Microbiology 002, Exam 4

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There are lots of pathogens and infections that can cause throat irritation and/or inflammation but in the following lecture I'll present 3 that specifically infect the throat:

- Adenovirus serotypes 1-7: cause pharyngitis, conjunctivitis and pharyngoconjunctival fever - Corynebacterium diphtheriae: cause Diphtheria - Streptococcus pyogenes (Group A strep): cause Strep throat and the possible complications of Strep throat like Scarlet Fever, Rheumatic Fever and Glomerulonephritis

There are 2 steps to protein expression

- Transcription is where the enzyme RNA Polymerase copies a gene from the DNA and the copy is made of mRNA (messenger RNA.) - Translation is where the mRNA is used to make a protein. This happens on the ribosomes and relies on tRNAs (transfer RNAs) reading the mRNA and bringing in amino acids (the building blocks of proteins.)

Transcription summary

-The small subunit binds to mRNA, when it finds that start codon AUG, then the large subunit attaches, at this point, we have mRNA, ribosome assembling around to the mRNA -The first tRNA is going to come in and bind to this P site of ribosome, and his anticodon is binding to the start codon of mRNA, bringing in first amino acid (methionine) -2nd codon of mRNA, lines up with A site, second tRNA, binds anticodon to codon to mRNA, binding thru complimentary based pair rules -This second tRNA is bringing in his amino acid, which is leucine. -A protein bond forms between the amino acids to attach them together -The ribosome begins to shift, pull the mRNA thru, that forces our first tRNA thru the exit tunnel and out -Gonna move this tRNA into the P site, and the 2 amino acids are connected to one another -Next the 3rd codon is now lining up with the A site, so the 3rd tRNA can come in, once tRNA is in there -The anti codon of the 3rd codon is binding with the mRNA, brought in 3rd amino acid, little peptide bond forming between these two -The mRNA is moved once more thru the ribosome, 2nd tRNA is kicked out thru the exit tunnel, this 3rd one in our P site, 3 amino acids connected together, the 4th tRNA enter into A site, gonna bind to the codon of the mRNA thru anticodon, bringing in 4th amino acid, peptide bond forms between them, then gonna pull mRNA thru, kicking out the old -Basic process here, the ribosome assembles around the mRNA, scans for that start codon, and then the tRNA enter in into ribosome sites one at a time binding their anticodon to the codon of mRNA, they bring in amino acids, the amino acids attach together to form protein, and then ribosome moves mRNA thru, kicks out the old tRNA, allows new tRNA in, and step by step, that's how protein is built.

Glycolysis (occurs in the cytoplasm)

1 glucose, 2 ATP and 2NAD+ in, 2 pyruvate, 4 ATP (net 2 ATP out) and 2NADH out.

Summary of transcription

1. RNA poly binds to the promoter upstream of the gene 2. RNA poly adds nucleotides complementary to the template strand of DNA in the 5 to 3 direction 3. Uracil is used in place of Thymine 4. RNA poly falls of the DNA and stops transcription at the termination signal.

Role and net production of: ATP, NADH, FADH2, CO2

2 pyruvate, 4 ATP (Net 2 ATP), 2 NADH (glycolysis) 2 ATP 8 NADH 2 FADH 6 CO2 (krebs) 30-32 or 32-34 ATP, 6 H2O and 6 CO2 (ETC) ATP is energy for all cells, pyruvate is used as product for the krebs cycle, NADH and FADH2 are products used in ETC to have energy released as H+. CO2 is a waste product from the reactions.

Electron transport system (occurs in the matrix of the mitochondria)

8 NADH and 2 FADH2 energy move into ETC, in which they are oxidized. Chemiosmosis occurs in which H+ ions are pumped into mitochondria inner membrane space. These H+ ions get pumped back into matrix by ATP synthase in which ATP is created from ADP and inorganic phosphate (PI) producing 30-32 ATP, 6 H2O and 6 CO2.

What is ARDS?

Acute Respiratory Distress Syndrome (ARDS) is a severe, life-threatening medical condition characterized by widespread inflammation of the lungs, fluid accumulation, and breakdown of the cells lining the lung's blood vessels.

Describe the transmission, life cycle, signs and symptoms, diagnostics of the Intestinal Nematodes: Ascaris lumbricoides:

Ascaris lumbricoides (intestinal Nematode) • Basics o Most common helminth infection worldwide. 2nd highest worm infection in the U.S. o Transmission is via ingestion of eggs (5 F's - feces, food, flies, fingers, fomites). o Low wormloads are well tolerated, but a large wormload can cause serious illness. • Pathogenesis o Larvae hatch in small intestine >> exit the intestinal wall >> migrate through the vasculature into the liver, heart and lungs. (Liver to Lung Migration) o In lungs: Larvae burst through the alveoli, they crawl up trachea/pharynx where they are coughed up and swallowed. o Once in the GI, they mature in adults. Females release eggs in stool (up to 200,00 eggs per day) • Infections o Ascariasis - Adults stay in intestines; low worm burdens are often asymptomatic. o Heavy worm burden > tangled mass > abdominal pain and intestinal obstruction. o Adults may move to other parts o In devolving nations, cause malnourishment, physical and mental damage by starving host.

Describe the transmission, life cycle, signs and symptoms, diagnostics of the Intestinal Nematodes: Hookworms: Nevator mericanus (New World and Ancylostoma duodenale (Old World). {Hookworms}

Basics and Pathogenesis o Larvae hatch from eggs in human feces >> contaminate soil >> larvae penetrate skin (usually between toes of bare feet) >> cause "ground itch." o Larvae enter the circulation and perform a liver-lung migration similar to Ascaris o Adults mature in small intestine with females releasing -20,000 eggs per day. o Diagnose by stool examination, looking for eggs. • Infections o Chronic anemia - Hookworms hang onto intestinal mucosa with teeth, secrete anticoagulant and suck the host's blood. o Loss of blood > chronic anemia and severity is proportional to worm burden. o Severe infections > weight loss and fatigue, particularly if nutrition is poor. Infection in young children may lead to developmental delays.

The overall equation for aerobic respiration

C6H12O6 + 6O2 >> 6CO2 + 6H2O

Protistan-Caused Diarrhea For the following protozoans that cause diarrhea, know name and type of protozoan, morphological characteristics, transmission, symptoms of infection, diagnosis, and unique information relevant to each. 1.

Cryptosporidium ➢ Cryptosporidium spp. is an Apicomplexan, a protistan group of animal parasites we first encountered when learning about malaria. ➢ The most common way to be infected with cryptosporidiosis is through the consumption of water contaminated with Cryptosporidium spp. cysts. o The cysts enter the water when fecal matter from infected vertebrates is introduced, and they can last for several days to weeks in the water. o Common sources of human outbreaks are in water parks or municipal water systems. ➢ Cryptosporidium is resistant to chlorine and oftentimes swimming pools have to be shut down and drained when fecally-contaminated. ➢ Symptoms arise within 2 to 10 days of consuming the contaminated water, and can last for a week or more. o The primary symptom is watery diarrhea, but other symptoms include stomach pain, nausea, vomiting, fever, weight loss, and dehydration. ➢ The illness is most severe for immuno-compromised patients, and healthy patients may not experience any symptoms. ➢ Proper diagnosis is made by examining the patient's stool. o The stool can be examined for cysts via microscopy using an acid fast stain, or it can be checked for Cryptosporidium anitgens via ELISA.

Describe the transmission, life cycle, signs and symptoms, diagnostics of the Intestinal Nematodes: Enterobius vermicularis(Pinworms)

Enterobius vermicularis (Pinworm) • Basics o Most common helminth infection in the U.S. and affects 200 million people worldwide. o Infection most prevalent among small children (infects 20% of all school children) and institutionalized persons. o Pinworms seldom produce serious disease but may cause considerable discomfort. • Pathogenesis o Eggs ingested in household dust, from contaminated clothing or bedding. o Eggs hatch in small intestines; larvae mature in large intestines. o Adult females migrate out of rectum to deposit eggs. o Infective eggs can spread to the same person (autoinfection) or others by putting contaminated fingers into their mouth. • Infections o Enterobiasis - The most typical symptom is intense perianal itching. o Anal pruritus in small children leads to loss of sleep, irritability and frequent scratching of the anal and vulval areas. • Diagnosis o Sample perianal skin for eggs using scotch tape early in the morning. o Microscopically check for eggs on tape.

Transcription

Making RNA copy (tRNA, mRNA, rRNA) from DNA. ➢ Major player here is mRNA. RNA molecules used during translation to make proteins.

Other common causes of acute otitis media are:

Moraxella catarrhalis (3rd most common cause) - a gram negative diplococcus Staphylococcus aureus Streptococus pyogenes

Describe the transmission, life cycle, signs and symptoms, diagnostics of the Intestinal Nematodes: Ascaris lumbricoides, Hookworms, Enterobius vermicularis(Pinworms)

Nematodes (Roundworms) o Intestinal nematodes mature in the small intestine. o Adults attach to the intestinal wall via anterior oral hooks or cutting plates. o Examples of intestinal nematodes include the giant intestinal round worm, hook worms and pinworms.

Compare and contrast the morphological characteristics of the 3 types of Helminths

Parasitic Worms (Helminths) ➢ Multicellular animals with organs for reproduction, digestion, movement, and protection ➢ Approximately 50 species parasitize humans ➢ Distributed worldwide; some restricted to certain geographic regions with higher incidence in tropics ➢ Acquired through ingestion of larvae or eggs in food; from soil or water; some are carried by insect vectors. ➢ Afflict billions of humans. Nematodes (Roundworms) • Round non-segmented bodies with a complete digestive trat. • Flatworms - flat, multi-cellular worms which include: o Trematodes (Flukes) o Which are flat, non-segmented bodies with "sucking" mouth parts. Cestodes (Tapeworms) o Which are long and segmented.

Human Rhinovirus (HRV) ➢

Rhinoviruses belong to the Picornavirus family which are non-enveloped, RNA viruses ➢ Main cause of the common cold (30-50% of cases) ➢ Over 110 serotypes cause rhinitis with many strains circulating in the population at one time. ➢ Infections peak around summer and early fall. ➢ Transmission from contaminated hands and fomites. ➢ Rhinoviruses are sensitive to acidic environments (stomach) and their optimum temperature is 33 C, the average temperature of the nose. ➢ Common cold symptoms: Headache, chills, fatigue, sore throat, cough, and rhinorrhea. ➢ The usual therapy is to relieve symptoms with various cold remedies and cough syrups that contain nasal decongestants, antihistamines, and analgesics. ➢ Best prevention is hand-washing and care in handling nasal secretions.

