Final Exam - Study Guide and Practice Questions

What is the difference/similarity between a bacteriophage and a virus?

Virus is the general class of an organism

Phage is a subclass of virus that infects bacteria

How big is a typical bacteriophage or virus?

MUCH smaller than the cell it infects; most are 30 to 300 nm (bacteria average 1000 nm in diameter)

What is the basic structure of a bacteriophage or virus?

Nucleic acid surrounded by protein capsid

What types of nucleic acids are present in their genomes?

All varieties - ssDNA, dsDNA, ssRNA, and dsRNA

What steps are involved in the reproductive cycle of a T4 lytic phage?

Early - takeover of host cell machinery

Middle - replication of phage genome

Late - capsomer production, capsid assembly, genome packaging, and host cell lysis

What is happening during the latent period of a phage lytic infection?

No increase in the number of phage-forming units = early and middle functions; PFU only increase during packaging

What is involved in the reproductive cycle of a lambda lysogenic phage?

Most phage go into lytic cycle, some go into lysogenic cycle where phage gene expression is silenced and the phage DNA is inserted into the host chromosome

The phage DNA is replicated along with the host DNA during all ‘LYSOGEN’ cell growth and division; eventually, the ‘PROPHAGE’ can be induced, it exits the host chromosome and starts the lytic cycle anew

How can you measure the abundance of bacteriophages?

Plaque assay: spread phage sample on plate along with many host cells, and incubate to get bacterial lawn; count the number of clear spots where cells were lysed = plaques (each plaque derived from one phage particle)

What is involved in the reproductive cycle of a retrovirus?

ssRNA is used as template to produce dsDNA by REVERSE TRANSCRIPTASE

• DNA inserts into host cell chromosome by INTEGRASE

• HIV genes are expressed from that PROVIRUS to produce mRNA, which is also the positive (+) strand RNA assembled into viral particles

• Translation produces polyprotein, which is cleaved into individual viral protein components by HIV protease

What is an enveloped virus and what types of molecules make up the envelope?

A virus that has a membrane surrounding the nucleocapsid, generally infecting animal cells

The envelope contains lipids from the host cell cytoplasmic membrane plus viral ‘spike’ proteins that were inserted into that membrane during viral growth

What is the difference between ‘RNA replicase’ and ‘reverse transcriptase’?

RNA-directed RNA synthesis vs. RNA-directed DNA synthesis

How do influenza viruses undergo antigenic shift?

They acquire as significantly different gene encoding one of the two major antigens (H or N) when a single cell is infected by two different influenza virus strains—this can happen only because of the Influenza genome is made up of 8 separate RNA molecules, each encoding a different protein

What is a viroid?

An infectious RNA molecule, infecting plants, that does not encode any protein

What is a prion?

An infectious protein molecule that is not produced from any infectious nucleic acid; the gene is in the host chromosome, and the protein is only infectious when it is improperly folded and able to catalyze the further misfolding of host-produce proteins

What is positive (+) strand RNA?

mRNA

What is negative (-) strand RNA?

The complement of mRNA, which can be used as a template by RNA replicase to produce positive strand RNA

What is the structure of the human airways?

Includes the nasal cavity, pharynx, larynx, trachea, bronchi, bronchioles, and alveoli

Air passes from the upper respiratory tract (nose and throat) into the lower tract (trachea and lungs)

What size particles can enter the alveoli of the lungs and how does this help prevent airborne infections?

Only very small particles (typically under 5 micrometers)

Size restriction helps prevent many airborne pathogens and larger particles from reaching the deepest parts of the lungs

What is the appearance of a strep throat infection and which tissues in the throat are involved?

Caused by Streptococcus pyogenes; presents with redness and swelling in the throat, often involving the tonsils and pharynx, and can include white pus spots

Where does a diphtheria infection occur in the body?

Primarily occurs in the upper respiratory tract, especially in the throat and nasal passages

Why is diphtheria toxin so deadly (what does it do to host cells)?

Inhibits protein synthesis in host cells, leading to cell death—this systemic effect can damage the heart, nerves, and kidneys

Where does a pertussis infection (whooping cough) occur in the body?

Upper respiratory tract, specifically targeting the trachea and bronchi

What aspect of whooping cough is so deadly to infected infants?

Intense coughing fits which can cause apnea (pauses in breathing), leading to oxygen deprivation and potentially death

How common are TB infections in people around the world?

2 billion people infected

10.8 million new cases/year (2023)

1.25 million deaths/year

What cells in the body are infected by TB bacteria?

Phagocytic cells like macrophages in the lungs

In what organ is the level of infection highest and in what part of that organ are the most bacteria found?

In the lungs, specifically in the apices (upper parts) of the lungs, where oxygen levels are highest and the bacteria thrive

What does measles look like in humans?

Red blotchy skin rash, high fever, cough, runny nose, and conjuctivitis (red eyes)

What are some of the long term and sometimes life-threatening consequences that can occur from measles?

