MicroBio 420

T/F The complement system is part of the specific immune response.

False Along with phagocytosis, the complement system is part of the innate immune response.

T/F There are no antigens that can stimulate B cells without T cell help.

False Antigens that stimulate B cells directly are called T-independent antigens.

T/F Both human cells and bacterial cells divide by mitosis.

False Bacteria divide by binary fission and human cells divide by mitosis. The processes are similar in the fact that both involve the division of one cell into two genetically identical cells

T/F. All viruses can infect any cell type or tissue type.

False Because a virus must attach to host cell cytoplasmic membrane receptors for entry into that cell, a virus may only be able to infect a single or a limited number of cells or tissues (tissue tropism).

T/F Generalized transduction is so called because specific bacterial genes are transferred during this process.

False In generalized transduction, any segment of bacterial DNA can be transferred. During specialized transduction, specific genes are transferred, depending on where the viral DNA is integrated into the bacterial chromosome.

T/F Generalized transduction involves the transfer of phage genes from one bacterial cell to another.

False The genes that are transferred are bacterial genes.

Activated complement proteins play a part in eliminating microbial invaders from a host. They belong to the group of non-specific immune responses. Which of these is NOT part of that group?

Plasma cells

T/F Environmental factors control microbial growth through their effect on enzyme activity.

true. Factors such as pH, temperature, and moisture have an effect on bacterial enzymes, which influence bacterial cell division.

Arrange the following experiments from the oldest to the most recent in the scientific journey towards disproving spontaneous generation.

Redi, Needham, Spallanzani, Pasteur

During viral infection of a host cell, which is the third step of the process?

Release of nucleocapsid into host cytoplasm

Which of the following is NOT one of the molecular Koch's postulates?

Replacement of the mutated virulence gene with a wild-type gene should have no impact on the virulence of the strain.

Which of the statements is FALSE?

Rhizobia transfer some of their DNA into the host plant

bacillus/bacilli

Rod shaped bacteria

Steriliants

destroy all microbes, including viruses and endospores. Destruction of endospores usually require 6 to 10 hours treatment. Steriliants are used to treat heat-sensitive materials critical instruments like scalpels. Example - ethylene oxide

By keeping food cold, the growth rate of food spoilage microorganisms is

decreased

What are molecules other than ATP that carry energy in the cell?

glucose-in cell respiration and glycolysis, pyruvate- krebs cycle, aceytyl coA, NADH=ECT, FADH2-ECT, GTP

Neutrophilic bacteria (pH)

grow at pH 6-8. All human pathogens belong to this group. includes the majority of bacteria

Spirochetes (shape)

helical cell with axial filament, spiral-shaped bacteria that have flexible walls and are capable of movement

Acid fast cell wall

highly hydrophobic •Thick layer of peptidoglycan covered by lipopolysaccharides and layer of hydrophobic mycolic acids, lipids, and waxy material, which makes the cell wall very hydrophobic. •Acid-fast bacteria are slow growing organisms. •Cells of Mycobacterium tuberculosis are dividing once in every 24 hours •Cells of Mycobacterium leprae are dividing once in very 12 DAYS •Compare to Gram-negative Escherichia coli (E. coli) that is dividing every 20 min •Microbes are highly resistant to antibiotic treatment •Clinically important acid-fast bacteria of the following genera: Mycobacterium, Nocardia

John Needham's experiment was clever and well accepted by the scientific community during his time because ______.

his method of "cooking" the broths was how they normally cooked during that time.

The complement system components react

in a cascade.

Which of the following are mechanisms pathogens use for avoiding recognition and attachment by phagocytes?

inactivating complement component Cb3, producing capsule that binds the host's complement regulatory proteins, producing M protein for inactivating complement component Cb3, producing receptors that allow binding of Fc region of antibodies and prevent osponization

Fluorescent dye

is a chemical capable of emitting the light of particular color (for example - green) upon absorption the light of another color (for example - blue). •Fluorescein absorbs light at 488 nm (blue) and emits light at 520 nm (green) •Rhodamine absorbs light at 540 nm (green) and emits light at 560 nm (red).

Pure microbial culture

is a culture containing only one microbial species. It can only be obtained (isolated) by growing microbe on solid medium like nutrient agar etc.

Pure Bacterial Culture

is a culture that contains only one bacterial species or strain - It can be isolated only by growing bacteria in the laboratory on solid culture medium

Culture medium/a

is a mix of nutrients and water required for bacterial growth

First line of defense

is a part of innate immunity and is directed at preventing the entry of microbes into human body. It has 3 main components: • •Skin is built of multiple layers of the cells that act as physical barrier between microbes and internal content of the body. The upper layers are made of dead cells that are bathed in skin antimicrobial secretions like: •Sebum has acid pH 4-5 and oily components inhibiting bacterial growth, •Sapienic acid produced only in humans and has antimicrobial activity, •Sweat has high salt content that has inhibitory effect on microbial growth •Lysozyme is secretory enzyme that digests bacterial cell wall • •Mucous membrane is made of 1-2 layers of live cells that act as physical barrier between microbes and the tissues of human bodies. It is bathed in various secretions like: •Mucus - a sticky material that traps entering microbes. Then mucus is removed along with bacteria by ciliated cells, •Ig A secretory antibodies that can bind to microbes and subjecting them to phagocytosis, •Lysozyme is secretory enzyme that digests bacterial cell wall •Stomach juice has strong acid pH 2 and proteases that kill most of the microbes upon their entry to stomach •Saliva contains lysozyme and also mechanically removes microbes. • •Normal flora (microbiota) is made up of microbes residing in/on healthy individuals. •They prevent colonization of host organism by pathogens by: •Producing antibacterial substances and inhibiting growth of pathogens •Covering the binding sites that can be used by pathogens •Sequestering nutrients that otherwise can be used by pathogens •Training immune system for possible invasion of pathogens •EXAMPLES: •Archaea - Methanobrevibacter smithii; •Bacteria - Escherichia coli, Lactobacillus acidophilus, Cutibacterium (Propionibacterium) acnes; Staphylococcus epidermidis; Staphylococcus aureus Streptococcus mutans; •Fungi - Candida albicans, Saccharomyces cerevisiae, •Gastric juice is produced by various cells of stomach lining •Hydrochloric acid is produced by parietal cells •Digestive enzymes are produced by chief (zymogenic) cells •Protease (pepsin) •Gastric lipase •Mucus is produced by foveolar cells tears, saliva

Pasteurization

is a process when bacteria causing spoilage are killed by a heat applied for a short time - beverage is heated to 60OC for 30 min, which kills vegetative bacteria

Antibody

is a protein capable of specific interaction and binding to macromolecule (like another protein), thus labeling any cellular structure containing this macromolecule. •If the antibody can bind to protein X and is tagged with fluorescent dye, it can be used in fluorescence microscopy to visualize the cells or even their organelles containing the protein X. •The cells and cellular organelles lacking protein X would not be stained by the antibody and, therefore, would not be visible during examination of the specimen under the fluorescent microscope.

Metabolism

is a sum of all chemical reactions that take place in the cell. It has two branches: •Exergonic (catabolic) •Endergonic (anabolic)

Exotoxin

is a toxin that can cause damage to the host by destroying cells or disrupting normal cellular metabolism. They are highly potent, highly specific and can cause major damage to the host. Exotoxins may be secreted, or may be released during lysis of the bacterial cell.

Normal Flora (NF) presence

is always beneficial to healthy host •Microbial antagonism - prevent and inhibit the growth of pathogenic microbes by: •Competing for binding sites needed for attachment to the host; Competing for nutrients making them scarce; Making pH of environments acidic - most of microbes can not grow at pH 6.0; Producing antimicrobial compounds •Stimulation of host immune system - •Vitamins K and B produced by E. coli are needed for immune system functioning; •Immune system may produce antibodies to NF cross-reacting with pathogen. Immune system can be exposed to NF due to injuries of the skin or mucous membrane injuries; •Aiding digestion - intestinal microbiota help extract energy from food more efficiently

T/F Rod-shaped bacteria such as Escherichia coli, Salmonella, and Bacillus species synthesize new cell walls over the entire surface of the cell.

true

The generation time of Mycobacterium tuberculosis is

12 hrs

What was the total number of people in the U.S. colonized with C. auris at the time this report was written?

122

For each glucose molecule broken down by glycolysis, how many net ATP molecules are produced?

2 n the investment phase of glycolysis, 2 ATP molecules are used. However, in the payoff phase of glycolysis, 4 ATP molecules are made. This yields a net ATP production of 2 ATP molecules per glucose molecule.

Arrange the following in the proper sequence in which they occur during a single PCR cycle .1. Addition of DNA nucleotides by Taq polymerase 2. Complementary base pairing between primers and target DNA 3. Heat separation of strands of target DNA

3,2,1

During glycolysis, a single 6-carbon molecule of glucose is converted to two 3-carbon pyruvate molecules. During the later steps in this process, how many molecules of ATP are generated?

4

tetrads (grouping)

4 cocci in a square

The decimal reduction time is the time it takes to kill 90% of a given bacterial population under certain conditions. If 90% of a population of 100,000 bacteria is killed in 10 minutes, how long would it take to reduce the population to 10 cells?

40 min

Approximately what proportion of women developed puerperal fever in Dr. Klein's ward once medical personnel started washing their hands?

6%

Which enzyme is NOT involved in DNA replication?

RNA Polymerase

Viral Taxonomy shapes of viruses

complex, Polyhedral, enveloped, Filamentous

O Antigen

composed of polysaccharides, used to identify bacteria strains, outermost part of LPS

Enterotube

contains 12 different nutrient media that allow to detect tested bacterium's ability to use or produce a particular chemical compound.

The membrane attack complex kills cells by

creating holes in cell membranes.

Spirillum/a (shape)

curved rod long enough to form spirals

All of the following cells have class II MHC receptors on their surface EXCEPT.

Red Blood Cells

In viral entry by endocytosis

the host cell's cytoplasmic membrane surrounds the whole virion and forms a vesicle.

Eliminated diseases

the ones that are no longer naturally occur

The germ theory of the disease

(also called the pathogenic theory of medicine) proposes that microorganisms are the cause of many diseases. It was established by Robert Koch

If the label in box A is "cold sores," what is the label in box B?

Cold sores (2 red pyramids, dark red in middle is A and B)

Classification

- It is arrangement of biological species into taxa (singular - taxon) of various ranks. •High ranked taxon may include multiple taxa of lower ranks •Taxa from highest-ranked to lower ranked: •Domain à Kingdom à Phylum à Class à Order à Family à Genus à Species •The closer two species related to each other, the lower taxon they will share.

Nomenclature

- It is the system of assigning names to biological species. •It uses binominal nomenclature or two-worded name system, where first word in name describes the genus to which organism belong and second name describes the species itself. •Homo sapiens - Homo is genus, sapiens is description of species. •Escherichia coli - Escherichia is genus, coli is description of species itself.

•Commensalism

- Microbes establish association with the host organism beneficial to the microbe. Host remains unharmed. These microbes can be opportunistic pathogens - causing the infections only when host is weak. •Examples : •Staphylococcus epidermidis - part of normal flora of humans residing on the skin. It lacks any virulent factors and kept by immune system in check. However, it may became a threat to immuno-compromised individuals. •Staphylococcus aureus - part of normal flora of humans, residing on the skin and in the nostrils, causing from time to time local infections like hair follicle infections or boils

•Mutualism

- Microbes establish mutually beneficial association with the host organism •Examples : •Escherichia coli inhabits intestine. It takes part in food digestion. It syntheses vitamins K and B. It trains immune system; •Lactobacillus spp. inhabit intestine and urogenital system preventing the growth of pathogens (like Clostridium spp) and opportunist pathogens like Candida albicans

Evolution of enzymes

- Over the years of evolution, the enzymes have adapted to perform best at specific conditions •DNA polymerase is the enzyme copying of chromosomes (in DNA synthesis) •Human DNA polymerase shows highest rate of enzymatic reaction at 37OC, which is the temperature of human body •Microbial DNA polymerase isolated from thermophilic bacterium shows highest rate of enzymatic reaction at 72OC, which is the temperature of hot springs where the microbe resides •Proteases are enzymes that can hydrolyze the proteins to small polypeptides or amino acids. These enzymes are important in digestion of food •Pepsin is a protease found in human stomach. It shows the highest rate of enzymatic reaction at pH 2, which is the pH of stomach juices •Trypsin is another human protease but located in small intestines. It shows the highest rate of enzymatic reaction at pH 8, which is the pH of digestive juices secreted in to the lumen of small intestines

Replication of DNA viruses

- Viral genome goes to nucleus - Herpesviridae; Poxviridae •dsDNA goes to nucleus to make mRNA and DNA copies. •ssDNA goes to nucleus and converted into dsDNA by host enzymes - Parvoviridae; •ss (+) DNA used to make dsDNA (replicative form), which is used to synthesize ss (+) DNA copies for new viral particles. •ss (-) DNA used to make mRNA for translation

Producers (photosynthetic autotrophs)

- are any organism that are capable of photosynthesis •They include all photosynthetic prokaryotes (archaea and bacteria), algae, lichens, and green plants (photo-auto-trophs) through process of photosynthesis accomplish: •Conversion of sunlight energy into energy of chemical bonds stored in producers •Extraction of carbon from inanimate world and returning it to living system in form of organic molecules - sugars •Production of free oxygen

Consumers (photosynthetic autotrophs)

- are any organism that is feeding on another living organism •Primary consumers are those that feed on producers - herbivores, plant viruses, plant pathogenic bacteria •Secondary consumers are those that feed on other consumers (carnivores or predators) or on other consumers and producers - viruses, pathogenic bacteria •Decomposers are those who consume only dead organic material - fungi, most of bacteria, scavengers (heterotrophs) by eating other organisms & cellular respiration accomplish: •Energy transfer from one organism to another •Transfer of nutrients from one organism to another •Returning carbon to inanimate world from living system in form of carbon dioxide •Release of energy from ecosystem as heat Types of consumers: •Primary consumers - herbivores •Secondary consumers - carnivores, omnivores •Decomposers - consuming dead organisms

Aerobic

- grow at normal atmospheric condition - 20% O2 -Most bacteria, including pathogens

Sterilization

- it is a procedure that kills or removes all microbes, including endospores and viruses •Destruction of microbes can be achieved by heat (autoclaving, dry heat, incineration), chemical treatment (ethylene oxide, peracetic acid ) or irradiation (X-ray, UV light) •Still, sterilized item may have prions present; •Removal of microbes can be achieved by filtration (however, the viruses can pass any filter);

Identification

- it is a process of description (characterization) of an organism to determine to which species or which taxon it belongs. •It is done by using dichotomous key, when questions about specific properties of an organism are asked. •The answer to first question determines which question is asked next. It continues until species or lowest possible taxon in determined. •Identification starts with the questions asking about the most common properties and as identification proceeds the questions become more and more specific.

Disinfection

- it kills or removes all pathogens. Non-pathogens and endospores may survive the treatment. Disinfection can be achieved by two types of chemical compounds: •Disinfectants are antimicrobial chemicals that are toxic to humans. •They are used on inanimate objects like floors, desks etc. •EXAMPLES: bleach; hypochlorous acid; chloramine; aldehydes; •Antiseptics are antimicrobial chemicals that have limited toxicity to humans. •They can be used on human skin •EXAMPLES: hydrogen peroxide; iodine-containing substances (5% solution, betadine, povidone), 60% - 95% alcohol

Preservation

- it prevents bacterial growth or germination of endospores •Addition of sugar, vinegar or any other Bacteriostatic compound like nitrites or sorbitol can prevent bacterial growth or germination as long as certain concentration of chemical is maintained.

Dynamic nature of normal flora

- its makeup depends on many factors like: • Physiology and activity of host affects the normal flora make up of the individual •Hormonal level; Food - many spices have some antimicrobial activity; Drugs taken - particularly antibiotics, immuno-suppressants; Travel - particularly to exotic countries • Presence and condition of other members of the Normal flora •Lactobacillus suppresses the growth of Candida albicans by lowering pH to 5-5.5. •Suppression of Lactobacillus increases pH and leads to candidiasis / enterocolitis

•Parasitism

- microbe benefits at expense of host. These microbes normally are not present on healthy individual and they have multiple virulence factors that help them break the defense systems of humans and cause the disease. •Examples : •Yersinia pestis - it infects lymph nodes or lungs and is causing plague in humans •Vibrio cholerae - it infects intestines and is causing cholera in humans •Viruses - they are all obligate parasites and some are causing diseases in humans

Reservoir

- natural habitat of pathogen suitable for its survival outside of host for extended time •Human reservoir - the most important source, since humans may carry microbes with no symptoms •Symptomatic infections - signs and symptoms of disease are obvious and can be easily observed •They are caused by Streptococcus pyogenes, Corynebacterium diphtheriae, Influenza virus, over 200 various types of viruses causing common cold •Asymptomatic carriers - people that have infections that have not developed (yet) in to the disease and thus do not display and signs and symptoms of the disease •These people quit often would carry Staphylococcus aureus, Mycobacterium tuberculosis, Hepatitis virus, HIV before infection develops in to AIDS, gonorrhea (particularly in females - up to 30% of cases) •Animal reservoir - zoonotic disease that potentially can be far more severe in humans than in animal host •EXAMPLES: Salmonella; Yersinia pestis (Plague); Vibrio cholerae; Rabies virus; Borrelia (Lyme disease) •Environmental reservoir (soil, water) - impossible to control •EXAMPLES: Clostridium botulinum, Clostridium tetani; Vibrio cholerae; Klebsiella spp, Legionella spp.

Cell rupture

- rapid release of viruses leading to host cell death within few hours or days

•Capnophilic

- require higher CO2 concentration -Candle jar or CO2 incubator are used -Microbes that digest cellulose in stomach of ruminant animals (cows)

Micro-aerophilic

- require low O2 concentration - 2-10% -Incubated in gas-tight jars where chemical packets are places to make hydrogen and CO2 -Helicobacter pylori (stomach infections); -Borrelia burgdorferi (causing Lyme disease)

•Anaerobic

- require strict oxygen-free environment -Grown in anaerobic jars in the presence of chemicals that convert free oxygen into other molecules, like CO2. or in anaerobic chamber where O2 replaced for N2. -Clostridium spp. -Bifidobacterium (used to prepare yogurt)

Budding

- slow release of viral particles over extended period of time. It enables viral survival in host organisms and infected cell over extended period of time, like months or even years

Growth and development (properties of life )

- the ability of organism to increase in size and build new complex structures that were initially absent •It involves catabolic reactions and results in increased weight of organism, increased number of cells, appearance of new features of organism

Reproduction (properties of life)

- the ability of organism to produce offspring •The genetic information is transferred from parental organism(s) to offspring

Plaque assays

1.Sample is mixed with bacterial cells in warm melted "upper agar" •This 'upper agar" has twice less agar content than normal solid medium, •Therefore, it solidifies at room temperature 2.The mix is overlaid on solid agar growth medium and left to solidify 3.Plates are incubated for 24 hours at temperature optimal for growth of bacterial host 4.As bacteriophages infect the cells and replicate, they lyse the bacterial cell forming plaques (clear zones) on bacterial lawn (cloudy background)

Replication of RNA viruses

- viral genome stays in cytoplasm •dsRNA - Viral RNA used to produce RNA-depended RNA polymerase, which is used to make copies (-)s-RNA and (+)s-RNA. Reoviridae (rotavirus). •ssRNA •(+)sRNA - Viral RNA used to produce RNA-dependent RNA pol, which is used to make copies of (-)RNA used to produce (+)RNA in cytoplasm. Picornaviridae (hepatitis A). Togaviridae (rubella) •(-)sRNA - RNA-dependent RNA polymerase present in virus makes (+)RNA in cytoplasm that is used as mRNA & as template for (-)s-RNA. Rhabdoviridae (rabies) •(+)sRNA and Reverse Transcriptase - replication of retroviruses see next slide. Retroviridae (HIV)

Gas production (cell products)

-Gas production monitored by using Durham tube •Inverted tube traps the gas produced by growing bacteria -This methods will be used in water testing lab by growing bacteria in lactose broth containing inverted Durham tubes

CD4+ T cells1. include helper T cells.2. include cytotoxic T cells.3. recognize antigen presented on MHC class I.4. recognize antigen presented on MHC class II.

1, 4

Label the prokaryotic and eukaryotic ribosomes with the appropriate subunits.

1. 50S, 60S 2. 30S, 40S 3. 70S, 80S

Animal virus replication

1. Attachment of virus to host cell occurs via viral surface proteins-adhesins and cellular receptors 2. Entry of viral particle into a cell 3. Uncoating and release of viral NA occurs with help of viral or cellular enzymes 4. Replication of virus: - If DNA, viral genome enters nucleus where copies of viral DNA and viral RNA are made using cell enzymes, then both exported to cytoplasm and RNA used to make viral proteins using cell resources - If RNA, viral genome stays in cytoplasm, where copies of viral RNA and viral proteins are made 5. Assembly of viral particles from viral NA and viral proteins occurs spontaneously, no energy required 6. Release of viral particle occurs: -- via budding or -- via cell lysis

Match each of the following aerobic chemolithotrophs with their characteristics.

1. Gram-negative bacteria that obtain energy by oxidizing inorganic compounds like ammonia. 2. Gram-negative obligate chemolithotrophs, use H2 as an energy source with O2 as a terminal electron acceptor. 3. Gram-negative rods/spirals, may form filaments, obtain energy by oxidizing hydrogen sulfide and thiosulfate with O2 as a terminal electron acceptor.

Rank the germicides from most to least potent.

1. Sterilants 2. High-level disinfectants 3. Intermediate-level disinfectants 4. Low-level disinfectants

Steps of productive infection (lytic cycle) in bacterial cells

1.Attachment - adhesins of bacteriophage bind to receptors of the cell 2.Entry - Viral tail contracts and inject viral DNA into the host cells, viral proteins remain outside of the cell 3.Replication - Virus hijack the cell and produce viral DNA and proteins 4.Assembly - viral DNA and proteins form viral particles 5.Lysis and Release - viral enzyme lysozyme digests bacterial cell wall, the cell bursts, viruses are resealed. •EXAMPLES: - measles virus, mumps virus

Steps of latent infection (lysogenic cycle) in bacterial cells

1.Attachment - adhesins of bacteriophage bind to receptors of the cell 2.Entry -viral DNA enters the cell •Integration - Viral DNA inserted into chromosome forming provirus. Viral genes are not expressed. If cell is divided, each daughter cell is supplied with a copy of viral genome. •Induction - viral DNA pop up from chromosome and virus enters lytic cycle. 3.Replication - Virus hijack the cell and make viral DNA and proteins 4.Assembly - viral DNA and proteins form viral particles 5.Lysis and Release - viral enzyme lysozyme digests bacterial cell wall, the cell bursts, viruses are resealed.

Infectious Disease Development

1.Establishing the infection- •Adhesion to the host •Colonization 2.Breaching barriers & invasion-•Entry via skin •Entry via mucous membrane 3.Avoiding host defenses- •Hiding inside the host cell •Inactivation of host defense systems 4.Damage to the host-•Indirect damage (immune reaction), Direct damage (microbial products) 5.Exit of pathogen from the host-portals of exit

Characteristics of infectious disease: Ability of a disease to be transmitted

1.Non-communicable infectious diseases •They can not be transmitted between the hosts - Tetanus, Botulism 2.Communicable infectious diseases They can be transmitted between the hosts. Two subtypes of communicable diseases 1.Non-contagious Transmitted via specialized routes: •vectors, vehicles, •non-casual transfer of bodily fluids - transfusion or sexual contact, needles, •Examples: −West Nile encephalitis, −HIV, Herpes, −Tuberculosis (non-active), Syphilis (latent), −Bubonic plague 2.Contagious Transmitted via: •direct contact, indirect contact, •casual transfer of bodily fluids or discharges - respiratory droplets •Examples: −Smallpox, Rabies, COVID-19 −Common cold, Measles, −Tuberculosis (active), Syphilis (2ndary), Pneumonic plague, Diphtheria

How many patients were initially identified with C. auris colonization in the U.S.?

77

Calculate how many generations it takes for a single bacterial cell to become 256 cells.

8

What percentage of the C. auris isolates sent to the CDC were resistant to fluconazole?

85.7%

Forty people attended the lunch party. Of these, 35 were interviewed by CDC personnel. The remaining 5 people were not available for the interview. What percentage of people were questioned?

87.5%

How many agar plates do you have to analyze at the end of your experiment?

90

bacterial flagellum

A. Filament (little bumps- flagellin) B. Hook F. Basal Body

Consider how an aerobically respiring bacterial cell uses glycolysis, the TCA cycle, and oxidative phosphorylation to break apart and oxidize glucose. What are the three main benefits these central metabolic pathways yield to the cell?

ATP, reduced electron carriers, and precursor metabolites.

Which of the following are examples of microbial evolution that may lead to disease emergence or reemergence?

Acquiring ability to form a capsule, Gaining a toxin gene by horizontal transfer, Developing resistance to antimicrobial medications, Gaining new reservoirs of infection.

naturally acquired adaptive immunity

Active immunity via infections Passive immunity via antibody transfer (breast milk and placenta)

Artificially acquired adaptive immunity

Active immunity via injection of antigen (immunization) Passive immunity via injection of antibody (antiserum, antitoxin)

Diversity of Prokaryotic Organisms

Aerobic bacteria •This term describes a group of bacteria that can grow in oxygenated environment and include: •Obligate aerobes •Facultative anaerobes •Microaerophiles •Aerotolerant bacteria

Growing aerobic bacteria in anaerobic environment would result in slow down or even inhibition of bacterial growth. Explain why.

Aerobic bacteria require O2 for growth (anaerobic environments lack O2). Aerobic bacteria use O2 for energy production and respiration by transferring e- and O2 is the final e- acceptor in the transport chain, therefore in the absence of O2 these bacteria have no way to produce energy to sustain growth

Classes of germicidal agents

Alcohols, ethylene oxide, halogens, Phenolic compounds, Peroxygens, Detergents

After Gram's iodine is added to the slide, what color do cells appear?

All cells appear purple in color.

Toxicity

All germicides are at least somewhat toxic to humans and the environment. •Therefore, the benefits of sterilizing or disinfecting an item / surface must be weighed against the risks associated with particular chemical. •In hospitals, benefits outweigh the risks due to specifics of the hospitals (overall - the stronger chemical, the better)

Which of the following were NOT tested for C. auris in this case? eyes, urinary catheters, cerebrospinal fluid, stool samples Which medication/class of medication do you think would most likely be prescribed for the 77 patients in this case?

An echinocandin

Host-Microbe Interactions

Anatomical barriers as ecosystem •Mucous membrane −It has one or two layers of living cells •Skin -It has multiple layers of cells -the upper most layers are remnants of the dead cells

Mucous membrane is penetrated by microbes more easily than the skin. However, anthrax develops if human skin is exposed to as little as 10 endospores of Bacillus anthracis, while the same disease develops in humans if at least 10,000 endospores inhaled. Explain why development of anthrax requires more endospores if they are inhaled than when they contact the skin.

Anthrax requires more endospores if they are inhaled than when they contact the skin due to many things: size of the endospore, the fact that the respiratory system has many defense mechanisms (the endospores can get trapped in the mucous and then blown out if your blow your nose, vs through the skin any break in the skin gets you directly into the blood stream. Bacillus anthracis causes anthrax, which is a bacterial illness. It's a Gram-positive, rod-shaped bacteria that form endospores. It's mostly found in dirt. Anthrax cannot be communicated or propagated directly from one person to another. It is communicated from one infected individual to another through the inhalation of endoscopes or direct contact with endoscopes. It has been shown that spreading anthrax through mucous inhalation necessitates a large number of endosperm, whereas spreading the infection by skin contact necessitates a small number of endosperm, also known as Cutaneous spreading. A lesion in the skin is required for the germs to enter the body. Cutaneous anthrax causes endospores to enter the body through the skin. When an endospore enters the skin or a cell, bacteria begin to multiply, and the number of bacterial cells grows in a short period of time, which is sufficient to cause disease. Whereas, in the case of mucous inhalation, a larger number of endospores are required to cause infection because mucous endospores must cross a number of barriers to reach a suitable place where they can germinate, and there is a significant loss of endoscopes during this journey from entry to germination, which is why for spreading infection via mucous infection, a large number of endospores are required.

cell wall functions

Antibiotics like penicillins and cephalosporins are killing actively growing bacteria by interfering with cell wall synthesis •These antibiotics prevent formation of cross-links between peptidoglycan fibers. •Certain bacteria (called mycoplasmas) are lacking the cell wall and just like eukaryotic cells use cholesterol to stabilize plasma (cytoplasmic) membrane. Bacterial cell wall can be digested by enzymes called lysozymes •These enzymes are encoded by bacteriophages (viruses infecting bacterial cells) and also present in human saliva and tears.

