Exam 4

Question 1

Define term: primary pathogen

Answer 1

Primary pathogens can cause disease regardless of the host’s microbiota or immune system.

Question 2

Define term: opportunistic pathogen

Answer 2

Opportunistic pathogens can only cause disease in a host with compromised defenses.

Question 3

Define term: pathogenicity

Answer 3

Pathogenicity is the ability of an organism to produce an infectious disease in another organism.

Question 4

Define term: infection

Answer 4

Infection: successful colonization of a host by a microorganism, which can lead to disease

Question 5

Define term: infectious disease

Answer 5

An infectious disease is caused by a primary pathogen that can be a bacterium, fungus, virus, etc.

Question 6

Define term: communicable

Answer 6

communicable, which means they can be spread from person to person either directly or indirectly though an object

Question 7

Define term: contagious

Answer 7

contagious, meaning that can be spread directly from person to person

Question 8

Define term: focal infection

Answer 8

Focal infection: localized infection spreads to a secondary location (localized infection gains access to bloodstream)

Question 9

Define term: iatrogenic disease

Answer 9

Iatrigenetic disease: Diseases that are a result of a medical procedure

Question 10

Define term: local infection

Answer 10

Local: localized to a small area (i.e., infected hair follicle)

Question 11

Define term: nosocomial disease

Answer 11

Nosocomial disease: Disease contracted in a hospital

Question 12

Define term: zoonotic disease

Answer 12

Zoonotic disease can be passed from animals to humans.

Question 13

Define term: noncommunicable disease

Answer 13

Noncommunicable disease cannot be passed from human to human.1

Question 14

Define term: noninfectious disease

Answer 14

Noninfectious disease is not caused by a pathogen like cancer or a genetic disorder.

Question 15

Define term: resistance

Answer 15

Resistance: the capacity of bacteria to withstand the effects of a harmful chemical agent.

Question 16

Define term: systemic infection

Answer 16

Systemic: infection spreads throughout the entire body (i.e. chicken pox)

Question 17

Define term: virulence

Answer 17

Virulence refers to the degree that a pathogen causes illness or “how sick you get.”

Question 18

Be familiar with the term human microbiota and describe why they illustrate a symbiotic relationship.

Answer 18

Human Microbiota is the types of microbes present in an environmental habitat such as those on the human skin or in the gastrointestinal tract.

Roles of the Human Microbiota:
- Aid in food digestion.
> Produce enzymes to breakdown proteins, carbohydrates, and lipids
- Make molecules that we need but cannot produce.
> Bacillus, Pseudomonas, and Lactobacillus make vitamin B12
> Bifidobacterium make folate and biotin
- Development of the immune system
> The immune system does not properly develop in the absence of microbial stimulation
- Occupy space to prevent pathogen colonization

Question 19

Explain the different between a sign and a symptom. Define the term syndrome.

Answer 19

Signs: objective and measurable indicators of disease
i.e., changes in body temperature, changes in breathing rate or blood pressure

Symptoms: subjective indicators reported by the patient. Can’t be measured.
i.e., Nausea, loss of appetite, pain
Subject to memory bias, sometimes can be reported on a scale

Syndrome: a specific set of signs and symptoms.

Different causes can lead to the same symptoms or signs

Question 20

Explain the difference between acute, chronic, and latent disease.

Answer 20

Acute disease has a rapid onset and goes away over days or a week. Example: Flu

Chronic disease can change over weeks, months or years. Example: Stomach ulcers from H. pylori

Latent disease is where the pathogen goes dormant in the body without replicating for long periods of time Example: the virus that causes chicken pox and then shingles

Question 21

Apply Koch’s Postulates to determine which pathogen causes a disease.

Answer 21

1. The suspected pathogen must be present in all cases of disease and absent from healthy animals.
2. The suspected pathogen must be grown in pure culture.
3. Cells from a pure culture of the suspected pathogen must cause a disease in a healthy animal.
4. The suspected pathogen must be reisolated and shown to be the same as the original.

Question 22

Understand how Koch’s Postulates can be modified to determine if a gene makes a microbe pathogenic (EHEC example).

Answer 22

1. The phenotype (sign or symptoms of disease) should be associated only with pathogenic strains of a species
   - EHEC causes intestinal inflammation and diarrhea, whereas nonpathogenic strains of E.coli
2. Inactivation of the suspected genes associated with pathogenicity should result in a measurable loss of pathogenicity.
   - One of the genes in EHEC encodes for Shiga toxin, a bacterial toxin(poison) that inhibits protein synthesis. Inactivating this gene reduces the bacteria’s ability to cause disease.
3. Reversion of the inactive gene should restore the disease phenotype.
   - By adding the gene that encodes the toxin back into the genome(ex, with a phage or plasmid), EHEC’s ability to cause disease is restored.

Question 23

Understand how LD 50 is used to quantify virulence.

Answer 23

Virulence is how severe the disease is that the pathogen causes.
> We can quantify the virulence of a pathogen by using an LD50 curve.
- The LD50 is the dose of pathogen that leads to death in 50% of the animals.

Question 24

Identify the four characteristics necessary for a microorganism to be a successful pathogen.

Answer 24

For a pathogen to be “successful,” it must accomplish the following steps:
1. Gain entry to the host and adhere.
2. Travel to the location where it can cause infection (invasion)
3. Evade the host’s immune system for a time.
4. Cause damage to the host by multiplication, production of virulence factors and toxins

Question 25

Discuss the routes of entry and transmission of microorganisms into a host.