Role of ribosomes in translation

Ribosomes provide the site of Translation ➢ The ribosome is just not protein, made of partial rRNA Has 2 subunits, large and small subunit ➢ Made of both protein and rRNA ➢ Has 2 main binding sites of tRNA, A and P sites, the E site doesn't really exist, exit tunnel for tRNAs ➢ When ribosome is functioning and active, the mRNA is between the 2 subunits and tRNAs, the anticodon can bind to codon of mRNA, and are bringing in 2 different amino acids Piece of mRNA made from transcription, out in the cytoplasm and here ribosome is going to assemble around mRNA, small and large unit will assemble around it. ➢ All activity starts at start codon, AUG. ➢ When it finds AUG, it allows 1st tRNA to bind its anti-codon to mRNA's codon, to bring in 1st amino acid, methionine. ➢ At the A site, we have tRNA coming in bind its 2nd anti-codon to mRNAs 2nd codon and bringing in the 2nd amino acid, peptide bond forms between the amino acids and wind up on the tRNA, and shifts, as it moves forward, it moves to the next codon and kicks out the 1st tRNA to make space for the new one, ejected out of the exit site.

For the enteric bacteria, also know the above information, including MacConkey agar results and how to identify if they are lactose and non-lactose fermenters. Which are invasive bacteria? Be sure to also know the mechanism of actions of the enterotoxins. Enterobacteriaceae Family

Small gram-negative rods, facultative anaerobes. ➢ All ferment glucose, reduce nitrates to nitrites, oxidase negative, and catalase positive ➢ Many inhabit soil and water and some are common occupants of the large intestine ➢ The enteric pathogens are the most frequent cause of diarrheal illnesses through the action of their enterotoxins. ➢ Divided into: o Fecal Coliforms (Lactose Fermenters) o Non-Coliforms (Non-Lactose Fermenters) ➢ MacConkey Agar is a Selective and Differential media for distinguishing between lactose and non-lactose fermenting Enterobacteriaceae. ➢ Enterobacteriaceae Antigens and Virulence Factors o Classified by 2 Surface Antigens: • O - Cell Wall Antigen • H - Flagellar Antigen • K - Capsule/Fimbrial Antigen o Virulence Factors: • Fimbriae - for adherence • Endotoxin - LPS • Exotoxin - mostly enterotoxins causing gastroenteritis

Prevention of dental carries? o

The best way to prevent dental caries is through dietary restriction of sucrose and regular brushing and flossing to remove plaque from teeth. o In the United States, fluoride is added to water to increase tooth hardness by remineralizing teeth that may have begun to demineralize because of plaque buildup. o New strategies of prevention include the use of probiotics which introduce a mix of bacteria found in healthy mouths. • These have been shown to reduce the levels of S. mutans and other bacteria associated with periodontal disease. o Several vaccines are in development that aim to prevent dental caries by producing antibodies that bind and block the proteins bacteria use to attach to teeth

Otitis Media (Ear Infection)

Viral infections of the upper respiratory tract (colds, flu, pharyngitis) can lead to inflammation of the eustachian tubes and the buildup of fluid in the middle ear. When this happens, it can lead to bacterial multiplication in those fluids and hence an ear infection called acute otitis media. ➢ Happens mostly to children than adults, more likely to experience because they have trouble fighting infections due to their immune systems still developing. ➢ Unusual irritability, difficulty sleeping, tugging at ears, fever, fluid coming out of ear, loss of balance, unresponsiveness to quiet sounds are common symptoms. ➢ The most common cause of acute otitis media is Streptococcus pneumoniae. ➢ Endogenous pneumococcus can gain access to the chamber of the middle ear by way of the eustachian tube thanks in part to the fluid build up and inflammation caused by a concurrent viral infection. ➢ When the pneumococcus encounters the mucus and fluid in the middle ear, it multiplies rapidly, leading to an increased inflammatory response and pus production. ➢ As the fluid and pressure increase in the middle ear, symptoms develop that include sensation of fullness or pain the ear and loss of hearing. ➢ The second most common cause of otitis media is Haemophilus influenzae (pictured below). Similar to the pneumococcus, it predominantly causes ear infection in young children and it may arise from endogenous infection following a viral upper respiratory tract infection. ➢ Haemophilus influenzae type B is especially notorious for causing epiglottitis (inflammation of the epiglottis). ➢ The epiglottis is a flap in the throat that prevents food from going down the trachea. ➢ Because of its location in the airways, inflammation of the epiglottis can interfere with breathing and is life-threatening. ➢ Shown in the image below is an inflammed epiglottis that appears cherry red in color. ➢ Children with epiglottitis have difficulty and painful swallowing and they are often seen drooling heavily to avoid swallowing at all. ➢ Other symptoms include fever, hoarseness of voice and wheezing due to airway obstruction. Epiglottitis can lead to a surgical emergency if the inflammation is too severe. ➢ Fortunately, with the introduction of the Hib vaccine, the incidence of epiglottitis has decreased dramatically

Krebs cycle (occurs in the mitochondria)

Yield per pyruvate (so since there is 2 pyruvates going into Krebs cycle, x2) o 1 ATP o 4 NADH o 1 FADH2 o 3 CO2

Sinusitis

an inflammatory condition of any of the four pairs of sinuses in the skull (see picture below). ➢ Sinusitis is commonly called a sinus infection and can be caused by allergy or by infectious agents which include a variety of viruses or bacteria. ➢ In fact, the same bacterial organisms that cause otitis media can also cause sinusitis (in the same order of most common to least common). ➢ Bacterial sinusitis is not a communicable disease and infections most often arise from the normal microflora of the host following a viral URI (e.g. common cold).

Leptospirosis has two phases:

o 1) An early phase where L. interrogans can be found in the blood and CSF. Symptoms include fever, headache, muscle aches, conjunctivitis and vomiting; o 2) The immune phase which causes meningitis, and Weil's Syndrome, a condition characterized by kidney invasion, liver disease, jaundice, anemia, and neurological disturbances. • Death can result if left untreated due to severe kidney and liver damage. ➢ Leptospirosis can be treated with antibiotics, the sooner the better. ➢ Prevention includes a vaccine only made available for military personnel who train in jungle regions and animal care and livestock workers. ➢ For the general population, the best prevention is wearing protective clothing and avoid swimming and wading in natural water sources that are frequented by livestock.

How do people acquire pneumoniae pneumonia? Is it contagious? Who is at a higher risk?

o If S. pneumoniae moves from the normal flora location of the nasopharynx into the lungs, it can cause pneumonia (hence being called the pneumococcus): o It is contagious

Understand the progression of pertussis (whooping cough and stages) including the tissues affected, major symptoms and vaccine

• B. pertussis produces fimbriaelike adhesion molecules that allow it to find and bind to the ciliated cells that line the upper respiratory tract. o These ciliated cells are tasked with removing particles from the respiratory tract before they can enter (and possibly damage) delicate lung tissue. • B. pertussis also produces exotoxins that destroy and remove the ciliated cells. • Without these cells, mucus will build up in the lungs and block the airways. • Symptoms include the "whooping noise" from coughing fits, runny nose, sneezing (most contagious during runny nose and sneezing). • Although there is a vaccine available (the DTap vaccine), whooping cough infections have reached epidemic proportions in California twice in recent history (2010 and 2014). • This is due to a combination of childhood vaccinations not lasting through adulthood and a low vaccination rate in general. • Teenagers and adults should obtain a booster vaccination prior to contact with small children and pregnant women, as whooping cough in infants can be deadly. o For example, infection in adulthood only requires hospitalization approximately 5% of the time, while infants and children up to age 4 will require hospitalization 50% of the time.

Blastomyces dermatitidis

• Causes blastomycosis • Thermally Dimorphic • Free-living species distributed in soil and rotting wood of a large section of the Midwestern and southeastern U.S. • Inhaled 10-100 conidia convert to yeasts and multiply in lungs • Symptoms include cough and fever. • North American Blastomycosis o Fungal pneumonia similar to histoplasmosis but not as common o Can disseminate into the skin and bones.

Coccidioides immitis

• Causes coccidioidomycosis • Lives in alkaline soils in semiarid, hot climates and is endemic to southwestern U.S. • Distinctive morphology - block like arthroconidia in the free-living stage. • Arthrospores inhaled from dust, creates spherules containing endospores in the lungs. o Dirt-Biking in the desert o Farming o Construction sites. • Events in Coccidioides Infection o 1. Digging in soil produces aerosol of Arthrospores (inset). o 2. Inhaled Arthrospores establish a lung infection. o 3. An arthrospore develops into a spherule that produces endospore; endospores are released into the lungs. o 4. Immunocompetent persons effectively fight infection and return to health. o 5. Compromised people can develop meningitis, osteomyelitis, and skin granulomas. • Valley Fever o Fungal pneumonia: Cough, fever, chest pain, flu-like o Common in children and newcomers to endemic areas. • For each fungal species, know its geographical distribution, transmission and life cycle of infection, and signs/symptoms of disease

Fungal Pneumonia • Know the three causative agents of fungal pneumonia presented in the lecture video

• Fungal pneumonia is an infection of the lungs caused by endemic fungi. It accounts for only a small portion of pneumonia cases in this country; however, fungal pneumonia generates concern in the ever-growing population of immunosuppressed people. In the following lecture, we will examine the three fungal agents that cause fungal pneumonia. These include: • Histoplasma capsulatum • Blastomyces dermatitidis • Coccidioides immitis Fungal pathogens • Portal of entry o Cutaneous and superficial - contamination of skin surface o Subcutaneous - inoculated skin; trauma o Systemic mycoses - respiratory portal; inhaled spores • Fungal pneumonia agents o True or primary fungal pathogens tha can invade and grow in a healthy, immunocompetent host o Thermal dimorphism - grow as molds as 30 C and as yeast at 37 C

Be able to explain why we need a new flu vaccine every year and how those vaccine strains are chosen

• Genome constantly changes o Antigenic drift (standard mutations, we are all controlled by antigenic drift, the random mutations that occur over time) o Antigenic shift (occurs if you have 1 influenza virus and infecting a cell and you have a red one infecting a cell, during packaging, you can get pieces of the two merging together to form new combo, the re-assortment of genomic segments) • Constantly have "new" flu strains occurring • Immunity to 1 strain doesn't protect against other strains.