Enhances (outcomes) of primary immune response

Antibody class switching •Initially B cells are programmed to differentiate into plasma cells producing IgM antibodies. Under direction of cytokines produced by T helper cells some of activated B cells switch the programming and differentiate into plasma cells secreting another class of Ig (usually IgG). Maturation of antibody affinity •Affinity is the measure of how strong antibody binds to antigen. Affinity maturation is resulting in production of antibody that binds to the antigen stronger, while production of weaker antibodies ceases . Formation of memory cells After antibody class switching, some of the activated cells are forming memory cells. Unlike plasma cells, memory cells are not currently producing antibody or producing them at low rate and can survive in the body for many years retaining the ability to be activatedupon next exposure to the same antigen and produce antibody in the future. Since memory cells are greater in numbers than original naïve cells, any subsequent immune response will be quicker and stronger than primary immune response

Primary and secondary immune response

Antibody titer •It is a measurement of antibody concentration. •It is expressed as the inverse of the greatest dilution that still gives a positive reaction with the antigen. •ELISA is a common means of determining antibody titers. First immune response •It is a reaction of immune system to first exposure to antigen •It requires up to 2 weeks to mount immune response sufficiently strong to halt microbial growth inside host body •During this delay, infected person might experience signs and symptoms of an infection •Even life-threatening situation may develop •Over the time, some B cells undergo changes that enhance immune response including: •Affinity maturation; •Class switching; •Formation of memory cells Secondary immune response •It is a reaction of immune system to subsequent exposures to the same antigen •It requires considerably less time to mount much stronger immune response •Memory cells are responsible for swift and strong reaction to secondary response. •Vaccination exploits this phenomenon of immune system's memory •Infection might be eliminated even before signs and symptoms of infection are developed. •So, person may not even notice secondary or consequent exposure to antigen

Nature of antigens

Antigen (Ag) •It is any compound that can induce the antibody production in the host. •Various macromolecules, particularly proteins, may act as antigens. Epitope •It is a part of antigen that can be recognized by a specific antibody. •In proteins, it is a stretch of 6 amino acids in proteins. •The same epitope may be present in different antigens. Hapten •It is small molecule that is not immunogenic (it does not cause immune response). •Hapten becomes immunogenic only if it forms a complex with a carrier molecule. •For example, penicillin is not causing immune response in 95% of human population. However, penicillin forms complex with albumin in 5% of human population due to mutation and causes allergic reaction. Antibody (Ab) •It is a protein produced by immune system in response to appearance of foreign antigens in the host. •Each antibody recognizes and binds to a particular epitope of the antigen. •Antibody would have cross-reactivity, if the same epitope is present in different antigens.

______ are molecules that stimulate a response in T cells and B cells.

Antigens

using chemicals to destroy microbes

Any potential disinfectant or antiseptic must be tested on various microbes

Review the chart*. How many total bacteria are on the hands of the people who wash their hands with water only, assuming that each colony arises from a single cell?

Approximately 450

A unicellular microorganism was recovered from a hot spring (95°C) in Wyoming. After observation, it was determined that the cells lacked a nucleus, had a cell wall that lacking peptidoglycan, and had 70S ribosomes. Analysis of the cytoplasmic membrane revealed lipids containing long-chained branched hydrocarbons with ether linkages. Determine how this organism would be classified, based on the description provided.

Archaea

Why must fresh cells be used for the Gram stain?

As cells age, they may not stain correctly.

Consider the biochemical pathway: A → B → CEnzyme 1 catalyzes A → BEnzyme 2 catalyzes B → CEnzyme 1 can use only A as a substrate. Consider the biochemical pathway: A → B → CEnzyme 1 catalyzes A → BEnzyme 2 catalyzes B → CIf enzyme 2 is inactive, which of the following compounds will accumulate?

B Only

The clonal selection theory states that

B cells that recognize a given epitope multiply to form a family of identical cells.

Microorganisms that have complicated nutritional requirements are

fastidious

Helper T cells

function in both cell-mediated and humoral immunity.

Identify the correct matching of shapes, based on the scientific names.

Bacillus species - rod; Staphylococcus species - spherical.

ATP yield in fermentation and respiration

Bacteria harvesting energy via cellular respiration are growing faster than those harvesting energy via fermentation. Fermentation- 2 total yield ATP Respiration- up to 38 total yield ATP

Endospore morphology

Bacteria producing endospores •Endospores are produced only by some Gram-positive bacilli. Among them species that belong to the following genera: •Bacillus - they produce spores with diameter smaller than that of cell. Therefore, if endospore is produced, the cell shape is not disturbed •Clostridium - they usually produce spores whose diameter bigger than that of the cell. Therefore, produced endospore disturbs the shape of the cell. •Streptomyces are producing endospores that do not disturb the cell shape. •Gram-negative bacteria or Gram-positive cocci never produce endospores.

The three-domain system of classification

Bacteria, Archaea, Eukarya The current three-domain classification system is based on comparison of sequences of 16S ribosomal RNA (18S rRNA for Eukarya). The system was introduced by Carl Woese

Comparison of vegetative cells vs endospore

Bacterial cells: •they are metabolically active and show activity of various enzymes. •Most bacterial cells have cell wall, Gram-positive, Gram-negative or acid-fast. •Bacterial cells are sensitive to heat, to antimicrobial treatments easily killed by heat, radiation or antimicrobial chemicals. Endospores: •they are produced by some of Gram-positive bacilli only. •Endospores are resting form of bacterial cells and, therefore, have no metabolism or enzymatic activities. •Endospores have multiple (five) protective coatings: •inner membrane, •Germ cell wall •cortex (contains dipicolinic acid, calcium and peptidoglycan), •outer membrane, •spore coat (made of spore-specific proteins). •These protective coatings make endospore highly resistant to heat, antimicrobial chemicals, and radiation. • All vegetative bacterial cells are easily destroyed by simple boiling during 5-10 minutes. •However, endospores of many bacterial species can easily survive the boiling •To kill the endospores a much tougher treatment is required, like autoclaving - a combination of overheated steam and high pressure.

Principles of prokaryotic growth

Bacterial growth properties 1.Very rapid rate of cell growth −Bacteria like E. coli are dividing every 20 min 2.Exponential growth −Bacterial population doubles after each generation −Bacterial population can be calculated as following: Nn = N0 x 2n, where N0 - it is initial number of bacterial cells; n - it is number of generations

In animal virus replication, an uncoating step is needed to release the nucleic acid from the capsid. Why is this step not needed in bacteriophage replication?

Bacteriophages inject their DNA into the host cell.

Is Staphylococcus epidermidis related closely to Escherichia coli or to Staphylococcus aureus? Explain your answers.

Based on their scientific names, S. Epidermidis is not closely related to E.Coli as they are not from the same genus. S. epidermidis is closely related to S. Aureus as they are from the same genus, but are different species.

Father Spallazani repeated John Needham's experiment but Spallazani boiled the broth for much longer and sealed the flasks by melting their necks closed. He observed that the broth remained sterile, basically forever. What do you think the vast majority of the people believe from his experiment?

Because the flask of broth was sealed, the vital forces of life could not enter

Thayer-Martin agar (selective)

Beef extract Casein hydrolysate Starch Sheep blood Agar Antibiotics: Vancomycin Colistin Nystatin Trimetoprim used to test rectal specimens. It is very similar to chocolate agar but supplemented with mix of antibiotics that inhibit any bacteria but Neisseria. •It is selective medium made of chocolate agar supplemented with mixture of antibiotics inhibiting Gram-positive bacteria (vancomycin), Gram-negative bacteria (colistin and trimethoprim) and fungi (nystatin). •The only microbes that can grow on the medium are species of genus Neisseria. •Neisseria spp. are Gram-negative bacteria but they still can grow in the presence of colistin and trimethoprim

chocolate agar (non selective)

Beef extract Casein hydrolysate Starch Sheep blood Agar contains lysed red blood cells. It can be used to grow practically any human pathogens •MacConkey agar is used to grow Gram negative bacteria and distinguish those that form lactic acid from non-formers •It is non-selective medium containing lysed red blood cells. •The iron released from lysed RBC is oxidized by oxygen from air turning medium color brown. •Since the iron is readily available to bacteria, chocolate agar support the growth of some human pathogens that can not grow on blood agar, where iron is still inside the RBC. EXAMPLES: Hemophilus influenzae

Most cultured bacteria tend to multiply by _____.

Binary Fission

Lithotrophs use non-organic source of energy

Biomining •It is a process of mineral mining with use of specific bacteria that can extract the desired minerals from low-grade ore Nitrogen cycling and bacteria •Bacteria are the only organisms capable of "nitrogen fixation", when free nitrogen (N2) is converted to ammonia (NH3) and nitrates, the nitrogen forms that can be used by other organisms Diversity of prokaryotic organisms •ChemoOrgano-trophs - use organic molecules like glucose as source of energy •Obligate aerobes are oxidizing glucose in aerobic cellular respiration with highest energy yield. •Obligate anaerobes are oxidizing glucose in anaerobic respiration with lower energy yield. •Facultative anaerobes are oxidizing glucose by aerobic cellular respiration (if oxygen is present) or by fermentation (if oxygen is absent). Fermentation has the lowest energy yield. •ChemoLitho-trophs - use inorganic compounds as source of energy, oxidizing them •Methanogenic bacteria use hydrogen (H2) as source of energy and carbon dioxide (CO2) as acceptor of electrons, which results in formation of methane (CH4) and water (H2O). •Iron (iron-oxidizing) bacteria derive the energy by oxidizing ferrous iron

During PCR, which primer anneals to DNA with its 3' end toward the center of the sequence to be amplified?

Both the forward primer and the reverse primer.

Early in glycolysis, two phosphates are added to the glucose molecule. These phosphates come from

Breaking down ATP

How are microbes killed and digested in the phagolysosome?

By hydrolytic enzymes

Which of the following refers to a descriptive epidemiological study?

Collecting data that characterize the occurrence, from the time and place of the outbreak to the individuals infected

The classical complement pathway is activated when

C1 binds to the antibody in an antigen-antibody complex.

Both the classical and alternative complement pathways create

C3 convertase.

C3 convertase cleaves C3 into

C3a and C3b.

The membrane attack complex is made from

C5b, C6, C7, C8, and C9.

Central metabolic pathways & Respiration

C6H12O6 + 6 O2 + 32 ADP + 32 Pi ® 6 CO2 + 6 H2O + 32 ATP

Expression of viral oncogenes in infected animal cells

Can mimic protooncogenes, causing imbalance in cell cycle control towards unchecked proliferation, leading the tumor formation

Cellular immune response

Cellular immune response Cell-mediated immunity effective against large parasites; cancer & infected cells It is mediated by T lymphocytes (helper and cytotoxic T cells) and Natural killers Activation of macrophages by helper T cells and vice versa •If bacterial species invades human for the first time, its cells will be opsonized by C3b. •If the same species invades the host second or consecutive time, then the cell will be opsonized primarily by antibodies. •Macrophage binds to opsonized bacterial cell either via C3b receptor or Fc receptor •After internalization, bacterial cell is digested and the fragments of its antigens are resented on surface of macrophage via MHC (major histocompatibility complex) class II molecules •Note that the same type of MHC class II molecules are also found in B cells •If at least one of the fragments presented by MHC class II molecules is recognized by T cell receptor (TCR) and CD4 co-receptor of helper T cell, the cell binds to macrophage •Macrophage and helper T cell mutually activate each other by interleukins' exchange •IL-1 is delivered to helper T cells, while IL-2 is delivered to macrophage Activated macrophage •It increases its motility rate, production of antibacterial substances like hydrogen peroxide and hydrolytic enzymes, which increases the ability of macrophage to destroy microbes. •Activated macrophage also secretes interleukin 1, which is delivered to hypothalamus via blood stream resulting in upregulation of body temperature (fever) Activated helper T cell •Helper T cells have T cell receptors (TCR) and CD4 co-receptor on their surfaces. Together, they define the specificity of the helper T cell. •Activated helper T cell goes via rounds of cell division producing the multiple self-copies thus increasing the chances of activation of other macrophages or B cells presenting the same antigens •Interleukin 2 secreted by activated helper T cells also activate cytotoxic T cells • Function of cytotoxic T cells •Cytotoxic T cells have T cell receptors (TCR) and CD8 co-receptor on their surfaces. Together, they define the specificity of the cytotoxic T cell. •Function of cytotoxic T cells is to recognize the antigens presented on MHC class I molecules of somatic cells. It allows to kill infected or cancer cells even if there are not antibodies present.

What is the name of the process by which phagocytes move towards microbial products?

Chemotaxis

Which of the following are possible labels for A and B?

Chickenpox (A) and shingles (B) (2 red pyramids, dark red in middle is A and B)

Determine what type of A-B toxin (cytotoxin, neurotoxin, or enterotoxin) the following microbes produce.

Clostridium Botulinium-Neurotoxin Vibro Cholerae -Cytotoxin Bordetella Pertussis- Enterotoxin

Properties and functions of T cells and Natural killers

Comparison of T helper cells, T cytotoxic cell and Natural killers •T helper cells have CD4 surface marker (TCR co-receptor). Their function is to stimulate other cells of immune system presenting antigens on MHCII complexes. The cells stimulated by T helper cell include T cytotoxic cell, macrophages (both are activated via interleukin 2) and B cells (activated via interleukin 4); •T cytotoxic cells have CD8 surface marker (TCR co-receptor). Their function is to kill cells representing foreign antigens on MHCI complexes that include some somatic cells that are dysfunctional, infected or cancerous. •Natural killers have Fc receptors that can recognize tails of antibody bound to surface of human cells or large parasites. Their function is to kill antibody-labeled parasites or human cells. It also kills cells lacking MHC-I. Major histocompatibility complexes I and II (MHC I and MHC II): •MHC I is found in various types of somatic (body) cells. It binds and presents endogenous antigen that is synthesized inside the cell and is of viral, parasitic or cancerous origin •MHC II is found in antigen presenting cells - macrophages, phagocytes, dendric cells, and B cells. It binds exogenous antigen that is synthesized outside of the cell and can be of various microbial origin. MHC II can be Co-receptors of T-cell receptors (TCR) •CD4 is found on T helper cells. This co-receptor together with TCR can recognize antigens presented on MHC II •CD8 is found on T cytotoxic cells. This co-receptor together with TCR can recognize antigens presented on MHC I •Both types of TCR co-receptors have variable and constant regions similarity to Fab domains of the antibody. Variable region can recognize specific epitope of antigen presented on MHCI or MHC II

Normal microbiota of Skin

Conditions: aerobic; dry; high salt content; low temperature •Staphylococcus aureus, Staphylococcus epidermidis, Propionibacterium acne, Candida albicans −Actinobacteria (52%), Firmicutes (24%), Proteobacteria (17%)

Normal microbiota of the throat

Conditions: aerobic; wet; low salt content; high temperature •Corynebacterium spp., Mycoplasma spp., Streptococcus spp.; -Obligate aerobes, facultative and aerotolerant anaerobes

Normal microbiota of the nasal cavity

Conditions: aerobic; wet; low salt content; low temperature •Corynebacterium; Staphylococcus aureus; Streptococcus spp.; Mycoplasma spp. −Obligate aerobes, facultative and aerotolerant anaerobes

Normal microbiota of the Intestines

Conditions: anaerobic; wet; low salt content; high temperature •Lactic acid bacteria, Enteric bacteria, Candida albicans, Clostridium spp. -99% are obligate anaerobes and facultative anaerobes

Which of the following bacterial genera is NOT described correctly?

Corynebacterium - spherical.

The structure that divides the bacterial cell in two is called the

Cross Septum

Gram Stain

Crystal violet (positively charged) binds to plasma (cytoplasmic) membrane (negative charged) •In Gram positive bacteria it binds to plasma (cytoplasmic) membrane that is beneath thick peptidoglycan layer •In Gram negative bacteria, it binds to outer membrane that is above thin peptidoglycan layer Iodine is mordant - it forms complex with crystal violet and prevents its washing out from Gram positive bacteria during VERY brief decolorization with 95% alcohol •In Gram negative bacteria crystal violet is washed out quickly along with outer membrane. •Gram positive bacteria will be falsely stained as Gram negative, if decolorization would last longer than a few (~5) seconds. Gram positive bacteria can also be stained as falsely Gram negative if the bacterial culture is older than 24 hours or if they are actively growing It establishes the type of cell wall bacterium has, Gram positive or Gram negative -gram positive- purple -gram negative- pink

Helper T cells secrete ______ to stimulate the proliferation of B cells.

Cytokines

T/F Semmelweis won the Nobel prize for his work.

False

T/F T-independent antigens will produce strong, high-affinity IgD responses from B lymphocytes.

False

T/F The presence of flagella can be determined by a Gram stain.

False

Based on the phylogenetic tree shown here, which organisms are most closely related?

D. radiodurans and T. aquaticus

PCR requires all of the following EXCEPT

DNA ligase

What general type of staining is used to separate various types of bacteria based on their cellular structures?

Differential

Evasion of compliment system by bacterial species

Digestion of C5a •It prevents the attraction of phagocytic cells to the site of infection, thus overall reducing inflammation reaction •EXAMPLES: C5a peptidase of Streptococcus pyogenes Inactivation of C5b •It prevents formation of membrane attack complex in plasma (cytoplasmic) membrane of bacterial cell •EXAMPLES: Lipo-polysaccharide complexes of Neisseria gonorrhoeae, Bordetella pertussis, Haemophilus influenzae Inactivation of C3 convertase •It prevents the activation of compliment system. •EXAMPLES: M protein of Streptococcus pyogenes binds compliment regulatory protein (factor H) and inactivates C3-convertase. It prevents: opsonization, formation of membrane attack complex, and inflammation.

Which of the following cell arrangements is described CORRECTLY?

Diplococcus - pairs of spherical cells.

Choose which of the following best describe the difference between a disinfectant and an antiseptic.

Disinfectants are antimicrobial chemicals used on inanimate surfaces or objects to remove most of the pathogenic microorganisms. Antiseptics are antimicrobial chemicals that can be used on skin or tissues to achieve the same result.

Nature of antibodies

Domains of antibody and their functions: −Fa domain is variable region, which defines the antibody specificity - there is an antigen-binding groove −Fb domain is a part of constant region which is species-specific - it connects light and heavy chains together via disulfide bonds and, therefore, it keeps Fa region active −Fc domain is a part of constant region which is species-specific - it is recognized by microphages, natural killers and complement system, if antibody tags a pathogen. Antibody •It is Y-shaped protein produced by immune system of the host in response to appearance of foreign antigen •It is made of 4 polypeptides - 2 light & 2 heavy chains that are hold together by four disulfide bonds Variable region •It is consisting of Fa domain •The tip of Fa domain defines the specificity of the antibody as it has antigen-binding groove, where a particular epitope can fit in tightly, in "key and lock" manner Constant region •It is consisting of Fb and Fc domains that are species-specific. •Constant region is exactly the same among all antibodies of all individuals of the same biological species •The antibody taken from one human can be injected into another human without immunological rejection by immune system of a recipient •Antibodies isolated from non-humans and injected into a human will cause immune response. Therefore, they can be used in treatment only once •Fb domain holds light and heavy chains together. •Fc domain of constant region is responsible for various immune reactions leading to elimination of microbes, infected or cancerous cells •Fc domain can trigger compliment activation, phagocytosis or attack by natural killer if antibody is bound to the surface of a microbe, infected/cancerous self-cell or large parasite.

Please use the dichotomous key below to identify a bacterium with the following characteristics: stains pink in the Gram stain, produces no color when exposed to oxidase substrate, and produces both acid and gas when inoculated in lactose broth.

E. coli or other coliform

Replication of reverse-transcribing virus (retrovirus)

Each retroviral virion has envelope, two copies of ssRNA(+), and three enzymes: −Reverse transcriptase; Integrase; Protease 1. Attachment and entry of the virus in to the host cell 2. After un-coating, viral ssRNA is converted into dsDNA with help of viral reverse transcriptase 2. dsDNA is inserted into chromosome of the host cell. Virus turns into provirus. If such infected cell divides, each daughter cell is supplied with a copy of viral genome 3. Viral genes are expressed at low rate 4. New virions are formed at plasma membrane and are released via budding. It prevents the lysis of the infected cells 5. Released virions infect new cells

Which reservoir is easier to control? Which reservoir is harder to control?

Easier-human as we are able to control what humans ingest or are surrounded by to a degree Harder- environmental reservoir, we can not control the environment

T/F The thinner peptidoglycan layer of Gram-positive bacteria allows the crystal violet-iodine complex to leave the cell.

False

Why do you think the CDC recommends cleaning patient's rooms with a disinfectant effective against Clostridium difficile endospores in facilities where C. auris is found?

Endospores are highly resistant, killed only by extreme heat or chemical treatment. A disinfectant that destroys spores will likely kill any other organisms as well.

After it was cooked, the perlo was left at room temperature overnight. On the day of the party, the food was heated for an hour at a high setting in a slow cooker. Even though the perlo was effectively heated, people who ate it still got ill. What can you conclude from this information?

Enterotoxin A is heat stable (not destroyed by heat).

Phagocytosis- cells of the immune system

Erythrocytes - red blood cells are supplying oxygen to the tissues and are removing CO2 Platelets - responsible for blood cloth formation that prevents bleeding in case of injury. Leukocytes - have various functions in innate and adaptive immune system. •Granulocytes - they contain cytoplasmic granules filled with biologically active chemicals •Basophils - 0.5-1% of leukocytes produce and store histamine in vesicles •They are needed in inflammation and also are responsible for allergic reactions as they carry receptors for IgE •Eosinophils - 2-4% of leukocytes cytotoxic and some are phagocytic. •They are needed in fighting parasitic worms. Granules contain enzymes, including histaminase. •Neutrophils - 60-70% of leukocytes. Short lived, lasting only a few days •They constitute the majority of phagocytic cells of human body. Granules contain many enzymes and antimicrobial substances. Die after releasing granule content. •Monocytes - making up mononuclear phagocytic system. They are lacking cytoplasmic granules visible under light microscope. •Macrophages - 3-8% of leukocytes. Phagocytic. Long-lived, lasting weeks or months. •Alveolar or Wandering macrophages are present in lungs, bronchi or tissues •Continuously regenerate lysosomes. Alert other immune cells to microbial invaders •Dendritic cells - antigen-presenting cells. They "inspect" tissues and bring material to B and T cells of adaptive immune system (all naïve lymphocytes) •Natural killers - cytotoxic cells that recognize any cells labeled by IgG and kill them •Lymphocytes •T-lymphocyte - helpers and cytotoxic cells •T helper cells modulate humoral immune response and activate macrophages •B-lymphocyte - antigen-presenting cells producing antibody upon activation by T helper cells and differentiation into plasma cells.

Nutritional factors influencing microbial growth

Essential (major) elements

Infectious Disease Development (cont)

Establishing the infection •Adherence - attachment of bacteria to host organism; •Virulence factors involved are adhesins of bacterial cells localized on Cell wall, Capsule, Fimbriae, Flagella •Colonization - multiplication of microbe in host and growth; •Virulence factors involved are Siderophores (iron-binding proteins); Hydrolases (DNase, protease, RNase, lipase); • Breaching anatomical barriers & invasion •Skin's portals of entry - Hair follicles (the most common) and Injuries (insect bites; wounds; parenteral route ) •Mucous membrane's portals of entry - Respiratory, Gastrointestinal, Urogenital tracts; Conjunctiva. •Virulence factors involved are Effector proteins; Type III secretion system; • Avoiding host defenses •Mechanisms - Hiding inside the host cell; Avoiding killing by compliment system; Avoiding killing by phagocytes; Avoiding antibodies. •Virulence factors involved are Capsules; Fimbriae; Cell wall component; Protein A; Antigenic variation; Very wide variety of enzymes like Ig A protease • Damage to the host - causes the appearance of signs and symptoms of the disease; •Indirect damage to the host caused by excessive immune response. •Virulence factors involved are Cell wall components (endotoxins); Superantigens (nonspecifically activate cytotoxic or helper T cell) •Direct damage to the host caused by toxins and enzymes produced by bacteria. •Virulence factors involved are Enzymes, Exotoxins, Exit of the host organism - it involves portals of exit, which are usually the same as portals of entry: •Skin as portal of exit - microbes are shed off along with dead cells of the skin •Mucous membrane as portal of exit - Respiratory, Gastrointestinal, Urogenital tracts; Conjunctiva

During the Gram stain procedure, bacteria can first be differentiated from each other after the application of ______.

Ethanol or acetone

What are the differences between bacterial chromosome and the chromosome of eukaryotic cell?

Eukaryotic chromosomes are located within the nucleus, whereas bacterial (prokaryotic) chromosomes are located in the nucleoid. The key difference between bacterial and eukaryotic cells is that eukaryotic cells have a membrane-bound nucleus (and membrane-bound organelles), whereas prokaryotic cells lack a nucleus.

Chemically defined media are the mix of

Exact chemical composition is known - the mix of inorganic salts as source of essential elements, glucose as source of carbon. •inorganic salts (source of essential elements) •Glucose (source of carbon and energy) •Agar (solidifying agent)

Complex media

Exact chemical composition is not known, as they are made complex organic components. They include clinically important media are those that contain very complex ingredients whose exact chemical makeup is not known, like •yeast extract, •beef extract, •digested proteins. •They are useful for isolation and maintenance of fastidious bacterial culture. They also include clinically important media.

acidophilic

Extreme pH - (low, acidic pH)

alkalophilic

Extreme pH -(high, basic pH)

All biochemical pathways have the same number of enzymatic reactions.

False

T./F In general, bacterial cells are larger than human cells.

False

T/F . Bacteria are only visible when using an electron microscope.

False

T/F All bacteria can be classified as either Gram-positive or Gram-negative.

False

T/F B lymphocytes cannot produce and secrete antibody without the assistance of helper T lymphocytes.

False

T/F Handwashing with regular soap removes all normal microbiota from the skin

False

T/F It is impossible to generate the diversity of immune responses needed in a typical human life span because there are only an estimated 25,000 genes in the human genome.

False

T/F Plant and animal viruses begin their infection cycles by binding to specific receptors on the cytoplasmic membranes of the target cells.

False

T/F After a B cell is activated to form plasma cells, those plasma cells each produce different antibodies.

False The plasma cells divide by mitosis to create a large clone of identical plasma cells, each making identical antibodies.

T/F Mitochondria contain hydrolytic enzymes.

False, Lysosomes contain hydrolytic enzymes.

T/F Cells cannot begin a new round of replication until they have completely finished dividing

False. A new round of cell division can occur before the cells complete division.

T/F Cell division is triggered exclusively when cells attain a threshold mass.

False. Cell division is triggered exclusively when cells attain a threshold mass and length.

T/F DNA helicase is responsible for adding nucleotides to the growing end of the DNA.

False. DNA helicase is responsible for unwinding the DNA double helix so replication can begin. DNA polymerase is responsible for adding the nucleotides to the chain.

Lines of Host defense

First line of defense prevention of microbial entry Second line of defense non-specific destruction of a microbe Third line of defense specific destruction of a microbe

Please select the mode of disease transmission being demonstrated in this scenario: A teacher walking through her first grade classroom pauses to pick up a used tissue that ended up on the floor instead of in the waste basket. Unfortunately, after discarding the tissue, she doesn't immediately wash her hands, and acquires a strain of rhinovirus. Several days later she begins to experience the symptoms of a cold.

Fomite

Application of Microbes

Food production •Lactic acid & ethyl alcohol fermentation Biodegradation •DDT, oil, other pollutants treatment Biotechnology Recombinant proteins, antibiotics etc

Why were people still so unwilling to dismiss spontaneous generation even after Father Spallanzani's experiment?

For about 1,900 years, spontaneous generation was shown to be "true" by repeated observations.

Gas vesicles (internal structure of cell)

Function: Provide buoyancy to the cell

Granules (internal structure of cells)

Function: Storage of excess of nutrients Metachromatic granules: Storage of phosphate reserves Polysaccharide granules: Storage of sugars reserves Sulfur granules: Storage of S as energy reserves Magnetosomes: Storage of iron oxide, which helps inactivate H2O2 (hydrogen peroxide)

Ribosomes (internal structure of cell)

Function: protein biosynthesis Chemical Composition: RNA (65%) and proteins (35%) Structural Composition: small 30S subunit, large 50S subunit •Prokaryotic cells •They have one type of ribosomes - 70S •Eukaryotic cells •They have two types of ribosomes - 70S and 80S •70S ribosomes (prokaryotic type) are localized in mitochondria and chloroplasts •80S ribosomes (eukaryotic type) are localized in cytoplasm

What are the two entry mechanisms used by enveloped viruses?

Fusion and endocytosis

World Mortality rates

Globally •the major cause of death in the world are non-communicable diseases •This also includes non-infectious diseases like a stroke or heart attack •Mortality rate from communicable (infectious) diseases are about 3 times lower than that from non-communicable diseases. •This indicates that overall infectious diseases are under control world-wide African region •The major cause of death in Africa are communicable diseases •Communicable diseases include infectious diseases only. •Mortality rate from non-communicable diseases is almost as high as from communicable diseases •This indicates that overall infectious diseases are rampant in African region •Low economic development contributes to •Shortages in supply of important vaccines against dangerous infectious diseases, •Shortages in supply of antimicrobial drugs •Lack of infrastructure that secures safe water supply

Glycolysis is the central metabolic pathway that involves the breakdown of ______.

Glucose

Lactic acid fermentation (in muscles/lactic acid bacteria)

Glucose ---> 2 lactic acid + 2 ATP

Which of the following compounds can be generated from precursor metabolites produced during glycolysis?

Glycerol, a component of lipids. Some small amino acids like alanine, leucine, and valine. Peptidoglycan, a component of bacterial cell walls.