Answer 25

Pathogens enter a host through a portal of entry.
> Encounter with a potential pathogen is called exposure or contact.
> Major portals of entry include the skin, mucous membranes (respiratory tract, gut), or parenteral routes (breach in skin or mucosal membrane).
> Most pathogens are suited to a certain portal of entry

Question 26

Understand the importance of adhesion factors and recognize different types.

Answer 26

Pathogens must adhere to host tissues at the portal of entry.
>How do they stick?
Via adhesion factors:
- Adhesins on fimbriae, flagella, cilia, or capsids
- Spike proteins on viruses
- Glycocalyces (slime layer or capsules)
- Biofilm growth: Cells secrete extrapolymeric substance - (EPS)
. Protects again immune systems and antibiotics
. Not fast growing, but persistent

Question 27

Explain why invasion is important for pathogenesis and how invasion can occur.

Answer 27

Invasion is the dissemination of the pathogen through local tissue or body.

• Some pathogens make toxins that allow them to colonize, damage tissue, and penetrate deeper into the body.
• Some pathogens enter cells: obligate or facultative
  . Can evade immune system and use cell’s nutrients

Example: Salmonella and Shigella enter intestinal epithelial cells.
- These pathogens enter by endocytosis.
- They secrete a molecule that causes the host cell to make ruffles in its membrane that bring the bacteria inside.

Question 28

Identify the four mechanisms presented for evasion of the host immune system.

Answer 28

To be successful, the pathogen must resist the host immune system for a time.
. Phagocytes are immune cells that engulf pathogens.

Mechanisms to Evade Immune System
1. Destroy the Phagocytes:
. Some streptococci and staphylococci secrete a substance called leukocidin: kills white blood cells
2. Decrease the Rate of Phagocytosis:
. The bacterial capsule blocks the attachment of the phagocytic cell to the bacteria and interferes with phagocytosis.
3. Coat themselves with host proteins
. Staphylococcus aureus may coat themselves with host proteins.
. This makes the bacteria invisible to the host antigen-antibody protection system.
4. Viruses change the proteins on the outside of the virus.

Question 29

Explain how a pathogen can damage the host using spreading factors and toxins.

Answer 29

Tissue Damage by Secreting Enzymes Called Spreading Factors
- Hyaluronidase: Breaks down hyaluronic acid that hold connective tissue cells together
- Collagenase: Break down tissue fibers and cell membranes and contribute to cell destruction associated with gangrene.
- Neuraminidase: Made by Vibrio cholerae to break apart epithelial cells in the intestine.

Some pathogens cause tissue damage
. Produce toxins that are important in disease progression:

• Exotoxins: Usually proteins that are secreted from the bacterial cell into the surrounding medium.
• Endotoxins: Part of the Gram-negative cell wall
• Exotoxins: proteins released from the pathogen cell as it grows

Three categories:
1. AB toxins
2. Cytolytic toxins
3. Superantigen toxins

Question 30

Differentiate between endotoxins and exotoxins.

Answer 30

• Endotoxins: Part of the Gram-negative cell wall
• Exotoxins: proteins released from the pathogen cell as it grows

Comparison of Exotoxins and Endotoxins:
- Exotoxins: High potency, inactive at 60-80 degrees Celsius, and protein composition
- Endotoxins: Low potency, stable(resists at 120 degrees Celsius), and Lipopolysaccharide composition

Question 31

Explain the mechanisms of action of botulinum toxin, tetanus toxin, and cholera enterotoxin.

Answer 31

The Activity of Botulinum Toxin (AB toxin):
(a: normal muscle contraction) Upon stimulation of peripheral and cranial nerves, acetylcholine (A: acetylcholine includes muscle contraction) is normally released from vesicles at the neural side of the motor end plate. Acetylcholine then binds to specific receptors on the muscle, inducing contraction. (b: botulism) Botulinum toxin acts at the motor end plate to prevent release of acetylcholine from vesicles, resulting in a lack of stimulus to the muscle fibers, irreversible relaxation of the muscles, and flaccid paralysis.

The Activity of Tetanus Toxin (AB toxin):
(a: normal) Muscle relaxation is normally induced by glycine (G) release from inhibitory interneurons. Glycine acts on the motor neurons to block excitation and release of acetylcholine (A) at the motor end plate. (b) Tetanus toxin binds to the interneuron to prevent release of glycine from vesicles, resulting in a lack of inhibitory signals to the motor neurons, constant release of acetylcholine to the muscle fibers, irreversible contraction of the muscles, and spastic paralysis. For the purpose of illustration, the inhibitory interneuron is shown near the motor end plate, but it is actually in the spinal cord.

The Activity of Cholera Enterotoxin (affects small intestine)—an AB toxin:
Cholera toxin is an A B enterotoxin that activates a second-messenger pathway, disrupting normal ion flow in the intestine, resulting in potentially life-threatening diarrhea. The thumbnail photo of the three-dimensional structure shows a side view of the toxin, with the separate cell-binding B subunit and the enzymatically active A subunit.

1. Normal ion movement, Na+ from lumen to blood, not net Cl- movement
2. Infection and toxin production by V. cholerae
3. Activation of epithelial adenylate cyclase by cholera toxin
4. Elevated cAMP blocks Na+; net anion movement to intestinal lumen
5. Massive water movement to the lumen and ion loss trigger cholera symptoms.

Question 32

Describe the mechanisms of action of cytolytic toxins and superantigens.

Answer 32

Cytolytic toxins: Hemolysins
Destroy red blood cells.

(a: blood cells tuned black) Zones of hemolysis around colonies of Streptococcus pyogenes growing on a blood agar plate. (b: cells turned white) Activity of lecithinase, a phospholipase, around colonies of Clostridium perfringens growing on an agar medium containing egg yolk, a source of lecithin. Lecithinase dissolves the cytoplasmic membranes of red blood cells, producing cloudy zones of hemolysis around each colony.