Know the steps of aerobic respiration, the cellular location of each (prokaryotes vs eukaryotes) and the basic idea of what happens during each step

• Glycolysis (occurs in the cytoplasm) • 1 glucose, 2 ATP and 2NAD+ in, 2 pyruvate, 4 ATP (net 2 ATP out) and 2NADH out. • Krebs cycle (occurs in the mitochondria) • Yield per pyruvate (so since there is 2 pyruvates going into Krebs cycle, x2) o 1 ATP o 4 NADH o 1 FADH2 o 3 CO2 • Electron transport system (occurs in the matrix of the mitochondria) o 8 NADH and 2 FADH2 energy move into ETC, in which they are oxidized. Chemiosmosis occurs in which H+ ions are pumped into mitochondria inner membrane space. These H+ ions get pumped back into matrix by ATP synthase in which ATP is created from ADP and inorganic phosphate (PI) producing 30-32 ATP, 6 H2O and 6 CO2.

Compare and contrast Aerobic Respiration, Anaerobic Respiration and Fermentation

• In anaerobic respiration o Uses Glycolysis, TCA cycle and the ETS. o The final electron acceptor is an inorganic salt instead of O2 (NO3, NO2, SO4, etc.) o Amount of ATP depends on the salt being used. • In aerobic respiration, glucose goes thru glycolysis and also does use oxygen, produces 2 pyruvate, 2 NADH and 4 ATP (2 net ATP). o Then goes into the krebs cycle, where each pyruvate molecule reacts with CoA to make 1 Acetyl CoA and 1 CO2, which does use O2 and occurs in the mitochondrion. Each Acetyl CoA goes into the citric acid cycle making 1 ATP, 4 NADH, 1 FADH2, and 3 CO2, totaling 2 ATP, 8 NADH, 2 FADH2 and 6 CO2. o NADH and FADH2 energy move into ETC. These two molecules are oxidized e- passed down ETS in series of redox reactions; Final E- acceptor is O2, combines with 2 e- and 2 H+ to produce H2O. o Energy released during ETS, some lost as heat and some pump into ATP synthase pathway, where ADP + PI makes ATP. H+ ions/protons going down gradient drive this reaction causing oxidative phosphorylation (production of ATP using energy from redox reactions). End total, 6 H2O, 30-32 ATP and 6 CO2. • Fermentation o Glycolysis pathway: o Uses 1 glucose to yield 2 pyruvate, 2 ATP & 2 NADH o Fermentation pathway: o Uses pyruvate and NADH to yield NAD+, acids or alcohols and sometimes, gas o Produces only 2 ATP per glucose along with the acid/alcohol and sometimes, gas.

Histoplasma capsulatum

• Most common true pathogen; causes histoplasmosis • Typically dimorphic • Distributed worldwide, most prevalent in eastern and central regions of U.S. • Grows in moist soil high in nitrogen content (bird and bat-droppings) • Inhaled conidia produce primary pulmonary infection o Cave dwelling (Spelunking) o Demolition work o Cleaning old chicken coops. • Events in Histoplasma Infection o 1. Soil containing bird droppings is whipped up the wind. o 2. Microconidia are inhaled. o 3. The patient develops mild pneumonitis, which might recur. o 4. In the tissue phase of infection, the yeast phase develops, is phagocytosed, and multiplies by budding intracellularly. Most patients recover w/o complications. o 5. In some cases, phagocytes enter the blood and cause disseminated disease in a number of organs. • Ohio Valley Fever o Asymptomatic to self-resolving fungal pneumonia in 95% of cases. o Cough, fever, malaise, chest pain, headache and weight loss.

Know the basic structure and replication cycle of influenza (genome, proteins, structure)

• Orthomyxovirus • Enveloped, segmented ssRNA genome • Causes influenza / "flu" • 2 important envelope glycoprotein spikes • Hemagglutinin (HA) - binds to host cells • Neuraminidase (NA) - assists in viral budding & release

Know the basic characteristics of Streptococcus pneumoniae including the Gram reaction, shape, arrangement, normal flora location, colony descriptions and virulence factor

• S. pneumoniae is a Gram positive cocci in pairs (diplococcus) and short chains. • The major virulence factor is a pronounced capsule, present in all pathogenic strains of S. pneumoniae. o The large capsule causes the colonies to be mucoid (see figure below) which means that they are thick, moist, smooth and kind of mucous-like in consistency. o This capsule is so important to the bacteria that if you remove the capsule, it can no longer infect! o This capsule is often identified in a patient's sputum sample by using a serological test called the Quellung reaction. • It can cause ear infections (otitis media) when it passes through the Eustachian tube into the middle ear (see week 11 module) and it can cause meningitis when it gets into the cerebral spinal fluid (see week 9 module). • Here is another time this pesky little guy can wreck havoc. o If S. pneumoniae moves from the normal flora location of the nasopharynx into the lungs, it can cause pneumonia (hence being called the pneumococcus):

Know the 3 examples of viruses causing ARDS

• Sin Nombre Hantavirus o Hantaviruses are enveloped, RNA viruses (shown below) that belong to the Bunyaviridae family. o In the U.S., the only hantavirus is the Sin Nombre virus (Sin Nombre is Spanish for the "nameless virus") • The Sin Nombre hantavirus is carried in the gastrointestinal tract of wild rodents in the southwest and is transmitted via inhalation of dried rodent urine/feces in dust. o In fact, it was breathing in rodent wastes from cabins in Yosemite that sparked the outbreak of acute respiratory distress syndrome in that famous national park. • The Sin Nombre virus is now considered an emerging virus in the United States ever since it was first isolated in 1993 from rodents collected near the home of one of the initial patients with hantavirus pulmonary syndrome in the Four Corner region of the western United States (Utah, Colorado, Arizona, and New Mexico). • A higher than normal rainfall (caused by El Niño) resulted in a bumper crop of piñon nuts, a favorite food of deer mice. Mouse populations increased, as did contact with humans. • The Sin Nombre virus causes Hantavirus Pulmonary Syndrome (HPS) - initial symptoms are fever, chills and myalgia (muscle pain). o Rapidly followed by a dry cough, shortness of breath, pulmonary edema, acute respiratory failure and death within days. o HPS has a ~50% mortality rate • SARS-Coronavirus • SARS is a viral respiratory illness caused by a Coronavirus. • It is often referred to as the SARS-associated Coronavirus (SARS-CoV). • SARS was first reported in Asia in February 2003. The illness spread to more than two dozen countries in North America, South America, Europe, and Asia before the SARS global outbreak of 2003 was contained. • The SARS-coronavirus originated in bats and previously infected only palm civets and ferret badgers. o Consumption of civets by humans in China selected for mutations that expanded the virus host range and facilitated human transmission. o From there, the virus was able to be transmitted through droplet or direct contact from human to human. o Symptoms of SARS included fever, body ache, and malaise. Patients may or may not experience respiratory symptoms with breathing problems but severe cases could result in respiratory distress and death. • MERS-Coronavirus (watch the video on your own time) • More recently, a new strain of Coronavirus called MERS-CoV has emerged in the Middle East. Most people infected with MERS-CoV develop severe acute respiratory illness, including fever, cough, and shortness of breath. Like SARS, this novel coronavirus had proved just as deadly. Watch the video below for a good overview of MERS-CoV. • For the 3 viruses, know the following (if presented in module page only) o Viral characteristics o Transmission o Symptoms o Geographical distribution

Understand antigenic shift and antigenic drift and why influenza has such a high mutation rate.

• The genome is constantly changing o Antigenic drift (standard mutations, we are all controlled by antigenic drift, the random mutations that occur over time) o Antigenic shift (occurs if you have 1 influenza virus and infecting a cell and you have a red one infecting a cell, during packaging, you can get pieces of the two merging together to form new combo, the re-assortment of genomic segments)

Understand how an inducible operon works and be able to explain the function of the Lac Operon as an example of an inducible operon

Understand how a repressible operon works and be able to explain the function of the Tryp Operon as an example of a repressible operon

• The lac repressor is synthesized in its active form by regulatory genes somewhere else in DNA, active repressors bind to operators, now what that does is when RNA poly comes in and binds promoter, cannot do transcription because repressor is in the way • If lactose shows up, acts as the inducer (binds to the repressor and deactivates it) • Tryptophan is an amino acid that can be made through transcription to create enzymes. o Low trp environment, needed for building block of proteins to make trp enzymes. o When you have lots of trp around, you probably don't want transcription to occur. Trp can act as a co-repressor of the trp repressor, attach to trp repressor that will attach to the operator on the operon and stop RNA poly from transcribing. o Lot of trp, don't create trp or some lying around, don't create trp.

Operons Know the parts of the operon and what they do (promoter, operator, termination sequence, structural genes, regulatory gene, repressor protein, inducer, corepressor)

• The structural genes contain the enzymes needed to catabolize lactose. • Normally transcription is off. o Why is transcription off? • Because cell is saying to itself, why should it make enzymes unless there is lactose around • Lactose turns transcription from the lac operon on. • Lac is an inducible operon. • A coordinated set of genes, all of which are regulated as a single unit. o 2 types • Inducible - transcription from the operon is turned ON by substrate • Repressible - transcription from the operon is turned OFF by the product synthesized • Here we have promoter (the binding site RNA poly, where transcription starts) • (RNA poly binds and starts here) o The region where RNA polymerase is going to bind o Marks the start of the gene, but does NOT contain DNA that is expressed • Next to promoter is operator (control site that regulates access to promoter, turns on or off transcription) • (Contains transcription) o DNA sequence after the promoter that controls whether or not RNA polymerase will proceed o Does NOT contain DNA that is expressed. • Structural genes (in this operon, encode the enzymes needed to digest lactose) • Regulatory gene (not in operon, separate somewhere else in DNA, encodes protein called the repressor protein) o CONSTANTLY expressed • But in low amounts o Produces a protein called the REPRESSOR • Whether it is ACTIVE or INACTIVE depends on the operon we are talking about. • Repressor (when active, bind to operators) • If lactose shows up, acts as the inducer (binds to the repressor and deactivates it) • This is why we call in an inducible operon, can be turned on or induced to produce those enzymes • The Termination Sequence o Sequence where RNA polymerase disconnects from the DNA o Marks the end of the transcribed gene, but does NOT contain DNA that is expressed.

Understand the progression of tuberculosis including the cells infected, symptoms and progression

• They do not produce exotoxins or enzymes characteristic of other bacterial pathogens. o Instead, the ability to produce the cord-like colonies is used as an indicator of virulence. • Cord formation is thought to impede the ability of macrophages to ingest and destroy M. tuberculosis. • Macrophages ingest M. tuberculosis and bring them to the lymph nodes, where they are being digested and referred to as latent tuberculosis. • These latent cells have the possibility of dividing and when they do, this is considered active TB and can occur in people that are immune-compromised, they go into the blood stream and to the bones, digestive system, nervous system, the liver, or the heart. • Symptoms include coughing, difficulty breathing, chest pains, night sweats, and weight loss. • Treatment, antibiotics rifampicin isoniazid for 6-9 months or a cocktail of pills and injections. Other treatments are in development and current ones are outdated. Vaccination!!