Phylum Actinobacteria

Gram-positive and acid fast bacteria with high content of G/C (69-73%) in their DNA •Some species are forming branching filaments that resemble hyphae of fungi

Phylum Firmicutes

Group of Gram-positive bacteria with low content of G/C (23-54%) in their DNA Properties of phylum Firmicutes •It is a diverse group of bacteria with Gram positive type of cell wall and different requirement for oxygen from obligate aerobes to obligate anaerobes and everything in between. •Some of the bacteria, in fact, are lucking of any cell wall (class Mollicutes) but they have high DNA homology to another members of this phylum and thus are closely related. •Bacteria have various cell shapes from cocci to bacilli, some are polymorphic (do not have constant cell shape) •Bacteria have low G/C content of DNA (23-54%) •Some bacilli can produce endospores; others - can not. •None of the cocci can produce endospores •The phylum is divided into four classes based on biochemical properties of organisms •Some can produce highly potent exotoxins and can be highly pathogenic - Clostridium; Mycoplasma; Staphylococcus; Streptococcus, some Bacillus species •Other species are beneficial to humans - various species have industrial applications and are used in •Biofuel production - Bacillus, Clostridium; •Dairy industry - order Lactobacillales (group of lactic acid bacteria) •Production of antibiotics - Bacillus

How did Semmelweis test his hypothesis?

He insisted that physicians and medical students wash their hands with disinfectant before aiding women in childbirth.

Avoiding host defenses

Hiding within a host cell •Prevents contact of immune system with a microbe. Avoiding killing by compliment system •M protein of S. pyogenes inactivates C3 convertase, which prevents opsonization, formation of membrane attack complex, and inflammation. •LPS of N. gonorrhoeae, B. pertussis, H. influenzae inactivate C5b which prevents MAC formation Avoiding killing by phagocytes •Avoiding ingestion by phagocytes •Killing of phagocyte at the distance by secretory toxins like Leukocidins of S. aureus; Streptolysins of S. pyogenes; Pneumolysin of S. pneumoniae •Prevention of phagocyte attraction by M protein and C5a peptidase of S. pyogenes •Prevention of phagocyte adhesion by biofilm, capsule, Protein A, Protein G •Avoiding digestion by phagocytes •Escape from phagosome, followed by the killing of phagocyte - Components of cell wall in Shigella spp. destroy membrane of phagosome formed after ingestion of microbe, releasing bacteria into cytoplasm of phagocyte. Then Shiga toxin produced by bacterial cell kills phagocyte. •Preventing phagosome-lysosome fusion - Salmonella once inside the cell, produces protein that blocks the fusion process; Mycobacterium tuberculosis and HIV both have ability to prevent formation of phagolysosome •Surviving within the phagosome - Coxiella burnetti (causes Q fever), once inside, delays the fusion of phagosome with lysosome and grow within the phagosome Avoiding antibodies •Digestion of IgA by IgA protease prevents immobilization and agglutination of bacterial cells. Gram-negative bacteria: N. gonorhoeae, N. meningitidis, Haemophilus influenzae. Gram-positive bacteria: S. pneumoniae, S. pyogenes •Antigenic variations - N. gonorrhoeae and N. meningitidis can change their surface antigens every two weeks or so. •Mimicking host molecules - some strains of S. pyogenes form capsule composed of hyaluronic acid, a polysaccharide found in human tissues. As a result, such capsule has reduced antigenicity.

halophiles

High salt concentration - up to 15-20% of NaCl

Thermophile

High temperature 70OC to 100OC

Medical Microbiology

Human and animal pathogens •Causing infectious diseases Producers of antibiotics •Penicillin, Nystatin, Tetracyclines Normal flora (microbiota) •Prevents some infectious diseases Normal flora (microbiota) •Prevents some infectious diseases Re-emerging diseases •Malaria; Cholera, Plague, Measles Eliminated diseases •Small pox, Rinderpest; Potentially polio

Branches of adaptive immunity

Humoral immune response Antibody-mediated immunity that kills extracellular microbes (outside host cell) Cellular immune response Cell-mediated immunity that kills intracellular microbes (inside host cell)

Dynamics of Prokaryotic Growth

In nature, microbes are living in mixed microbial communities -They can grow at various conditions, including the most harshest and severe -To study bacteria, they must be grown in the laboratory as pure culture Robert Koch is the greatest contributor to methods of bacterial cultivation in the lab −He was the first to isolate bacterial pure cultures, including pathogens

Course of infectious disease

Incubation period •It is a time between initial exposure and onset of first signs & symptoms. •It may last from a few hours to up to two weeks. •Patient may already be infective to the others. It is particularly true for viral infections. Prodromal phase •It is a short period of early mild symptoms. •The number of pathogen has already increased enough to start causing the damage to host. •Immune system is already activated to produce immune response against the pathogen, which is not mounted yet. •Patient is infective to the others. Illness •It is a stage of disease when the signs and symptoms are most prominent & severe. Patient's organism has high count of microbes that are causing extensive damage to a host. •Sign is what everybody can observe; Symptom is what only patient feels •Immune system is mounting the immune response by producing the antibodies, whose titer (concentration) in the blood is rapidly rising. •At the end of the phase the rate of bacterial growth is reduced due to mounted immune response. •Patient is infective to the others. Decline •It is a stage of the disease when patient starts feeling the relief from symptoms •Immune response is mounted & strong. It is eliminating the pathogen from the host. •As the body spent considerable resources to fight primary infection, there is a high risk of getting secondary infections (complications). •Patient is infective to others Convalescence •it is a stage of recuperation and recovery. •Patient can still be infective to others

Damage to the host

Indirect Damage It involves immune responses (allergies) Direct Damage •Host is damaged directly by microbial products like toxins or enzymes

What part of the body would you expect to be affected by enterotoxin?

Intestines

antimicrobial substances

Iron-binding proteins •Transferrins, Lactoferrins, Ferritins, Hemoglobin •Iron is essential trace element required for bacterial growth Antimicrobial peptides •Short peptides (15-50 AA-long) that have broad spectrum of antimicrobial activity - defensins etc. •They are produced by macrophages and mucous cells Interferons •Antiviral proteins produced by virus-infected host cells •They prevent the spread of virus infection to neighboring cells

Which of the following have been recommended by the CDC to reduce the risk of C. auris transmission?

Isolating an infected patients, Cleaning patient's rooms with disinfectants on a daily basis, Notifying facilities to which a patient with C. auris may be transferred.

Select the statements about ionizing radiation that are true.

It can be used to reduce spoilage organisms on food, it can be used to sterilize medical equipment.

Francisco Redi performed an experiment in which he put meat in jars, covering some with gauze and leaving others open. He then observed the meat over a few days. While this experiment is very well known in biology, it still did not completely change everyone's belief in spontaneous generation. How was the experiment lacking?

It didn't explain that the meat could still "rot".

Differential Media (can also be selective)

It differentiates the growing bacteria into various bacterial groups as some components of the media make bacterial species to look differently from each other •It contains some components that allow differentiate growing bacteria into different groups. •Differential medium can also contain selective agents and, therefore, be selective.

Why is Gram's iodine added to the slide?

It forms complexes with the crystal violet, decreasing its solubility

Decontamination (Sanitization)

It is a procedure that reduces overall the number of microbes present. Some pathogens or opportunistic pathogens may survive the treatment. •It can be achieved by using soaps or detergents

Pathogenicity

It is ability of a microbe to cause the infectious disease in a host. For balanced pathogenicity Pathogens •They have multiple virulence factors •They cause primary disease in healthy individuals •Strains of S. aureus producing: ‒Capsule ‒Exfoliative toxin Opportunistic Pathogens •They have some virulent factors •They are causing secondary disease in the hosts whose defense system is down •Strains of S. aureus producing: ‒Capsule Nonpathogens •They have no or very few virulence factors •They do not cause infections in humans • •Strains of S. aureus producing: ‒No Capsule

Pure culture

It is microbial culture consisting of just single biological species of a microbe

Which of the following statements about interferon is TRUE

It is produced in response to double-stranded RNA.

Which of the following statements about interferon is TRUE?

It is produced in response to double-stranded RNA.

Chain of infection

It is the series of events that infectious disease must follow to spread in population Salmonellosis •Reservoir of etiological agent •gastric system of animals •Portal of exit from reservoir •feces of animals •Route of transmission •contaminated food or water-fecal oral route •Portal of entry in to the host •mouth-ingestion Susceptible host humans NOTE: All strains of Salmonella enterica can be found in animals and birds with one exception: •Salmonella enterica subsp. enterica serovar Typhi causing typhoid fever is found only in humans.

Liquid Media

It is used to grow large quantities of bacteria or run the biochemical tests. The growth is judged by changes in media (color, gas, turbidity, sediments) Luria-Bertani broth (LB) -Tryptone, Yeast extract, NaCl

Solid Media

It is used to isolate and maintain pure cultures. Bacterial growth is judged by appearance of colonies. Each colony contains pure culture Luria-Bertani agar (LB agar) -Tryptone, Yeast extract, NaCl, Agar

Which of the following statements about Thiomargarita namibiensis are TRUE?

It stores nitrate, its terminal electron acceptor. It stores sulfur, its energy source. Its name means "sulfur pearl of Namibia."

Controls of Microbial growth

Joseph Lister, British surgeon, was the first to control microbial growth by dressing wounds with carbolic acid, which has increased survival rate of wounded soldiers. Microbial growth can be controlled by physical or chemical methods Selection of particular method depends on circumstances & level of control required

Microbial evasion of killing by phagocytic cells

Killing of phagocyte at the distance •It prevents encounter of phagocytic cell and a microbe. •It can be achieved by bacteria that make secretory toxin that binds to phagocytic cells and kills them. •EXAMPLES: •Leukocidins bind to phagocytes and kill them by forming pores in their plasma membrane. •Streptolysin O, Streptolysin S produced by S. pyogenes bind to any membranes that contains cholesterol (found almost exclusively in membranes of Animalia) and forms large pores •Pneumolysin produced by S. pneumoniae s similar to leukocidins produced by S. aureus Prevention of phagocyte's adhesion to microbe •It does not prevents encounter of phagocytic cell and a microbe, but prevents binding of a microbe by phagocytic cell •Microbes achieve it by various means. EXAMPLES: •Biofilm formed by S. aureus, S. pyogenes completely embed the bacterial cells in extracellular material, forming large structures and preventing physical contacts of phagocytes and bacteria •Capsule formed by S. aureus, S. pyogenes, S. pneumoniae prevent contacts of C3b or antibodies present on bacterial cell wall and C3b and Fc receptors present on phagocytic cells •Protein A, Protein G, Coagulase are covering bacteria by host proteins: proteins A and G (formed by S. aureus, S. pyogenes) are binding IgG inverted; coagulase (formed by S. aureus) precipitates human fibrin on to bacterial cell •Ig A protease, M protein are interfering with opsonization of bacteria: Ig A protease (formed by S. aureus, S. pneumoniae) digests Ig A antibodies bound to bacterial cell, M protein (formed by S. pyogenes) inhibits the activity of C3 convertase Escaping phagosome, followed by killing and escaping macrophage •It does not prevent encounter and ingestion of microbe by phagocytic cell, but it allow microbes to escape the phagocytic cell •Components of cell wall in Shigella spp. destroys membrane of phagosome formed after ingestion of microbe, releasing bacterial cell into cytoplasm of phagocyte. Shiga toxin (secretory exotoxin) produced by bacterial cell kills phagocyte. Prevention of phagolysosome formation •It prevents digestion of microbe inside the phagocyte enabling microbial survival for long time and turning phagocytes into reservoir of infection. •Components of cell wall, Components of virus envelopes prevent fusion of phagosomes containing microbes and lysosomes containing hydrolytic enzymes thus preventing the destruction of microbes by phagocytes. Mycobacterium tuberculosis, HIV (human immunodeficiency virus)

Establishing the cause of infectious disease

Koch's postulates •To prove that a microbe is causing the disease, this microbe must be: 1.found in all cases of the disease 2.isolated from diseased host as pure culture and must be maintained "in vitro" 3.causing the same disease in healthy host upon injection of the isolated culture 4.isolated again as a pure culture from experimentally injected and diseased animal. And newly isolated microbe must be identical to the microbe isolated early in step two.

During glycolysis, a single 6-carbon molecule of glucose is converted to two 3-carbon pyruvate molecules. During the later steps in this process, how many molecules of ATP are generated?

NAD+ is converted to NADH.

Select which of the following might impact the results of this experiment.

Length of time washing hands, type of soap, Section of lab floor sampled by each volunteer.

Which of the following describes a latent viral infection?

Long periods of time with essentially zero viral replication, punctuated by outbreaks of active replication and disease manifestation. Infected individuals are largely non-infectious between outbreak periods.

A ______ contains hydrolytic enzymes to digest foreign bacteria.

Lysosome

Antigenic fragments are complexed with ______ and displayed on the surface of the infected cell.

MHC class I molecules

Which of the following are antigen-presenting cells?

Macrophages and B cells are both APCs.

When present, of what is the viral envelope composed?

Mainly lipids

Vital Activities of microbes

Major decomposers •Dead organic material is recycled The only players in nitrogen fixation •N2 à NH3 which can be used by others The only players in nitrogen fixation •N2 à NH3 which can be used by others

What is a probable reason why corked glass jars were not suspected in the transmission of microbes?

Many other things have been placed into jars and corked without any perceived microbial contamination.

What would be a "good" argument against Spallanzani's experiment and in support of spontaneous generation?

Melting the flask neck closed kept the "vital forces" from entering and prevented spontaneous generation of life.

Catabolism of other organic compounds

Microbes are always use simple sugars (mono-, or disaccharides) as preferred source of energy •Glucose is universal source of energy as extraction of energy from it requires the least investments. •If simple sugars are not available, microbes would turn to polysaccharides or fats •Proteins are the least favorable source of energy as the energy extraction from them requires considerable investments and, therefore, yields less energy.

Breaching anatomical barriers & invasion (Skin)

Microbes penetrate skin via wound (cut or bite) or via hair follicle Breaching the mucous membrane by Shigella species - occurs in two distinct steps: •Step 1. Exploiting antigen sampling function of microfold (M) cells •M (microfold) cells are localized in the small intestines. They transport the samples of gut content across epithelial cells and present it to macrophages. •Along with gut content sample, Shigella is taken in by M cell at apical membrane. •The microbe is moved across M cell. At basolateral membrane Shigella cell is presented to macrophage and then bacterium is ingested. •Due to specific properties of its cell wall, microbe inhibits the formation of phagolysosome and survives inside the macrophage •Shigella produces secretory exotoxin that is killing macrophage & freeing microbe •Step 2. Directed uptake by host cell •Freed from macrophage Shigella cell binds to basolateral membrane of epithelial cell via adhesins •Using type III secretion system microbe injects effector molecules that are disturbing cytoskeleton of the host cell and are causing membrane ruffling. •Shigella sinks into the ruffles and forces the host cell to take it in via endocytosis •NOTE: Shigella virulence factors involved are highlighted Various bacteria can by-pass M cells and use directed uptake mechanism to cross or infect epithelial cells directly. •EXAMPLES: •Salmonella spp are using this mechanism to directly enter epithelial cells in the intestine and cause gastroenteritis (salmonellosis) •Streptococcus pneumoniae, Haemophilus influenza, Neisseria meningitidis are using this mechanism to enter blood stream in the respiratory system and after delivery to the nervous system infect meninges and cause meningitis.

Molecular postulates

Molecular postulates help to establish virulence factors of the pathogen 1.The gene(s) for virulence factor(s) must be present and be expressed in the pathogenic strain 2.Disruption of the gene(s) expression in the pathogen should reduce or abolish the pathogenicity of the strain 3.Expression of the gene(s) of the virulence factors in non-pathogenic strain should change it to pathogenic 4.Antibodies against virulence factors should be protective

Diffusion

Movement of molecules across a gradient from an area of higher concentration to an area of lower concentration.

passive membrane transport

Movement of molecules across a membrane without the input of energy (ATP)- transport of H2O into the cell

Consider the figure of a lichen. In this symbiotic relationship, the photosynthetic alga provides the fungus with organic nutrients. The fungus provides the alga with water and protection. Which of the normal microbiota relationships described below is most similar to this association?

Mutualism - intestinal bacteria providing host with vitamins E and K.

M9 minimal agar (Chemically defined media)

Na2HPO4 KH2PO4 NaCl NH4Cl MgSO4 , CaCl2 Glucose Agar (solidifying agent)

Clonal deletion, selection & expansion

Naïve B cells •They are produced in bone marrow, hence they were named B cells •Each of them has B cell receptor with specificity analogous to that of the antibody to be produced by the cell. •However, the cells have not encountered the antigens yet Activated B cells •These are the B cell that had encountered the antigen and bound it to the B cell receptor •This is also known as clonal selection •After binding antigen, B cell made a contact with T helper cell and became activated •The activated B cell goes through proliferation (rounds of cell divisions) and each descendant becomes either plasma cell, producing antibody, or memory cells, which would be activated in the further upon next encounter with the same antigen •This is also known as clonal expansion Effector cells •It is common name for all descendants of the activated B cell - plasma and memory cells Plasma cells •They are activated B cell that has stopped cell division and actively producing the antibody Memory cells •They are descendants of activated B cells that can persist in the host for years. •They are responsible for prompt and strong secondary immune response.

B lymphocytes and the antibody response

Naïve B cells can be activated with or without participation of T-helper cells T-helper cell dependent B cell activation It is most common pathway and involves T-helper cells Naïve B cell is activated and it goes via rounds of cell divisions forming multiple memory and plasma cells T cell-dependent activation of B cells •Naïve B cell has B cell receptor and MHCII on its surface. •The B cell receptor has exactly same specificity that the antibody to be produced by the cell. •B cell receptor of naïve B cell binds the antigen. •The bound antigen is internalized (taken inside) by the naïve B cell. •Inside the cell the antigen is shredded to fragments, which are presented on MHC II complexes localized on the surface of B cells. •At least one of the antigen fragment / MHC II complexes is recognized by complex of T helper cell receptor and CD4 localized on the surface of T helper cell. •It results in binding of T helper cell to naïve B cell. •T helper cell delivers cell interleukin 4 to naïve B cell, which activates the later - naïve B cell goes via rounds of cell division. •Some of the resulting cells would form memory cells, while others would be converted into plasma cells producing the antibody whose specificity is exactly the same as specificity of B cell receptor.

Which cell type is capable of phagocytosis?

Neutrophils and macrophages.

Review the chart*. Which bar(s) represent(s) the control in this experiment?

No washing

Routes of transmission

Non-contagious infectious diseases are spread from person to person via specialized routes, like vectors or vehicles: •Vectors - is any living organism that can carry a disease-causing microbe •Mechanical vectors - just mechanically carry the microbe from one place to another. They are NON-SPECIFIC as the same vector can spread a variety of the diseases. •Houseflies can carry Escherichia coli, Shigella, Entamoeba, Giardia, eggs of Ascaris •Fleas can carry Yersinia, Rickettsia, Trypanosome, Bartonella •Biological vectors - are part of the life cycle of pathogen. These vectors are DISEASE-SPECIFIC as they are carrying selected pathogens. •Anopheles mosquito is required for Plasmodium to become pathogenic to humans. •Vehicles - is any non-living object that can carry a disease-causing microbe: •Water - waterborne disease - can be prevented by chlorination of water supplies •Food - food borne disease - can be prevented by following the sanitary standards that were designed to prevent the spread of this type of diseases •Air - airborne disease - can be prevented by using HEPA filters •Non-casual body fluids transmission (including sexual contacts and blood transfusion) - can be prevented by using protective gowns, gloves, blood screening etc. •Drugs that are contaminated by microbes - can be prevented by not sharing needles or abstention. •Parenteral route - microbes are transmitted via inserted medical devises, needles, or cuts done during surgery Contagious infectious diseases are spread from person to person directly by •Direct contact - physical contact with another individual. EXAMPLES: Syphilis, Smallpox •Indirect contact - via fomites, the objects like clothing, doorknobs, drinking glass. EXAMPLES: Syphilis, Smallpox •Droplet transmission - via sneezing and inhalation of infected droplets. It is the most important source of contamination in crowned locations. EXAMPLES: Tuberculosis, Measles, Common cold, Diphtheria, Bacterial viral pneumonia •Large droplets (> 10 micrometers) can travel for about meter •Droplet nuclei (less than 5 micrometers) are suspended indefinitely and can travel for very long distances. For example, can spread though out entire building via ventilation system. Vertical transmission - from mother to a child during pregnancy Horizontal transmission - between unrelated individuals

Why did CDC personnel interview people who became ill within 24 hours after party, and not only people who became ill within 2-3 hours of the party?

Not everyone who ate the contaminated food would necessarily develop illness or go to the hospital within 2-3 hours. Factors such as how much food they ate must be taken into account.

Anatomy of Eukaryotic Cell

Nucleus - the place where genetic information of the cell is stored •Consist of chromosomes, nuclear envelope with nuclear pores Plasma (cytoplasmic) membrane - is semi-permeable natural boundary of the cell Endoplasmic reticulum - the system of intracellular membrane •Rough endoplasmic reticulum carry ribosomes bound to the surface of the membrane. It is the place where membrane and secretory proteins are produced •Smooth endoplasmic reticulum is a place of lipid and sterol biosynthesis and detoxification Golgi apparatus - is where the proteins are received from ER, sorted, modified & shipped out Mitochondria - the power plant of the cell. It is the place where cellular respiration occurs, during which ATP molecules are produced upon glycose oxidation. •The organelle has its own genome (prokaryotic type), 70S ribosomes (prokaryotic type), and double membrane (outer and inner membranes). •Inner membrane folds into cristae, the place where oxidative phosphorylation take place) Cytoskeleton - sets of proteins that perform various functions •It has 3 types of elements - actin microfilaments, microtubules, and intermediate filaments Ribosomes - machinery for protein synthesis •In their composition and structure they are similar to that of prokaryotic ribosome but larger consisting of small (40S) and large (60S) subunits that form 80S ribosomes. •Ribosomes bound to membrane are producing membrane or secretory proteins; Ribosomes freely floating in cytoplasm are producing soluble proteins Centrosome is build of microtubules and plays role in segregation of chromosomes Lysosomes are filled with hydrolyses involved in intracellular digestion and housekeeping Flagella are locomotive organelle build of microtubules Microvilli are the folding of plasma (cytoplasmic) membrane, which increases the surface of the cell enabling it to absorb nutrients more efficiently.

What did Semmelweis hypothesize?

Physicians and students were inadvertently transferring something from cadavers to women in labor that caused illness and sometimes death in the women.

Which of the following statements about plant virus transmission are TRUE?

Plant viruses enter their host through wounds. Grafted plants may be at risk of virus infection. An insect may transmit viruses between plants. Parasitic fungi may transmit plant viruses.

The antibody-producing progeny of an activated B cell are called ______.

Plasma Cells

Environmental factors for microbial growth

temperature, pH, O2 requirement, water availability

You observe bacteria growing on the surface of a Petri dish of nutrient agar you left on the counter in your lab. You can be confident that your bacteria are NOT which of the following?

Obligate anaerobes (cannot multiply if oxygen is present.)

Plant cells

Organelles found in plant cells only •Central vacuole is membranous sack •The organelle stores excess of water and can serve as nutrient depository •Cell wall is tough structure that can withstand mechanical stress •It is build of cellulose and functions as exoskeleton that prevents osmotic lysis of the cell and provides support to large organisms like grass and trees •Plasmodesmata are channels make in the cell wall. •They enable the cells communicate with each other and share nutrients and water with each other •Chloroplasts are organelles where photosynthesis takes place •It contains its own genome (prokaryotic type), •It contains its own 70S ribosomes (prokaryotic type), •It has outer and inner membrane, and third membrane - thylakoids (membrane sacks with chlorophylls)

Pathogen Properties

Pathogen properties affecting the spread of disease •Virulence is ability of microbial strain to cause the disease. It depends on set of virulence factors produced. •Highly virulent strains produce many various virulence factors, easily cause the disease that is more likely to be severe and easier to spread. •Non-virulent strains produce none or very few virulence factors and cause no disease or very mild disease that is harder to spread. •Incubation period is the time between exposure to pathogen and onset of first signs and symptoms of the diseases. The longer incubation period of the disease, the easier disease can spread. •Infectious dose 50 (ID50) is an average number of microbes required to cause the disease in 50% of exposed population. The lower ID, the easier disease can spread. Host properties affecting the spread of the disease •Immunity is resistance of the host to infection. •Innate immunity is inborn, is not specific and is not very strong •Adaptive immunity is acquired via diseases or immunization. It is microbe-specific and provides the strongest resistance against the infection. •Anatomy of an organism may predispose it to a particular type of infectious diseases . •For example, specifics of female body anatomy make them more predisposed to urogenital infections than males. •Genetics is genes makeup of an organisms. Any genetic mutation interfering with binding of pathogen to human body increases resistance to that infectious disease. •For example - some tribes in Africa are immune to HIV or to malaria due to their genetic background. •Health & Behavior. •Taking the drugs may reduce resistance to the infections. Immuno-depressants reduces the resistance of patient to any infection. Prolonged antibiotic treatment may suppress to normal flora and reduce the resistance to infections. •Travel increases the spread of infectious diseases. •Consumption of specific food may increase or reduce the risks of getting particular diseases. For example, consumption of raw meat or fish increases changes of getting intestinal and other internal parasites. Consumption of spicy food overall reduces of risks of infections.

Please select the TRUE statements about lymphocyte disorders.

People with defects in their late complement system components are at risk for repeated Gram-negative bacterial infections. People with selective IgA deficiency are at risk for repeated infections of the respiratory tract. Children with DiGeorge syndrome are at risk for virus and obligate intracellular bacterial infections

Samples of the 4 main dishes were tested for bacterial toxins. The dishes were perlo (chicken/sausage/rice dish), chicken wings, pulled pork, and green beans with potatoes. Storage, preparation and handling of the dishes is summarized in the table. Which food do you think is likely to have caused the reported illness, and why?

Perlo, because it was stored at room temperature for 8 hours, giving plenty of time for bacterial contamination and toxin production

After being engulfed, a microbe is found within a _______.

Phagosome

You inoculate fern spores onto the surface of a growth medium in Petri dishes and wait for them to develop into gametophytes, a stage in the life cycle of a fern. The medium contains sources of nitrogen, phosphate, and a number of other macro- and micro-nutrients, but no carbon. After a few weeks, you see a contaminant growing on your plates. Assuming the organism is not digesting the agar itself, which of the following is most likely your contaminant?

Photoautotrophic species of bacteria, archaea, or protists.

What was the control in Semmelweis's experiment?

Physicians and medical students who delivered babies without washing their hands first.

Plasmids (internal structures of cell)

Plasmids are extra-chromosomal DNA. They are: 1.Circular double-stranded DNA molecules that are much smaller than the chromosome and replicate autonomously 2.They are build of the same chemical components as the chromosome: dA, dT, dC, dG deoxyribonucleotides 3.They often carry one or more genes for antibiotic resistance

RNA

Plus strand single-stranded viral RNA •It can be directly used as messenger RNA to produce viral proteins, some of which will be used to build a capsid and others to replicate the viral genome •Minus strand single-stranded viral RNA •It is complimentary to messenger RNA •Therefore, it must be converted to plus strand before it can be used to synthesize viral proteins

Potency of germicidal chemical formulations

Potency can be tested by various approaches, including disk-diffusion method 1.Paper disk is soaked in chemical being tested and is overlaid over bacterial lawn 2.Appearance of clear zone indicates the antimicrobial activity of tested compound -The bigger clear zone is, the more effective compound is against microbe

Forms of energy

Potential energy It is associated with objects due to their location or structure - P.E. is stored, i.e. −Energy of water behind the dam Chemical energy is stored in molecule & is released in chemical reaction: CH4 + 2O2 = CO2 + 2H2O Kinetic Energy It is associated with moving objects - K.E. is being used or it performs a work, i.e energy of falling water Thermal energy is associated with moving molecules and atoms − Heat is thermal energy transfer 'Energy is a capacity to do work. It is transferable between objects. It also can be transformed from one form to another

Bacterial defenses against bacteriophages

Preventing viral attachment •To cause infection, virus must bind to bacterium via cell receptors •Viral infection is prevented, if these receptors are modified or covered: −Modification of cell receptors - it occurs via genetic mutations −Covering cell receptors - it can occur via production of biofilm or masking by another protein: S. aureus produces biofilm & protein A. Both of them cover such receptors. Restriction-modification system •It is responsible for cleavage and destruction of foreign DNA •Restriction-modification system consist of two bacterial enzymes: −Restrictase - it is endonuclease that recognizes short stretch of DNA (~ 6 nucleotides), called restriction sites. Restrictase binds to the site and cleaves the DNA −DNA methylase - it is DNA modifying enzyme that protects self DNA from restrictase. CRISPR system •It is responsible for destruction of foreign genome (DNA or RNA) •The mechanism is somewhat similar to that of siRNA: −If survives viral attack, bacterium inserts small fragments of viral DNA into it's genome −These fragments are expressed as RNA that form complex with CAS9 protein. •If expressed RNA binds to viral genome, viral genome is cleaved by CAS9.

Prions

Prions (PP) can be acquired •via mutation in the gene of the cell •via direct contact of normal protein (NP) with the prion •They are infectious agents that contain protein only. •Prions are linked to a number of fatal diseases (all of them cause brain degeneration). EXAMPLES: •Transmissible spongiform encephalopathies •Sheep scrapie •Creutzfeldt-Jakob disease •Mad cow disease •Prions are similar to a normal prion protein found in all vertebrates. They arise from the gene that encodes normal protein. •A gene mutation causes the protein to have different folding properties and as result to become resistant to proteases and UV light. •However, prions still can be inactivated by chemicals that denature proteins - phenols for example. •Prion protein has ability to convert the normal protein in to pathogenic one (prion).