Superantigen Exotoxins
> cause an overstimulation of the immune system
> can lead to shock and death
> generally due to a localized infection, but with systemic effects
> Gram-positive bacteria Staphylococcus aureus and Streptococcus pyogenes are major producers of exotoxin superantigens
- Superantigen poisoning can be triggered by food poisoning (in particular, that caused by the enterotoxins of S. aureus), by toxic shock syndrome, or by pyrogenic fever

Question 33

Explain the function of endotoxins in disease.

Answer 33

Endotoxins: (less potent)

Part of the Gram negative cell wall

Only small amounts may escape into the surrounding fluids from living bacteria.

Greater amounts of endotoxin are released when bacteria die and their cell walls disintegrate.

Large amounts needed to induce disease symptoms

Composed of polysaccharides and phospholipids.

Examples:
Salmonella typhi - > typhoid fever
Neisseria meningitidis -> meningococcal meningitis

Question 34

For the following diseases describe the characteristics of the organism, pathogenesis mechanism,
diagnosis/treatment/prevention methods (see the slides for details and an example)
o Whooping cough, rubella, Chikungunya, Lyme disease, cholera, botulism

Answer 34

For the diseases listed on the next slide research the following:

> Characteristics of the organism:
Name, morphology, other distinguishing features
Pathogenesis (How does it cause disease?):
System affected, symptoms, mechanism
Diagnosis and treatment/prevention

> Person to person diseases:
- Whopping cough
- Rubella

> Vector-borne diseases:
- Chikungunya
- Lyme disease

> Food-borne or water-borne diseases:
- Cholera
- Botulism

Question 35

Define the fields of epidemiology and public health.

Answer 35

• Epidemiology:
  the study of the occurrence, distribution, and determinants of health and disease in a population
• Public health:
  the health of the population as a whole
  > Identifying the nature of a disease and its transmission is a major goal of epidemiology
  > In developed countries, infectious diseases cause fewer deaths than noninfectious diseases. However, in developing countries, infectious diseases account for nearly half of all deaths.

Question 36

Describe the contributions of John Snow and Florence Nightingale to the field of epidemiology.

Answer 36

• John Snow (1813-1858) is the Father of Epidemiology.
  > Was able to tie an outbreak of cholera to a contaminated water pump in the Soho neighborhood of London
• Florence Nightingale (1820-1910):
  > Part of a group of nurses dispatched during Crimean war to take care of wounded soldiers
  > Took meticulous notes and presented a monthly report of cause of death, which turned out mostly be infectious disease

Question 37

Explain the different ways we can define a population.

Answer 37

Epidemiology looks at the prevalence of a pathogen in a population.
- How is a population defined?
> Can be geographically or if only some people are susceptible, may be more complicated.
> Is there a condition, behavior, or membership that makes an individual more susceptible?

• Once the population is defined, then we can analyze the disease with empirical measurements.

Question 38

Understand the main categories of Epidemiological studies.

Answer 38

There are two main types of epidemiological studies: observational and experimental.

1. Observational:
   > Data are gathered from participants through measurements or answers to interview questions.
   > No manipulation by scientists
   > Explores associations but doesn’t determine cause

Observational studies explore correlation, not causation.
There are different observational methods:

• Descriptive: gathers info to see how disease spread over time
  > Who gets sick, how many get sick, where do they get sick
• Analytical: goal is to generate hypothesis for cause
  > Compares affected and unaffected individuals
• Retrospective: gather data from past to present cases
• Prospective: follow patients and monitor their disease state throughout study

2. Experimental:
   - Scientists manipulate the subjects to explore the causative agent associated with a disease or assess treatment options or prevention
   - Much less common because of ethical reasons
   - Can use animals or human subjects
   > Koch’s Germ Theory of Disease
   - Example: Drug efficacy
   > Most often double-blinded to avoid the placebo effect

Question 39

Describe morbidity rate vs mortality rate, incidence vs prevalence, and common source epidemics
vs propagated epidemics.

Answer 39

Morbidity: the state of being diseased

> Morbidity rate:
- Number of affected individuals during a set period compared to the total population (cases per 100,000)
Mortality rate:
- Number of deaths due to the disease of a period compared to total population (deaths per 100,000)
Incidence: number of new cases in a population
Prevalence: total number infected with a disease (almost always higher than incidence since prevalence is cumulative)
Common source epidemics: contact with a contaminated material(eg: contaminated egg salad at a picnic)
- Many cases in a short time period
Propagated epidemic: spread person to person
- Slower spread, more difficult to track and eliminate

Question 40

Distinguish between sporadic, endemic, epidemic, and pandemic disease patterns.

Answer 40

Diseases in population can show different patterns.
- Sporadic disease: seen occasionally and without geographic concentration (example: tetanus, plague, etc.)
- Endemic disease: present continually in a population in an area at a low level (example: malaria in Brazil)
- Epidemic disease: sudden higher than expected incidence of a disease in a population (example: influenza with increased ER visits in a season)
- Pandemic disease: epidemic spreads world-wide (example: coronavirus)

Question 41

Understand how epidemics arise for disruptions in equilibrium of disease frequency due to changes in conditions/environment and antigenic drift or antigenic shift.

Answer 41

Epidemics signal a disruption in equilibrium of disease frequency.
> Why does this happen?
- Change in conditions or environment
- Antigenic drift (point mutation) or antigenic shift (gene shuffling between 2 different strains) in viruses can lead to evasion of immune system

Question 42

Explain how we can understand etiology by using the Germ Theory of Disease.