Pneumonia, encephalitis (brain inflammation), permanent hearing loss, and, in rare cases, a fatal brain disorder called SSPA (subacute aclerosing panencephalitis)

What vaccine is used to prevent measles?

MMR (measles, mumps, rubella) vaccine

What does rubella look like in humans?

Mild pink rash that starts on the face and spreads, often with low fever and swollen lymph nodes

What are some of the long term and sometimes life-threatening consequences that can occur from rubella?

Congenital rubella syndrome in infants, causing birth defects like deafness, heart defects, and intellectual disabilities if infection occurs during pregnancy

What vaccine is used to prevent rubella?

MMR (measles, mumps, rubella) vaccine

What does mumps look like in humans?

Noticeable swelling of the salivary glands, especially the parotid glands on the sides of the face

What are some of the long term and sometimes life-threatening consequences that can occur from mumps?

Orchitis (testicle inflammation), oophoritis (ovary inflammation), meningitis, hearing loss, and rarely, infertility

What vaccine is used to prevent mumps?

MMR (measles, mumps, rubella) vaccine

What does chicken pox look like in humans?

Itchy rash with red spots that turn into fluid-filled blisters, then scab over; it may also include fever and fatigue

What are some of the long term and sometimes life-threatening consequences that can occur from chicken pox?

Pneumonia, encephalitis (brain inflammation), and bacterial skin infections—the virus can also remain formant and reactivate later as shingles

What vaccine is used to prevent chicken pox?

Varicella vaccine

What are the symptoms of colds?

Sneezing, sore throat, runny nose, mild cough, and congestion

What are the symptoms of the flu (Influenza)?

High fever, body aches, fatigue, cough, chills, and headache

How are colds and flu spread from person to person?

Both are spread via respiratory droplets from coughing, sneezing, or contact with contaminated surfaces

Do colds or the flu occur at a higher frequency?

Colds occur more frequently than the flu

How do flu viruses use infections in pigs and birds to change their antigens on a yearly basis?

Antigenic shift happens when different strains infect the same animal, mixing their segmented RNA genomes; this creates new virus strains with surface antigens (hemagglutinin and neuraminidase) unfamiliar to the human immune system

What does a flu pandemic look like if you draw it on a map showing the spread of the disease?

Rapid, global spread of infection across continents, often radiating outward from an epicenter as new regions become affected over time

What are perishable foods?

Fresh foods (highest water content)

What are semi-perishable foods?

Potatoes and nuts

What are stable or non-perishable foods?

Flour and sugar (least water content)

What are common ways that foods can be prepared to improve their shelf-life?

Acidity (pickling)

Drying, or add sugar or water to reduce water activity

Chemical preservatives

Canning

Irradiation

Pasteurization

What is food poisoning?

Microbe grew in the food and produced a toxin; the microbe may or may not survive ingestion, but the toxin still acts (generally ‘self-limiting’)

What is food infection?

Microbe is in the food but then grows inside body (once consumed) causing infection

How is an enterotoxin the same or different in comparison to endotoxins and exotoxins?

Exotoxins are proteins secreted by bacteria and include enterotoxins

Endotoxins are lipopolysaccharides (LPS) from the outer membrane of the Gram-negative bacteria, released upon cell death

Enterotoxins are a type of exotoxin that specifically targets the intestines, causing diarrhea and vomiting

What are main characteristics of food poisoning caused by Staphylococcus aureus?

Heat stable enterotoxins

Nausea, vomiting, diarrhea (1-6 hours)

• Egg/meat salads, salad dressing, desserts, meat, improper heating/chilling

What are main characteristics of food poisoning caused by Clostridium perfringens?

Spore former (can survive cooking)

>10^8 cells ingested, sporulation occurs in small intestine

Produces CPE (C. perfringens enterotoxin)

Diarrhea and cramps (7-15 hours)

• Chili, salads containing meat, improper heating/chilling

What are main characteristics of food poisoning caused by Clostridium botulinum?

Spore former (can survive cooking)

Botulinum toxin (heat labile), cosmetic applications

Few cases, but high mortality

Paralysis (18-24 hours)

Treatment with ventilation and antitoxin

Where can organisms—such as Staphylococcus aureus, Clostridium perfringens, and Clostridium botulinum—be found naturally and how do they end up in food products?

Staph is on your hands

Clostridia spores are everywhere

How does botulism toxin work?

Blocks the release of acetylcholine at neuromuscular junctions, leading to flaccid paralysis

It is heat-liable and can be fatal if respiratory muscles are affected

Where can infant botulism be found naturally and how do they end up in food products?

Often from honey, can be environmental

Due to immature immune system and immature intestinal flora

Hypotonia

Treatment with ventilation and tube feeding

Generally self-limiting (3-6 weeks)

Where is Listeria monocytogenes commonly found in nature and food?

Water, soil, meat, dairy products, and fresh produce

Contamination often occurs during food processing

What environmental conditions can Listeria monocytogenes survive?

It tolerates acid, salt, and cold; it is psychrotolerant (can grow at refrigerator temperatures)

What type of pathogen is Listeria monocytogenes?