Chromosome (internal cell structure)

Prokaryotic chromosome (with few exceptions) is : 1.Single, circular double-stranded DNA molecule that holds all genetic information required by the cell 2.Prokaryotic DNA is build of the same chemical components as the eukaryotic one: dA, dT, dC, dG deoxyribonucleotides 3.It is directly localized in cytoplasm, forming nucleoid

Adaptive immunity (3rd line of defense)

Properties of adaptive immunity highly specific matures during lifespan requires time to develop has microbe specific memory •Specific antibody and lymphocyte response to appearance of antigen •Antibody (Ab) - Y-shaped proteins made in response to antigen appearance in the organism. These proteins specifically bind to antigen •Antigen (Ag) - A substances that causes the body to produce specific antibodies •Immunogen - A compound inducing any immune response, including T-cell activation. •Globulins - Serum proteins •Gamma (g) globulin - Fraction of serum proteins containing antibodies •Serology - Studies the reactions between antibodies and antigens •Serum - Content of the blood minus any blood cells •Antiserum - Generic term for serum that contains specific antibody

In addition to perforins, what else is secreted by cytotoxic T cells?

Proteases (e.g. granzymes)

If you viewed the slide microscopically after the ethanol/acetone step, Gram-positive cells would appear ______, while Gram-negative cells would appear ______.

Purple; colorless

If you viewed the slide microscopically after the crystal violet step, Gram-positive cells would appear ______ in color while Gram-negative cells would appear ______ in color.

Purple; purple

The two 3-carbon molecules that glucose is split into during glycolysis are converted through a series of steps ending in what 3-carbon molecule?

Pyruvate

Principles of infectious disease

R. Koch was first to establish connection between a microbe & a specific disease Infectious disease is the disease caused by etiological agent or agents (microbe or microbes) Colonization is establishment of a microbial presence in the host organism via attachment & initial growth. •Examples: intestines of infants, initially sterile, become colonized by enteric and lactic acid bacteria within a few first days after the birth. Infection occurs when microbe establishes initial parasitic relationship with host. However, due to low numbers the microbe have not caused any major damage to the host yet. Therefore, symptoms (what is felt by patient) and signs (what can be observed by anyone) are very mild or non-existent. •Examples: hair folliculitis caused by Staphylococcus aureus; fungal infection of a skin Disease is an abnormal state of the body in which it does not function properly. •Non-infectious disease is caused by failing systems of the organism due to •Aging; Malnutrition; Inherited genetic mutations; Ingested microbial products •Infectious disease is caused by an invading microbe that causes noticeable impairment of body function (causes the damage to the host) leading to development of strong specific symptoms, signs or their combination (called syndrome) •Primary infectious diseases are caused by pathogens in healthy people. Examples: Plague caused by Yersinia pestis, Tuberculosis caused by Mycobacterium tuberculosis, HIV infection and AIDS caused by HIV •Secondary infectious diseases are caused by opportunistic pathogen, a microbe that causes infectious disease only when host's defenses are down. Examples : Pneumonia caused by Pneumocystis in HIV-infected humans due to failing immune system Etiological agent •is a microbe that is causing an infectious disease. It is also known as causative agent Balanced pathogenicity •It is host-parasite relationship in which the parasite persists in the host while causing minimal harm. The pathogen becomes less virulent while the host becomes less susceptible.

Selective culture media

Selective media are tailored to specific applications by addition of selective agents that allow the growth of some bacteria, while inhibiting the growth of others •It contains selective agent that allows one group of microbes to grow while growth of others is inhibited.

Which of the following observations led Semmelweis to his hypothesis?

Semmelweis's friend cut himself with a scalpel being used for an autopsy and developed the same signs and symptoms as women with puerperal fever, Women in childbirth aided by medical students who also did autopsies developed puerperal fever more often than those being aided by midwives who did no autopsies,

The FtsZ protein is needed to form the ______.

Septum

Complement proteins are found in

Serum

Comparison of three bacterial phyla

Similarities •All three phyla belong to domain Bacteria that include prokaryotic unicellular organisms lacking nucleus and membrane-bound organelles. •They have cell wall made of peptidoglycan and single circular chromosome. •All three phyla include bacteria that are chemoorganotrophs that use organic molecules as source of carbon and energy. •All three phyla include aerobic bacteria and include species that can cause infections in humans. •Differences: •Phylum Proteobacteria include Gram-negative organisms with approximately 45% GC content in their DNA that can be obligate aerobes or facultative anaerobes and form no endospores. They do not produce antibiotics but have endotoxins as part of their cell wall. Some species are coccobacilli. •Phylum Firmicutes include Gram-positive bacteria with low GC content in their DNA. Some species are obligate anaerobes or are pleomorphic. A few species can produce antibiotics that can be used only apically due to their high toxicity to humans. •Phylum Actinobacteria include Gram-positive bacteria with high (~70%) GC content in their DNA. Some species are obligate anaerobes or can have filamentous or branching cell shape and form large colonies on solid media. Phylum contain many species that produce various antibiotics used in treatment of bacterial infections in humans.

Which of the following compounds can be generated from precursor metabolites in the TCA cycle?

Some amino acids like aspartate, glutamate, and proline, certain protein components.

Which of the following bacterial groups is described CORRECTLY?

Spirochetes - move by axial fibrils.

During ancient times, people claim to have observed living creatures emerge from non-living organic materials (e.g., decaying food, stagnant water). When they purposefully left some meat out on a table, they observed that after several days, maggots appeared. Based on these observations, what can they (and you) conclude?

Spontaneous generation is occurring. The maggots came from the meat.

John Needham designed an experiment in which he boiled some broth and then corked the flask it was in, thereby sealing the flask. After a few days, he noticed that the broth had microbes in it! What did people conclude from Needham's experiment?

Spontaneous generation of small things like microbes still occurs

The term used to describe a cluster of spherical bacteria is ______.

Staphylococci

What is the name of the organism causing the illness in the people who attended the lunch party?

Staphylococcus aureus

T-cell independent B cell activation

T helper cells are not involved in this pathway of naïve B cell activation. Naïve B cell is activated and it goes via rounds of cell divisions forming multiple memory and plasma cells •Naïve B cell is activated when large antigen like polysaccharide cross-links several B cell receptors •This pathway does not work in children −For this reason, polysaccharide-based vaccines are reserved for immunization of adults

Which of the following could be another "good" reason for the meat still rotting?

The "vital force" required for life could still penetrate the cloth and cause the meat to spontaneously change.

Bacteriophage MS2 is an icosahedral, (+) sense, single-stranded RNA phage. It infects E. coli and other members of the Enterobacteriaceae. It only infects strains of these bacteria that have produced a sex pilus. Based on the information given, which of the following are true about MS2?

The bacterial receptor for MS2 is on the F (sex) pilus. MS2 is a virulent phage. The phage carries a replicase. MS2 can only infect F+ bacteria

If wet mount slide freshly prepared with motile bacteria in drop of water is left under microscope for 15 minutes, bacteria would stop moving. Why?

The cover slip used in preparation of wet mount slide prevents evaporation of water. Heat produced by a bulb of light microscope will be insufficient to kill bacterial cell. However, water does not supply the source of energy. Therefore, if motile bacterial cells are left in water for a few minutes, they will be alive, but run out of ATP and stop moving.

Naming of the enzymes

The enzymes can be named for: •the substrate they act on and adding suffix -ase •Protease - breaks down proteins •Pepsin - in human stomach •Trypsin - in human small intestines •Lipase - breakdown lipids •RNase - breaks down RNA •DNase - breaks down DNA •type of catalyzed reaction and adding suffix -ase •Ligase - joins DNA fragments together •Restrictase - cuts DNA into fragments •Polymerase - catalyzes polymerization reaction •DNA or RNA polymerases •Synthase - catalyzes the synthesis of a molecule •ATP synthase in mitochondria •Oxidase - catalyzes the oxidation of a molecule

The energy source for contraction of the FtsZ ring during cell division comes from ______.

The hydrolysis of GTP

Comprehension: Ignaz Semmelweis and Disinfection- What is the main point of this reading?

The incidence of bacterial infections in women giving birth is greatly reduced if medical personnel wash their hands before touching patients.

Cells prefer to use carbohydrates as energy sources because they are such good donors of hydrogen and electrons What is oxidation?

The loss of electrons from a molecule.

Endosymbiont theory

The theory suggests that chloroplasts and mitochondria have prokaryotic origin Eukaryotes had originated from the ancestor that is common to prokaryotes as well Metabolically active intracellular parasites like rickettsia gave rise to mitochondria Blue-green photosynthetic bacteria gave rise to chloroplasts Data supporting the theory: DNA of mitochondria and chloroplasts are similar to the prokaryotic one. Ribosomes of mitochondria and chloroplasts are of prokaryotic type. Composition of inner membrane of mitochondria & chloroplasts are similar to that of prokaryotes

Members of the genus Mycoplasma have no cell wall, making them somewhat unique in the microbial world. How do they prevent osmotic lysis?

Their cytoplasmic membrane is rich in sterols to help provide added strength and rigidity.

House sparrow and field sparrow look practically identical to non-specialist. Do house sparrow (Passer domesticus) and field sparrow (Spizella pusilia) belong to the same or different species? Explain your answer

They are not the same species, they do not share the same genus in their scientific name. They also have different patterns and behaviors.

Methods of bacterial cultivation

They are techniques of growing bacteria in laboratory's sterile settings

Other acellular infectious agents

They are the simplest infective agents as they are built of either RNA or a protein Viroids prions

What happens to the protons received from NADH in bacteria?

They are transported across the cytoplasmic membrane, setting up a proton motive force.

Which of the following statements accurately describe biochemical pathways?

They convert an initial substrate through a series of steps into an end product. They are well-organized and structured. They can be linear, branched, or cyclical. They are carefully regulated.

Which of the following cells can be a target for cytotoxic T cells?

Transplanted cells. Virus-infected cell. Cancer cells. Only cancer cells and virus-infected cells.

T/F A disease with a long incubation period is potentially more of a problem than one with a short incubation period.

True

T/F In a biochemical pathway, the product of the first reaction becomes the substrate in the second reaction.

True

T/F It is sometimes difficult to obtain pure cultures of microbes that grow naturally in mixed communities

True

T/F Mycoplasma pneumoniae lacks a cell wall and has a pleomorphic morphology.

True

T/F Nitrogen-fixing cyanobacteria are critically important ecologically.

True

T/F PCR reactions are carried out in machines called thermocyclers.

True

T/F A helper T cell must be activated before it can stimulate a B cell to produce antibody.

True A helper T cell must be activated before it can stimulate a B cell to produce antibody.

T/F Both antigen-presenting cells and B cells have class II MHC receptors on their surface.

True Both cell types have class II MHC receptors on their surface.

T/F Both enveloped and non-enveloped (naked) viruses can enter a cell by endocytosis.

True Both enveloped and non-enveloped (naked) viruses can enter a cell by endocytosis.

T/F Complement factor C3b coats a bacterium and binds to C3b receptors on phagocytes, making the bacterium more susceptible to being phagocytized.

True C3b coats a bacterium and binds to C3b receptors on phagocytes, making the bacterium more readily phagocytosed. This is referred to as opsonization.

T/F Cytotoxic T cells produce cytotoxins and perforins which cause death of the infected cells.

True Cytotoxic T cells do not recognize self proteins of infected cells

T/F Apoptosis occurs in infected host cells, as well as during positive and negative selection in lymphocyte development.

True During the clonal deletion process, T cells that react with self proteins are destroyed by apoptosis.

T/F f a bacterium could escape from a phagosome, it would be able to resist digestion by that phagocyte.

True If a bacterium can escape the phagosome, it may continue to survive within the phagocyte.

T/F In order for viruses to enter host cells, they must bind to receptors on the host cytoplasmic membrane.

True No matter how a virus enters the host cell (fusion or endoxytosis), the first step for entry is binding to host cell receptors.

T/F Phagocytosis is part of the body's innate immune defenses.

True Phagocytosis is part of innate immunity.

T/F Antigen fragments are presented at the surface of macrophages along with self proteins.

True The antigenic fragment is presented at the macrophage cell surface along with MHC class II proteins.

T/F Almost immediately upon entry, the viral nucleic acid alters the gene expression of the host cell.

True The viral nucleic acid alters the gene expression of the host cell soon after infection.

T/F More than one mechanism of viral entry into a host cell exists.

True Viruses can enter a host cell by membrane fusion (enveloped viruses) or by endocytosis (non-enveloped or enveloped viruses)

T/F A person deficient in cytotoxic T cells may be more susceptible to developing cancer.

True correct due to the role cytotoxic T cells play in killing cancer cells.

T/F The energy captured in the phosphorylation of ADP to ATP comes from the proton motive force created in respiration.

True. The flow of electrons down the electron transport chain moves protons across the membrane, resulting in the formation of a proton motive force. The flow of protons back through ATP synthase drives the phosphorylation of ADP to ATP.

Tryptic soy agar (complex media)

Tryptone Pancreatic digest of casein Soytone Papaic digest of soybean meal NaCl Agar (solidifying agent)

Please categorize the statements according to the type of hypersensitivity.

Type I:-hives -asthma -shock-mediated by histamine -involves basophils and mast cells -causes wheals and flares Type II: -transfusion reactions -hemolytic disease of the newborn -mediated by ADCC -involves NK cells -causes no skin reactions -disseminated intravascular coagulation -mediated by neutrophil enzymes Type III: -involves phagocytes -causes arthus reaction in skin -serum sickness Type IV: -causes skin inflammation -contact dermatitis -involves dendritic cells -mediated by T cell cytokines

Removal of the capsid to release the virus nucleic acid into the host cytoplasm is called ______.

Uncoating

Categories of infections caused by human virus

Viral infections can be either acute or persistent (lasting short or long time, respectively

Cultivating viruses in the laboratory

Viruses can grow only inside of the actively metabolizing cells -Bacteriophages -Animal & human viruses All viruses are obligate parasite and require live host cells for their growth.

What conclusion can you make from the data* presented?

Washing your hands with water removes some bacteria, but adding soap is more effective.

Escherichia coli is facultative anaerobe. In your opinion, when the growth rate of E. coli would be the highest - when it is growing in aerobic or anaerobic condition? Explain your answer.

While E. Coli can grow with or without O2, this bacteria prefers aerobic respiration. This is because aerobic respiration is more efficient than other methods. This is because the presence of O2 allows complete oxidation of growth substrates.

Dogs and wolfs look quite different from each other. Do dogs (Canis lupus familiaris) and wolfs (Canis lupus) belong to the same or different species? Explain your answer.

Wolves and dogs are the same species. Dogs are a subspecies of wolves. Not only is this implied by the their shared genus and species in their scientific names but when bred together they also are able to create fertile offspring.

Which of the following about microbes is false?

Yeasts are unicellular prokaryotes

Generalized transduction occurs when

a bacteriophage packages a piece of bacterial DNA during replication.

An antigen-presenting cell presents antigen to a helper T cell on its surface using ______.

a class II MHC molecule

During maturation or formation of phage particles

a few phage heads may surround fragments of host bacterial DNA.

A patient is suffering from a severe case of influenza, caused by influenza virus. He takes analgesics (painkillers) and also a fever-reducing medication, and after a few days begins to feel better. However, just as he thinks he will be able to return to school, the patient suddenly worsens, developing chest pain, and a productive cough (coughing up sputum). When he notices that his sputum contains blood, he goes to the doctor who diagnoses pneumonia, caused by the bacterium Streptococcus pneumoniae. In this scenario, the influenza virus is ______ while the S. pneumoniae is _______.

a primary pathogen; an opportunistic pathogen

Hypothesis

a testable explanation of a hypothesis

Apoptosis is

a type of cell death that does not initiate inflammation

Homeostasis (properties of life )

ability of organism to regulate and stabilize its internal conditions regardless of environment •It requires selective exchange of chemical compounds between cell and environment

Does "spontaneous generation" make sense to people from ancient times?

absolutely, yes. This is a fairly testable and repeatable experiment for people in ancient times—since they can leave all sorts of decaying matter out and witness all types of transformations to the decaying matter (e.g., food). As viewed through the lenses of their technology, spontaneous generation just made sense and it continued to make "sense" for 1,900 years! But then, here comes Francesco Redi.

Phagocytosis can be enhanced by immunological mediators such as ______.

activated complemented proteins

Pour Plate method

add melted cooled agar to plate and gently mix-some colonies appear on surface, many are below the surface

The energy released during the reactions of glycolysis is used to form ______.

adenosine triphosphate

Normal Flora suppression

always has negative impact on human health: •Antibiotic-associated colitis - antibiotic overuse leads to overgrowth of Clostridium difficile. •Candidiasis - is overgrowth of Candida albicans due to suppression or flashing out of lactic acid bacteria (LAB) from the digestive or urogenital tracks.

The basic parts of a bacteriophage are

an isohedral head, tail, tail pins, and fibers.

Lipid A

anchors LPS in outer membrane, alerts immune system to gram-negative Bactria, composed mostly of fatty acids, causes endo-toxic effects

Helper T cells interact with target cells by recognizing

antigen-MHC protein complexes.

A helper T cell becomes activated by a(n) ______.

antigen-presenting cell

•Restriction enzymes (restrictases, endonucleases)

are enzymes that cut DNA at specific nucleotide sequence called restriction sites forming DNA fragments •Endonucleases are part of restriction-modification systems of bacterial cell •Restriction sites are palindromic sequence of 4 to 8 nucleotides •the left part of restriction site is complimentary to its right side. •This increases efficiency of restriction enzymes

Alkalophilic bacteria (pH)

are growing at pH above 8.5. No human pathogens in this group.

Acidophilic bacteria (pH)

are growing at pH below 5.5. No human pathogens •To maintain neutral pH, they pump H+ (protons) out of the cell continuously.

Probiotics

are live microbes applied to the body or ingested with intend of a beneficial effect. •Bifidobacterium, Lactobacillus - found in yogurt and are beneficial to digestive system

Enzymes

are mainly proteins (some can be RNAs) that act as catalysts, a chemical agent, that speeds up a chemical reaction without being consumed by the reaction can speed up the chemical reactions from 10,000 to billion times •without enzymes, the rate of chemical reactions would be so slow, that the cell would not be able to function and exist

Exergonic (catabolic) reactions

are those that break down complex, energy-rich molecules (reactants) to simple molecules (products) with less energy stored. •The change of free energy is negative (after completion of chemical reaction, the system has less free energy) - the difference between the energy stored in reactants and energy stored in products is released ENERGY IS RELEASED

Endergonic (anabolic) reactions

are those that produce energy-rich, complex molecules (products) from simple molecules (reactants) with less energy stored •The change of free energy is positive (after completion of chemical reaction, the system has more energy than before the reaction) - the difference between the energy stored in reactants and the energy stored in products are consumed ENERGY IS CONSUMED

Viral spikes

attach specifically to host cell receptors.

Streptobacillus (grouping)

bacilli growing in chains, chain of rods

pleomorphic (shape)

bacteria that characteristically vary in their shape

Streptococci (grouping)

bacteria that form a chain

The most common organisms causing food spoilage are

bacteria, yeasts and molds

Viruses that infect bacterial cells are called ______.

bacteriophages

C3b

binds to the surfaces of microorganisms and phagocyte receptors.

After entry of the bacteriophage into the host cell, a phage enzyme

breaks the host DNA into fragments

Rod-shaped bacteria

can be either Gram-positive or Gram-negative.

Animal and human viruses

can be grown in cell culture, in embryonated eggs or in infected animals. Embryonated eggs contain various types of tissues and virus's type would determine what part of egg would be infected with the virus.

Bacteriophages

can be growth on bacterial lawn. Growing virus would lyse bacterial cells and form clear plaques on bacterial lawn. These plaques contain remnants of bacterial cells and high number of viral particles (virions).

A positive (+) strand of RNA

can directly act as mRNA.

Halophilic bacteria

can grow in the presence of high salt concentration. They produce small organic molecules that are effectively increasing the tonicity inside the cell enabling them to survive in hypertonic environment. •survive hypertonic environment •Obligate halophiles tolerate up to 20% of salt concentration. They are constantly producing these molecules and, therefore, can live in environments with high salt concentrations. •grow only in hypertonic environment •Facultative halophiles tolerate up to 10% of salt concentration. They can regulate tonicity inside their cells by switching on and off the production of small organic molecules. Therefore, they can live in environments with normal and high salt concentrations. EXAMPLES: Bacillus subtilis (free-living organism), Staphylococcus epidermidis (human normal flora), Staphylococcus aureus (human opportunistic pathogen). can grow in isotonic and hypertonic environment

When the bacteriophage transfers bacterial DNA into a recipient bacterial cell, this DNA

can integrate into the chromosome

Non-halophilic bacteria

can not survive hypertonic environment. EXAMPLES: Escherichia coli (human normal flora), Streptococcus pyogenes (human pathogen).

Essential Major elements

carbon, nitrogen, hydrogen, oxygen, phosphate, sulfur •Carbon is essential element as it forms the carbon skeleton of any organic molecule. •Autotrophic bacteria use inorganic molecules as source of carbon - CO2 in process of photosynthesis. •Heterotrophic bacteria use organic molecules as source of carbon •Nitrogen is found in NA and proteins. As source, microbes may decompose NA, proteins. •Some may use inorganic molecules - NH4+ or NO3-, A very few bacteria can use N2 in nitrogen fixation that is a highly important process for earth biosphere (WHY?) •Phosphorus is found in NA and phospholipids and chemically modified proteins. As source, microbes may use DNA, RNA, and phospholipids, or inorganic - PO43- . •Sulfur is found in proteins. Most are getting from proteins, others use SO42- or H2S

Surface receptors on immune system cells function in ______.

cell development communication identification of self/non-self molecules

T-dependent antigens

characteristically have a protein component.

Why some bacterial cultures, when they grow, turn clear medium cloudy, while other bacterial cultures form sediment, leaving the rest of medium clear?

cloudy medium indicates Aerotolerant anaerobic bacteria- they are evenly dispersed throughout the culture, they can live anywhere in the culture because they neither require or are damaged by O2 sediment indicates Obligate anaerobic bacteria- they can't survive in the presence of oxygen, so they clump together at the bottom of the culture. top layer indicates Aerobic bacteria, which require oxygen to live, form a layer at the top of the medium. This allows them to be as close as possible to the oxygen source.

packets (grouping)

cocci in cubical arrangements

clusters (grouping)

cocci in groups resembling grapes

Diplococci (grouping)

cocci in pairs

High-level disinfectants

destroy all viruses and vegetative microorganisms but they do not kill all endospores. In most cases it is steriliants that are used for short time periods that are not long enough to kill endospores. They are used to treat heat-sensitive semi-critical instruments like gastrointestinal endoscopes. Example - bleach

Low-level disinfectants

destroy fungi, vegetative bacteria (except mycobacteria) and enveloped viruses. They do not kill endospores or naked (non-enveloped) viruses.

Intermediate-level disinfectants

destroy vegetative bacteria, including mycobacteria, fungi, and most but not all viruses. They do not kill endospores. They are used to disinfect non-critical instruments like stethoscopes Example - carbolic acid

Every virus particle contains ______.

either DNA or RNA

Glycolysis makes products that feed into

electron transport chain, TCA cycle AND fermentation

Active membrane transport

energy (ATP) required; occurs only in living cell membranes; substance moves up or against its concentration or pressure gradient; utilizes pumps and vesicular transport -- transport of glucose into the cell

The three primary functions of complement activation are

enhancing phagocytosis, causing inflammation, and killing target cells.

Phagocytes are attracted by all of the following EXCEPT

enzymes released by lysosomes.

Eukarya

eukaryotic organisms that have nucleus and membrane-bound organelles. Eukaryotes are in turn classified into 4 kingdoms •Kingdom Protista (or protozoa - simple animals) - unicellular or di-cellular organisms. Some of them are photosynthetic and have cell wall made of cellulose. •Kingdom Plantae (plants) - are multicellular organisms capable of photosynthesis and have primitive tissues. The cells of these organisms have cell wall made of cellulose. •Kingdom Fungi (yeasts, molds, and mushrooms) - uni- and multi-cellular organisms that can not do photosynthesis and their cells have the cell wall made of chitin •Kingdom Animalia (animals) - multicellular organisms that can not do photosynthesis and their cells have no cell wall

Protozoa

eukaryotic, members are always unicellular, some members are photosynthetic, members do not have a cell wall

Algae

eukaryotic, single cell or multicellular membranes, all members are photosynthetic, members have a cell wall

Fungi

eukaryotic, single cell or multicellular membranes, members are not photosynthetic, members have a cell wall

In phagocytosis, the digested contents are eliminated by ______.

exocytosis

Antibiotic

is an agent produced in a microbe (bacteria or fungi) and it can inhibit the growth of other microbes. The first antibiotics widely used in medicine were penicillin produced by fungus Penicillium and streptomycin produced in bacteria of the genus Streptomyces.

Fermentation

is anaerobic process of incomplete oxidation of sugars resulting in synthesis of limited amount of ATP and formation of various organic molecule like ethyl alcohol or lactic acid.

fermentation

is coupled to glycolysis to regenerate NAD+ in the absence of O2. •During glycolysis, only 2 ATP molecules are produced from each glucose molecule. •In fermentation itself, electrons from NADH are dumped on to pyruvic acid resulting in its oxidation and regeneration of NAD+ molecules from NADH. •It enables the cell to continue glycolysis and extraction of energy from glycose. •Fermentation can occur in over-exercised skeletal muscles, when oxygen is depleted in the tissue and then cells had to get rid of NADH oversupply via fermentation. At this point, lactic acid is formed as a result of partial oxidation of glycose. •Later, lactic acid would cause muscle pain, which can be dealt with by mild exercise or by taking hot shower - both of them would speed up metabolism in skeletal muscle leading to breaking up of lactic acid. Two most common types of fermentation are •Ethyl alcohol fermentation •Lactic acid fermentation

flouresence microscope

is designed to produce very clear, highly contrast images of cellular structures that were specifically stained with fluorescent dye. •It has the source of bright light that includes entire spectrum of visible light •The first filter set allows the light of particular color (particular wavelength, l) to pass, while blocking all other colors •Light of selected color passes though the specimen stained with fluorescent dye inducing the emission of light with different color •Second filter set allows induced light to pass, while blocking all other colors. •As a result, a very crisp contrast image is formed on black background.

Normal flora

is established within first year from the time of birth. •Resident flora inhabit body for extended periods; •Transient flora is present for a short time

Endotoxin

is large molecule consisting of a lipid and a polysaccharide composed of O-antigen, outer core and inner core joined by a covalent bond. They are found in the outer membrane of Gram-negative bacteria and are triggering strong immune responses in humans and animals. They are released only from dead bacterial cells. Massive release of LPS results in rapid shock, loss of blood pressure and death.

Plasma (cytoplasmic) membrane

is natural boundary of the cell •It is semi-permeable structure that allows some molecules to cross, while other molecules will be prevented from crossing

•Tonicity

is the ability of solution to take or give water to the cells •Hypotonic; Isotonic; Hypertonic •Most bacteria do not survive hypertonic environment

Generation time

is the time required for population to double. •For bacterial cells like E. coli, the generation time is 20 min •For bacterial cells like Mycobacterium spp., the generation time is about 20 hours

The negative (-) sense strand of RNA

is used to synthesize more (+) strands.

In transduction, bacterial DNA is transferred to a new cell when

it is injected by the virus.

Pasteurization

it kills vegetative cells of pathogens and reduces the number of spoilage microbes. It does not affect the endospores at all.

After glycolysis, pyruvate can be converted into ______ under anaerobic conditions.

lactic acid

What type of infection is shown in the figure?

latent (2 red pyramids)

Spontaneous generation can be explained as

life arising from dead matter

active transport using ATP

light yellow transport protein, binding protein (blue) attaches to purple circle molecules (?) yellow P's attach to red oval ATP/ADP

The microbe is digested within the phagocyte by enzymes delivered by a _______.

lysosome

Bacteriophages involved in generalized transduction are ______ phages.

lytic

Antigen-presenting cells

may be dendritic cells. may be B cells. may be macrophages. present antigen fragments on their surface.

B cells differentiate into plasma cells and ______.

memory cells

______ are the precursors to macrophages.

monocytes

Place the labels to explain the concepts behind how spectrophotometry works.

more opaque tube should generate a higher absorbance reading, the clearer tube should generate a lower absorbance reading, How-light shines through the tube light that is lost is called the absorbance

If the Gram's iodine step was skipped in this technique, what would likely be seen under the microscope, providing all other steps were performed correctly?

most cells would appear red/pink

In the electron transport chain, protons are pumped across the cell membrane. This results in

the formation of a proton motive force.

Prior to using microscopes, do you think most people knew of biological activities such as flies laying eggs?

no, Before microscopes were available, people could not see anything that small and so the power of speculation and superstition generally prevailed.

Fluid mosaic model

of membrane suggests that the proteins are freely move within the phospholipid bilayer

Bacteriophages adsorb or attach

only to members of the same bacterial species.

Which of the following would prevent global eradication of polio?

opposition to polio vaccines in some countries, lack of health system infrastructure in some countries, civil wars and other disruptive happenings

Group Translocation

orange transport protein, blue triangle molecules, attach to yellow round P, then square light blue R

Capsule

overlays cell wall and serves various function •It serves as depositary of nutrients. •It may play role in attachment of the microbe to substrate or to host cells. •Capsule also may help pathogen to avoid the attacks by phagocytic cells of host organism, thus facilitating development of infectious disease.