Answer 42

When studying an epidemic, scientists must first find the etiological (causative) agent;
- It’s not enough to observe an association
- Need to determine direct causation…how do we do that?
- Remember: GERM THEORY OF DISEASE by Robert Koch
1. The suspected causative agent must be absent from all healthy organisms but present in all diseased organisms
2. The causative agent must be isolated from the diseased organism and grown in pure culture
3. The cultured agent must cause the same disease when inoculated into a healthy, susceptible organism
4. The same causative agent must then be reisolated from the inoculated, diseased organism

Question 43

Explain the concept of a reservoir and the different kinds of reservoirs, including the example of Typhoid Mary.

Answer 43

Reservoirs are places where pathogens normally reside.
- Reservoirs can be living or non-living
> some pathogens can reside in soil or water, either naturally or as a result of contamination
- Humans: Communicable disease
> Carriers:
1. Passive carrier: not sick but, passes the pathogen to next host
2. Active carrier: those who harbor (and shed) and infective agent
> Might be during incubation period or convalescence
> Asymptomatic: do not show signs or symptoms: Typhoid Mary (Salmonella typhi)

Question 44

Describe the three main types of transmission. Know the three types of direct contact and contrast them with indirect contact. Compare mechanical vectors vs biological vectors.

Answer 44

3 main types of transmission:
1. contact: direct or indirect through fomites
- direct contract: when the pathogen is spread by physical contact of 2 people.
> Vertical direct contact: from mother to child during pregnancy, birth, breastfeeding
> Horizontal direct contact: other forms of contact
> Droplet transmission: when an individual coughs or sneezes, small droplets of mucus that may contain pathogens are ejected (Spread of <1m (if over 1m: airborne transmission))
2. Indirect contact: involves fomites that have become contaminated
- example: droplets on a doorknob
- A new host must touch the contaminated fomite and touch a susceptible portal of entry
2. vehicle: through water, food, or air
- Contamination water leads to 500,000 deaths worldwide according to the WHO
- Dust, aerosols, and long-distance droplet transmission are considered airborne vehicle transmission
- Food borne illness: often spread by the oral-fecal route
3. vector: an animal that carries the pathogen from one host to another
- Mechanical vectors: carry the pathogen from one host to the next without infecting themselves
- Biological vectors: animals that become infected themselves and pass the pathogen

Question 45

Understand the importance of herd immunity in disease control.

Answer 45

Herd immunity: Defined as the resistance of a group to infection due to immunity of a high proportion of the group
- If a high proportion of individuals are immune to an infection, then the whole population will be protected
- Immunized people protect nonimmunized people because the pathogen cannot be passed on, and the cycle of infectivity is broken

Question 46

Explain the missions of the CDC and the WHO.

Answer 46

The Centers for Disease Control (CDC) is the main national public health agency in the US.
- It protects the public from disease and injury
- Certain diseases called notifiable or reportable diseases must reported by a physician if he/she diagnoses a patient with one. 58 on the list
- Helps keep records on morbidity.
- The CDC publishes the Morbidity and Mortality Weekly Report (MMWR).
- Helps healthcare professionals keep on top of the latest epidemiological data

The World Health Organization is an agency of the United Nations that looks a disease data globally.
- Analyzes data about diseases.
- Implements strategies to prevent their spread
> Isolation of those with the disease
> Quarantine; includes healthy individuals who were exposed
> Immunization
> Vector control

The CDC and WHO prepare for emerging or reemerging diseases.
- Diseases that are either new to the human population or have become more prevalent in the last 20 years.

Question 47

Give examples of successful public health initiatives.

Answer 47

Public health agencies can recommend controls against spread of disease.
- Controls directed against common vehicles and major reservoirs
. Controls directed against the reservoir
> If reservoir is animal, it can be immunized or destroyed
> When humans are the reservoir, eradication can be difficult
- Those with disease can be quarantined, immunized, and treated
> Used by the W H O to eradicate smallpox
- Isolation, quarantine, and surveillance: controls directed against transmission of the pathogen
1. Immunization
- Diseases have been controlled using immunization Examples: smallpox, rubella, and tetanus
2. Quarantine
- Restricts the movement of an individual with an active infection
3. Surveillance
- The observation, recognition, and reporting of diseases

Question 48

Understand why emerging and reemerging infectious diseases are a threat.

Answer 48

Emerging and Reemerging Infectious Diseases
- Emerging and reemerging diseases
> Worldwide distribution of diseases changes rapidly
> Diseases that suddenly become prevalent are called emergent
> Reemerging diseases are those that have become prevalent after having been under control

Question 49

Distinguish between innate and adaptive immunity.

Answer 49

1. Innate (anatomical/physical barriers; first line of defense)

• General defenses
  Born with this type
• No memory of past exposures
• Every response is the same
• Immediate response

2. Adaptive

• Specific defense
• Learns how to kill specific pathogens when exposed
• Remembers this information for later exposures
• Each time we are exposed, we can kill the pathogen faster
• Delayed response

Question 50

Describe how the body knows something is foreign.

Answer 50

• Patrolling immune cells read the chemical “flags” on the outside of cells to determine whether they are foreign or not…
• Pathogen-associated molecular patterns (PAMPs) are components of pathogens that can be recognized by immune cells. Some examples of PAMPs are LPS, peptidoglycan, and flagellin.
• When the defense cell finds a cell without a “self flag”, the pattern recognition receptors (PRRs) on its surface such as Toll-like receptors bind to PAMPs on the outside of the microbe.
• This interaction leads to immune system response.