Know the basic characteristics of Legionella pneumophila including the Gram reaction, shape, normal habitat, etc

• This gram-negative bacillus is a strict aerobe that grows in close association with an amoeba in lots of fresh water environments including ponds, pools, cooling towers and air conditioning units.

Know the basic characteristics of Mycobacterium tuberculosis (acid fast, cords, lack of virulence factors)

• Tuberculosis is a complicated illness caused by Mycobacterium tuberculosis, an acid-fast bacillus that has a tendency to grow in cords. • They do not produce exotoxins or enzymes characteristic of other bacterial pathogens. o Instead, the ability to produce the cord-like colonies is used as an indicator of virulence. • Cord formation is thought to impede the ability of macrophages to ingest and destroy M. tuberculosis.

How do people acquire Legionnaires disease? Is it contagious?

• When aerosolized droplets of contaminated water are inhaled, it can result in Legionnaires' disease, which presents with a high fever, cough, diarrhea, abdominal pain and possibly, pneumonia (mainly in the elderly and debilitated patients who are diabetic or alcoholics). • Cannot be contracted from person to person and contracted from infected water sources. • Know the people at risk for acquiring RSV pneumonia and what treatment is available for those patients. • We learned about this virus last week because it usually causes colds (upper respiratory tract infection) in both children and adults but unfortunately in very young children (6 months and under) it can progress to the bronchi and lungs. • RSV is highly contagious via respiratory droplets and fomites and outbreaks are common during the winter. • While there is no vaccine for RSV, passive immunization is available for high-risk babies.

Whooping Cough and Tuberculosis • Know the basic characteristics of Bordetella pertussis (gram reaction, shape, virulence factor)

• Whooping cough (aka pertussis) is a common early childhood infection caused by Bordetella pertussis, a small gram-negative coccobacillus pictured below. • B. pertussis produces fimbriaelike adhesion molecules that allow it to find and bind to the ciliated cells that line the upper respiratory tract. o These ciliated cells are tasked with removing particles from the respiratory tract before they can enter (and possibly damage) delicate lung tissue. • B. pertussis also produces exotoxins that destroy and remove the ciliated cells. • Without these cells, mucus will build up in the lungs and block the airways.

Pharyngitis

➢ "Sore Throat" as the major complaint ➢ Severity of the pain ranges fro moderate to severe depending on the causative agent ➢ Reddened mucosa, swollen tonsils, possible white puss, difficulty talking and/or swallowing, sometimes foul breath. ➢ Causative Agents o Bacteria • Swollen uvula, whitish spots, red swollen tonsils, throat redness, gray furry tongue o Viral • Red swollen tonsils, throat redness.

Know the 3 viruses that cause gastroenteritis, including virus type, prevalence, susceptible age groups, symptoms and transmission. 3. Adenovirus serotypes 40-42

➢ Adenovirus serotypes 40 - 42 are classified as the enteric adenoviruses because they primarily infect the gastrointestinal tract. ➢ Infection by these serotypes can be attributed to 5-20% of hospitalizations for childhood diarrhea worldwide, but they can infect any age group. ➢ Adenoviruses 40-42 are the only DNA viruses that cause viral gastroenteritis. ➢ Symptoms last 7 to 8 days and include diarrhea, vomiting, and fever. ➢ Transmission is thought to be contact with contaminated food, water, or surfaces.

Leptospira interrogans - Know morphological characteristics, transmission, disease symptoms and phases of infection (present on other flashcard), and prevention.

➢ Another bacterium that we are including in this UTI section is Leptospira interrogans, a spirochete with very tight coils and characteristic hooked ends. ➢ An infection with this organism is known as Leptospirosis. ➢ Leptospirosis is a zoonotic infection (primarily an animal disease accidentally transmitted to humans) that is transmitted to humans via contact with contaminated animal urine. ➢ L. interrogans can affect the kidneys, along with the liver, brain, and eyes. ➢ In infected domesticated or wild animals, Leptospira interrogans invades and grows inside the kidney. ➢ Animals shed the spirochete in their urine and contaminate water (rivers, streams, swimming pools). ➢ Once in the water, humans can come in contact with Leptospira interrogans through broken skin or the mucous membranes. ➢ Leptospirosis is an occupational hazard of sewer workers, rice farmers, slaughterhouse workers, veterinarians, dairy farmers and military personnel. ➢ There has even been a case of athletes competing in the swimming phase of a triathlon contracting leptospirosis from the water. ➢ The incidence of Leptospirosis increases in times of natural disasters like hurricanes and floods where humans and animals are wading in water.

For the following causative agents of acute food poisoning, know gram stain reaction, morphology, the exotoxins they produce, and what foods are associated with each: 2. Bacillus cereus

➢ Bacillus cereus is an endospore-forming gram-positive bacilli that is a common soil microbe that can be an airborne and dust-borne contaminant. o As a result, it is a common resident on vegetables and food products in close contact with soil. o B. cereus multiplies very readily in cooked foods, most notably fried rice. • In fact, outbreaks of food poisoning from this bacterium are often associated with Chinese restaurants. o Other foods implicated with B. cereus are cooked potatoes and meat and vegetable dishes. ➢ Bacillus cereus spores and toxins survive short periods of cooking and reheating; when the food is stored at room temperature, the spores germinate and release exotoxins. o B. cereus produces two exotoxins, one of which causes an emetic (or vomiting) disease, the other causes a diarrheal-type disease. o The emetic form of the disease is the most frequently linked to fried rice and food intoxication results from ingestion of a heat-stable exotoxin that causes acute vomiting, usually within 1-4 hours post-ingestion. o The diarrheal form of the disease is associated with cooked meats or vegetables that are held at warm temperatures for long periods of times. o These conditions cause B. cereus to produce a heat-labile (or heat-sensitive) exotoxin that causes watery, profuse diarrhea, nausea, and abdominal cramps. o The symptoms generally disappear in 24 hours with no lasting effects or required treatments.

Parainfluenza Virus

➢ Belongs to the Paramyxovirus family (Enveloped, RNA virus with helical capsid) ➢ Widespread as influenza but more benign. ➢ Spread by respiratory droplets or fomites. ➢ Causes about 5% of common cold cases in older children and adults ➢ No specific treatment available; supportive therapy. ➢ In infants and young children, parainfluenzal disease can cause bronchitis, bronchopneumonia and Croup (laryngotracheobronchitis) ➢ Croup manifests as labored noisy breathing with "seal bark cough"

For the following causative agents of acute diarrhea, know gram stain reaction, morphology, special characteristics and/or virulence factors, transmission (any food products involved), if they produce exotoxins and how they cause disease. 5. Campylobacter

➢ Campylobacter jejuni causes bloody or watery diarrhea after ingestion of raw poultry or unpasteurized dairy. ➢ Causes bacterial gastroenteritis ➢ Transmitted by food (raw poultry and unpasteurized dairy) ➢ Adheres to the intestine, burrows through the mucus and mulitples ➢ Secretes C. jejuni enterotoxin. o (Means it works on GI tract and type of exotoxin) stimulates stomach cramps, watery or bloody diarrhea, and sometimes vomiting, abdominal pain). ➢ Usually self limiting within a week ➢ Often undiagnosed and untreated.... Most common food infection?

Carbohydrate Fermentation Broth and how it works

➢ Carbohydrate fermentation medium (phenol red broth in your lab manual)- contains sugars that can be fermented and converted to acids, along with a pH indicator to show the reaction; helps identify bacteria ➢ Reducing medium - contains a substance that absorbs oxygen or slows penetration of oxygen into medium...

Describe the different sections of the Tapeworms. Compare and contrast the life cycle, signs and symptoms, diagnostics of Taenia saginata (Beef Tapeworm)

➢ Cestodes (Tapeworms) o Cestodes (also called tapeworms) are long, very thin, segmented flatworms that are divided into 3 sections: • Scolex = the head, which attaches to the intestinal wall via hooks and/or suckers. • Neck, and • Body, which is ribbon like and resembles tape; made up of individual segments called proglottids (Proglottids absorb nutrients directly and filled with eggs). o Definitive hosts (humans) ingest larvae from infected tissues (cysticercus), e.g., undercooked beef, pork or fish. Larvae develop into adult tapeworms in the intestine. o Adult tapeworms develop in the intestines and can grow up to 5 meters long. o Tapeworm infections are often asymptomatic unless there is a heavy worm burden. ➢ Taenia saginata (Beef Tapeworm) o Basics • Humans acquire by ingesting inadequately cooked beef containing the cysticerci (encysted larval stage). Larvae hatch in intestine and mature to an intestinal tapeworm. • Adult beef tapeworms remain the intestines. o Infections • Taeniasis - Intestinal infection: asymptomatic to mild > diarrhea and weight loss. • Adult tapeworms grow to 5 m > live in intestine for several decades. o Diagnosis • Microscopy: Thick-walled, spherical, dark brown eggs and/or proglottids in stool.

Be able to explain the process of Electron Transport and Chemiosmosis to make ATP

➢ Chemiosmosis: generation of adenosine triphosphate by the movement of hydrogen ions across a membrane o 3 ATP made per NADH o 2 ATP made per FADH2 ➢ NADH and FADH2 energy move into ETC, in which they are oxidized. Chemiosmosis occurs in which H+ ions are pumped into mitochondria inner membrane space. These H+ ions get pumped back into matrix by ATP synthase in which ATP is created from ADP and inorganic phosphate (PI) producing 30-32 ATP.

➢ Clostridium difficile can cause pseudomembranous colitis (also called antibiotic-associated colitis) after antibiotic therapy kills the competing micro flora of the gut. ➢ Gram + spore-forming anaerobic bacillus ➢ Normal resident of colon, in low numbers ➢ Treatment with antibiotics eliminates C. difficile's completion and it can cause pseudomembranous colitis (antibiotic-associated colitis, a super infection by C. difficile) when it grows unchecked. o Produces enterotoxins that damage the intestine and can cause "pseudomembrane" development. (major symptom is severe diarrhea with cramps and possible fever and colon perforation and death is possible.) • Will cause diarrhea, nausea, vomiting, gastroenteritis and damage by diarrheal fluids may cause necrotic lesions. ➢ Highest risk patients are those on board broad spectrum antibiotics fro an extended time period.. Nursing home patients are #1. o C. difficile's super infection can be a severe infection but is brought on by excessive antibiotic use • Somebody who's been using an antibiotic is at a high risk and nursing patients are the ones who use the most antibiotic and are higher risk for this ➢ Treatment by removing the antibiotic in weak cases, using a strong antibiotic targeted to anaerobes is possible, probiotics and even fecal transplantation to restore normal flora.