An intracellular pathogen that polymerizes host cell actin to move and spread between cells

What are the symptoms and risks of Listeria food infection?

Most infections are mild or unrecognized, but severe cases can cause bacteremia and meningitis, especially in pregnant or immunocompromised individuals

What kind of virus is Norovirus and what illness does it cause?

RNA virus that causes stomach flu or viral gastroenteritis

What are the main symptoms of Norovirus infection?

Fever, chills, headache, muscle aches, diarrhea, and vomiting

How is Norovirus transmitted?

It is highly contagious and spreads through contact with infected people, surfaces, or contaminated food

How long does Norovirus illness typically last?

It is self-limiting and typically resolves in 1-2 days

How are bacteria used to help leach copper metal from crude ores?

Oxidize iron to produce ferric iron (Fe3+) which reacts with copper sulfide in ores to release copper ions; the bacteria work after acid (H+) is added to help solubilize the metal during leaching

What chemicals are added to the ore during copper leaching, and at what stage do the bacteria play an important role?

Sulfuric acid (H2SO4) is added to solubilize metals

Bacteria like Acidithiobacillus species oxidize ferrous iron (Fe2+ to Fe3+) and sulfur compounds during the leaching process, enhancing copper recovery

What is the toxic chemical produced in most acid mine drainage from coal mines?

Sulfuric acid (H2SO4) which is produced when bacteria oxidize pyrite (FeS2), with iron playing a key role in the oxidation process

How are bacteria used to remove uranium from contaminated environments?

Reduce soluble U^6+ (uranium VI) to insoluble U^4+ (uranium IV, uraninite), which precipitates out of groundwater

What property of uranium ions is important in the process for bacterial cleanup?

The solubility of uranium - U^6+ is water-soluble, while U^4+ is insoluble and precipitates from the solution when reduced by bacteria

Why was the Valdez oil spill in Alaska so difficult to clean up?

The cold water slowed bacterial metabolism and growth, making it harder for microbes to degrade the oil efficiently

What metabolic property of bacteria is used in oil spill clean-up?

Bacteria can use hydrocarbons in oil as a carbon and energy source, breaking them down biologically

How is the organic pollutant 2,4,5-T broken down by bacteria and what are the products?

Through enzymatic breakdown which produces CO2 and biomass (cell material) as end products

Give an example of a difficult plastic to break down.

Polyethylene (plastic bags)

Give an example of a plastic that is easier to break down using bacterial action.

Biodegradable plastics like polylactic acid (PLA) are more easily broken down by microbial enzymes

In wastewater treatment, how many stages are there? What takes place at each stage?

Primary - physical removal of solids (screening and sedimentation)

Secondary - biological degradation of organic matter using microbes

Tertiary/Advanced - chemical or biological processes to remove nutrients like nitrogen and phosphorus

What are the two types of secondary treatment in wastewater treatment, and how do they differ from one another?

Aerobic treatment - uses oxygen and aeration tanks to support bacteria that degrade organic matter

Anaerobic treatment - no oxygen; uses anaerobic microbes to break down material, producing methane and CO2

What process is used to remove NH4+ from wastewater? What is the NH4+ converted to that is not toxic to the environment?

Nitrification - NH4+ is biologically converted to nitrate (NO3-), which is less harmful to the environment

What chemical is added to water to kill most bacteria remaining after treatment?

Chlorine is added to disinfect the water

How is water distributed to a town and how is water pressure maintained even if the electricity is shut down?

Water is stored in elevated water towers that use gravity to distribute water and maintain pressure, even if electricity is off

The protein coat that surrounds the viral nucleic acid is called a ___.

Capsid

Class I viruses are examples of ___ viruses.

dsDNA

What enzyme do T4 phages use to help them inject their nucleic acid through the cell wall into the cytoplasm?

Lysozyme

What phage is lysogenic?

Lambda

What enzyme must retroviruses carry the gene coding for?

Reverse transcriptase

Which virus can be transmitted even in the absence of symptoms?

COVID

Shingles are an adult-onset infection caused by what virus?

Chicken pox

M. tuberculosis infects and lives inside which type of cell in the lung?

Macrophage

What is the main cause of death in children from whooping cough due to?

The cough itself

How many molecules of diphtheria toxin does it take to kill a single human cell?

1

What type of food-borne infection is associated with cruise ships?

Norovirus

What food is often contaminated and leads to an infant botulism infection?

Honey

What is typically the most common food-borne infection in the US?

Campylobacter species

T/F: Pasteurization leads to complete sterilization of the treated food.

False

What is the number one cause that contributes to food-borne disease outbreaks?

Inadequate refrigeration

What gas is a major waste product of an anaerobic sludge digestor?

CH4

What plastic is most easily broken down by bacterial action?

PHB/PHV

In acid mine drainage, what is the main form of acid seen with coal mines?

H2SO4

The bacterium Acidothiobacillus ferroxidans is used to mine which metal (not the obvious one)?

Copper

What is used as a substitute for chlorination to kill contaminants, especially in Europe?

UV irradiation