Question 51

Describe and give examples of anatomical and physical barriers that protect us from infection including the skin, mucous membranes, tears/saliva, sweat glands, stomach acid and secretions, and the normal microbiota.

Answer 51

Anatomical/ Physical Barriers:
1. Skin
- Comprised of tightly packed epithelial cells
- Top layers dead
> Comprised of keratin (protective waterproofing)
- Top layer is continuously shed to help remove microbes
- Dryness of skin helps inhibit growth
- It’s impossible for microorganisms to penetrate intact skin
- When skin is broken due to an injury (cut, burn, etc.) a subcutaneous infection develops
> If you have a cut, this line of defense is breached
> Using a band aid or disinfectant on the wound will prevent unwanted bacteria from coming inside the body
- Sebaceous glands on skin (chemical barrier):
> produces sebum (oil) which lowers the pH of skin and secretes antimicrobial fatty acids
> Some bacteria can metabolize sebum and cause the inflammatory response associated with acne
2. Mucous membranes
- Line gastrointestinal, respiratory and genitourinary tracts
- Less protective than skin.
- Outer epithelial cells secrete mucus (viscous glycoprotein) to trap microbes
- Mucus removed from body by cilia
Skin and mucosal membranes are made of tightly packed epithelial cells.
These structures between cells limit pathogens from gaining access to the bloodstream.
3. Tears/Saliva and Sweat Glands
- Tears :
> Protect eyes by constantly washing and preventing microorganisms from “settling down”
- Saliva:
> Produced by salivary glands
> Contains lactoperoxidase enzyme which can oxidize components of bacteria and viruses.
. Our sweat, tears, saliva, nasal secretions, and urine also contain an enzyme called lysozyme that breaks down peptidoglycans in cell walls of bacteria.
- Sweat Glands:
> Produce perspiration, which helps maintain body temperature at a constant level and remove microorganisms from the surface of the skin
> High lactic acid content and electrolytes inhibit microbial growth.
> Also has antimicrobial peptides
4. Stomach acid and Secretions
- Stomach Acid:
> Contains hydrochloric acid, enzymes, and mucus
> pH ~1.2-3 -> destroys most pathogens and toxins
> Food particles shield some bacteria.

• Secretions:
  > Defecation, urination, vaginal, vomiting all expel microorganisms
  . Helicobacter pylori can survive in acid conditions (neutralizes stomach acid).
  If it gets into the stomach, it causes ulcers because it triggers immune response.

5. Normal Micrbiota Function in Innate Immunity; If something is already living in a space, there is no room for new bacteria to grow
   - Normal microbiota:
   > Colonize the host without causing disease (“good niches”)
   > Prevent the overgrowth of pathogenic microorganisms
   > Maintains or alters pH levels, nutrient availability, oxygen levels
   > May inhibit growth of pathogen growth through competition
   Examples:
   - Vaginal secretions via Lactobacillus acidophilus produce lactic acid and keep pH too low for microbial growth by Candida albicans (causative agent of vaginitis).
   - In the large intestine, E.coli produce chemicals that inhibit the growth of Salmonella and Shigella.
   When the human microbiota is disrupted, pathogens can take advantage
   - taking broad spectrum antibiotics can affect the human microbiota
   - when the normal strains are wiped out in the gut, pathogens such as Clostridium difficile can colonize and cause severe diarrhea and even death
   - Fecal implants have been used to recolonize the normal flora to treat C.difficile infections.

Question 52

Describe the composition of blood, how blood cells are produced, and the functions of the thymus and lymph nodes.

Answer 52

What’s in our blood?
- Blood composed of plasma (liquid) and formed elements (cells and cell fragments)
- Erythrocytes (red blood cells)
platelets
- Leukocytes (White Blood Cells)
Thymus:
- Site of T cell development
- Produce T cell receptors (TCRs) as they develop.
- TCRs bind antigens on a pathogen to stimulate an immune response
Lymph nodes:
- Connected by lymphatic vessels which absorb fluid (lymph) that leaks out of blood vessels
- Lymph circulates through lymph nodes and back to the blood.
- Any pathogens that are in the lymph can be targeted by immune cells in the lymph nodes.

Question 53

Explain the process of phagocytosis and recognize the different types of phagocytes.

Answer 53

Phagocytosis: Non-specific mechanism
- When pathogens penetrate the skin and mucous membranes, they are attacked by phagocytes
- Phagocytosis- engulfment of microbes by phagocytic cells (neutrophils, dendritic cells, eosinophils, and macrophages).
- When an infection occurs, immune cells move to the infected area.
> Monocytes mature and become active phagocytic macrophages and dendritic cells.
- At the beginning of infection, neutrophils dominate the infected area, however as infection progresses macrophages concentration increases.
> The pattern of white blood cell activity during infection can be seen in the differentiated white blood cell count.

Stages of Phagocytosis:
1. Chemotaxis:
- Chemical signals attract phagocyte.

2. Adherence:
   - Phagocyte plasma membrane interacts with microbe.
   - Microbial capsules interfere with adherence.
3. Ingestion:
   - Microorganism brought into the phagocyte in a membrane bound vesicle called phagosome.
4. Killing/Elimination:
   - The phagosome fuses with a lysosome and the microbe is killed and digested.
   -Digested material is removed from cell (exocytosis)

Question 54

Describe how interferons and natural killer cells act in defense against viral pathogens.

Answer 54

Interferons protect cells from viral infection
- Interferons: small proteins produced by certain WBCs and tissue cells with anti-viral activity
> Infected cell produces interferons in response to infection by a virus.
> When cell dies it releases both new viruses and interferons.
> Interferon binds to cell surfaces of nearby cell to induce expression of anti-viral proteins by healthy cells.