Cell wall

overlays the plasma (cytoplasmic) membrane and serves as exoskeleton •Cell walls can be of different types - Gram positive, Gram negative or acid-fast Peptidoglycan monomer is made of NAM-NAG heterodimer Structure: It is mainly made of peptidoglycan, a polymer of alternating N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) monomers forming a fiber Fibers are cross-linked by pentapeptide bridges forming the 3D structure

the terminal electron acceptor in aerobic respiration is ______.

oxygen

After host cell DNA is broken down by a viral enzyme

phage DNA is replicated and phage coat proteins are produced.

phosopholipid bilayer

phospholipids have hydrophilic heads and hydrophobic tails. The tails are hidden between the layers, while heads are exposed to water

plasma (cytoplasmic) membrane

phospholipids, proteins, steroids

A difference between plasmids and fragments of DNA that have been transferred between cells is

plasmids can replicate independently.

Normal microbiota play a number of essential roles, including

preventing disease by competing with disease-causing microbes, helping degrade foods that would otherwise be undigestiblepromoting immune system development.

facilitated diffusion

process of diffusion in which molecules pass across the membrane through cell membrane channels

A farmer would encourage the growth of Rhizobium species near certain plants because the rhizobia

produce a nitrogen source that can be used by plants

Viral capsids are composed of ______.

protein

The complement system comprises a group of ______ found in the bloodstream.

proteins

Low-temperature storage

refrigeration- slows down growth freezing- prevents growth

Cytotoxic T cells cause death of infected cells by

releasing cytotoxins, perforins, and enzymes that destroy the cell.

Which of the following is a function of the mucociliary escalator?

remove microbes from the respiratory tract

Which of the following is a function of the mucociliary escalator?

removes microbes from the respiratory tract

Cells must ______ their DNA prior to cell division

replicate

What is molecular basis for high mutation rate of RNA viruses?

selection for faster replication is stronger and faster polymerases make more mistakes. The fabled mutation rates of RNA viruses appear to be partially a consequence of selection on another trait, not because such a high mutation rate is optimal in and of itself. HIGH REPLICATION SPEED?

Vibro (shape)

short curved rod

cocobacillus (shape)

short rod shape bacteria

Gram-positive bacteria retain the crystal violet-iodine complexes because the ethanol/acetone

shrinks the thick peptidoglycan cell wall, making it impermeable.

binary fission

simple

In which of the following sites would you expect to find normal microbiota?

skin, vagina, colon

Coccus/Cocci (shape)

spherical/rounded cells

Below is an outline of Louis Pasteur's swan-neck flask experiment. What can you conclude from his results?

spontaneous generation is incorrect, only life can beget life. microbes can be found in the air

Spread Plate method

spread cells onto surface of pre poured solid agar-bacterial colonies appear only on surface

Helper T cells ______.

stimulate B cells and other T cells

The advantageous genes that can be transferred by transduction are genes for

sugar fermentation. toxin production. drug resistance.

Environmental factors that influence enzyme activity

temperature, pH

Re-emerging infectious diseases

the ones that once were major health problems globally or in a particular country, and then declined dramatically, but are again becoming health problems for a significant proportion of the population •Factors playing role - the same as that in case of emerging diseases

Cellular organization (properties of life )

the organism is built of cells that have intracellular structures and organelles - Please, see lectures 3 and 4

What about Pasteur's experimental design was uniquely directed at dismissing the notion of "vital forces" and spontaneous generation?

the swan-neck flasks, which allowed "vital force" but not microbes to enter the broth.

In aerobic respiration, oxygen acts as

the terminal electron acceptor.

Today, microorganisms are consistently classified based on

their ribosomal RNA sequences, the similarity of their nucleotide sequences to other organisms, nucleic acid amplification tests.

Some phages are medically important for all of the following reasons EXCEPT

they also infect eukaryotic cells.

Sterols

they stabilize the fluidity of a membrane - reduce fluidity at higher temperatures and increase fluidity at lower temperatures

what is the function of antibody in human body?

three main functions: 1) Antibodies are secreted into the blood and mucosa, where they bind to and inactivate foreign substances such as pathogens and toxins (neutralization). 2) Antibodies activate the complement system to destroy bacterial cells by lysis (punching holes in the cell wall).

Archaea

unicellular prokaryotic organisms that have no nucleus or membrane-bound organelles and their cell wall is made of pseudo-peptidoglycan or proteins. •Prokaryotic means "pre-nuclear" - organisms are lacking nucleus and, therefore, genetic material is localized directly in cytoplasm. •Form only one kingdom Archaea. They are also known as archaebacteria - literally "ancient bacteria" •They were first to appear on Earth and tend to inhabit the environments with harsh conditions like high temperature, high salt concentration; high (basic) or low (acidic) pH. As a result, there are no human pathogens among them.

Bacteria

unicellular prokaryotic organisms whose cell wall is made of peptidoglycan •Prokaryotic means "pre-nuclear" - organisms are lacking nucleus and, therefore, genetic material is localized directly in cytoplasm. •Some of bacteria are photosynthetic, others extract energy by oxidizing minerals, still others are extracting energy by oxidizing organic molecules

Cytotoxic T cells recognize ______.

viral antigens and class I MHC molecules

A microbiologist discovers a new infectious agent. In an effort to identify the type of agent, the microbiologist exposes the agent to the following: i. RNAse ii. DNAse iii. Protease iv. Heat v. Acid After the different treatments, the microbiologist determines that the agent is destroyed by treatments (i), (iv), or (v). This result leads the scientist to conclude that the agent likely is a(n) _____.

viroid

Emerging infectious diseases

• the ones whose incidence has increased recently (in the past 50 years) and could increase in the near future. •Factors playing role - microbial adaptation, climate change, use of antibiotics in agriculture, travel and increased population density; war and famine; poverty and social inequality, bioterrorism, land use, anti-vaccination or vaccine hesitancy, wildlife trade

Mycobacterium

•Acid-fast (Gram positive); Obligate aerobes; Non-motile, form no endospores; •Slender bacilli that exhibit "corded growth" cell arrangements. Slow growing •Generation time is about 24 hours •It is a pathogen causing tuberculosis −Infectious dose (ID50) is as little as 10 −After phagocytosis, microbe survives inside macrophage •Infection treatment takes few months •Generation time is about 12 days •It is a pathogen, causing leprosy −It is the only bacterium that infects periphery neurons −It can survive inside macrophage •Infection treatment takes few months

Classification of infectious disease By duration of symptoms

•Acute infection develops fast and lasts for few days - Common cold, Strep throat •Chronic infection develops slow lasts for months or years - Tuberculosis, Leprosy Latent infection never completely eliminated and it can be reactivated - Herpes zoster, Chickenpox (varicella zoster

Reducing the available water

•Adding sugar or salt •Drying the food Both prevent the growth of microbes

Sources of antibiotics

•Antibiotics are compounds produced by a microbe and can interfere with growth of other microbes •Phylum Proteobacteria - no bacteria produce antibiotics useful to humans; •Phylum Firmicutes - some bacteria of Bacillus genus produce some antibiotics that have limited use due to their high toxicity to humans (polymyxin, bacitracin); •Phylum Actinobacteria - genera Streptomyces and Actinomyces are major source of antibiotics for humans (streptomycin, neomycin). •Fungi, like Penicillium and Cephalosporium (penicillins and cephalosporins, respectively)

Glossary

•Antitoxin - antibodies directed against a specific toxin. •Injection of these antibodies protects he patient against toxin's activity •Toxemia - presence of toxin in the host's blood stream; •Toxigenic - microbe that can produce a toxin; •Toxin - substances that contribute to pathogenicity of the microbe; •Toxoid - Inactivated toxin. It can be used as a vaccine;

Glossary (epidemiology)

•Attack rate is the percentage of people who become ill after exposure to microbe •Herd immunity is the protective effect of non-immunized population by majority (at least 85%) of population immunized against the disease. •Incidence of disease is the number of new cases occurred in a specific period •According to occurrence of the disease in population, there are Endemic disease is constantly present in a given population; Sporadic disease occurs occasionally in a given population; Epidemic disease is when unusually large number of new cases in a population; Pandemic disease is when epidemic disease is spread world-wide. •Outbreak - a cluster cases occurring in specific population during brief time interval •Index case - the first identified case in outbreak •Prevalence of disease is total number of cases in population during specific period •Mortality is overall the death rate from disease in population during given period

Comparison of properties of Corynebacterium and Mycobacterium genera:

•Bacteria from both genera, Corynebacterium and Mycobacterium, belong to phylum Actinobacteria, which is a group of Gram positive bacteria with high content of G/C (69-73%) in their DNA. However, Mycobacterium has hydrophobic acid-fast cell wall. •Bacteria from both genera are aerobic filamentous bacteria that do not form endospores. •If lysogenic for beta virus, Corynebacterium diphtheriae produce potent diphtheria toxin, while species of Mycobacterium do not produce any known toxin. •In humans, C. diphtheriae is causing diphtheria, while M. tuberculosis is causing tuberculosis and M. leprae is causing leprosy (Hansen disease). Mycobacterium •It is a genus of Gram positive acid fast aerobic bacteria that may form filaments. They do not form endospores. •They have waxy cell wall that defines acid fast stain, •slow growth rate and resistance to antibiotic treatment. •Species pathogenic to humans: M. tuberculosis is causing tuberculosis; M. leprae is causing leprosy Nocardia •It is a genus of Gram positive obligate aerobic bacteria forming rudimentary filaments •They have waxy cell wall that defines acid fast stain, •They show slow growth rate and resistance to antibiotic treatment. •Found in rich soil and oral microflora - in healthy gingival and periodontal pockets. •Some species are opportunistic pathogens - N. asteroides - can cause pneumonia • Streptomyces •It is a genus of Gram positive endospore forming aerobic filamentous bacteria. •About 500 species predominantly found in soil. They generate distinct "earthy" odor. •Most important source of antibiotics - Streptomycin (S. griseus); Neomycin (S. fradiae); Kanamycin (S. kanamyceticus); Chloramphenicol (S. venezuelae) •Few species are pathogenic to humans: S. somaliensis, S. sudanensis •Corynebacterium diphtheriae •It produces metachromatic granules where excess of phosphate is stored. •The granules are revealed by Albert - Ponder stain •the different parts of an organism are stained in different colors by single dye due to pH differences •Principal human pathogens: •Corynebacterium diphtheriae is causing diphtheria, •Mycobacterium tuberculosis is causing tuberculosis •Mycobacterium leprae is causing leprosy (Hansen disease).

Properties of enteric bacteria

•Enteric bacteria belong to order Enterobacteriales of class gamma-Proteobacteria. •The group's name reflects the fact that these bacteria mainly are associated with human and animal intestines. However, some species can reside in soil. •They are Gram-negative bacilli, mainly peritrichous. •They are facultative anaerobes that can ferment sugars with production of acid. •Enteric bacteria have adhesins localized on their pili (fimbriae).

Exponential growth of bacteria

•Bacteria have prokaryotic type of cell with no nucleus or other membrane-bound organelles. •It divides via simple division (binary fission). Single circular chromosome is attached to plasma membrane via special proteins. Before cell division, chromosome is replicated and the cell is enlarged. The copies of chromosome are segregated with help of plasma membrane and moved into would-be daughter cells. The components of cell wall are deposited between the chromosomes and the cell is divided. •After each cell division, two independent organisms are formed and the bacterial population is doubled. Therefore, bacterial growth is exponential. •Time required for bacterial population to double is called generation time, which is different for various bacterial species: 20 min for Escherichia coli, 30-120 minutes for Bacillus subtilis, 22 hours for Mycobacterium tuberculosis, 12 days for M. leprae. •Bacterial population can be calculated as following - Nn = No x 2n, where No is initial number of bacterial cells, n is number of generations.

Negative Stain

•Bacterial cells are suspended in negatively charged dye •Suspension is spread on slide and dried before examination It shows morphology of delicate bacterial cells that is not altered by heat-fixation, dye binding

Host specificity

•Bacteriophages; Plant viruses; •Animal viruses; Human viruses •Any virus can infect unique or limited range of host. It is called host specificity. •Host specificity is defined by −Specific interaction of Viral Adhesin and Host Cell Receptor (both are surface antigens) −Host cell defenses called Restriction-Modification System •Restriction-modification system is consisting of two proteins (enzymes): −Restrictase −DNA modifying enzyme

Chemical preservatives

•Benzoic acid •Sorbic acid •Propionic acid •Nitrates and nitrites -all Affect the state of plasma membrane Nitrites •When added to processed food they inhibit the germination of Clostridium botulinum endospores.

Metabolic capabilities

•Biochemical tests are run to characterize metabolic capabilities of bacterial culture by growing it on various growth media. •For example, bacterial culture can be tested for its ability to use different sugars as source of carbon and energy. •These studies establish the biochemical profile of a particular microorganism and it helps to identify the microbe.

Difference between a biotype and a serotype

•Biotype is the biochemical profile of a particular microorganism, •Serotype is the difference in its surface structures/antigens that will lead to separate immune responses from an organism (characterized by presence of different antibodies in the individual's serum)

Examples of complex media

•Blood agar contains whole red blood cells. It is routinely used in clinical labs. Many human pathogens can grow on it. It can be used to identify hemolytic bacteria •Chocolate agar contains lysed red blood cells. It can be used to grow practically any human pathogens •MacConkey agar is used to grow Gram negative bacteria and distinguish those that form lactic acid from non-formers •Thayer-Martin agar is used to test rectal specimens. It is very similar to chocolate agar but supplemented with mix of antibiotics that inhibit any bacteria but Neisseria.

Comparison of non-contagious and contagious diseases

•Both non-contagious and contagious diseases are classified as communicable disease, which means that they can be transmitted between the hosts. •Non-contagious diseases •They are transmitted from person to person via specialized routes involving •Vectors (living non-human organisms), •Vehicles (non-living objects like droplets from mist machine) or •Non-casual bodily fluids exchange (like semen, blood transfusion). •These diseases can cause outbreaks but usually do not cause epidemics. •Microbes causing these diseases usually have high infectious dose. •Contagious diseases •They are transmitted from person to person directly involving •Direct contact (physical contact with infected), •Indirect contact (contact with objects that were in contact with infected) •Casual bodily fluids (like respiratory droplets). •These diseases can cause outbreaks and epidemics •Microbes causing these diseases have very low infectious dose.

Metabolism - the set of all chemical reaction of the organism (properties of life )

•Catabolic reactions break down large complex molecules into small and simpler ones •Anabolic reactions are opposite to catabolic reactions - in anabolic reaction the larger and more complex molecules are produced (synthesized) from smaller and simpler molecules

Internal Structures

•Chromosome - single copy, contain genetic information •Plasmid - it is extra-chromosomal DNA, often carrying genes for antibiotic resistance •Ribosomes are machinery for protein synthesis. They are made of small (30S) and large (50S) subunits forming 70S ribosomes •Storage granules and vesicles play role in storage of nutrients and other functions •Endospores are lacking from actively growing cells. They are formed only when the cell encounters harsh conditions and help it to survive.

Risk for infection (affecting antimicrobial treatment)

•Critical instrument comes into the contact with an open wound - scalpel −Must be sterilized (all microbes killed) •Semi-critical instrument contacts mucous membrane - endoscope −Can be disinfected (pathogens killed) •Non-critical instrument contacts intact skin - stethoscope; blood pressure cuffs Can be sanitized (microbes reduced)

Principles of control & Situational considerations

•Daily life usually requires only decontamination (sanitization) measures −Washing and scrubbing of hands, cooking utensils, clothes that leads to removal of most microbes is sufficient •Water treatment requires disinfection to stop the spread of diseases via water −Disinfectant (chlorine) kills all human pathogens. However, non-pathogens and endospores survive •Hospital & Microbiological laboratory require the most stringent antimicrobial measures and employs variety of antimicrobial treatments: −Sterilization - by use of UV light irradiation, autoclaving, incineration resulting in killing all microbes, including endospores −Disinfection - by use disinfectants in floor mopping or by use of antiseptics in hands/skin treatment resulting in killing most human pathogens but others may survive.

Growing viruses in vivo (in live organism):

•Embryonated eggs are infected with virus at various dilutions. •The dilution at which 50% of inoculated eggs are infected called infectious dose 50 or ID50

Transmittance

•It measures amount of light passed through the sample. •It is expressed as a per cent of control sample (T%) •100% indicate that all light has passed through the sample •0% indicates that no light has passed through the sample

Mechanism of enzyme action

•Enzymes are mostly proteins but some of them are RNAs. •They function as catalysts that speed up chemical reaction without being consumed during the process: •An enzyme binds a substrate at active site forming enzyme-substrate complex in highly specific fusion like "key & lock". •Active site provides local conditions that reduce activation energy (EA) and promote the chemical reaction. •Substrate is converted to the product and the product is released from the enzyme active site. •The enzyme becomes available for another round of enzymatic reaction.

Principal pathogenic species of enteric bacteria that cause diseases in humans

•Escherichia coli - it is a part of normal flora in human guts, However, some stains can cause colitis, food poisoning and other diseases •Klebsiella pneumoniae - it is a part of normal flora in human guts. However, if it enters the lungs, it causes severe form of pneumonia with high mortality rate. •Salmonella enterica - it is a part of normal flora in birds and reptiles guts only. If ingested, microbe causes gastroenteritis or food poisoning only in humans •Salmonella typhi - it is a part of normal flora in birds and reptiles guts only. The microbe can cause typhoid fever in humans •Shigella dysenteriae - it infects humans and apes that are the only natural reservoir of this bacteria. Microbe causes dysentery in humans and apes. •Yersinia pestis - it is a part of normal flora in human guts. But it causes plague if enters human body via bite of infected flea or via inhalation of respiratory droplets. •Proteus mirabilis - it is a part of normal flora in human guts. However, if it enters circulatory system and is delivered to the kidneys, it can promote formation of the stones in kidneys.

Required elements

•Essential (major) elements are those that make up 0.1% or more of cellular weight: −carbon, nitrogen, hydrogen, oxygen, phosphate, sulfur •Trace elements are essential elements that make up 0.01% or less of cellular weight: −Zn, Mg, Mn, Fe, Cu (enzyme cofactors)

Comparison of general properties of exotoxin and endotoxins

•Exotoxins are produced by Gram positive and Gram negative bacteria. •They are proteins that can be secreted from the cell or stay inside. •Most of exotoxins are sensitive to heat inactivation & can form toxoids suitable for use in immunization as vaccines. EXAMPLES: botulinum toxin, cholera toxin, diphtheria toxin. •However, some exotoxins heat-stable. EXAMPLE: enterotoxin TSST1 of S. aureus •Exotoxins are target-specific and highly potent. Patient can die before immune response is mounted. •As a result, antitoxins are the most important part of treatment of any disease resulted from exotoxins. •Endotoxins are produced by Gram negative bacteria only •They are liposaccharides and can not be secreted as they are part of Gram-negative cell wall. •Due to its nature , endotoxins cannot be heat-inactivated. Therefore, they are not suited for toxoid production that can be used as vaccines. EXAMPLE: lipid A of LPS. •The mechanism of endotoxin's action is non-specific (can cause septic shock) and they are not very toxic •Massive quantities of endotoxin are required for it to have an effect (which may occur when bactericidal antibiotics are used to treated the infection caused by Gram negative bacteria).

Growth Factors

•Fastidious bacteria must be grown on the medium supplemented by growth factors (vitamins, amino acids, nucleotides), the organic molecules that cannot produced by the bacterial cell: −Neisseria gonorrhoeae requires blood agar; −Hemophilus influenzae grow chocolate agar −Treponema pallidum requires live cells. However, it (T. p.) is not intracellular parasite

Bacterial classification systems

•First attempt at bacterial classification was undertaken by Ferdinand Cohn in late XIX century. Classification was based on shape of bacterial cells. •Second attempt at bacterial classification was undertaken by S. Orla-Jensen in early XX century. In 1908 he had proposed to classify bacteria according to their physiology ( in other words - biochemical phenotype). •Third attempt at bacterial classification was undertaken by Albert Kluyver and Cornelis van Niel. In 1930-ties they had proposed to classify bacteria according to their evolutionary relationships. •Forth attempt at bacterial classification was undertaken by Roger Stanier in second half of XX century. He proposed to classify bacteria by comparing DNA sequence (in other words - according to DNA homology).

Filamentous protein appendages

•Flagella - organ of locomotion. It also may play a role in bacterial attachment •Pili (fimbriae) - play role in attachment of the bacterium. It may also play role in specific DNA transfer between the cells

Compare conditions and outcomes of flaming and hot air sterilization

•Flaming (over 1500OC) instantly kills everything; •Dry heat - 170OC for 2 hours. •It kills everything (Prions?) •Both are sterilization methods

Simple Stain

•Flood the heat-fixed slide with methylene blue •Methylene blue is positively charged dye and, therefore, it binds to negatively charged plasma (cytoplasmic) membrane •Incubate for 1.5 min •Rinse the slide in cold clean tap water •Air dry slide •Examine it under microscope, starting with 4X low magnification objective,

Acid Fast Stain

•Flood the slide with Carbol fuchsin and steam it for 10 min •Do not let the smear dry by watching the slide and adding the dye if needed. •Also avoid excessive heat - if slide starts steaming, reduce/remove the heat. •Rinse in water, decolorize in drops of acid alcohol until the red-colored runoffs are gone. •Counter-stain with methylene blue for 1 min •Rinse the slide in water and examine the slide under microscope. It shows if sample contains bacteria with highly hydrophobic acid-fast cell wall Acid-fast M. smegmatis is stained red and shows "corded growth" grouping

Biofilm's negative impact on humans

•Formed biofilm allows the bacteria to control the environment, including pH and concentration of antimicrobial drugs •Cells within biofilms can produce harmful chemical compounds (like toxins) that can be harmful to humans. •At the same time, the treatment of infection becomes far more difficult since the architecture of biofilm allows microbes to avoid phagocytosis (killing by phagocytic cells of immune system) and provides microbes with better possibilities to resist to antimicrobial treatments •Teeth decay starts with formation of tooth plaques - form of bacterial biofilm. Bacteria inside this biofilm produce large quantities of lactic acid, effectively reducing pH. This leads to wash out of calcium from the teeth and development of dental carries. •Implant-associated infections always involve biofilm-forming bacteria like Pseudomonas aeruginosa or Staphylococcus aureus

Temperature requirements for microbial growth

•Optimal growth temperature is a temperature at which the microbe's growth rate is highest •Minimal / maximal growth temp are the lowest / highest temp when microbe still can grow

Other solidifying agents that can be used to prepare culture media

•Gelatin - it is a protein extracted from animals. •However, it can be digested by many microbes •Starch - it is a polymer of glucose found in plants •It can be digested by microbes that can produce enzyme called amylase •It is also used in tests run to identify the microbes

alcohol fermentation (in yeasts)

•Glucose ---> 2 ethyl alcohol + 2 CO2 + 2 ATP

Vibrio

•Gram negative curved-rod shaped (comma-like) bacteria; Facultative anaerobes; Motile, possessing single polar flagella with sheaths •Microbe can survive in brackish water and at alkaline pH for extended time. −It is readily found in mollusks and crustaceans. •V. cholerae becomes pathogenic only if it is infected with lysogenic CTXj virus −Gene of CTXj virus encodes cholera toxin that causes cholera in humans −Microbe is sensitive to stomach acid. Large number of bacteria must be ingested to cause the disease. If antacids taken, the ID50 of V. cholerae is significantly reduced. Cholera •The most characteristic sign and symptom of cholera is watery diarrhea called "rice water stool" resulting in profound loss of fluids and electrolytes. •Diarrhea is caused by cholera toxin that is encoded in viral genome •The most efficient treatment of cholera is prompt replenishment of fluids (rehydration) of infected person.

Haemophilus

•Gram negative, typically coccobacilli, but can be pleomorphic bacteria; Aerobic, Non-motile, Form no endospores •It is not a part of human normal flora, but people may be asymptomatic carriers −However, humans can be asymptomatic carriers - H. influenzae may be present in humans without any signs and symptoms of infections or diseases −Microbe is fastidious and some strains would not grow even on regular blood agar. It can produce various virulence factors, including capsule, b-lactamase, endotoxin. Encapsulated stains are causing pneumonia, meningitis in humans

Corynebacterium

•Gram positive with some mycolic acid present; Non-motile; No endospores; Facultative anaerobes; Straight to slightly curved bacilli •It is a part of human normal flora −Microbe can not invade human body and always remains on body's surface −It produces diphthin (IgA protease), the virulence factor that helps to survive •Microbe turns pathogenic only if it becomes lysogenic for b bacteriophage −Viral gene encodes diphtheria toxin, the virulence factor causing the disease −Lysogenic C. diphtheriae causes in humans deadly infectious disease, diphtheria

Coliforms

•Gram-negative motile or non-motile bacilli that can ferment lactose by using enzyme b-galactosidase •Free-living or non-fecal coliforms are associated with human and animals guts but also can survive outside of the hosts. Examples - Citrobacter, Enterobacter, Klebsiella •Fecal coliform is associated with human and animal guts and CAN NOT survive outside of the hosts - Escherichia . Therefore, presence of fecal coliform in water indicates he fresh fecal contamination and possible presence of human pathogens => the water is not safe to drink, unless it was boiled for at least 10 min.

Streptococcus

•Gram-positive aerotolerant (obligate fermenters). •Salt-sensitive; Catalase-negative; Cocci growing in chains •It prefers to grow on mucous membrane of mouth and trachea. •Opportunistic pathogen causing infections only if ciliary escalator non-functional •It prefers to grow on mucous membrane of mouth and trachea •Pathogen producing various virulence factors & their combinations Streptococcus •S. mutans, S. pneumoniae, S. salivarius, S. viridans all of them are part of normal flora • Streptococcus pneumoniae - it is OPPORTUNISTIC PATHOGEN. However, microbe can be carried asymptomatically. The only known virulence factors produced by S. pneumoniae are •Capsule (highly immunogenic). It is interfering with phagocytosis. •IgA protease, digesting IgA class antibodies •Pneumolysin - pore-forming exotoxin that can interfere with functions of soluble molecules and cells of the immune system. •Microbe can cause infections only if it produces capsule AND it enters lungs, which can occur only if ciliary escalator is non-functional. If capsule is not produced, then strain can not even colonize the host. Streptococcus pyogenes - it is HUMAN PATHOGEN that is not a part of normal flora in humans. Severity of the infection is depending on what set of virulence factors is produced: •Capsule/Biofilm interfere with ingestion by phagocytes and helps microbe survive treatment by antibiotics •Adhesins - M protein acts as adhesin but it also inhibits the activity of C3 convertase, thus preventing activation of compliment system and interfering with attraction of phagocytes to the site of infection. Protein F is fibronectin-binding protein and it is analogous to FnBPA of S. aureus •Protein G binds IgG inverted thus interfering with phagocytosis (prevents ingestion). •Enzymes - Hyaluronidase breaks connections between the cells in human tissue thus increasing microbe invasiveness. Streptokinase - dissolves blood clots thus increasing microbe invasiveness; C5a peptidase digest C5a thus preventing inflammation reaction and attraction of phagocytic cells to site of infection. •Exotoxins - Superantigens (SpeA, SpeC) nonspecifically activate T-helper cells leading to "cytokine storm"; Lipid digesting enzymes; Streptolysin O, Sreptolysin S are secretory toxins that form pores in cholesterol-containing membranes (i.e. plasma membrane of human cells), which results in cell lysis. •Due to frequent very serious complications, even mild infection caused by S. pyogenes MUST BE TREATED with antibiotics.