Coronaviruses

➢ Coronaviruses are the second most common cause of the common cold. ➢ Relatively large RNA viruses with distinctively spaced spikes n their envelopes. ➢ Common in domesticated animals ➢ Grow best in 33-35 C ➢ Infections peak around winter and spring (colder months) ➢ Symptoms similar to rhinovirus but with greater nasal discharge.

Transmission of Cold Viruses

➢ Coughing, and sneezing discharge viral particles into the air in small (cough) or large (sneeze) droplets (40,000 droplets) ➢ The most common means of spread is through transmission from contaminated fingers/hands to the mucous membranes of the nose or eye. ➢ Practically everyone gets colds and fairly frequently. ➢ People can acquire some degree of immunity to a cold virus that they have encountered before but minimal overall protection because of sheer number of cold viruses. Causative Agents ➢ Most Common Causes o Rhinoviruses o Coronaviruses o Parainfluenza Virus ➢ Other causes o Influenza virus o Respiratory Syncytial Virus o Adenovirus

Know how dental caries develop and the main cause. How can they be prevented?

➢ Dental caries is considered the most common infectious disease of humans. o Over time, oral microbes found living in dental plaque can destroy enamel and cause infection in the deeper layers of teeth containing soft tissue, called the pulp. o The pulp contains blood vessels and nerves and infections in this region lead to pain, referred to as a "toothache." ➢ The main cause of dental caries are oral alpha-hemolytic viridans streptococci such as Streptococcus mutans. o The viridans streptococci are the most numerous and widespread residents of the oral cavity, nasopharynx, genital tract, and skin. o At least 24 species have been identified and have been divided into 5 groups. o Some other examples include Streptococcus sobrinus, Streptococcus mitis, Streptococcus salivarius, and Streptococcus sanguinis. ➢ In the presence of sucrose and other sugary substances, these bacteria produce sticky polymers of glucose called fructans and glucans. ➢ These polymers initiate the formation of plaque biofilm. o If these biofilms are not removed through good dental hygiene practices, the streptococci and other oral bacteria begin to produce acid as they ferment the carbohydrates and start to erode away at teeth.

➢ Entamoeba histolytica is an Amoebozoan, a protistan supergroup we first learned about when discussing amoebic encephalitis. ➢ Amebiasis symptoms include loose stool, abdominal pain, weight loss, and fatigue, but only 10 to 20% of infected individuals will display these symptoms. ➢ Amebic dysentery is the term given to severe E. histolytica infections, with the added symptoms of bloody diarrhea and fever. o Symptoms typically take one to two weeks to arise, although there has been cases of symptoms taking longer to develop. o Diagnosis is achieved through microscopical analysis of stool samples. o During diagnosis, it is important not to confuse E. histolytica with another amoeba, Entamoeba coli which is a non-pathogenic amoeba that may be found in the human GI tract. o To distinguish the two, the E. histolytica trophozoite often presents with ingested human red blood cells. o Cysts released in the feces of infected vertebrates can persist in soil or water for weeks up to several months.

What are the most common bacterial causes? For the bacteria listed below, know gram stain reaction, morphology, virulence factors, and distinguishing characteristics of each. 1. Escherichia coli (UPEC)

➢ Escherichia coli (a gram negative bacillus) is by far the most common cause of urinary tract infection, accounting for 80-85% of acute cystitis. ➢ The species of E. coli that cause UTIs are different from those that cause diarrhea and are known as UPEC - Uropathogenic E. coli. ➢ UPEC strains do exist as normal flora in the GI tract and they have a variety of virulence factors that facilitates their infection in the urinary tract. ➢ These include: o 1) Numerous fimbriae with adhesions that specifically attach to the epithelial cells lining the urinary tract, and o 2) Motility that is adapted to allow UPEC to ascend the urinary system quickly. Other factors promoting UTI with E. coli include sexual intercourse and urinary catheters, the latter accounting for UTIs being the most common of nosocomial infections.

Excision Repair of Mutations:

➢ Excision repair enzymes cut out mutated pieces of DNA and DNA poly 1 will fill in with new DNA and ligase will seal up the gaps, we call this excision repair. o Happens in all points in the lifetime of our cells, happens in prokaryotes as well.

Bacterial Infections with Acute Diarrhea and Vomiting Know the signs and symptoms of acute food poisoning

➢ Food poisoning, also called foodborne illness, refers to symptoms in the gastrointestinal tract that are caused by a preformed exotoxin produced by a pathogen. Symptoms include severe nausea, frequent vomiting accompanied by diarrhea, and abdominal cramping.

Strep Throat

➢ Found on choc agar ➢ Extreme pain ➢ Bright red and pus ➢ Foul smelling breath ➢ Must be treated immediately to avoid complications

➢ Giardia intestinalis is a protist in the supergroup Excavata, more specifically the Diplomonads. ➢ Many Diplomonads are parasites, thrive in oxygen poor environments, and are symmetrical - with two equal-sized nuclei and four flagella on each side. ➢ This symmetry can be seen in the image above of Giardia, the two dark circles are the nuclei of the cell. ➢ Giardiasis is the most common intestinal parasite found in the United States, although the majority of infections are asymptomatic. ➢ Human infection is often seen in campers and hikers who drink water from rivers and streams without proper filtering or boiling the contaminated water. ➢ Symptoms such as loss of appetite, diarrhea, stomach cramps and upset, projectile vomiting, excessive gas, and lactose intolerance, can arise within one to three weeks of exposure to contaminated water. o The symptom of lactose intolerance is typically temporary, but can become permanent. ➢ Cysts are shed in the fecal matter of infected vertebrates, which can survive in cold water for up to three months. ➢ Diagnosis is achieved through examination of the patient's stool for trophozoites (pictured above) and cysts.

Translation

➢ Going from mRNA to protein, not 1 to 1 relationship like transcription ➢ (In yellow) 3 nucleotides, a A, U and a G, we call this a codon, an info for 1 amino acid ➢ In the next codon, C, C, U, the info for the next amino acid (in green). ➢ tRNA are the ones that read this codon and figures out what amino acid this encodes through complementary base pairing. o Anti-codon in tRNA is going to bind to the codon in mRNA to bring in the 1st amino acid, and the 2nd tRNA anti-codon is going to the bind to the codon in mRNA and bring in the 2nd amino acid, and so forth, etc. (shown below) ➢ Translation will always occur at AUG (methionine), which is the start codon, and there are also stop codons where translation stops. ➢ Code is universal, and ensures which amino acids will be made based on codon sequences. Also the information from mRNA to make amino acids, proteins

Corynebacterium diphtheriae

➢ Gram + ➢ Club-shaped bacilli ➢ Palisades arrangement ➢ Metachromatic granules

Streptococcus pyogenes (Group A)

➢ Gram + Cocci in chains ➢ Causes a variety of infections like cellulitis, erysipelas, impetigo, necrotizing fasciitis. ➢ Carried as normal flora in 15% of humans ➢ Transmitted via droplets and direct contact. ➢ Strict parasite, beta hemolytic ➢ Inhabits throat, nasopharynx, occasionally skin ➢ Surface antigens o C-Carbohydrates o M-protein (fimbrae) ➢ Enzymes o Streptokinase o Hyaluroidase ➢ Toxins o Hemolysins o Erythrogenic toxin

Stomach Helicobacter pylori - Know gram stain reaction, morphology, virulence factors, and distinguishing characteristics. What is this organism specifically known for causing?

➢ H. pylori is a curved, spiral-shaped, gram-negative bacilli with a lophotrichous flagellar arrangement. ➢ Humans are the only reservoir of this pathogen and to date, the transmission of Helicobacter pylori still remains a mystery. o The current consensus is that the bacterium is spread through the oral-oral or fecal-oral route. o Once in the host, the primary habitat is the harsh human stomach! o Approximately two-thirds of the world's population are infected with H. pylori, occurring in the stomachs of 25% of healthy middle-age adults and in more than 60% of adults 60 years of age or older. ➢ Helicobacter pylori is highly motile and quickly bores into the stomach epithelium where it binds to specific binding sites on these cells and entrenches itself. o In fact, one specific receptor that Helicobacter binds to is the same molecule on RBCs that confers the O blood type, hence the higher rates of stomach ulcers caused by this pathogen in people with this blood type. o To protect itself against stomach acids, Helicobacter pylori secrete urease which hydrolyzes stomach urea to produce an alkaline ammonia cloud. o This cloud neutralizes stomach acid and protects the pathogen as it makes its way through the stomach. ➢ Helicobacter pylori is Implicated in 90% of stomach and duodenal ulcers (also called peptic ulcers). o Before this bacterium was discovered, it was believed that spicy foods and stress caused these ulcers, but now it appears that these factors merely aggravate the ulcers caused by the pathogen ➢ Immune responses cause inflammation of the stomach (gastritis), and subsequent infiltration of white blood cells lead to deeper erosion of the stomach epithelium and more ulcers. ➢ H. pylori and the host immune response against it are a major factor in the development of stomach cancer.

For all the hepatitis viruses, know viral characteristics, genome, transmission (fecal oral vs bodily fluids), whether they can establish a chronic condition, and if they are curable or preventable through vaccines 1. Hepatitis A

➢ HAV is a nonenveloped, single-stranded RNA enterovirus that belongs to the Picornavirus family. o Remember that many viruses from this family can result in viral meningitis and we will see that other enteroviruses can cause gastroenteritis next week. o Here we will focus on the one member of this family that specifically infects the liver, HAV. ➢ Infection by HAV is quite mild compared to many of the other Hepatitis viruses. ➢ Patients are likely to experience "fluish" symptoms possibly accompanied by nausea and vomiting. ➢ In severe cases you might see jaundice and abdominal tenderness (from the inflamed liver) but that is pretty rare in this mild and self-limiting infection. ➢ Transmission of HAV is through the fecal-oral route meaning that you ingest something contaminated by feces from an infected person. o This infection is more common in places suffering from poor hygiene and sewage treatment. o In this country we see HAV usually as an outbreak associated with poor hygiene with food prep. o The last multi-state outbreak of HAV in the US came from packaged pomegranate seeds sold by Costco stores in multiple states (including California). o The CDC traced the cases and using epidemiological information, identified the cause and stopped the epidemic. ➢ There is a vaccine available for HAV that is recommended for children but most adults are unvaccinated. ➢ You can request the vaccine from a healthcare provider or the health department but since good hygiene can prevent this infection, most Americans are at a small risk for this relatively mild infection by HAV.