Natural Killer Cells
- NK cells activate to destroy the target, which is likely a virally infected or cancerous host cell:
> Granzyme: an enzyme that induces programmed cell death (apoptosis)
> Perforin: pokes holes in (perforates) the target membrane

Question 55

Explain the process and steps of inflammation including fever and systemic inflammation/septic shock.

Answer 55

The four classic signs are redness, fever, swelling, and heat.
- An injury creates an opening in the skin, allowing pathogens to enter body tissues.
- Mast cells release histamines and macrophages release cytokines
- These chemicals attract more immune cells, such as neutrophils and dendritic cells, to help fight the infection.
- Histamines make blood vessels “leaky,” which allows immune cells and fluid to leak out of blood vessels into the tissues where the infection is occurring.

1. Fever
   - Certain cytokines, particularly I L-1, will cause the host’s body temperature to rise, causing a fever
   - Fever-causing cytokines are called pyrogens because they generate (gen) heat (pyro)
   - A fever is beneficial because it increases circulation rate, which allows leukocytes to get to the site of infection
   - It is also beneficial because some pathogens cannot tolerate the increased temperature
2. Systemic inflammation and septic shock
   - Widespread (systemic) inflammation can lead to shock as the increased vascular permeability decreases a host’s blood pressure, which can cause damage to multiple organs at the same time
   - Gram-negative bacteria are particularly dangerous because they contain L P S, which triggers a proinflammatory cytokine response
   > Examples: Salmonella species or Escherichia coli, which can be introduced into the peritoneal cavity or the bloodstream by a ruptured or leaking bowel

GOAL: to remove the injurious agent and its by-products or at least isolate it and to repair damaged tissue.

Question 56

Indicate what antigens are and how they relate to the immune system.

Answer 56

• Antigens are substances that causes your immune system to produce antibodies
  > Capsules, cell walls, flagella, fimbriae, toxins of bacteria, coats of viruses, proteins on surface of foreign blood or cancerous cells
  > The certain part of the antigen that is recognized is the epitope

Question 57

Describe the general structure and function of antibodies.

Answer 57

• Antibodies are produced to match each specific foreign antigen’s marker
  > Antibodies are produced by activated B cells
• Antibodies aid in the removal of antigens or prevent the ability of pathogens to cause widespread infection.

Question 58

Describe T and B lymphocytes in terms of where they are produced, and where they mature, and their functions including the types of t cells –cytotoxic T cells, helper T cells, and regulatory T cells.

Answer 58

Mediated by two types of cells:
B cells and T cells

> They undergo maturation, learning how to recognize an antigen as a foreign molecule and how to recognize self-antigens as the body’s own molecules, in different tissues

• B cells mature in the bone marrow and are important for antibody production in humoral immunity. (B-cells build an army of antibodies and let them do the fighting)
• T cells mature in the thymus and play a role in cell-mediated immunity. (T-cells fight with bacteria in hand-to-hand combat)

Steps in adaptive immune response:
- Antigen presentation by phagocytes and other infected cells
> Presented on MHC surface proteins
- T-cell activation
> Helper T-cells activate B-cells (also T-cell independent activation)
> Cytotoxic T-cells destroy infected cells
- B-cell expansion
> Antibody production
> Memory

T-independent antigens activate B cells without the help of T helper cells.
- Different antigens: usually lipopolysaccharides and polysaccharides
- Bacterial capsules can contain repeated T-independent antigens and produce weaker immune response without generating any memory cells.
- Infants usually do not have T-independent immune response until the age of 2.

Cell-mediated Immunity: T cells
- T-cells cellular-mediated immunity
- T-cells are SPECIFIC for a particular antigen:
> Through the T cell receptor (TCR) present on the surface of a T-cell
- T cells act directly against antigens and foreign cells when the antigen is presented by macrophages

Types of T cells
- Helper T cells
> Stimulate B and T cells
> B cells must be activated by helper T cells before they can produce antibodies
> AIDS: loss of helper T cells-no antibodies produced

• Cytotoxic T cells
  > Responsible for cell mediated immunity
  > Specific for a certain antigen
  > Directly attack cells physically and chemically by releasing perforins (which makes holes in the plasma membrane of the target cell) and granzymes which induce cell death.
• Regulatory T cells (used to be called Suppressor T cells
  > Inhibit B and T cell activity
  > Modulate (turn off) the immune response; Help prevent autoimmune disorders

Question 59

Understand how memory is acquired in adaptive immunity

Answer 59

Memory: The first antigen exposure induces multiplication of antigen-reactive cells, resulting in multiple copies, or clones. After a subsequent exposure to the same antigen, the immune response is faster and stronger due to the large number of responding cells.

Question 60

Describe the difference between active and passive immunity. Give or recognize examples of natural active and passive immunity and artificial active and passive immunity.

Answer 60

Naturally acquired:
1. Active immunity: antigens enter the body naturally; body induces antibodies and specialized lymphocytes (ex: immunity to chicken pox after you have it)
2. Passive immunity: antibodies pass from mother to fetus via placenta or to infant via the mother’s milk

Artificially acquired:
1. Active immunity: antigens are introduced in vaccines; body produces antibodies and specialized lymphocytes (ex: immunity to chicken pox after getting the vaccinated)
2. Passive immunity: preformed antibodies in immune serum are introduced by injection (ex: anti-venom)

Question 61

Explain what a vaccine is and how it relates to adaptive immunity.

