)
the lowest concentration of a drug that prevents growth of a particular organism
Minimal lethal concentration
the lowest concentration of a drug that kills the pathogen
Dilution susceptibility test
- drug is diluted in regular intervals (normally 2x)
- mueller-hinton broth is normally used
Kirby-Bauer method
Fresh bacteria are inoculated on a Myeller-Hilton plate. dried for 5 min and disks with antibiotic are added
E-test
- convenient for use with anaerobic pathogens
- similar to disk diffusion method, but uses strip rather than disk
- E-test strips containa gradient of an antibiotic
- intersection of elliptical zone of inhibition with strips indicates MIC
Antibiotics
Inhibitors of cell wall synthesis
Penicillins, Cephalosporins, Vancomycins
WHere is penicillin derived?
Derivatives of 6-aminopenicillanic acid. have as Beta-lactam ring
Clavulanic Acid
- B-lactamase inhibitor (enzyme that degrades Beta-lactam antibiotics)
- similar looking to Beta- lactamin to fool
- marketed with amoxicllin as “augmentin”
Caphalosporins
- orignially isolated form a fungus, Cephalosporium
- contain Beta-lactam ring
- 4 broad generations
Vancomycin
- Glycopeptide antibiotic
- produced by Streptomyces orientalis
- Binds to D-ala - D-ala
- Inhibits transpeptidation
- last resort drug
Protein synthesis inhibitor
Aminoglycodides
- Diverse class of antibiotics
- All contain: cyclohexane ring & amino sugars
- Most synthesized by different species of Streptomyces
- Bind to the 30S ribisomal subunit
- Bacterocidal (Kill)
3 common resistance mechanisms of Aminoglycoside
- Acetylation of an amino groups of the 30S subunits
- ATP-dependeent adenylation of a hydroxyl group
- ATP-dependent phosphorylation of a hyrodxyl group
protein synthesis inhibitor
Tetracyclines
- family with a common 4 ring structure
- similar to aminoglycosides (they bind the 30S subunit)
- Resistance Mechansims
- Efflux: pumps out the drugs from cytoplasm
- Ribosomal modification
- Drug modification, so if cant bind to the subunit
- Bacterostatic
protein syntehsi inhibitor
Macrolides
- 12-22 carbon lacton rings linked by one or more sugars
- Erythromycin binds to the 23S rRNA of the 50S subunit
metabolic inhibitors
Sulfanilamide
- analog of p-aminobenzoic acid (PABA)
- mutates by point mutation
metabolic inhibitor
Trimethoprim
- analog of dihydrofolic acid
- mutation is point? mutation
nucleic acid synthesis inhibitors
Quinolones
spontaneous mutation
- Nalidixic acid
- Norfloxacin
- Ciprofloxacin