➢ HBV is an enveloped DNA virus from the family Hepadnaviridae. ➢ Interestingly, the DNA of this virus is partly single-stranded and partly double-stranded. ➢ HBV is often called a "Dane Particle" and can be identified in serological tests by looking for a protein in it's envelope called it's "Surface Antigen". ➢ HBV is a more severe infection than HAV. Patients usually experience fever, chills, malaise, anorexia, abdominal pain, diarrhea and nausea. ➢ In addition to commonly seeing jaundice in HBV patients, you might also see a rash and/or arthritis. ➢ HBV is a very serious infection and can be life-threatening. ➢ Most patients will recover fully after an acute case of HBV but for some patients, HBV becomes chronic and that long-term infection can result in liver cirrhosis (permanent scarring to the liver tissue). ➢ These chronic HBV patients also have a substantially higher risk for liver cancers. ➢ Some patients become latent carriers of HBV after recovering from the infection and continue to be infectious to others even after they have fully recovered. ➢ Although HBV is growing in the liver, it releases active virus into the blood which makes it easily transmissible through small amounts of blood and other body fluids including semen. ➢ This makes HBV a highly infectious disease through sexual contact, mother to baby during birth, sharing needles, tattooing, even sharing things that have trace amounts of blood or fluid like utensils and razors. o It is a major concern for healthcare workers because of the risk of needle sticks and their likelihood to encounter patient body fluids. ➢ There is an effective HBV vaccine that is recommended by the CDC for all children and those adults that may not have received it and are considered high risk (healthcare workers, partners of HBV patients, homosexual men, injection drug users, etc.)

➢ HCV is an RNA virus from the flavivirus group and is sometimes referred to "non-A non-B" hepatitis in the medical setting because it was identified as an infection before the actual virus was isolated and identified. ➢ Unfortunately HCV infection is often subclinical for months or years before the patient begins to experience symptoms of liver damage: jaundice, malaise, abdominal pain, etc. o Since most HCV infections do become chronic, this leads to long-term damage and even death in the patient. o In fact, chronic HCV infection is the most common cause for a liver transplant in the US. ➢ HCV is infectious through blood contact and too a lesser degree, sexual contact. o This unfortunately means that patients are infectious for months or years while their infection is subclinical and they have no idea they are infected. o By far, the most common transmission for HCV is sharing needles with injection drug use but it is also possible to transmit the virus via sexual contact and of course, healthcare workers have some risk with their patient contact: ➢ We don't currently have a vaccine for HCV so prevention and screening are the best options.

➢ HDV is a weird one. It can only infect as a co-infection with HBV because it is an incomplete virus particle on it's own. ➢ It appears that the presence of HDV along with HBV causes a more severe form of HBV infection. ➢ Although we don't have a vaccine specific for HDV, the HBV vaccine protects against both.

➢ HEV is a relatively mild infection rarely seen in the US. ➢ It is transmitted through fecal-oral route and is usually associated with contaminated water supplies in countries without good sewage treatment protocols. ➢ HEV is a self limiting disease and there is no vaccine available for HEV.

Gastrointestinal Helminths

➢ Helminths are parasitic worms that are covered in the parasitology branch of microbiology. ➢ These organisms may be large enough to be seen with the naked eye, ranging from tapeworms that can grow up to 50 feet long, to small roundworms that are less than 1 mm in length. ➢ Yet, we still include them in microbiology because they are pathogenic to humans and because microscopes are necessary to identify their microscopic eggs and larval stages (see image below).

Role of Oxygen à H2O

➢ In anaerobic respiration, Oxygen is not the final electron acceptor, in the aerobic respiration, oxygen is the final electron acceptor combing with 2 electrons 2 H+ to produce H2O.

➢ Listeria monocytogenes causes listeriosis upon ingestion of contaminated foods which starts with diarrhea and can progress to septicemia and meningitis particularly in high risk groups like pregnant women, immunocompromised adults and the elderly. o Listerosis results in a food poisoning particularly after refrigeration of unpasteurized dairy products, poultry and prepared meats. ➢ Non-spore-forming , gram + bacillus. ➢ Resistant to cold, heat, salt, pH extremes and bile. ➢ Primary reservoir is soil and water. ➢ Outbreaks have been traced to contaminated foods such as produce, deli meats, soft cheeses and other dairy products. ➢ Individual cases arise from the organism growing in the fridge ➢ Treated with antibiotics. ➢ High risk groups need careful monitoring because complications and death are possible.

Diphtheria

➢ Local infection: o Sore throat, low fever, lack of appetite o Inflammation of the pharynx and tonsils o Pseudo-membrane (formed by dead bacterial cells, extremely difficult to remove) forms which can cause deadly asphyxiation o If patient survives, may recover fully or...

Toxemic Diphtheria

➢ Lysogenic Corynebacterium diphtheriae produces an exotoxin o (Has an A-B toxin, B portion binds to tissue cells in host, grows in the throat, toxin enters blood stream and toxin goes all over the body. A portion of toxin does the damage, blocks translation of proteins. ) • Can shut down 90% of protein synthesis ➢ Symptoms show up all over the body o Heart failure o Nerve atrophy

Rhinitis, or the Common Cold

➢ Many viruses (>200 different kinds) cause the common cold, called rhinitis (inflammation of the nose) ➢ Symptoms of rhinitis include rhinorrhea (runny nose), sneezing, coughing, scratchy throat, headache, malaise, and possibly low-grade fever ➢ Symptoms usually being 2 or 3 days after infection and are largely due to the immune response to the infection.

Know terms like metabolism, anabolism, catabolism, energy coupling

➢ Metabolism - The total of all chemical reactions and physical processes occurring in a cell. ➢ Catabolism - degradation, releases energy, end products with reduced energy, CO2 and H2O. (Cat destroys) ➢ Anabolism: biosynthesis, requires energy (Ana builds). ➢ Energy coupling: cell uses an exergonic rxn to drive the endergonic rxn(above), breakdown of ATP for ex -ATP when it gets broken down to ADP, highly exergonic process, ADP is a simplistic molecule than ATP and you get energy out You get -7.3 kcal/mol to do this

DNA Mutations

➢ Mutations are changes in the genetic material ➢ Spontaneous mutations occur constantly in all organisms' DNA. ➢ Mutagens drastically increase the frequency of mutations o Chemicals (asbestos, acrylamide, etc.) o UV light (i.e. thymine dimers) and Radiation ➢ How DNA mutations affect protein structure and function? o Messes up DNA sequence which would affect protein structure ➢ 2 main mutations: o Substitution mutation • When 1 nucleotide is mutated and gets mixed, it changes. • Missense mutation (encode a diff amino acid.) and Non-sense substitution mutation (we've changed one nucleotide and could now create a stop codon, which will end translation, could be destructive.) o Frameshift mutation • Inserting or deleting nucleotides, if we insert or delete, not only do we affect one amino acid, we affect every amino acid after that. o Silent mutation, • Type of substitution mutation (the redundancy in the code, where we have changed the DNA but not the protein)

Adenoviruses

➢ Non-enveloped, double-stranded DNA ➢ 30 types associated with human disease ➢ Infect lymphoid tissue, respiratory mucosa and intestinal epithelia and conjunctiva of the eye o Serotypes 1-7 for upper respiratory and conjunctiva ➢ Spread by respiratory and ocular secretions ➢ Causes colds, pharyngitis, conjunctivitis and pharyngoconjunctival fever.

➢ Non-motile Gram negative rods ➢ Does not produce H2S ➢ Etiological agent of Bacillary Dysentery - a disease marked by crippling abdominal cramps and frequent diarrhea with mucus and blood ➢ Important species are S. dysenteriae (severest form), S. boydii and both S. sonei and S. flexneri (found in U.S.) ➢ Only found in human and ape gastrointestinal tract ➢ Transmission through fecal-oral spread. ➢ Feces-contaminated food or water is ingested and the non-motile Shigella is phagocytosed into the large intestines where they survive in the phagosome and multiply ➢ They are invasive and spread to adjacent cells that stimulate an inflammatory immune response that causes extensive tissue destruction ➢ Also releases endotoxin and exotoxins (Shiga toxin) ➢ Shiga toxin cleaves the 60s ribosome, inhibiting protein synthesis ➢ Shigellosis symptoms vary widely, depending on the patient's nutritional status and age, the infective strain and dose.

Viral Gastroenteritis Know the 3 viruses that cause gastroenteritis, including virus type, prevalence, susceptible age groups, symptoms and transmission. 1. Norovirus

➢ Norovirus is a highly contagious naked, RNA virus that is thought to be the cause of almost 90% of all viral gastroenteritis infections. ➢ It is the most common cause of food-borne illness in the United States, sickening nearly 21 million people each year. ➢ Norovirus is transmitted by coming in contact with an infected person, consuming contaminated food or water, or by coming in contact with contaminated surfaces. ➢ The virus causes inflammation in your stomach and/or small intestine, leading to stomach pain, nausea, diarrhea, and vomiting. ➢ Symptoms usually appear within 12 to 48 hours of exposure and patients recover within 1 to 3 days. ➢ Norovirus is easily transmitted in crowded situations, such as schools, cruise ships, nursing homes, or restaurants, and is not restricted to particular age groups. ➢ Because the Norovirus is so contagious, it commonly crops up as an epidemic in people that are in close contact with one another like school children:

Differences in Eukaryotic Transcription/Translation

➢ Nucleus sequestered ➢ Exons/Introns ➢ Only Proks have operons ➢ In a Prokaryote, transcription and translation can occur at the same time (much faster, don't need to get rid of introns, both happen in cytoplasm) o For a prok, both happen in cytoplasm o Proks don't have introns, only exons o Only proks have operons. ➢ In a Eukaryote, not possible in euk. (much slower in protein production) o Transcription in euk happens in nucleus, translation happens in cytoplasm o In a euk, introns and exons o Here we have DNA template, complimentary anti-parallel o o You'll see introns periodically between exons o During transcription, we have direct copy of that DNA in RNA, we have to get rid of introns because they are non-coding o We have to splice out introns and attach exons together to form mRNA before mRNA leaves nucleus. o Therefore, two can happen in prok but not in euk because of diff of areas o When we seq euk DNA, we find large pieces of DNA that don't encode anything, introns (non-coding sections of DNA), exons (are coding sects of DNA) ➢ Why in the world would euks have non-coding sects of DNA? We don't know

Understand Oxidation-Reduction

➢ OIL RIG NAD+/NADH and FAD/FADH2 Gylcolysis and TCA load electrons onto NAD+ to form NADH. o NADH delivers the electrons to the ETS and is turned back into NAD+. o FAD / FADH2 works the same way.