Staphylococcus

•Gram-positive facultative anaerobes ; •Salt-tolerant; Catalase-positive; Cocci growing in clusters •It prefers to grow on the skin. •Plays vital role in limiting colonization of the skin by pathogen •Does not produce any virulence factors and lacks ability to invade. −However, it can form biofilm •It prefers to grow in nasal chambers but is also readily found on the skin •Opportunistic pathogen •It can produce multiple virulence factors Firmicutes are Gram-positive bacteria that have low GC-content in DNA (24-50%). Staphylococcus epidermidis It is part of normal flora in humans. It does not produce virulent factors and has no ability to invade human host. •However, some strains may form biofilms: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807625/ •It is the principal staphylococcal species found on skin that plays a vital role in limiting the skin colonization by pathogens •It may represent danger to immuno-compromised patients only Staphylococcus aureus - it is OPPORTUNISTIC PATHOGEN that is part of normal flora in humans. Still, various strains of S. aureus can cause various infections in humans depending on what virulence factors are produced: •Capsule/Biofilm interfere with ingestion by phagocytes and helps microbe survive treatment by antibiotics •Adhesins - Clumping factor A binds to fibrin, fibrinogen, plastic devices; FnBPA (fibronectin-binding protein A) binds to acellular tissue substances and plastic devices. •Protein A binds IgG inverted thus interfering with phagocytosis (prevents ingestion) •Enzymes - penicillases and b-lactamases - digest penicillins and b-lactam antibiotics, Catalase - inactivated hydrogen peroxide produced by attacking macrophages; Coagulase - deposit human proteins on bacterial cell and, thus interfering with phagocytosis. It is found in the most virulent strains. Hyaluronidase - breaks connections between the cells in human tissue thus increasing microbe invasiveness. Staphylokinase - dissolves blood clots thus increasing microbe invasiveness •Exotoxins - Superantigen (TSST-1) nonspecifically activates T-helper cells resulting in "cytokine storm". Exfoliative toxin - protease digesting desmoglein I that holds keratinocytes (skin cells) together; a-, b- toxins - membrane-disturbing toxins (pore-forming and lipid-digesting, respectively); Leukocidin is secretory toxin that kills phagocytes by forming pores in their plasma (cytoplasmic) membrane. •Penicillin-binding protein 2a - does not bind penicillin, resulting in bacterial resistance to penicillin. •Staphyloxantin inactivates hydrogen peroxide produced by attacking macrophages

PCR (polymerase chain reaction)

•It is an enzymatic reaction of making multiple copies of gene of interest using •Limited amount of template DNA - theoretically one copy of gene is enough •Number of gene copies doubles with each cycle N(n) = 2n •In 25 cycles, 1 copy of DNA would be multiplied to 3,3 x 107 copies of the gene •Pair of primers flanking the gene •All 4 deoxynucleotides (dA, dT, dC, dG) •Thermostable DNA polymerase •This method is particularly useful if •Pathogen is very slowly growing, •Pathogen present in very small numbers or mixed with other bacteria Applications of PCR: •Cloning the gene of interest (recombinant DNA); •Amplifying DNA to detectable levels; •Sequencing DNA; •Diagnosis of genetic disease; •Detection of pathogens

Clostridium

•Gram-positive; Obligate anaerobes; Endospore-forming bacilli •Growing without growth arrangement; Endospores may deform the cells •It is normally present in humans colon •Opportunistic pathogen −Growth is inhibited by normal flora −It is causing antibiotic-associated colitis •It can produce some virulence factors −See slide noted for more details •Endospores are abundant in soil. •Pathogen, −Only, If anaerobic conditions present −Causes gas gangrene, food poisoning It produces multiple virulence factors Genus Clostridium is belonging to phylum Firmicutes - bacteria that have low GC-content in DNA (24-50%). Species of Clostridium are •Gram positive bacilli that are obligate anaerobes •They form endospores, which often have diameter bigger than that of the bacterial cell •Some of clinically important clostridial species produce the most potent biological toxins known Clostridium botulinum •It produces botulinum toxin, the most potent biological toxin known. LD50 (lethal dose for 50% of exposed people) is 1 ng per 1 kg of body weight. That means about 70-75 ng of toxin can kill an average person. •In humans , it causes botulism Clostridium difficile •it produces protein-modifying TcdA and TcdB toxins that are damaging intestinal mucosa. •It also forms biofilms •In humans, it causes antibiotic-associated diarrhea, pseudo membrane colitis, perforation of colon, sepsis. There were 15,461 cases of C. difficile-associated infections were identified in the USA in 2011, with total burden of the infection estimated at about 453,000 cases. Clostridium perfringens •It produces a-toxin and various enzymes that cause tissue necrosis and increase invasiveness. •As very strong fermenter, it is producing a lot of gas (hydrogen and carbon dioxide) that further increasing bacterial invasiveness. •In humans, it causes gas gangrene and may also cause food poisoning: Clostridium tetani •It produces tetanospasmin, the second deadliest known biological toxin. LD50 is 2.5 ng per 1 kg of body weight. •In humans, it causes tetanus

Water availability

•Hypotonic solution gives water to red blood cells (RBCs are burst); Isotonic solution does not take or give water from or to RBC; Hypertonic solution takes out water from red blood cell;

Infectious Dose

•ID is a number of microbes required to establish infection in individual host •ID50 is number of microbes required to cause infection in 50% of exposed population

Morphology of microbial colonies on special media

•If Escherichia coli is grown on EMB agar, bacterial colony has unique appearance - it develops green metallic sheen. •It ferments lactose with production of a lot of acid that precipitates dyes present in the medium. •If bacteria are grown on blood agar, their hemolytic activity can be determined •Alpha-hemolytic bacteria develop cloudy greenish halos around colony as they are partially hemolytic. •Beta-hemolytic bacteria develop clear halos around colony as they are lysing red blood cells completely •Gamma-hemolytic bacteria do not develop halos around colony as they are non-hemolytic and can not lyse red blood cells.

Residue

•If chemical leaves residue after treatment, it must be removed

How to measure evolutionary relationship of macromolecules?

•In this approach, the sequences of polymeric macromolecules (RNAs, DNA or proteins) from various species are aligned and compared to each other letter by letter (nucleotide by nucleotide or amino acid by amino acid). •The similarity of two sequences is expressed as PERCENT OF HOMOLOGY •Percent homology reflects the percent of nucleotides or amino acids identical in two sequences from various species. •The higher % of homology, the closer compared sequences are related •The sequence comparison of the same gene or protein from multiple species allows to build phylogenic tree of that macromolecule and see how it was evolving over the time. •Comparison of nucleotide sequence of 16S or 18S ribosomal RNAs from different species allows to build phylogenic tree of Life as those molecules are the most conservative and change extremely rare.

Proteins (there are 2 types)

•Integral or transmembrane proteins are exposed on both sides of plasma (cytoplasmic) membrane •Peripheral proteins are exposed only on one of the sides of the plasma (cytoplasmic) membrane

Fluorescence microscopy

•It allows the use of multiple fluorescent dyes of different colors to simultaneously visualize various structures in the same cell. •Each dye is visualized with help of specific filter set •Resulting images can be overlaid, which leads to formation of composite image containing information on localization of multiple structures in the same cell. •It also allows the visualization of structures in live cells in real time.

Formation of biofilms

•It begins when planktonic bacteria attach to the surfaces. •Additional bacteria attach and grow in the initial layer. •Growing bacterial cells produce and secrete sticky material that fills the space between the cells •Completely formed biofilm has open channels that allow the nutrients to move in and waste to move out of microbial community. Biofilm is any group of microorganisms embedded within a 3D slimy extracellular matrix that is composed of extracellular polymeric substances (EPS) made of extracellular DNA, proteins, and polysaccharides.

Types of cellular respiration

•It can be aerobic or anaerobic. It requires electron transport chain & acceptor of electrons •In aerobic respiration, oxygen is used as terminal acceptor of electrons. •In anaerobic respiration, terminal acceptor of electrons is iron, manganese, cobalt, uranium, sulfur, carbon dioxide, nitrate or organic molecule other than pyruvic acid (i.e. fumaric acid). •During anaerobic respiration there is less energy extracted than it is in aerobic respiration. Therefore, obligate anaerobes are growing slower than obligate aerobes. [EXTRA] Electron transport chain (ETC) is set of membrane proteins. The energy-rich electrons are damped by electron carriers (NADH and FADH2) on ETC. As these electrons travel along ETC, protons are pumped across the membrane, creating proton gradient. ETC includes: •Complex I - NADH dehydrogenase removes 2 electrons from NADH and transfers them onto ubiquinone, and pumps 4 protons across membrane, creating proton gradient. Complex I is principal place where electron leakage can take place producing harmful superoxide radical by transfer of electrons on to oxygen, instead of moving them along ETC. •Complex II - Succinate dehydrogenase (4 subunits) binds electron-rich ubiquinone and delivers electrons to complex III. This is also the place where electrons from FADH2 are accepted and transferred on to ubiquinone. •Coenzyme Q - •Complex III - Cytochrome bc1 complex transfers electrons from ubiquinone onto cytochrome C. Additional 6 protons are translocated across membrane, increasing proton gradient. This is another place where electron leakage can take place producing harmful superoxide radical by transfer of electrons directly on to oxygen, instead of moving them along ETC. •Cytochrome C - •Complex IV - Cytochrome C oxidase accepts electrons from cytochrome C and transfers it onto molecular oxygen (O2), producing two molecules of water. At the same time, additional 4 protons are translocated across the membrane, further increasing proton gradient.

Culture characteristics

•It describes appearance of microbial colony and includes: •Form - describes to the following characteristics of the colony: •Shape - Most common shapes are Circular, Irregular, Filamentous, Rhizoid •Size - diameter of colony is measured in millimeters. •Tiny colonies are described as punctiform •Surface - Shiny (glistening) or dull; Smooth, Rough, Veined, or Wrinkled •Texture - Dry, Moist, Mucoid, Brittle, Viscous •Color - It may also include optical characteristics like opaque, cloudy, translucent •Elevation - describes the profile (side view) of the colony. •The most common are Flat, Raised, Umbonate, Crateriform, Convex, Pulvinate (cushion-like). •Margin - describes the edge of the colony. •The most common are Entire, Undulate, Lobate, Curled, Filamentous. •NOTE: The appearance of bacterial colony is affected by •Temperature and atmospheric conditions at which the bacterial culture was grown, •Time of incubation •Medium used to grow bacterial culture

TRICARBOXYLIC ACID (Krebs) CYCLE

•It is taking place in mitochondrial matrix •2 acetyl-CoA are completely oxidized to 4 CO2 and H2O. •Production - 2 ATP, 6 NADH, 2 FADH2

Phylum Proteobacteria

•It includes Gram-negative bacteria that have different cell shape, from cocci (rounded cells) to coccobacilli (short rod-like cell shape) and to bacilli (rod-like cell shape) •They are aerobic bacteria that is they can grow in the presence of oxygen •Proteobacteria are including obligate aerobes, facultative anaerobes, microaerophiles and aerotolerant species •There are motile and non-motile species. •The phylum is divided into 5 classes based on analysis and comparison of ribosomal RNA sequences •All proteobacteria produce LPS (lipopolysaccharides) as part of cell wall. •In some species LPS contains lipid A, which turns LPS into endotoxin •Some species may also produce exotoxins, •Order Enterobacteriales or Enteric bacteria include species that are tightly associated with human intestines. •Human pathogens: phylum Proteobacteria includes many bacterial species that are pathogenic to humans and animals, infecting digestive, respiratory, nervous, urogenital and circulatory systems.

DNA methylase

•It is DNA modifying enzyme that is part of restriction-modification system •It chemically modifies the restriction

standard curve

•It is a graph of bacterial growth when cell concentration is plotted against absorbance of bacterial culture (OD). •Therefore, when built the standard curve allows the conversion of absorbance (OD) units into the microbial cell concentration (cells/ml) without actual count of the cells. •The useful range of standard curve is between 0.1 to 0.6 OD units.

Group of lactic acid bacteria

•It is a group of bacteria that ferment sugars with production of lactic acid. •The following genera are part of lactic acid bacteria group: Lactobacillus; Lactococcus; Streptococcus

Biofilm

•It is a group of bacterial cells embedded within self-produced matrix of extracellular polymeric substance. •Biofilm provides effective protection against viral infection, phagocytosis, and antibiotic treatment

Virulence

•It is a measure of microbial ability to produce virulence factors and cause the disease •Virulence factors are molecules and structures produced by a microbe •Examples : adhesins, capsules, secreted enzymes, toxins •Combination of produced virulence factors defines the virulence of a microbe - •Examples : •Staphylococcus aureus - common strains are causing Folliculitis, harmless skin condition. 5% of strains of S. aureus are producing exfoliative toxin and are causing Staphylococcal scalded skin syndrome, a life-threatening disease. •Streptococcus pyogenes - common strains are causing Streptococcal pharyngitis (Strep throat), relatively harmless disease. However, stains of S. pyogenes producing streptolysins are causing Necrotizing fasciitis (flesh-eating disease), a life-threatening disease •Highly virulent strains are producing various virulence factors and are more likely to cause infectious disease. •Non-virulent strains are producing very few virulence factors or are not producing any at all and can not cause infectious disease.

DNA gel electrophoresis

•It is a method of separation of DNA molecules (fragments or whole chromosomes) in electric field •Separation of molecules occurs according to their -Charge - by the force of the applied electric field §Negatively charged molecules would move toward positively charged electrode (anode) §Positively charged molecules would move toward negatively charged electrode (cathode) -Size - by the dragging force produced by interaction of moving molecules with the matrix of the gel -The bigger molecule, the slower it moves through the gel -The smaller molecule, the faster it moves through the gel

Commercial canning process (commercial autoclaving, commercial sterilization)

•It is a process of destroying the endospores of Clostridium botulinum in food to be canned. It is 12D process - should destroy 1012 endospores. •However, the autoclaving time is shorter than usual, which enables endospores of thermophilic bacteria to survive. However, it is not a concern as thermophilic bacteria can not grow at room temperature. •Therefore, the commercially canned food can not be considered sterile •Conditions - 121OC, pressure 15 psi for 3 min

metabolic pathway

•It is a series of chemical reactions in which the product of one chemical reaction becomes the reactant of the next one. •Metabolic pathway starts with precursor molecule that is going through series of chemical reactions until the end product is formed. •Each chemical reaction is in metabolic pathway is served by specific enzyme and may require energy supplied by ATP or electron carriers like NADPH or NADH

Metabolism

•It is a sum of all chemical reactions that take place in the cell. •It has two branches - catabolism and anabolism. •Catabolism is a sum of catabolic (exergonic) reactions that break down energy-rich, complex molecules and harvest energy in form of ATP. •Anabolism is a sum of anabolic (endergonic) reactions consume energy (mainly in form of ATP) and build up complex molecules out of simpler ones. •Catabolism and anabolism are coupled (interconnected) via ATP molecules which allows the flow of energy from catabolic reactions to anabolic reactions.

Taxonomic hierarchy

•It is a system of taxa (classification units) of various ranks. •The high ranked taxon may include multiple taxa of lower ranks. •The higher taxon, the more common and older characteristics it describes •The lower taxon, the more specific and relatively recent characteristics it describes •Taxa from highest to lowest: Domain --> Kingdom --> Phylum --> Class --> Order --> Family --> Genus --> Species. •These taxa are used to classify biological species. •The closer two species related to each other, the lower taxon they will share. •Domain (highest taxon) Eukarya includes all organisms made of the cells with nucleus and membrane-bound organelles (the most common and oldest characteristics) . This domain includes four kingdoms: •Kingdom (second highest taxon) Procista includes eukaryotic organisms that made of single or two cells. Some are photosynthetic, while others are not. They include all eukaryotic organisms that can not be classified in to other 3 kingdoms of domain Eukarya •Kingdom Fungi - includes multi- or unicellular non-photosynthetic eukaryotic organisms that have cell wall made of chitin •Kingdom Plantae - includes multicellular photosynthetic organisms that have cell wall made of cellulose - green plants •Kingdom Animalia includes multicellular non-photosynthetic organisms that have no cell wall. They are mobile (with very few exceptions) and form blastula during embryonic development. •Phylum Chordata includes multicellular animals with spinal chord •Class Mammalia includes animals with spinal chord whose females nurse their young with milk •Order Carnivora includes flesh-eating mammals •Family Ursidae includes carnivores with large bodies, long snouts, small rounded ears, shaggy hair, paws with non-retractive claws and short tails •Genus (next to lowest taxon) Ursus includes various bears •Species (lowest taxon) americanus is smallest bear that inhabits North America and has black fur Ursus americanus is scientific name for the animal known by its common English name as American black bear.

Pasteurization methods and conditions

•It kills vegetative bacterial cells. However, endospores and naked viruses survive. Therefore, it is not sterilization •Conditions: •Classical method - 63OC for 30 min •HTST (high temperature, short time) - 72OC for 15 sec •UHT (ultra high temperature) - 140OC for 2 sec

Allosteric regulation

•It is an example of non-competitive inhibition of enzymatic activity •It is used in regulation of some metabolic pathways in the cell. •The end product of the metabolic pathway acts as reversible non-competitive inhibitor of the first enzyme of the same metabolic pathway. •Binding of the end product to first enzyme at allosteric site effectively turns down the activity of the enzyme and shuts down the metabolic pathway entirely. •The pathway remains turned off as long as the concentration of the end product remains high. •Allosteric regulation enables the cell to quickly turn off and turn on the metabolic pathway depending on concentration of the end product. •The shutting down of the metabolic pathway is achieved without enzymes' destruction and their re-synthesis, thus conserving the cellular resources.

Pathogen

•It is an organism that can infect host organism and cause a disease

Genetic mutation

•It is any change to nucleotide sequence of DNA or structure of chromosome that occurs spontaneously or induced by exposure to chemical or physical mutagens. •Changes in nucleotide sequence of DNA can lead to changes in amino acid sequence of proteins which may result in resistance to viral infection if mutation affects the structure of cell receptors recognized by viruses.

ATP

•It is energy currency of the cell. ATP is build of adenine, ribose, and 3 phosphate groups •It carries the energy stored in third phosphate group in immediately available form. •Upon hydrolysis, ATP is split into ADP and P, a phosphate group that carries the energy. •The phosphate group along with energy is transferred on to target molecule turning it into activated state in which the cellular work, like biosynthesis of macromolecules, can be done in the cell •After ATP hydrolysis, resulting ADP molecule is used to regenerate ATP needed for various cellular functions, including biosynthesis •Therefore, ATP allows the energy flow from catabolic reactions to anabolic reactions

endospore

•It is extremely resistant to heat, desiccation, UV, •It can survive for 100s of years •It is abundant in the soil •Process of endospore formation (sporulation) may coincide with toxin production. •It consists of: •Core contains cell wall, plasma (cytoplasmic) membrane, nucleoid, cytoplasm. Water content 10-30% of active cell. Low pH. Special small acid-soluble proteins (SASPs) condense and stabilize the DNA. •Inner membrane •Cortex contains peptidoglycan, dipicolinic acid that cross-links with calcium ions leading to extreme resistance of endospore. •Outer membrane •Spore coat - layers of spore-specific proteins

Symbiosis ("together living")

•It is intimate interactions between microbe and host (human) •Types of symbiosis: −Mutualism (Lactobacillus spp., Escherichia coli); −Commensalism (Staphylococcus aureus); −Parasitism (Yesinia pestis, Vibrio cholerae, any virus)

Adaptive immunity (3rd line of defense)

•It is microbe-specific, has memory, and can mature during the life span of individual. •It includes the third line of defense Third line of defense •It is directed at specific destruction of microbes that entered human body •It includes •Humoral immune response which is based on specific antibody (activity of B cells) •Cellular immune response which is based on activity of T lymphocytes (helper and T cytotoxic cells) and natural killers.

Innate immunity (1st and 2nd line of defense)

•It is non-specific, has no memory, and can not mature over the life span. •It includes the first and second lines of defenses First line of defense •It is directed at prevention of microbial entry into human body •It includes •Skin and its secretion, •Mucous membrane and its secretion, •Normal flora (microbiota); Second line of defense •It is directed at non-specific destruction of microbes that entered human body •It includes •Phagocytic cells; •Compliment system; •Fever •Antimicrobial substances of a host.

bacterial motility

•It is observed during examination of freshly prepared wet mount slide under the microscope •Wet mount slide is prepared as following: •bacterial culture is suspended in drop of water and suspension is covered by cover slip

Budding

•It is observed in replication of some animal and human viruses, not in plant viruses or bacteriophages. •It is the process of slow virus release from the cell with active participation of host cell plasma membrane. •It is characteristic to enveloped viruses •EXAMPLE - Human Immunodeficiency Virus (HIV)

Agar

•It is polysaccharide isolated from marine kelps •It is inert as it can not digested by bacterial cells with very few exceptions

RTF agar

•It is rich culture medium containing not only common components (yeast extract, peptone, starch etc) but it is also supplemented with sheep blood (source of hemin or X-factor) and niacin (NAD or V-factor), which makes this medium suitable for growing Haemophilus influenzae

IgG class

•It is secondary antibody produced in response to exposure to microbe. •It can activate compliment system but can not cross-link (agglutinate) microbes. •As a monomer, it is found in blood (up to 85% of total antibody content) and lymph •Due to its size, it can cross placenta and found in tissue •It is the antibody of memory - it will be produced upon secondary exposure to a microbe

Complement system (second line of defense)

•It is set of soluble proteins present in blood stream that "complement" or enhance the action of antibodies and phagocytic cells Activation of complement •Classical pathway - works only in the presence of antibody (that is on second and consecutive exposure): 1.Antibody binds to microbial surface antigen & recruits C1 complement protein 2.Bound C1 activates C2 and C4 by cleaving them into 2 subunits each. 3.C2a and C4b subunits form C3 convertase that splits C3 protein to C3a and C3b. •Lectin pathway - works only if bacteria have mannose-containing carbohydrates (these carbohydrates are absent in human cells and tissues): 1.Mannose-binding (M-B) lectins, the proteins produced by liver, are binding to microbial mannose-containing surface carbohydrate. 2.Bound M-B lectins activate C2 and C4 by cleaving each of them into 2 subunits. 3.C2a, C4b subunits are forming C3 convertase that splits C3 protein to C3a and C3b. •Alternative pathway - works only if bacterial cell has lipo-polysaccharide complexes on its surface (primarily Gram negative bacteria). 1.Endotoxin, polysaccharides or cell wall components bind C3b which is constantly produced in tiny amounts. 2.Bound C3b recruits factors B, D, and P (properdin). 3.B, D, and P factors form C3 convertase, which is dramatically accelerating production of C3a and C3b.

RESPIRATION

•It is taking place on mitochondrial inner membrane. •It requires the presence of electron transport chain (ETC, acceptor of electrons, AND electron carriers •ETC is a set of membrane proteins that can accept electrons from electron carriers and transfer them on to electron acceptors •Aerobic respiration is the process when oxygen is used as terminal acceptor of electrons. •Anaerobic respiration is the process when terminal acceptor of electron is not oxygen but Fe, Mn, S, U, NO3 or organic molecule other than pyruvic acid. •Aerobic respiration is more efficient as there are more ATP produced than during anaerobic respiration. •Production: up to 34 ATP

Lysogenic conversion

•It is the change of bacterial phenotype due to viral infection, when viral genome is inserted into bacterial chromosome and virus become provirus. •Usually it results in increased pathogenicity as bacterial cell acquires ability to produce toxins. •EXAMPLES: •Corynebacterium diphtheriae is non pathogenic, unless it is infected with b virus resulting in production of diphtheria toxin. •Vibrio cholerae acquires ability to produce cholera toxin when it becomes lysogenic for CTXj virus •It may increase pathogenicity (ability to cause the disease) of the bacterial cell

Chemical energy

•It is the energy stored in molecule's structure and it is released in chemical reaction •For example - burning of cooking gas releases energy used to prepare the food

IgM class

•It is the first antibody produced in response to first exposure to microbe. •They are most effective at activation of compliment system by classical pathway. •It can also cross-link (agglutinate) microbes, •Both these activities make IgM particularly useful during first exposure to microbe •As a pentamer it is found in blood (up to 10% of total antibody content) and lymph •Due to its size, it can not cross placenta and it is not found in the tissues •It is the only antibody that can be formed by fetus

IgD class

•It is the monomeric antibody found on surface of B cells surface •It does not activate compliment system but it plays crucial role in activation of naïve B cell

IgE class

•It is the monomeric antibody found on surface of mast cells and basophils •It does not activate compliment system but it plays crucial role in setting off certain types of allergic reactions

Chemiosmosis

•It is the movement of protons across membrane along the proton gradient that was formed with help of energy-rich electrons and electron transport chain. Chemiosmosis is used for synthesis of ATP during cellular respiration and photosynthesis

Glycolysis

•It is the oldest pathway to generate ATP from glucose and can be found in all types of cells. It takes place in cytosol. •In bacteria, it is also known as the Embden-Meyerhof-Parnas pathway. •Glucose is broken into two molecules of pyruvic acid. •Formed: 2 Pyruvic acids (to be used in next step), 2 ATP and 2 NADH (to be used later in last step of cellular respiration)

IgA class

•It is the secretory antibody and the most abundant immunoglobulin made by the body •It can not activate compliment system but it can cross-link (agglutinate) microbes. •Secretory component also protects against destruction by proteases. •As a dimer it is found in blood, lymph and in the secretions of mucus, saliva, tears, breast milk.

Fever

•It is triggered by appearance of microbial products −Example: endotoxin (LPS) of Gram-negative bacteria Benefits of fever: Inhibition of bacterial growth by affecting bacterial metabolism Increased activity of T helper and T cytotoxic cells in the host Increased production of antimicrobial substances by the host Fever development caused by Gram-negative bacteria: •Gram-negative bacterium is ingested by macrophage •Formed phagosome is fused with lysosome and ingested bacterium is destroyed •Endotoxin released from the cell wall of Gram-negative bacterium triggers production of interleukin 1 by macrophage. •Interleukin 1 secreted by macrophage enters blood stream and is delivered to hypothalamus •In response to appearance of interleukin 1, hypothalamus produces prostaglandin that causes development of fever. NOTE: Gram-positive bacteria can also cause a fever, but mechanisms involved are different from that of Gram-negative bacteria

Biofilm's positive impact on humans

•It is used in bioremediation - cleaning toxic spills •It is used in treatment of waste water.

Streak plate

•It is used to isolate or maintain pure culture from microbial sample grown on solid or liquid media Spread sample on medium sector by sector

Spread Plate

•It is used to test liquid or solid sample for microbial presence. Solid sample must be suspended first Put ≤1 ml of liquid or solid sample suspended in water and spread it on plate using sterile spreader

Scanning Electron Microscope

•It is used to visualize the structural details of the surface. •Magnification up to 10,000´; Resolution up to 20 nm •Resulting images have characteristic 3D appearance •The image provide fine details of surface structure, the inner content is not visible

Transmission EM

•It is used to visualized the structural details inside the cells. •Electron micrographs are taken from serial thin sections. •These images can be used as is or they can be used to reconstruct 3D structure of the sample using computer technology •Magnification up to 300,000´; Resolution up to 0.5 nm

Dichotomous key/identifying bacteria

•It is widely used in identification of biological species, including bacteria. •The key is based on system of questions that have only two answers. •The answer to the first question determines the second question to be asked •And it continues so, until the species is identified.

Autoclaving

•It kills vegetative bacteria and endospores, viruses and all other microbes. Therefore, it is a sterilization procedure. However, prions can still survive the treatment •Conditions - 121OC, pressure 15 psi for 20 min •Biological indicators such as thermophilic bacteria or heat-resistant endospores (for example those of Geobacillus stearothermophilus) are used to ensure that autoclave is working properly

Boiling (using heat to destroy microbes)

•It kills vegetative bacteria and viruses. However, endospores of most bacterial species survive the treatment. Therefore, it is not a sterilization •It is particularly very effective at killing most common waterborne pathogens •Conditions - 100OC for 10 min

Absorbance (or optical density)

•It measures the amount of light absorbed by the sample •It is expressed in optical density units (OD) •0 OD indicates that the sample optically clear •Any OD above zero indicate that the sample had absorbed some light •For practical purposes, the absorbance of any cell suspension, including bacteria, is measured between 0.1 to 0.6 OD units •Any readings below 0.1 or above 0.6 OD are inaccurate.

Hygiene hypothesis

•It proposes that lack of exposure to normal flora can lead to development of allergies

Turbidity of a Solution

•It results from scattering and absorption of visible light by suspended insoluble particles or cells. •More particles or cells suspended in the liquid medium, more light is scattered and absorbed, more turbid solution looks. •Turbidity can be measured using spectrophotometer.

Inflammation

•It results from the damage done to human tissue and/or appearance of microbial antigens, which leads to local activation of compliment system and vasodilation of blood vessels, which results in locally increased blood flow. It is one of the outcomes of compliment system activation triggered by microbe −It results in vasodilation and attraction of phagocytic cells to affected site −Neutrophils (residing in the blood) would be attracted first, then macrophages (tissue) •It is triggered by −Appearance of C3a and C5a produced due to appearance of bacterial products like LPS, Proteins, Mannose-containing sugars −Appearance of Histamines, Cytokines, Prostaglandins, Leukotrienes released by damaged human cells Signs and symptoms •Redness of the affected area and heat (increased temperature) due to vasodilation and increased blood flow; •Swelling due to accumulation of fluids in affected area. •If swelling is excessive, then pain and loss of function may be experienced; • Functions •Destruction and removal of the invading microbe. •If destruction is not achievable, then walling off the microbe (for example, formation of tubercles in case of infection caused by Mycobacterium tuberculosis). •Repair or replacement of the damaged tissue; Types of inflammation •Acute inflammation is short and intense in response. •Due to short duration, it may be less damaging to host, particularly if it affects least sensitive tissues - EXAMPLES: acne vugaris affects epidermis and leaves no scares. •However, sepsis, also acute systemic inflammation, involves sensitive tissues - blood stream, and, therefore, it is life-threatening condition that can result in quick death. •Meningitis is another acute inflammation involving meninges around brain and spinal cord. It is also can result in rapid death. •Chronic inflammation is less intense in response but it may last months or years leading to more damage done to the host. •EXAMPLES: tuberculosis, rheumatoid arthritis.

Tricarboxylic acid cycle (TCA) (Citric acid cycle or Krebs' cycle)

•It takes place in mitochondrial matrix or in cytoplasm of bacterial cell. •2 Acetyl-Co A are completely oxidized to CO2 and H2O. •Formed: 2 ATP, 6 NADH (to be used later in last step of cellular respiration), 2 FADH2 (to be used later in last step of cellular respiration)

Cellular Respiration

•It takes place on mitochondrial inner membrane (if the cell is eukaryotic) or plasma membrane (if the cell is prokaryotic). •10 NADH, 2 FADH2 produced in previous steps are used to create proton gradient with a help of electron transport chain. •In second step, called chemiosmosis, the proton gradient is used to synthesize ATP. •Formed: up to 34 ATP - it varies from species to species (28 ATP in humans) •10 NAD+ and 2 FAD are regenerated and can be re-used again

Transition step

•It takes place on mitochondrial outer membrane. •Pyruvic acid is converted to acetyl-CoA •Formed: 2 acetyl-CoA (to be used in next step), 2 CO2 and 2 NADH (to be used later in last step of cellular respiration)

Fermentation is alternative to respiration

•It uses an organic molecule as the final electron acceptor

Mycoplasma

•Lacking cell wall; Obligate aerobes; Some exhibit gliding motility •Pleomorphic bacteria; Form punctate (microscopic) 'fried egg" colonies •Not part of human normal flora •Pathogen causing human diseases −Pelvic inflammatory disease −Bacterial vaginosis in women −Infertility in men 1 report suggests it is intracellular •Not part of human normal flora. •Pathogen, −It is causing atypical, "walking" pneumonia •If P1 adhesin is not organized into tip structure, microbe loses pathogenicity Genus Mycoplasma is belonging to phylum Firmicutes - bacteria that have low GC-content in DNA (24-50%). Species of Mycoplasma are •Lacking cell wall and, therefore, at the end of Gram stain will have pink color. •Do not produce endospores and are naturally resistant to b-lactam antibiotics (penicillins and cephalosporins) •They do not produce any known toxins.