Answer 61

Vaccine:
- Inject a tiny amount of weakened non-infectious virus or bacteria
- The body’s immune system will generate an immune response (antibodies).
- If the person becomes affected with the virus again in the future:
> Body already knows how to kill it and will kill it fast
- The person will not develop severe symptoms of the infection

Question 62

Explain the 3 different kinds of immune system failures, including allergic reactions.

Answer 62

1. Immunodeficiencies: these are cases when the immune system is compromised, so that it doesn’t work as well
   > Example: AIDS (acquired immune deficiency syndrome) is a virus that destroys helper T cells, thus reducing the effectiveness of cell-mediated immunity to fight infection or cancer.
2. Autoimmune diseases: The immune system incorrectly labels certain cell of its own body as foreign and eliminates them.
   > Example: Multiple sclerosis or systematic lupus erythematosus
3. Hypersensitivities: when the immune system starts to fight a perceived threat such as pollen or a food protein that is indeed harmless.
   > May be mediated by antibodies and give almost immediate response or may activate T cells and cause a delayed response.

What’s an allergy?
- Known as an immediate hypersensitivity
- Body has detected that matter as “foreign” and made antibodies and memory cells against it
- All further exposures to the agent will be classified as an attack on the body
- A full immune response will be mounted

Question 63

Understand how immunotherapy can be used to fight cancer.

Answer 63

• Immunotherapy is treatment that uses certain parts of a person’s immune system to fight diseases such as cancer. This can be done in a couple of ways: Stimulating, or boosting, the natural defenses of your immune system so it works harder or smarter to find and attack cancer cells
• Immunotherapy is a type of cancer treatment. It uses substances made by the body or in a laboratory to boost the immune system and help the body find and destroy cancer cells. Immunotherapy can treat many different types of cancer. It can be used alone or in combination with chemotherapy and/or other cancer treatments.

Question 64

Name the six elements that are most associated with organic molecules.

Answer 64

1. Carbon
2. Hydrogen
3. nitrogen
4. oxygen
5. phosphorous
6. sulfur

Question 65

Definite the term biogeochemical cycle.

Answer 65

Biogeochemical cycle: the cycling of inorganic material from organisms to their non-living environment

Question 66

Be able to explain the carbon cycle in terms of cycling between heterotroph and autotrophs and cycling between organic and inorganic pools.

Answer 66

The Carbon Cycle
- Living things on earth require carbon to build biological molecules.
- Photoautotrophs and chemoautotrophs can use external energy sources to reduce inorganic carbon (CO2) to organic carbon (glucose, etc).
- Heterotrophs require organic carbon they can break down for energy.
- Autotrophs take CO2 and convert it to organic carbon.
- Both autotrophs and heterotrophs take organic carbon and oxidize it to CO2.
- Phototrophic organisms produce organic or fixed carbon and reduce the level of carbon dioxide in the atmosphere
> Oxygenic phototrophic organisms can be divided into two groups: plants and microorganisms
= Plants dominate terrestrial environments
= Microorganisms dominate aquatic environments
- Carbon is cycled through all of Earth’s major carbon reservoirs
> Includes atmosphere, land, oceans, freshwater, sediments, rocks, and biomass
> All nutrient cycles are linked to the carbon cycle, but the nitrogen (N) cycle links particularly strongly because, other than water (H2O), C, and N make up the bulk of living organisms
- Reservoir size and turnover time are important parameters in understanding the cycling of elements
- C exists in different forms in different reservoirs:
> Inorganic carbon in rock (limestone): largest reservoir
> Organic carbon
> Gaseous carbon (CO2, methane, CO)
- Exchange between reservoirs can be very slow or very fast
> Fastest for atmospheric CO2

Carbon turnover
- CO2 is returned to the atmostphere by respiration and decomposition as well as by human-related (anthropogenic) activities
> Microbial decomposition is the largest source of CO2 released to the atmosphere
> Since the Industrial Revolution, human (anthropogenic) activities have increased atmospheric carbon by 40%

Question 67

Define greenhouse effect and how it relates to the carbon cycle.

Answer 67

Greenhouse gas: This rise in carbon dioxide has led to steadily increasing temperatures worldwide (global warming) because carbon dioxide

1. Some solar radiation is reflected by the Earth and the atmosphere
2. Most radiation is absorbed by the Earth’s surface and warms it
3. Some of the infrared radiation passes through the atmosphere.
   - Some is absorbed and re-emitted in all directions by greenhouse gas molecules.
   - The effect of this is to warm the Earth’s surface and the lower atmosphere.
   - Infrared radiation is emitted by the Earth’s surface

• The 2 major end products of decomposition are methane (CH4) and carbon dioxide (CO2)
  > CH4 is potent greenhouse gas and is produced in anoxic (or oxygen-free) environments
  > Most methane is converted to carbon dioxide by methanotrophs; however, some enters the atmosphere

Question 68

Distinguish between methanotrophs and methanogens.

Answer 68

• Methanotrophs: microorganisms that use methane for their energy source
• Methanogens: microorganisms that produce methane as a byproduct of metabolism

Question 69

Understand how methane plays a role in climate change and methods that can be used to mitigate its effects.

Answer 69

Methanogens and methanotrophs: considerations for climate change

• Methane is about 30x more potent as a greenhouse gas than CO2.
• Responsible for about 30% of global warming.
• About 70% of total methane emissions are from biological sources.
• Produced biologically by methanogens as the final step in the degradation of organic matter.

Question 70

Describe the nitrogen cycle and identify the roles that prokaryotes play in nitrogen fixation, nitrification, and denitrification.