Fusobacterium & Porphyromonas gingivalis - Know gram stain reaction, oxygen tolerance, how they contribute to periodontal disease and bad breath.

➢ Periodontal disease is one of the most common human infections with nearly 100% of the population developing some form of this disease by age 45. ➢ Like dental caries, the causative agent of periodontal disease is not attributed to a single organism, but to a community of oral biota. o When plaque biofilms consist of the right combination of bacteria, such as the anaerobes Fusobacterium and Porphyromonas gingivalis, the periodontal destruction process begins. o These bacteria are obligate anaerobes that are gram negative rods. o These organisms naturally produce metabolic byproducts that are foul-smelling and are the cause of bad breath in individuals.

What is the best way to prevent food poisoning?

➢ Prevention comes from proper food handling which includes washing hands, fruits and vegetables, and keeping cooked hot foods hot [140°F (60°C) or above] and cold foods cold [40°F (4°C) or below]. (S. aureus). ➢ Be wary of fried rice that has been left out for long periods of time (B. cereus). ➢ Refrigerate food after it has cooled down sufficiently (C. perfringens).

Transcription

➢ Promoter (the start site for transcription) o A sequence in the DNA where RNA poly binds o Similar to ORI, the location of where helicase bound to unwind DNA. ➢ RNA polymerase (the enzyme that does transcription) o Reads DNA and synthesizes a complementary antiparallel strand of RNA. o Goes on until it reaches the termination sequence and the mRNA will just fall off. ➢ Termination sequence o Where transcription will stop.

What are the most common bacterial causes? For the bacteria listed below, know gram stain reaction, morphology, virulence factors, and distinguishing characteristics of each. 3. Proteus

➢ Proteus mirabilis is a gram (-) bacillus and an opportunistic non-coliform enteric that can also cause urinary infection. ➢ P. mirabilis is of particular importance because it can lead to the formation of kidney stones in patients through its production of urease. ➢ Urease is an enzyme that catalyzes urea (a major solute in urine) into CO2 and ammonia. ➢ Proteus can grow well in urine and its urease activity causes an increase in ammonia which in turn increases the urine pH(alkaline). ➢ Ammonia and the alkaline environment are factors in the formation of kidney stones. ➢ Proteus mirabilis has fimbriae for attachment to epithelial cells of the urinary tract and is highly motile, especially when hyperflagellated. ➢ P. mirabilis can swarm on the surface of moist agar and create distinguishing concentric rings which can be used for laboratory identification. ➢ Proteus can also be identified by testing positive for urease and H2S (hydrogen sulfide) production. ---All UTIs are treated with antibiotics and prevention comes by way of basic practices such as emptying the bladder frequently and (especially for females) wiping from front to back after a bowel movement. Scientific studies have found that components in cranberry juice discourage attachment of UPEC to the urinary tract, hence drinking cranberry juice is encouraged for people who are predisposed to UTIs.

RNA:

➢ RNA is also a nucleic acid that is made of nucleotides. ➢ The RNA nucleotides are made of the sugar ribose, a phosphate group and a nitrogenous base. ➢ There is a change in the nitrogenous bases because we don't have Thymine in RNA, instead we have Uracil. ➢ So the base pair rules for RNA would be: C-G and A-U. RNA is a single stranded molecule so you don't have the same helix structure.

DNA:

➢ Remember that DNA is made of building blocks called nucleotides and those nucleotides are made of a sugar (deoxy-ribose), a phosphate group, and a nitrogenous base (Adenine, Thymine, Guanine or Cytosine). ➢ The nucleotides are assembled into strands and two strands come together to form the DNA double helix.

Know the 3 viruses that cause gastroenteritis, including virus type, prevalence, susceptible age groups, symptoms and transmission. 2. Rotavirus

➢ Rotavirus is also a naked, RNA virus that is most common in infants and young children, and is the leading cause of severe diarrhea in these age groups. ➢ Older children and adults can be infected with rotavirus, but they will typically exhibit milder symptoms. ➢ Symptoms appear approximately 2 days after exposure to infected individuals or contaminated surfaces and include severe watery diarrhea, vomiting, fever, and abdominal pain. ➢ Rotavirus is a very serious illness and is responsible for the deaths of over 500,000 infants and children each year, worldwide. ➢ The CDC recommends an oral vaccine be given to infants in the US.

Intro to URIs (upper respiratory infections)

➢ Runny nose, high fever, stuffy nose, congestion, symptoms due to URI. ➢ Disease causing agents are bacteria or viruses. ➢ When the nasal cavity has an infection, we call that rhinitis. ➢ If we have an infection in the pharynx, we call that pharyngitis. ➢ If the epiglottis is infection, we get epiglottitis. ➢ If the larynx gets infection, we have laryngitis. ➢ And so forth to the trachea, we get tracheitis. ➢ Majority of viruses are rhinoviruses. ➢ Influenza virus can cause a URI, but more than 200 can cause URIs. ➢ Streptococcus are bacteria that can cause URIs, strep A, G, but most common is strep A. ➢ The viruses or bacteria cause the symptoms to occur, immune response. Body causes an inflammatory response to get rid of these pathogens, which is why we get a lot of mucus and stuffiness, fever and sore throat.

For the following causative agents of acute food poisoning, know gram stain reaction, morphology, the exotoxins they produce, and what foods are associated with each: 1. Staphylococcus aureus

➢ S. aureus (gram + cocci) is also one of the most common causes of acute food poisoning, especially from eating foods that are rich in carbohydrates such as custards, cream pastries, and especially potato salad. It is also associated with processed meats, chicken salad, and ham (recall that Staphylococcus are halotolerant). ➢ Staph food poisoning is caused by release of an enterotoxin. o Enterotoxins are a type of exotoxin that act upon the gastrointestinal tract of humans which induce nausea, vomiting, and diarrhea. o The illness does not require the actual bacteria to be present or alive in the contaminated food as the toxin alone is sufficient for causing symptoms. o If the bacterium is allowed to multiply in the food, it produces its toxin. o Even if the bacteria are subsequently destroyed by heating or reheating, the preformed toxin will act quickly once it is ingested. ➢ The Staph enterotoxin is heat-stable; inactivation requires 100 degrees C for at least 30 minutes. o As a result, heating food after toxin production may not prevent disease. o Ingestion of the enterotoxin causes acute symptoms of vomiting, diarrhea and abdominal cramping within 1-6 hours post-ingestion. o Recovery is also rapid, usually within 24 hours. Often, a single food source will cause disease in several people, leading to a mini-outbreak. ➢ Prevention comes from proper food handling which includes washing hands, fruits and vegetables, and keeping cooked hot foods hot [140°F (60°C) or above] and cold foods cold [40°F (4°C) or below].

➢ Salmonella enteritidis o About 1,700 serotypes (including S. typhimurium) o Normal animal intestinal flora (cows, chickens, rodents, reptiles) o Transmission mainly from raw poultry or eggs, reptilian pets, or raw milk. o One of the leading causes of gastroenteritis. o Bacteria is ingested and they invade small intestine epithelial cells o Usually self-limiting in the healthy, causing fever and an inflammatory but water diarrhea with abdominal pain, nausea and vomiting.

Systemic S. pyogenes disease (possible complications of Strep throat)

➢ Scarlet fever o Lysogenic S. pyogenes makes Erythrogenic toxin. o Bright red "sandpaper" rash. o High fever o Immune response damages the vasculature o Deadly if untreated. ➢ Rheumatic Fever o Cross reaction of antibodies made against M protein attack the heart muscle o Can cause permanent heart valve damage o Joint damage can happen too. ➢ Glomerulonephritis o Antibodies made against S. pyogenes form antigen-antibody complexes that deposit in the kidneys (blocks the kidneys normal functions) o Nephritis develops. • Hands, feet and eyes show signs of inflammation, heart failure, and kidney damage.

➢ Staphylococcus saprophyticus is an opportunistic gram-positive staphylococci that is responsible for 5-15% of acute cystitis. ➢ S. saprophyticus can be a resident of the skin, gastrointestinal tract, and vagina. ➢ UTIs caused by this organism is found almost exclusively in sexually active young woman and is the second most common cause of urinary infections in this age group. ➢ Cultures of S. saprophyticus can be differentiated from Staphylococcus aureus because they lack Coagulase (thus referred to as Coagulase-negative staphylococci) and S. saprophyticus is Novobiocin resistant, unlike S. aureus, which is sensitive to Novobiocin.

Describe the different sections of the Tapeworms. Compare and contrast the life cycle, signs and symptoms, diagnostics of Taenia solium (Pork Tapeworm)

➢ Taenia solium (Pork Tapeworm) o Basics • Life cycle mirrors T. saginata but with pigs as intermediate host. • Infection: ingestion of cysticerci in undercooked pork causes tapeworm (Taeniasis): Asymptomatic to mild > diarrhea and weight loss. o Infections • Cysticercosis - infection can also occur via ingestion of eggs in contaminated food and develop a serious condition known as cysticerosis. (Cysticerosis can occur in the eye, brain and muscle tissue) • Larvae hatch from eggs and migrate throughout the body and become encysted in muscles, bladder, eyes, and brain.

Mumps Virus - What viral family this virus belongs to and what are the viral characteristics. Transmission, symptoms, and best form of prevention.

➢ The Mumps virus is a Paramyxovirus that belongs to the same family of viruses which include measles and parainfluenza. ➢ All members of the Paramyxoviruses are RNA, enveloped viruses. ➢ The mumps virus targets the salivary glands (shown above). ➢ Humans are the only reservoir and transmission is via salivary and respiratory secretions. ➢ Symptoms of a mumps infection includes fever, malaise, and inflammation of the salivary glands (especially the parotid glands - Parotitis). ➢ The best form of prevention against Mumps is through the live, attenuated MMR vaccine. o Recall that Mumps infection can often lead to meningitis and possible neurological damage so vaccination is highly recommended.