Bacterial growth curve phases

•Lag phase - the number of bacterial cells does not increase as the cells are adapting to environment & prepare to grow. The cells are metabolically very active, but they still are not dividing yet. •Log phase (exponential) - period of exponential growth. Population doubles with each generation time passed: •Early & advanced log phase. the cells are producing primary metabolites (proteins, lipids, NA) required for cell growth and cell division. At this time, bacteria are most sensitive to antibiotics due to active metabolism (targeted by antibiotics) •Late log phase, the cells become crowded and start producing secondary metabolites (antibiotics, toxins etc) that help them to compete with others for dwindling nutrients supply and produce endospores. The cell are becoming resistant to antibiotics. At the end of log phase, some Gram-positive bacilli would produce endospores •Stationary phase - the population remains relatively stable as the rate of cell growth equals to the rate of cell death. Nutrients are exhausted in media and are available from the dead cells only. The cells are resistant to antibiotics. •Death phase - the population rapidly declines as the rate of cell death exceeds the rate of cell growth. The population shrinks and total number of viable cells rapidly decreased by more than 99%. •Prolonged decline phase - once the population is reduced by 99%, remaining live cells enter prolonged decline that is marked by very gradual decrease of population. This phase may last for many months.

Classification of infectious disease By distribution of pathogen

•Localized infection - pathogen is limited to a small area - Inactive (early) tuberculosis •Systemic infection - pathogen enters the circulatory system and is spread in the body -Bacteremia - Sepsis, Active tuberculosis -Viremia - HIV, Measles, Poliomyelitis

Filtration (physical method)

•Mechanism: Objects bigger than filter's pores are mechanically removed •Microbes are mechanically removed from air or liquids if they are bigger in size than the size of pores in the filter. •Filtration is not effective against viruses

Alcohols

•Mechanism: They remove water and dissolves lipids of membrane or envelope. •Ethanol or Isopropanol must be at least 60%-strong, but less than 100%. •Treatment must be for 10 sec or longer. •It kills bacterial cells and enveloped viruses. Other microbes can survive -exception for prions, endospores, mycobacteria, & naked viruses •It is not sterilization method. ‒Antiseptic, not sensitive to organics NOTE •Regardless of concentration, alcohols are not effective against non-enveloped viruses, endospores, mycobacteria and prions.

Phenolic compounds

•Mechanism: it destroys microbes by denature proteins & destroy membranes •Conditions: exposure to solution containing phenol, phenolics, or bisphenolics ‒Disinfectants (phenol) or antiseptics, not sensitive to organics •Outcome: Kill microbes, including mycobacteria, except prions, endospores •They denature proteins and destroy cytoplasmic membranes, remain effective in the presence of detergents or organic material, AND phenolics such as triclosan, have been used widely in various lotions and soaps. •Phenol - it was the first chemical used as 5% aqueous solution (carbolic acid) in antimicrobial treatment. It causes severe skin irritation and, therefore, can be used as disinfectants only. •Phenolics - They are phenols with attached aromatic ring. They are less irritating and toxic to humans, practically odorless and more effective as antimicrobial agents. Antiseptics. •Lysol - Used as household disinfectant cleaners. During 1918 influenza pandemic, it was used as disinfectant effective against the virus. •Proventil - brand name for O-phenylphenol used as biocide. Used in agriculture as fungicide and in hospitals, households, nursing homes as disinfectant of the surfaces. •Bisphenols - two phenols are connected via additional atom like carbon or oxygen. •Triclosan - used as antibacterial and antifungal agent. In hospitals it is used for decontamination of hands. Recently it has been shown that showering or bathing with 2% of triclosan helps in decolonization of patients whose skin is carrying methicillin-resistant Staphylococcus aureus (MRSA). Also used as part of sewage treatment. •Hexachlorophene - used as topical anti-bacterial agent. Often added to the toothpaste and soaps. Used as soil anti-fungal, plant bactericide and acaricide (killing the ticks and mites) in agriculture.

Halogens

•Mechanism: it destroys microbes by oxidizing their organic molecules Chlorine •Conditions: exposure to solution containing one of the following - bleach; hypochlorous acid (HOCl); chlorine (Cl2); chloramine (NH2Cl) for few minutes −Disinfectant, sensitive to organics −It is used in water & sewage treatment •Outcome: Kill microbes, with exception for prions, mycobacteria, some endospores Iodine •Conditions: exposure to 3% - 5% solution containing iodine-releasing organic molecules (iodophors) like betadine, povidone. −Antiseptic, sensitive to organics −It is used in skin & wound treatment •Outcome: Kill microbes, with exception for prions, mycobacteria, some endospores •Iodophors - a combination of organic molecule and the iodine from which iodine is released slowly. They do not stain, lesser irritants, long-lasting. Usually are used in combination with nonionic detergents. •Betadine •Povidone-iodine •Chlorhexidine - chlorine-containing substance used as a hand scrub in surgery.

Ethylene Oxide

•Mechanism: it destroys microbes by oxidizing their organic molecules •Conditions: exposure to gas for 3 to 5 hours ‒Disinfectant, not sensitive to organics. Traces must be removed by blowing hot air for another 8-12 hours •Outcome: Steriliant that kills everything 100% ethanol •It is dehydrating the uppermost layers of bacteria (capsule and cell wall) too fast forming a crust on bacterial surface which prevents further dehydration of bacterial cell •The formed crust helps bacteria survive the treatment by 100% ethanol. •Alcohols are not effective against non-enveloped viruses AND endospores. 40% ethanol •It contains too much of water, which prevents damage to plasma membrane and dehydration of the cell. 60-95% ethanol •It is the most effective concentration against bacterial cells as the cells are killed within 10 seconds of exposure 60-70% ethanol •It is a preferred concentration of alcohol in hand antiseptics as it is •still effective at killing bacterial cells within 10 seconds of exposure •not excessively dries the skin as it does at higher concentrations •cheaper to produce than antiseptics with higher ethanol concentration.

Radiation (physical methods)

•Mechanism: producing reactive molecules - superoxide and hydroxyl-free radicals •There are various types of radiation - ionizing (x-rays, gamma-rays), non-ionizing (UV light), microwaves. •All of them carry large amount of energy that causes excessive damage to proteins and nucleic acids due to formation of highly reactive molecules and free radicals. •The molecules like proteins and nucleic acids are denatured or even shredded to fragments depending on the strength of radiation and exposure time. •Radiation is used to sterilize material that is sensitive to heat or moisture. •Ionizing radiation is approved for sterilization of grounded meat that is destined for supermarkets in the USA

Detergents

•Mechanism: they are surfactants that primary remove microbes from surface •Conditions: exposure to solution containing one of the following - soaps, anionic or cationic detergents from 20 seconds to up to few dozens minutes ‒Antiseptic or low level disinfectants Soaps Outcome: these antiseptic-sanitizers remove microbes from surface Anionic detergents Outcome: these antiseptic-sanitizers remove microbes from surface, some bacterial cells may be killed Cationic detergents (quats) Outcome: these low level disinfectant-sanitizers kill bacterial cells and inactivate enveloped viruses while remove other microbes from the surface

Peroxygens

•Mechanism: they destroy microbes by oxidizing their organic molecules Hydrogen peroxide •Conditions: exposure to 3% solution for few seconds ‒Antiseptic, highly sensitive to organics ‒Cheap and excellent way to treat fresh skin cuts and pimples ‒It is more effective when combined with peracetic acid •Outcome: Kills microbes, with exception for prions, endospores, mycobacteria Peracetic acid •Conditions: exposure to solution for ~ 1h ‒Disinfectant, sensitive to organics but less than hydrogen peroxide ‒It irritates skin and eyes •Outcome: it is steriliant that kills all microbes, including endospores and mycobacteria.

Adhesion to the host

•Microbes are using their surface proteins (adhesins) to attach to the host cells. Adhesins specifically interact with receptors of host cells in highly specific manner. •The presence of multiple adhesins broaden the host range of a microbe •EXAMPLES : •M protein of S. pyogenes is bacterial adhesin located on the cell wall. It also has strong anti-phagocytic activity due to its ability to destroy C3-convertase and, thus, preventing compliment activation. •Opa protein of Neisseria gonorrhoeae is bacterial adhesin located on tips of pili. It also binds to receptors of immune cells preventing them from mounting immune response. •Tip structure of Mycoplasma pneumoniae contains multiple copies of P1 adhesin concentrated on leading edge of bacterial cell. This makes adhesion to host far more effective. Colonization of the host •It occurs when microbe attached to the host starts growing, increasing the number of microbes present in the host. •To do this, microbes should find the source of nutrients and ward off the defenses of the host. It is achieved by the following virulence factors: •Hydrolytic enzymes are enzymes that break polymeric molecules to monomers •Siderophores are proteins that make iron available to bacterial cells •Ig A proteases are enzymes that digest IgA antibodies, which prevents ross-linking of bacterial cells.

Composition of the item (affecting antimicrobial treatment)

•Moisture-sensitive material −Methods involving water or steam can not be used in antimicrobial treatment −Dry heat, radiation, not autoclaving or boiling •Heat-sensitive materials −Methods involving heat can not be used in antimicrobial treatment −Filtration, radiation, not autoclaving •If an item to be sterilized is made of moisture-sensitive material, sterilization methods based on use of water or steam can not be used - dry heat or gaseous steriliants must be used; •If an item to be sterilized is made of heat-sensitive material, sterilization methods based on use of high temperatures can not be used - gaseous steriliants, irradiation, chemical solutions must be used; •If an item contain certain chemical components it may reduce the effectiveness of antimicrobial treatments that are based on use of halogens (for example, bleach) - using high temperature or combination of steam, pressure and high temperature may be far more effective antimicrobial treatment.

Classification of exotoxins based on their target

•Neurotoxins cause damage to nervous system by blocking transmission of nerve signals, which leads to paralysis. Example - tetanospasmin •Enterotoxins cause damage to digestive system by damaging intestinal cells, which leads to diarrhea. Example - cholera toxin •Cytotoxins cause damage to a variety of cell types by affecting cell signaling functions, which leads to stop of protein synthesis and cell death. Example - pertussis toxin Lysogenic conversion means that the genes encoding exotoxins are not of bacterial origin. These genes are introduced into bacterial cells by bacterial virus Botulinum toxin is AB toxin that blocks transmission of nerve signals to the muscles by preventing the release of acetylcholine. It leads to flaccid paralysis. Encoded by plasmid and/or chromosomal DNAs Cholera toxin is AB toxin that modifies a regulatory protein in intestinal cells, causing those cells to continuously secrete electrolytes and water. It leads to watery diarrhea. Encoded by CTXj virus. Diphtheria toxin is AB toxin that inhibits host protein synthesis by inactivating a eukaryotic elongation factor. It leads to cell death of targeted cells and formation of highly characteristic "pseudomembrane" located on mucous membrane. Encoded by beta virus. Tetanus toxin is AB toxin that inhibits signal transduction between inhibitory neurons and skeletal muscles. It leads to muscle spasm. Encoded by plasmid DNA

Blood Agar

•Non-selective medium - various bacteria grow, even pathogens •Differentiate a - hemolytic, b - hemolytic, g - hemolytic bacteria Growth of a - hemolytic bacteria •It is non-selective medium that supports the growth of many bacterial species, including pathogens •But it allows differentiate growing bacteria into three groups: •Alpha-hemolytic bacteria lyse red blood cell partially and form greenish halos around their colonies. They are opportunistic pathogens. •EXAMPLES: Streptococcus pneumoniae; some strains of Staphylococcus aureus. •Beta-hemolytic bacteria lyse red blood cells completely and form clear halos around their colonies. They are highly aggressive pathogens. •EXAMPLES: Streptococcus pyogenes, Clostridium perfringens, some strains of Staphylococcus aureus. •Gamma-hemolytic bacteria do not lyse red blood cells and they do not produce any halos around their colonies. They are non-pathogenic or are moderate opportunistic pathogens •EXAMPLES: Enterococcus faecalis, Staphylococcus epidermidis, Streptococcus mutans, some strains of Staphylococcus aureus

Normal microbiota (flora)

•Normal flora are the microbes found on the body of healthy individuals •It includes over 1,000 species and it is dynamic and depends on various of factors

Terminal acceptors of electrons

•Not all electron acceptors are the same •Some are closer in terms of electronegativity to their high-energy electron carrier molecules (e.g., NADH) than others, and this impacts the amount of produced energy. •Oxygen has the highest electron affinity of the terminal electron acceptors used.

Domain ARCHAEA

•Oldest prokaryotic organisms that have cell wall built of pseudopeptidoglycan and proteins. In plasma (cytoplasmic) membrane, they are using hydrocarbons not fatty acids linked by glycerol. They are often living in extreme conditions - high temperatures, high salt concentrations, extreme pH. •Pyrodictium - "pyros"="fire", marine anaerobic lithotrophs that are extracting energy from sulfur (S->HS). They are growing at above 100OC. •Thermoproteus - anaerobic lithotrophs that are extracting energy from sulfur (S->HS). They are growing at temperatures up to 95OC •Methanogens - "the one producing methane" anaerobes that are extracting energy from H2, converting CO2 to methane & use it as source of carbon. They can grow at high and normal temperatures •Halophiles - "salt-loving" are capable of growing in brine (salt concentration of up to 20%)

Outcomes of complement activation

•Opsonization - After cleavage of C3 into C3a and C3b, •C3b binds to the surface of a bacterial cell, which makes it a target for the attack by phagocytic cells •Inflammation - After cleavage of C3 into C3a and C3b, •C3b and factor P form complex that splits C5 into C5a and C5b. •Produced C5a attracts macrophages and neutrophils to the site of infection, •while released C3a binds to mast cells causing their degranulation and massive release of histamines resulting in vasodilation that helps phagocytic cells migrate from blood stream into the infected tissue. •Formation of membrane attack complex - After cleavage of C3 into C3a and C3b, •C3b and factor P form complex that splits C5 into C5a and C5b. •C5b binds to plasma (cytoplasmic) membrane of bacterial cell and recruits additional proteins of compliment system proteins C6, C7, C8, and nine copies of C9. •It leads to formation of large pores (channels) that results in lysis and death of bacterial cells.

Protective mechanisms of antibody-antigen binding in the host organism

•Opsonization - If antibody is bound to the cell surface, it's free sticking out Fc domain can be recognized by Fc receptors of phagocytic cell. Binding of Fc receptor to Fc domain of this antibody promotes the bacteria's phagocytosis •Complement activation - Antibody binding to bacterial cell triggers compliment cascade reaction via binding of C1 compliment protein to Fc region of the antibody. It leads to activation of C3-convertase and splitting of C3 compliment protein in to two subunits, C3a and C3b, which eventually leads to opsonization, Inflammation reaction and MAC formation in bacterial plasma membrane •Antibody-dependent cellular cytotoxicity - If antibody binds to a large pathogen, cancerous or infected cell that is too big to be ingested by phagocytic cell, it can be recognized by Fc receptors of Natural killers. Natural killers would attack such antibody-labeled cell eventually killing it by delivering to the cell various toxic substances that either lyse the targeted cell or trigger apoptosis (programmed cell death) in it. •Neutralization reaction - it is the binding of antibody to viral particles or soluble toxins that render them biologically inactive. Coating of toxins or viruses with antibody would prevent them from binding to the host or targeted cells as the antibody would interfere with interaction of antigens and their corresponding receptors on the host or targeted cells. •Immobilization and prevention of adherence - Antibodies bind to flagella, pili and interfere with its functions. •Agglutination - it is reaction of cross-linking of the cells by antibodies. It results in formation of microbial clumps, which makes phagocytosis more effective - macrophage does not have to chase individual microbes. •Precipitation - it is reaction of cross-linking of soluble proteins (for example - toxins) by antibodies resulting in formation of large insoluble protein precipitates. That alone inactivates toxins as all biological reactions occur in solutions only. In addition, precipitates are more effectively removed from the host by phagocytic cells than soluble proteins.

Exceptions from Koch's postulates

•Pathogen is difficult or impossible to grow -Treponema pallidum causes syphilis and it can not be grown "in vitro" at all •Pathogen has humans as unique host -Human Immunodeficiency Virus (HIV) causes AIDS & it grows in humans only •Same disease is caused by a variety of microbes -Pneumonia can be caused by Mycoplasma pneumoniae, Streptococcus pneumoniae, Neisseria pneumoniae •Same microbe is causing multiple diseases -Streptococcus pyogenes can cause Impetigo; Scarlet fever; Toxic shock syndrome; Necrotizing fasciitis

Persistent infections

•Persistent viral infections are those when virus is continuously present in the host for extended period, often for life. •The virus is released from infected cell via budding without causing lysis of infected cell. •The infected cells are likely to be killed by immune system rather than by replicating virus. •Three type of persistent viral infections •Chronic infections •the virus presence can be detected in the blood at any time. •Symptoms and signs of disease appear at the beginning of the disease but can disappear later and be absent for extended period time. Sometimes signs and symptoms may develop late. EXAMPLES: - Hepatitis B; •Latent infections •Infectious virus can be detected in the blood at the beginning of infections. Then, virus disappears from the blood and may be absent for extended period. Then, virus reappears in the blood after extended period (weeks or months). •Symptoms and sign of disease appear at the beginning of the disease. After the virus became dormant in the host cells, the symptomless period begins. Virus disappears from the blood. Infected person become non-infective. Symptoms re-appear after reactivation of virus and may be different; EXAMPLES: - Chickenpox-Zoster, Herpes simplex viruses 1 and 2 (HSV1 and HSV2). •Slow infections •The presence of infectious virus in the blood is gradually increasing over prolonged period. •No significant symptoms may be apparent during this period. EXAMPLES: - retroviral infections, including HIV (human immunodeficiency virus).

Killing of microbes by phagocytic cells

•Phagocytic cell is actively pursuing microbe using chemotaxis to localize the microbe. •The killing by phagocytic cell involves phagocytosis (binding and ingestion) and digestion of a microbe by hydrolytic enzymes or killing by produced hydrogen peroxide. •Phagocytosis is binding, engulfing and ingestion of a microbe by phagocytic cells. It involves the following steps: •Opsonization - the surface of microbe is covered by opsonins (proteins like C3b) or antibodies •Binding of opsonized microbe to a phagocytic cell - via corresponding receptors •If microbe is covered by C3b, then C3b receptors of phagocytic cell are involved in binding •If microbe is covered by antibodies, then Fc receptors of phagocytic are involved in binding •Ingestion of a microbe and formation of phagosome - microbe bound by phagocytic cell is internalized (taken in) with formation of vesicle called phagosome. •The content of phagosome, including microbe, is separated from cytoplasm of phagocytic cell by a membrane •Digestion is disintegration of a microbe with help of hydrolytic enzymes located in lysosomes •Formation of phagolysosome - phagosome containing a microbe is fused with lysosome containing hydrolytic enzymes •Digestion - the microbe is disintegrated upon enzymatic action •Some nutrients can be absorbed by the cell, forming residual bodies •Excretion of residual bodies - non-digested microbial remnants are removed from the phagocytic cell •Microbes can also be killed by hydrogen peroxide produced by activated phagocytic cells •If phagocytic cell attacks the organism that is too big, then it uses help of other phagocytic cells to kill invader.

Plasma membrane composition:

•Phospholipid bilayer •Proteins - there are of two types: •Sterols

Classification of microbes based on energy and carbon sources

•Photo-auto-trophs - photosynthetic bacteria like Cyanobacteria •Photo-hetero-trophs - Heliobacteria, purple non-sulfur bacteria •Litho-auto-trophs - they are using inorganic chemicals (H2, NH3, NO2-, Fe 2+ , H2S) as energy source and they are using CO2 as carbon source - i.e. nitrogen fixing bacteria, methanogenic bacteria •Organo-hetero-trophs - they are using organic compounds (sugars, amino acids) as source of energy and carbon - i.e. any bacteria that are pathogenic to humans.

Domain BACTERIA

•Prokaryotic organisms that have cell wall built of peptidoglycan. In plasma (cytoplasmic) membrane, they are using fatty acids linked by glycerol (lipids). •Aquifex - "the one producing water" lithotrophs that are growing best at 85-95OC. They are capable of anaerobic (N->NH3) and aerobic respiration (O->H2O). 16% of their genes similar to genes of Archaea. •Thermotoga - anaerobic lithotrophs (reducing S->HS) that are living at 70OC in oil deposits. •Green filamentous bacteria - capable of photosynthesis •Cytophaga - means "the one that eats the cells", earliest predator? Prefers cold water.

Redox reaction

•Redox reactions are used by the cells in extraction of energy from chemical compounds. •Transfer of electrons from one compound to another does occur during these reactions. •The compound that loses electrons becomes oxidized and is called electron donor. •The compound that accepts electrons becomes reduced and is called electron acceptor. •The protons (H+) are often follow the movement of electrons. •Amount of energy harvested by the cell depend on electron donor (the energy source) and terminal acceptor of electrons. •Glucose is the most universal source of energy (electron donor) used by living organisms. •Oxygen is the terminal electron acceptor used by living organisms in aerobic cellular respiration. •If carbon dioxide (CO2), sulfates (SO42--), nitrites (NO2--) nitrate (NO3--) or organic compounds (other than pyruvic acid, i.e. fumaric acid) are used as terminal acceptors of electrons, then the cellular respiration is anaerobic. There is always less energy extracted in anaerobic cellular respiration than in aerobic respiration. •If pyruvic acid used as terminal electron acceptor, then energy is extracted from glucose in process of fermentation. Fermentation is less effective in extraction of energy than any type of cellular respiration.

additional properties of life

•Response to stimuli (Sensitivity) and Adaptation to changing environment (Evolution)

Human pathogens

•They are microbes (bacteria, fungi, viruses, algae, protists) that can infect humans and cause the disease. •Human pathogens from phylum Proteobacteria (Gram-negative bacteria) are from the following genera: •Bordetella, Brucella, Escherichia, Haemophilus, Helicobacter, Klebsiella, Legionella, Neisseria, Pseudomonas, Rickettsia, Salmonella, Shigella, Yersinia; •Human pathogens from phylum Firmicutes (Gram-positive bacteria) are members of the following genera: •Clostridium, Listeria, Mycoplasma, Staphylococcus, Streptococcus, Ureaplasma; •Human pathogens from phylum Actinobacteria (Gram-positive and acid-fast bacteria) are members of the following genera: Actinomyces, Corynebacterium, Mycobacterium, Nocardia.

Replication of retroviruses

•Retroviruses are enveloped viruses that have two copies of single-stranded RNA (+) and three enzymes (reverse transcriptase, integrase, and protease) packed in their capsid. •They belong to lentiviruses as the infections they case are slowly developing over extended period of time. •Infection starts with interaction of viral adhesins with receptors of the host cells and attachment of virion to the surface of the host cell. •Upon entry to the cell, the viral ssRNA (+) genome in uncoated and converted to double stranded DNA with the help of viral reverse transcriptase. •The produced viral DNA transported to nucleus of infected cells, where it is inserted into one of the chromosomes with help of viral integrase. The virus becomes provirus. •The viral genes are expressed at low rate resulting in slow but steady assembly of new virions at the surface of plasma (cytoplasmic) membrane. •Newly assembled virions are released from the host cell via budding, which enables infected cells to survive for extended period of time. •Infected cell is not killed by replicating virus but rather the immune system, involving T cytotoxic cells or/and natural killers.

MacConkey agar

•Selective medium - it inhibits Gram-positive bacteria growth •Differentiate lactose fermenters from non-fermenters Peptone NaCl Agar Lactose (color) Bile salts (selective agent) Neutral red (pH indicator) •It selects against Gram-positive bacteria, allowing only Gram-negative bacteria to grow. •It also differentiates bacteria into fermenters and non-fermenters of lactose. •If lactose is fermented by growing bacterium, the produced lactic acid changes the color of neutral red, the pH indicator, to pink. •The growing lactose non-fermenter does not change the color of the medium.

EMB Agar

•Selective medium - it inhibits Gram-positive bacteria growth •Differentiate lactose fermenters from non-fermenters Peptone, K2HPO4, Agar Lactose (color) Eosin (selective agent, color) Methylene blue (selective agent, color) •It selects against Gram-positive bacteria, allowing only Gram-negative bacteria to grow. •It also differentiate bacteria into lactose fermenters and non-fermenters of lactose. •The colonies of non-ferments appear colorless. •If lactose is fermented, produced lactic acid cause precipitation of eosin and methylene blue that stains the colony of lactose fermenters dark. •The colonies of Escherichia coli, a strong fermenter, are not just dark - they also acquire distinctive green metallic sheen.

DNA Probe Technologies

•Short DNA molecules of known sequence used to detect the presence of specific genes or their expression in the sample Genotype is the genetic makeup of biological species or an individual •DNA probes are single stranded 18 to 28 nucleotide-long fragment DNA or RNA •DNA microarray is a solid support with the attached gene-specific DNA probes DNA microarrays are solid supports with fixed patterns of single-stranded DNA probes that are specific for particular genes. •Based on ability of NA strand form a duplex with complimentary strand of NA •Enable researchers to do gene expression profiling and diagnostics •Some companies are already offering patient's profiling for a fee. •It can provide insights on presence of alleles responsible for inheritable genetic disorders •It can predict behavior patterns of a patient.

Comparison of genera Clostridium and Mycoplasma:

•Similarities: •both genera belong to phylum Firmicutes, that includes Gram-positive bacteria with low GC content. •Both genera include species that are human pathogens. •Differences: •Genus Clostridium •It includes Gram-positive bacilli that are obligate anaerobes •They produce the most potent known exotoxins (neutotoxins). •Due to its large diameter, endospores produced by clostridia are distorting the shape of bacterial cell. •Some species have flagella and are mobile. •Principle human pathogens are C. botulinum causing botulism, C. perfringens causing gas gangrene, C. tetani causing tetanus. •Genus Mycoplasma •It includes the smallest bacteria with smallest known genome that are obligate aerobes. During evolution, mycoplasmas have lost the genes involved in synthesis of cell wall and, therefore, are lacking cell wall. •As a result, mycoplasmas are pleomorphic •They have the plasma (cytoplasmic) membrane fortified by cholesterol. •Mycoplasmas are naturally resistant to penicillins. •Mycoplasmas do not produce any known toxins. •Mycoplasmas do not produce endospores •Mycoplasmas have no flagella but some species still exhibit gliding motility •Principle human pathogens are M. pneumoniae causing pneumonia, M. hominis causing urogenital infections and infertility.

Comparison of genera Haemophilus and Vibrio

•Similarities: Both genera belong to class gamma-Proteobacteria consisting of Gram-negative bacteria. Species of both genera are facultative anaerobes, sensitive to stomach acid and produce endotoxin and cause infections in humans. •Differences: •Genus Haemophilus includes fastidious non-motile coccobacilli that can form capsule, produce no exotoxins and have humans and animals as their natural reservoir and cannot survive outside of host. Principal human pathogen is H. influenzae that is causing meningitis in humans. •Genus Vibrio includes motile monotrichous curved rods that can produce exotoxin if lysogenic for virus. They have humans, shells and brackish water as their natural reservoirs. Principal human pathogen is V. cholerae that infects human intestines causing cholera. Some strains of Vibrio cholerae can be hemolytic.

Viruses vs Bacteria

•Similarities: they both are built of proteins and use nucleic acids as genetic material. Both bacteria and viruses can cause infections and diseases in humans or infect and kill bacteria. •Differences: unlike bacteria, viruses contain only one type nucleic acid, DNA or RNA, but never both. Also, viruses do not have cellular organization and are obligate parasites, while bacteria have cellular organization of prokaryotic type and may be free-living organisms.

Activity in the presence of organic matter

•Some antimicrobials can react with organic material present in item, which reduces the effectiveness of the antimicrobial and can damage the item

storage and stability

•Some chemicals can be sold as concentrates and very stable, while others have limited shelf life

Environmental risks

•Some germicides retain their activity after use and can interfere with wastewater treatment system, which relies on use of specific microbes. Such germicides must be inactivated before disposal

Endospore Stain

•Spores are formed during the late phase of bacterial growth and help bacteria to survive the harsh environmental conditions. It is much harder to kill endospores than actively growing cells. Pasteurization does not kill endospores. •Spore formation may coincide with production of toxin. It shows if bacteria present in sample have formed endospores. Endospores are stained in green. Bacterial cells are stained in red

Comparison of cellular properties of Staphylococcus aureus and Streptococcus pyogenes

•Staphylococcus aureus •It is salt-tolerant, coagulase-positive, catalase-positive cocci growing in clusters. •They are facultative anaerobes that can produce various virulence factors, like capsule, adhesins (clumping factor A, fibronectin-binding protein A), proteins covering bacterial cells with human proteins (coagulase, protein A), various enzymes and toxins. •Depending on set of virulence factors produced, strains of S. aureus can cause various infectious diseases in humans, from boils to food poisoning, to pneumonia and to scalded skin syndrome. •Streptococcus pyogenes •It is salt-sensitive, coagulase-negative, catalase-negative cocci growing in chains. •They are aerotolerant bacteria that can produce various virulence factors, like non-antigenic capsule, adhesins (M protein, protein F), protein covering bacterial cells with human proteins (protein G), various enzymes and toxins. •Depending on set of virulence factors produced, strains of S. pyogenes can cause various infectious diseases in humans, from impetigo, to streptococcal pharyngitis, to necrotizing fasciitis. Due to frequent very serious complications, even mild infection caused by S. pyogenes MUST BE TREATED with antibiotics.