Answer 70

Nitrogen Cycle:
Nitrogen
- key constituent of cells
- exists in several oxidation states
- four major nitrogen transformations:
1. nitrification
- Nitrification: oxidizing ammonia compounds (NH3, NH2) to nitrate (NO3) or nitrite (NO2)
- Nitrifying bacteria are aerobic chemoautotrophs that use this oxidation to produce energy.
- Once nitrification is complete, the nitrogen can then be assimilated into organic molecules by organisms.
- In marine systems, nitrates can contribute to eutrophication (accumulation of nutrients) in the aquatic environments, which causes algal blooms then death of aquatic organisms.

2. denitrification
   - Nitrate and other nitrogen oxides are converted to N2
   NO3–>NO-2–>NO–>N2O–>N2
   - Process is strictly anaerobic, but most denitrifiers are facultative aerobes and prefer to use oxygen as their terminal electron acceptor
   - This activity reduces soil nitrogen content and therefore its fertility
   - But is important in waste treatment to remove nitrogen from effluent
3. anammox
4. nitrogen fixation
   - Symbiotic bacteria incorporate atmospheric nitrogen into organic molecules: Nitrogen fixation
   - Atmosphere is almost 80% nitrogen, but it is in the form N2 or N≡N
   - Eukaryotes cannot break this triple bond
   - Some bacteria can reduce N2 to NH3

Many biological molecules including proteins and nucleic acids include nitrogen
- Getting nitrogen into organisms is difficult because much of the earth’s nitrogen is environmental N2, which is triple-bonded and unusable by plants.
- Prokaryotes play an important role by doing nitrogen fixation.

Question 71

Define eutrophication and how it relates to the nitrogen cycle.

Answer 71

• Human activities put more nitrogen and phosphorous into the environment via runoff.
• This leads to eutrophication in the aquatic environments and anerobic conditions.

Examples:
1. Excess nutrients are applied to the soil. 2. Some nutrients leach into the soil and later drain into surface water. 3. Some nutrients run off over the ground into the body of water. 4. The excess nutrients cause an algal bloom. 5. The algal bloom reduces light penetration. 6. The plants beneath the algal bloom die because they cannot get sunlight to perform photosynthesis. 7. Eventually, the algal bloom dies and sinks to the bottom of the lake. Bacterial communities begin to decompose the remains, using up oxygen for respiration. 8. The decomposition causes the water to become depleted of oxygen if the water body is not regularly mixed vertically. Larger life forms, such as fish die.

Question 72

Describe the sulfur cycle.

Answer 72

Sulfur is essential for the synthesis of certain macromolecules
- It is part of certain amino acids and in certain vitamins.
- Several microorganisms are responsible for carrying out the sulfur cycle in complex processes.
- Anoxygenic photosynthetic bacteria and chemoautotrophic archaea and bacteria use hydrogen sulfide as an electron donor.
- H2S is oxidized it first to elemental sulfur (S0), then to sulfate.
- Decomposing bacteria remove sulfate groups and make hydrogen sulfide and release it back into the air.

Question 73

Explain what bioremediation is and how prokaryotes are involved including the examples of oil spill cleanup, plastic degradation, and wastewater treatment.

Answer 73

Bioremediation uses microbial metabolism to remove xenobiotics and other pollutants.
- Xenobiotics are substances made by humans and released into the environment.
- Examples of such contaminants: adhesives, dyes, lubricants, oil and petroleum products, pesticides, etc.
- Two very concerning xenobiotics:
> polycyclic aromatic hydrocarbon (PAH, carcinogen from crude oil)
> trichloroethylene (TCE) which is a ground water contaminant

Bioremediation can happen at the site (in situ) or transported to another location (ex situ).
- In situ is when the remediation happens at the original contamination site.

Bioremediation can happen at the site or transported to another location.
- Can use native species or introduce foreign species who can degrade certain contaminants.
- Scientist might alter conditions to encourage degradation.
> For example, Rhodococcus and Pseudomonas are known for their ability to degrade many environmental contaminants, like those found in oil.

Environmental Consequences of Large Oil Spills and the Effect of Bioremediation
- Prokaryotes have been used in bioremediation of several major crude oil spills
- The rectangular plot (arrow) was treated with inorganic nutrients to stimulate bioremediation of spilled oil by microorganisms, whereas areas above and to the left were untreated.

Bioremediation and Microbial Degradation of Major Chemical Pollutants: Chlorinated Organics and Plastics
- Plastics of various types are xenobiotics that are not readily degraded by microorganisms
- The recalcitrance of plastics has fueled research efforts into a biodegradable alternative (biopolymers or microbial plastics)

Wastewater Treatment
1. Wastewater
- Domestic sewage or liquid industrial waste
- “Gray water” is the water resulting from washing, bathing, and cooking
- Sewage is water contaminated with human and animal fecal material
2. Wastewater treatment
- Relies on industrial-scale use of microbes for bioconversion
- Following treatment, the discharged treated wastewater (effluent water) is suitable for
> release into surface waters
> release to drinking water purification facilities

Question 74

Explain how bacteria are involved in the food industry.

Answer 74

The food industry also uses bacteria to make certain foods
1. Fermentation
- Bread
- Beer and wine
- Cheese, yogurt
- Pickles, sauerkraut, kimchi, olives
> Acids produced during fermentation lower the pH enough to suppress the growth of spoilage organisms
- Soy sauce, tofu, miso
- Lactic acid bacteria such as Lactobacillus, Lactococcus and Streptococcus are used in the manufacture of dairy products
2. Food preservation
- Preventing the incorporation of microorganisms into food
> Sanitation
- Preventing the multiplication of microorganisms in food
> Chemical preservatives
> Processing at high temperatures
> Refrigeration
> Pasteurization
> Radiation
> Desiccation
> Bacteriophage (FDA, 2006, ready –to eat meat products)