➢ The best-known fecal coliform and the most abundant intestinal facultative anaerobe. ➢ Most species are nonpathogenic and motile. ➢ Causes an opportunistic infection when it enters the urethra and is the most common cause of UTIs ➢ Some strains are pathogens with differing virulence factors and effects. ➢ True Pathogenic Escherichia coli strains o All are spread via fecal-oral route, from poor sanitation and fecal contamination. • Enterotoxigenic E. coli • ETEC is a major cause of "travellers diarrhea" and infant diarrhea in developing countries - both are watery diarrheas • ETEC is non-invasive and causes severe diarrhea due to heat-labile toxin and heat-stable toxin - stimulate secretion and fluid loss • ETEC is transmitted in developing countries through poor sanitation and use of human feces as fertilizer on food crops. • Enteroinvasive E. coli • EIEC invades the intestinal wall and causes inflammatory disease of the large intestine leading to bloody diarrhea. • EIEC virulence is due to invasion of intestinal epithelium (via invasion proteins) Transmission may be associated with contaminated food. • Enteropathogenic E. coli • EPEC causes chronic diarrhea. Also infantile diarrhea in developing countries (but rotavirus is more common). • EPEC attachment an subsequent injection of proteins directly into small intestine epithelia leads to small intestine microvilli damage and surface effacement causing watery diarrhea. • Enterohemorrhagic E. coli • Also called: o -STEC (shiga toxin-producing E. coli) o -VTEC (verotoxic E. coli) • EHEC is non-invasive but causes attaching and effacing lesions, similar to EPEC but in the colon (EPEC = small intestine) • EHEC produces a hemorrhagic toxin called the shiga-like toxin (Stx) or verotoxin, which nicks the colon cells 60s ribosomes, shutting down eukaryotic protein synthesis. • EHEC Shiga-like toxin can also enter the bloodstream and travel to the kidney, whose cells are particularly vulnerable to the toxin. Disease may thus progress to hemolytic uremic syndrome (HUS and acute renal failure.

Have an understanding of the structure and importance of ATP to the cell

➢ The energy of ATP is in the bonds between phosphate groups. Putting a phosphate group on ADP stores energy and taking a phosphate group off ATP releases energy... ➢ The removal of terminal phosphate releases energy

Why are women more susceptible than men?

➢ The greater frequency of UTI in women is attributable to a shorter urethra compared to males, and a closer proximity of the urethra to the anus, where fecal material harboring enteric bacteria can contaminate the urethral opening. ➢ A shorter urethra makes it more likely that bacteria can quickly make its way to the bladder, resulting in a urinary tract infection.

The Respiratory system is divided into two parts:

➢ The upper respiratory tract (which includes the mouth, nose, nasal cavity and sinuses, the throat (or pharynx), the epiglottis and larynx (or voicebox). ➢ The lower respiratory tract (which begins with the trachea and also includes the bronchi, bronchioles, and the lungs. ➢ To defend against dust, debris, and microorganisms that are always found in the large volumes of air we breathe, the inner lining of the respiratory tract contains mucus that acts as a natural trap for invading microbes and ciliated epithelial cells that propel these particles stuck to the mucus upward and out of the respiratory tract. o These combined first line of defenses are known as the mucociliary escalator.

Diphtheria Transmission, Prevention and Control

➢ Transmission: droplets, direct contact and fomites ➢ Antibiotics and antisera for an infected patient along with heart and respiratory monitoring ➢ Vaccine: DTaP contains the diphtheria toxoid. Interesting History Side Note ➢ Gnome, Alaska, had a Diphtheria epidemic before the vaccine was produced with children dying left and right. ➢ Anti-toxin was in Fairbanks, Alaska, but was way too far from Gnome. So Dr. Welsh sent a panic telegram to try get this anti-toxin.

Describe the general characteristics of Trematodes (Flukes), along with the specific information for the GI Fluke - Fasciolopsis buski

➢ Trematodes (Flukes) o Trematodes (or flukes) are flat, fleshy, nonsegmented flatworms with ovoid leaf like bodies. o All Trematodes have complex life cycles involving snails are their intermediate hosts and water (or aquatic animal or plant) transmission to humans. o Trematodes that infect humans include intestinal, liver, lung and blood flukes. ➢ Fasciolopsis buski (Giant Intestinal Fluke) o Basics • Exceptionally large parasitic fluke (up to 7.5 cm) and largest known to parasitize humans. • Found in Asia and India • Larval form is ingested on water plants, especially water chestnuts and bamboo shoots • Strict vegetarians are susceptible! o Infections • Most infections are mild and symptoms increase with fluke burden. • Signs and symptoms: local inflammation, diarrhea and anorexia. o Diagnosis • Eggs are released into stool and used for diagnosis.

➢ True Enteric Pathogens: Salmonella and Shigella o Non-Coliform members of the Enterobacteriaceae Family. o Non-Lactose fermenters o MacConkey Agar is a Selective and Differential media for distinguishing between lactose and non-lactose fermenting Enterobacteriaceae. ➢ Salmonella o Highly motile, encapsulated organisms o >1,700 serotypes o Of all the serotypes, Salmonella typhi is uniquie in having no nonhuman animal reservoirs o Produce H2S ➢ Salmonella typhi o The most serious pathogen in the genus Salmonella. o Etiological agent of Typhoid Fever. o Humans are the only host and reservoir. o Fecal-oral transmission o Some people are permanent carriers (typhoid Mary) o Infections are uncommon in developing countries (~500 cases/year in the US), versus the underdeveloped world (17 million cases/year w/ 600,000 deaths). ➢ Feces-contaminated food or water is ingested and motile bacilli attaches to intestinal cells. ➢ Gradual onset of headache, loss of appetite, lethargy and fever, with abdominal pain followed by a few short bouts of diarrhea after the second week. ➢ Disease varies from a prolonged, mild, self-resolving fever, but can lead to perforations in the small intestine leading to death.

Urinary Tract Infections Know the signs and symptoms of a urinary tract infection.

➢ Urinary tract infection (UTI) is one of the most common bacterial infections in humans. ➢ By the age of 30, at least 20% of all women have experienced an episode of UTI, and over 50% have one or more lifetime UTIs. ➢ The greater frequency of UTI in women is attributable to a shorter urethra compared to males, and a closer proximity of the urethra to the anus, where fecal material harboring enteric bacteria can contaminate the urethral opening. ➢ A shorter urethra makes it more likely that bacteria can quickly make its way to the bladder, resulting in a urinary tract infection. ➢ Urinary tract infections usually occur when normal flora in the gastrointestinal tract ascend up the urethra into the bladder. ➢ Normally, the flushing action of urine helps to keep infections at bay but if urine flow is reduced or bacteria are introduced into the bladder, a bladder infection (known as cystitis) can occur. ➢ If the infection then spreads to the kidneys it is called pyelonephritis. ➢ Signs and symptoms of cystitis include burning pain upon urination (dysuria), frequent urges to urinate even when the bladder is empty, pain in the pubic area, fever and nausea. ➢ Cloudy urine is indicative of the presence of bacteria and white blood cells, and an orange or red tinge from the presence of red blood cells (hematuria) may be found in the urine. ➢ If back pain is present, this is a sign that the kidneys are now involved in the infection (pyelonephritis).

➢ Vibrio cholera causes the disease cholera resulting in rice-water stools when the bacteria is ingested in contaminated water or from fecal contamination from infected people. ➢ Comma-shaped bacterium that causes cholera ➢ In some humid environments and infected people are the reservoirs. ➢ Ingested with food or water and attaches to intestinal cells. ➢ Vibrio cholera and Cholera o Infects surface of small intestine, noninvasive o Cholera toxin causes electrolyte and water loss through secretory diarrhea, resulting dehydration leads to muscle, circulatory and neurological symptoms.

➢ Vibrio parahaemolyticus and Vibrio vulnificus cause watery diarrhea after ingesting contaminated raw seafood. ➢ Salt-tolerant inhabitants of coastal waters, associate with marine invertebrates. ➢ Vibrio parahaemolyticus - gastroenteritis from raw seafood. ➢ Vibrio vulnificus - gastroenteritis from raw oysters. o Remember that if V. vulnificus gets in to the skin it can cause a necrotizing fasciitis.

Viridans streptococci (Strep. mutans & Strep. sobrinus) - Know gram strain reaction, morphology, hemolytic pattern, and how they promote caries.

➢ Viridans streptococci and alpha hemolysis on blood agar plate. Also, gram positive streptococci arrangement. ➢ The main cause of dental caries are oral alpha-hemolytic viridans streptococci such as Streptococcus mutans. o The viridans streptococci are the most numerous and widespread residents of the oral cavity, nasopharynx, genital tract, and skin. o At least 24 species have been identified and have been divided into 5 groups. o Some other examples include Streptococcus sobrinus, Streptococcus mitis, Streptococcus salivarius, and Streptococcus sanguinis. ➢ In the presence of sucrose and other sugary substances, these bacteria produce sticky polymers of glucose called fructans and glucans. ➢ These polymers initiate the formation of plaque biofilm. o If these biofilms are not removed through good dental hygiene practices, the streptococci and other oral bacteria begin to produce acid as they ferment the carbohydrates and start to erode away at teeth.

Liver Describe hepatitis and the symptoms of hepatitis (jaundice)

➢ When a virus infects the liver tissue the result is hepatitis (an inflammatory disease of the liver that interferes with liver function.) ➢ One of the major symptoms of hepatitis is jaundice (a yellow coloring to the skin and eyes.) o Jaundice results from the lack of liver function which means that old RBCs and their components are left in the blood and tissues. o One of the components in these RBCs is bilirubin, a yellow pigment which deposits into the fat of the skin and the whites of the eyes when it's not properly processed and removed by the liver. ➢ In addition to the distinct yellowing of the skin, you can often see yellowing in the whites of the eyes. The whites of the eyes are sometimes the first place you notice the jaundice:

For the following causative agents of acute food poisoning, know gram stain reaction, morphology, the exotoxins they produce, and what foods are associated with each: 3. Clostridium perfringens

➢ You may remember Clostridium perfringens as being the causative agent of gas gangrene, but the endospores of this gram positive bacillus can also contaminate many kinds of foods. ➢ The foods most likely to cause food intoxication from this organism are meat dishes, stews and gravies that are improperly reheated. o When these foods are cooled, kept only warm for long periods of time, or left unrefrigerated, spores can germinate and the cells begin to multiply. o If the food is eaten without adequate reheating, C. perfringens enters the small intestines and releases exotoxin. ➢ The C. perfringens exotoxin is an enterotoxin that acts upon the epithelial cells of the small intestines, causing watery diarrhea, nausea (usually without vomiting), and severe abdominal cramping and pain. ➢ Symptoms begins to arrive in 8 to 16 hours post-ingestion of contaminated food. ➢ The recovery is rapid and no treatment is required as deaths are extremely rare.

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