How to build a standard curve

•Take aliquots of microbial culture growing in liquid medium at different time points while it is growing •Alternatively, make serial dilutions of grown microbial culture •Determine the optical density and count the cells in all collected aliquots (or serial dilutions) •After cell count, calculate cell concentration, express it as # cells per milliliter (cells/ml) •Make a graph by plotting cell concentration versus optical density •Next time growing the same microbial culture in the same medium, the standard curve would allow to establish the cell concentration at any given time point without actually counting the cells by converting the optical density in to the cell/ml. •Method works only for OD range between 0.1 and 0.6, which corresponds to roughly 106 to 10x107 cells per ml. •If OD of bacterial culture is above 0.6, then to get accurate data the culture must be diluted until OD is reduced to 0.1-0.6. •After cell concentration is established it must be multiplied by dilution factor.

Environmental conditions affecting antimicrobial treatment

•Temperature −Bleach kills Mycobacterium tuberculosis at 55OC twice fast than at 50OC −Flaming (over 1400OC) - dry heat kills bacteria and endospores instantly −Hot air sterilization (170OC) - dry heat kills bacteria and endospores in 2 hours •pH −bleach is more effective if pH is acidic - it facilitates release of chlorine •Volume of fluid -it takes 2 min to bring 200 ml of water to boiling - needs short time treatment -It takes about 5 min to bring 1000 ml of water to boiling - needs long time treatment

Pleomorphic bacteria

•Term originates from greek πλέω- more, and -μορφή form •They are micro-organisms that can alter their shape or size in response to environmental conditions.

Bright-field microscopy

•The light emitted by the source is collected by condenser lens and focused on specimen •Light interacts with specimen and is partially scattered by it •The light scattered is lost, while the light that is not scattered by specimen enters into objective lens •As a result the image has bright background and darker specimen on it -Light scattered by specimen does not enter the objective lens. -Light not scattered by specimen is the only one that enters the objective lens. -Darker objects are visible against bright background - low contrast

Dark-field Microscope

•The light emitted by the source is partially blocked by opaque disk. The unblocked light is collected by condenser lens and focused on specimen •Light interacts with specimen and is partially scattered by it •The scattered light enters objective lens, while the un-scattered light is lost •As a result the image has black background and light specimen on it Dark-field microscopy -Light scattered by specimen is the only one that enters the objective lens. -Light not scattered by specimen does not enter the objective lens. -Lighter objects are visible against a dark background - high contrast

The use of sulfanilamide in treatment of bacterial infections

•The mechanism of sulfanilamide action is an example of competitive inhibition of enzymatic activity •Sulfanilamide has structural similarities to PABA, a substrate for dihydropteroate synthase, the enzyme catalyzing one of the steps of folic acid biosynthesis. •Sulfanilamide acts as competitive inhibitor for the enzyme. •Folic acid biosynthesis is the metabolic pathway present in bacterial cells. However, it is absent in human cells. •Humans must get folic acid from their diet. •Folic acid is used as a precursor in nucleotide biosynthesis •Therefore, there is no target for sulfanilamide in human cells and the drug can be effectively used in treatment of bacterial infections in humans and the drug has side effects on very rare occasion.

Number of microbes (use the graphs reviewed in lecture)

•The more microbes are present in the sample the longer time is required for treatment to sterilize the sample.

Modern three domain system of biological classification (it was proposed by Carl Woese)

•The system is based on differences in nucleotide sequences of 16S (in prokaryotes) and 18S (in eukaryotes) ribosomal RNA genes. •It divides all cellular forms of life into 3 domains, Archaea, Bacteria, and Eukaryota •All three domains have common ancestor •The first two domains (proposed by C. Woese), Archaea and Bacteria, include prokaryotes •The third domain, Eukarya, include all eukaryotic organisms and is divided into four kingdoms Protista, Plantae, Fungi, and Animalia •Domains Archaea and Eukarya are closer related to each other than domains Archaea and Bacteria

Calculation of time required for antimicrobial treatment

•The time required for antimicrobial treatment depend on •Number of microbes present in sample •Decimal reduction time for hardest to kill microbe present in sample •Some of antimicrobial treatments would not be able to sterilize (kill all microbes present) sample if it contains prions, endospores, mycobacteria •The time required for treatment to be completed can be calculated as the following: •t = D x (Log10N + 1), where •t is time required for treatment; •D is decimal reduction time; •N is number of microbes present in the sample.

Growing viruses in vitro (in cell culture):

•The tissue is separated into individual cells •The cells are suspended in liquid growth medium and mixed with virus to be grown •The mix of viruses and cells (1:100) are plated on plastic dishes and allowed to grow •As virus replicates in the cells, the number of cells is declining, while concentration (or titer) of viral particles in the medium is growing •When all cells are killed by the virus, the replication (growth) of virus stops.

Factors limiting host range of a virus

•The viral host range is limited to a single or a few closely related bacterial species or one type of the cells in host organism due to •Specific interaction of viral adhesins and host cell receptors •To cause infection, virus must bind to host cell: •The viral surface antigens-proteins (also called adhesins) interact with receptors on surface of host cell. •Interaction is highly specific, like in antibody-antigen interaction •Restriction-modification system of the host cell •It functions as defense mechanism of the cell against invasion of any foreign DNA. •It consist of two types of enzymes: •Restriction enzyme (endonuclease) may recognize viral DNA at restriction sites and cut it in small fragments Modification enzyme attaches methyl group to the host DNA at restriction sites and prevents

Cost and availability

•There are some germicides that are very cheap (bleach), while others are very expensive and may require special equipment to use (ethylene oxide).

The enzymes have their 3D-structure (folding) stabilized by hydrogen bonds.

•Therefore, enzymes are sensitive to change in temperature, pH (acidity), and salinity of the environment •Each enzyme has narrow range of temperature and pH, where the activity of the enzyme is highest. This is what is called "optimal range". •High temperatures have stronger negative effects on enzymatic activity than low temperatures as they disrupt hydrogen bonds causing denaturation (more likely irreversible) of the enzymes.

Fungal colonies

•They appear fuzzy and larger than bacterial ones •This is due to the fact that after cell division completed the fungi cells stay connected to each other and form hyphae - the very long structures made of connected cells. •Some of these hyphae would be protruding in to the air and will be used to form the fungi spores.

Yeasts colonies

•They are also fungi but form colonies similar bacterial one. •This is due to the fact that yeast cells like bacterial break off after cell division and do not form hyphae.

Mechanism of type III exotoxins action

•They are called intracellular as they enter the cytoplasm of targeted cell and interfere with some cellular function. This kills the affected cell. They are two kinds of type III exotoxins: •Toxins injected via type III secretion system are directly delivered to host cell via syringe-like system when bacterium binds to the surface of the host cell •EXAMPLES: Various effector proteins of Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, Yersinia pestis •AB toxins are produced and secreted from bacteria in inactive form, with A and B subunits connected. Toxin is delivered to targeted cell via blood and binds via B subunit. In some cases toxin is delivered via Type III secretion system. In cytoplasm, subunit A is cleaved from subunit B and becomes active. Active subunit A interferes with some cellular function and kills the cell. •EXAMPLES: Diphtheria toxin of Corynebacterium diphtheriae and Shiga toxin of Escherichia coli inhibit protein synthesis; Cholera toxin of Vibrio cholerae activate adenylate cyclase leading to increased cAMP production & massive loss of fluids and electrolytes; Botulinum toxin of Clostridium botulinum and Tetanus toxin of Clostridium tetani interfere with signal transduction between skeletal muscles and neurons

Mechanism of type II exotoxins action

•They are called membrane damaging as they bind to plasma (cytoplasmic) membrane of host cells and compromise its integrity. It leads to cell lysis and development of tissue necrosis, which in turn increases the invasiveness of a microbe. They are two kinds of type II exotoxins: •Lipases are enzymes that bind to plasma membrane and digest phospholipids. •EXAMPLES: a toxin of Clostridium perfringens has phospholipase & hemolytic activity. It contributes to developing of gas gangrene; b toxin of Staphylococcus aureus •Cholesterol-dependent cytolysins are secreted by bacteria as non-active monomers. They bind only to cholesterol-containing membranes (cholesterol is not found in bacteria, with Mollicutes as exception). In the presence of cholesterol, monomers are assembled into complexes with large pores causing cell lysis EXAMPLES:Perfringolysin O of Clostridium perfringens; Streptolysin O (oxygen-sensitive) and Streptolysin S (oxygen-stable) of Streptococcus pyogenes; a toxin (also called a-hemolysin) and leukocidin of Staphylococcus aureus; Pneumolysin of Streptococcus

Bacteria pili (fimbriae)

•They are considerably shorter and thinner than flagella. •They are hollow inside •They play crucial role in bacterial attachment and may also be responsible for twitching and gliding motility •Sex pili that are lager and thicker than regular ones are involved in DNA transfer between the cells •Bacterial species that have pili but do not have flagella: Bordetella pertussis, Corynebacterium diphtheriae, Haemophilus influenzae, Neisseria gonorrhoeae, Neisseria meningitidis, Shigella spp., Staphylococcus aureus, Streptococcus pyogenes, Yersinia pestis

Trace Elements

•They are essential elements that are required in time amounts (less than 0.01% of cell weight). They are enzyme cofactors. •EXAMPLES: Zn (zinc) - DNA polymerase (replication of DNA); Mg (magnesium) - DNA polymerase; glucose 6-phosphatase (transport of glucose across membrane); Mn (manganese) - arginase; Fe (iron) - catalase (breaks H2O2 to H2O and O2); nitrogenase (fixing N2); hydrogenase (oxidizing H2 - important for anaerobes); Cu (copper) - cytochrome C oxidase (part of electron transport chain used in cellular respiration),

Aerotolerant anaerobes

•They are indifferent to the presence of oxygen as they do not have electron transport chain involved in cellular respiration and extract the energy via fermentation only and no toxic forms of oxygen produced. EXAMPLES: Streptococcus pyogenes. Lactobacillus acidophilus (part of normal flora) Harvest energy via fermentation only

Viruses, Viroids, and Prions

•They are lacking cellular organization and are inert when outside of host cell

Bacterial flagella

•They are long proteinaceous appendages composed of subunits of flagellin that provides a mechanism of motility. •Flagella also can participate in bacterial attachment to substratum or host cells. •Flagella are attached to plasma (cytoplasmic) membrane via rod. •When ATP is hydrolyzed, flagella rotate pushing the cell forward •Bacterial species that have flagella and, therefore, are motile: Bacillus subtilis, Escherichia coli, Helicobacter pilori, Pseudomonas aeruginosa, Salmonella enterica, Salmonella typhimurium, Vibrio cholera •NOTE: Bacterial species listed above also have pili, in addition to flagella.

Enzyme activators

•They are molecules that increase the activity of enzymes. •Cofactors •Non-organic components that bind to the enzymes and activate them. Same cofactor may interact with numerous enzymes •Examples: •Zn2+ •Ca 2+ •Coenzymes •Organic compounds that act as carriers for electrons and energy. Same coenzyme may interact with more than one enzyme •They transfer atoms from one molecule to another. •They may bind to a number of different enzymes. •They are synthesized from vitamins. •Examples: •Coenzyme A •Coenzyme Q •NAD+ •FAD •NADP+ •Vitamins

Enzyme inhibitors

•They are molecules that reduce or inhibit enzymatic activity. •If enzyme inhibitor binds to active site of enzyme, it is called competitive inhibitor as it competes with substrate for active site. •The effect of competitive inhibitor can be reduced by increasing concentration of the substrate. •If inhibitor acts on enzyme by binding to enzyme at site different from active site, then it is called non-competitive inhibitor as it does not compete with substrate for active site. •The effect of non-competitive inhibitor on enzyme can not be diminished by increasing concentration of the substrate.

Electron carriers

•They are molecules used to ensure more efficient extraction of energy from the energy source. •Electron carriers hold energy in the form of loosely bound electrons and hydrogen atoms. •Examples of electron carriers are NADH, FADH2 and NADPH. •The energy stored in electron carriers is mainly used to produce ATP in process of cellular respiration. •Electron carriers used in cellular respiration NAD+ + 2 e- + 2H+ à NADH + H+ FAD + 2 e- + 2 H+ à FADH2 •Electron carriers used in photosynthesis NADP+ + 2 e- + 2H+ à NADPH + H+ Oxidized forms Reduced forms

Endotoxins

•They are produced by Gram-negative bacteria only •They are consisting of lipopolysaccharides that are part of Gram-negative cell wall •Lipid A is the most toxic part of LPS •Endotoxins are released from dead cells only •Endotoxins are heat-stable •Endotoxins have no specificity and are not very potent toxins •Only large quantities can have effect •If massively appear in blood stream, they cause shock •Due to wide spread vasodilation and drop in blood pressure •They also have pyrogenic effect - they cause fever •Infections caused by Gram-negative bacteria are not treated by bactericidal antibiotics •To prevent massive release of endotoxins

General properties of exotoxins

•They are produced by Gram-positive and Gram-negative bacteria. •They are proteins that can be secreted from the cell or stay inside. •Most of exotoxins are sensitive to heat inactivation & can form toxoids suitable for use in immunization as vaccines. EXAMPLES: botulinum toxin, cholera toxin, diphtheria toxin •Some exotoxins heat-stable. EXAMPLE: enterotoxin TSST1 of S. aureus •Exotoxins are target-specific and highly potent. Patient can die before immune response is mounted. As a result, antitoxins are the most important part of treatment of any disease resulted from

Interferons

•They are produced in response to viral infection •They are produced in response to viral infection Outcomes of interferon production: •Increased resistance of the host cells to virus attacks •Up-regulation of antigen presentation by the host cells •Activation of natural killers & macrophages Mechanism of interferon's antiviral activity •Virus enters host cell (1) and starts replication, producing dsRNA •In response to appearance of dsRNA, infected cell produces and secretes interferons. •Secreted interferons are taken up by neighboring cell (2). •It triggers in them the production of inactive antiviral proteins (iAVP), resulting in cell resistance to possible viral infection. •When virus enters alerted cell armed with iAVP, the iAVP is activated. Activation of iAVP triggers the apoptosis of the cell (2), thus limiting or stopping the spread of viral infection into surrounding areas.

Enzymes

•They are protein catalysts that speed up the rate of chemical reaction by reducing the activation energy needed for chemical reaction to start.

Portals of entry

•They are routes used by a microbe to enter the host. •Same microbe can enter the host using different portals of entry. •Same portal of entry can be used by various microbe •Preferred portal of entry used by pathogen to enter the host leads to disease. •For Streptococcus pneumoniae it is respiratory tract: •If inhaled (microbe enters via respiratory tract), S. pneumoniae causes pneumonia - preferred portal of entry •If ingested (microbe enters via gastrointestinal tract), S. pneumoniae does not cause the disease - portal of entry

Portals of exit

•They are routes used by pathogen to leave (exit) the host. •Usually but not always it is the same portal used to enter the host. •Measles, Chickenpox viruses are entering human host via mucous membrane of respiratory system but leaving human host via skin •Rabies virus enters via skin when is bitten by an animal, but leaves via saliva. •Most important portals of exit are: •Respiratory tract - microbes are exiting in respiratory droplets of saliva •Gastrointestinal tract - microbes inhabiting it are shed in feces •Skin - microbes are constantly shed along with skin cells as they slough off

Bacterial colonies

•They are small and compact. •This happens because bacterial cells do not form hyphae

Acute infections

•They are usually short in duration; Host may develop long-lasting immunity; •Results from lythic infections - large number of viral particles is produced in short time with infected cells killed; Disease symptoms result from tissue damage and infection of new cells; •EXAMPLES: Mumps; Measles; Influenza; Polio

TCA Cycle

•To completely oxidize one glucose molecule, the TCA must turn twice. •It takes place in cytoplasm of prokaryotic cell or in mitochondrial matrix of eukaryotic cell •In citric acid cycle, the introduced acetyl-group is completely oxidized to carbon dioxide and water. •Formed: 4 CO2, 6 NADH (to be used in cellular respiration) and 2 FADH2 (to be used in cellular respiration). STEPS: 1.acetyl-CoA enters citric acid cycle by being attached to oxaloacetate molecule (C4-molecule) and forming citric acid (C6-molecule) 2.Chemical rearrangement of citric acid to isocitric acid 3.A redox reaction generates NADH + H+. CO2 is released converting isocitric acid to a-ketoglutaric acid 4.A redox reaction generates NADH +H+. CO2 is released and coenzyme A added converting a-ketoglutaric acid to succinyl CoA 5.Energy harvested while CoA are being removed. ATP and succinic acid are formed. 6.A redox reaction generates FADH2. Succinic acid is converted to fumaric acid. 7.Fumaric acid is converted to malic acid 8.A redox reaction generates NADH + H+. Malic acid is converted to oxaloacetatic acid

General characteristics of viruses

•They are very small in size, ranging from about 10 nm to about 800 nm •All viruses are obligate parasites - to replicate a virus must infect the host cell −If outside of host cell, they are inert particles incapable of metabolism and replication −However, when viruses find their way to host cell, they hijack cellular replication machinery forcing infected cell to produce new virions (viral particles) Structure: Capsid •Made of proteins (capsomers) •Optional proteins, spikes, •If present, they are involved in virus attachment to the host cell •It houses viral genome Envelope (optional optional lipid membrane) •It is lipid membrane wrapping the capsid •If present, it hosts viral adhesins •It is made of phospholipid bilayer and proteins •If envelope present, it hosts viral adhesins that are involved in virus attachment to the host cell. •Enveloped viruses are very unstable outside of the host and can be easily inactivated by disinfectants' and/or antiseptics' treatment. Genome •Any virus has a genome that can be either DNA or RNA, but never both •In viruses, both types of nucleic acids can be either single- or double-stranded. •Regardless of type of nucleic acid involved, viral genome can be either linear, circular or segmented. •The genome is in capsid made of proteins. •DNA or RNA •Single-stranded or double-stranded, regardless of NA type •Circular, linear or segmented

Obligate anaerobes

•They can grow only in the absence of oxygen and extract energy via anaerobic cellular respiration or fermentation. They do not produce superoxide dismutase and catalase and, therefore, oxygen is toxic to obligate anaerobes. EXAMPLES: Clostridium tetani; Clostridium perfringens, Clostridium botulinum. Harvest energy via anaerobic cellular respiration or fermentation

Obligate aerobes

•They can grow only in the presence of oxygen as they extract energy via aerobic cellular respiration only. To neutralize toxic forms of oxygen (superoxide radical and peroxide) formed during aerobic cellular respiration, they produce superoxide dismutase and catalase. EXAMPLES: Mycobacterium tuberculosis, Bordetella pertussis, Neisseria gonorrhoeae Harvest energy via aerobic cellular respiration only

Microaerophiles

•They can tolerate 2-10% of oxygen as they extract energy via aerobic cellular respiration and produce small quantities of superoxide dismutase and catalase that are easily overpowered by atmospheric oxygen (21%). EXAMPLES: Helicobacter pylori. Campylobacter jejuni, Borrelia burgdorferi Harvest energy via aerobic respiration only

Contagious diseases

•They cause outbreaks and epidemics •They can be transmitted between hosts via •Direct contact with infected •Indirect contact with infected (via shared objects) •Contact with casual bodily discharges (respiratory droplets formed after sneezing or coughing) •They have low infectious dose •Examples : as little as 10 cells of ingested Shigella or inhaled Mycobacterium tuberculosis is required to cause the infectious disease.

Facultative anaerobes

•They grow best in aerobic conditions. However, they also can grow (much slower) in anaerobic conditions by switching from aerobic cellular respiration to fermentation. They also produce superoxide dismutase and catalase. EXAMPLES: Escherichia coli; Staphylococcus aureus. Harvest energy via aerobic cellular respiration or fermentation

Psychrotrophs

•They have optimal growth rate at room temperature. Therefore, they are abundant around humans. •They can also grow at +4OC and cause food spoilage in refrigerators. EXAMPLES: Bacillus cereus).

Mesophiles

•They have optimal growth temperature around +37OC. They are tightly associated with birds, animals and humans. •Some of them are part of normal flora, while others are pathogens causing infectious diseases. EXAMPLES: Clostridium tetani, C. botulinum, S. aureus and many more.

Psychrophiles

•They have optimal growth temperature around +5OC. They inhabit Arctic and Antarctic regions and the lakes fed by glaciers. •They have no major importance to humans as they are hardly present around humans

Thermophiles

•They have optimal growth temperature around +65OC. They inhabit hot springs and also can be found in compost heaps. •They do not cause infections in humans but can be a source of useful enzymes

Extreme thermophiles

•They have optimal growth temperature around +90OC. They inhabit hydrothermal vents located on the ocean floor. •They do not cause infections in humans but can be a source of useful enzymes.

Non-contagious diseases

•They may lead to outbreaks but do not cause epidemics •They can be transmitted between hosts via •Specialized routes of transfer •Vectors (insects, rodents) - West Nile disease; Viral encephalitis, Bubonic plague •Vehicles (water, dust particles, food) - Cholera; Food poisoning; Botulism; •Non-casual transfer of bodily fluids •Transfusion, Needles, Sexual contact - AIDS, Syphilis •Microbes causing non-contagious diseases usually have high infectious dose •Examples : millions of ingested Salmonella or Cholera cells required to cause the infectious disease

gram positive cell wall

•Thick layer of peptidoglycan is on the top of plasma (cytoplasmic) membrane •Teichoic acids attach the cell wall to plasma (cytoplasmic) membrane •The microbes are likely to be sensitive to penicillin •Clinically important Gram positive bacteria of the following genera: Bacillus, Clostridium, Corynebacterium, Listeria, Staphylococcus, Streptococcus,

gram negative cell wall

•Thin layer of peptidoglycan sandwiched between two membranes - plasma (cytoplasmic) membrane and outer membrane •Outer membrane contain lipopolysaccharides and lipid A •Lipid A is a part of endotoxins that is released only from the dead bacterial cell •Microbes are likely to be resistant to penicillin and are generally less sensitive to antibiotics than Gram positive bacteria •Clinically important Gram negative bacteria of the following genera: Borrelia, Escherichia, Helicobacter, Klebsiella, Legionella, Neisseria, Pseudomonas, Salmonella, Shigella, Vibrio

Photosynthesis

•Two steps of photosynthesis: −Light reaction - the energy of sunlight is converted into the energy stored in ATP and NADPH (instead of later, some bacteria may use NADH2) •It requires the use of antennae pigments (bacteriochlorophyll of chlorophyll) to absorb the energy and chemiosmosis to synthesize ATP and NADPH (NADH2) −Dark reaction - the energy stored in ATP and NADPH (or NADH2) is used to "fix" carbon - carbon dioxide (CO2) is converted into organic molecule (sugar). Anoxygenic phototrophs •They include archaea and bacteria that do not produce free oxygen as a by-product of photosynthesis. Examples of anoxygenic phototrophs: •Purple sulfur bacteria; •Non-purple sulfur bacteria; •Green sulfur bacteria; •Filamentous anoxygenic phototrophic bacteria; •Other anoxygenic phototrophs like Heliobacterium. •These prokaryotes do not use H2O as source of electrons as it done by oxygenic phototrophs •They use sun light as source of energy, CO2 as source of carbon, H2S as source of electrons, producing elemental sulfur as a by-product of photosynthesis: •6 CO2 + 12 H2S = C6H12O6 +12 S + 6 H2O Oxygenic phototrophs •They include cyanobacteria, algae, green plant that produce free oxygen as a by-product of photosynthesis. •These prokaryotes and eukaryotes use H2O as source of electrons •They use sun light as source of energy, CO2 as source of carbon, H2O as source of electrons, producing molecular oxygen as a by-product of photosynthesis: •6 CO2 + 12 H2O = C6H12O6 + 6 O2 + 6 H2O

Mechanism of type I exotoxins action

•Type I exotoxins are cell surface-active and act via binding & linking two cells together. •They are collectively called superantigens as they over-ride specificity of T-cell response. •Type I exotoxins are non-specifically bridging (linking) T cell receptors of T helper cells and MHC class II receptors of antigen presenting cells like phagocytes, B cells, dendric cells. •It results in activation of up to 50% of all T helper cells, which leads to massive release of cytokines and interleukins (called cytokine storm) followed by wide-spread vasodilation of blood vessels and massive loss of fluids from circulatory system •Resulting signs and symptoms are - rashes, nausea, vomiting, diarrhea, fever, shock, multi-organ failure, death •Diseases associated with superantigens: rheumatic fever, rheumatoid arthritis; scarlet fever; toxic shock syndrome •EXAMPLES: •Enterotoxin TSST-1 of S. aureus. It is called enterotoxin as it causes food poisoning that leads to nausea and vomiting. It is heat stable and is not inactivated by food re-heating. •Pyrogenic exotoxins SpeA and SpeC of S. pyogenes. They are called pyrogenic as they are causing fever.

Enzyme activators: Cofactors and Coenzymes

•Upon binding to enzyme cofactors and coenzymes increase enzymatic activity -They adjust the shape of the active site so that it acquires a perfect fit with a substrate •Cofactors are non-organic enzyme activators like −Fe2+, Zn2+, Ca2+ •Coenzymes are organic enzyme activators like -Coenzyme A, -Coenzyme Q -All vitamins, -NAD+, FAD+

Exposure plate

•Used to test the air for microbial contamination Remove the lid of petri dish and keep the plate open for certain period of time

Viroids

•Viroids are made of small SS-RNA (240-380 nucleotides long and have no protein coat •Viroid RNA is circular and resistant to digestion by RNases •They are replicating autonomously in the host cell •Single viroid is capable of infecting the host cell

Virulence factors

•Virulence factors are molecules & structures that define the virulence of microbe −Virulence (pathogenicity) is a measure of microbe's ability to cause a disease Adhesins •They are molecules (mainly proteins) localized on surface of microbes and they are responsible for microbial attachment to the host; •Adhesins can be part of specialized cellular structures like capsules, flagella or pili •In Mycoplasma pneumoniae adhesins are clustered together forming "tip" structure Antigenic variations •Some pathogens can continuously alter their surface proteins, which enables the microbe to avoid immune response in the host. •Neisseria gonorrhoeae (gonococci) changes surface antigens every two weeks Antibody inverting & modifying proteins •IgA proteases are digesting secretory antibodies of IgA class; •Protein A, produced in Staphylococcus aureus, or protein G, produced in Streptococcus pyogenes, are binding antibody inverted, thus making the bacteria similar to the host cell Capsules •It is extracellular structure made of proteins and polysaccharides that interfere with phagocytosis, •Capsules also can promote adhesion of microbe to the host •Streptococcus pyogenes capsule made of hyaluronic acid that is found in human body. •Capsules of some bacteria may also inhibit the digestion of bacteria ingested by phagocytic cells Enzymes - Alter proteins and other molecules of the host •Collagenase (hydrolyzes collagen) enables the spread of the pathogen deep in the tissue; •Hyaluronidase (hydrolyses hyaluronic acid of host cell) provoking autoimmune response; •Coagulase (coagulates blood) precipitates blood's proteins on microbial cell; •Kinases (digest clots' fibrin) prevents localization of microbes in single place and stimulates its spreading via circulatory system; Waxy component of cell wall - waxy lipids of Mycobacterium tuberculosis prevent digestion of microbe inside macrophages;

Compatibility with the material being treated

•You want to use gaseous germicides on electrical equipment instead of liquid one

route of transmission, viruses are divided into following groups

•enteric viruses that are transmitted via fecal-oral route (polio virus, rotavirus), •respiratory viruses that are transmitted via respiratory droplets (influenza virus, measles virus, rhinoviruses), •zoonotic viruses that are transmitted from animals onto humans •either via vectors (flavivirus is causing West Nile encephalitis) or •direct contact with infected animals (rhabdovirus is causing rabies); •sexually transmitted viruses that are transmitted via sexual contact and are causing genital herpes (herpes simplex virus) or AIDS (human immunodeficiency virus).

Plasma (cytoplasmic) membrane function

•formation the semi-permeable barrier between content of the cell and environment. •Small and uncharged molecules can easily cross the membrane - Water, gases, neurotoxins •Large and charged molecules can not cross the membrane - ions, glucose, proteins etc. •Proteins involved in the movement of small molecules into the cell are called transport proteins, permeases, AND carriers.

Effect of type of microbes present (use the graphs reviewed in lecture)

•some microbes can be easily killed by an antimicrobial procedure, while killing of other microbes can be harder to achieve by the same treatment or not be achieved at all. •The most resistant microbial forms are prions, endospores and mycoplasmas, the east resistant microbial forms are Gram-positive bacteria and enveloped viruses. •The microbial sensitivity/resistance to the procedure is measured by D-value (decimal reduction time - a time required to reduce bacterial population by 90%). •The larger D-value, the more resistant microbe is to the treatment.

Acid production (cell products)

−pH indicator detects acids that result from sugar breakdown −This methods will be used in water testing lab by growing bacteria in lactose broth supplemented with neutral read (pH indicator) •Medium would turn yellow, if bacteria grow and produce acid.